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Department of Biochemistry,
Hislop College,
Nagpur (M.S.)
Department of Biochemistry,
Lady Amritabal Dga College, Shankarnagar,
Nagpur (M.S.)
Retired Professor,
Department of Blchemistr,
Nagpur University, LIT Premises,
Nagpur (M.S.)
%Iimalaya PublishingHouse




Nag u r
No part ofthis book shall be reproduced, reprinted or translated for any purpose
whatsoever withou
prior permission of the publisher in writing.
First Edition
: 1993
Second Revised Edit/on
: 1997
Third Revised Edition
2002 (May)
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One of the problems facing the writers of textbooks in fast moving subjects is t
obsolescence of old information and sprouting of new knowledge. Luckily, for us,
with tremendous growth in biochemistry, the basic techniques of study have remai
unaltered. Yet, variations and improvi.ations of the old techniques have been pe
since the book was last revised. The present resion is an attempt to take into a
these changes.
The Achilles' heel of the previous edition was the chapter on centrifugation. Th
was brought to our notice time and again by students and teachers of the subject
diverse corners of the nation. We are happy to state that the chapter has been t
revised, almost rewritten, and the scope of the discussion has been greatly expa
Another aspect that has been completely revised is infrared spectrometry. Again
was brought to our eyes by people who have taken critical notice of the book. Th
e current
discussion of the aspect is again much wider in its scope and care has been take
n to
give several examples of its use in biochemistry and allied sciences.
New techniques such as fluorescence energy transfer, fluorescence polarization,
non-radioactive labeling, etc. have been added. Also, radioimmunoassay has been
discussed more extensively along with a good discussion of its variant,
A sore point with the previous editions was the lack of anindex. This shortcom,
has been addressed and the book now has a detailed index.
The above are the major additions. Numerous small changes in virtually all the
will become visible to the teachers of the subject who have seen the first two
editions. New problems have also been added at the end of the chapters.
Late in the day, when we had already submitted the revised draft for publication
we received the UGC syllabi for Biochemistry, Microbiology, Botany, Zoology,
Biotec.hnology, and otherallied life science subjects We were pleasantly surpris
ed to
draftnot only covered all major points but had more to offer leaving
in the syllabi. The. current edition will be of good use to students
any life science subject.

In its revised form, we feel confident that the book win be much more useful to
We would like to thank the great number of teachers and students who have praise
our book; they provided us the support that eyery author nxis so much. We are eq
to those who criticized the book for providing the motivation to revise it.

A book of this expanse does not bcome possible without contribution of
several willing souls. We have been lucky that several colleagues and students
helped us in our endeavour in whichever way they could, sometimes even
going out of the way to do it.
We would like to thank Prof. H. F. Daginawala, former Head of the
Department of Biochemistry, Nagpur University, for his constant
encouragement and help. We are also highly indebted to Dr. N. V. Shastri,
Head of the Department of Biochemistry, Nagpur University, for his
suggestions regarding the changes to be made in the revised edition. The
fact that he taught this very subject to two of the authors (AU & KU) has
!.everything to do with the writing of the textbook.
. Heartfelt thanks are due to Ms. Ragi Radhakrishnan, one of our
,cherished students, for designing the cover for the 3rd edition and for
going through much of the 2rid edition in search of mistakes, typographical
Dr. Rajnish Kaushik and Dr. Shibani Mitra Kaushik, St. Louis, Missouri,
out of the way to provide us as much current literature as they could
of the fact that both of them were laden with their own research work.
cannot really express our feeling of gratitude towards them.
We are indebted to Dr. Saraswati Sukumar (Johns Hop.kins), and Dr.
Runnebaum, The Salk Institute, La Jolla, USA, who provided us
of much of the recent literature.
Thanks are also due to several of our colleagues, friends and students
Dr. Irfan Rahman, Dr. Ashish Bhelwa, Dr. Saibal Biswas, Dr. S.N.
Sadhana Naidu, Ms, Ramfla Bhojwani, Dr. Raymond Andrew, Dr.
Deshpande, Mr. Amol Amin, Mr. S. Wankhede, Dr. Shyam Biswal,
Ms. Anjali Gadkari.
We record our appreciation of Mrs. Harsha Dave who was involved in
,g the Ist edition.
Finally, we would like to thank Shri Gokul Pandey and Shri D. P.
of Himalaya Publishing House for their constant help and valuable

1 - 65
66- 74
75 - 99

Electrolytic Dissociation and Electrolytes -- Ionization: Basis of
Acidity and Basicity w Bronsted-Lowry Theory: Acid is a Proton
Donor, Base is a Proton Acceptor -- Strength of Acids and Bases -Acid-Base Equilibria in Water -- Function and Structure of
Biomolecules is pH Dependent w Measurement of pH: Use of
Indicators m Electrometric Determination of pH -- Buffers: Systems
which Resist Changes in pH -- Titrations: The Interaction of an
Acid with a Base.
Ion Selective Electrodes Measure the Activity of Metal Long m Glass
Membrane Electrodes m Solid-State Ion Exchanger Electrodes Solid-State Crystal E
lectrodes Liquid-Membrane Electrodes w Gas-Sensing Electrodes.
Classification of Colloids -- Properties of Colloids -- Donnan
Equilibrium. . .
A Molecular-Kinetic approach to Diffusion m Methods of
Determination of Diffusion Coefficient Significance of Diffusion Coefficient w D
iffusion of Electrolytes -- Diffusion of Water Across
Membranes: Osmosis Measurement of Osmotic Pressure Van't HoiTs Laws of Osmotic P
ressure --Theories of Osmotic Pressure
and Semipermeability m Osmotic Behaviour of Cells m Molecular
Weight Determination from Osmotic Pressure Measurements -Significance of Osmosis in Biology.
Factors Affecting Viscosity Measurement of Viscosity Applications of Viscornetry

Significance of Viscosity in Biological Systems.

I00- 121
122- 144

Factors Affecting Surface Tension w Measurement of Surface

Kinds of Adsorption Interactions -- Adsorption Characteristics -Molecular Orientation Adsorption Isotherms: Quantitative
157- 174

Relationships -- Adsorption from Solutions n The Importance of

Adsorption Phenomena.
Basic Principles -- The Laws of Absorption n Significance of
Extinction Coefficient (Box) Problems (Box) -- Preparation of Standard Graph (Bo
x) Deviations From Beer's Law -- Absorption Spectrum -- Why is Absorption Spectr
um Specific For A Substance?
-- The Chromophore Concept -- Instrumentation For UV-Visible
And Infrared Sprectrophotometry -- Radiant Energy Sources -Wavelength Selectors -- Detection Devices -- Amplification And
Readout Double Beam Operation -- Double wavelength Spectrophotometer Application
s of UV-Visible Spectrophotometry Qualitative Aalysis -- How to Interpret Absorp
tion Spectra of Biological Macromolecules (Box) -- Quantitative Analysis Enzyme
Assay n Molecular Weight Determination -- Study of Cis-trans
Isomerism Other Physicochemical Studies -- Control of Purification Difference Sp
ectrophotometry Turbidimetry and Nephelometry -- Theory and Applications of Infr
Spectrophotometry -- Calculation ofVibrational Frequencies -Modes of Vibration Infrared Spectra of Common Functional Groups -- The Carbon Sk
eleton -- Carbonyl Group -- Hydroxy
Compounds Nitrogen Compounds -- Infrared Spectrophotometer: Mode of Operation Sa
mpling Techniques -- Applications of Infrared Spectrophotometry -- Disadvantages
of Infrared
Spectrophotometry -- Spectro.fluorimetry Structural Factors Which
give Rise to Fluorescence -- Fluorescence and Phosphorescence (Box)
-- Fluorometry: Theory and Instrumentation -- Applications -Fluorescence Spectra and Study of Protein Structure -- Extrinsic
Fluorescence -- Fluorescence Energy Transfer -- Fluorescence
Polarization n Luminometry -- Flame Spectrophotometry -Instrumentation for Emission Flame Photometry Instrumentation for Atomic Absorpt
ion Spectrophotometry -- Atomic Fluorescence
-- Nuclear Magnetic Resonance Spectrophotometry -- Magnetic
Properties of the Nucleus -- Nuclear Resonance Chemical Shifts: Position of Sign
als '-- Hyperfine Splitting -- Instrumentation Applications Electron Spin Resona
nce Spectrometry n Applications -- Spin Labeling -- Mossbauer Spectrophotometry
-Applications Some Solved Problems
Circular Dlchrolsm and Optical Rotatory Dispersion -- Rotational
Diffusion -- Flow Bircfringence D E1ectrlc Birefringence D
Polarization of Fluorescence -- Light Scatterlng-- X-ray Diffraction.


Basic Principles of Centrlfugatlon m Relative Centrifugal Force (RCF)
-- Other Factors Affecting Sedimentation -- Instrumentation -Desktop Centrifuge -- High Speed.Centrifuge The Ultracentrifuge
-- Analytical Ultracentrifuge Fixed-angle Rotors -- Vertical-tube rotors Swingin
g-bucket Rotors n Wall Effects Preparative Centrifugation -- Differential Centri
fugation -- Density Gradient
Centrifugation -- Rate Zonal Centrifugation -- Isopycnic
Centrifugation Gradient Materials Preparation of Density Gradients --Choice of R
otors Centrifugation in Zonal Rotors --Centrifugation Analytical Basic Principle
s of Centrifugation --Factors Affecting Sedimentation Velocity -- Sedimentation
-- Factors Affecting Standard Sedimentation Coefficient Measurement of Sedimenta
tion Coefficient Concentration Distribution -- Applications Of Boundary Sediment
ation -- Band
Sedimentation Determination of Molecular Weights


Survey of Chromatographic Procedures -- Techniques of Chromatography

-- i. Plane Chromatography -- A. Paper Chromatography
B. Thin-Layer Chromatography 2. Column Chromatography --Types of Chromatography
-- 1. Chromatography 2.
Partition Chromatography A. Liquid-Liquid Chromatography B. Gas-Liquid Chromatog
raphy (GLC} -- 3. Gel Permeation
Chromatography 4. Ion Exchange Chromatography 5. Affinity
Chromatography High Performance Liquid Chromatography Some Specialized Technique
s -- Hydroxyapatite Chromatography
-- An Affinity System for Base Dependent Fractionation of DNA -An Affinity System for Fractionating supercoiled and NonSupercoiled DNA -- DNA-Cellulose Chromatography.


Migration of an Ion in an Electric Field m Factors Affecting

Electrophoretic Mobility -- Types of Electrophoresis 1. Free Electrophoresis 2.
Zone Electrophoresls. General Techniques of Zone
Electrophoresis -- 1. Paper Electrophoresis 2. Cellulose Acetate
Electrophoresis 3. Gel Electrophoresis. Specialized Electrophoretic
Techniques I. Discontinuous (Disc) Gel Electrophoresis 2. Gradient Electrophores
is 3. High Voltage Electrophoresis (H.V.E.)
4. Isoelectric Focussing 5. Two-Dimensional Gel Electrophoresis
6. Immunoelectrophoresis 7. Pulse-Field Gel Electrophoresis
8. Electrophoresis on Cellular Gels. Electrophoresis in Genetic
Analysis 1. Restriction Mapping. 2. Southern Transfer. 3. Gel Retardation or Ban
d Shift Assay. 4. DNA Sequencing. 5. DNA Foot
printLng. -

,Radioactive Decay =- Production of Isotopes -- Synthesis of Labeled
Compounds -- Interaction of Radioactivity with Matter m
Measurement of Radioactivity -- 1. Methods Based Upon Gas
Ionization --A. Ionization Chambers B. Proportional Counters
C. Fundamentals of Geiger Counters 2. Photographic Methods
3. Methods Based Upon Excitation w A. Liquid Scintillation
Counting Use of Stable Isotopes in Biology -- The TracerTechnique
-- Use of Isotopes as Tracers in Biological Sciences -- Some
Information About Commonly Used Isotopes -- Safety Aspects -Dosimetry.
Polymerase Chain Reaction -- Enzyme-Linked Immunosorbent
Assay (ELISA) -- Flow Cytometry.
479 - 54,
546 - 56!

567593 - 60:

A history of the quest to understand the molecular basis of acid - base properti
es ,m.akes
for a very amusing reading. For instance, in 1773 Doctor Samuel Jhonson averred
that acids
iare composed of pointed particles which affect the taste in a sharp and piercin
g manner".
iAnother attempt to explain the nature of acids was made by Lavoisier when he pr
oposed that
the characteristic behaviour of acids was due to the presence of oxygen. Stimula
ted by this
observation, Sir Humphrey Davy went to great lengths to show that hydrochloric a
cid also
contalns oxygen. He, of course, failed in his attempt thereby disproving the the
ory of Lavoisier.
Even the later history of acid - base research is not without its share of amuse
ment, albeit in
:a manner different to the above described instances. In 1884 Svante August Arrh
enius in his
dissertation proposed the theory of electrolytic dissociation and ionization on
current understanding of acid - base character is based. The doctoral dissertati
on was,
greeted by the lowest possible pass-mark by the University of Uppsala, Sweden. F
, Arrhenius was awarded Nobel Prize in Chemistry in 1903.
Let us consider a simple experiment. A pair
F.Jcperlmental system for determining
electrical conductivity of a solutWn. The
bulb does not light when there is a nonbulb l@hts when the beaker cohtalns
eteces n
of electrodes is connected in series to a light bulb
and to a source of electricity (Figure 1.1). As long
as the electrodes hang separated in the air, no
electric current flows through the circuit, and the
bulb does not light. If however, the two electrodes
are touched to each other, the circuit is completed
and the bulb lights. If the electrodes are dipped
into a beaker containing water purified by
repeated distillations, the bulb does not light. This
tella us that water is not a good conductor of
electricity and is not capable of completing the

circuit. If we dissolve an acid, a base, or a salt in

water in which the electrodes are dipped, the bulb
lights up. Obviously, these substances are able
to carry the current and thereby complete the
circuit. Substances produc/ng solutions capable
of conductlng electric'.tty are called electrolytes. On
the other hand, substances producin9 solutions
incapable of conducting electricity are known as
non-electrolytes. Table 1.1 provides a few
examples of electrolytes and non-electrolytes.

Bophs. Chemis
What is the mechanism by which, electrolytes conduct electricity? Arrhenius' the
ory proving
an answer. The theory proposes that acids, bases, and salts undergo dissociation
in water
varying degrees, each molecule giving rise to oppositely charged long. For examp
le, if gase
hydrogen chloride is bubbled into water, virtually all the hydrogen chloride mol
ecules re.
with .water (Figure1.2) giving rise to a hydronium ion (positively charged) and
a chloride i
{negatively charged}. These long can now be carried to the cathode and the anode
thereby completing the circuit. This theory of Arrhenius is known as the theory
of electrol3

Collision 'Complex'
Hydronium Ion
Chloride Io:

Figure 1.2. When gaseous hydrogen chloride is bubbled in water, HCI mo/ecu/es co
llide with water molecu
Collisions of sufficient energy and proper orientation produce hydronlum long an
d chloride long.
Going back to the experiment we discussed, a diligent observer would note that c
substances cause the bulb to be brightly lit, whereas other substances cause the
bulb to
only dimly lit. This experimental observation permits us to subdivide the electr
olytes into groups. Substances that dissociate almost completely and produce sol
utions that are very go
conductors of electricity are known as strong electrolytes; substances which dis
sociate only part
and produce solutions which are poor conductors of electricity are known as weak
The difference between strong and weak electrolytes was attributed by him to a d
ifference in t
degree of ionization.

Arrhenius Theory : H Ion is the Acid, OH- Ion is the bae

Fom the experiment that we have discussed above, one can safely conclude that ac
base reactions are a function of ionization p-nciple. Thus, based on ionization
nhenius defined acids and bases. These definitions are elaborated below.
Acls : Acids were described by Arrhenlus as compounds containing hydrogen will
upon addition to water become ionized to yield 14+ long. Nitric acid (14N03), wh
ich is a solut
strong electrolyte or srong ac [Le,, it dissociates completely in water to produ
ce t4+ long), m
be cited as an example.
Nitrous acid (HNO2) , a weak electrolyte {Le., dissociates only partially to pro
duce H+ iont
may be cited as an example of a weak acid.
HNO2 # H+ +NO.
(A single arrow ----> denotes reactions that go completely to
the right; a double arrow x--- denot
re.actions that go only partially to the right).

Acids and Bases
Table 1.1 Examples of Electrolytes and Nonelectrolytes
Strong Electrolytes

Hydrochloric acid, HCI [H+ + Cl-] .

Nitric acid, HNOa [H+ + NO]
Sulfuric acid, H2SO4 [H+ + HSO]
Sodium hydroxide, NaOH [Na+ + OH-]
Potassium chloride, KCI [K+ + CI-]
Silver nitrate, AgNO3, [Ag+ + NO ]
Sodium chloride, NaCI [Na + CI-]
Copper fib sulphate, CuSO4 [Cu2+ + SO-]

Weak Electrolytes

Acetic acid CH3COOH [CHaCOOH]

Ammonia, NH3 [NHa]
Hydrogen sulphide, H2S [H2S]
Mercury (II} chloride, HgC12 [HgCI2 ]
Glucose C6H1206 [C6H1206 ]
Sucrose C12H22011 [C12H22011 ]
Ethyl alcohol, C2HsOH [C2H5OH ]
Methyl alcohol, CH3OH [CH3OH ]
Acetone CH3COCH3 [CHaCOCHa ]

Species in parentheses are predominant in solution. The difference between weak

nonelectrolyte is that weak electrolytes dissociate very lltfle (not shown in th
e table) whereas the
nonelectrolytes do not dissociate at all.
Bases : According to the Arrhenius definition, bases are compounds which upon io
in water yield OH- (hydroxide) long. Sodium hydroxide, which dissociates complet
ely to produce
OH- long, may be cited as an example.
NaOH Na+ + OHThe Arrhenius concept is important in that it has provided us with the first mec
approach to acid - base behaviour and has been instrumental for the development
of more
sophisticated theories. There are, however, two major shortcomings in the Arrhen
ius model.
"- (0 In the AIThenius model the acid-base reactions are limited to aqueous solu
tions (this
is not a problem as far as biological systems are concerned since all reactions
take place in aqueous solutions).
The theory limits bases to hydroxide compounds. This is very unsatisfact
ory because
it is well known that many organic compounds which are not hydroxides, for examp
ammonia, show basic properties in their chemistry.
In the year 1923, two more theories defining acid-base character were proposed.
The first
theory, Bronsted and Lowry theory, is very satisfactory for understanding physio
logical processes
and will therefore form the basis of all further discussions. The second theory,
proposed by
G. N. Lewis is much more general than the Bronsted - Lowry concept. A brief disc
ussion of this
theory is given in Box 1.1.

Biophysical Chemistr
Bronsted - Lowry Theory :' Acid is a Proton Donor, Base is a Proton Acceptor
This theory defines an acid as any compound that yields protons (H+ long) and a
as any compound that combines with a proton. In other words, acids are proton do
nors and
bases are proton acceptors. It should be noted that as-far as acids arc concerne
d, Arrhenius
and Bronsted - Lowry theories are similar ; in both cases acids give off H+ long
. However, the
concept of a base is much broader in the Bronsted theory, hydroxyl ion being jus
t one of the
possible bases. Cited below are a few examples which will illustrate the point m
uch better.

general equation
H+ "
H+ [
H+ [

H+ I
CO -

H+ I

Concept of conjugate ac/d and conjugate base : Each of the compounds listed abov
e as acid,
pon ionization, produces. H+ long. Their ionization also produces long or molecu
les which can
ombine with a proton (HSO , Cl-, H2PO , CHsCOO-, etc). According to the definiti
on, these
which can combine with a proton are bases: Thus, we can say that every acid diss
ociates to a proton and a base (if the reaction is reversed, a base can combine
with a proton to
an acid}. The Bronsted -Lowry theory thus conceives of an acid base 'pair'. An acid
its corresponding base are said to be 'conjugate', i.e., 'joined in a pair'. Thu
s, CI- is the
of HCI, likewise H20 is the conjugate base of H30+.
An acid is a proton donor. Its strength would depend upon the ease with which it
a proton. An acid will yield a proton with comparative ease if its conjugate bas

e is weak.
HCI as an example. Its conjugate base, CI-, is a weak base; it is not a very goo
In solutions, therefore, HCI is completely ionized to produce H and CI-. HCI IS
i strong acid because/ts conjugate base/s wea/ Let us consider another example,
that of
Its conjugate base CH COO- is stronger base compared to CI-. The acetate ion,
binds the proton much more tenaciously with the result that in solution acetic a
cid is
' ionized. CHCOOH Is a weak ac/d because/ts conjugate base Is strong. Similar co
e drawn for bases also and their strength would epend upon the strength of their
The Bronsted Lowry theory gives us the following reciprocal relations :
-- ff an acid is strong, its conjugate base is weak:
-- if an acid is weak, its conjugate base is strong.
-- if a base is strong, its conjugate acid is weak.
if a base is weak, its conjugate acid is strong.
Concept of an a/ka/i : In the previous pages NaOH was regarded as an Arrhenius b
ionized to produce OH- long. NaOH, however, is not a Bronsted base because, as a
it has little ability to accept a proton. NaOH can act as a base solely because
it gives rise to OH- long which are very good proton acceptors. NaOH and other
hydroxides like KOH, therefore act as bases by proxy. Such compounds, under the
theory, are known as alkalies.

Biophysical Chemisl
Amphoteric substances : Substances which can behave both as an acid and as a bas
referred to as amphoteric. Thus, under the Bronsted concept, liquid ammonia qual
ifies as
NH3 NH + H+
and as a base too
NH3 + H+ NH
Similar is the case with water which behaves as an acid
HOH x- H + OHand as a base
HOH + H+ --- I-IO*
Sa/ts : Under this tleory salts are thought to be compounds which are formed by
the ionizable hydrogen with a metal ion or with any other positively charged gro
up. Thu
CH3COONa is the sodium salt of CH-COOH formed by replacement of the proton by th
e N
ion. KCI is a salt of HCI formed by replacement of the proton by K+ ion.
(Throughout the dlscussiori, acids will be treated as examples. However, the dis
applies equally well to bases, albeit, in a reverse manner).
In a preceding section we have said that the strength of an acid depends upon th
e strength
weakness of its conjugate base. This, however, is not the only determinant of st
rength. Apm
from strength of conjugate base, the strength of an acid depends upon (i) the ba
sic strength
the solvent, and (ii) the dielectric constant of the solvent. Both these factors
are discusse

The Basic Strength of the Solvent
So far we have been writing the ionization reaction of HCI as
HCI .--x H+ +
and the general ionization reaction of acids as
HA --- H++A
It is, however, well known that H+ long do not exist in acid solutions. This is
because th
H+ long combine with the solvent molecules to give rise to 'lyonlum long'. Let u
s illustrate th
caseby considering a specific example, that of water, as a solvent. In water, th
e H long {formec
due to ionization of an acid) are known to combine with water molecules to give
rise to H30+
the. hydronlum long (also known as the oxonium or hydroxonium ionsl.
H++H20 ---- H30+

iAds m Boes 7
Recall that Bronsted - Lowry concept states that a base is a proton acceptor, Th
us water
the above cae (and solvents in general} is acting as a base.
We can now rewrite the general lonition reaction of an acid In water
HA+H20H30+A- '
The strerth of the acid, HA, now is a function of the competition between the tw
o bases,
, and H20 to accept the Ionlzable hydrogen.
Coe I : A= is strorer than H20, In th-is cae A- Is a stronger base and bind to t
bI hydrogen much more tenaciously than H20. A a consequence, the dissociation of
acld, HA, will be less and it not be a stror acld in water.
Case 2 : A- is weaker than H-O. In this case, once the acid is dissolved in wate
r, A= Mill 10se
ionlzable hydrogen to water Zhich is a stronger base. The dissociation of the ac
id, HA, Mill
and the acid may even be completely dissociated. The acid, HA, will be a strong
in water.
We can now generalize the above observations./f the basic strength of the solven
t is less
base, the ac will be v,,,eak in that solvent. If the basic strength
greater tbn that of the conjugate base, the ackl will be strong in that solvent.
To drive the point home, let us consider the strength of the same acid in two so
I : Acetic acid in water. The acetate ion is a stronger base than water.
is a weak acid in water.
CH3-C-OH+H-OH CH--C--O:+H30+ "
2 : Acetic acid in liquid ammonia. Acetate ion is a weaker base as compa
red to
Therefore, acetic acid which was a weak acid in water, is a strong acid in liqui

The above examples show the relative nature of the designations strong and weak.
that an acid is strong does not convey much sense unless we know in relation to
directlon of proton transfer and its extent depend upon these relative proton donating proton-bindlng abilities of the potential acids and the solvent. It can
thus be said that the
ran acid s always relative to.the basic strength of the solvent used.
Constant of the Solvent
Upon ionization the acid splits into two oppositely charged long, H+ and A-. The
se long
attract each other and recombine. However, solvents of high dielectric constant
attraction between oppositely charged partlcles dissolved in them. This action o
f the
acid and consequently is important for the strength of acid.
acid in a solvent of high dielectric constant Mill dissociate greatly and will t
herefore be
The same acid, in a solvent which has a low dielectric constant, will not dissoc
iate much

+ H+
B/ophysicat Chemts
and will consequently be weak.Water is a solvent which has a very high dielectri
c eonstan'
room temperature, almost 80. On the other hand, petroleum ether has a very low d
constant, just 2.2. A given acid can therefore dissociate to a much greater exte
nt in water tt
in petroleum ether. The dielectric constant is thus of great importance in deter
stre.ngth of an acld.
Effectof Structure on the Strength of -cids
It is a commonly accepted fact that carboxylic acids are stronger than other org
anic aci
Why is that so? The reason usually given is that the carboxylate anion (the conj
ugate ba
formed upon dissociation is stabilized by resonance (two equivalent resonance st
such a manner that it is more stable than the original acid molecule.
u" +
Resonance stabilized anion
On the other hand, in the alkoxide ion, TO-, the negative charge is not delocali
zed an(
concentrated on the single oxygen atom. This anion, therefore, is not as stable
as the resonar
stabilized carboxylate anion. The resonance stabilization promotes dissociation
in the carboxy
acids making them stronger in relation to the organic acids where lack of resona
nce stabfllzati
decreases dissociation.
If resonance stabilization were the only factor all carboxylic acids would have
had t
same strength. This is not so. Carboxylic acids which contain strong electron at
tracting grou
(halogens) on the alpha - carbon are stronger than the unsubstituted acids. On t
he other ha
carboxylic acids bearing electron releasing groups (methyl) on the alpha - carbo

n atom a
weaker than the unsubstituted acids. These electrostatic factors, in which elect
rons are eith
attracted to or repelled from one atom or group of atoms with respect to another
are known
inductive effects. Electron attracting groups withdraw electrons from the carbox
ylate grou
This weakens the oxygen - hydrogen bond thereby facilitating ionization and rele
ase of a proto
Moreover, these groups also help stabilization of the conjugate base by resonanc
(I) CI-----C<---- C
Cl<---- C <------ C
O <--- H

Acids and Bases

Inductive effects are additive and increase with the number of substitutions by
withdrawing or electron releasing groups. These effects also are sensitive to di
stance. Thus,
substitution by a halogen on the beta carbon of a carboxylic acid is not as effe
ctive as one on
the alpha - carbon.
What Do We Mean by 'Strength of an Acid'?
So far we have not reviewed this term critically. We, however, have been using t
he term
loosely to convey in essence the H ion concentration [H+] . Thus, when we said th
at HCI is a
strong acid, what we meant was that HCI ionizes t give a high [H]. When we said th
is a weak acid, we meant that CH3COOH ionizes to only a little extent giving a l
ow [H+]. AIIhough
this is the way we are going to use this term subsequently in this chapter, we m
ight as well
understand its actual meaning.
The concept ofactW/ty : The long in soluUon, are separated from one another by s
layers of solvent and thus have little attraction for each other. If, however, w
e increase the
concentration of the solution, the intervening distances between different long
start decreasing.
In a dilute solution, the long move about freely without the hindrance of attrac
tive forces from
oppositely charged long. In a concentrated solution, however, the long can not m
ove freely
because they are closer to each other and therefore are affected by oppositely c
harged long. The
long then assume a certain degree of orientation. Each ion is surrounded by an '
ion atmosphere'
of opposite charge which reduces its movement. Thus the effective concentration
of the long is
sllghfly less than its absolute concentration. This effective concentration is k
nown bya better
term, activity. Thus, in true sense, the strength of an acid is a measure of the
activity of H long
and not of its concentration. It may be said that the activity and concentration
of H long might
be identical in dilute solutions. It is only in the concentrated solutions that
they start to differ.
Activity coejc/ent : Activity is a measure of the effective concentration of the
solutes in
The activities might be related to the absolute concentrations by a proportional

called activity coefficient. The symbol used for activity coefficient is . The eq
uation for
the relationship is as follows
a is the activity and C the concentration. Units of both a and C are moles per l
itre. The
r coefficient approaches unity at infinite dilution.
Does Not Reflect The Strength of an Acid
We know that HCI is a considerably stronger acid as compared to CH-COOH. HCI ion
'and almost all the hydrogen of HCl is present as H+ at any point of tim. HCI al
so conducts
current much better than CHsCOOH. The two acids, however, have similar titration
25 ml of 0.01 N NaOH are required to fully tltrate 25 ml of 0.01 N HCI. The same
of 0.0 IN NaOH is required to fully titrate 25 m. of 0.0 IN CH3COOH. Both acids
titration response because of the following scheme of events. Acetic acid is wea
1.3% of its hydrogen is present as H+. When we add alkali to this solution, the
long liberated from it combine with the H present and remove them in the form of
CHsCOOH --- CH3CO0- + H+

NaOH Na +

in which two reactants A and B interact to form two products, C and D. Note that
reaction is reversible. According to the law of mass action the rate of the reac
tion to the righ
will depend upon the molar concentrations of A and B (throughout the discussion
we assum
that the solution is dilute and thus activity is equal to concentration) Thus
I 0
Bophyslcal Chemls
To achieve equilibrium with respect to dissociation, more acetic acid molecules
to give rise to another 1.3 % H*. These too are removed as water in the manner d
escribed abov
The process continues till all acetic acid has ionized to give up protons which
get removed =
water. A similar process takes place with HCI also
' HC1 C1- +


+ ,
NaOH -------> Na +
The two acids therefore end up giving similar titration profiles. The acidity me
asured titration is known as the total or the titratable acidity and reflects th
e concentration of an a
in solution. It does not, however, reflect the strength of an acid or its actual
The free hydronium ion concentration, [H3 O]' doininates chemical reactions In ph
systems. Since all physiological fluids are aqueous based, the concentration of
hydronium for
may determine the extent to which the reaction proceeds, the rate at which it go
es, or tt
detailed mechanism of how it takes place in such solutions. For example, in both
, living and t
vitro physiological systems, specific enzyme activity is often quite dependent o
n the effectiv
concentration of the hydronium ion.
Adjusting and controlling the free hydronium ion concentration is a necessity in
biochemical experiment. To understand the complex equilibria which are always pr
esent in acid - base system is therefore of paramount importance.

The Law of Mass Action

The law of mass action, evolved mainly by Guldberg and Waage, states that the ra
te of
chemical reaction at a given time is proportional to the active masses of reacti
ng substances prese
at that time. The active mass for molecules is essentially equal to their molar
However, for long, as one would recall, the active mass means the effective conc
entration or t13
activity (which might be equal to molar concentration in dilute solutions).
Let us consider the reaction
Vr a [Al. IBI
where [A] and [B] are expressions of molar concentrations of A and B, and V is t
Apart from the molecular concentration, the'chemical afllfities
reaction velocity to the right,
the reactants should also be taken into account. The chemical affinities are con
stant at a give:
temperature and other reaction conditions. In the above equation, therefore, we
might introduc
a proportionality constant which corrects for the particular chemical affinity.

Bophgsical Chemistry
To achieve equilibrium with respqqt to dissociation, more acetic acid molecules
to give rise to another 1.3 % H+. These too are removed as water in the manner d
escribed above
The process continues till all acetic acid has ionized to give up protons which
get removed a
water. A stmflar process takes place with HC] also
C1- +



The two acids therefore end up giving similar titration profiles. The acidity me
asured b]
titration is known as the total or the titratable acidity and reflects the conce
ntration of an acia
in solution. It does not, however, reflect the strength of an acid or its actual
The free hydronium ion concentration, [H30], dominates chemical reactions in phys
iological systems. Since all physiological fluids are aqueous based, the concent
ration of hydronium long
may determine the extent to which the reaction proceeds, the rate at which it go
es, or the
detailed mechanism of how it takes place in such solutions. For example, in both
. living and h
vitro physiological systclns, specific enzyme activity is often quite dependent
on the effective
concentration of the hydronium ion.
Adjusting and controlling the free hydronlum ion concentration is a necessity in
biochemical experiment. To understand the complex equilibria which are always pr
esent in an
acid - base system is therefore of paramount importance.
The I,w of Ma ,tion
The law of mass action, evolved mainly by Guldberg and Waage, states that the ra
te of a

chemical reaclon at a 9hen time s proportlonoJ to the active masses of reactj su

bstances present
at that time. The active mass for molecules is essentially equal to their molar
However, for long. as one would recall, the active mass means the effective conc
entration or the
activity (which might be equal to molar concentration in dilute solutions).
Let us consider the reaction
in which two reactants A and B interact to form two products, C and D. Note that
reaction is reversible. According to the law of mass action the rate of the reac
tion to the right
will depend upon the molar concentrations of A and B (throughout the discussion
we assume
that the solution is dilute and thus activity is equal to concentration} Thus
V a [A]. [BI
where [A] and [B] are expressions of molar concentrations of A and B, and V is t
reaction velocity to the right. Apart from the molecular concentration, thechemi
cal aiIties of
the reactants should also be taken into account. The chemical affinities are con
stant at a given
temperature and other reaction conditions. In the above equation, therefore, we
might introduce
a proportionality constant which corrects for the particular chemical affinity.

vr = K1 IA). IB]
Since the reaction is reversible, the products C and D will react to give A and
B. Writing
expression for the velocity of the reaction to the leR
V! = K2 It). [D] ....
At equilibrium, the rate of the reaction to the right and that to the left will
be equal. So
and / [A]. [BI = K2 [Cl. [D]
[C].[D] KI
[A].tB] K,. =
where ,.is the equilibrium constant and is an expression of the chemical affinit
ies of
obvious from the above equilibrium equation that if K is large the
the right predominates, which means that affinity between A and B is higher than
that at equilibrium the concentration of C and D is higher than that of A and B.
when Kis small.
The equilibrium equation may be stated in words : at equilibrium the product of
of the substances formed in a chemical reaction divided by the product of
of the reactants in that reaction is a constant referred to as the equilibrium
/v We may stress again that the activities of the reacting species will give the
and not the molar concentrations which are used only for the sake of simplicity.
The law of chemical equilibrium may be applied to virtually all reversible react
ions and
including the ionization of acids and bases.
of Water
As per the collision theory, it is expected that water molecules constantly coll
ide with
water molecules. It may further be expected that at any instant a minute fractio
collisions might give rise to the following change:

This reaction is better illustrated in Figure 1.3.

Biophysical Chemistry
Figure 1.3. A collision between two water molecules can result n the formation o
f a hydronlwn ion and a hydrox
ion. The collision should be of su.clent energy and proper orlentation ,
It is obvious from the above equation that for every single hydronium ion formed
, a hydros.
ion is also produced. Thus ionization of water forms these two long in equal num
bers therek
ensuring that pure water is essentially neutral. The dissociation of water has b
een confirme
by electrical conductivity experiments. These experiments also tell us that at e
quilibrium a
small percentage of water molecules becomes ionized; actually Just slightly more
10-7%. This means that water is almost a nonelectrolyte. At higher temperatures
the number
collisions between water molecules will be higher producing a sllghtly higher nu
mber hydronium long. But the water will stay essentially neutral because an equa
lly higher numb
of hydroxyl long will also form.
The Equilibrium Constant and Ionization Constant of Water
We have seen that water has only a very slight tendency to ionize, However, the
of ionization, H30+ and OH- have very profound biological effects. It is therefo
re necessary th
we express the extent of ionization of water quantitatively.
We can represent the ionization of water simply as
H--OH H++OH(although we have said before that H long do not exist as such and the correct re
would be H,O, we can think that hydronium ion is the hydrated form of H and take t
he liber
to express tas H for the sake of simplicity). The equilibrium constant of such a
according to the law of mass action would be
We have seen that water has a very slight tendency to ionize. This means that t!
.. concentration of water should be virtually unchanged by ionization. T
he concentration of wat.
per lit-re in pure water is equal to the number of grams of H20 in 1 L d
ivided by the gra

molecular weight, Le. 1000/18 = 55.5

M or 0.55 x 10 M. Substituting this value in
equilibrium constant expression we get

[H+] [OH-]
From electrical conductivity measurements of water thevalue of Keq has been calc
il very carefully and has been,found to be 1.8.-x 10-16 at 25C. Substituting this
value for K in
the above equation, we get
[H+l [OH-]
1.8 x 10-16 55.5
" Rean'angg
(1.8 x 10-Ie = [H*] [OH-]
99.9 x 10-18 = [H+] [OH-]
1.0 x I0-14 ffi [H*] [OH-]
The product of the equilibrium constant of water He. and concentration of water,
is taken to be constant, is known as ion7,atlon constant or the dssocfation cons
tant or
ion product of water and is symbolically denoted as K Thus,
/ = 1.0 x I0=14 = [HI [OH-] at 25"C,
The above equation is substantially true for water and for dilute aqueous soluti
ons. In
olutions the product of hydrogen ion concentration and hydroxyl ion concentratio
n is
constant value 10-I,4 (at 25"C) whether the solution is acidic, basic or neutral
. Value of Kw
widely with temperature as shown in Table 1.2. When concentrations of [H+] and [
as in pure water, the solution is said to be neutraL. Under such conditions,
of the value of Kw allows us to calculate the concentration of H+ and OH-.
I I0-14-- [I-gl [OH-]
I X 10-14-- [H+]2
solving for H+, we get
[H+I = I x 10-7

[H+]= [OH-] = 1 x 10-TM

Ionization Constant of Water at Var/ous Temperatures
Temperature ('C}
Ionization Constant (K


37 (Normal body temperature)
Thus when a solution is neutral, the concentrations of H and OH- are both 10-7 M.
ther hand, ff the solution is acidic, the concentration of H+ would be higher th
an 10-7 and

I 4 Bphysmd Chem
that of OI-I- would be less than 10-7 M. Furthermore, when the solution is basic
, the concen
of H should be less than 10-7 M while the concentration of OH- would be higher th
Thus, the ionization constant of water, Kw, is of great help to calculate the co
ff the concentration of OH- is known, and vice versa.
The relationship [H*] [OH-] = Kw = 1 x 10"4 helps in elcution of [H*] if[OH-] is
known and
Vke versa. The following examples demonstrate it.
(1) Calculate the [H+] of the solution which is 0,01 Nfor NaOH at 24=C,
Ans. NaOH is a strong alkali and by definition dissociates fully. Thus a solutio
n which is 0.01 N
with respect to NaOH is also 0.01 Nwith respectto OH-. Therefore [OH-] of the so
lution is 0.01
g tool per litre or 1 x 10" g tool per litre. Putting this value into the equati
[H*] [OH"] = K=, = 1 x 10-4
we get
[H+].I X 10-= = I x 10"4
IH* =

= 1 x 1 Og tool per Iltre


(2) Calculate the [OH'] of the solution which is 0.001 N for HCI at 24'C.
Ans. HCI is a strong acid and by definition dissociates fully
respect to HCI is also 0.001 Nwith repect to H+. Therefore, [H+]of the solution
is 0.001
litre or I x 10"a g tool per lltre. The [OH-] of this solution will be

OH- = lx10"
=1x10"11 g rnol per litre

(3) Calculate the [OH-] for each of the following

neutral. The temperature is 24'C.

(/) [H+] = 1 x 10"e mole/litre.

(ii) [H+] = 4 x i0-e mole/litm.
(iii) [H7 = 2.5 x 10"mole/litre.
(iv) [H+] = 2 x 10-2mole/litre.
Arts. (i) lx10-s mole/litre. (ii) 2.5x10-s
(iv) 5 x 10-13 mole litre.
mole/litre. (ill) 4x 10-e

Simple Way of Denoting H+ and OH- Concentrations: The Concept of pH

Because of the importance of trace concentrations of hydrogen and hydroxyl long,
routinely have to make hundreds and thousands of measurements. The manipulation
of sucl

and Bases


wkward figures as negative exponents (e.g., 10-7) or even their decimal equivale
nts (0.000000 I)
cumbersome and tedious. As a matter of simple convenience, the chemists, chiefly
Sorensen, ng ago devised a shortcut. This shortcut is thepH scale which is a co
nvenient tool to designate
the actual concentration of H (and therefore of OH-) in any aqueous solution in t
he range of
acidity between 1.0 MH and 1.0 M OH-. Mathematically, the term pH is def'med by t
he equation
Let us see how convenient is the pH scale. We know that the hydrogen ion concent
n a neutral solution at 25 is 1 10-7 M. The pH of this solution would be given by
pH = log-lx10-7
= log (1 x 107) = log 1.0 + log 107
pH= 7
Thus the cumbersome figure of neutrality, hydrogen ion concentration of 10-7 M,
into the simple pH value of 7. Solutions which are acidic will have pH values le
7, and conversely, the solutions which are alkaline will have pH values larger t
han 7.
ion product of water (1 x 10-), forms the basis for the pH scale, the scale rang
es from
to 14 (Table 1.8).
1.3 The pH Scale
[H*], M
[OH-], M



It is necessary to understand that the pH scale is logarithmic and not arithmati

c. Thus,
is said that two solutions differ from each other by 1 pH unit, it ineans that o
ne solution
I0 times the hydrogen ion concdntration of the other. Thus, vinegar (pH 3.0) has

approximately 10,000 times greater than that of blood (pH 7.4). Table 1.4 lists
values of some important and commonly used aqueous fluids.

Table 1.4
Place of Various Materials in the pH Scale
Biophysical Chem

pH value
Household bleach
Household ammonia
Baking soda
Sea Water
Egg white
Hepatic duct bile
Intestinal Juice
Pancreatic Juice
Blood (human}
Tears (human)
Cerebrospinal fluid
Kupffer cells (intracellular)
Black coffee
Tomato Juice (ripe)
Orange juice
Lemon Juice
Pure gastric juice

7.4 7.5 7.5 7.357.4


6.354.8 6.6 6.4 5.0


4.2 - 4.9
2.6 - 4.3

If we take the negative logarithm of the equation

Kw = [H+] JOWl = 10-4
we get
log IHI - log IOH-] = - log Kw = 14
but, - log [H] = pH, slmflarly - log [OH-] = pOH, and - log Kw = pKw
pH + pOH = pKw (at 24"C)
Sometimes the expression pOH is used to denote basicity (OH- concentration) of a
It is important to note that the pH scale is applicable accurately only to solut

ordinm-y temperature (approximately 24"C) where the value for pKw is 14. Only at
this temperatu
pH of neutral solutions will be 7.
Measurement of pH is of utmost importance to biologists in general and to bioche
particular. This is so since pH determines not only the activity of blomolecules
such as enzyme
but may also be important for the stability of their structures. Moreover, measu
rement ofpH blood and urine can give us important diagnostic information.

It must be emphasized that the actual meaning of pH is the negative log of hydro
gen ion
r and not the hydrogen ion concentration. However, in dilute solutions with whic
h we
[ deal, activity is essentially equal to the concentration.
Measurement of pH of an aqueous solution can be-performed by using such indicato
r dyes
Isee later) as phenolphthalein, phenol red, litmus, etc. Accuratemeasurements, h
owever, require
specially glass electrodes which are very accurate (see later).
of Weak Acids
A biologist is more concerned with the behaviour of weak acids which are not com
when dissolved in water. Weak acids (and weak bases) occur commonly in biologlca
are responsible for metabolic regulation.
The law of mass action can be applied to formulate equilibrium equations for the
If weak acids are given the genera/formula HA, their dissociation equation can

Bophystcal Chem
According to the law of mass action the equilibrium expression for this dissocia
be written as "
where Ka is the dsn cot or the nan t ofwe acid. A hler vue
obviously means higher degree of ionization. Thus, lactic acid with a Ka of I.
I 0 is much more iod aeflc acid wch has a vue of I. 74 x I 0-s. s aut0mafl prodes
e oaon at lacc acid is a songer acid as comped to acec acid.
dlssociaon constt us deles e tendency of y acid, , to lose its proton.
A discussed eer in the secon on pH, it is cumbersome to hdle negave eo
vues. ese vues c be better hdl if e conveed to e negative log us,
og = p
fle mng use of p, it should be remembered at s vue would be less stronger ad d m
ore for a weber acid. us, lactic acid wch is songer acetic has a p vue of 3.86 a
s comped to 4.76 of acetic acid. Table 1.5 ts e d pv of some coon we acids.
Phosphoric acid (H3PO4)
Formic acid (HCOOH)
Lactic acid (CHaCHOHCOOH)
Acetic acid (CH^COOH)
Propionic acid CHaCH2COOH)
Carbonic acid (H2CO3]
Ammonium ion (NH )
7.25 x 10-3
1.78 x 10-4
1.38 x 10-4
1.74 x 10-3
1.35 x 10-s
7.9 x 10-7
5.62 x 10-1


We have so far considered the dissociation of monobasic acids only. However, the
certain polybasic acids, like H2C03, H3PO4 etc., whose dissociation should also
be conside
Polybasic acids dissociate in stages and an equilibrium expression for each stag
e, involvi
dissociation constant for each stae, may be written. We will take H2CO3 as an ex
ample. '
dissociation of H2CO3 takes place as follows:
2HCO xH+ + CO 3
We can write equilibrium expressions for each of the two stages
-- =K2-- 6.31 x 10-11
where K and K are the first and the second dissociation constant of the acid. Th
e dissociat
of the first hydrogen ion from H2CO3 IS opposed by the force of attraction of it
s linkage to I

Rgds and Bases

molecule. The dissociation of the second proton is more difficult. It is held no
t only by the
primary union with the molecule but also by the attraction of the negative charg
e left on the
molecule by the dissociation of the first proton. The value of K2 is therefore l
ess than KI.
The dissociation constant of a weak acid may be employed to calculate the pH of
01ution of a known concentration. The procedure for such calculation is enumerat
ed below.
For the dissociation of a weak acid HA
HA : H+ + A
flae equilibrium expression may be written as
H+ A-]
le encentrations of H A- would be equal as they are formed In equal amounts.
v.erefore, [H+ 12 = Ka [HA] or [H+ ] = -/-a [HA]
We know that weak acids are only slightly ionized. Thus, we can safely assume th
at not
!note than 1% exists as H+ and A-. One can therefore assume that the concentrati
on of the
imdissociated acid, HA, is equal to the normality of the acid. This value can th
en be substituted
the above equation and the hydrogen ion concentration can be calculated. The val
ue of
.[!ydrogen ion concentration so calculated will be approximate as we have not co
rrected it for
slight dissociation which the weak acid has undergone.

Biolhysal Chemis
Ionization of Strong Acids
Strong acids (and bases) dissociate completely or almost completely in dilute aq
solutions (HCI, H2S04). Thus, a 0.1 N solution of HCI is essentially 0.1 N in hy
coneentration also. It iS therefore nonsense to write equflibrlum equations and
constants for their dissociation. On the other hand, the higher number of long p
roduced by
strong acids promotes interactior between these long and ttlerefore, the activit
y of strong ac
might be less than the hydrogen ion concentration produced by ionization. Th pH
of str
acids of a given concentration is therefore slightly differerit than what is pre
dicted by th
Hydro13is of lts ,
.. There are numerous salts which, from an Inspect.ion of their chemical formula
e, cannot i
any possible way provide either hydrogen long or hydroxyl long in water, Yet, in
solution, many
of these salts test either acld/c or basic: Thus sodium, acetate, CHsCOONa, test
s basic when-ll

and Bases


. relydissolved in water. Obviously sodium acetate solution has more OH- long th
an it has H30 + .
, ammonium chloride, NH4CI, tests acidic in water which means that this solution
3 long than itlhas OH-. Inspection of the formulae of these salts tells us that th
ey can
jt podkibly provide H30* or OH" ions..What then is the mechanism by which extra
OH- or
tr. a H3O long are being produced in such salt solutions?
H' To .answer this qqestion let us find out which long will be present i
n a solution of these
lalts tn water. First let us consider sodium acetate: Upon dissolution i
n water, sodium acetate
mpletely dissociates, into the Na+ !ons and acetate, CH3COO-, long. Apa
from these two
S, some H,O* and OH- will also be present through dissociation of water.
This inspection
us that t.e only way sodium acetate can test basic is by decreasing the
HsO+ concentration
thus relatively increasing the oH- concentration, Let us find out whetle
r any of the two
COO" and Na, produced by sodium acetate, have the ability to combine with
effectively reduce their concentration. Can Na+ long bind H30+ ? Obvious
ly no. Can
* long combine with OH, long ? No. Because NaOH is a strong base (Ikali)
, and by definition
ium long readily relgase OH- long. The answer, thus, does not lie in Na+
long. If now we
nsider CH3COO- long, we will see that this ion is derived from a weak ac
id, the acetic acid. We
.ve already seen that weak acids are weak because their conjugate bases
are strong and bind
th protons rather tenaciously reducing the extent of dissociation. The s
trong conjugate base,
ion in this cse, can. therefore bind with protons (H3O+) and effectively

remove them
solution leaving an excess of OH- long. This makes a so/llum acetate sol
ution test basic
1.4). Is i that all salts of weak acids and strong bases (sodium acetate
is an example)
basic in soltion? Yes, by definition all of them have strong conjugate b
ases which can
protons iom solution. We therefore can generalize the situation. Sa/ts o
f weak acids
bases test basic when dissolved in water.
Long from the sal : Na CH3CwO-

Long from water:

OH' Tenden'y to combine
No posslbility of Interaction

Hydrolysis of sodgun acetate (salt of strong base and weak acid). Na and OH" do n
ot have a tendency
to combffe because they are derWed from strong alkali. CHo CO0-, however, has a
tendency to combine
w[tn H* of water becaus [t s a base covate to a weak ad. Th depletes long of wat
er wh{le OH"
rerna unchared. The olution #:Lcomes alkal{ne. (HO shown as H'for the sake of stl

Biophysico2 Cherr
The same train of logic can be adapted to find out what will happen when
salts of st
acid and weak base {Figure 1.5}, and salts of strong acid and strong base {Figur
e 1.6}
dissolved in water. We can generalize these situations also and state that (0 sa
lts of strong c
and.weak bases test acidic when dissolved in water; and (il) salts of strong aci
ds and strong I
test neutral when dissolved in water.
Long from salt : NH
CILong from salt : Na

Long from water

Long from water ;

Figure 1.5. Hydrolysis of ammonium chloride (salt of

strong acid and weak base). Cl- and I-I* have
no tendency to combine. NH on the other
hand can combine with OH- long. This
depletes OH- tons of water while-14+ tons
remain constant. The solution becomes acidic
Figure 1.6. Hydrolysis of sodium chloride (salt of s
acid and strong base). As evldent fror
figure, none of the salt lons has any tenc
to combine with either l-I* or OH-.pro
by tonlzatton of water. The solution re

If any ion from the salt interacts with water in such a manner as to change its
pH, hydro:
is said to occur.

The Effect of Salts Upon the Dissociation of Acids

Let us see what happens when a salt of a weak acid is mixed with the weak acl
solution. Experimental results with such mixed solutions tell us that the pH of
such solui
increases as compared to the pH when only the acid was present. This obviously m
the addition of salt to acid solution has decreased the dissociation of the acid
. If we appl)
same principles which we considered in the above section, we can provide an answ
er for
decrease in dissociation. Let us consider the solution of acetic acid and its sa
lt, sodium ace
as an example. From our discussion above we know that sodium acetate is complete
ly dissoci
in solution, whereas acetic acid is only weakly dissociated. We, therefore, have
the follo
dissociation equations :
CH3COONa ---) CH3COO- + Na+
We have seen that acetic acid is a weak acid and dissociates very little. This i
s becaus
conjugate base, CH3COO', is very strong and binds protons tenaciously. Since sod
ium ace
dissociates completely, by adding this salt we are further increasing the concen
tration o!
conjugate base, /.e., the acetate ion. These extra long then combine with the sm
all numb
protons dissociated from acetic acid. Thus, the H ion concentration gets reduced
and the
increases. We can therefore say that the pH of a solution of weak acid and its s
alt is determ
-by the ratio of salt to acid in the solution. The higher the salt concentration
, the higher the
Table 1.6 elaborates the effect of changing salt to acid ratio on the pH of salt
-acid solution

tdds and Bases
sble 1.6 Effect ofChanging Salt/Acid Ratio on the pH of Salt-Acid Solution
Sodium Acetate
Acetic Acid

' 0.75

The same set of principles discussed above apply in the case of solutions of wea
k hydroxides
d their salts also. We might cite the example of NH OH and NH4CI, where the diss

NH4OH NH + OHNH4CI --> NH + ClUe NH4OH is only partially dissociated, NHCI dissociates completely, The extra N
H long
ue to the dissociation of NH CI depress the dissociation of NH.OH thereby decrea
sing OHcentration
and thus a drop in pH restflts. The higher the sal concentration the lower the
Solutions which contain both weak acids and their salts are known as buffer solu
tions Ooy
same logic, solutions containing weak bases and their salts are also buffer solu
tions) because
[]/have the capacity to resist changes in pH when confronted with either an acid
or a base.
..]he principle behind this resistance of pH by buffers remains the same as desc
ribed in the
section. However, we will consider it once again in a more explicit manner. Let
a system of acetic acid and sodium acetate. From the discussion in the previous
know that sodium acetate dissociates fully and acetic acid dissociates only a li
solution therefore contains undissociated acetic acid molecules, CHsCOOH, acetat
e long,
and Na+ long. Let us now see what happens when an acid or a base is added to thi
When an acid (HCI) is added :
CH3COO- + H+ + CI- ---> CH3COOH + CIIn solution HCI dissociates completely to produce hydrogen long and chloride lon
g. The
could have decreased the pH, combine with the strong conjugate base
are thus removed. The pH of the solution does not decrease appreciably (it fails
to the change in ratio of salt to acid in solution).
When an alkali (NaOH) is added :
CH3COOH + Na + OH- ---> CH3COO- + Na + H20
The strong alkali, NaOH, dissociates completely into its constituent long Na + a
nd OH-.
have increased the pH, bUt in the buffer solution they react with CH3COOH to giv
to water and acetate long. The pH does not increase appreciably (it increases on
ly in

to the change in the ratio of acid to salt in the solution).

pH = pKa - log
Biophysical Chemlstr
To what extent can a buffer solution resist change in pH ? A simple example will
be citec
If 10 ml of 0.1 N HCI is added to 990 ml of pure,water (pH 7.0), the pH of water
drops 4 unil
and becomes 3. Similarly, if 10 ml of 0.1 N NaOH is added to 990 ml of pure wate
r, the p]
increases by 4 points and becomes 11. However, if 10 ml f 0.1 N HCI is added to
990 ml of
buffer consisting 0.1 N acetic acid and 0.1 M sodium acetate (pH 4.76), the drop
in pH is on]
0.01 points. The pH changes merely to 4.75. Similarly, addition of 10 ml of 0.1
NNaOH to 99
ml of above buffer solution elicits a rise of merely 0.01 units on the pH scale.
The pH become
4.77. We thus see that buffer solutions resist chariges in pH to a very signific
ant extent (we wi
consider the same example quantitatively a little later).
We have seen that the conjugate base provided by salt dissociation is actually i
nvolved i
the buffering action. The metal long (like Na in sodium acetate) are not involved
. We shoul
therefore rewrite the definition of buffer solutions. Buffers are mixtures of we
ak acids and the
conjugate bases.
The Henderson-Hssselbslch Equation
Henderson-Hasselbalch equation is important for understanding buffer action and
base balance in the blood and tissues of the mammalian system. The equation is d
erived in following way. Let us denote a weak acid by the general formula HA, an
d its salt by the genen
formula BA (B being the metal ion and A- being the conjugate base). The salt diss
completely, while the weak acid dissociates only partly. We can write the equtli
brium reactior
for the dissociation of HA and BA in the buffer solution as follows :
HA -I-I + ABA -B+ + AWe will soon find that Henderson-Hasselbalch equation is simply another way or w
the expression for the dissociation constant of a weak acid.
Solving for {H], we get

Taking the negative logarithm of both sides, the equation becomes

However, - log [H+] = pH, and - log Ka = pKa. Therefore,

[conjugate base]
pH = pKa + log
necessary because the values of pK and activities vary
strength. The value of pKa on the basis of activities can be calculaled with the
help of
relationship :
and Bases
the negative sign, we invert - log [HA]/[A-] and obtain
pH = pKa + log
This is Henderson-Hasselbalch equation'Now, the weak acid, HA, is only slightly
the absence of the salt. Thus very little of the A- long come through the dissoc
iation of
bak acid. On the other hand, we have seen that the salt BA is completely dissoci
ated and gives
Ehlgh concentration of A- long. It can, therefore, be safely assumed that the co
ncentration of
he undissociated acid [HA] is equal to the total acid concentration. We can also
assume that all
." has dissociated from BA and therefore the concentration of the conjugate base
, [A-] is equal
the concentration of the salt, [BA]. Taking into consideration these assumptioBs
, he equation can take many differont forms.
pH = pKa + Iog [acid]
[proton acceptor] "'..
pH = pKa + log [prot.0n donor] . .?w .
As with all the equations considered so far, the
more accurately when concentrations are converted to

pK (activity) = pK (concentration) - 1.018 f

Is the ionic strength of the solution. For most calculations, however, concentra
fairly accurate results. Now, that we have derived an equation which relates pH
concentration (conjugate base Concentration) and the weak acid concentration,
;us see the quantitative basis of buffer solutions rslsting a large change in pH
. We have seen
addition of 10 ml 0.1 NHCI to 990 ml of pure water brings its pH down from 7 to
3. Let us
add this acid to 990 ml of 0.1 N acetic acid and 0.1 M sodium acetate
long disgociating from HC1 are neutralized by the acetate long.
The addition of HCI therefore lowers the concentration of the acetate ion slight
ly and
the concentration of acetic acid by the same amount. If we assume that all I-I+
long have
neutralized, the drop in acetate ion concentration will be 10-3 mole/litre. The
acid would rise by the same amount. -

pH = pKa + Iog-pKa of acetic acid is 4.76. Therefore,
pH = pKa + log 1.0
pH = pK + 0
pH = pKa
Thus to calculate the pK of any acid one only needs to dissolve that acid and it
s salt equal concentrations and thenaexperimentally determine the pH of the solu
tion. It will be equ to the pK of the acid. Some extremely important problems ab
out buffers which can be solw using Hederson-Hasselbalch equation are provided f
or in Box 1.6.
Henderson-Hasselbalch equation makes it clear that the pH of a buffer solution d
upon the pKa of the acid and upon the salt to acid concentration ratio. The lowe
r the pK oft]
acid the lower will be the pH. The buffer pH will increase with increasing salt
Again, according to Henderson-Hasselbalch relationship, the actual salt and acid
can be varied widely without any change in pH if the ratio between the two is un
ity. Thus,
lactate buffer containing 0.01 M lactate and 0.01 N lactic acid will have the sa
me pH even if fl
buffer is diluted 10 times or even 20 times. In actual cases, however, the pH of
the dilut
buffer increases slightly. This increase is not signii2cant enough.
Biophysical Chemistr
[CH3COO- i
-- 0.1---0.001
= 0.0999-NAL

j[CH3COOH]FINAL = 0.1 -- + 0.001 -- = 01101
Substituting the final salt and acid concentrations in the Henderson-Hasselbalch
we get
pH = 4.76 + log 0.0999
= 4.75
The pH of the buffer solution after addition of I0 ml of 0.1 N HCI changes from
4.76 to 4.751
drop of merely 0.01 units of pH.
Henderson-Hasselbalch equation gives a very important relationship which makes
possible to calculate the pK 0f-any given acid with extreme ease. The relationsh
ip is, that if tt
molecular ratio oLIt to acid is unity in a solution, the pH of that solution wil
l be equal to tt
pK of flleacl tTind "<
: ::- r the ;.
!i.: ".
pH = pKa + log [acid]

Btophys/cal Chel
Buffer Capacity
By buffer capacity we mean the capacity of the buffer to resist changes in pH. T
he ca
to resist changes in pH depends upon (i) the actual concentrations of salt and a
cid pre
the buffer, and (//) the salt to acid concentration ratio.
' First, let us consider the effect of actual salt and acid concentration on the
buffer ca
Let us add 1 ml of 0.1 N HCI to a lactate buffer solution containing 10 ml of 0.
1 M lactal
10 rnl of 0.1 N lactic acid {pH of this buffer will be equal to the pK- of lacti
c acid, 3.86, sin
ratio of salt to acid is unity). What will be the change in pH of thebuffer solu
tion ? The H
convert 1 ml of the salt to 1 ml of acid. The pH of the solution will therefore
pH = 3.86 + log = 3.86 + log 9-1og 11
= 3.86 + (0.9542 1.0414) = 3.77 (App.)
the change in pH of the buffer solution is therefore 3.86 - 3.76 = 0.09. Thus, o
ne ml of
HCI causes a decrease of about 0.09 pH unit.
Suppose we add 1 ml of 0.1 N HCI to a buffer solution containing I0 ml of 0.025
and I0 ml of 0.025 N lactic acid. What will be the change in pH ? The HCI, in th
is cas
convert 4 ml of salt to acid. The pH of the solution will therefore be
pH = 3.86 + log -6 = 3.86 + log 6-1og 14
= 3.86 + (0.7782 - 1.1461) = 3.49
the change in pH of the buffer solution is therefore 3.86 - 3.49 = 0.37. Thus, i
n this c
ml of 0.1 N HCI causes a decrease of about 0.37 pH unit.
The above example tells us that the first buffer has a higher buffer capacity th
second. This means that buffers containing higher concentrations of salt and aci
d have a buffer capacity as compared to solutions with lower salt and acid conce

Let us now consider the effect of salt to acid concentration ratio upon the buff
er cap
To understand this, let us consider a lactate buffer composed of 15 ml of 0.1 Ml
actate ano
of 0.1 N lactic acid. The pH of this buffer would be
pH = 3.86 + log "" = 3.86 + (1.176-0.6989) = 4.34
Let us now add 1 rnl of 0.1 N HCI to this buffer. The HCI would convert 1 ml of
salt to 1
acid. The pH of the buffer will be
pH= 3.86+ log 14 = 3.86+ (1:1461-0.7782)= 4.23
Thus the pH of the buffer is lowered by 0.1 . pH unit. As shown previously, 1 ra
l of 0.1 h
added to a buffer composed of 10 ml of 0.1 M lactate and 10 ml 0.1 Nlactic acid
changes it
by 0.09 pH unit. This example elaborates the effect of salt to acid concentratio
n ratio on b
capacity. The generalized statement based on the above example can be that when
the ra
salt to acid concentration is unity, the buffer has maximum efficiency.

and Bases
The buffer range of any given buffer is about 2 pH units. It consists of one pH
unit on
side of the pK of the buffer acid. Thus, lactate buffer should be a good buffer
in the pH
. 2.86 -- 4.86. Iwe increase the concentration of buffer solution, we can also i
ncrease its
to a little extent. The selection of a proper buffer system for a given experime
a common problem. Some examples arc provided. For the pH range 3 to 4, phthalic
acid phthalate can be used; for the pH range 4-6, acetic acid-sodium acetate
is satisfactory; for the pH range 6 t-0 8, monosodium dihydrogen phosphate (acid
) monohydrogen phosphate (salt) buffer is useful (see Appendix).
How important buffers are for normal functioning of a body can be .understood fr
om the
.that the pH of blood is maintained strictly within the range 7.3 to 7.5. Death
is more or less
pH of 7.0 and above a pH of 7.9. In the laboratory, buffers are used for two mai
: (/) as reference standards for pH determination, and (//) to maintain optimum
acid reaction of a medium such as bacteria or tissue culture or an enzymatic rea
ction mixture. discuss more about some important biological buffers in a later s
As mentioned earlier, it is the pK value that is of utmost importance when decid
ing about
buffer has to be used. However, each buffer has other.chemical characteristics p
eculiar which must be borne in mind. Several buffers may fit the pH range one is
working in.
a few of them may have characteristics that are detrimental to the experimental
This becomes even more important considering the fact that most of the commonly
designed for biochemical use. The most common problems that plague .these
inhibition of some enzymes, precipitation of polyvalent cations, toxicity, absor
light, strong effect of concentration and temperature on pH, and lack of good
activity in the most used pH range in biochemistry. A few most commonly used
are discussed below individually.
The advantages of phosphate buffers are numerous. They have a high buffe
ring capacity.
Na and K salts are very highly soluble and thus any ratio of Na and K long can be
Because the long are highly charged, high ionic strength can be obtained without

The last named advantage can become a disadvantage too, It is impossible to prep
are a
buffer with a high buffering capacity and a low ionic strength!
The actual disadvantage of the phosphate buffers are as follows. They ma
y bind polyvalent
Chiefly, they bind Ca , and to a lesser extent, Mg2 . More importantly,
are known to be toxic to mammalian cells. Another disadvantage isthe lac
k of buffering
in the range 7.5 to 8.0.
They are good buffers between the pH range 12.0 - 12.5.
The principal disadvantages of these buffers result because of relative
insolubility of most
of the sensitivity of pH to temperature chauges. High temperatures
extreme pH changes due to loss of CO2.
The buffering range in which these buffers work well is 10 - 10.8.
This buffer is probably the most used in biochemistry and for obvious reasons. C
; advantages. (1) Since the pKa is , it has a high buffering capacity between 7.
5 and 8.5.

(2)Very low toxicity. (3) Does not intei-fere with most biochemical reactions. (
pure forms.
. The disadvantages are as follows: (1) Like carbonate buffers, its
to a very high extent. (2) Like phosphate buffers, it reacts with a few metal lo
ng like
Ni2+, Ag+ etc. (3) It reacts with some glass electrodes and thus may lead to err
EDTA Buffers
EDTA (ethylenediaminetetraacetate) is not normally used for its buffering. It is
chelating agent of divalent cations and is added to other buffers mainly to redu
concentrations of the divalent cations. Thus, one finds that EDTA buffers are us
ed very
when working with nucleic acids; the reason is that Mg2 is a cofactor for nucleas
of EDTA therefore abolishes the activity of these enzymes. This is exactly why E
DTA buffer
used when nucleic acids are to be stored. One precaution here. EDTA suffers from
disadvantage of absorbing very highly in the UV range. As such, if nucleic acid
has to be estimated, the concentration of this buffer should be kept yery low (0
.001 M).
Another buffer that suffers from high absorbance in the UV range is the barbitur
Boric Acid and Glycine Buffers
Borate has weak toxicity and glycine, of course, has none. Both these buffers ha
ve a I
UV absorption. Borate is good between pH range 8.7 to 9.7 and glycine between 9.
5 to 10.
Additionally, borate is chosen for work with bacteriophages since it stabilizes
Glycylglyinc Buffer
This is often a buffer of choice for enzymo10gical work and works well in the pH
to 8.0. It also has very low UV absorbance. This is another major plus since enz
assays in the UV range will not be impeded. One more great advantage is that it
for the divalent cations Ca2+ and Mg2+. These are precisely the cations that are
used very
for enzymological work.
The disadvantage with glycylglycine springs from its being a peptide : it is

proteases and as such cannot be used with these enzymes. Additionally, it cannot
crude protein preparations since such preparations may have protease contaminati
Triethanolamine Buffer
This is another favorite for enzymological work. It has all the advantages
glycylglycine. It buffers at the same pH range and it doesn't suffer from the li
glycylglycine, namely protease susceptibility. Also, it is a volatile buffer and
therefore may
chosen for purification work where the buffer is to be subsequently removed.
The Good Buffers
These buffers are so named after their discoverer, Norman Good. Because of sever
problems with the buffers just discussed, Good looked at a large number of zwitt
erionic buffer
The buffers that he found good lack the drawbacks mentioned above. They are not
toxic, the,
do not absorb appreciably in the UV range, they do not precipitate divalent cati
ons, their pH
not sensitive to temperature changes, and they are quite soluble. These buffers
are given bel
in a tabulated form (Table 1.7). Since they have very long names, they are usual
ly known
their abbreviations. However, their full names are being provided in the table.

ethane acid
6.2 - 7.2
and Bases
1.7. Good's Buffers
Buffer Abbreviation
pH range where
best used
-2- ACES 6.88 6.4 - 7.4
[(carbamoylmethyl) imino]acid

-hydroxyethyl)- I -piperazineacid

6.6 - 7.6
7.8 - 8.8
9.7- 11.1


7.0 - 8.0
7.6 - 8.8

known as EPPS.
The old definition of neutralization states that an acid and a base react with e
ach other to
water. The Bronsted-Lowry concept offers a much broader view 3333of the process
to this concept, neutralization is a process of proton transfer from an
a base. Neutralization need not result in the formation of a recognizable salt a
nd may
involve water.

Biophysical Chemistn.


Although, in the following pages, we shall be considering acid-base interactions
in aqueot
media, the above discussion will help us in identifying the conjugate acid and b
ase produced:
any neutralization process.
Titration is normally used to determine the amount of an acid in a given solutio
n. In th
procedure a known volume of an acid is titrated with a base (usually NaOH) whose
is accurately known. Small aliquots of the base are added till the acid is total
ly neutralized. T,
titration can be followed by adding an indicator to the acid solution or by cont
measurement of the pH by a pH meter. The concentration of the base and the volum
e requir
for fully neutralizing the acid are sufficient for calculations which will revea
l the concentratic
of the acid in solution.
Titration Curves of Weak Acids
Let us again take the example of acetic acid. Figure 1.7 represents the characte
titration curve of acetic acid when it is titrated against a strong alkali. The
figure traces fl
course of titration of a 0.1 N solution of acetic acid with 0o I N NaOH at 25C.
Before tl
titration is started (i.e. before any NaOH is added), the acetic acid is slightl
y ionized and the I:
of the solution is due to acid alone. When successive aliquots of NaOH are added
, the OH= fro]
dissociation of NaOH will combine with the free H+ in solution to form water. As
soon as the fr
H+ is neutralized by OH- to water, some of the undissociated acetic acid immedia

tely dissociat(
further to satisfy its dissociation constant. Thus with each addition of NaOH, m
ore water
formed and more and more acetic acid gets converted to the acetate anion.
CH3COOH + Na+ + OH- ----) CH3COO- + H20 + Na
As the titration progresses, the concentration of acetate ion increases
continuously am
that of acetic acid decreases. Have we come across this situation before
? Yes. We know th
solutions of weak acids and their conjugate bases are known as buffers.
With the progress
titration, the solution is fast becoming a mixture of the conjugate base
, acetate, and the we
acid, acetic acid. The pH of this solution will now change in accordance
with the Hendersor
Hasselbalch equation, i.e., at any stage of titration, we should be able
to calculate the pH ofth
solution using the Henderson-Hasselbalch relationship. If we plot the pH
values against th
volume of alkali added we get the characteristic curve shown in Figure 1
.7. The titration curve
of all weak acids have similar shape (Figure 1.7). They differ only in t
heir location on the pl
scale. The position of the curve on the pH scale depends upon the pK of
the acid being titrate(
While dealing with the Henderson-Hasselbalch relationship, we havre alre
ady considered th
the pK, of an acid is equal to the pH of the solution containing equal c
oncentrations of both
salt anl the acid. Such a situation will clearly be present at the mid-p
oint of the titration. Th
the pH of the solution when the acid is half titrated represents the pK
of the acid being titrate
(Figure 1.7).
The titration curve of a weak acid is usually spread over about 4 pH units. Thus
, for
weak acid whose pK is 5, the titration begins at around pH 3. This acid will be
half titrated pH 5 and will stand c%mpletely titrated at around pH 7. If the pK
of the acid being titrated is the titration begin's at pH 5, is half completed,b
y pH 7, aad is complete at around pH 9. Th
tiI4".ation curves of these two acids will be displaced along the pH scale accor

ding to their respectiv


and Bases
pH 7

: 9-2S



Equlvalente of OH------1.7.
Characteristic titration curves of weak acids. The midpoints of the titr
a(-ions have been indicated. Also
indicated are the predominant ionic species at the beginning, midpoint and end o
f the titrations. The
buffering zones have been shown.
From Figure 1.7, we note that the titration curves are relatively flat in their
centre sections.
zones are the buffering regions of the acid-conjugate base pair (Figure 1.7). On
of these curves one can select the salt acid concentrations that will give a goo
d buffer
One can see that the titration curve assumes greatest degree of flatness at its
the acid to conjugate base concentration ratio is unity. This ratio obviously ha
s the
capacity. This is the proof for what we have already considered mathematically
: the buffer is most efficient in resisting pH changes when the ratio of salt
is unity. Figure 1.7 also shows that at both the. ends the titration curve
sharply. This means that the composition of the acid-conjugate base solution in
is not good foi- a buffer. It is obvious that at both the ends the ratio of conj
ugate base to
is far removed from unity.
Titration curves of weak bases follow the same pattern as seen for weak acids, b
ut in a
order as evident from Figure I.8.

of titration
pkw" pkb = 9.26 =
PH 7
0 0.5 1.0
------ HCI
Figure 1.8. Characteristic titration curve of weak bases.
Titration of a Strong Acid with a Strong Base

pH 3
0.5 1.0
Equivalents of OH100%
0.1N NaOH Salt

lgure 1.9. Titration of a strong acid with strong base (0.1 N HCI against 0.1 N

Figure 1.9 represents the titration curve of 0.1 N HCI titrated against 0.1 N Na
OH. The
Striking thing about this titration curve {in general for titration curves of al
l strong acids) is the
very sluggish change in pH as successive aliquots of NaOH are added. To change t
he pH by one
unit, almost 80% of the NaOH is required. However, at the later stages the titra
tion curve shows
a sharp break and the pH changes rapidly. Thus the HCI solution has a good buffe
ring capacity
between pHI and 3. As this pH range is seldom used in biology, titration curves
of strong acids
are not so important to a biochemist.
Titration Curves of Polybasic Acids
Let us now consider titration curves of polybasic acids which can donate more th
an one
proton and can consequently possess more than one pK, corresponding to the succe
dissociation of each of the protons. A good example is affored by phosphoric aci
d, H3PO4, for
which three ionization steps and there corresponding pKa are

and Bases
I-13PO4 H2PO +H+, pKa = 2.24
H2PO HPO+ H+. pKa - 7.2
HPO- PO--'+ H+, pKa = 12.4
Thus, in a titration of phosphoric acid the first stage consists of titration of
H3PO to
the second in the titration of H2PO to HPO -, and the third in titration of HPO
: to phosphoric acid the three pK are much separated from each other. The titrat
therefore, shows a sharp break after each pK and at these regions the buffering
'the solutions is very poor (Figure 1. I0). However, there are three different p
H zones at which
hosphoric acid system can act as a very good buffer. This example of phosphoric
acid has
r chosen because many biological molecules contain phosphate-related groups.
groups enter into multistep acid-base processes closely analogous to those of ph
11:[ orHPO--- PO +Hp/G=12.4 .
8t ,----for H,P4 HPO- + H+p = 7.2
* p 2 24
25 -.50 . .75
ml of 0.1N NaOH
Titration of 25 mls of O.1 N H3PO4 solution by 0.1 N NaOH solution, pKa of three
different stages are
shown. Three buffering zones, although not shown, are self evldent.
What happens if the polybasic acid happens to have different pKa values very clo
se to each
Let us answer this question with the help of an example of citric acid. Citric a
cid has
values which are relatively close to each other (pK1 = 3.1, pK2 = 4.7, pK3 = 6.4
). In
, case what will happen is that by the time the first H* is fugy titrated the se
cond H* also
titrating. Likewise, the titration of the second H* is not complete before the t
hird H*
In such cases there are no sharp breaks in the titration curve between successiv
and one observes a relatively flat curve throughout. Such systems are well buffe
red over a
range of pH. This is evident from the titration curve of citric acid shown in Fi
gure 1.11. If
acids having pK= values not far away from each other are mixed together, one wou

similar type of curve for such a mixture also. This is what happens in the body.
pKa relaUvely close to each other. Their titration curves therefore
thereby enhancing their efficiency in the pH range maintained by the body fluids

Biophysical Chemt
Figure I. I I. Titration of citric acid by NaOH equivalent strength. Compare thi
s cun with Fig. I, I O. Citrate ti
gives a characterlstlc jlat curve because of overlapping flrst, second, and thir
d stages of hydrog
dissociation. Citric acid therefore has a large buffering zone.
The death of a human being below a blood pH of 7,0 and above a pH of 7.9 is en
testimony for the importance of pH to life in general. Examples may also be cite
d of dea,
tissue cultures and bacterial cultures in inadequately buffered media. It is the
refore a
obvious conclusion that biomolecules are profoundly affected by changes in pH. I
n any c
most of the important conponents of the living cell are acidic, basic, or amphot
eric and
alteration in the pH of the environment profoundly affects their state of ioniza
tion and the:
their conformation and biological activity.
In this section we will deal with pH-dependent properties of proteins and their
blocks, amino acids. We will also discuss in brief the pH-dependent properties o
f o
Ionization of Amino Acids is pH-Depenflent
All amino acids are amphiprotic compounds and can be denoted by the general forn
H -- C k NH2
Their a-amino group is weakly basic and has a pK in the range 9-I0.5.

a-carboxyl is acidic with the pK in the range 1.7 to 2.4. All amino acids are th
erefore ioniz
an aqueous solution depending on the prevailing pH.
The amino acids which do not possess any dissociable group in the side chain exi
three ionic forms :
H-- C --NH ,r
a.. H--C -- NH r
- H -- C--NH2

E/iv of O H--curve for alanine.
pKal is for -COOH andpl
is for the a-NH .
At a low pH only the a-amino group is ionized and the amino acid is a cation. If
the pH is
a-carboxyl group starts dissociating. This process leaves a hgative charge on th
which already has a positive charge due to the amino group. The charges cancel o
the amino acid possesses no net charge. This state is known as the zwitterionic
state and
; amino acid may be called a zw/tter/on. If the pH is still further raised, the
hydrogen ion from
group dissociates. This leaves only the negative charge on the amino acid due to
dissociation and the amino .acid behaves as an anion.
Thus, on the basis of the principles we have discussed earlier (Henderson-Hassel
it can be said that at a pH equal to the pKa of the carboxyl group (PKal) the am
as partly cation, partly zwitterion. Similarly, at pH equal to the pK of the ami
the amino acid will exist partly as anion and partly as zwitterion. In a solutio
n in
water the amino acid exists mostly as a zwitterion. Let us take the example of a
H-- C -- NH2
zwitterion form in solution will be
H-C --NH

acid, HCI, to this solution of alanine in water it will behave as a base. The re
can be represented by the equation
+H3N- CH- COO- + H + Cl- +H3N- CH- COOH + Clthe other hand, if an alkali is added, alanine solution behaves as an acid. The
can be expressed by the equation
HaN--CHCOO- +Na+ OH- H2N--CH--COO- + Na + H20
in the zwitterionic alanine, a-amino group behaves as an acid and the
a-carboxyl group as a base.
What would the titration curve of alanine look like?
Figure 1.12 shows that the titration curve for a
lanine looks
like that of a diprotic weak acid. Prom the midp
oint of the
first titration curve we can calculate the PKal
(for the
dissociation of carboxyl group) and from the mid-point of
the second titration curve we can calculate the pKa2 [fo
r the
dissociation of the amino group). From these two pKavalu
we can calculate the pH of the solution of alani
ne in its
zwitterionic form by the equation


Thus for alanine
Biophysical Chern

2.34 + 9.69
pH =
= 6.02
Thus, when we dissolve crystalline alanine in pure water, the pH of the solution
is 6..
Or if an alanine solution is brought to the pH 6.02, alanlne wI exist as a zwitt
erion. This p}
known as the/so/on/c po/nt of alanine as alanlne at this pH does not possess any
net chin
This pH is also known as the tsoelectrtc pH of alanine as at this pH alanine swi
electrophoretically immobile. In general the pH at which an amino acid exists as
a zwitterio]
known as the isoionic or isoelectric point of that amino acid.
We may now write the ionization of alanine indicating the specific pK

H -- C NH3+
PK =2.34
H C -- NH

C --' NH3
pH 6.02

There are many amino acids which have side chains containing dissociable groups.
groups might be acidic or basic in character. Some of them might contain an extr
a carboxy]
group in their side chain (e.g., aspartic acid, glutamic acid) while some others
might contain extra amino group (e.g. lysine}..Their titration curves look like
those of polyprotic acids. Titrati(
curves for aspartic acid and lysine are given in Figure 1.13 and 1.14 respective
ly. Their isoior
points and different pKa are also shown in the figures. The student can thus wri
te th<
dissociation sequence from the data provided in the figures ( the sequence would
be much li
that of alanine represented above). It may be mentioned, as evident from the fig
ures, that tt
Isoionic pH of dicarboxylic amino acids are quite low somewhere around 3, while
the isoion
pH for the diamino-monocarboxylic amino acids such as lysine is quite high, some
where arour
10. Table 1.8 lists the pKa and the pI values of important amino acids.

Equivaleflla of OH:
EClUiValenl of OH-

Figure 1.13. Tltratlon cw for aspartlc ac pK is for

a-COOH, pK,,, for -COOH, and pl for
Figure 1.14. Titration curve forlysi+ne, pK= is fo=
-COOH, pl for a-NH 3 ' and pK


and Bases

1.8 pKa and pl Values of Some Common Am/no Acids

Conjugate acid
Aspartic acid
Glutamic acid
a-COOH ,


What is it that we learn from the acid-base properties of these amino acids?
1.8 it becomes clear that the only amino acid which has a p/Q near to the pH of
body fluids is histidine. Its imidazole is half ionized at that pH. We have alre
ady considered
importance of pKa for the buffering action of solutions. Because it has a pKa ne
ar to the

PH, histidine possesses a significant buffering action in blood.

protein of erythrocytes is a unique protein in that it contains a large number o
in its structure. These histldine residues impart considerable buffering power t
o haemo
near pH 7, which is important to the role of red blood cells in the transport of
carbon dioxide by the blood.

of Amino Acids are pH-Dependent
"All the properties of amino acids which depend upon their ionization would natu
rally be
prevailing pH. We can cite the example of solubility of amino acids. Amino acids
least soluble at their isoionic pHs. They are much more soluble at pHs lower and
pHs. Thus, at a given pH different amino acids will have different solubilities
upon how far removed is the pH of the solution from their own isoionic points.
Other properties which are affected by the extent of ionization are the. metal c
optical rotation, the ultraviolet absorption at a given wavelength and even the
Can be Separated on the Basis of Charge
Can we utilize this pH-dependent ionization of amino acids for their separation?
A small
are given a mixture of three amino acids, alanine, aspartic
It is required thatwe separate these three amino acids from each other and
/hem in a more or less pure state. From Table 1.8 we can find out that the pl of

Aepertio Imid
Net hargo zero
Itet charge- 1
Figure 1.15. pH dependent separutWn of amlno acids. If the pH of a solutWn of th
ree arnlno acids, vz.,
aspar acld and argIne s brought to 6.0, due to ther different pK values alantne
becomes zwltterlon
the anode; argnlne becomes positively charged and moves toword the cathode.
If a potential difference is now applied across the vessel containing this solut
ion, aspart
acid will move towards the anode by virtue of its negative charge. Lysine on the
other hand wi
move towards the cathode and alanlne will remain immobile because it contains no
net char
(Figure 1.15). We can thus effectively separate a mixture of amino acids by elec
trophoresis o.
the basis of the differential charge they possess at different pHs. Amino acids
are usual.
separated by paper electrophoresis using high voltages (see chapter 12).
A better method to separate amino acids .on the basis of the charge they possess
at differen
pHs is ion exchange chromatography. We, however, defer a discussion on this tech
nique to later Chapter (chapter 1 I) where it is discussed in reasonable details
Ionization of Proteins i pH-Dependent
We have seen that ionization of amino acids is pH-dependent. It is therefore a c
that ionization of proteins should also be pH-dependent since proteins are amino
acids Itnke
together by peptide bonds. There are, however, significant differences. Since th
e a-amlno an
a-carboxyl groups of.successive amino acids are involved in the formation of pep
tide bon
(Figure I, 16) they ar unavailable for ionization. Thus, only the terminal, free
a-amino group a
the amino end of the protein, and the free a-carboxyl group at the c-termlnal en
d of the protek
remain ionizable. But since a protein consists of manyamino acids possessing dis

sociable side
chain groups, these dissociable groups will provide a protein with its character
istic charge
pattern at a given pH. As we have seen that the dissociation of these side chain
groups is also
pH-dependent, the ionization of proteins also is pH-dependent.
Biophys.d Chemist
aspartic acid, and arglnine are6.02, 2.98, and 10.76 respectively. Now if we bri
ng the pH off
solution containing a mixture of these three amino acids to 6.0, what will be th
e state ofionizatl,
of these amino acids? Since the pH is extremely near the pI of alanine, this ami
no acid will
present as a zwitterion with no net charge. Aspartic acid on the other hand will
be negativ(
charged at this pH and arginine will bear a positive charge.

and Bases
- (CH2).NH.C,NH2
- NH
- (CH2),I.N
pH 12
- NH2

Biophysical Chemts
The Three Dimensional Protein Structure is pH-Dependent
The conformation of a protein molecule in space is a result of a specillc coilin
g and fok
of the polypeptide chains. The molecule may be very large with molecular weight
several million daltons. The stability of the three dimensional structure is not
entirely du
the peptide bonds. Other types of bonds such as the electrostatic bonds between
ionized gro
of opposite charges are important for maintaining this stability. Since the numb
er of the ioni
groups and the extent of ionization both are a function of changes in pH, the st
ability of
three dimensional structure of proteins is also pH-dependent (also see Box 1.10)
Most globular proteins fold themselves up in a manner that most of the amino aci
ds v
potentially ionizable polar side chains are clustered together in one part of th
e molecule, wl
other amino acids with non-polar side chains are clustered together in another p
art of
molecule. Example may be cited of myoglobin in which all the polar side chain am
ino acids
clustered at the periphery of the molecule and the non-polar amino acids are clu
stered centr
The core of the molecule is therefore hydrophobic while the periphery is hydroph
Proteins Can Act as Buffers
Figure 1.17 shows the titration curve of protein taking gelatin as an example.'
characteristic feature of the curve is that it does not break sharply at any pH
and is relati,
flat at many pH ranges. This type of a titration curve is a hallmark of a good b
uffer with a I
buffering range. The absence of sharp breaks and the relative flatness at many p
H range,
due to the multi dissociab!e character of the protein. There are many ionlzable
groups wh
ionize successively and simultaneously throughout most of the pH range. We will
discuss ra
about proteins as buffers a little later.
78 910111213
Figure I. 17. Dissociation curve of standard gelatin preparatR)n in hydrochloric

acid or sodium hydroxide solutio

The isoelectric pH of a protein is the pH at which the protein is immobile in an
field. At this pH, the protein exists as a zwitterion having equal number of pos
itive and negal
charges, the net charge being zero. The isoionic point of a protein is defined a
s the pH at wh
the total number of H taken up by a protein is equal to the total number of H diss
ociated fr
it. Isoionic and isoelectric point of a protein will essentially be the same if
the protein does
bind long other than H. Since this is an ideal condition and not usually obtainab
le, the isoio
and isoelectric points of a given protein differ.
.Separation Methods for Proteins Depend on Ionization
Just as discussed for amino acids, proteins are also separated on the basis of t
he extenl
their ionization, i.e., on the basis of the charge density they possess. Thus, i
n an electrophore

and Bases
the mobility of a protein is a funcUon of its charge density, crcnt proteins
:with differing mobflities because their charge density is different and become
each other. The process is discussed in details in Chapter 12.
A much better technique of protein purification is that of isoelectxic focussing
. Use is
e of the isoelectric point of a protein. Suppose that the isoelectric point of a
protein is 6.0.
a pH gradient in a column so that the pH varies from 1-10 and place all the
the sample on top of the column and start the current, all the proteins will mig
the charge that they possess. At the space where pH of the gradient is 6, while
r proteins will continue moving, the desired protein will become immobile since
it possesses
charge; the pH is isoelectric for it. The method is discussed in reasonable deta
ils in
Another powerful tool for protein purification which also depends upon the charg
e density
ion-exchange chromatography. We defer a discussion of this technique to Chapter
of Proteins is pH-Depenflent
We have already seen that the three dimensional structure of proteins is depende
nt upon
stability. Biological activity of proteins is known to be an attribute of one sp
of the protein molecules (also see Box 1.10), Thus, any change in pH, which is
to the three dimensional structure of protein molecules is definitely detrimenta
l to
We know that enzyme activities are a function of pH of the medium. Large
from optimal pH alter the activity of an enzyme drastically. At extreme pHs the
might become denatured losing its function completely. Even slight changes in pH
r not be of a destabilizing nature, alter the activity of an enzyme in particula
r, and
in general, This was primarily the evidence which led to the suggestion that the
an attribute of a small part .of the whole molecule, the active site (the site
is engaged in catalysis). Small pH changes which might not alter the structure o
f a
substantial enough to alter the ionization of a single dissociable group within
site. This is the reason why slight alterations in pH cause a change in the acti
vity of a
may also be mentioned that the effect of pH on the biological activity of protei
ns may
evidence about the dissociable groups present in an active site.


In reactions catalyzed by general acids or bases the catalyst functions as an ac
ceptor or
protons. Often the critical proton transfer step is to or from a carbon atom of
state species. How can we ascertain that a proton transfer is the mechanism behi
can carry out the reaction (which we suspect to be acid-base catalyzed)
(heavy water) rather than H20. Deuterium is an isotope of hydrogen and has twice
mass as hydrogen. Due to isotope effect (see Chapter 13) deuterium ion will reac
t much
' than the hydrogen ion. Thus, "ff the reaction is catalyzed by a proton transfe
r step,
!take place at a much slower rate in heavy water. Using such strategies many enz
have been shown to be acid-base catalyzed. Many times both a general acid and a
base are involved in catalysis; the acid donates a proton to the reaction interm
he base accepts one.
be expected, the strength of the general acid or base, i.e., its proton dissocia
of reactions catalyzed by proton transfer steps. The most significant
at physiological pH is the imidazole group of histidine which has a pKavalue
6.0. This pKa enables it to act both as a proton donor and a proton acceptor at
pH. Another factor which can affect the rate of acid-base catalyzed reactions is
or accepts a proton. The imidazole
is particularly effective in this case also. It has an equal rate of protonation
physiological pH with a half-time of less than 0.1 us. There are several enzymes
catalytic properties to the tmidazole group of histidine.
general acid-base catalysis is, can be proved by a simple example. To hydrolyze
bonds without enzymatic mediation, very high concentrations ofH+ and OH- are req
long reaction periods. Chymotrypsin achieves this hydrolysis
pH and at body temperature fairly quickly.
of Most Biomolecules is pH-Dependent

which pos.sess multiple dissociable groups will be affected by changes in

similar to the proteins described above. Thus, nucleic acids, mucopolysaccharide
will be affected by changes in pH. Their three dimensional structures and
their biological activity would be affected by changes in pH.
t only biopolymers but even smaller metabolites may be affected by pH. One of th
e main
t of the cellular metabolites being charged is that the plasma membrane is
lmpex?meable to charged species. It is therefore easier for the cell to retain t
the cell. Important ionizable groups possessed by cellular metabotites

are carboxyl and amino groups, and the phosphate group. Even the rate of catalys
metabolites may be dependent upon their extent of ionization and will therefore
upon pH.
Biologically Important Buffers
We have seen how all major biomolecules are affected by pH changes. The conclusi
we have derived is that the biological activity of most biomolecules is dependen
t on pH. We
therefore grasp the importance of maintenance of the pH of physiological fluids
limits conducive for normal functioning of cellular processes. The control of pH
in biolo
systems is achieved by the action of efficient buffering systems whose chemical
that they can resist pH changes due to the metabolic production of acids such as
lactic a
and bases such as ammonia. The major buffering systems found in cellular fluids
are I
bicarbonate buffers, phosphate buffers and protein/proteinate buffers.
Buffering of Blood
An interesting example of buffering in biological systems is provided by what oc
blood. The pH here is maintained within extremely narrow limits of 7.36-7.4 for
venous bl
and 7.38-7.42 for arterial blood. Three distinct buffering systems are responsib
le for maintair
the pH within these narrow limits : (/) H2CO3 and HCO , (//) the acid and base s
oxygenated haemoglobin, and (///) the acid and base species of deoxygenated haem
A detailed description of haemoglobin is uncalled for here, but what can be ment
that this iron containing protein resides within the red blood cells in relative
ly abundant quant
14-16 grams/I00 ml of whole blood. The predominant function of haemoglobin is to
oxygen from lungs to respiring tissues. Within the lungs, oxygen from the incomi
ng air ent
the erythrocytes and becomes bound to the iron atoms of haemoglobin. The oxygena
haemoglobin, while it is being carried by the blood, donates its oxygen to vario
us respi
tissues. In this process the oxyhaemoglobin becomes deoxygenated and via venous
blood retu
to the lungs to indulge in the oxygen transport cycle again. While engaging thus
in its prim

role of oxygen transport, haemoglobin also contributes importantly to the buffer

ing of bl
How? Let us consider the following points before we elaborate the whole mechanis
It is known that oxygen binding to haemoglobin is weakened by decreasing
the pH.
other words, oxygen dissociation from haemoglobin is promoted by increasing hydr
ion concentration. This phenomenon is known as the Bohr effect after its discove
CO2 (diffusing from the tissues into the erythrocytes) does not reside i
n the erythroc
as such. It is converted by the enzyme carbonic anhydrase to H2COa.H2C0a ionize
HCO and H so that the ratio of HCO /H2CO3 becomes 20/1 (substitute this r in Hend
erson-Hasselbalch equation along with 6.1 as the pKa for H2CO3 and calct
the pH; it comes to 7.4, the pH of blood l). The ionization of H2CO8 can cau
decrease in pH because it increases the hydrogen ion concentration. In allwe may
that input of CO2 can decrease the pH if H is not eliminated.
BLOOD. VII= 7.4 .

HC03 +H+

CO2 1-12J 1-12J3

How is the H+ generated by incoming CO2 quenched? To answer this question,
have to consider the acid-base properties of haemoglobin.

Acids and Bases
We have already mentioned that haemoglobin is rich in histidine, an amino acid
which has a pK of about 6.0 (imidazole group) making it predominantly ionlzable
the blood pH. We denote haemoglobin by the symbol Hb. We can include another H i
this symbol to denote the ionlzable hydrogen. Experimental determination proves
that oxygenated haemoglobin (HHbO2) has a pK of 6.-62, while deoxygenated
haemoglobin (HHb) has a pK, of about 8.18. This automatically means that oxygena
haemoglobin is a stronger acid as compared to deoxygenated haemoglobin. Thus,
at pH of blood, 7.4, the base form of oxygenated haemoglobin would predominate
(HbO . ). On the contrary at the same pH, the acid form of deoxygenated haemoglo
(HHb) would be predominant.
(pKg. = 6.62)
BLOOD. pH = 7.4
HbO. + H+
BLOOD, pH = 7.4

Hb- + H

(pK = 8.18)
With these points in background, let us consider the bufferLng of btood. We have
seen that
incoming C02 causes an increase in H ion concentration which has to be eliminated
. This H
reacts with the base form of oxygenated haemoglobin, HbO . (which is predominant
at pH 7.4)
converting it to its acid form HHbO2, At this point the Bohr effect comes into p
lay and oxygen
dissociates from haemoglobin and diffuses into the tissues. The acid form of oxy
becomes deoxy. We have already seen that deoxyhaemoglobin has a higher pK and do
es not
dissociate to a great extent. It thus remains as HHb. What has taken place now i
s that not only
the H released by incoming CO2 has been buffered, but in the process the objectiv
e of oxygen
transport to the tissues has also been achieved.
The CO2 in the form of HCO now leaves the erythrocyteS and is carried to lungs t
hrough the venous blood. To counterbalance the exit of HCO , CI- moves into the
erythrocytes from
plasma. This is known as the chloride shift.

When the venous blood reaches the lungs, HCO and 02 enter erythrocytes and CI- e
xits. 02 binds to HHb converting it to HHbO2. The Bohr effect, however, does not
take place because
the ionizable hydrogen is quickly donated to HCO to convert it to H2CO3.HHb02 ge
ts converted to HbO .HbO . can now indulge in transporting oxygen while it is ca
rried by the blood to different tissues. H2CO3, by the reverse action of carboni
c anhydrase is converted to H20 and

"::::) .::::::::::i!!ii!!!i!
H,CO= H+ + HCO= :!:!:!:::: 7,
n :::::::::::
.:.:.:-.. o
.:::::::::: u
I=:: ::::::.
" :::::::::::!
(A} Events in enjthrocyte when arterial blood reaches the respiring tissue.
: :Z ::;:::::::
(B) Events "in enjthrocyte when venous blood reaches the lungs.
Figure I, 18. Buffering of blood. Role of HCO / H 2 CO3 and HbO / HHbO2 buffers,
From the foregoing discussion we can conclude that the main buffering systems
are the HCO ;/I-I2CO3, HbO ;/HHbO., and Hb-/HHb. In addition, blood contains
proteins and m'ay substances possessin phosphate groups. Thus, two additional
systems which operate in blood are HPO4-/HPO and proteinate-/protein systems. Th
systems, however, contribute less to the buffering of blood than the main system
s discusse
Buffers of Tissue Fluids and Tissues
The main buffering system present in spinal fluid, lymph, and exudates are simil
ar t
those present in blood. The HCO /H2CO system is much more predominant in these f
As compared to this the contribution of potein buffers is much smaller.

Adds ar Bases
In tissues, the buffering systems are mainly the HCO /H2CO3, and the pro
The contribution of the latter, however, is much more here as compared t
o their contribution in
tissue fluids. Within the cell many organic acids and their conjugate ba
ses also exert buffering
actions. We have already seen citrate in this light.
Indicators are substances which demonstrate characteristic color properties. The
y show
one color above a characteristic pH and another color below that pH or pH range.
They are often
used for pH measurement when high levels of accuracy are not required (their use
has decreased
in modern days and the pH meter is the most often used instrument). The indicato
r with which
we are all familiar is litmus which is red when acidic and blue when basic. Othe
r indicator
substances also exhibit characteristic change in color with change in pH; their
colors might,
however, be different from those of litmus. What is the mechanism behind such co
lor change by
indicators? The indicators act like a weak acid dissociating in the following ma
nner :
Him H + In(acid)
(conjugate base)
In acid solutions where [H] is high, the indicator dye does not dissociate apprec
iably. As
pH is raised and [H+] decreases, the dissociation of dye becomes predominant til
l a stage comes
when the dye is predominantly dissociated. The dye exhibits different colors in
the dissociated
and undissociated states.
We can write an equation for the dissociation constant of indicators.
When the dye is half dissociated
[HInl=1 Thus [H+] = KI.

LIn- .J
The dissociation constant at equilibrium for an indicator is therefore the value
of H at
which the color change of dye is half complete. A negative log of this value wil
l give us the pKa
of indicator.
Table 1.9 gives a list of the commonly used indicators. By using two or more ind
icators we
determine the pH of a given sample within one to two units. For example, a given
sample is
colorless for p, henolphthalein, The pH of the sample must be less than 9. The s
ame sample
however tests blue for bromothymol blue. Its pH, therefore: can not be below 8.
The pH of the
given sample, therefore, must be within pH 8 and 9.

Table 1.9 Some common Acid-Base Indicators
pH Range
Acid Color
Base Color

Methyl Violet
Thymol Blue
Methyl Yellow
Methyl Orange
O.5- 1.5
1.2 - 2.8
2.9 - 4.0
3.1 - 4.4

Bromophenol Blue
Bromocresol Green
Methyl Red
Chlorophenol Red
Bromothymol Blue
Phenol Red
Cresol Red
Thymol Blue

Alizarin Yellow R
3.0 - 4.6
3.8 - 5.4
4.2 - 6.3
4.8 - 6.4
6.0 - 7.6
6.2 - 7.5
6.4 - 8.0
7.2 - 8.8.
8.0 - 9.6
8.0 - 9.8
9.3- 10.5
10.1 - 12,0

Papers impregnated with several dyes are commercially available. The change in t
colors when dipped into a sample iscompared with a color-pH code on the dispense
r. These
papers are very efficient and can determine the pH of a given sample to about 0.
1 of a pH unit.
These papers are, however, useless when the test solutions are highly colored or
when very
high accuracy is needed. For such measurements, pH meters are used. These are di
Earlier on we have seen that indicators are unsatisfactory for measuring pH of s
which are colored. We have also seen that for works which require absolute accur
acy, indicators
are not a good tool for pH measurement. Such situations call for electrometric d
etermination of
pH. For a student of biochemistry, probably the most familiar instrument is the
pH-meter. Its
operation is quite simple; it consists of a glass electrode which when dipped in
to a solution
develops an electrical potential depending upon the hydrogen ion concentration a
nd this potential
is read off the display which is calibrated into a pH scale. Let us try to under
stand the basic
principles underlying the working of a pH meter.
Electrode Potentials
When a strip of metal (electrode) is dipped into water, it tends to dissolve owi
ng to its
solution pressure, P. While the atoms of metal go into solution, they leave behi
nd their loosely
bound valence electrons as a negative charge on the electrode. Since the electro
de has developed
a negative charge, it now attracts the positively charged metal long which have
already gone
into solution. Some of the positively charged metal long might reattach themselv
es to the
negatively charged electrode. The tendency of the atoms to leave the metal and t
he tendency of
metal ion.s to reattach themselves, finally becomes balanced and an equilibrium
is reached. At

Acids and Bases

equilibrium some positively charged metal long remain in solution and the opposi
te charge of
the electrode and the metal long gves rise to a potential difference.
Let us now alter the conditions a bit by dipping the metal int( a solution of on
e of its salts.
This is an altogether different situation because there are many metal long alre
ady in solution.
These metal long will oppose the separation of more metal long from the electrod
e and an
equilibrium will be achieved early..The point of'equilibrium in this case will b
e dependent upon
the relative values of the two opposing forces: the solution pressure (P) of the
metal and the
osmotic pressure (p) of the metal ions-in solution. Three possibilities arise (F
igure 1.19):
"Figure I. 19. Diagram indicating how electrode potentials arise when a metal st
rip is dipped into a solution of one of
its salts.
P = Solution pressure of the metal; p = Osmotic pressure of the metal..
P > p. Since the solution pressure is higher, the atoms from the metal s
trip continue
to dissolve as positive long till the accumulated charge is strong enough to opp
further dissolution. The metal strip in this situation acquires a negative charg
e as
compared to the solution which becomes relatively positive.
P < p. The opposite takes place. Since the osmotic pessure of metal long
in solution is
higher, they attach themselves to the metal strip increasing the positive charge
on the
electrode. The solution becomes relatively negative.
P = p. Since both the opposing forces are equal, metal long neither leav
e the electrode
nor the metal long in solution get attached to the electrode. No potential devel
Taking thermodynamic reasoning into consideration, the potential difference betw
een a
metal and a solution of one of its salts is given by Nernst equation

E = --In-... (1)
nF p
where E = electrode potential, R = gas constant (8.316joules per degree), T= abs
olute temperature,
n = valency of metal ion, F= faraday (96,500 coulombs), P= solution pressure, an
d p -- osmotic
pressure of metal long in solution. The natural logarithm is denoted by '/n'.
We know that RT/F is constant for any given temperature. Therefore, the magnitud
e and
the sign of the electrode potential, E ,will be dependent upon n, P and p. If we
use the same
metal, the electrode potential will depend solely upon osmotic pressure, p, of t
he solution in
which the electrode is dipped. Since osmotic pressure can be regarded as proport
ional to
concentration, we can say that the electrode potential is a function of concentr
ation of the
metal long in solution (actually the electrode potential is dependent upon activ
ity and not
concentration). We may therefore rewrite equation (1) by replacing the osmotic p
ressure term
with a term for concentratiort.-

E = RYlnP
where C = concentration of the metal long in solution.
Since the electrode potential developed by a metal strip is dependent upon the c
of the metal long, is it not possible to measure the concentration of metal long
in any given
solution by measuring the potential developed by the electrode? Theoretically th
e answer is in
affirmative. However. practically it is impossible to measure the potential Of a
half cell (one
electrode dipping in a solution). This problem can be circumvented ff we provide
for a second
electrode of the same metal dipping into a solution of a different concentration
. The two electrodes
will now develop different potentials. If the two electrodes and the two solutio
ns are suitably
connected, an electric current will pass from one electrode to another, the elec
tromotive force of
which will be equal to the difference between the two electrode potentials. Thus
E =E1-E2
RT In C2 ( l and P2 cancel out since they 1
= nF C kate identical for the same metal]
If we can flx:the potential of the second electrode then the potential of other
half-cells can
be determined relative to it. In other words, the problem of measuring the poten
tial of a half-cell
in the presence of another half-cell is solved by referring all potentials to a
standard reference
potential. The electrode(s) which is used as a standard is known as the referenc
e e/ectrode. We
will consider some of the reference electrodes used in electrometric determinati
on of pH in the
following pages.
The basic function of a reference electrode is to maintain a constant electrical
against which deviations may be measured, The. desirable characteristics that a

electrode should possess are (0 it should be easy to construct, and (//) it shou
ld develop potentials
which are reproducible even if small currents are passed.
Various reference electrodes are in use and some of them are discussed below.
The Hydrogen Electrode
The hydrogen electrode consists of a piece of platinum foil dipped in a 1 M solu
tion of
hydrogen long. The solution used to provide this hydrogen ion activity is 1.18 M
HC1 (the potential
produced is dependent upon the activity and not the concentration: see Box 1.5).
To increase
its surface area, the platinum foil ts coated vth platinum black. Hydrogen gs at
one atmosphere
pressure is bubbled over the platinum foil, The platinum strip saturated with hy
drogen gas.
acts exactly as the metal electrodes described above when dipped in a solution c
hydrogen long. This arrangement in toto is known as the standard hydrogen electr
(Figure 1.20) and it is arbitrarily assigned a potential of zero under all condi

lx 96, 500 Ige 2
Acids and Bases
------ Hydrogen gas inlet
Gas outlet
Platinum strip
Hydrochloric acid
Fgure 1.20. Construction of a Hydrogen Electrode.
We can measure the pH of an unknown solution if two hydrogen electrodes are imme
into two solutions of differing hydrogen ion concentrations, the [H] being consta
nt in one of
these solutions. The electromotive force developed in such a system will be an i
ndex of the [H+]
in the unknown solution. If we consider the potential of normal hydrogen electro
de as Eho, and
that of the hydrogen electrode in the unknown solution as Eh, the e.m.f, obtaine
d on c,ompleting
the circuit will be
e.m.f. (volts) = Eh- Eho
If we denote the hydrogen ion concentration in two different solutions in which
we have
dipped the hydrogen electrodes by [H+]I and [H+]2, hen by. the Nemst equation th
at we have
discussed previously, the e.m.f, is given by
e.m.f. = Eh- Eho = --log [ H+ ]i
Substituting the values of R, n and F in the above equation we have
But loge = logo x 2.30258. Substituting this value we get,
8.315 x T x 2.30258
I x 96,500

Biophysical Chemistry
We have already seen that the H actity around a standard hydrogen electrode is fi
xed at
I. The above equation therefore can be written as
e.m.f. = 0.00019837Tlog
but log can be written as log 1 - log [H+]2. Since log 1 = 0, we have - log [H]2.
As we have
seen in the previous chapter, - log [H] = pH. The above equation therefore become
e.m.f. -- 0.00019837 T pH.
At 25C e.m.f. = 0.059 pH


From (3), it is evident that if the potential difference (e.m.f.) between the st
andard hydrogen
electrode and the electrode in the unknown solution is experimentally determined
, the pH of
the unknown solution can be easily calculated.
Although hydrogen electrode is the standard of reference, it is extremely inconv
enient to
construct and maintain it for everyday work. A source of ultrapure hydrogen is r
equired and it
is essential to maintain the correct partial pressure within the cell. Even trac
es of impurities
either in the gas or in the solution are enough to poison the electrode. Moreove
r, the electrode
responds to numerous redox couples and therefore strong oxidants or reductants a
re detrimental
for pH measurement, Due to these disadvantages its use is extremely limited. It
is, however,
used exclusively .for calibrating other reference electrodes. It is also used fo
r measuring hydrogen
ion concentrations of solutions in which no other electrode will operate satisfa
The Calomel Reference Electrode

The design of calomel electrode varies for different applications, but a general
calomel electrode can be illustrated as in Figure 1.2 I. The electrode consists
of a strip of platinum
sealed into glass and allowed to dip into mercury. A paste of calomel (Hg2CI2, 0
.1 M.) is held
against the mercury by means of a sintered glass plug or cotton wool. The whole
electrode is
filled with saturated KCI. Contact with an outside electrolyte is maintained thr
ough a porous
ceramic plug.
Side arm for
filling KCI
Sintered Glass
KCI crystals
Ceramic plug
Figure 1.21. Structural features of a calomel reference electrode

pH =
E - 0.246
Acids and Bases
The calomel electrode is a lalf-cell and can be represented as
Pt I Hg] Hg2C12 I KC1 (saturated)
(Every vertical line denotes an interface at which a potential is developed).
If the KC1 solution is kept saturated, all the potentials developed in the calom
el half-cell will be
constant. All calomel electrodes have a side arm to replenish KC1 solution.
The potential in a calomel hf-cell is derived from the primary reaction
H ++
g2 +2e-2Hg
The corresponding Nernst equation for this reaction is
e.m.f. = E
connects calomel and hydrogen electrodes to a voltmeter, a potential of 0.246 my
(at 25C). Thus, if we connect a calomel and hydrogen electrode together and the
electrode is made to dip in a solution of unknown [H], the potential which will d
be 0.246 my higher than the situation where both the electrodes used were hydrog
The equation of pH, when a calomel electrode is used as reference would therefor
Calculation of pH
From the text we know that at 25C using saturated calomel electrode pH =

0.246)/0.059. When the electrodes are dipped in a solution the voltmeter reads
0.652. What is the pH of the solution ?
0.652 - 0.246
= 6.9
pH of the given solution is 6.9
(2) Calculate the potential developed if the pH of a given solution is 2.6.
Ans. 0.4
Calomel electrode is extensively used as a reference electrode for pH measuremen
t. It is easy to
prepare, cheap and quite easy to maintain. The potential developed by this elect
rode is
reproducible and constant.
The Silver/Silver Chloride Electrode
Basic design of this electrode is provided by Figure 1.22. It consists of a meta
llic silver wire
coated with silver chloride and immersed in a saturated potassium chloride solut
ion. The potential
of this system is derived from the primary reaction

Biophysical Chemistry
The potential developed may be calculated from the Nernst equation
e.m.f. = E,--lg[Cl= 0.222-0.0509 log [CI-] (at 25C1
From the above equation it bec.omes clear that the potential of the reference el
ectrode is a
function of the chloride ion concentration (activity). In order that the chlorid
e ion concentration
remains constant at all conditions of humidity, a saturated potassium chloride s
olution is
used. Electrical contact between the reference electrode and the solution being
tested is
maintained through a potassium chloride salt bridge. This Junction is made throu
gh a porous
ceramic membrane embedded in the bottom of the reference electrode.
Silver/silver chloride electrode is extremely easy to maintain and it develops a
potential. It is being used as a reference electrode in most of the current Inst
Side arm for
filg KCI
Saturated KCI -..
KCI crystals -Ceramic plug
Figure 1.22. Structural features of an Ag : AgCl reference electrode.
The measurement of pH by glass electrode involves the use of two reference elect
separated by a glass membrane whose function is to establish an electrical poten
tial depending
upon the hydrogen ion activity of the solution being tested. The design of glass
electrodes is
enormously variable, but a basic construction is shown in Figure 1.23. It consis
ts of a high
resistance glass tube with a thin. low resistance glass bulb fused at the bottom
. The bulb is
- responsible for the pH sensitivity; the rest of the electrode is insensitive t
o [H+]. The tube is filled

up with 0. I N solution of HCI. Dipping in this solution is a silver/sflverchlor

ide electrode. The
other reference electrode might be a calomel electrode, but in most current inst
ruments this
electrode also is an Ag/AgCl electrode. When both electrodes are dipped Into a s
ample, the
resulting e.m.f, gives the pH of the solution.

and Bases
Glass stem
: AgCl
eiectrode J
0. IN HCI -. -- pH sensitive
glass membrane
Figure 1.23 Diagram of a glass electrode.
It is essential to understand the nature of the pH sensitive glass membrane to u
electrode works. X-ray diffraction studies have revealed that the glass membrane
ia network of silicate and aluminate long (Figure 1.24). The holes in this latti
ce-like structure
be occupied by cations of varying size. These holes, however, cannot accommodate
because of the strong repulsion of the oxygen containing long. By careful manipu
lations during
it is possible to obtain a membrane whose holes can accommodate only H long.
membranes will then be sensitive to hydrogen ion activity.
) gen atoms

con atoms
Figure 1.24. Structure of a pH-sensitive glass membrane as revealed by X-ray dif
fraction studies.
How does a glass membrane respond to differences in hy4rogen ion activity?. The
belief is
that the glass electrode works by an ion exchange process. It is believed that t
he membrane
consists of three layers, a dry glass layer sandwiched betweentwo hydrated layer
s. Let us now
see what events can occdr when this glass electrode is placed in aqueous solutio
ns of neutral,
basic, and acidic reactions (Figure 1.25). We begin with the basic assumption th
at in the holes
of the lattice-like network of the two hydrated layers, hydrogen long are presen
(i) When the electrode is placed in a neutral solution : In this situation hydro
gen long from

the concentrated HCI in the inside of the glass electrode become bound to the in
ner hydrated
surface. This results in the release of an equal number of protons from the 'hol
es' of the outer
hydrated surface and the neutrality of the membrane is maintained (Figure I..25


CF ' H
H Tj
u H+
Cl" H ."
Cl" H

Biophysical Chemistry
H+ + OH'Na+----H20

H+ + OH" Na+-) H20

Cl" H :---b H+ + OH'Na+ H20
.- H+ + OH" Na+.b, H20
=--b H+ + OH" Na+---- H20
H + + OH'Na +-- H20


Internal External
internal External
solution solution
solution Solution
Figure 1.25. The glass electrode works by ion exchange mechanism. A schematic di
agram showing events at different
go When the electrode is placed in a basic solution : Consider that the basic so
lution is
that of NaOH which dissociates fully to give Na and OH-ions. Since a high number
of OH- long are present outside, the H long from the outer hydrated layer leave t
heir 'holes' and go
into the sample solution where they combine with OH- long to give H20. The Na lon
g remain
unquenched and therefore positive charge at the outside of the glass membrane in
creases. Let
us see what is happening at the inside of the membrane. Since the outside 'holes
' are becoming
vacant, more and more protons from the HCI solution inside, become bound to the
inner hydrated
surface. This leaves the Cl-ions unquenched and consequently the inner side of t
he glass
membrane develops an excessive negative charge. The separation of charge on two
sides of the
glass membrane gives rise to the electrode potential which is an index of the pH
of the solution
(Figure 1.25 B).

(iii) When the electrode is placed in an acidic solution : In this situation, th

e concentration
of H+ long at the outside of the membrane is high. Consequently, the 'holes' in
the outer hydrated
surface are occupied by H long. Now, to maintain the electroneutrality of the mem
brane, H
long from the 'holes' of the inner hydrated layer are released. These H+ long de
crease the excess
of negative charge inside due to CI- long. Thus, while the inside becomes less n
egative, the
outside is becoming less positive. Again, this separation of charges is the sour
ce of the electrode
potential (Figure 1.25 C).
The overall potential of the glass electrode is a contribution of several potent
ials: (/) the
potential of the internal silver/silver chloride electrode; (//) the potential d
eveloped at the inner
glass surface; (No the potential developed due to imperfections in the glass sur
face; and (iv) the
po.t.ential developed at the outer glass surface. However, potentials (/), gO, a
nd (///) are all constant

Hg/Hg C12)
Acids and Bases
for a given electrode and it is only (iv) which changes with the pH of the test
solution. For a given
glass membrane, then, all these constant potential may be collected into a gener
al constant EG,
and an equation may be written.
2.303 RT
e.m.f. = Eo +
(pH outside)
We know that E,., R, and F are donstant. Thus, e.m.f, depends only on the pH and
temperature. This equation therefore tells us how important it is to maintain th
e temperature
of the buffer used to standardize the pH meter and the temperature of the test s
olution at the
same level for the pH reading to be correct.
When a pH sensitive glass electrode and a reference electrode are dipped in a so
lution, a
galvanic cell is set up. The cell can be written as follows:

(0.1 N HCI)
Each vertical line in the above representation denotes an interface and a .poten
tial is
developed at each interface. The potential of the whole galvanic cell is the alg
ebraic sum of the
potentials developed by the glass (indicator) and the reference {Ag/AgCI or Hg/H
ggCI2) electrodes.
e.m.f. (cell) = e.m.f. (re0 3, e.m.f. (glass) -Since e.m.f. (ref) is constant, e.m.f. (ceil) varies only with a variation in th
e pH of test
solution (if the temperature is constant). The modem glass electrodes develop po
tentials which
give a linear relationship with pH .changes.
Floure 1.26. Various kinds of pH-s.e.nsttive electrodes. {a) general purpose gla
ss and reference electrode: (b) combination electrode for pH measurement of flat
moist surfaces; (c) combination micro-spear electrode
for small sample volumes.

Bophysical Chemistry
The glass electrode can be combined with an external reference electrode. In oth
er words,
the reference electrode can be built in the same unit. Such an electrode known a
s a combination
electrode is illustrated in Figure 1.26. Also illustrated in the same figure are
various.kinds of
combination electrodes used for different purposes.
The glass electrode can be dsed to measure pH of virtually all kinds of solution
s, including
those containing strong oxidizing and reducing agents. It may be embedded in sem
isolid materials
such as cheese or butter and give a satisfactory pH value. It is also suited for
pH measurement
of biological fluids. It however, has certain disadvantages {which can be circum
vented}. Firstly,
the electrical .resistance of the glass membrane is high. Use of high impedance
amplifiers is
therefore mandatory for potential measurement. Secondly, at high pHs (higher tha
n 9) the
electrode may start developing potentials due to sodium long rather than due to
H long. This
problem has to be ameliorated by manufacturing a special glass with low sodium c
The pH meter is basically an electronic voltmeter (or potentiometer) designed fo
r use with
a glass electrode system. It is composed of(/) a reference electrode, (//) a gla
ss electrode responsive
to the pH of the solution surrounding it, and (rio an electrometer, which is a d
evice capable of
measuring very small differences in electrical potentials in a circuit of extrem
ely high resistance.
The pH meters are usually so constructed that the true zero of the voltmeter is
at or near
pH 7. Before use, the pH meter must be standardized with a pH 7 (or pH near 7) b
adjusting the zero calibration to give the correct reading with the temperature
control. Then a
second buffer, whose pH is near to that of the sample is substituted and the met
er is adjusted
to give the correct reading with the temperature control, This procedure helps t
o establish the
correct linear relationship between my and pH. Moreover, this standardization mu
st be done
each time a pH measurement is to be done. This is essential because there are su
btle changes
in various potentials due to the ageing of the electrode. The standardization ju
st before a

measurement tends to nullify these potential changes due to electrode ageing.

To be of use, the meter of pH electrometer must give a reading consonant with th
e pH of
the sample. This needs the signal to be amplified greatly before it is strong en
ough to activate a
standard milliammeter or a millivoltmeter. The following equation states that th
e pH sensitive,
galvanic cell potential (E3 to be amplified is
e.m.f. (cell) -- e.m:f. (rei + e.m.f. (glass)

e.m.f. (glass)
2.303 RT
= E +pH

2.303 RT
e.m.f. cell
= e.m.f.tref +Eo
e.m.f. {cell)
= E + mpH
where E = e.m.f. {rel) + EG, and m = 2.303 RT/F
The amplified signal is then directed to a meter which produces a deflection rel
ated to the
pH of the solution.

Acids and Bases

In general, the determination of pH using a pH meter is quite simple. The soluti
on is
placed in a small container. The glass and the reference electrode (or the combi
nation electrode)
are dipped into this solution so that the glass bulb is dipped completely. The p
circuit is closed and adjusted till the null point is obtained. The pH can then
directly be read off
the display. Two general precautions must be taken; (t) As stated above, the pH
meter must be
standardized before every measurement, and (//) when not in use, the reference a
nd the glass
electrode must be kept immersed in water so that the pH sensitive membrane does
not become
dehydrated. The following points must be kept in mind while measuring the pH.
Sodium Error
General purpose glass electrodes are to a certain extent permeable to sodium lon
g also.
Thus they can produce a potential for Na in the same way that they do for H. There
fore in
solutions where Na is present, the actual pH determined by glass electrodes is l
ower than what
it should be. This is so because the electrode reads a sum of both H and Na long,
i.e., the
recorded pH is -log |H and Na] and not just-log [H]. NaturaLly, as the concentratio
n of Na
increases, the pH decreases. The effect of this problem is not so noticeable whe
n the pH is low.
But when one is working at high pH (due to NaOH), the pH reading could be off by
as much as
two units if I M NaOH is used.
There aretwo ways to correct this problem. The first is to use Na impermeable gla
electrodes. However, if this is not possible, then one should work preferably wi
th KOH when
working at high pH and avoid NaOH if possible. The general purpose glass electro
de is not
permeable to the bigger K long.
Electrode Contamination
It is a common precaution to wash electrodes frequently with acid or With deterg
ents or
sometimes both. The reasons are not fa to see. In our discussion on glass electr
odes we have
seen that these glass membranes have holes for H. Naturally, if these holes are b
locked, the

electrode Will give a faulty reading owing to reduced permeability. For biochemi
sts this
permeability problem is quite common since they work With proteins. Proteins can
form a thin
film on the glass. This impedes permeability. This film can be washed away compl
etely with
either acid or detergents. Thus, it cannot be emphasized enough that if one is w
orking With
proteins, the electrode must be washed very frequently with acid or detergents.
Certain commonly used buffers react With the components of glass electrodes. One
is that of Tris[tris-(hydroxymethyl)aminomethane] buffer. This buffer can cause
large changes
in pH readings. One should read the manual supplied along With the electrodes ca
refully. The
- buffers that can cause changes in the electrode areusually listed there. One s
hould then avoid
working with these buffers as far as posslble.
Concentration of Long
Previously we have. discussed that the pH is actually a negative log of H activit
y and not
H+ concentration. At low concentration the activity and concentration are the sa
me, However,
at high concentration the activity actually becomes lower than the concentration
. Thus, one
must avoid measuring pH of very concentrated solution. There is another reason f
or doing so.
Other long can also affect the activity of hydrogen long. Thus the pH of a buffe
r will vary both
with its own concentration and with the concentration of other salts in the solu
If one is preparing a stock buffer solution which is very concentrated, it is wr
ong to adjust
the pH of the stock so as to give the correct pH upon dilution.. Rather the conc
entration should
be so prepared that upon dilution it gives the correct pH; the pH of the diluted
buffer should be

Biophysical Chemistry
pH papers are for rough use. The commercially available pH papers claim that
measurements can be very sensitive - difference of 0.2 pH units can be detected.
there are numerous pitfalls involved here. For biochemists, the pitfalls are hig
her, and, again
these pitfalls result from having to work with proteins. Many proteins are known
to cause
errors of several pH units when working with pH papers. High salt concentration
can also
cause large errors.
Additionally, some components of the solution may react with the pigments on the
and cause color changes not related to pH at all.
Suggestions For Further Reading
1, Henderson, L.J., The Fitness of the Environment, Beacon Press, Boston, 1958.
2. Edsall, J.T. and Wyman, J., Biophysical Chemistry, Academic, New York, 1958,
Vol. I.
West, E.S., Todd, W.R., Mason, H.S. and Van Bruggen, J.T., Textbook ofBi
ochemlstry, 4th
ed., Macmillan, 1966.
4. Segel, I.H., B/ochem/ca/Ca/cu/at/ons, 2nd ed., Wiley, New York, 1976.
5. Bates, R.G., Determination ofpH ; Theory and Practice, 2nd ed., Wiley, New Yo
rk, 1973.
Wfllard, H.H., Merritt, L.L., Dean, J.A. and Settle, F.A., Instrumental
Methods of Analysis,
6th ed., CBS, New Delhi, 1986.
Carbonic acld has two pKa. pK = 6.35 and pK2 = 10.3. (a) Draw a titratio
n curve indicating
the p, attern of ionization of carbonic acid as a strong base is added. (b) Iden
tify the pH ranges
where buffering occurs. (c) Identify the predominant chemical species at each of
the following
pH values : 4,5,6,7,8,9, I0, I 1 and 12. (d) Identify the pH at which HCO specie
s would exist in a 50-50 equilibrium with its conjugate base.
You are given two buffers : (a) 0.1 M phosphate buffer of pH 7.7 and (b} 0.1 M p
buffer at pH 6.71. If acid is to be added to these buffers, which of them, do yo
u think, will
resist the pH changes better?

When the ratio of salt to acid concentration is unity, the buffer has maximum ef
Prove this statement mathematically taking an example of acetate buffer, pK of a
cetic acid is
What is the major ionic species present at pH 7.5 in 0.15 Msolution of (
a) leucine, (b) glutamic
acid, and (c) arginine.
The living cell contains several phosphoester compounds. 3-phosphoglycer
aldehyde, whose
structure is given below, is Just an example of such compounds.
The hydrogen at position 3 are dissociable. The first pKa is 2.1 and the second
is 6.8. Can
you now draw the structure of the species of the compound that would predominate
physiological conditions7
How is it that buffers of different compositions can have the same pH? F
or example it is
possible to prepare 0.01 M phosphate buffer of pH 7.0 and 0.1 M phosphate buffer
of pH 7.0.

Acids and Bases

/k man suffering from untreated diabetes mellitus is admitted to a hospi
tal. Doctors fear that
his blood pH may have dropped because of ketoacidosis. Analysis of his blood rev
eals that
[HCO ] = 16 mM and Pco 2 = 30. If pK of HCO is 6. I., determine whether the pati
ent runs a risk of acidotic coma. (Note. In plasma under physiologic conditions,
concentration of CO2
and Pco2 are related by the solubility constant for CO2 in plasma which is 0.03
mM/mm Hg,
8. After a course of insulin the man is feeling good and his blood pH has become
7.4. [HCO ]
has increased to 21 mM. Cm you calculate the concentration of CO2 in the blood p
lasma of
the patient at this point? Can you also calculate the Pco2?

It is a well known fact that metal long have a profound effect on cellular proce
sses. The
importance of the role that long play in cellular activity can be gauged by the
fact that most cells
maintain a very critical Na and K balance between the extracellular and the intrac
spaces. Any disturbance in this critical balance is detrimental to the cellular
metabolism through
a drastic change in the osmotic pressure resulting in cellular swelling. Another
metal ion, Caz,
is known to act as a minatory intracellular messenger stimulating such diverse p
rocesses as
insulin secretion, chemotaxis, endocytosis, and even cellular proliferation. The
se examples are
sufficient to underscore the importance of studies evaluating the activity of me
tal Long in various
metabolic states and processes.
The realisation of the importance and increased number of such studies involving
prompted a swift development of glass electrodes so useful for measuring ion act
ivity in biological
Ion Selective Electrodes Measure the Activity of Metal Long
Biological fluids contain many different types of Long such as Ca2+, Na+, IC, CI
-, HPO4-,
HCO-s, etc. The ensuing electrical interactions between these long will assure t
hat every ion,
while repelling like charged long, will surround itself with oppositely charged
long. Any given
ion can therefore exist in two forms in a biological system; (0 it can exist in
its free ionized form,
or (//1 it can exist complexed with an oppositely charged ion(s), where the net
charge of the
complex is zero. To understand the point better, let us take an example of calci
um. Calcium
can exist in its free ionized form. Ca2+, or as a chargeless specie(s} like CaCO
3, CaCI2, etc. It is,
however, well known that the effects of calcium, such as nerve conduction, muscu
lar contraction,
cellular proliferation, etc., all depend upon the free ionlzed calcium, Ca2. It i
s therefore much
better ff the study conducted and the instrument employed measures the concentra
tion of free
ionized calcium (or the activity of calcium long) rather than measuring the tota
l calcium
concentration. The same logic applies to the study of other long too. In the lat
er pages of this

text book, we will discuss about a technique known as flame photometry (emission
and absorption
flame photometry} which has been employed as an useful tool to measure mineral c
ontents in
biological samples. This technique, however, measures the total quantity of the
mineral present
(domplexed or free ionized form}. On the other hand, ion selective electrodes me
asure the
concentration of the active species of the metal long.
Basic Principles
An ion selective electrode operates on exactly the same principles as a pH elect
rode (see
Chapter 1). In fact, a pH electr0de is a type of ion selective electrode sensiti
ve to hydrogen long;
Just like a pH electrode, the electrode body contains a reference solution and a
n internal
reference electrode. On to this electrode body is sealed an ion selective membra
ne which acts as

Ion Specific Electrodes

the ion sensor. Four different types of ion selective membranes are in use. They
are (i) specially
formulated glass, (//) an ion exchanger dispersed inan inert matrix, (/tO a crys
tal, and (/v) a
liquid ion exchanger. The external reference electrode is either a calomel or a
chloride electrode. The potential developed across the ion selective electrode c
an be measured
on a millivolt scale available in a pH meter. This is proportional to the activi
ty of ion in the
sample. More sophisticated instruments employ specific ion meters (high impedanc
e millivoltmeters) which have readout scales directly calibrated in concentration.
The presently available ion selective electrodes may be divided into four catego
ries depending
upon the ion selective membranes that they employ. The four types are discussed
in brief in the
following pages.
Glass Membrane Electrodes
The selectivity of a glass electrode is a function of the composition of the gla
ss. Three
subtypes of glass electrodes and their selectivity characteristics are presented
Type : pH, order of selectivity : H >> Na > K, Rb, Cs .

>> Ca2

Type : cation sensitive; order of selectivity : H > K > Na > NH, Li >> Ca2
Type : sodium sensitive, order of selectivity : Ag+ > H > Na >> K. Li .... >
> Ca2
The second two subtypes are in general responsive to monovalent cations and are
more or
less unresponsive to anions.
Appropriate adjustments ofglass composition Change the degree of electrode selec
and also the selectivity order depicted above. Thus, glass can be made more resp
onsive to
cations by adding to it elements which have coordination numbers greater than th
eir oxidation
numbers to alkali metal-silicate glasses (20% Na20 - 10% CaO - 70% SiO2). This t
excessive negative change to the glass making it suitable to attract cations
having a proper charge-size ratio. Glasses with a composition of 27% NaO - 5% Al
2Oo - 68%
, show a general cation response. If the above composition is modifiea to 11% Na

2( 18%
7 lO./o SiO, the glass becomes highly sodium selective as compared to other alkali metal
. elecfrodes are very sensitive to silver long also, but this does not pose a pr
oblem in
their biological applications.
Electrode stem
- Internal reference
ljure 2.1. Construction of a typkal glass electrode
Glass electrodes are preferred where the studies involve measurement of sodium,
or silver long because of their high specificity for these long. Other desirable
feature of the glass
is that due to its relative inertriess it can be used in non-aqueous media, orga
nic solvents, and

also in the presence of lipid soluble or surface active molecules. They also sho
w an indifference
to anions present in the sample unless the anions chemically attack the glass.
The glass electrode consists of a stemof non-cation responsive, high resistance
glass on
which is fused a thin walled bulb of cation responsive glass. Figure 2.1 depicts
typical glass
electrode. For further details about the working of a glass electrode the reader
is advised to
refer to the chapter on acids and bases.
Solid-State .Ion Exchanger Electrodes
In these electrodes, the glass membrane is replaced with a solid-state ionically
membrane. The ion responsive material is an insoluble or sparingly soluble salt
dispersed in an
inert matrix. Often used inert matrices include silicone rubber, polyvinyl chlor
ide, and other
polymeric materials. In order to prepare the membrane, the ion exchange material
is dispersed
through the inert matrix. Such membranes have good mechanical properties and giv
reproducible potentials. The membrane so prepared is then cemented to a glass or
epoxy resin
electrode body. The body holds an internal-reference solution and a reference el
Sometimes, the back Of an ion responsive membrane is coated with mercury, and a
wire is connected to it which works as the reference electrode.
These electrodes are mainly anion responsive and several varieties are available
measuring the halide ion concentrations. The ion responsive material for such ha
lide response
electrodes is usually a silver halide.

halide solution
rubber wiib
silver halide)

Figure 2.2. Diagrammatic representation of a solid

/on exchanger electrode.

Solid-state ion exchanger electrodes have

two drawbacks. The first drawback is that they
have a relatively short working life. This problem
has been circumvented by building the sensor
membrane into a removable cap which can be
replaced as required. The second drawback
concerns itself with the extremely high resistance
of silicone rubber and other matrices. In order to
tackle this problem it is necessary that the'
embedded ion exchange material should provide
enough electrical conductivity across the
membrane. This is achieved by careful dispersion
of the ion exchanger so that each exchanger
particle is in contact with each other within the
matrix. Figure 2.2 is a diagrammatic
representation of a solid-state ion exchanger

Solid-State Crystal Electrodes

A crystal or pressed pellets of an insoluble salt can act as ion sensiti
ve elements operating
in much the same way as the salt dispersed in an inert matrix. The cryst
al is precision ground
into a disc shape and fixed onto an electrode body. The manufacturing pr
ocess is closely controlled
to avoid the crystal developing an internal crack or leak. The crystal s
hould also not have high
resistance. Examples can be cited of the lanthanum fluoride electrode (m
easure fluoride) and
silver chloride electrode (measures chloride).
A single crystal of LaF3 acts as the sensing membrane in a fluoride elec
trode. However,
LaF3 has a very high electrical resistance. To cancel this detrimental p
roperty LaF- crystal is
usudly doped .with europium (II) which lowers the crystal resistance and facilit
ates ionic charge
transport. The LaF3 crystal, sealed into the end of a rigid plastic tube, is in
contact with the
internal solution arid the external solution. The internal solution is 0.1 M wit
h respect to NaF

Ion Specific Electrodes

and NaCI. The fluoride ion activity controls the potential of the inner surface
of the.lanthanum
fluoride membrane. NaCI is present in the internal solution so that the chloride
ion can fix the
potential of the internal Ag/AgCI reference electrode. This fluoride electrode c
an measure the
fluoride ion activity as less as 10- M. The fluoride ion may also rspond to hydr
oxide ion concentration. However, this does not pose a problem as hydroxide ion
concentration is kept
constant with a buffer.
In a similar manner, as described for fluoride electrode above, polycrystalline
membrane gives a good sulphide ion electrode. Mixed crystals of AgX-Ag2S compose
the anion
selective electrodes for chloride, bromide, iodide, and thiocyanate.

Figure 2.3. Cross sectional view of a
crystal electrode.
Conductance in the crystal is a function of lattice
defect. A mobile ion adjacent to the vacancy defect moves
into the vacancy. Only the mobile ion may move into this
vacancy since this vacancy is tailor made for the charge,
size and shape of the particular ion. Thus only the mobile
ion takes part in conductance, all other long being rejected
by th crystal membrane. For example, in a fluoride
electrode only fluoride long can move into the vacancy
defect thereby taking part in conductance. The electrode
thus responds only to fluoride long.
Solid-state crystal electrodes have a life of about 1-2
years. However, if used at high temperatures, their life
gets shortened considerably (1-3 months). Figure 2.3 is a
diagrammatic representation of the crystal electrode.

Liquid-Membrane Electrodes

The sensing element of these electrodes is a layer of organic solvent in which a

n ion
exchanger is dissolved. Most available electrodes use a porous diaphragm (glass
or ceramic
disc) which separates the inner ion exchanger solution from the test solution. T
he ion exchange
solution keeps the disc always saturated (see Figure 2.4). This type of electrod
es are used for
the measurement of calcium, nitrate, perchlorate and other long.
Reference electrode
Ion-exchange reservoir
Internal filling solution
(Reference solution)
Porous membrane
Figure 2.4. Cross section of a liquid ion ehange electrode.
The design of such electrodes is discussed briefly. They have a typically double
tube arrangement in which the inner tube contains the aqueous reference solution
and the
internal refence electrode. The outer tube contains the ion exchange solution wh
ich saturates
the pores of a hydrophobic porous disc. The pores of the disc are roughly 100 rn
in diameter.
The porous disc, also known as the membrane, is replaceable. Thus, the ion excha
nge solution
can be changed after removing the disc. This process allows change in the ion se
lectivity of the
electrode, selectivity being a function of the ion exchange solution. The liquid
ion exchanger
used for calcium sensitivity is the calcium salt of his (2-ethylhexyl) phosphori
c acid (d2EHP)
dissolved in various straight ch.ain alcohols. Another type of liquid ion exchan
ger used for

BoplujscoJ Cherrtstrtj
calcium is didecylphosphorie acid dissolved In di-n-octylphenyl phosphonate. Thi
s calcium
electrode can be changed Into a nitrate electrode ff the calcium sensitive Ion e
xchanger In the
electrode Is replaced by a substituted nickel (II}-1, 10-phenanthrolIne Ion exch
anger which ts
sensitive to nitrate.
Due to the loss of ton exchanger with each measurement, life of such electrodes
Is extremely
short (1-3 ,months). At the end of such periods, the ion exchanger Is refilled a
nd the porous
membrane replaced with a new one. The electrode Is sensitive enough to measure f
airly low
concentration of tons.
Two main types of interferences are encountered by ion selective electrodes. The
y. are
(0 method interference, and (tO electrode Interference.
Method Interference can occur when either
c strength
or temperature of the sample beIng tested
asuring fluoride
long, a low pH might give very low values
so sInce fluoride long
form complexes with the hydrogen long and
ivity. The
method Interference can therefore be done

or all of such factors as the pH, ioni

are not properly fixed. Thus, while me
for the activity of this ion. This is
consequently lose their measurable act
away with by fixing the measurement co

Electrode interference.s are mostly due to the passage of an Interfering ion Int
o the membrane
In lieu of the Ion being measured. Thus, high barium ion concentration In a samp
le beIng
measured for calcium can be detrimental to the experiment as barium long can com
pete with
calcium long for passage Into the membrane. Another type of electrode Interferen
ce occurs
chiefly with crystal electrodes. Surface reactions between long present In the s
ample with one of
the components of the crystal can lead to formation of a second Insoluble comple
x on the
crystal. The crystal electrode consequently loses its sensitivity to the desired
ion. Example may
be cited of a bromide electrode (AgBr crystal) which forms a complex with thiocy
anate ion
(AgSCN) altering its sensitivity to bromide long. Sometimes one of the component
s of a crystal
may form a stable cbmplex with anion In the sample being measured. For example,

citrate long
form a very stable complex with lanthanum long. This results In Increased solubi
lity of the
membrane thereby IncreasIng the lower limit of detection of the fluoride ion.
Activity measurements are valuable because the activities of Long determ
ine rates of
reactions and chemical equilibria. Thus, ion electrodes have been used for predi
corrosion rates, extent of precipitation, degree of acidity, formation of comple
solution conductivities, and effectiveness of electroplating bath solutions. The
se are
some of the Industrial uses of ion selective electrodes.
Ion selective electrodes can have many diagnostic applications In biolog
y. For example,
the chloride electrode is beIng used to assay chloride ion activity In the sweat
of babies
as a diagnostic test for cystic fibrosis. Another application with a potential f
or direct
health .use falls In the area of dental research. Calcium and fluoride electrode
s are
beIng used to study the relationship between tooth decay and saliva ion composit
Ion selective electrodes are used to study the control of ion transport
b-y tissues and
cells. Example can be cited of very recent studies by Prentll eLa/where Ca2+ home
of human neutrophlls was studied under various stimulating and resting condition
Such studies have provided a deep understanding of the role of long In triggerin
neutrophil response to an InvadIng antigen. Transport of Na and C1- long have al
been studied In various ceils usIng the correspondIng electrodes.

"'X I I Ion-selective
f" ------ "M .----'-',- -" membrane t--.--.--.----.. Re fe r en c e solution
Ge, i .ob ed
subtrate or enzyme
- 10-I
- 10-2 - 100 - 100 - I0
Ion SpecIj Electrodes
(/v) Another very stimulating biological application of ion selective electrodes
is that they
can be converted into enzyme electrodes. These electrodes can then measure the a
of an enzyme in a given sample [the only action required
on the part of the investigator is to dip the electrode in
the desired sample). For example, the ammonium ion
electrode can be converted into an enzyme electrode
' measuring the activity of urease. Urea is fixed in a gel
membrane which is fastened onto the bulb of ammonium
electrode. The enzyme urease (kO present in the sample
will then act upon urea in the membrane to give rise to
ammonium long which can diffuse through the
membrane to be sensed by the electrode. The ammonium
electrode thus, is converted into a urease sensitive
electrode and can measure the activity of urease in
various samples. There are thousands of other enzyme

substrate combinations that yield products measurable

Figure 2.5. Construction of an enzyme With ion selective electrodes. The design
of an enzyme
electrode is provided in Figure 2.5.
As is obvious from some of the applications listed
above, ion selective electrodes can provide much useful information about cellul
ar processes.
to this tremendous utility potential, a lot of ion selective electrodes having s
ensitivity for
long have been developed in recent years. A list of such electrodes along With t
and the long which can interfere in their functions is provided in Table 2.1.
2. I Particulars of Some lon Selective electrodes

Material Detected
10.5 - 100
I0-5- I0
i0-s10-7 10-6 -10-7 lO-5
Range (M} Interfering Long and Compounds
CO2, volatile amines
S2-, I-

Zn2+, Fe2+, pb2+, Mg2+

I-. Br-, NO, SO-, F-, HCO;
S2-, Hg2+, Ag2+
S2-, V
S2NO, Br-, ICO
K, Li
H, Cs, NH
Ag. Cu .

Two gas electrodes are Widely used in biology; the oxygen electrode and the carb
dioxide electrode. Whereas the oxygen electrode is used in many diverse branches
of biology,
the carbon dioxide electrode is chiefly used to measure carbon dioxide in the bl
ood. Both of
these electrodes are described b.riefly in the following pages.

Biophysical Chemistnj
The Oxygen Electrode
Although a variety of different anode-cathode combinations for oxygen electrode
available, the platinum with silver/silver chloride is the most used cathode-ano
de combination. The often found arrangement of these electrodes is annular with
the tubular silver/silver chloride
anode enclosing the platinum cathode. The electrodes dip into an electrolyte sol
ution (usually a
buffered pgtassium chloride solution) which is held inside an electrode by an ox
ygen permeable
membrane. The membrane might be a very thin polypropylene. Polarization of elect
rodes at 0.6
V is achieved with the help of a mercury cell.
The gas electrodes, including the oxygen electrodes measure the partial pressure
of a gas
in solution rather than its concentration. The term partial pressure is often ab
breviated to pX,
where X stands for the gas whose partial pressure is being indicated. Thus, the
partial pressure
of oxygen is indicated as pO2, and that of carbon dioxide as pCO2.
When the oxygen electrode is dipped into a solut/on containing oxygen, the follo
reactions happen :
The oxygen molecules from the sample diffuse through the membrane into t
he electrolyte
so that within a short time the electrolyte and the sample come to equilibrium w
respect to the pO2.
The outermost valency shell of each oxygen atom has a vacancy for two el
ectrons upon
acceptance of which it can be turned into an oxygen ion. These electrons are sup
by the platinum cathode. The reaction at the cathode is :
4e-+ 02 + 2H20 = 4OH(//0
The hydroxyl long so produced at the cathode then react with potassium c
hloride in
the electrolyte solution. The reaction in the electrolyte is :
OH- + KCI -- KOH + CI(iv)
The negatively charged chloride ion produced in the electrolyte solution
are attracted
to the positive anode and donate their electrons. The reaction at the anode is :

CI- = C1 + eAg + Cl = AgCl

There is thus a deposition of silver chloride on to the anode.
The overall result of the above reactions is a transfer of electrons from the ca
thode to
anode. This transfer represents a current flow which can be measured and is prop
ortional to
pO2 of the sample.
Calibration of the oxygen electrode is done with the help of an oxygen free samp
le (5 mg
sodium sulphite in 5 ml 0.01 M borax, or water through which nitrogen gas has be
en bubbled)
and another sample with a known pO2 (equilibrating a liquid with air with a know
n oxygen
content). The response of the calibrated-electrode is exactly linear to the part
ial pressure in the
The current produced by an oxygen electrode is affected by variation in temperat
ure. If the
oxygen concentration remains constant, a temperature variation of IC would induc
e a 5%
variation in the current. It is thus imperative that the sample measurement shou
ld be done at
the same temperature at which the calibration was performed. If this can not be
done, then
temperature correction must be applied before one reaches to a conclusion about
pO2, of the

Ion Specific Electrodes
A diagram of a typical oxygen electrode is provided in Figure 2.6.
Electrode body
Platinum cathode Ag/AgCI anode
Membrane Electrolyte
Figure 2.6. Construction of an oxygen electrode.
The Carbon Dioxide Electrode
The constituents of a carbon dioxide electrode are (/) a conventional glass pH e
with a calomel reference electrode, (/0 a thin plastic or teflon membrane which
is permeable to
carbon dioxide and not to other long, and (///) a standard bicarbonate solution,
usually 0.005 M
NaHCO3 between the membrane and the glass electrode.
When the electrode is dipped into a sample containing dissolved carbon dioxide 0
carbon dioxide is allowed to diffuse into the bicarbonate solution by the permea
ble membrane.
The pH of the bicarbonate solution changes, and this change is read by the glass
electrode. This
pH change is reflected by the pH meter which is directly calibrated for pCO2. Th
e response time
of a carbon dioxide electrode is higher because the standard bicarbonate solutio
n has to come
Into equilibrium with the sample. The same temperature variation relationship di
scussed with
respect to the oxygen electrode applies here too.
A diagram of the conventional carbon dioxide electrode is provided in Figure 2.7
Combined pH and calomel
reference electrode
Standard bicarbonate solution
F/gure 2.7. D/agram of/t carbon d/ox/de e/ectrode.

The oXygen electrode is being widely used in many different biological experimen
ts wherever
there is a need of measuring oxygen. The carbon dioxide electrode on the other h
and is mainly
used for clinical purposes, oft.e.n for measuring the carbon dioxide dissolved i
n blood or plasma.

Biophysical Chemistry
Suggestions For Further Reading
I. Lakshmlnarayanaiah, N.. Membrane Electrodes. Academic, New York, 1976.
Koryta, J., lon Selecave Electrodes, Cambridge monographs in Physical Ch
emistry, No. 2.
Cambridge University, New York, 1975.
Willard, H.H., Merrltt, LL. Dean, J.A. and Settle, F.A., Instrumental Me
thods of Analysis,
6th ed., CBS, New Delhi, 1986.

Until the middle of the nineteenth century colloidal systems were regarded as be
ing outside
the realm of well behaved chemical systems because they did not behave in a mann
er expected
of an aqueous solution. Such physico-chemical properties of colloidal solutions
as the exhibition
of osmotic, pressure, electrolytic conductance, lowering of vapour pressure, ele
vation of boiling
point, depression of freezing point etc. were different. However, colloids must
constitute extremely
well behaved systems because life is a manifestation of various colloidal states
. All protoplasm
i8 in colloidal form. Most of the biological fluids, notably blood, lymph, milk,
bile, and digestive
secretions are colloidal solutions. Moreover, the biomembranes may themselves be
to be a manifestation of the colloidal state.
Historical Perspective
The study of colloids as a system began with Selml in 1843 when he prepared coll
suspensions of Prussian blue, sulphur, and casein. He observed that the preparat
ions were not
true solutions but suspensions of a finely divided state of matter in water.
Michael Faraday, a British scientist, prepared aqueous suspensions of gold in 18
57 and
studied the optical properties of this preparation. On passing a narrow beam of
light through
this preparation he observed the path marked out by a cloudy haze. This could no
t be observed
in a true solution. The above phenomenon, which is due to diffraction or scatter
ing of light by
colloidal particles was further studied in 1969 by Tyndall and is today known as
the Tyndall
The breakthrough in colloidal chemistry came with the work of Thomas Graham, an
Englishman who performed certain fundamental experiments to prove the existence
of colloidal
systems. He observed that solutions of certain substances diffused at a slower r
ate and were
unable to pass through a parchment membrane. Because of their sticky nature he s
them to be noncrystallizable and called them co//o/ds (Kolla in Greek means glue
). Substances
belonging to the other class which were readily diffusible through membranes and
also could
be crystallized were termed crystalloids. This primitive system of classificatio
n was not fortunate
as it was seen later that many substances which formed glue-like solutions could

be crystallized.
On the other hand from almost all the crystalloids colloidal solutions could be
obtained. It was
soon recognized by Von Weiman that any substance can under suitable conditions,
be brought
into a state of subdivision to be appropriately termed colloidal. Wolfganf Ostwa
ld in 1907 pointed
out that any matter in finely divided dispersed condition implies the presence o
f another phase,
the dispersion medium. Only when these two phases i.e., the dispersed phase and
the dispersion
medium exist as separate phases, the system can be said to be colloidal in natur
e. Thus a
colloidal system is a state of matter and not a type of matter.
With the invention of the ultramicroscope in 1903 the study of the properties of
sols became possible. The appearance of a colloidal solution under an ultramicro
scope is like a
milky haze of counfless points too minute to be separately observed. Based on th
e various size
-of partlcles which could be distinguished, a rough classification was suggested
by Siedentopf &
Zsigmondy. According to them, the particles which were distinct in the ordinary

Spinal fluid dilutions with 0.4% NaCI 76 Boptu3sc Chemlstrg
and appeared as well focussed images in We u]tramJcroscope were called mcrons. T
hose wltch
could be observed only in the ultramicroscope were the submcrons and the others
which were
invisible both in ordinary and ultramicroscope were the am/crons.
The stability of colloidal systems was studied at great length. The importance o
f valency
and its influence on stability of sols was studied by Schultz. Hardy added to th
is information by
looking at it from a quantitative angle. Their findings, formulated as "the Schu
ltz-Hardy rule"
are still in practical use today, one of them being clarification of drinking wa
ter by adding small
amounts of calcium salts. Zsigmondy introduced the term gold number while explai
ning the
protective action of one colloid over another. Later, the gold number of cerebro
spinal fluids.was
introduced into medicine as a diagnostic aid to obtain information about certain
types of
diseases, such as meningitis, neurosyphilis etc. (see Figure 3.1).
5 Colourless
4 Pale blue
3 Blue
2 /Lilac/purple
A = Neurosyphilis
B = Meningitis

Normal spinal fluid

lgure 3. I, Gold sol curves for cerebrospinal Jluld give djnostic information
Outstanding contributions in the field of colloidal chemistry have been made by
other scientists, notably Freundlich {phenomenon of adsorption), Donnan (Donnan
Svedberg (sedimentation) and Einstein.
What are Colloids?
As stated earlier, colloids represent a state of subdivision of matter. The matt
er, finely
divided, is uniformly distributed in a continuous medium. However, the dispersed
particles are
neither so large that they separate on standing, nor so small that they can be s
aid to be in
solution. This means that the colloidal state is an intermediate state between a
suspension and
a true solution.
A colloidal system is characterized by particles ranging in size from 1 ml to 0.
1 in diameter. They can be formed either by aggregation of small molecules like
sodium chloride or
by disintegration of large polymers. The particles are non-filterable and can be
observed under
the ultramicroscope as illuminated discs engaged in a kind of random zig-zag mot
ion. This type
of movement is called Brownlan movement after the name of its discoverer Robert
Brown. The
smaller the particles, the more rapid is their movement. This unpredictable chao
tic movement

The Colloidal Phenomena

of molecules was explained by Albert Einstein in 1905. The surrounding molecules
of the
dispersion medium continuously collide with the colloidal particles. These colli
sions impart
sufficient kinetic energy to the colloidal particles so as to enunciat a Brownia
n movement.
This movement is, however considerably slower than that of the molecules of the
medium and
can therefore be observed under an ultramicroscope.
If the particles cross the upper size limit they will form suspensions. In that
case, the two
phases separate on standing and the particles can be filtered off easily. An ord
inary microscope
is enough to observe the participants of the dispersed phase in a suspension. In
contrast are
the true solutions whose individual members are invisible even in the ultramicro
scope. Only an
electron microscope can be used for this purpose as the size of the particles in
such a system is
always less than I m.
Another characteristic property exhibited by colloidal system is the Tyndall eff
ect. If a
narrowly defined concentrated beam of light is allowed to pass through a colloid
al system it
appears as a white path. The same is not observed in a true solution (see Figure
3.2). The above
effect can be illustrated as follows. Consider a room with a small shutter on on
e of its walls. As
long as the room is uniformly illuminated the air inside the room seems perfectl
y clear and
transparent. But ff the room is now darkened and a concentrated beam of light al
lowed to enter
shutter, we can see the dust particles in the path of the light clearly. This is
due to
', of light by dust particles. Minute dust particles affect the visible light wa
ves to produce
the phenomenon called diffraction. The same principle is followed by colloidal p
articles. True
solutions do not respond to such a phenomenon because its particles are too smal
l to scatter
(A) Copper sulphate solution
(B) Colloidal solution of blue ink n water.

Fre 3.2. Tyndall effect. (A) No licjht scattering by a concentrated solution of

copper sulphate; (B) lJht beam is
scattered and appears as a white path through a colloidal solution of blue ink i
n water

The "I,ndall effect is utilized in the ultramicroscope. In this instrument an in

tense light
.beam from an arc lamp is focussed by the lenses of a compound microscope on the
stage of
another high-power microscope with its optical axis at right angles to the first
one. Other light
is excluded from the field. The individual sol particles scatter light and appea
r as bright discs
gainst a dark background (see Figure 3.3). Modern methods have made the use of u
light to extend the range of microscopic work. Its. short wavelengths permit for
mation of focussed
images of objects as small as I0 mm in diameter. The images though not visible c
an be recorded
photographically. Figure 3.4 shows a simplified version of an ultramicroscope.
View under ultmmlcroscope. (A) Colloidal panicles appear as illuminated discs of
light (B) Particles of
true solution an: not visible " "

Bophysal Chemtry
'i Scattered light
Source o
Colloidal solution

Figure 3.4. Tyndallization and observation in an ultramicroscope

As mentioned earlier, colloidal systems are composed of two phase of matter. The
phase, also called the discontinuous or internal phase is made up of colloidal p
articles while the
dispersion medium, also called the continuous or extema/phase is made up of the
solvent in
which the dispersion takes place. Numerous types of combinations of these two ph
ases are
possible (Table 3.1) and it is difficult to classify colloids strictly. However,
various attempts have
been made and the classification of colloidal systems as two distinct types the lyophilic colloids
and the lyophobic colloids, based upon the interaction of phases has fdund wide
Table :S.1 Typee of Colloidal 8ytem
DiIrd Diponslon Medium Type

Solid sol
Solid aerosols
Solid emulsion

Liquid aerosol
Solid foam
Liquid foam

Alloys, glasses coloured with.

dispersed metals, e.g., ruby
glass, gemsl pearls,
Gold sol, ferrichydroxide
sol, starch in water.
Smoke, dust in air, volcanic dust.
Butter, cheese,
Milk, water in oil, off in water,
Fogs, mist, clouds.
Pumice stone.
Whipped cream, froth on beer.
Not known (this type is not seen
because of the high rate of
diffusion of gases).

The Colloidal Phenomena

Lyophilic Colloids
The word lyophilic stems from the Greek word philos meaning loving (lyo means so
Needless to say that the these are colloidal systems where there is strong attra
ction between
the solvent and the particles. Numerous substances of biological interest such a
s proteins,
nucleic acids and the starches fall in this category. Other significant compound
s are the cholic
acids, soaps, synthetic detergents, and the emulsifying agents. Lyophilic colloi
dal solutions
differ from true solutions only with rspect to the size of the particles which l
eads to a change
both in the properties as well as techniques of study of these systems,
A lyophilic colloidal system can take up different names depending on the nature
of the
dispersion medium. When it has water as the continuous phase it is called a hydr
osol, while
With alcohol as its dispersion medium it is called an. alcosol. But the general
term for this type
of system is the emulsoid.
The emulsoids are easy to prepare and though they resemble the true solutiohs in
respects, the great disparity in size of the solute particles confer upon them s
ome distinct
physical properties. Additional properties are conferred upon them because of th
eir charged
polyelectrolyte nature. One unique property of colloidal solution is the Donnan
effect. It is
unequal distribution of diffusible long across a semipermeable membrane due to t
concentration of colloidal particles on one side of the membrane.
Due to the high degree of solvation of the particles in an emulsoid, the precipi
tation or
flocculatlon of these systems is difficult..They are stable and therefore are pr
ecipitated only by
high concentration of electrolytes. Also, they exist in a state of true reversib
le equilibrium. To
explain this further, the dispersed phase of lyophilic colloids when separated b
y evaporation or
precipitation clump together in loosely packed aggregates. Theseflocs can be rec
onstituted into
the colloidal form easily by removing the electrolyte from the medium and by mix
The hydrophillc colloids show a higher viscosity than that of the medium. It has
also been
found that the viscosity ihcreases with"concentration. Two reasons are attribute
d to these

The hydrophflic colloids have strong attraction for water. This extensiv
e solvation of
the particle immobilizes the bound water and resists its freedom of movement thu
. increasing viscosity.
With higher concentration of solute, there is more trapping of solvent.
Also the colloidal
particles try to orient themselves in a lattice like structure. This systematic
affects the flow of the solvent as the solvent now has to find gaps in this stru
cture to
escape or it has to break down this structflre to enable its flow.
, The optical properties of lyophilic systems are also different. Tyndall effect
for these systems
is minimum. Besides the size of the particles, the difference in refractive indi
ces between the
dispersed phase and the dispersion medium also affect tla In emuloid this differ
ence is not appreciable because of the high solvation character of this system.
the Tyndall effect is not s.o prominent.
The lyophobic colloids derive their name from the Greek word phobe (meaning fear
ing or
hating) and thus mean 'solvent-hating'. But we carmot call these ystems 'solvent
hating' in the
strict sense because if it was so, no dispersion would be formed. If the solute
molecule completely
repelled the dispersion medium it would have remained dry. No wetting and theref
ore no
dispersion was poible. However, lyophobic systems do form dispersed systems in w
hich the
molecules remain detached from the solvent though not in complete isolation. Thi
s is one of the
reasons of.their instability. -.-

Biophysical Chemistry
The lyophobic systems are also called suspensoids. They easily precipitate out f
irreversible flocculates. But if they are left Undisturbed, despite their intrin
sic instability they
remain unchanged for long periods (see Box 3.1). Research has shown that it is t
he electrical
potential difference between the surface and the solution far away from the part
icles that
determirtes the diuturnity (stability) of the lyophobic system. This electrical
potential difference
arises due to the charge carried by the particles of a sol, and the charge carri
ed by the long in
the surrounding medium.
The optical properties of lyophobic systems are worth mentioning. These systems
characterized by solute molecules which stay apart from each other. This allows
scattering of light as the difference in refractive indices of the solvent and s
olute particles is
quite high. The.-ndall effect is distinct and therefore the particles of a suspe
nsoid are more
clearly visible in an ultramicroscope. The viscosity, though, is not so affected
as the solvent flow
is not hindered.
In the early 1900's when the physico-chemical behaviour of solutions was being s
there was a misconception that the basic principles of physical chemistry were n
ot applicable
to colloidal solutions. Since diffusion was very slow, viscosity was high and fr
depression was not so remarkable in these solutions, workers were doubtful wheth
er the laws
of thermodynamics would be obeyed. We now know that colloids do conform to certa
fundamental physico-chemical laws as systems containing only. small molecules or
long, only
the scale is different. To understand this, let us first look into the factors w
hich are the sources
of non-ideality of colloidal solutions.
The two factors which determine the solution behavi0ur of biopolymers are (1) th
e great
difference in size of the molecules of the solute with the solvent. (ii) the bon
ding interactions
and frequently charged nature of the solute.
( Size: A feature of solutions of macromolecules is that the solute molecule is
many times

larger in size than the solvent molecule i.e,, the solutions are more concentrat
ed in terms of
weight or volume percent while their molarity is still very low,
One of the determinants of the equilibrium state of a system of many particles i
s the
randomness or disorder of the system. According to the second law of thermodynam
ics, the
term entropy is used to denote such a randomness in a system. In an ideal soluti
on it is assumed
that the solute molecules are of the same order of size as the solvent molecules
so that the
distribution of solute molecules in the solvent is entirely random as is seen in
the case of true
solutions. But this cannot hold true for macromolecular solutions because of the
high solute to
solvent size ratio. In these solutions the centre of each molecule is excluded f
rom a volume of
solution because of the high solute to solvent size ratio. In these solutions th
e centre of each
molecule is excluded from a volume of solution because it is temporarily occupie
d by some part
of another macromolecule. The departure from ideality thus depends on this molec
ular xcluded

... (I)
... (2)
... (3)
... (4)
The Colloidal Phenomena 1
volume (6). The quantity B, the second virial coefficient, which serves as a con
venient measure
of solution non-ideality is related to '#' by the equation.
B- 2M2
where N is the Avagadro's number, and M is the mo!ecular weight.
The excluded volume is determined.by the actual molecular dimensions.
For spheres, N
so that
and for rods, 6 Nd
so that
B dM

v is the specific volume,

L is the rod length,
d is the diameter of the rod.
The globular macromolecules contribute less to non-idcality of a solution than t
asymmetric rods or random coils because the permutations and combination of arra
possible in a solutiol for the latter are always less in number than the former.
(ii) The bonding interactions : When a colloidal dispersion is prepared, the sol
i Interactions and the solvent-solvent interactions are broken with utilization
of energy and new
bonding nteractions, the solute-solvent interactions are formed with release of
energy. This
liberation of energy is the driving force for mixing. If we do not consider the
'entropy' term
described earlier, dissolution of a solute in a given solvent will be favoured o
nly if the solventsolute interactions are great enough to overcome the solute-solute interactions
and the solventsolvent interactions.
The description of thestate of a solution needs to specify the amount of compone
present and the temperature and pressure. If the temperature and pressure are as
sumed to be
constant, in an ideal solution,
The internal energy = sum of internal energies of its components in thei
r standard
states, i.e. E or energy change between system and surroundings is zero, and
The volume = sum of the volume of the components is their standard state
s, i.e. AV
or volume change for mixing is zero. When the volume change is nil at constant p
the change in enthalpy (heat content) is also zero.
(C) On mixing, there is a great disorder so that AS or change in entropy is posi
The combination of the statement of the first and second laws of thermodynamics
us the equation,
.F= &H -T&S
... (6)

Biophysical Chemistry
It follows from the above equation that if AS. for mixing is positive, &
F for mixing will be
negative. Only under these conditions, the reaction will proceed spontaneously t
o form an idea]
Since it is the free energy of a solution which is a property of interest, we mu
st know the
contribution of each component of a system to the total free energy. The partial
molar energy is
the amount of free energy contributed by each component of the system. It is an
variable and is often called the chemical potential, symbolized by ''.
The total free energy Of the solution is then
F = Z nl]i
... (7)
where ni is the number of moles of component L The chemical potential is the int
ensity factor of
a chemical reaction and may be regarded as its driving force. It also determines
the direction in
which the net reaction will proceed. When the value of AF = 0, the system is sai
d to have
attained equilibrium. In that state, the chemical potential of any com .ponent m
ust be constant.
It also follows that tl must be identical at all places in the system, Otherwise
there will be
further reaction or migration of matter from a region of higher chemical potenti
al to a region of
low chemical potential.
For solutions of macromolecules, the chemical potential of the solvent is import
ant as
many macromolecules interact strongly with the solvent or with one another. In '
poor' solvents,
the solute-solute interactions are preferred. This increases the solvent chemica
l potential and
enthalpy change then is not equal to zero (AH 0). The virial coefficient win be
negative. On the other hand, in 'good' solvents, there is preferential attractio
n between the solvent and solute
molecules so that the solute molecule tends to extend itself and the entropy inc
reases. The
excluded volume is larger in such solvents and the virial coefficient is positiv
e because there is
a great decrease in solvent chemical potential. Both the above cases are deviati
ons from ideallty.

There. are of course, other sources of nonideality in a macromolecular solution

in addition
to the excluded volume. To make a solution behave as an ideal one, a temperature
can be found
(0 temperature or Flory temperature) at which the above enthalpic and entropic t
erms cancel
each other. The second virial coefficient, B, then becomes nll and the solution
behaves ideally.
The lyophilic colloids mostly behave as true solutions, form spontaneously and a
re stable
thermodynamically. On the other hand, the lyophobic colloids are always unstable
thermodynamically. Despite inherent instability, many of the lyophobic colloidal
persist indefinitely. This is attributed to the electrical charge carried by the
system. A detailed discussion of the electrical properties of colloids will be d
ealt with
elsewhere in this chapter.
When a warm concentrated solution of starch is cooled, it gradually sets into a
more or
less rigid mass. This product is called a gel and the process by which it is for
med is termed
gelation. Gelation is a property possessed by lyophflic systems. Many factors li
ke pH, temperature
and, concentration of solute as well as electrolytes in the medium have profound
influences on
this process. Change in H concentration can bring about a change in the molecular
of a colloidal particle thus altering its power to gelate. At higher temperature
s gels generally
liquefy, while cooling favours gelation. With increasing concentration of the co
lloidal particle,
gelatlon is favoured. Also, the gel structure is more firm with higher concentra
tion of solute.
The gIs are thought to possess a definite structure. Nageli described a mesh lik
e structure
for gels. The gels are so firmly set that it becomes very difficult to squeeze o
ut any solvent which

The Colloidal Phenomena

is trapped or absorbed within the network of the interlacing fibrils. On standin
g for a sufficient
period of time, most gels gradually contract, extruding a portion of the dispers
ion medium, the
process being known as syneresis. Avery good example of a colloidal system trans
iting into the
gel form is blood clotting. Blood exuding from the wound gets more and rore visc
ous to form
the clot eventually. The clot when examined under the microscope appears as a cl
ose network
of fibrils (fibrin) in which are trapped the blood cells and other liquid compon
ents. The clot is a
rigid structure but on standing it shrinks, exuding a transparent fluid, the ser
Gel formation is not always an irreversible process. Though coagulation of prote
in .and
clotting of blood axe irreversible, solid agar or gelatin formed by the cooling
process can be
brought back to their original lyophilic colloidal solution forms by gentle warm
ing. Gels may
thus be classified into two types, elastic and non-elastic. The elastic gels eve
n after complete
dehydration can be brought back to their original state by addition of water. So
me examples of
this class are agar agar, gelatin etc. The non-elastic ones, like silica gel are
An entirely different process may also form gels. Lyophilic colloids, in their s
olvent free
forms, spontaneously imbibe considerable amounts of liquid solvent or solvent va
pour, increasing
in volume and setting into a more or less rigid mass. This process is known as s
welling. The
amount of solvent imbibed may be very large and it is held firmly within the hon
structure of the gel. If this process is not checked, swelling may continue inde
finitely, leading to
a lyophflic dispersion which gets diluted more and more. But as observed, swelli
ng does have a
limit. It continues as long as the free energy of the system decreases. Once the
chains have become fully extended, swelling will virtually stop. This can be exp
lained in terms
of entropy. As the chains extend to their full, they become more and more ordere
d. This decreases
the entropy of the system with a concomitant increase in free energy. A balance
which results
between the decrease in free energy, (due to solvation of the macromolecule by t
he solvent) and
increase in the free energy brings the whole swelling process to a standstill.
Presence of long in the medium affects swelling. This is due to the high solvati
characteristics of the individual long. Some long increase the limit of swelling

while some decrease

it. Viscosity of the gel decreases as swelling continues.
Some gels which are in a semi-solid state can revert back to liquid sol on agita
tion. On
standing the sol reverts back into a gel. This sol-gel transformation without ch
ange of temperature
is referred to as thttropy and it has great biological significance. It can also
be brought about
by a change in hydrogen ion activity or by changing electrolyte concentration. P
rotoplasm is
said to have thlxotropic properties. In fact, the complete mechanism of muscle c
involves an elaborate gel-sol transition process controlled by the activity of c
alcium long.
Association Colloids
We have a little earlier discussed the nature of lyophobic systems which are inh
ffnstable and the lyophilic systems which ae thermodynamically stable and are ma
de up of
macromolecules having great solvation power. There exists another class of collo
idal systems
which, though thermodynamically stable, are made up ofmicelles. A micelle is a s
formed aggregate of micromolecules. This aggregate achieves colloidal dimensions
and is a
thermodynamically stable structure. The dispersion finally formed is called the
colloidal system.
A striking feature of the association colloids is that the molecules formlng it
are amph/path/c
in nature i.e., the molecules possess both lyophilic and lyophobic groups in the
ir structure. The
lyophobic components form the core of the micelle (aggregate) while the lyophili
c components
are on the surface extending their polar groups into the aqueous solution.

Biophysical Chemistry
Because of tiffs dual character of its molecules, association colloids are of gr
eat practical
utility. Most of them are surface-active substances. Examples of this class are
the soaps and
detergents like sodium dodecyl sulphate. While some are excellent solubflizers o
f various types
of organic compounds in water, others are good dispersion stabilizers.

The Colloidal Phenomena
There are many insoluble constituents in the biological fluids like urine and bi
le. But,
they do not-precipitate out normally. Only under abnormal conditions they
the form of gallstones and kidney stones. How is a normal person safeguarded
pathologies ? The answer lies with protective colloids. Protective colloids or p
as they are often called, do not form a separate type or class of colloidal syst
nothing but lyophilic colloidal systems which when added in sufficient quantitie
s to a
sol hinder its precipitation by electrolytes (see Figure 3.5). In other words, t
is protected by the emulsoid. The emulsoid therefore, acts in this,case as a pro
An opposite phenomenon occurs if the recipe is altered, the ingredients remainin
g the
called sensit/zat/on. In this, if a small amount of the lyophflic system is adde
d to the

Biophysical Chemistry
lyophoblc system, precipitation is facilitated. The suspensold gets sensitized a
nd is precipitated
out by a very small amount of electrolyte. This is because the lyophflic colloid
is now enveloped
by the lyophobic system facilitating flocculation (see Figure 3.6).
Aggregates form
(1 ml, 10%) Na. , --Na
The particle is charged Na
due to adsorption
of anions
. Albumin or
Charge on the
particle is reduced
to zero by the
electrolyte added
of charges lead
to aggregation
and precipitation

,,.- -.-,.=. -: - -'

-- J"-- ,
t- - .--.,,
.- L' .-.a' --'..--" --'.?
Water film
a,----*'on of water
narge on me


- o de
thou reduced
further proection)
is not effective to
cause precipitation
Protective Gelation Albumin film
Fjure 3.5. Protective colloidal action on a hydrophobic so/.
7 Lyophobic colloidal particle
& Lyophllic colloidal particle
Figure 3.6. llustratlon of sensltlzation and protection by a lyophoblc colloidal
The protective action of various lyohflic substances was studied by Zsigmondy. H
e advised
a quantitative measurement called the Go/d Number in order to measure the relati
ve protective
powers of hydrophflic colloids. The Gold Number is the weight in mgs of protecti
ve colloids that
when added to 10 ml ofa Zsigmondy gold sol (contains negatively charged hydropho
bic colloidal
particles), just fails to prevent the colour change from red to blue on the addi
tion of I ml of a
10% solution of sodium chloride. The smaller the gold number, the greater is the
action of a particular lyophilic substance. With the unprotected gold sol, the a
ddition of sodium
chloride brings about charge neutralization, aggregation of the sol particles, a
nd finally,
The .gold number of various fluids of our body presents a picture of our health
profile and
thus c.ap be used for diagnostic purposes by a clinical chemist.
Examples of protective colloids are gelatin, gum arabic, albumin etc.

Th Co//o/da/Phenomena
We have earlier discussed the kinetic properties (Brownian movement) and the opt
properties (Tyndall effect) of colloids. The behaviour of colloidal systems can
be understood
properly only when we consider the electrical properties of its constituents as
well as the system
-as a whole.
Electrical Properties of Colloids
The colloidal systems we frequently ncounter are the solutions of biological mac
or biopolymers as they are often called. Majority of these biopolymers are elect
rically charged.
The charges may be 'strong' or Xveak' depending on the ionization constants of t
he acidic or
basic groups: The distribution of the charges on the macromolecules may be symme
tric or
asymmetric, and this is independent of the net charge carried by the macromolecu
le. The origin
of these charges may be either extema/or/nternaL When the charges are acquired b
y adsorption
of positive or negative long from the medium, it is called external. It may also
happen that the
charges arise due to active acidic or basic groups present in the inherent struc
ture of the
macromolecule which remain exposed on the surface. In such a case the origin is
said to be
Consider a spherical colloidal particle witha negatively charged surface. This p
will tend to attract the positive long from the dispersion medium around itself.
As a result, the
macromolecule will soon be surrounded by an/on atmosphere, a region in which the
re will be a
statistical preference for long of the opposite sign. Helmholtz likened this sit
uation to the charge
distribution in a parallel plate condenser. The condenser consists of two concen
tric spheres of
opposite signs, and the two plates of the condenser constitute the so called r/g
/d doub/e/ayer
(see Figure 3.7).
Q --Charge due to adsorbed layer of long
Q = particleCharge carried by the spherical colloidal

Outer sphere of oppositely charged long

Figure 3.7. Helmlwltz "Double layer" model.
With more contributions from Gouy, Debye and Huckel0 a modified theory was propo
to explain the charge distribution around a macromolecule. According to this ele
ctrical double
layer .theory, the long of charge opposite to that of the surface (called gegen/
ons, from the
German gegen meaning against) concentrate and tend to orient as an immobile laye
r on the
surface. As the distance from the surface increases, mobility of the long increa
ses and the ion
layers become more and more diffused (see Figure 3.8}.
If +Q is the charge on the spherical macromolecule, r is the radius of the spher
e, -Q is the
charge on the adsorbed ion layer, and d is the thickness of the double layer, th
e potential at any
point on the surface of the macromolecule will be given by +Q/Dr where D is the
constant of the medium. The outer layer of oppositely charged long reduce the po
tential on the
spherical colloidal particle by -Q/D (r+d).

Biophysical Chemistry
.- -[ , Compact layer (surface of shear)
- I---.-.--" 4. ,. ---\
-- - --" "----',- - ....
r" "" -.parttc-t-e- q+ -#- \- -r---- Mobile long in liquid around X.-- .- -- /" -- -v --- -" the particle {
Diffuse layer)
-[L-r.- Positively charged colloidal particle
, Immobile layer of negatively charged
long adsorbed upon the surface
from the liquid
Fire 3.8. The electrical double layer around a spherical colloquial particle whi
ch is posvebj charged
The net potential between the immobile layer of long and the diffused mobile lay
er of long
is called the e/ectrok/twttc or zeta potential and is represented by 4.
= Dr D(r+
= (r +d}-r@
Dr (r+d)
" .
Dr(r +d)
The electrical double layer in the phase boundaries produces the -potential as a
result of
lectrostatlc and adsorptive interactions. The zeta potential has a very close re
lationship to the

stability of a sol. The zeta potential of a sol can be very effectively reduced
by addition of
elee'rolytes. The electrolytes decrease the zeta potential to a critical value,
after which
neutralization of the charges takes place resulting in the collapse of the doubl
e layer. When this
happens, flocculation of the colloid takes place. Various other factors which af
fect zeta potential
are surface charge density, dielectric constant of the medium and thickness of t
he double layer.
Great slgrtiflcance has been attached to zeta potential in understanding various
reactions of our body, one of them being blood coagulation. During this process,
zeta potential
is reduced below the critical value (mainly due to the increase in calcium long
in the medium)
enabling the dispersed particles to form aggregates. This occurs because the dou
ble layer breaks
down at the 'critical potential' facilitating coalescence of the particles. A fl
occulate in the form of
a clot appears subsequently to stop blood flow.
Existence of charged layers on and around a colloidal particle gives rise to man
y other
potentials besides the zeta potential. The layer of oppositely charged long whic
h is in immediate
contact with the colloidal particle, i.e., the immobile layer, is also called th
e Stem layer. The
potential between this layer and the particle surface is called the Stern potent
/aL The potential
difference between the surface of the particle and all the ionic layers in the s
olution surrounding
the particle is called the electro chemical potential and is represented by E.

Colloidal Phenomena
The three potentials mentioned above are related to each other by the fo
Stem Potential = E ... (9)
(Electro chemical - Zeta Potential)
The above relationship shows that zeta potential is a little lower than the Stem
I this is because it is located further out from the surface of the macromolecul
e. The zeta
of any colloidal solution can be calculated by electrokine*ic measurements like
electro-osmosis and streaming potential. Though the methods are different, all
the same calculated value of the zeta potential fcr any particular system. All t
he methods
the relative motion of the two surfaces in contact.
For the quantitative treatment of electrokinetic phenomena, various assu
mptions have to
First, the double layer is likened to a parallel plate condenser where the plate
s are 'd'
apart and each carry a charge 'q' per sq.cm. The potential difference created be
tween the
plates may be assumed to be equal to zeta potential which now can be written in
C ... {lO)
D represents the dielectric constant of the medium. With the above equation the
deduction of the zeta potential by the different types of electrokinetic phenome
(i) By electrOlahore$i: Movement of macromolectles in an electric field may be o
measured with a microscopic equipment known as the microelectrophoretic cell. Th
e design
[such an apparatus can be seen in Figure 12.3.
If oppositely charged electrodes are dipped in a solution of macromolecules, the
to migrate in the electric field which is thus created. The velocity of movement
given by

law would be :
V = -... (11)
E = electric field in volts per cm felt by the particle
Q = moving charge
= viscosity of the medium.
There will also be a frictional force operating which will tend to drag the solv
ent in the
direction resulting in retardation of the velocity of movement of the particle.
When the
force and the frictional force balance each other the particles move with a less
velocity given by
... (12}
= --

... (13)

Boptujsc Chemtrv
us, measurement of ze pote revolves the measemet of e ve]ocl of e
cogod pc]es der pressed e]ecc e]d as e vue of oer components of e equaon (13) be
o eas.
iO e: In 1808 Reuss t obseed e flow of water mu a membe of powdered qu when a po
ten derence was applied. Based on is ely eeent,
eoreflc studies elecoecs were made d sever tecques have been ds to study effecve
ly e behaour of macromolecules soluon.
In o preous scuion we studied bef e movement of e cooid pcles under e uence of e
lecc fld. If e pcles e now forcibly stopd from mog, we see at e dispersion meum
now ss mog. is movement of fld elecc field is ced ecss or ecoss.
To delve equation reg e -poten to e eleco-osmoc flow, appatus c set up as foows.
: A U-tube is dided to o m compen bya blk of gel ed side e tube (s gure 3.9). e
whole to is now a solvent.e gel, wch is fact a ckened fo of a lyopc cooid cot mo
ve but it c ow e Ivent molecules to
svee ou it. en elecc coecon is made beeen e o s of e U-tu ou a p of elodes. e so
lvent is seen to se one ofe . Ife solvent ter, e ter flow u e gel tod e negave p
ole because e ter acqs a sive chge (it t be mfloned here at e pous gel membe beh
aves as enoous set of cap robes). Dung e flow of ter ou e gel, e is pferen
adsoon of OH- long. e s of e 'pes' lea e H long to chge e war molecules posively
Original - " Flow of : :
Blek of gel
Figure 3.9. Illustration of electro-osmosls
If W" is the volume of liquid flowing through the capillary per second, then
V = -r2ED
{ = r2ED

The Co//o/da/Phenomena
where r = radius of the capillary,
E = potential applied in volts,
= Zeta potential,
length of the capillary,
dielectric constant of the medium,
viscosity of the medium,

For a parchment membrane or a colloidal gel 'r" and T are very difficult to dete
rmine. To
clrctunvent, these factors, a different term 'K' was evolved. 'K' is the specifi
c conductance of the
liquid in the capillary, and is equal to
I = strength of current,
a .= cross-sectional area of the capillary,
E = potential gradient in volts cm-:
The relation between the ,potential and the rate of electro-osmotic flow through
then stands as
4 K rIV

... (15}

The above equation can be used to determine -potetial. The equation states that
at a
electr/c current I, the volume of liquid 'V" flowing through a membrane is direc
to the zeta potential and the dielectric constant of the medium and inversely
to the viscosity '' and the specific conductivity 'K' of the I/quid.
{i//) By streamh potent/a/: A third type of electrokinetic phenomenon observed i
s the
streaming or flow potential when a liquid like water is forced to flow through
A potential develops on either side of the capillary at its two ends (see figure

H" H*
H* H*
The nature of the potential depends upon the pressure applied as well as nature
of the
It has been suggested that the streaming potential results due to forcible flow
of liquid
tends to separate the oppositely charged layers of the electric double layer. St
is related to zeta potential '' by the equation.
= .4 KS
... (16}

Biophysical Chemistry

= streaming potential
= pressure applied to the streaming liquid
= dielectric constant of the medium
= specific electrical conductivity of the liquid, and
3 = viscosity of the medium.
Another method for study of electrokinetics is the determination of sedimentatio
n potential.
The phenomenon is known as Dom effect after the name of its discoverer. It measu
res the
electric potential established by the movement of the colloidal particles with r
espect to a Sationary
dispersion medium. The particles move under the impact of a mechanical force, th
e gravitational
force. Normally the potential derived by this method is very negligible, but it
assumes great
significance during centrifugation. When a colloidal solution is allowed to sedi
ment in an
ultracentrifuge under the centrifugal force, a potential difference of measurabl
e dimensions
develops across the ends of the solution.
Precipitation of Colloids
The stability of the two general classes of colloids, the lyophllic and lyophobl
c systems,
differs mainly due to two factors.
(0 charge on the colloidal particle, and
(/0 the degree of solvation.
The hydrophobic colloids (suspensoids) can be flocculated easily by addition of
quantities of electrolytes. When a dilute electrolyte solution is added dropwise
to a colloidal
solution and mixed thoroughly after each addition, it is observed that a point c

omes when after

addition of a single drop, rapid aggregation takes place leading to the formatio
n of a coarse
flocculate. The volume of the added electrolyte at this point gives the.floccula
tion value of the
colloidal system.
The flocculation values of lyophobic colloidal systems are lower than those of l
colloidal systems. This in turn means that the lyophillc systems are more stable
. Why? Two
movements take place continuously in a colloidal dispersion. One is the Brownian
motion and
the other is the convective movements of the dispersion medium. Both of these wo
uld normally
bring the particles close to each other continuously. Though there are ample cha
nces of contact
of particles, it is seen that coalescence does not occur. This is due to the fac
t that the colloidal
particles are charged. The hydrophobic colloidal particles are electrically char
ged alike and
repel each other. The electrolyte long gets adsorbed upon some of the colloidal
neutralizing or reversing the charges of the latter. These colloidal particles n
ow serve as nuclei
which grow rapidly by aggregation of other particles finally leading to precipit
ation. If the
electrolyte solution is added rapidly and in excess, with vigorous stirring, pre
cipitation does not
take place. The reason is that charges on the colloidal particles get reversed s
imultaneously so
that the particles continue to repel each other and remain separated.
The effectiveness of a-salt solution to precipitate a colloidal solution also de
pends on the
valency of the oppositely charged ion. Higher the valence, greater is the effect
The stability of lyophilic systems (emuIsoids) lies in the fact that the particl
es have a very
strong attraction for the solvent in addition to the electrical charge which con
fers stability to a
sol. As long as the particles remain solvated, neutralization of the charges alo
ne will not bring
about precipitation. Similarly, dehydration alone will only convert the emulsoid
to a suspensoid
but not precipitate it. This property of lyophilic colloids has great biological
significance as most

Colloidal Phenomena
physiological colloidal dispersions are of the lyophilic type. Living matter the
refore can
slight changes in its content of inorganic long without disaster. Effective prec
lyophilic colloid requires the addition of a large quantity of soluble salt. Thi
s is known as
process, thepower of which depends upon the nature of both the cation and the
anion of the salt. Depending on their ability of dehydration of other particles,
the long are in series called the /yotrop/c or the Hofmeister series. This seri
es determines the
i out power of the different electrolytes (see Box 3.4). Thus addition of large
amounts of
dehydrates as well as neutralizes the charges on the colloidal particles simulta
md causes precipitation. The reversibility of the precipitate of an emulsoid to
the dispersion
forri is also vez difficult to achieve and for this reason they are also known a
s irreversible

Biophysical Chemistry

Colloidal Phenomena
Besides electrolytes, H and OH- also affect the stability of colloids. While OHLong
the negative zeta potential H long have an opposite effect. Thus by varying the v
alue of
potential to a 'critical potential', precipitation is facilitated. Various other
physical and
heat, UV radiation, acids and alkalies,
mechanical disturbances like ultrasonic vibrations, high speed shaking or stirri
ng can
the conformation of the colloidal particle and thus precipitate it.
Another effective method of bringing about precipitation .is by mutual cancellat
ion of charges.
can be done by adding a negative suspensoid to a positive suspensoid or vice-ver
sa. This is
as mutual precipitation of colloids.
In a
dispersion, if the particle is a macromolecule o polyelectrolyte nature,
the genel:al physicochemical propexies may arise. The British physicist
in 1911, showed that when two solutions of electrolytes are separated by
membrane, potentials arise at the junction. This happens when movement o
of the long through the semipermeable membrane is hindered. The hindranc
e may
to the colloidal nature of the ion or the electrolyte may be chemically bondedto
like an ion-exchange resin on one side. In addition,
Losmotic pressure difference between the two compartments is observed at equilib
rium. The
for these apparent anomalies was provided by Donnan and therefore the
Donnan membrane equilibrium bears his name to this day.
Let us consider a system to be divided into two compartments by a semipermeable
water to pass through but not the large long of colloidal
In compartment A is present a solution of salt NaR of concentration 'a' where Ris
anion of polyelectrolyte nature. Compartment B is occupied by a solution of NaCl
'b'. NaCl will now diffuse from (B) to (A) and some of it may reversely diffuse

(B). This continues till the system attains equilibrium.
rlf 'x' represents the net concentration of NaCI that has diffused from (B) to (
A), then at
the situation in the compartments will be depicted as in Figure 3.11 (a and b).
(a mols)
(b tools)
CI(b mols)
Figure 3. I i. (a) Distribution of ions.across a semipermeable membrane at zero
(A) (B}

(a + x mols}
(a mols)
Cl{x tools}
(b x mols}
CI(b - x mols}

Figure 3.1 I. (b) Distribution of long across a semipermeable membrane at equili


Biophysical Chemlstr
The rate of diffusion of NaCI from (B) to(A) is proportional to the product of t
he concentration
of Na and C1- in (B) and the rate of diffusion of NaCI from (A) to (B) is proport
ional to the
product of the concentrations of Na and CI- in (A). It might be mentioned here th
at in very
dilute solutions, activity terms can be replaced by concentrations. The situatio
n is represented
as below :
[Na]B [CI-]s = [Na]A [CI-]^
to-x) to-x} =(a+x} (x}
The above equation shows that while in compartment B the concentration of Na and
CI- is the same, in compartment A the concentration of CI- is less than the conc
entration of
But as electroneutrallty requires the presence of equal numbers of cations and a
nions in each
compartment, it follows that
[Nals = [CI-] and
iNal^ = [R'l^ + |el-|^
where [R-I^ is the concentration of the restricted ion in compartment A. The abo
ve equation
points out the fact that the concentration of the diffusible anion is less in th
e compartment
containing the non-diffusible ion than in the other compartment. The restriction
of the nondiffusible anion at the membrane while the cation is tending to diffuse through
it, sets up.a
potential difference between the two solutions. At equilibrium, the solution in
the compartment
A acquires a positive potential with respect to the other because of the slight
excess of Na long.
Thus we have seen that the presence of a non-diffusible ion on one side of a dia
lyzing membrane
causes unequal distribution of every diffuslble ion on the two. sides of the mem
brane. While the
positive diffusible long concentrate in the compartment containing the negative
ion, the negative diffusible long are more to be seen on the opposite side. The
concentrations of the non-diffusible and the diffusible long is important in a s
ystem in Donnan
equilibrium. If the concentration of the non-diffusible ion is increased, a grea
ter inequality in
ion distribution is observed. This leads to a further increase in membrane poten
tial. On the
other hand, the greater the concentration of diffusible long, smaller is the mem
brane potential

due to the masking of the effect of non-diffusible long. Therefore, the Donnan e
ffect can be
decreased considerably at high electrolyte concentrations.
The osmotic pressure difference observed at equilibrium due to inequalities of d
of diffusible long in the two compartments can be minimized by dissolving the po
lyelectrolyte in
a salt solution of high molarity (0.1 M or higher) and then using the same salt
solution in the
other compartment. Another modification which can be adopted for protein solutio
ns is to
select a pH very near to the isoelectrlc pH of the protein so that the net prote
in charge is
reduced to a minimum value. Under these conditions, the flow of the oppositely c
harged diffusible
ion across the membrane and its concentration in the compartment containing the
molecules will be decreased. The osmotic pressure in a system exhibith-lg Donnan
effect can be
calculated by the formula
where c = concentration of the long
R ffi gas constant T = temperature
At 27C, the osmotic pressure of a system of the following type can be calculated
thus :

5.10 mols

The Colloidal Phenomena

Na (a)
Na {b}
Cl- {b}

(at zero time)

Semipermeable membrane
Let a = 3 mols and b = 4 mols, then amount of NaCI diffusing from (B) to (A), re
by 'x' will be,
a +2b
This is so because at equilibrium
[Na+]s [CI-]s = [Na+]A [CI-]A

(b-x}(b-x} = {a+x}(x}
b2-2bx + x2 = ax + x=
b== ax + 2bx
b= = x {a + 2b}
a+ 2b

Putting the value of a and b n the above equation, we get

= 1.45approx.
x - (3 + 2 x 4) - 3+8
Now, calculating the concentration of each of the long in the two compartments w

(a.+x) = 4.45
(b-x) = 2.55

CI(x) = 1.45
R(a} = 3.0
8.90 tools
Cl(b-x) = 2.55

Since the osmotic pressure is given by the equation,

P =.cRT

Biophysical Chemistry
by substituting all the values we get,
P = (8.9 - 5. I) x 0.082 x 300 (as 27C = 300K)
= 3.8 x 0.082 x 300
= 93.48 atmospheres
Biological Significance of Donnan Membrane Phenomenon
The Donnan effect plays a significant role in our body because of two basic stru
Most of our body membranes are dialyzing membranes, i.e., they allow the
of water, gases like O and COa, long and small organic molecules across them whi
disallowing colloidal particles, and
The non-diffusible protein anions are present in large quantities in cel
ls and in plasma
but not in interstiUal fluid.
Both the above factors promote unequal distribution of diffusible long on either
side of
biological membranes which in turn would result in establishment of a pH differe
nce and.an
osmotic difference between the compartments. Minor pH changes are tolerable for
most of the
tissues but drastic pH changes may pose problems. The body saves itself from the
h .armful
influence of the latter with the help of its buffer systems. But sometimes maint
enance of a
drastic pH difference is a necessity, as is in the case of stomach. Gastric dige
stion cannot
proceed ff the pH is not maintained at a very low level. In this case, the gastr
ic mucosal membrane
gears up to permit the hydrolysis reaction
where P represents the non-diffusible protein long. The H long, with associated C
I- long (to
maintain electroneutrality) will move from gastric mucosa to the gastric lumen b
ecause of the
non-diffusible P* long in the protoplasm. This leads to a greater concentration
of H long in he
lumen and subsequently the pH of the gastric secretion fails to very low values.

The Donnan effect applies to all kinds of diffusible long. The red blood ceils p
rovide another
case where Donnan effect determines the distribution of long between the content
s of the cell
and the surrounding plasma. The erythrocyte membrane is freely permeable to HCO
and Cl-anions but is impermeable to the protein haemoglobin which exists in the
anionic form. When
blood flows through capillaries, HCO diffuses into the plasma by passive diffusi
on. About 70% of the HCO formed in the red cells enters the plasma. Na md K are n
ot available for free diffusion due to the operation of sodium-potassium pump. T
o maintain electroneutrality, CIfrom the plasma enters the erythrocytes. But at equilibrium the Cl- ion concentr
ation in RBC
and plasma is not found to be equal. Only 70% of the CI- long present in the blo
od plasma enter
the cells. The unequal distribution of this diffusible ion is mainly due to the
Donnan effect. As
the RBCs of venous blood has more of riCO long, there is a greater concentration
of Cl- long in these RBCs during this exchange phenomenon.
The above examples have made us understand the usefulness of Donnan membrane
equilibrium in biology. However, there are cases where the same effect becomes a
bane to the
system. An example that can be cited is that of oedema in ttssues. When the plas
ma .albumin
content falls below the normal value, salt and water retention tares place in th
e tissues. The
movement of the concerned electrolytes in and out of the ceil membranes occurs m
ainly due to the Donnan effect. Other developments like increased secretion of a
ldosterone and vasopressin
fotlow soon to result in a full-fledged oedema state.

ne CoY.ol Phenomeng
The Donnan equilibrium has played a very important role in interpretation of oth
physiological phenomena like absorption of glucose by the intestine, the distrib
ution of diffusible
long between blood and the cerebrospinal fluid and in urine formation in the kid
Besides its role in physiology, it is also being exploited for the benefit of ma
nkind. Kidneys,
apart from being one of the main organs involved in acid-base regulation, also e
xcrete many
toxic substances through urine formation. Naturally, both these functions are al
tered in kidney
pathology with life-threatening repercussions. For such patients, artificial kid
neys are used.
These artificial kidneys have dialyz'ng membranes which form minute channels for
blood on
one side and a dialyzing fluid on the other side. The thin dialyzing cellulose m
embrane allows
all constituents of blood to .diffuse freely in both directions with the excepti
ons of plasma proteins
and cellular components. In this way, the toxic substances accumulated in the bl
ood can
diffuse through the cellulose membrane into the dialyzing fluid. This diffusion
can be tailored
as per the needs of the patients by altering the concentrations and compositions
of the non diffusible long. It is obvious that Donnan effect plays a major role
in the,functioning of artificial kidneys.
Suggestions for Further Read/ng
Edsa]l, J.T., The S/ze, Shape and Hydration of Protein Molecules in The
Proteins, Vol. I,
Part B (H. Neurath and K. Bailey, eds.), Academic, New York, 1953.
Haschemeyer, R.H., and Haschemeyer, A.E.V., Proter: A Guide to Study by
Physfcal and
ChernfcaIMethods, John Wiley and Sons, Inc. 1973.
Ward, A.G., Co[[ofds, Their Propertfes andApplfcatfons, Blackle and Sons
Ltd., London, 1948.
Me Ba/n, J:W., Co//ok/Science, Reinhold Pub]/shlng, CoG., New York, 1950
Kruty, H.R., Co//ofd Sdence, Elsevier Publishing Co., New York, 1952.

Adamson, A.W., Physical Chemistry of Surfaces, Intersc/ence Pub]/shers I
nc., New York, 1960.

Matter tends to move spontaneously from a region of high concentration to a regi
on of
lower concentration until the composition is homogeneous throughout. This moveme
nt of
molecules without any energy expended is called passive transport or diffusion.
The molecules in a solution are in a state of continuous motion as a result of b
by solvent and other solute molecules if present. The direction of movement is c
changing in a zig-zag fashion. The velocity of this movement, also called Browni
an movement
(see Chapter 3) is given by the equation,
... (1)
where C is the root mean square velocity in cm sec-,
'R' is the gas constant having a value of 8.314 10 ergs/degree/mole,
T is the absolute temperature in Kelvins, and
M is the molecular weight of the moving particle.
Due to Brownian movement, the displacement of the molecules per unit time is not
in a
straight line. The small molecules and long (crystalloids) diffuse rapidly while
the macromolecules
owing to their large size and shape have a sluggish motion. Another factor affec
ting the movement
of molecules is the concentration difference. Greater the concentration gradient
, more rapid
will be the diffusion.
Biomembranes are selectively permeable in nature. Diffusion of solutes across th
membranes is mainly of two kinds :
(/) Simple diffusion,
(//) Facilitated diffusion.
Simple diffusion may take place directly through a lipid bilayer, through "holes
" created in
the membrane by membrane proteins or by discontinuities in the lipid bilayer. Bu
t there is no

active participation of any membrane protein in this type of solute movement.

On the other hand, facilitated diffusion compulsorily occurs with the participat
ion of a
carrier molecule, usually a membrane protein, It may perform its task in any of
the three ways
mentioned below :
it may move across the membrane with the substance to release it on the
other side
and then return to its original position to continue the cycle, or

Diffusion and Osmosis

a conformational change may take place in the transport protein on bindi
ng to the
solute which may help in the translocation of the latter to the opposite side, o
the solute may be shuttled from one membrane protein to another till it
reaches its
Diffusion is a process of equilibration thatis directed along a concentration gr
adient from
a region of higher concentration to a region of lower concentration. At equilibr
ium the molecules
will be uniformly randomized throughout the system leading to an increase in ent
ropy. It is
therefore a spontaneous process, according to the second law of thermodynamics.
Due to the random walk of individual molecules owing to vibrational and thermal
it is difficult to measure the actual displacement per unit time for each molecu
le. However, a
statistical consideration of all the diffusing molecules as a whole shows that a
t each point
time a net flow exists, which is proportional to and follows the concentration g
radient. This rate
of net movement of molecules can be described by Fick's laws of diffusion.
Fick's Laws of Diffusion
Let us first assume that the solute molecules are moving in one dimension only.
A molecule
situated at the origin initially is capable of moving either to the left or to t
he right in distances
of average length W. We shall call these small displacements as 'steps'. The net
movement of a
molecule can now be given by the excess steps taken to the right over the left o
r vice versa. The
probability of the steps taken in either direction remains the same. If 'n' is t
he total number of
steps covered by the molecule in unit time, the total distance travelled will be
equal to 'r', 'n' is
constituted of the steps taken by the molecule to the right and to the left indi
cated by symbols
'mr', and 'm,' respectively. As already stated that the chances of a leftward or
rightward step are
equal, the most probable end point of any particular molecule will be at the ori
gin itself, i.e., rn
is equal to mr, therefore rn-mr is equal to zero. However, the system contains a
large number of

molecules and some of these molecules might move excessively to the left or to t
he right. As the
time increases, the total number of steps 'n' also increases and with it increas
es the possibility
of more and more molecules moving away from origin by purely random motions lead
ing to
Rather than one, let us now consider a model having two origins separated by a p
From both the origins molecules radiate out into the solution across the plane l
ying between
the two origins. Naturally such a variation would change the concentration profi
les of not only
the two origins but of the plane also. From the above paragraph we know that the
change in the
concentration profile depends upon the total number of steps taken by the molecu
les (n), distance
covered (.) and on the initial concentration. Therefore, the net displacement pe
r unit time
across the plane in any one direction will be determined by the difference in th
e initial
oncentration of the two origins and by 'n' and W. This is the molecular basis of
lck'sfirst law
of diffusion which is in effect described by rate equation. It states that the a
mount of solute 'da'
diffusing across the areaA (1 sq. cm) in a length of time 'dt' is proportional t
o the concentration
gradient dc/dx at that point, or
' ...
where D is a constant of proportlonallty, also called d{1sion lent. It is indepe
ndent of the
concentration at 'x' and x + dx, and related to 'n' and ',' mentioned above. The
negative sign
arises since diffusion takes place in the direction of decreasing concentration

... (3)
Biophysical Chemistry
While formulating the first law, Fick assumed that the laws of diffusion were an
alogous to
the news governing the transfer of heat derived by Fourier earlier.
One of the methods to determine 'D' is to measure da/dt, also called the flux, a
nd then
find dc/dx frbm it. From this value we can obtain D as the flux obeys Fick's fir
st law. Due to
diffusion the composition and therefore the refractive index of thesolution chan
ges. Most of the
methods for measuring rate of diffusion involve measurement of such changes in t
he refractive
indices with the help of such techniques as light absorption, fluorescence and T
yndall effect,
More recenfly the interferometric methods of studying the boundary changes have
been preferred.
Experimentally, the measurement of diffusion constant is done by two methods :
(/) the porous disc method and
(//) the free diffusion method.
(0 In the porous disc method the particles are allowed to pass through a porous
disc made
of sintered glass or alundum. A concentration gradient is thus created across th
e porous disc.
A solute is now chosen whose diffusion constant is known and its rate of diffusi
on is measured
by this method. The molecule whose diffusion constant has to be evaluated is now
treated in
identical manner and its rate of diffusion through the porous disc is measured.
From the
obtained data, the diffusion constant of the unknown solute molecule is calculat
ed. The value
of 'D' thus obtained is of a relative nature.
For absolute measurements of'D' by the free diffusion method, Fick's second law
of diffusion
has to be applied. It is a partial differential equation derived from Fick's fir
st law of diffusion.
The simplest assumption during appication of this second law is that the diffusi
ng particles do
not participate in any chemical reaction within the diffusing space. This law ca

n be expressed
by the equation,
where - = rate of change of concentration with time
and- = first derivative of concentration gradient with respect to distance.
For three dimensions, the equation becomes
x, y and z are the space variables. The above equation has ALSO been expressed a
de B2
--- DVc
... (5)

Diffusion and Osmosis

-2 is the Laplace operator, in this case operating on 'c'. To use equation (5),
it has to be
where We
solved first. The solution takes into consideration the boundary conditions and
initial conditions
operative in the system under investigation. These conditions determine which of
the multitude
of possible solutions of a differential equation is applicable to the system. To
simplify the
mathematical dealing, one may employ a specially designed diffusion apparatus wh
ich is
geometrically simple or use an analytical centrifuge The spread of an initially
sharp boundry
between the solute and solvent is observed as the solute diffuses into the solve
nt layer.
Diffusion in biological system is, however, mostly associated with chemical reac
tions. In
such situations the. simplest assumption that can be made regarding the diffusin
g system is
that within the diffusing space the rate of utfllzation of the diffusing solute
is constant, i.e.
independent of time and place. Equation [5) in such conditions will take the for
-- = DVc - A
... (6)
where 'A'. represents the rate of consumption. Another frequent observation in b
iological system
is that due to stationary boundry conditions the concentration is independent of
tirne at all
positions of the diffusing.space. Under this condition, dc/dt = 0 and equation (
6) becomes,
D.Vc = A, assuming again the constant consumption of the diffusing solute.
The speed of movement of a particle is characterized by its diffusion coefficien
t which is a
function of the size and shape of the molecule. Knowledge of the diffusion coeff
icient is necessary
for ultracentrifuge studies as it provides us with information regarding the sha
pe of the particles
in solution. Perhaps it is of more importance during the determination of moecul
ar weight of

macromolecules as there is a distinct relationship between the molecular weight

of a substance
and its diffusion coefficient. Before we proceed to the mathematical treatment f
or obtaining the
relationship between molecular weight and 'D', we shall discuss the molecular na
ture of a
liquid film.
The /atttce theory explains beautifully the
molecular nature of a liquid film. According to this
theory the liquid film appears as a network of
molecules with empty spaces in between (see Figure
4. I). These empty spaces or 'holes' as they are called
are the regions where molecules are trapped during
their translational movement. Molecules thus move
from hole to hole, creating in the process new holes
to trap other molecules. This movment of molecules
from one hole to another is called diffusion.
However, since the molecules of a liquid are
attracted by other molecules adjacent to them, they
are unable to move swiftly in the holes created for
them. Therefore, in order to move a molecule into
a hole energy has to be expended. IfaE is the total
energy required to break the bonds a molecule
makes with its nelghbours to flow into an adjacent hole, will represent the dist
ance travelled by a molecule to fall into a hole. If the initial concentration o
f the sample at the origin is 'c', on

Figure 4.2
'dc. . +dx
Distance travelled (.x)
Diffusion of molecules across an energy
barrier. , is the dstance between
successive equtltbrrn posons, and aE
Is the total energy required to enable a
molecule to free from its neghbours and
j'Iow into an acent hole
Bophsca Chemstr
diffusion of the molecules through a distance dx
the concentration at the new equilibrium position
would change to c + - (see Figure 4.2).
Therefore, in order to move into an adjacent hole
the molecules should possess an energy equivalent
to or greater than AE.
Not all molecules possess AE. The fraction
which does possess AE can be represented by the
number e-/R, according to the Maxwell-Boltzmann distribution law.
As time 'dr' lapses, some of these molecules
will acquire the most favourable orientation to move
faster into the hole, so that the total number of
molecules per unit volume diffusing from left to
right will be depicted as

N = cQe-/T
where Q = the number of molecules possessing the correct orientation.
Similarly, the ones crossing over from right to left will be given by
The net movement from left to right direction would now be

Nm = N- Nr
Nm = -X --.Q.e-E/T per unit volume
... (7)
If the diffusion has occurred across a plane of area 'A', the net total number o
f particles
that have corssed over from leil to right along the concentration gradient per u
nit time would be
given by
Nm ..2A.Q.eA/RTdc
-... (8)
Comparing eqn. (8) with eqn. (3), we see that
D = ,2.Q.e-Z/RT "
Thus, if the values X, Q and E are known, D can be easily obtained.

4n r3N
... (13)
Di.Jiusion and Osmosis
The hydrodynamic properties of a molecule are strongly related to its size and s
Diffusion is of two main types -- translational and rotational. Out of these, th
e latter is
characteristic of the type of molecule. A large spherical molecule will have a s
ingle rotary diffusion
coefficient. An ellipsoid of revolution is characterised by two coefficients as
it possesses two
axes while a general ellipsoid molecule will have three coefficients, one for ea
ch of the axes.
These rotary diffusion coefficients of macromolecules of various shapes can be d
etermined by
flow birefringence (see Chapter 9) and by electrical methods if the molecules ar
e dipolar in
Einstein in 1905 gave a relationship between diffusion coefficient and radius of
macromolecule on the basis of Stokes' law of diffusion. The assumptions for this
are that the size of the diffusing molecule is many times greater than that of t
he solvent molecule
and secondly, the solvent is a continuous medium.
Einstein provided the relationship between diffusion coefficient (D) and frictio
nal coefficient
(f} as
D =-... (10)
k = 1.38 x I0-=3 JK- (Boltzmann's constant) and
T = Temperature in Kelvin.
The coefficient T depends on the shape and size of the macromolecule, but not on
mass. For spherical particles, Stokes provided the relationship

... (11)
where r = radius of the particle, and
-- viscosity of the solvent.
Combining eqns. (10) and (11) we get the Einstein-Stokes' equation as
D = (12)
Since the volume of a sphere of radius 'r' is -- ra, and the volume of a spheric
al molecule is
-- where ; is the partial specific volume, M being the molecular weight and N th
e Avagadro's
number, we can write

.., (16)
Do = -- (as 'K' .the Boltzmann's constant is
equivalent to the gas constant per
molecule, it Is replaced by R/N)
where fo is the frictional coefficient of a spherical particle.
Do =
As the macromolecules being studied are of various shapes, the experimentally de
values of'D' are usually smaller than those calculated theoretically on the assu
mption that the
molecules arespherical in shape. The ratio f/fo i.e., the ratio of the frictiona
l coefficient for nonspherical particles (f) to the frictional coefficient of spherical particles (fo
) is termed asfr/ct/ona/
rat/o or dtssymetry constant. The value off/fo for spherical particles is 'one'
and as the deviation
from spherical shape increases for macromolecules, the value of f/fo becomes pro
Earlier we have discussed the zlg-zag movement of molecules in solution on accou
nt of
Brownian motion. However, the same theory does not apply to solutions of electro
lytes. The
long here are influenced by the electric field and the net movement is according
to the sign of
their charge. One ion attracts around itself other long of opposite sign and ten
ds to drag them
along with itself. As a result, long of opposite charge do not move singly but r
ather in the form
of pairs. A faster ion is thus slowed down by its 'sluggish' partner while the l
atter is speeded up
by its association with the former. Thus it is difficult to obtain the diffusion
coefficient of any

single ion. What we find actually is the diffusion coefficient of the ion pair,
If an electric connection
is made after the solution of electrolytes has come to diffusion equilibrium, a
flow of current will
be observed. This is due to the dissociation of the ion pairs which under the in
fluence of the
extemally applied electric field now move independently to their respective oppo
sitely charged
electrodes. It is now possible to measure the ionic mobility of individual Long.
Each ion will have a different ionic mobility and the mobility is a measure of t
he speed of
the long as it moves through the solution. Therefore, there is a distinct relati
onship between the
mobility of an ion and its diffusion coefficient. It is given by
RT (v, + v2)
D = "
... (171
N Vla2 + v2D
where D is the diffusion coefficient of the electrolyte at infinite dilution, N i
s the Avagadro's
number, R is the gas constant equivalent to 8.314 x 107 ergs/degree/mole, T is t
he temperature
in Kelvins, bt and 12 are the absolute mobility of the two oppositely charged lo
ng and v and v2
represent the number of positively, and negatively charged long respectively obt
ained on
dissociation of the electrolyte (for e.g., ff one molecule of NaC1 dissociates i
t will give rise to one
positively charged ion, Na and one negatively charged ion, CI'. Similarly CaCI2 w
ill give one
positive ion Ca2 and two negative long of CI'}.
The value of 'D' obtained by equation (17) is of limiting nature as it is obtain
ed on the
assumption that the electrolytic solution is infinitely diluted. However, at low

Dtffuslon and Osmosis

the actual value of D can be found by taking into consideration the activity of
the solution. The
equation now takes the form : ,
D=DO +(l+dln+ /
... (18)
where 7 represents the "mean ionic actlty" coefficient and 'c' the concentration
of the solution.
At higher concentrations the above equation has to be modified further to take a
ccount of
the solvation of long which we shall,'discuss subsequently.
A stable solution is one in which the solute-solvent bonds are of the same order
of magnitude
In the same manner an aqueous solution will be stable only ff the
is capable of forming hydrogen bonds with water in a manner similar to the hydro
gen between the water molecules. When the solute has to diffuse, i.e., move from
hole to
In the lattice, its hydrogen bonds haveto be broken. The energy required to brea
k one
bond is approximately 4.2 kcal at 27"C. Now if the molecule has to move in water
, all
hydrogen bonds that it makes with water need not be broken at the same time. But
ff it
In a lipid layer, all the hydrogen bonds have to be broken together which will r
equire a
mergy. Therefore, the diffusion coefficient will be reduced in lipid solvent
solutes. Some solutes form many such hydrogen bonds with water molecules. If all
these bonds have to be broken when the solute moves, then diffusion will be slow
Having gained knowledge about the various types of interactions in a solution wh
ich affect
and on the basis of lattice theory we can now. give an explanation on diffusion
:solutes across bio-membranes. It will be appropriate to mention here some struc
characteristics of living membranes as per.the model provided by Davson and Dani
elli. Biological
membranes have a lipid bflayer sandwiched between two layers0f proteins, the lat
ter providing
integrity to the membrane. The lipid layer acts as an effective diffusion barrie
Several reasons have been attributed to this behaviour of the lipid layer. We sh
all discuss them

A molecule has to break all its hydrogen bonds with water if it has to p
enetrate the lipid
In an aqueous environment this would not have been difficult as the H-bonds coul
d be
one at a time and similarly reformed one at a time. Therefore, the diffusion rat
e of a
is lowered when passing through a lipid medium.
(10 The lipid bilayer is a closely knit structure with intermolecular hydrophobi
c bonds
acent side chains of the fatty acids making it even more difficult for a molecul
e to
it. To create even a single hole for a moving solute molecule, a large amount of
to be expended in breaking the hydrophobic bonds.
For a lipid membrane 50A thick, the resistance becomes too much and diffusion is
(li0 For large polyelectrolytes, diffusion is slowed down because larger holes h
ave to be
by displacement of a large nnmber of solvent molecules. Larger the molecule, les
ser is
value of 'D' as can be seen in equation (12).
(iv) A hydrated molecule has to shed its bound water molecules to penetrate into
the lipid
again requires a considerable energy. Diffusion thus is retarded. Greater the de
of a molecule, lesser is the diffusion. The values of spherical molecules are gr
affected by hydration. Cations are slow in diffusion than the anions because of
their bulk, the

... (19)
Biophysical Chemistry
bulk being chiefly contributed by the water molecules around them. Hydration cau
ses a swelling
of the molecule by binding water, and thisincreases the frictional effect. For m
acromolecules ff
the frictional ratio is more than 2.5, the effect of hydration becomes negligibl
(v) Lastly, there are several sophisticated membrane processes affecting diffusi
on of solute
molecules in and out of the cells.
The anions and cations of an electrolyte solution move at different rates. As a
result a
potential is set up across the membranes through which these long diffuse. It ca
n happen when
two solutions of the same electrolyte at different concentrations are separated
by a membrane
and also when two different electrolytes of the same concentration are kept sepa
rate due to the
membrane. These potentials are called diffusion poten'.ti, and are a characterist
ic of the
membrane as well as the long. If the membrane has the pores of a size that would
not allow
entry of one particular ion through it, the diffusion potential will be high.
Two equations have been provided to calculate the diffusion potentials of membra
They are :
Case a
E = 0.058 log laA + lab
c + ga
when there are two different salts AB- and CB- of a single concentration separated
by a membrane, and
E = 0.058 laA+ ]an logt
... (20)
1C + laB C2
when there are two different concentrations C and C= of the same salt across a m
embrane. ^,

B, c are the ionic mobilities of the long A, B and C respectively.

The above equation tells us that the relative mobilities of the diffusing long a
nd their
concentrations are the factors determining the magnitude of the diffusion potent
ial developed
across a membrane. However, these potentials are unstable as concentration diffe
rences are
bound to occur on further diffusion.

Due to
and Osmosis
always foundto be less than the expect value.This is due to the physiologicaldea
d space. The
anatomical dead
cpacity. The value of K for oxygenin human beings,can be determined from measure
ments of
diffusio.,capacity for oxygen, llng area and the istance through which diffusion
occurs. The
rate of diffu.
lungs, by the
So far we have discussed the free diffusion of molecules and diffusion of solute
s across
process which is complimentary to the ones described above and obeying
mechanism is osmosis. Osmosis is one of the major exchange processes which is
to the living body and therefore has to be regulated carefully. It is not only t
of the various long in the body fluids but also their content which is important
functioning individual. Osmosis takes care of both of these. By definition it s
a dilute to a concentrated solution, across a semipermeable membrane till the
equilibrium. The semipermeable nature varies from membrane to membrane. For
it is semipermeable to small long and molecules but not big colloidal particles,
for others
be differentially permeable to certain long, excluding others, while some may be
Biological membranes, though, are mostly specific. They have a vast range of
systems embedded within them which will carefully 'sniff the metabolite to be
while it waits outside and only allow one kind to enter, that which is needed.
the one to go out also has to face scrutiny. This flux of metabolites is associa
ted with of solvent. Some of these movements require energy and thus are termed
others just move on across the gradient and therefore called passive. Osmosis be
longs to
It is concerned with the spontaneous flow of solvent only. We can demonstrate
A glass tube open at both ends is chosen and at one end is tied an
membrane in the form of a sack. Now the tube is half-filled with concentrated su

in a beaker of water (see Figure 4.3). After some time we observe that
in the tube has risen. The level of the liquid rises until the hydrostatic press
ure so
sufficient to stop the flow of solvent, or osmosis, into the tube. This hydrosta
developed as a result of osmosis is called the osmotic pressure of the solution
and is
as the excess pressure that must be applied to the solution to prevent the passa
ge of the
t into it thorugh the semipermeable membrane separating the two solutions.

Btophysicat Chemistr

Final level
h,--- ---- Initial level
-----* Sucrose solution
I---- Water
i" -- = -- Animal membrane
---4 (semipermeable)
Figure 4.3 Osmosis through animal membrane
The osmotic behaviour of molecules was first reported by Abbe NoIlet in 1748.
on, the search began for an ideal semipermeable membrane. M. Traube in 1867
membrane of a gelationous precipitate of copper ferrocyanide, Cu2Fe(CN)6 for low
weight solutes in water. For high molecular weight solutes in organic solvents,
made of cellulose, cellulose nitrate or animal membrane have been found suitable
Why Exactly Does Osmosis Take Place ?
The answer becomes very simple if we look at it thermodynamically. When a solute
dissolved in a solvent, the energy of the solvent molecules is reduced considera
the solute-solvent interactions. When this solution is separated from the pure s
olvent by',
semipermeable membrane rapid movement of the solvent molecules across the barrie
in the direction of the solution. The hydrostatic pressure so developed in the
containing the solution is enough, to increase the free energy of the solvent mo
lecules in
solution. When the free energy of the solvent molecules in the solution is resto
red to
equal to that of the pure solvent, an equilibrium is achieved and osmosis stops.
number of solute particles in the solution, greater is the osmotic pressure deve
osmotic pressure is one of the four. colligative properties that a solution poss

pressure, rise in boiling point, depression of freezing point, being the others)
. Under
conditions it is just like gas pressure, directly proportional to the absolute t
emperature and
concentration, and is independent of the chemical nature of the dissolved materi
When working with a colloidal solution, mention has to be made about the nature
semipermeable membrane. Protein solutions, in general, are prepared in dilute sa
If the membrane is impermeable to both salt and colloidal particles, we obtain t
pressure. With a membrane impermeable to protein but permeable to
osmotic pressure. The latter is useful while deducing the molar mass of the coll
oidal particles
The first determination of osmotic pressure of macromolecular solutions began wi
in 1899 He filtered blood serum through a semipermeable membrane made of
successfully freed the serum from its crystalloid constituents. Osmotic pressure
of the filtrate devoid of protein constituents and the raw (unfiltered) serum sh
owed that
proteins gave osmotic pressures of 30-40 mm Hg. This experiment provided an insi
osmotic behaviour of cells in various physiological processes, namely, the renal
the secretory processes. Since then, various attempts were made to design the os
measurement apparatus to a type where the osmotic pressures of the biological
not be affected adversely by extraneous factors.

and Osmosis
Sorensen in 1917 first published the data of his measurements of osmotic pressur
e of
solutions under carefully controlled conditions. His results and those of Starli
ng's on
which was reproduced using collodion membranes and better designed modem
showed that a strict control of pH and salt concentration, and knowledge of the
of protein are mandatory while determining the osmotic pressures of protein
The osmometers which were. used by Sorensen and others in the first half of 20th
though efficient, took several days for standardization. The osmotic event was r
:the rise due to capillarity in themanometer tube required several days to reach
an equilibrium
osmometers designed later were easy to handle and more accurate. The manometers
these latter type of instruments contained organic liquids, paraffin, toluene or
alcohols with
could be attained in a very short time. The sample requirement also was low.
instruments required a rigorous thermostatic control within 0.004o. Later, this
s circumvented by the invention of an electronic osmometer by Rowe andAbrams in
could be operated without thermostatic control and the sample for determination
small volume (only 0.5 rnl). A detalled discussion of the apparatus is given in
pressure (P)
Electrical cireuit
An osmometer adaPted for rap dmeasurements of,osmotic pressure using
ample was designed as above by,Rowe and Abrams in 1957. The U;tube has
platinum foil which isconnected

o = 1
Biophysical Chemistry:
We rarely come across biological membranes which are perfectly selectlvely
the solvent and exclude solute molecules completely. However, due to small pore
membranes, though the movement of the solute molecules will be impeded, there
a very slow diffusion of low molecular weight solutes. Let us consider a vessel
and divided into two compartments (A and B) by a porous membrane. The membrane
impermeable to solute molecules. If a solute like sugar is now added to compartm
ent B,
will flow from A to B because the osmotic pressure of the solution in B is great
er than in
There will also be a diffusion of sugar molecules from B to A at a very slow rat
e. Due to this,
effective osmotic pressure as judged by the movement of solvent from A to B will
the osmotic pressure calculated from the solute concentration alone.
The effective osmotic pressure of a solution can be calculated by including a te
Staverman's reflection coefficient, symbolized by o, in the osmotic pressure equ
ation, so that
neff =
The reflection coefficient has an inverse relationship with permeability coeffic
ient. It depen&
on the nature of the selectivly permeable membrane and the nature of the solute.
If AsoLv
represents the effective fraction of the area on the membrane available for diff
particles and ASOLVET, the effective fraction of the area on the membrane availa
ble for
diffusion, then
If the pores in the membrane are of size which would not allow the solute molecu
les to
diffuse, the second half of the equation, i.e.,
ASOLUTE approaches zero and o
approaches I.
The significance of o is better understood when we study-the osmotic behaviour o

f living
cells. Living cells have selectively permeable membranes which are very permeabl
e to water and
some low molecular weight solutes, but much less permeable to other substances.
This leads to
the inflow of some solute molecules along with the solvent while others are reta
ined. Under
these conditions, the solution exhibits only that fraction of its total osmotic
pressure that is due
to the solutes which are retained. This fraction of the total osmotic pressure o
f a solution is
termed as its ton/city. If the cells are placed in a medium whose osmotic pressu
re matches that
of the cell contents inside, there is no unidirectional flow of solvent and the
cell size remains the

lon and OsrnosLs

same. The medium then is said to be isotonic with the cell. If the medium is con
centrated, its
osmotic pressure is greater than that of the cell interior. Water then will be a
bstracted from the
cell resulting a shrinkage of the cell. The solution is said to be hypertonic. O
n the other hand, a
cell will swell if it is placed in a dilute medium because the osmotic pressure
of the cell Contents
being higher will cause the cell to absorb water from outside and increasein siz
e. The medium
then is said to be hypotonic, The extent of swelling depends on the osmotic pres
sure differences
between cell contents and the surrounding fluid. Tonicity of a solution is there
fore expressed
always in terms of response of cells immersed in solutions. It is a function of
the cell membrane.
In contrast to tonicity, which refers to increase or decrease in size of ceils,
refers to the concentration of solutes in the solution. In osmometry, concentrat
ions should
always be expressed as molal concentratlons Molal concentrations are expressed i
n terms of
weight of the solvent, and this is unaffected by temperature. Molar concentratio
ns, i.e., grams
per Iitre though are preferable because of the inconvenience of weighing liquids
. This however,
has one important disadvantage in being temperature dependent. Ideal solutions o
f equal molarity
exert same osmotic pressure and therefore they are called/sosmotic. In exerting
a. greater osmotic
than another, a solution is said to be hyperosmotic and hyposmot/c if it exerts
a lower
The osmolarity of a solution is best expressed as osmoles. In quantifying the os
of body fluids, it is convenient to use a smaller unit, the milliosmol (abbrevia
, which equals 1/1000 of an osmoL The milliosmol is equivalent to a solution of
I millimole
a non-electrolyte per litre of water. If a substance iordzes, each ion contribut
es the same
molecule. Thus for example, one mol of glucose, a non-lonizable
has an osmolar value of 1; one mol of sodium chloride (NaCI) will produce 2 osmo
long while one mol of calcium chloride (CaCI) will PrOduce 3 osmoles
s it dissociates into one cation and two anions, the total being 3 long.
The osmolarity of the erythrocytes is approximately 280 mflliosmoles. When eryth
mM mannitol no change in the size of the ceils is observed. The reflection
for mannitol is approximately equal to 1, and therefore mannitol at 280 mM
is isotonic for red blood cells. If the same erythrocytes are suspended in 280 m

the cells will swell, i.e. 280 mM glycerol is hypotonic to the same cells. To ma
ke glycerol
a concentration of 318 mM is necessary to give an effective osmolarity
!280 milllosmoles. The reason for this is the value of G, which is 0.88for glyce
rol. Similarly
solution has to be prepared at a concentration of 337 mM to be isotonic for red
equal to 0.83 for malonamide. Thus knowledge of reflection coeiTcient can serve
during preparation of isotonic solutions for living cells.
The above observations make it clear to us that/sosmotic is not synonymous to so
hyperosmotic and hyp0smotic are not synonymous to hypertonic and hypotonic.
' of a solution cannot be predicted solely from its known composition. A solutio
n isotonic
can be slightly hyperosmotic to it and vice versa. Consider, for example a tank
which is permeable to solvent and the solute
being completely impermeable to sucrose (see Figure 4.4 case 1). Chamber 1 is
with an squeous solution containing 1.0 M sucrose and 1.0 M glycine while chambe
r 2
a 2.0 M aqueous solution of sucrose. Chamber I is thus isoosmotic with chamber 2
the tonicity of the solution in chamber 1 is less than that of the solution in c
of this hypotonicity of the mixed solution, water escapes to the 2.0 M solution
by osmosis. If we empty out the tank now and fill chamber 1 again with the same
of sucrose and glycine while chamber 2 now is filled with 1.0 M sucrose solution
;Figure 4.4 case 2) we observe no net transfer of water from any of the chambers
. This is, in
; of the fact that the solution in chamber I was initially hyperosmotic to that
in chamber 2.
reason for this is the isotonicity of the two solutions. Thus the pattern of sel
ectivity of the
plays a great role i.n the osmotic behaviour of living cells.

2.0 M
1.0 M
1.0 M
1.0 M
CASE 2 ]
(1) Chamber 1
is hyperosmotic to chamber 2,
(II) Chamber 1 and chamber 2 are isotonic to
each other.
Chamber 1
1.0 M
Biophysical Chemistry
Chamber 2
Chamber 1
Chamber 2
Selectively permeable membrane :

permeable to glycine
CASE i I but not to sucrose

(I) Chamber 1 is isosmotic with chamber 2.

(II) Chamber 1 is hypotonic to chamber 2.
.'. direction of osmosis =====
.'. no osmosis.
Figure 4.4 Osmotic behaviour of cells
Osmotic pressure measurements for molecular weight determination is seldom used
because of several disadvantages. Firstly, since osmotic pressure is a colligati
ve property and
therefore depends on the number of solute molecules, an impermeant molecule of s
mall mass
has the same effect as a molecule of large mass. Secondly, in practice, since th
e van't Hoffs
equation is followed for osmotic pressure measurements, the osmotic pressure-mol
ecular weight
relationship holds only for very dilute solutions. However, this method has impo
rtant theoretical
advantages. For example, it is indifferent to the size, shape, charge and so for
th of the solute
particles, at least in the dilute solution limit where interaction effects are a
voided. Therefore
this method can be put to use in determining molecular weight of such high molec
ular weight
compounds as polymers, proteins, plastics, etc.
In determining the molecular weight of a protein, measurement of the osmotic pre
ssure of
solutions having different small concentrations of protein are made. The van't H
offs equation is
used for the purpose in the following manner.
l-IV = nRT
n = C, i.e., concentration of solute in moles/litre,
But as 'C' is equal to c/M


and Osmosis
".oncentration is gms/lltre, R is the gas constant, T is the
temperature In Kelvins and H, the osmotic pressure In atmospheres. A graph ofl'[
/c is
against c. The linear curve obtained is then extrapolated to zero concentration
the value of the Intercept as equ. to RT/M. From this the molecular weight of th
e proteIn
(see Figure 4.5).
to i
0 &l O 03 0.4 05 (6 0.70
Concentration in gm protein/litre solution
The osmotic pressure measurements give a value of M., the average weight of a mo
iis equal to the weight of the sample divided by the total number of moles In th
e sample. Thus,
Weight of the sample (w
M. =
or number of moles Number of moles (n)
Suppose n' of the sample is made up of several fractions, each of a different mo
weight, i.e., the sample contains nI moles of molecular weight Mi,- n moles of m
olecular weight
M, us moles of molecular Ms and so on. Then,
n]M] + n2M2 + n3M3 +... niMi
Run ffi
n +n. +na .,.nl
Is the number of moles In the l fraction of molecular weight Ml

Run - '-niMi
Such an average molecular weight Is known as a number average mo/eadar weight.
Measurement of any of the colligative properties of a sample will lead to the ca
lculation of
number average molecular weight as they are proportional only to the number of u
nits In
The weight average molecular weight gives representation, to various molecular s
pecies In
proportion to their given weights In the given sample. The 'number' term therefo
re is replaced
by 'Ight' of that species In the formula represented as :
My = wlM +W2M +wsMs +"" wIMi

ffi hiMI,
and so on.
Table 4.1 enlists the molecular weight of certain proteins as deduced from measu
of their osmotic pressure.

Table 4. I Molecular weights of certain proteins from masuremnts of their omotio

Name of Protein

Insulin (in acid medium)

Lysozyme {egg white)
Trypsin inhibitor (Soyabean)
Bovine Serum Albumin
Human Serum Albumin
Flbrinogen. Huma plasma
44.9- 45.1


Most of us believe that life began millions of years ago in the form of minute s
organisms dwelling in an aquatic environment. These primitive living things live
d in an
environment which was more or less constant with respect to the composit/on of v

substances. As time passed, the organisms gradually evolved into more complex an
d highly
organ/zed individuals. This process of evolution finally gifted the with theh- o
wn 'personal' internal environment while the world surrounding them formed the e
environment (see Box 4.3)

Diffusion and Osmosis

BiophyslcaI Chemistry
Gradually the constancy of internal.environment became vital for existence of li
fe. It had
to be maintained at all costs. Many physlological processes and most of the orga
n systems
therefore got involved in maintenance of this constancy of composition of the in
environment, which is also known as homeostasis, by an incessant replacement and
phenomenon. It is at this point of evolution that the different exchange mechani
sms for the to
and fro passage of molecules in and out of cells got an upper hand. The body, di
vided into many
many compartments by an effective network of membranes worked in a perfectly coordinated
manner. Fluids containing dissolved matter were exchanged continuously between t
he "internal"
and 'external' compartments. In other words, a dynamic equilibrium was achieved.
Osmotic pressure plays a major role in the maintenance of this dynamic equilibri
within an individual. The factors responsible for compartmentalization of body f
luids appear to
be largely osmotic and related to electrolyte concentration. This is further mod
ified by 'the
selective nature of the biomembranes. The body fluids distribute themselves acro
ss membrane
structures such a way as to equalize osmotic pressure. This state is one of osmo
tic equilibrium.

/Mffuslon and Osmosis

Greater the concentration of non-diffuslble particles on one side of a membrane
as compared to
the other side, more Is movement of water towards It, i.e., towards high solute
The organs responsible for malntaining homeostasis in an individual are many. Bu
t the
homeostatic mechanisms or their end organs mainly lle in the intestine for absor
ption and for
exction in the kidney, skin, lungs, liver, pancreas and agaln intestine. These m
echanisms are
well adapted for exchange of water, minerals and metatlotds extstLng as cations
(see Box 4.4).

Biophjsical Chemistry
te/eost, probably due to the similar nature of their functions, r
The plasma proteins, being macromolecular polyelectrolytes, are large bulky mole
which cannot normally diffuse through the blood capillary membranes into the rel
atively protein
free tissue fluids. They thus exert an inward force, the co//o/da/osmotic pressu
re (also called
ondotic pressure) which has a magnitude.of approximately 25 mm Hg. This force is
enough to
hold a certain volume of water within the blood. Though its value is quite less
than the total
osmotic pressure of blood,, it exerts a great influence in maintaining fluid bal
ance across the
capillaries, The colloidal osmotic pressure of the plasma proteins is opposed by
the cap///ary
pressure which tends to direct the fluids out of the capillary into the tissue.
This filtering force
differs in its magnitude at either ends of a capillary. At the venule end it is
as low as 9.0 mm Hg
whereas at the arteriole end it rises to 25.0 mm Hg. At the arteriole end additi
onal outward
forces like the interstitial.fluid pressure (approx. 7.0 mm Hg) also exert their
effect with the
result that there is net fluid shift at this end from the capillary to interstit
ial space.
The opposite occurs at the venule end of the capillary with fluid flowing in fro
m the tissues
into the blood. However, if this balance between the two opposing forces is upse
t under certain
abnormal physiological conditions, fluid accumulates in the interstitial space r
esulting in a
condition known as edema. In this diseased state, a normally negative interstiti
al fluid pressure
becomes positive. This may happen due to cumulative or singular effect of severa
l factors like
high blood pressure, increased capillary porosity and/or low plasma protein cont
Albumin contributes to around 80/0 of the total osmoUc pressure of the plasma pro
Because of its considerably low molecular weight compared to globulin, it is a m
ore effective
species osmotically. Therefore, a loss or deficiency of plasma albumin has a mor
e negative
effect on fluidbalance in the body. Lowered plasma albumin leads to diminished b
lood volume
which precipitates into a state of haemorrhagic shock.
- Besides the plasma proteins, an appreciable variation in the concentraUon of c
electrolytes retained in body fluids can drastically affect a large number of ph
ysiological functions.
The total osmotic pressure of a body fluid is equal to the sum of the osmotic ef

fectiveness of all
the long present. The osmolar concentration of plasma is approximately 0.33 (i.e
., blood plasma
is 0.33 Min its total concentration of dissolved p -rarUcles inclusive of all lo
ng andhon-electrolytes). The cationic components of blood require precise regula
Uon in order to matntaln the osmoUc
balance of blood. The three important cations which require special mention are
potasslumand calcium. A major loss of sodium from the body leads to asignificant
lowering of
osmotic pressure of the body fluids which may be enough to cause dehydration whi
le increased
serum sodium leads to fluid retention. An increase in potassium concentration in
blood mainly
affects funcUoning of the heart and also causes dilatation of blood vessels. The
vascular system
thus loses ittonicity. Decreased serum calcium may lead to a generalized muscle
spasm called

Diffusion .and Osmosis 121

Osmotic pressure has a key role to play in the functioning of normal healthy pla
nts. The
constant osmosis of water into the cell creates a surplus hydrostatic pressure w
hich keeps the
cell strong and elastic. In this state, the cells are called 'turgid'. When thes
e healthy cells are
placed in.solutions of low and high osmotic pressure respectively the cells eith
er swell or shrink.
But due to the rigidity of the outer cellulose walls, plasmoptysis, i.e., swelli
ng of the cell in not
observed. However, plasmolysis, i.e., shrinkage of the protoplasm from the walls
is a regular
phenomenon observed due to leakage 0fwater from the interior of the cell through
the membrane
to the exterior when cells are placed in hypertonic medium.
Suggestions for Further Reading
I. Glasstone, S., Textbook of Physical Chem/stry, Van Nostrand, New York, 1975.
2. Crank. J., The Mathemat/cs of D/.rusion, Oxford University Press, 1956.
Stein, W.D., Diffusion and Osmosis in Comprehensive Biochemistry (Florki
n, M. and Stotz,
E.H. eds.), Vol. 2, Elsevier, New York, 1962.
Edsall, J.T.. The Size, Shape and Hydration of Proteins in The Proteins,
Vol. 1B (H. Neurath
and K.,Bailey, eds.), Academic, New York, 1953.
5. Robinson, R.A., and Stokes, R.H., E,ctrolyteSolutions. 2nd ed.. Butterworths.
London, 1959.

If equal volumes of water and castor .oil are allowed to flow out through I0 ml
pipettes under identical conditions, we observe a time difference between the tw
o liquids in the
emptying out process. This means that one liquid flows faster than the other. Th
is difference in
the rate of flow of liquids is attributed to the phenomenon of viscosity. In the
following text we
shall elaborate this term to understand its nature and impact on the living syst
Stationary plane

Moving plane

Stationary plane
Figure 5. I Velocity gradient in a fluld flowlng through a glass tube
In a liquid sample, a layer of liquid experiences resistance when it flows over
layer. If a shearing forceI is applied to overcome the attractive forces between
the molecules of
the adJacenta,, layers, Each layer will move with a different velocity (see Figu
re 5.1). The velocity
, so formed can be related to the shearing force applied per unit area b
y the equation.
F dv
n = q
A dx
where = shearing force per unit area (also called shearing stress),
viscosity of the liquid,
=dx difference in velocity between two layers separated by a distance dx.

S Force : If a piece of metal is subjected to a force at its upper surface while

being held fixed at
its lower surface, it will be deformed. The deformation is proportional to the a
pplied force. Such an
apl]led force is called a shearing force.

The coefficient of viscosity, l, can be defined from the above equation as the f
orce per unit
required to maintain unit difference of velocity between two parallel liquid sur
faces which
unit distance apart. The units of viscosity are dynes sec- cm-2. More common uni
ts are the poise) and millipoise (10- poise), after the name of poiseuflle who p
ioneered r of viscosity. Therefore, a liquid is said to have a coefficient of vi
scosity as one poise
a force of one dyne maintains a difference of velocity of one cm sec- between tw
o parallel one cm apart and have an area of contact equal to one sq.cm.
The reciprocal of the coefficient of viscosity is called the fluidity and is giv
en by the symbol

... {2)

The term fluidity expresses the tendency of a liquid to flow

s a measure
!the resistance a liquid offers to this flow. Liquids having
viscosity are
'mobile' due to their ease in flowing. On the other hand the
e high
of viscosity and do not flow easily. Most of our body fluids

whereas viscosity i
low coefficients of
iscous' liquids hav
are viscous due to

of particles of macromolecular size. Therefore, our main concern in this chapter

r viscosity with an eye on the solutions of macromolecules.
When we define viscosity, we assume that the fluid concerned is undergoing a lam
the flow lines of the solvent will cause a change in the viscosity of
the solvent. Now, let us consider the viscosity of a solvent lo. On addition of
particles to this solvent, the viscosity of the solvent increases to a new value
q. The ratio of
solution to solvent viscosity (q/qo) is the relative viscosity. The ratio of the
change in viscosity to
the original viscosity of the solvent is called the specific viscosity and is de
noted by qsp. As the
concentration of the macromolecules in the solution increases, the specific visc
osity also
increases. The concentration 'C' is expressed in grams/ml or grams/100 ml. Many
equations have been proposed to describe the change of specific viscosity with c
but the equation proposed by Huggins has found wide acceptance. It is expressed

A plot of q,p/C verses C is shown in Figure 5.2. Such plots are normally linear
for dilute
solutions. On extrapolating the curve to zero concentration, we get an intercept
on the Y-axls.
The value oflp/C at this dilution gives us the b-ttrtns/c viscosity of a solutio
n, depicted by [q]. We
also call it the//m/ring vlscos/ty number. The Huggins constant 'k' in the equat
ion (3) is obtained
from the slope of the curve. The quantity ,plC is sometimes called the reduced v
lure 5.2 Plot of reduced viscosty versus concentmt

... (4)
... (9)
For moderately concentrated solutions, another equation proposed by Solomon and
has been used extensively. The value of [B] determined by this method is only mo
accurate because it requires the measurement of.p at a single concentration only
. Nevertheless,
It is necessary for determination of viscosity for those solutions whose protein
denature easily when a very dilute solution of the protein is allowed to flow th
rough a capillary.
The equation is stated as
where In I = In (1+ l)
When macromolecular particles are suspended in a solvent they assume different
conformations. The increase in viscosity then depends primarily on the effective
volume occupied
by the macromolecules. Scientists have made several attempts to quantitatively r
elate viscosity
to the axial ratio of t-he macromolecules as
.p= v$ ... (5)
where v = the viscosity increment which increases with increasing axial ratio p
ffi l/d (the ratio
of length to diameter) of the macromolecule and $ = fraction of the volume of th
e solution
occupied by the particles.
Einste/n gave an equation relating spec/flc viscosity of a di/ute soluti
on of macromolecules
to the volume fraction occupied by the particles. The equation
1sp-- 2.5 $
... (6)
is based on the following three assumptions :
(a) the solute particles have a Very large size ratio to the solvent molecules a

nd are rigid,
(b) the flow rates are very low, and
the capillary through which the liquid flows must have a large radius co
mpared to
the radius of the spherical particle.
When the solution is moderately concentrated, there is interaction between the f
low lines
of the solute too and to quantify it; another term is addedto equation (7), so t
hat the. equation
now takes the form,
1sp = 2.5 $ 12.6
As the volume fraction $ VeC

... {8)

where We is the effective hydrodynamic volume of one mole of macromolecular solu
te particles
of molecular weight 'M' and concentration 'C' gm/ml, equation (8} gives
"q, = 2.5V= +
-- -- 12.6// C
As the concentration reaches Lnflnite dilution-, the equation becomes,
|'q) = 2.5 V/M

... (12)
factor {V}.
{Approx. 165 %}
Simha provided an equation for the viscosities of ellipsoids of,revolution. The
e//Ipsolds of revolution are clgar-shaped while the oblate ellipsoids of revolut
ion are dlsc-shaped
(see Figure 5.3). According to derivations by Einstein and later by R. Slmha,

or v


+ (11)

15(In2p- 1:5)
5(ln2p-0.5)' 15
The above equation is applicable to prolate ellipsoids. For oblate ellipsoids, t
he equation takes
the form,
15 tanp
O Oblate
(Approx. 108 %)

(Approx. 94.%)
a>> b
Figure 5.3 Ellpsolds of revolutlon
(Approx. 63 %)

Figure 5.4 shows a graph of the axial ratio for ellipsoids of revolution against
15 Oblate
lC Prolate
25 5 I0 15 20 25
Simha's factor
Figure 5.4 Plot of Simha" s viscosity increment v as a functWn of axlal ratio (a
/ b) for prolate and oblate ellpsokls of
(til) Linear Random Coils
No particular three dimensional structure can be allotted to a linear random col
l. This is
because the molecule exhibits a .great deal of rotation about the various segmen
ts in the

Bfphysfcal Chemistry
macromolecular chain. Hence, a large number of conformations are possible. The r
cotled macromolecules occupy a very large effective volume in solution. For the
same reason,
the intrnsic vscosltles of solutions of such polymers are often found to be vast
ly larger tha
those for spheres or ellipsoids. The intrinsic viscosity for such soluUons becom
es a measure of
the particle volume. As the conformation of the molecule continuously changes by
the npacts
of the surrounding solvent molecules, only average dmenslons of the molecule can
be deted.
Table 5.1 Itsts the values of intrinsic viscosities, vlscosRy increments and axi
al ratio for a
number of proteins,
Table 5.1 Intrlas/e viseoIt/es, viscosity increments, and calculated axial ratio
s for various
St. No. Name of Prote/n
I00 []
Tropomyosin (a)"
Serum albumin
Serum albumin
y-Globulin (human)
Flbrlnogen (human}

Tooacco mosaic virus

Axial Ratio Prolate Axial Ratio Oblate
w = 20.1
w = 0.3

The values of tropomyosin vary with different conditions of the experiment. The
values expres%-d

here are for acid Solutions at pH 2. I.

intrinsic viscosity,
v' = viscosity increment
w =
degree of hydration, i.e., if hydration is to the extent of I0%, w = O.
if 30% then w = 0.3 and so on.
The radius of gyratOrS, Rg, gives a rough measure of the effective radius of a m
olecule (see
Box 5.1). When the molecule is a linear chain, the radius of gyration will be a
function of the
chain length of the polymer and hence of the molecular weight.
Rod/J ofGyratlon : It is the square root of the mean square distance of
all individual electrons from
the centre of gravity of a particle. It is a measure of the three dimensional ex
tension of a particle.


Biophysical Chemistry
(ii) For rods,
where Mo isthe
Now, the intrinsic viscosity of a solution of macromolecuIes is related to the m
weight by an equation stated by Mark Houwink as
(I) = KILL .... (13)
where K and a are constants for a particular solute-solvent system and temperatu
re, and M is
the molecular weight, a is also known as an expansion factor. It depends on the
number of
bonds in a chain and takes account of the expansion of the flexible coil due to
the continuous
bombardment of the solvent molecules on it. If the polymer is dissolved in a 0-s
olvent, (see
Chapter 3) the intrinsic viscosity [I]0 becomes
[1] = KILL'


as a = I/2 in such a solvent.

If the flexible polymer is placed in a "better" solvent where there iS much inte
between solute and solvent, then the radius of gyration will increase more rapid
ly with M. As a
is dependent on molecular weight, it will also increase. The maximum value Of th
e exponent a
in 'good' solvents is 1.0. The parameters K and a are are determined by measurem
ents of [I] for
each s01ute-solvent system using for calibration samples of known molecular weig
When a liquid is heated, the molecules in the liquid become more active. This in
molecular activity or molecular motion occurs at the expense of cohesive forces
acting between
the molecules. As a result, the liquid now faces lesser resistance to its flow.
We observe a
decrease in viscosity, and the liquid now flows easily or we ma, say the liquid
has become more
The variation of the viscosity of a liquid with temperature is best expressed by
the equation,

I = Aesj ..; (15)

... {16)
log I = T
where A = constant depending.upon the molecular weight and molar volume of the l
T = temperature of the liquid;
and E = the activation energy per mole.

Stage B
According to equation (16), the plot of log l against the reciprocal of the abso
i.e., l/T, should yield a straight line. This is found to be true for a large nu
Figure 5.5). The explanation offered for such a plot is that astemperature incre
number of molecules which acquire sufficient energy (activation energy) to take
part in
[ flow increases. This increase in the number of molecules is in proportion to t
he Boltzmann
e-E1er, and hence viscosity decreases in a reciprocal manner.
60 40 20 0
2.9:3.0:3.1. :3.- :3.:3:3.4 :3.5:3.6 :3.7
lure 5.5 Temperature de1rtence of vscost plotted as log r vs. T
The opposite is seen in gases, i.e., with an increase in temperature, viscosity
For liquids having many hydrogen bonds some of the energy obtained will be utili
zed in
the H-bonds. The molecules thus require a higher amount of activation energy to
the resistance and increase flow. As a result, viscosity of such solutions is al
57C 60oc
Flgue 5.6 Plot of log of tlme of JIow through
vlscometer of an albumin solution
as a function of temperature,
The temperature effects on viscosity of

lyophilic colloidal solutions are very queer. The

viscosity of albumin solution with changes in
temperature have been studied in detail .by
Ostwald (see Figure 5.6). As the temperature is
raised, the viscosity of the solution decreases.
upto a certain stage (stage A) after which there
is a sudden shoot up and an equally sudden fall
in viscosity of the albumin solution (stage B)..
After crossing this fluctuating stage the viscosity
curve appears even (stage C) and as if in
continuation to stage A. It seems as though just
before coagulation, albumin increases its degree
of hydration and as coagulation is completed it
is left bereft of water. The coagulated albumin is
hydrophobic in nature. The other lyophilic

Blophysa Chemistry
systems like those of starch and gelatin also show such anomalous behaviour thou
gh they may
be quite different from that shown by albumin.
The effect of pH on viscosity of colloidal solutions is very distinct. The macro
contain a nurn'tmr of positlveand/or negative charges on them (therefore called
The charges produce electrostatic effects which can profoundly influence the sol
ution behaviour
of the macromolecule.
The charges on the molecules induce opposite charges in the surrounding solvent.
electrical double layer which is thus formed moves along with the particles resu
lting in an
increase in friction thereby increasing the viscosity. This increase in viscosit
y arising from the
movement of the ionic atmosphere when the charged molecules move is called the e
effect. It is affected by changes in pH and ionic strength of the solution. Kras
ny-Ergen derived
an equation for the electroviscous effect. It is written as
3 1 D
r)r = I+2.5 1+
j j
where k = specific conductance of the surrounding medium,
o = viscosity of the medium,
D = dielectric constant of the medium,
r = radius of the spherical macromolecule.
Fi = potential difference between the surface of the particle and a point in the
medium where the charge density is zero.
Fr = potential difference between the surface and centre of the particle.
As per equation (17), (Fi - Fr ) means the potential difference between the inte
rior of the
particle and the interior of the liquid. However, for practical purposes it is a
ssumed that (FI - Fr )
is equal to the potential difference across the double layer and the term (zeta

potential] replaces it.

When working with proteins, the electroviscous effect is minimized by c out visc
measurements in 0.1 to 0:2 M sodium chloride solution. This greatly reduces the
extent of the
electric double layer and hence leads to reduction of the electroviscous effect.
At the isoelectric pH [the pH at which the net charge on the molecule is zero),
the electrostatic
forces of attraction within the molecule cause it to contract resulting in a dec
rease in the
-viscosity of the solution. Above or below this pH, there is either an excess of
negative charges or
positive charges and the molecule expands. This leads to an increase in the visc
osity. But, there
are some exceptions to this rule. Globular proteins, for example ribonuclease, d
o not show a
appreciable increase in viscosity even when they have attained their maximum pos
itive or
negative charge. This is due to the fact that the molecules of this type lack fl
exibility in the
native state.
If the polyelectrolyte expansion, has to be controlled, the dilution of the macr
can be done with a solution of the same ionic strength (isoionic dilutionl. This
will keep th
ionic atmosphere around the macromolecule unchanged during the dilution process.

Viscosity bears a linear relationship with pressure in the case ofllqulds. This
means that
as pressure increases, viscosity of the liquid also increases.
Chemical Compotion
The viscosity of liquids generally depends upon the size, shape, flexibility and
diffusion coefficient (see Chapter 9) of the particles. The degree of orientatio
n ofa particle is
dependent on these factoi's. Liquids with large, elongated molecules show a high
When the solute molecules interact strongly with one another, they form
aggregates and the.
viscosity of the solution increases. Large amounts of dissolved Solids also incr
ease viscosity.
Specific Volume
.J.Batschinski in 1913 ave an equation relating viscosity to the specific volume
of" a
liquid as

... (18)

where vl = viscosity, v = specific volume of a liquid and b and c are constants.

On rearranging
Eqn (18) we get.
v = b+-...(19)
The equation shows that as specific volume increases, viscosity decreases and vi
ce versa. This
elationship is applicable only over a range of temperature.
The viscosity measurement employs the use of atleast three different instruments
(0 capillary flow,
(i0 rotation of a cylinder immersed in the solution, and
(//0 the rate of fall of a ball through solution.

The time required when a liquid flows through a capillary under specified condit
ions can
be used to determine the viscosity of the liquid. This. method is based on PoLse
ug/e's Law which
embodied in the equation
- 8 IV- ... (20)
where = viscosity of the liquid,
R = radius of the eapillary in cm.
P = pressure applied in dynes per sq. cm.
t = time of flow in seconds,
V = volume of the liquid in milliliters,
I = length of the capillary in cn

..i (21)
... {22)
Biophysical Chemistry
The Poiseuille's Law states that the volume of a liquid flowing through a capill
ary is directly
proportional to. the flow time, the pressure under which the liquid flows, and t
he fourth power
of the capillary radius. Also, the volume of liquid that flows is inversely prop
ortional to the
length of the capillary and to the viscosity of the liquid.
The values R, V, I can be made constant by using a capillary of known dimensions
for all
the liquids. A glass capillary viscometer can serve the purpose. If we measure t
he time of flow of
two different liquids through the same viscometer, then according to Poiseuille
equation, the
ratio of the viscosity coefficients of the two liquids is given by
Since the pressure P and P2 are proportional to the densities of the two liquids
p and Q2
we may write
r12 t2P2 tp
Thus, once the densities of the two liquids are known, the viscometer is calibra
ted for the
measurement of the flow time tt and t2 of the two liquids. This permits us to ca
lculate the
viscosity of the unknown liquid i provided of the reference liquid is known. Wat
er is generally used as the reference liquid. The value /p is also known as the
k/nernat/c vlscostty of the liquid.
Thus, by capillary viscometer the viscosity of one liquid can be determined by m
of its flow relative to another liquid whose viscosity is known.
Design of a Viseometer
The Hess viscometer is often used to measure viscosity of blood. It utilizes hor
capillaries instead of the vertical ones usually found in other capillary viscom
eters (see Box

... (23)
Fre 5.7 A Couette rotatlng-cyllnder viscometer
where T =
r, =
h =
Once the values ofT and 0 are known, l can be calculated by equation (23). The c
of the viscometer appearing in the equation can be determined by accurate measur
Alternatively, two liquids, whose viscosities are known can be used for calibrat
ion. The type of
flow obtained in this type of coaxial rotating cylinder viscometer is simpler th
an that in a
capillary viscometer. The only difficulty lles in con.trolllng the temperatureof
the system.
Liquids or solutions for which the viscosity is constant and is not affected by
the shearing
stress are called Newtonian liquids. For thesellquids, the thermal motion of the
molecules is
capable enough to counteract any effects due to flow itself and the liquid thus
exhibits Newtonian
ilow. On the other hand, the non-Newtonian liquids-display a change in viscosity
with variation
in the shearing stress. Non-NeWtonian behaviour is shown by molecules which are
Rotation of a Cylinder Immersed in,the Solution
When a rotating body is immersed in a liquid it experiences a resistance in its
This is due to the viscosity effect of the liquid. The amount of retardation dep
ends on two
(/) the viscosity of the liquid, and

() the speed of rotation of the body.

-- I
't-- Ptnter
The above principle was utilized by Couette
in- 1890 while designing a viscometer to measure
the viscosity of high molecular weight systems. The
apparatus consists of a rotating cylindrical cu.p.
The inner cylinder is held by a torsion wire (see
Figure 5.7). In the Couette rotating cylinder
viscometer, the liquid rotating in the outer cylinder
causes a torque. This torque and the angular
velocity of the rotating cylinder is recorded. The
viscosity of the solution is related to the torque
produced by the equation,

r2 r2

. .

=T o
torque required to maintain a constant angular velocity,
angular velocity of the rotating cylinder,
radius of outer cylinder,
radius of inneT cylinder,
height of cylinder immersed in the liquid.

Biophysical Chemistry
asymmetric or extremely flexible or are in the form of stiff coils as in DNA. Th
e capillary
viscometers produce a very high shearing stress and are therefore unsuitable for
measurements of DNA solutions. As the Couette viscometer tends to minimize the n
behaviour of solutions, it can be efficiently used for viscosity measurements of
DNA solutions
Rate of Fail of a Ball Through a Solution
The falling ball viscometers are designed to measure viscosity of solutions by a
Stoke's formula. A particle whose volume is much greater than the molecules of t
he solvent falls
through a liquid with a constant velocity. This constant velocity is attained du
e to two opposing
forces acting on the particle at the same time. They are (/) the centrifugal for
ce acting downwards
to accelerate the body, and (//) the frictional force acting in the opposite dir
ection which causes
an upward drag.6 When these two opposing forces just balance each other, as stea
dy state is
reached and the body now continues to fall with a constant velocity.
Let us consider the particle to be a sphere of radius 'r' and density p. The liq
uid through
which it fails has a density PL" The gravitational force acting on the particle
pulling it downwards
is given by
F = 4/3 r3 (p - pL) g

.,. (24)

where g is the acceleration due to gravity. The frictional force acting simultan
eously on the
particle leading to a visco .us drag can be given by
F2 = 6 r l v

... (25)

At equilibrium, F, balances F2 so that,

4/3 r (0 - P) g = 6 r
2r (P-p)g
q =
... (26}

Equation (26) is called the Stoke's equation and is applicable to the fall of sp
herical bodies
in all types of liquid media, provided the radius of the falling body 'r" is lar
ge compared to the
size of the solvent molecule. If the difference is not large, the body tends to
"drop" instead of
failing with a constant velocity.
Inlet -- -Steel bali
] : -- -- Sample
A small steel ball of density p is dropped
through the neck of a cylindrical tube (see Figure
5.8) filled with the liquid whose viscosity is to be
determined, and the time of fall of the ball between
two marks is measured. The same procedure is
followed replacing the unknown liquid by a reference
liquid whose density and viscosity are known. The
viscosity of the unknown liquid can now be
determined by the relative time of flow of the two
liquids as given by the equation

Figure 5.8 The falllng-ball vtscometer

... (27)

-- viscosity of the unknown liquid,

-- viscosity of the reference liquid,
= density of the steel sphere,
= density of the unknown liquid,
= density of the reference liquid.
= time of flow of the unknown liquid,
= time of flow of the reference liquid.
For viscosity measurements of macromolecular solutions, which generally exhibit
nonNewtonian behaviour, the Couette viscometer is routinely used. In this instrumen
t viscosity
measurements of macromolecular solutions can be attempted over a wide range of s
stress. Continuous measurements for a length of time under a specified shearing
stress can
also be performed. However, for asymmetric macromolecules with a molecular weigh
t exceeding
400,000 daltons, which show pronounced non-Newtonian behaviour, extrapolation to
shearing stress is necessary to measure the viscosity. The method which is gener
ally followed is
of extrapolation to zero rate of shear, but in this case, the former is to be pr
eferred. The procedure
for such a measurement is as follows :
A concentration is chosen at which the specific viscosity of the macromolecular
solution is
measured at differing known values of shear stresses. This is to be followed by.
plotting a graph
of specific viscosity versus shearing stress. The graph is then extrapolated to
zero shearing
stress. The value of (Isp) = 0 ('T' represents the shearing stress) so obtained
is plotted along with
values obtained similarly by repeating the procedure at sever.al different conce
ntrations, with
concentration denoting the X-axls in a manner similar to the Huggin's plot (see
5.2). We can thus find the intrinsic viscosity of the macromolecular solution at

zero shearing
stress. The apparatus which can be used for the above experiment is a modified t
ype of capillary
visoometer proposed by Yang. It is a multigradlent capillary viscometer which ca
n accommodate
particular ranges of shearing stress. The equations given below for maximum shea
ring stress
and maximum rate of shear can be used for calculating the value of the various s
stresses applied which are in fact, necessary for the extrapolation. For the mac
solutions whose intrinsic viscosity can be measured using the Couette viscometer
operated at
varying shearing stresses, equation (30) can be applied.
If the maximum shearing stress is denoted by,? and if Rm represents the maximum
of shear,
. =


Rm =


where V is the volume of the liquid passing through the. capillary of .radius 'r
' length 'L' in 't'
seconds under a pressure amounting to P dynes per square cm.

... (30)
Blphysaxl Cherrdstnj
where 7 is the shearing stress, T is the torque applied to maintain a constant a
ngular velocity,
rd is the difference in radius of the two cylinders of the Couette viscometer an
d h is the height of
the cylinder'immersed in the solution.
Viscometry has found wide application in the study of macromolecular properties,
more so, for proteins. Though among all physical techniques viscosity measuremen
ts are simple,
caution is required in interpreting the obtained data. More often viscometry is
combined with
other physical techniques to obtain fool-proof information about the macromolecu
le being studied.
But in many cases viscosity measurements alone provide definitive information. T
hey are
particularly useful in a showing structural changes in a macr.omolec, e associat
ed with physical
or chemical changes in the environment such as (0 protein denaturation, and/or (
) associationdissociation behaviour of subtmits of macromolecules. In the following text we s
hall discuss in
detail the relationship of some of these properties of proteins with viscometry.
Determation of Aymmetry, Siza md Shal of Maeromollu
Asymmetric particles do not rotate evenly in a velocity gradient and tend to ori
ent themselves
in the direction of the streamline of flow of the liquid. Thus their behaviour i
s non-Newtonlan,
since with increasing stress the degree of orientation of the molecules will inc
rease, The intrinsic
viscosity of such a solution will decrease with increasing shearing stress. Edsa
ll and Mehl
(I 940] working with 0.2% solution of myosin had observed a viscosity ratio of 1
.6 and a viscosity
increment (intrinsic viscosity divided by partial specific volume) of 340 at hig
h shear rates. This
indicated a very . degree of asymmetry of the myosin molecule.
The degree of orientation of a particle depends on its size, shape, flexibility,
and rotational
diffusion coefficient (see Chapter 9]. The combination of viscosity with data ob
tained by other
techniques like viscosity and radius of gyration(obtained from light scattering)
, can give us
Information about the shape of the molecule.

The spherical molecules are compact and therefore give rise to relatively small
effects. The rod-llke proteins have a high axial ratio and give rise to very hig
h viscosity increments
because they tend to take up positions with the larger dimension oriented in the
direction of
current. In this position, the degree of orientation increases as the shear stre
ss increases. The
molecules thus lose their randomness.
Staudinger (1932) on the basis of experimental considerations had given an empir
equation relating viscosity to the molecular weight of a macromolecular solute a
[l = KILL
Later, Mark and Houwlnk on the basis of theoretical considerations modlfiedthe a
equation and gave a better expression as
[] = KMa
The empirical constant a is dependent on the shape and solvation of the macromol
For non-solvated rigid molecules of spherical shape, a = 0. For rigid rods, a 1.
5 whereas for.
semi-rigid rods the value of a should range between 1.0 and 1,5. The flexible ra
ndom coils have
an a value falling in the range 0.5 to 0.8. In the 0 solvent a is equal to 0.5 f
or random coils.
To obtain molecular welghts of macromolecules, the intrinsic vlscosity data may
be combined
with those of diffusion or sedimentatiom The Schachman equations can be appropri
ately used
in such situations which are stated as

... (31)
4690 ($2o) [rl]/
and M =
where Szo Is the sedimentation coeffic|ent in Svedberg units at a temperature of
9.0"C. Water is
used as a solvent for this purpose, V is the partial specific volume of the subs
tance (the volume
increment when I gram of dry substance is added to a large volume of solvent) D=
0 is the
diffusion coeiTcient at temperature 20"C.
Protein Denaturation
Denaturation is an alteration of the native structure of a protein. It is genera
lly accompanied
by a drastic change in one or more of the properties of the protein molecule. It
is more often an
unfolding process, for e.g., a globular form might change to a random coil confo
rmation thus
Increasing the disorder of a system. DenaturatiOn can be brought about by a vari
ety of agents
like acids, alkalies, heat, UV irradiation, ultrasonic waves, etc.
The intrinsic viscosity is sensitive to changes in macromolecular structure. The
viscosity measurements on proteins are useful In indicating changes in molecular
due to denaturation. When a rigid molecule of low axial ratio is unfolded into f
lexible chains,
there is an observed increase in viscosity, This can be illustrated by the actio
n of heat on the enzyme ribonuclease (see Figure 5.9). At 40"C there is an abrup
t viscosity change indicating a
partial uncoiling of the compact globular form that exists at lower temperature
into the flexible
at higher temperatures. In contrast, myosin when treated with guanidine hydrochl
. [denaturing agent) shows a decrease in viscosity number. It is said that a dec
rease in viscosity
when rigid rods are converted into flexible coils. To obtain a detailed account
of the
denaturation process other techniques have to be combined with viscometry.

20oC 30oc 40oc 50oC 60oc 70C
Figure 5.9 Vscosity changes by the action of heat on the enzyme ribonuclease
Tanford et.al., after measuring the [rl] of a series of proteins in 6 M guanidin
e hydrochloHde
have shown that an empirical correlation between [r] and the number of amino aci
d residues
written in the form

Biophysical Chemistry
[T]] = 0.716 n.ss
... (33)
where 'n' is the number of amino acid residues in the chain. The above equation
is applicable to
protein molecules of all sizes upto 3,000 residues. Thus, viscosity measurements
of solutions
that convert compact proteins to the random cot configuration can be related to
the size of the
polypeptide chain. This can also tell us whether different denaturants acting on
a protein produce
molecules differing in shape or properties.
Chemicai Modification
Most proteins can be modified by drastic treatments. If the modification is of t
he covalent
type where some covalent bonds are broken or formed accompanied by a change in t
he shape
of the protein molecule, the viscosity change is appreciable. Thus measurement o
f intrinsic
viscosity can also help us in detecting chemlcal modification of a protein molec
ule. Splitting of
a peptide bond in a polypeptide chain may result in unfolding of a compact struc
ture resulting
in a considerable increase in intrinsic viscosity, Same can be said about the br
eaking of disulphide
linkages in a flexible coil which may lead to molecular extension.
Association-Dissociation Studies
Association (aggregation) or dissociation of proteins can be studied by viscosit
measurements. By convention, if rod like molecules associate end to end, the vis
cosity of the
solution should increase. This is so because such an association is thought to i
ncrease the
asymmetry of the molecule. On the other hand, since side-by-side association dec
reases the
asymmetry, it should also decrease the solution viscosity. These conventions, ho
wever, should
not be taken at face value. To cite an example,, association of myosin increases
the intrinsic
viscosity giving the indication that myosin association occurs end to end. Other
techniques like
sedimentation and light scattering, however, clearly show that myosin associatio
n is side -toside. The 'increase' in viscosity in this experiment can be attributed to an art
ifact whereby.
higher aggregates are produced by the shearing stress in the viscometer. From th
is, it is very
clear that viscosity is not very useful in association-dissociation studies and
is used as an
adjunct technique to absolute methods such as osmometry and light scattering.

Since viscosity is not dependent upon molecular weight of unsolvated spherical p

it is of limited use in association-dissociation studies of essentially spherica
l particles. However,
if dissociation of globular proteins involves considerable unfolding producing a
random cot, a
considerable increase in the intrinsic viscosity can be observed. Viscosity can
be useful for
understanding such types of dissociations.
Given below are a few examples based on the discussion above.
Studies About Interaction Between Actin and Myosin
Today we understand the mechanism of muscle contraction and the role of actin an
myosin in this intriguing phenomenon. However, barely four decades back we were
in dark
about this mechanism. At this time important insight into the relationship betwe
en actln and
myosin and the relationship of ATP with these two proteins was obtained with the
help of
scosity studies.
Albert Szent Gyorgyi and coworkers mixed purified actin and myosin in concentrat
ed salt
soultion. They observed that this mixing resulted in a large increase in the vis
cosity of the
solution (Figure 5. I0). The inference was straight- these two proteins must be
interacting to
generate large polymers. Today we know that this polymer is the actomyosin filam
ent that
primarily constitutes the contractile apparatus of the muscle. They further obse
rved that addition
of ATP to this mixture caused the viscosity to drop to the original level (Figur
e 5.10). The
scientists explained the results in the following way

Actin + Myosin ----> Actomyosin
Actomyosin + ATP ----->Actin + Myosin
0 0.2 0.4 0.6 0.8 1.0 F-actin
1 0.8 0.6 0.4 0.2 0 Myosin
When actin and myosin are mixed the viscosity of the solution rises. Addition of
ATP makes the viscosity
drop. |O)Actin-myosin mixtures; I actin myosin mixtures after addition of A TP.
that Actin from Different Species Acts Sim/larly
In an extremely interesting experiment Oosawa nd his colleagues proved that acti
n from
species indeed can act similarly. All they did was mix actin derived from the sl
(a myxomycete) with myosin from striated rabbit muscle. In purified state the so
lution of
proteins showed low specific viscosity. The moment these two proteins were mixed
shot up (Figure 5. I I). Moreover, when ATP was added, the viscosity dropped
of.the previous experiment stated above. This means that actin and myosin from
removed species still interacted to give rise to actomyosin.
.--- 0.5 mM ATP
- - to" 5 mM-A- -TP- # 0.5 mM ATP
0 I0
20 30 40
Time (min)
Figure 5. I I. Effect of A TP on the viscosity of actomyosin in which the actin
was derlved from the $11me mold and the
myosin.from striatedrabbit muscle. Dotted line - pure actin from slime mold; das
hed llne - myosin from
rabbit striated muscle; solid line - mixture of acttn and myosin.

Biophysical Chemistry
Idea about the Native Structure of a Protein
Incubation of a protein in 6 M guanidum chloride denatures it. In the denatured
the protein assumes a completely random coil configuration. Thus, if upon incuba
tion i-n 6 M
guanidinlum chloride, one sees an increase in viscosity of the protein solution,
one can safely
infer that the protein was quite compact in its native conformation. An example
is the enzyme
ribonuclease (Figure 5.9). Although in that figure the enzyme was denatured by i
ncreasing the
temperature, the same effect would follow with guanidinium hydrochloride treatme
nt also.
On the contrary, it is observed that with some proteins, the viscosity actually
when they are treated with 6 M guanidinium chloride. In such cases, one assumpti
on is that f
the protein may be fibrous in nature and that denaturation has given it more fle
xibility as a (
random coil. An example of such a case is afforded by poly(/-benzyl-L-glutamate)
. The viscosity \
of this polypeptide solution actually decreases upon denaturation meaning that t
his polypeptide
exists as a rigid rod in its native condition and the random coil conformation u
pon denaturation
is the more flexible form. The same is true about the protein collagen also.
However, such a conclusion may not be always correct. It could be that the prote
in contains
several polypeptide subunits that have dissociated upon guanidintum chloride tre
atment and
that this is the real cause of decrease in viscosity.
Detection of Intrastrand Disulfide Bonds in Proteins
Assessment of viscosity can easily lead one to detect whether or not a given pro
tein possesses
intrastrand disulfide bonds. When such bonds are present, the polypeptide will n
aturally be
present in a more compact shape owing to the folding that will result through su
ch covalent
bonds. Such proteinh will not give. much change in viscosity if they are treated
with 6 M
guanidinium chloride. However, if such bonds are broken, the same polypeptide wi
ll experience
a decrease in its compactness and in the presence of 6 M guanidinium chloride it
will assume
a random coil formation. The viscosity will increase.
[-mercapt)ethanol can reduce the disulfide bridges into individual sulfhydryl gr
oups, and
if one uses iodoacetate in the reaction mixture one can prevent these bonds from
Thus, if consequent to such a chemical treatment, one finds the viscosity of the

protein solution
increasing, it means that the protein, in all probability, has disulfide bridges
. If no change in
viscosity occurs, it may mean the absence of such bonds. Thus calf brain tubulin
has [1] = 36.0
ml/gm when it has not been treated with [-mercaptoethanol. After this treatment
though, [1]
climbs to 44.0 ml/gm. This is a sure indication that disuffide bridges are prese
nt in this protein.
The compactness of a given polypeptide will differ depending upon which cysteins
involved in disulfide bond formation. If the cysteins involved in disulfide link
age are situated
wide apart in the polypeptide, the molecule will be more compact as compared to
the molecule
which has disulfide linkage between two cysteins situated very near each other i
n the polypeptide
backbone. Thus, a great change in viscosity upon mercaptoethanol treatment would
mean that
the polypeptide has disulfide bridges formed between distant cysteins, while a s
mall ar
indistinguishable change in viscosity would mean the presence of a disulfide bri
dge between
cysteins that are more or less adjacent on the polypepttde backbone.
Polymerization of DNA
Later, in the chapter on radioactivity, you will come across an example to study
polymerization using DNA. The example there involves incorporation of radioactiv
ity in the
growing chain of DNA. DNA polymerization can be studied without the use of radio
activity also.
The logic is simple. When polymerization takes place, the chain length of DNA in
creases. When
this occurs, the viscosity of the reaction mixture must increase. Thus, if DNA,
all four 5'triphosphate nucleotides, and Mg2 are incubated with DNA polymerase I, a short wh
ile later,
an increase in viscosity can be demonstrated. This increase will not take place
if one of the

not put in the mixture or if Mg2 is absent. This proves that DNA polymerization
all the components in the reaction mixture described above.
of DNA
If a circular. DNA molecule is incubated with a nuclease, what should happen to
r of the solution? As long as the nuclease is causing single strand breaks, noth
ing much
happen. This is because the DNA will retain its configuration despite the single
due to the rigidity of base stacking. However, the moment a double strand break
will be rendered linear. This will cause an. increase in the axial ratio and the
r will increase. If the nuclease action is allowed to continue, multiple double
breaks will eventually occur resulting in multiple linear fragments of smaller s
izes. This will
result in a decrease in viscosity. Thus, with circular DNA molecules, the viscos
ity will initially
and then fall (Figure 5.12).
With linear DNA molecules, the viscosity will not increase at all if it is incub
ated with a
Initially, nothing will happen and then the viscosity will start going down.
One can determine whether the genome of an organism is circular or linear using
5.12 (A) Circular DNA. Initially the viscosity increases. (B) Linear DNA, Vscosi
ty never Increes. From a
plateau it starts decreasbg with time.
. .
that Certain Dyes Intercalate in DNA
The dye, proflavine binds to double-stranded DNA tightly. When DNA is incubated
the viscosity of the complex increases. This can happen only when the length of
For this, the dye must get inside the DNA structure in a manner that it lengthen
s the
Other techniques can be applied to study the same phenomenon. When DNA is incuba
with proflavine, the sedimentation coefficient of the complex decreases. This ca

n happen if DNA
becomes depolymerlzed due to proflavine. It may also happen if the axial ratio o
f the complex
increases. With the first possibility, a decrease in viscosity must take place.
This is not observed.
With the second possibility, viscosity should increase, and this is observed. Th
us, it seems that
the second possibility is correct. Thus, DNA length indeed increases when it is
treated with this
Employing fluorescec polarization, one learns that the dye becomes immobilized a
seems to be in the same place as the bases are. This indicates that the dye gets
in between the
bases and pushes them apart thereby lexgthening the DNA chain.
The importance of viscosity in human health and disease stems from the fact that
the vital
fluid circulating through each and every part oF the human system, the blood, is
highly viscous
and is affected profoundly by even a small change in the viscosity of the medium
. Generally

142 Biophysical Chemistry

blood flow varies inversely with the viscosity of the blood. Viscosity depends o
n the hematocrit
value, i.e., the percentage of the blood occupied by the erythrocytes, one of th
e major components
of the blood. The large vessels like the aorta and vein have a high hematocrit v
alue whereas the
capillaries and small veins have a very low value due to the difference in the n
ature of flow of
blood through the different vessels (see Box 5.3).
Nature of Blood Flow through Different Vessels
Newtonian fluids (viscosity independent of shearing stress) under conditions of
laminar flow and
constant temperature obey the relationship,
where q = viscosity, y = rate of shear and = shearing stress.
/ 1494Fm
i1111 m115 Prn
0 " i
2O 40 60 8O
Haematocrit (%)
Figure 1 Plot of apparent viscosity of erythrocytes in physiological saline agai
nst hematocrit.
Temperature is regulated at 25C. Figures in rectangles indicate the diameter of t
tubes chosen for the experiment
Blood; though inhomogeneous due to the presence of blood cells, behaves as a New
tonian fluid
in blood vessels with internal diameter 1 nm and above, But as the blood vessels
get narrower,
viscosity of blood decreases with increasing shearing stress. This anomalous beh
aviour of blood
is attributed to the erythrocytes as they are the predominant particles of blood
. The apparent

blood viscosity is indicated by the value of hematocrit which is about 45% for m
an (see Fig.l)
The figure indicates the change in apparent viscosity of blood with respect to h
ematocrit values
in vessels of varying internal diameters. At smaller diameters, flattening of th
e curve is observed.
The behaviour can be explained well if we go into the characteristics of the red
blood cells. The
red blood cells are biconcave having extremely flexible membranes. Because of th
is property and
the fluid content of the cells, the R.IB.C.s have a high degree of fluidity. Wit
h increasing shearing
stress, the erythrocytes assume shapes which facilitate their movement. In capil
laries, which
have a diameter smaller than 15 m, even upto 3 m, the red cells undergo extreme
(they assume an "arrow head" shape). As the shearing stress in these vessels of
narrow bore
increases the.red cells align themselves obliquely along the tube axis. This pro
cess is known as
dal migration. AS a result, the concentration of the R.B.C.s increases in the co
re region and

blood gets thinned out near the walls of the vessel.The layers in the peripheral
region now have
a lower viscosity and a high shear rate This lowered viscosity facilitates the m
ovement of the
central column of blood (predominantly R.B.C.) with an increased velocity. Thus,
the average
time spent by an erythrocyte in a narrow vessel like a capillary is shorter than
its counterpart
plasma, the volume element. The hematocrit value is therefore smaller in an acti
ve capillary than
the hematocrit of blood at rest.
Apart from the above parameter, the blbod pressure and the hysteretic (elongatio
n and shortening)
behaviour of the smooth muscles forming the vessel wall are important determinan
ts of the flow
of blood through a blood vessel.
Besides the hematocr/t, the other constituents of blood plasma, mainly the immun
and other plasma proteins also play a significant role in altering the viscosity
of blood leading
to many pathological states. In diseases such as hereditary spherocytosis, the r
ed blood cells
are very rigid and because of this abnormality, viscosity rises.
Variation in the viscosity of blood influences the working of the heart. In seve
re polycythemia,
the increase in viscosity of the blood increases the work of the heart. It was o
bserved by Mackson
in 1936, that the blood of patients suffering from congestive heart failure was
more viscid than
normal, The anaemic person presents a totally different but interesting picture.
In severe anaemia,
peripheral resistance is decreased but the cardiac output increases resulting in
overwork of the
heart. Blood viscosity is increased in several diseased states such as cyanosis,
diabetes mellitus, multiple myeloma, icterus and pneumonia.
Amoeboid movement which is a characteristic of all naked protozoa, leukocytes an
embryonic nerve cells has very close connection with viscosity changes. During t
hese movements
striking changes in viscosity take place. These changes are of the reversible ty
pe, the jelly like
gel state being converted to the fluid or sol state and vice versa. The changes
in Amoeba proteus
have been well described by Mast (1932). The cytoplasm in these organisms is sur
rounded by a
thin membrane, the plasmalemma. A thick rigid layer of plasmagel lies beneath th

e membrane,
with a thin fluid hyaline layer sandwitched in between. The plasmagel surrounds
a fairly fluid
plasmasol. As locomotion begins the plasmagel at the retreating end is converted
into the
plasmasol. The plasmalemma however, remains attached to the plasmagel and the su
bstratum. The newly formed plasmasol at the retreating end now advances forwards
and is transformed
into the plasmagel at the front. The forward flow of the plasmasol is facilitate
d by the alternate
contraction and relaxation of the plasmagel at the retreating and advancing ends
Owing to these differences in the elastic strength of the two regions the cell i
s propelled ahead.
Locomotion is thus affected by the reversible gel-sol transformations as explain
ed above. Similar
gelation changes are observed in many other cells of physiological origin i.e.,
the WBC,
m.acrophage, connective tissue cells and malignant sarcoma cells during cell loc
omotion and
cell division.
Suggestions For Further Study
Edsall, J.T., The Size, Shape and Hydration of Protein Molecules in The
Proteins, Vol. ]
(H. Neurath and K. Bkiley, eds.), Academic, New York, 1953.
2. Tanford, C., Physical Chemistry of Macromolecules, Wiley, New York, 1961.
Yang, J.T., The Viscosity of Macromolecules in Relation to Macromolecule
s, Adv. Protein Chem,
16, 323 (1961).
4. Scheraga, H.A., Protein Structure, Academic, New York, 196 I.
Haschemeyer, R.H. and Haschemeyer, A.V.E., Proteins : A Guide to Study b
y Physical and
Chemical Methods, John Wiley, New York, 1973.

Biophysical Chemistry
If poly 7-benzyl-L-glutamate is denatured with 6 M guanidinium chloride
the viscosit}
decreases. What does this tell you about the structure of the polypeptide?
You are given a plasmid and a linear DNA fragment. Using viscosity measu
rements how can
you prove which is which?
You are given an unknown proteip,When you denatured it with 6 M guanidin
ium chloride,
the viscosity decreased. What possibilities will you consider about this protein
based on thk
One can manipulate the activity of enzymes by manipulating the pH, ionic
strength, or the
temperature. Suppose hat you have incubated a double stranded linear DNA with a
manipulating the conditions so that one single stranded break results every 10 m
inutes. On
an average, it takes about I 0 single stranded breaks before a double stranded b
reak results.
After what time do you think the viscosity of the solution undergo a significant
5. A DNA solution has inadvertently been mixed with another unknown chemical and
in viscosity can be observed. No definite conclusions can be derived from this o
However, how many possibilities can you imagine which can give rise to reduction
in vlscosi!
in such a situation?
When one heats DNA, it 'melts', The optical density increases. What shou
ld happen to viscosity
under such a situation? When a salt, say NaCl, is added to the solution and then
the solution
is heated, what should happen? If the salt concentration is increased, what shou
ld happen?

If a polypeptide is incubated with a protease, what should happen to the

viscosity of the

Dry sand, when sprinkled gently upon water readily floats. The water surface beh
aves as
flit were covered by a fine elastic skin. The same sand particles, if introduced
below the surface
r sink. This anomalous behaviour of the sand particles nearia surface and in the
of the liquid is related to the phenomenon of surface tension. Before we proceed
what this phenomenon means, we shall discuss some properties of matter and
matter appears on a molecular scale.
Matter may exist in three different states in nature - solid, liquid, and gas. A
n assembly of
can exist in any of these states provided temperature and pressure are favourabl
e to
equilibrium which is established between the kinetic energy of the molecules and
forces between them determines the state of the matter. A solid has molecules co
in a regular pattern. All kinetic energy possessed by the molecules is confined
energy. A liquid has molecules arranged at an average constant distance but thei
do not remain flied due to 'not so strong' attractive forces. Further, the addit
ion of
and translational energy makes them more mobile. As a result, on the macroscopic
the liquid is shapeless but has a definite volume. A gas, however, is not only s
has lost its volume definition too. It is because the molecules in the assembly
are only
attracted to each other and the translational energy of the particles has gained
an upper
over the attractive forces. "
In a system where matter is present in more than one state, each state is called
a phase.
or may not be chemically identical with each other. The region of contact of two
is referred to as an interface. Interfaces may be of various types, viz., solid
- liquid, two
luids, gas-liquid or gas-solid. Two solids cannot ordinarily come into close con
trapping any gas or liquid between them. Also, two gases do not form an interfac
of their high diffusibility. An interface between a solid and a gas, or between
a liquid
a gas is more commonly termed as a surface. An interface made up of two phases o
f the
compound is highly dynamic in the sense that molecules are continuously leaving
entering into another and returning to the original phase. When one moves from t

across the interface to the interior of the adjacent phase, one experiences an
m many measurable properties such as density, heat capacity, viscosity, dielectr
electrical conductivity, refractive index, absorption behaviour etc., at the int
after moving a considerable distance away from the interface, the properties beg
in to
in accordance with the physical state and chemical nature of the material making
body of the individual phase.
On examining the arrangement of molecules in a phase, it is observed that in the
body or
phase, take a liquid for example, the molecules attract each other with a cohesi
: which is uniform in all directions because they are surrounded by other molecu
les of the
kind. They are thus free to move in all directions, and free forces of attractio
n are not

Biophysical Chemistry
exhibited. At the surface, .on the other hand, the molecules are only partially
surrounded by
other molecules, and as a consequence they
experience an inward pull (see Figure 6.1). The
result of this inward attraction is that the
number of molecules at the surface tends to be
reduced to a minimum and the surface contracts
until its area is the smallest possible for a given
volume of liquid. This behaviour of the surface
is responsible for the nearly spherical shape of
Figure 6. I Cohesive forces acting upon
falling water or oil drops. Drops or bubbles canj
molecules of a liquid so as to
resume a variety of shapes under the Influenc
result in surface tension
of gravity, compression, and stretching but a
soon as they are released, they resume their spherical shape. It !s because a sp
here is a body
having the least area for a given volume.
The special strain that the surface layer experiences as a consequence of the un
forces is called surface tension. By definition it is the force in dynes acting
along the surface at
right angles [90) to any line one cm in length. The units are dynes/cm. The surfa
ce possesses
a considerable amount of potential energy. It is much higher than the potential
energy carried
by the molecules in the body of the liquid. The surface is eager to accommodate
certain types of
molecules (surface active) always in order to decrease its free surface energy.
If the surface has
to be extended, molecules have to be forced out from the interior to the top and
this requires
.energy. Work has to be done to overcome the attractive forces between the molec
ules and create
the new surface. The work required to increase the surface area by I square cm i
n called the free
surface energy. It is expressed in ergs/cm. Both surface tension and surface eli
iergy have the
same dimension in the CGS system of grams per second2. Numerically they have ide
values, for e.g., liquid with surface tension of 60 dynes/cm possesses a free su
rface energy
value of 60 ergs/cm2. Therefore, though surface tension is an intrinsic property
of liquids and
surface energy a fundamental property of the surface of the liquid, they are som
etimes used
synonymously for convenience during calculations. The relationship between surfa

ce tension,
surface area and the Surface free energy can be summarized as
Surface Tension x Total Surface Area = Surface Free Energy
Thus, ff the surface tension of liquid is y dynes/cm, the work done in increasin
g the
surface area by 1 sq cm will be ergs, and the surface free energy will be y ergs
The total surface energy per unit area, however, may not be equal to the surface
energy alone. As heat must be supplied to the expanding surface to keep the temp
erature in the
surface constant, a heat term has to be added to the surface free energy. The to
tal energy at the
surface per sq cm then will be equal to
p=y-T -...(I)
where is the rate of change of surface tension with a change of temperature, and
is the
total energy at the surface. The differential term is always negative as surface
tension always decreases with an increase in temperature.

Box 6.1
Surface Tension
The surface tension of a given liquid is a constant value. It depends on the nat
ure of the
liquid. Greater the magnitude of the attractive forces operating between the mol
ecules of a
liquid, higher is the surface tension.
When two immiscible liquids come in contact wit each other, an interracil tensio
develops. This is because the dividing surface or interface contracts spontaneou
sly in response
to the attractive forces of the molecules in the interior of each liquid respect
ively. However, this
interracil tension is not an additive property of the surface tension of the two
different liquids.
Instead it is seen that the value is often slightly lower than the larger of the
two surface tensions.
The relation between the interracil tension and the surface tension of the two i
liquids is given by Antonofi's rule which stands as
],2 = ], - 2'
... {2}
where y,2 -- interracil tension between liquids 1 and 2,
/, = surface tension of liquid 1, and
Y2' = surface tension of liquid 2.
The molecules at the interface of two immiscible liquids are more or less satisf
ied and
to this decreased number of unbalanced forces, interracil tension is lowered. It
is for the
same reason that the potential energy at the surface of the molecules of each li
quid is far below
than that seen for molecules in the body of the two liquids individually.
When a drop of liquid is placed gently on a slide, it either spreads out into a
thin fdm or
a drop on the surface depending upon its affinity towards the solid surface. For
of solid-liquid interface, interracil tension can be expressed in terms of conta
ct angle. A
angle (e) is the angle between a solid surface and a liquid meniscus (also see B
ox 6.1).
magnitude of this angle is influenced by the forces acting along the surface of
the Solid.,
Useful information regarding the wetting quality of a surface can be obtained by

contact angle and there lies its importance. If the contact angle is zero, the l
iquid wets the
completely. For contact angle values upto 90 the extent of wetting is good but no
t perfect.
For values above 90, wetting is poor or non-existent. (see Box 6.1)
Wetting of Solids and Contact Angle
It haslong been surmised that interracil energies play an important role in phag
ocytosis (engulfing
and killing) of bacteria and other solid bodies by mammalian leukocytes. It migh
t be mentioned
here that the mammalian phagocytic defense consists of the circulating polymorph
leukocytes (PMNL) as the first line of defense and the reticuloendothelial syste
m, comprising of
the monocytes and the macrophages, as the second line of defense. For phagocytos
is to occur,
the bacterium and the phagocyte have to be brought into sufficient contact with
each other.
Naturally, the surface energy of the bacter um and the phagocyte are intimately
related to the
degree of phagocytosis. Thus 'a knowledge about the interracil energies of the b
acter um and
the phagocyte can allow us to predict the extent of phagocytosis.
The solid-liquid interracil tensions of solids have been studied using contact a
ngle measurements.
It is one of the oldest techniques devised byYoung in 1805 for studying the natu
re of solid surfaces.
A contact angle e is the angle between a solid surface and a liquid meniscus, as
shown in the
figure below.


Surface Tension
Haemophilus influenzae (rough)
Mycobacterium butyricum
Streptococcus pyogenes
21 3
Sa/monella typhimurium
Sa/rnonella arizonae
Streptococcus pneumon, iae
Klebsiella pneumoniae and
Human Neutrophils
18.0 approx.
As temperature rises surface tension of a liquid decreases, i.e., surface tensio
n has a
temperature coefficient. The relationship between surface tension and temperatur
was first provided by Baron R. von Eotvos in 1886. The relationship may be writt
en as
7(MV)2/3 = K (to - t)
... (3)
where te represents the critical temperature of the liquid, (MV)2/a is proportio
nal to the molecular
surface, and 7 and V are surface tension and specific volume respectively, at an
y temperature t,
expressed in degrees centigrade. K is a constant called the temperature coeffici
ent of molar
surface energy having a value of 2.12 for a number of "normal" unassociated liqu
ids, e.g.,
i carbon tetrachloride, ethyl ether, benzene, etc. For another batch of liquids
like water, alcohols,

md carboxylic acids, the temperature coefficient is not only less than 2.12 but
varies with
This abnormal behaviour is attributed to the associated state of the liquids. In
a state the actual molecular weight of the liquid is not M but xM, where "x" is
the factor of
association, i.e., the average number of single molecules combined to form an ag
gregate. The
above particulars for explaining the nature of the temperature Cdefflcient were
given by Ramsay
: and Shields in 1893, They found that at temperatures not too near the critical
point, the molar
:i surface energy could be expressed by a modified form as
y(MV)2/a = K (t - t - 6) ... (4)
is equal to molecular volume can also be written as M/p where p is equal to the
of the liquid. The Ramsay and Shields equation then takes the form
7(M/P)21 = K(q - t - 6)
... (5)
According to J.D. Van der Waals, the surface tension of a liquid at temperature
't' should
to the critical temperature to by an equation of the form,
7 = to (] - t/t)"
... (6)
a universal constant and to depends on the critical constants of the liquid. 'n'
has a
close to 1.2. Later in 1916, M. Katayama proposed modified form of equation (3)
which is
7----- p;) = K(t -t) = Kt (1- t/to) ...(7)
p" are the densities of the liquid and its vapour respectively at the same tempe

Biophysical Chemistry
The above equation holds quite accurately for normal liquids at temperatures muc
h nearer
to the critical value than does the original form of Eotvos. In equation (4), ac
cording to Ramsay
and Shields, the surface tension of the liquid becomes zero when the temperature
reaches a
value which is lesser than the critical temperature to, by 6C. It follows that at
critical temperature
the surface tension of a normal liquid will become negative. The above predictio
n, however, is
not univerl. Several liquids have shown a value of zero only at the critical tem
perature and
not earlier. For such liquids. Katayama's equation is found to be the most suita
ble. It is expressed
y'"/(p- p') = c
... (81
where C is a constant for each substance. For associated liquids the value of C
slightly as the temperature is raised, but the effect is relatively small.
The above interesting relationship (8) between the surface tension and density o
f a liquid
is also called Macleod's equation (1923) and it holds over a wide range of tempe
ratures. It is
obeyed with considerable accuracy by many organic compounds nearly upto their cr
temperatures. If both the sides of equation (8} are multiplied by the molecular
weight of the
substance M, we get
MY i--= ME = P (constant)
The constant 'P' also called the "parachor" by S.Sudgen {1924) is essentially a
volume modified to eliminate some of the influence of the cohesive forces which
are different for
different liquids. Parachor may be defined as the molar volume of a liquid at a
temperature at
which the surface tension is unity. Two liquids of molecular weight M and M2 hav
ing densities
p and P2' and surface tensions 71 and 72 respectively, will have parachors of th
e value
P] = p] V]7/ and P2 -- 92 V2 Y2]/
where V and V are the molar volumes of the two liquids.

With an increase in temperature, kinetic energy of the molecules of the liquid I

This will weaken the cohesive forces acting between the different molecules. As
a result, the
inward pull exerted by the molecules in the interior of the liquid upon those on
the surface, is
lessened. Hence a decrease in surface tension of a liquid is observed with risin
g temperature.
Effect of Solutes on the ,Surface Tension of a Solvent
Lowering or raising the surface tension of a solvent on addition of a solute dep
ends largely
on the chemical structure of the solute. Substances which decrease the surface t
ension of a
solvent are said to be cap///ary active. Soaps, proteins, organic acids, alcohol
s, esters, ethers,
amines, and ketones belong to this class. Other like inorganic salts, salts of o
rganic acids,
bases of low molar mass, sugar, glycerine, etc., increase the surface tension of
the solvent,
though slightly, and are therefore called cap///ary/nact/ve.
A majority of organic compounds are neither typically polar nor completely non-p
Consider for example an aqueous solution of fatty acids. The fatty acids possess
a hydrophflic
head (polar) and a hydrocarbon chain (non-polar). The polar part of the molecule
makes it
reasonably soluble. The hydrocarbon residues in the fatty acids are not at ease
in the interior of
the solution and therefore if they are to be brought to the surface, little work
will be required.
Once they accumulate at the surface, surface tension of the solvent will be lowe
red. The capillary

Surface Tension
activity of these amphipathic molecules thus depends largely on the predominance
of the non
of the molecule. A similar movement towards the surface is seen when non-polar
olutes are dissolved in water. These solutes concentrate preferentiallyat the su
rface and lower
the surface tension of the solvent. They are then said to be positively adsorbed
. Positive adsorption
can be visualized in the form of a surface crust when beaten white of egg is lef
t standing. The
a lbdmin in it accumulates at the surface of each bubble as a result of surface
md coagulates there. As a result a rigid film is formed at the surface. Saponin,
a plant glucoside,
nd bile salts have remarkable surface tension lowering ability. A very dilute so
lution of saponin
In water exhibits a surface tension of only 20 dynes per cm as compared to 73 dy
nes per cm of
pure water.
On the other hand, inorganic electrolytes in general, raise the surface tension
of water and
are, accordingly, negatively adsorbed at a water surface. In as much as surface
tension is
primarily dependent on mutual attraction of molecules, salts which are ionic and
polar in nature, by virtue of ion-dipole attractions, tend to pull the water mol
ecules into the
of the solution. In such a situation, if the surface has to be extended, addonal
be done to overcome the electrostatic forces. Polar substances are therefore, ca
above observations are summarized in Figure 6.2. The graph shows three types of
Type I curve corresponds to surface inactive substances. The increase in surface
concentration of these substance is infinite. An opposite effect occurs on addit
surface active substance (type Ill). However, the curve is remarkable in the sen
se that the
in surface tension occurs only upto a particular concentration. Beyond this, any
in concentration will not alter the surface tension of the liquid. Type II curve
the changes in surface tension of a liquid on addition of non-electrolytes or we
The graph depicts a gradual and regular decrease in surface tension of solvent
olute addition.

Figure 6.2 Effect of dlssolved substances on the swface tension of the solvent.
Surface inactive substances [strong electrolytes {ionic salts} alkali].
Non-electrolytes and weak electrolytes.
Surface active substances {soaps. proteins, etc.}.
The behaviour of amino acids also differ according to their polar nature. Figure
6.3 shows
surface tension of aqueous solutions of amino acids varies with concentration of

Biophysical Chemistry
Solutes which show a decrease of surface tension with increasing concentration a
re said
to exhibit positive surface activity, while those that raise it are said to have
a negative surface
activity; The solutes of the former type arc
Figure 6.3 Surface tensions of amino acid solutions at 25C.
I Glyclne
V Lysine
II -alanine
VI y - amino butyric acid
Ill a-alanine
VII y - amino caproic acid
IV -aminobutyric acid
Solutes which show a decrease of surface tension with increasing concentration a
re said
to exhibit positive surface activity, while those that raise it are said to have
a negative surface
activity. The solutes of the former type are also called surfactants. The role o
f surfactants has
been extensively studied in man and it is seen that lung function is intimately
linked with the
amount of surfactant present in the alveoli (see Box 6,2).
Box 6.2 ....
Role of Pulmonary Surfactant: Stablllty of Alveoll
Lungs, the respiratory organs
agraduatedseries oftubes that
medium cimulates through these airways usually
occurs by means of diffusi
and relaxation (inspiration) of the alveoli. The alveoli are
during expiratioD the expiratory muscles

the surface
tension generated bythethin ,aqueous film or
the,pressure suffiCletlyto, eollapsethe alveoli. Because tl
to theradius accord=n.to katlace's lawwhiCh is given as ,

end expiration would lead to

as the smller alveoli wou!d empty into the larger alveoli, andso on.
Thisproblem iscircumvented by
mixture oHipidsand proteins, the
interfacewithin'.,the. <

Surface Tension
of thelung at the end of each expiration. The collapsed alveoli,, like collapsed
-balloons would
require-greater pressure to inflate them than partially collapsed alveo i and th
is would hamper
smooth:gaseous exchange. ,
Pulmonary surfactant is acomplex mixtureof about 90% lipid 10% protein and small
lmitoylphosphatidylcho ine
generated by the aqueous
..yelin is,the
;r, but investigations regarding
:n=sare inco
studies on surfactant proteins suggesttht these
prgteins may play a prominent role in tPie organization of thelipids int
he airway
In man, a direct relationship has been reported between the amou
nt of surface active mater a
11 :
and the pulmonarysurface area. In premature infants, the normal pattern
of ung development s
= interrupted frequentiyresulting in suffactant insufficiency. A consequ
ence of this is the respiratory
distresSsyndrome (RDS)wh ch isa eading cause of morb d tyjn these infant
s. An established
treatment of this Complication is introduct on oflhigh concentrations of
oxygen through nspiration
accompanied by ventilatory support.This =treatmitis reported to have sho
wn an alteration n the
levels of surfactnt protein, leading to their increased acumu ation!n th

elngs: However, current

..: ..= treatment of the diseae lnvolvetracheal administraton of multipledoseof
mixture of.the
iil : . surfactant materials, namelyphospholipid and thesurfactant"prote us. An
alternate approach for
i... " resolution of acuIeRDS inv es plarmacoiogical internt on but mCich rema u
s to I: elucidated
,.-i regarding the regulation and expiession of the genes itiv01ved in surfactan
t protein synthesisand enzymes involved in surfactant phospho!ipid synthesis bef
ore th s approach can be applied
The tendency of molecules to either concentrate at the surface or remain in the
assumes great significance in the human body. It is this property that is respon
sible to some
extent in forming the limiting membranes (see Box 6.3).
Biomembranes show

Bio1hysicca Chemistry
proteins adhering to lipid-aqueous interfaces because very small amount of prote
ins were effective
in reducing the surface tension of a model ]ilid-water system considerably (see
Figure 1).
Protein film
Polar head
Lipold film

Protein film
Figure 1 TheDanielt and Davson model for cell membrane
Untilthe late 1960's bilayer models were often pemeived to be static structures
but studies with a
series of,biophysical techniques involving X-ray diffraction, nuclear magnetic r
esonance (NMR) "
and electron spin resonance (ESR) spectroscopy,-fluorescence microscopy, electro
n microscopy
and others have revealed the dynamic nature of thecell membranes which have been
in the Singer and Nicolson's fluid mosaic model proposed in, 1972 (see Figure 2)
Carbohydrate chains
attached to polypeptide
\i 3-'."

Llpold film

{ chainSpolar Hydrocarbon ]head ---- . '] ' Protein

Figure 2 The Singer and Nicolson model,for cell membrane

Hydrogen-Ion Concentration
Surface tension of protein solutions changes with hydrogen ion concentration. A
in the surface tension Is observed in the isoelectric zone.
Surface Tension and Vapour Pressure
The surface of a liquid assumes different shapes in different situations. Whenwa
ter is in
a pipette, it has a concave surface. When on a glass slide as a film, it has a p
lane surface, and
in the form of drops it has a convex surface (see Figure 6.4}, When liquid from
a plane surface
forms a drop, there is an increase in surface area. This increase requires more
surface energy.
The molecules of the convex surface are attracted by other liquid molecules to a
less extent now
than they were in a plane surface. The drops also have a higher vapour pressure
than earlier
(plane surface). The opposite is observed for a concave liquid surface. There, t
he surface liquid
molecules are attracted more than they are in a plane surface. The vapour pressu
re here is also
the lowe. st amongst the three surfaces. These observations are compiled in an e
quation given by

P 2M7
In Po RTpr
... (10)
Po are the vapour pressures of the plane surface of the liquid and convex surfac
drop) respectively, M is the molecular weight, y is the surface tension in dynes
cm-, p is
density of the liquid, R is the gas c.onstant expressed in ergs per degree per m
ole (8.31 x
T is the absolute temperature, and r is the radius of the liquid drop or the cap
illary (if it is
oncave surface, r is negative).
The Kelvin equation indicates that liquid drops have a considerably higher vapov
.r pressure
@ @ O0
. ()

lgure 6.4 Surface of llquid JIlms.

(AJ Concave surface when in a pipette.
(B) Plane surface when as aJIlm on a glass slide.
{C) Convex surface when as a drop.
tension of liquids can be measured by either of the tv, methods: static and dyna
mic. static methods are based on the assumption that the liquid has attained sur
face equilibrium.
uids and solutions of crystalloids the process of attainment, of equilibrium is
the static methods are best suitable. But for colloidal solutions a considerable
time is
reach the equflibrium state and therefore the dynamic methods of measuring surfa
preferred. The dynamic methods measure the tension of a liquid before the surfac
has had time to form. There are other methods too which fall between the static
and the
methods. Among the static methods, the most commonly used ones are.(/) the capil

(//) the du Nouy ring method, (it/) the Wilhelmy balance method, and (iv) the dr

Biophysical Chemistry
Automated Recording Devices
In the middle of the 20th century many automatic recording instruments making us
e of
either the Wilhelmy vertical pull method or the horizontal one were devised. The
se automatic
devices record the pressure exerted by a fflm as a function of the area occupied
. Surface pressure
may be changed by altering the area occupied by a film either by compressing or
expanding the
iflrn. This' force-area relatioriship can be recorded as a curve on a kymograph.
.In another
instrument described by Anderson and Evett a mirror is attached to the horizonta
l float of a
horizontal idm balance. A lens system is placed in such a way that it directs a
beam of light
from a light source on this mirror. Reflected beam of light now illuminates a tw
in phototube.
Any change in the film pressure displaces the light beam and this serves as a si
gnal to the
phototubes to bring about the firing of either of the two thyratron tubes which
in turn activate
a motor. The motor works to restore the float to its original position by means
of a torsion wire.
In doing this, the angular dplacement taking place is tr .ansformed into an elec
trical message
which is captured in a potentiometer recorder.
In 1963, Mendenhall and Mendenhall described an instrument which can carry out t
compression and expansion cycles of surface iflms automatically upto a ratio of
70:1. This
phenomenon of alternate compression and expansion is called hysteresis. Study of
loops, i.e., surface tension as a function of area, are of physiological importa
nce. It has been
observed that a surfactant found in the alveoli, responsible for the pressure-vo
lume hysteresis
following contraction and relaxation of the whole lung, exhibits hysteretic beha
viour and thus
prevents the lung from collapsing after a contraction wave (see Box 6.2).
Suggestions For Further Reading
Vold, M.J. and Vold, R.D., Colloid Chemistry, Reinhold Publishing Corpor
ation, New York,
2..Shaw, D.J Introduction to Colloid and Surface Chemistry, Butterworth, London,
3. Adamson, A.W., Physical Chemistry of Surfaces, John Wiley & Sons, New York, 1

Weaver, T.E. andWhitsett, J.A., Function and Regulation of Expression of
Pulmonary Surfactant
-- Associated Proteins, Biochemical Journal, 273, 249-264 (1991).

In the preceding chapter on surface tension we discussed the nature of cohesive
between the molecules of liquids and solids. We observed that surface atoms cann
in the three dimensions as the atoms in the interior do, and thus bonding forces
at the
urfaces are not completely satisfied. In order to satisfy their residual forces,
surfaces of liquids
tend to attract and retain on them gases or dissolved substances with which they
contact. This phenomenon of concentration of molecules or long on the surfaces o
f all
is called adsorption. The substance which is thus adhered to the surface is said
to be the
phase or adsorbate while the substance to which it is attached is the adsorbent


//////////S//////////// AdsorUe.t
Figure 7. I Adsorption : Concentration at tim surface
Adsorption should be carefully distinguished from absorption. In the latter proc
ess a
' retainedon the surface, but penetrates to the interior to become distributed
the phase (see Figure 7.2). However, at times, both adsorption and absorption ta
side by side and it is difficult to distinguish between the two processes experi
general term sorption (J.W.McBain, 1909) is implied in such cases.
-- Surface

of light.
Biohysico Chem/stry
The forces operating between the molecules of an adsorbate and the adsorbent are
short-range forces as suggested by I. Langmuir. These forces may be non-specific
like the
dispersion forces, the orientation forces and the Induction forces. Sometimes ch
emical bonds like
ionic and covalent bonds which are specific in nature may also be involved in th
e adsorption
process. In such a case, when a strong chemical bond appears between a molecule
of the
adsorbate and the surface of the adsorbent, the phenomenon is called chemical ad
sorption or
The physical forces involved in the adsorption process are non-specific in natur
e like the
dispersion forces or van der Waals forces, These forces arise from attraction be
tween temporary
,r instantaneous dipoles. The origin of an important part of the van der Waals f
orce can be
elaborated thus: owing to the continuing motion of all the electrons in their or
bits within the
atoms of a substance, a constantly changing electromagnetic field is set up outs
ide the substance.
At any gtven instant it may influence upon the electrons in neighbouring matter
in a way that
the electron cloud may be more concentrated at one side of the atom producing fl
dipoles. When two dipoles approach each other, their motions are no longer indep
endent. Instead,
two dipoles oriented in the same direction produce an attractive force (see Figu
re 7.3). These
forces are called dlspersionforces because fluctuating dipoles cause the phenome
non of dispersion
iVgure 7.3 Model of dlspersion forces
Even distribution of electron density of an isolated atom.
Instantaneous dlpole formatlon due to uneven distrtbutlon of electrona.

Attraction of two instantaneous dipoles.
Other physical forces of attraction like the orientation forces appear upon adso
rption of
polar molecules carrying constant electrical charges. The electrical charges app
ear on surfaces
either as a result of electrolytic dissociation or preferential attraction of ch
arged long from the
sunndings incompletely satisfied atoms of the surface. For example, charcoal, if
placed in
an aqenvironment is negatively charged because certain valence of the carbon ato
(secondary valence) at the surface which are incompletely satisfied attract hydr
oxyl long from
the medium. These hyflroxyl long holds on to the surface conferring upon it a ne
gative charge.
Polar molecules (these have a net separation of positive and negative charge in
molecules) have weak electrostatic forces between molecules resulting from attra
ction between
opposite ends of individual molecules. Polar molecules tend to orient, themselve
s with their
positive poles toward the negatively charged surface or negative poles toward th
e positively
charged surface (see Figure 7.4). These orientation forces are much weaker than
the electrostatic
forces of attraction between long, but somewhat stronger than the dispersion for
ces between
non-polar molecules.

( Polar molecule
circles represent adsorbent
,=: Surface
..-----. Iositively
e 7.40ntatn of molecs
ducon forces so play pot role e adsofion process. e elecosc which elecons ier at
tracted to or repelled fro one atom (or groups of atoms)
to oer, e cled inductive effects. adsorbate may not contn dipoles to , but e ele
cc chge on the suace of the adsorbent may duce dipoles in the
molecules ereby attracting them. It may so happen that dipole moments appe
adrbent suace due to inducHon by the dipoles berg adsorbed.
e molecules of e adsorbate approach those of the adsorbent suace, the above
e opposed by forces of repulsion. AdsoHon d desoHon conue till
is reached. A molecule being adsorbed is not associated a sine cene.
centres (see Figure 7.5).

0 0 0 0

o o o o o
I Adsorbate molecules
Dotted lines represent residual
forces of attraction of surface

Figure 7.5 Adsorption of adsorbate molecules at multiple sites of the adsorbent

In addition to the non-specific interactions discussed earlier, molecular comple
xes with
bonds are often formed on adsor)ents. Hydrogen bonds are much weaker than normal
bonds but are stronger than thee/dipole-dipole interactions between polar molecu
bonding occurs beositively charged hydrogen atom in one molecule and a
highly electronegtive atom in a second m61ecule (see Figure 7, 6). Further, if t
he adsorbent
of donor-acceptor interactions with the adsorbate, unstable complexes are usuall
H -- 0 --H..- ..... H
Figure 7.6 Hydrogen bonding represented by the doffed line, between two water mo

Biophysical Chemistry
Finally, sometimes the association of the adsorbate and adsorbent may result in
a strong
chemical bond. In such a case a new surface chemical compound is formed which ma
y further
take part in the adsorption phenomena.
As adsorption phenomenon involves concentration of a substance on the surface, t
extent of adsorption depends on the surface area. The larger the surface of the
adsorbing agent,
the greater is the adsorption. Therefore, matter in finely divided or colloidal
state exhibits great
powers of adsorption. Finely divided metals like nickel and platinum and porous
like charcoal, fuller's earth, silica gel etc., provide a large surface area and
are best solid
Physical adsorption is due to the operation of relatively weak electrostatic for
ces of attraction
like the van der Waals forces. These forces are characterized by low heats of ad
sorption (approx.
1 Kl mole-). Therefore, physical adsorption proceeds best at low temperature and
with increasing temperature ([ Chatelier's principle). The latter occurs due to
the increased
kinetic energy of the adsorbed molecules which causes them to escape more rapidl
y from the
adsorbing surface. Physical adsorption can also be easily reversed by lowering t
he pressure.
In contrast to physical adsorption, chemisorption is associated with high heats
of adsorption
(approx.50-100 kcal mole-). The chemical bonds formed between the adsorbate and
the adsorbent
cannot be broken easily and therefore chemisorption is seldom reversible. Only a
fter heating to
high temperatures, the process is reversed. However, it may happen that the subs
tance desorbed
at higher temperature is not the same as the one originally adsorbed. The heat o
f adsorption
decreases as the amount of substance adsorbed increases, apparently due to progr
decreasing attractive forces as multilayers of molecules are built up on the sur
face of the
adsorbent. Some systems may show physisorption at low temperatures and chemisorp
tion at
some higher temperature.

Adsorption proceeds best from dilute solutions, i.e., it is more nearly complete
when the
ratio of adsorbent to the adsorbate is high.
The surface charge of the adsorbent is an important criterion in adsorption. A n
charged surface will adhere upon it more of a positively charged adsorbate than
it will do of a
negatively charged one. As for e.g., cellulose strips will adsorb more of the dy
e methylene blue
(positively charged) than of congo red (negatively charged).
The adsorbing powers of many substances can be increased by temperature treatmen
Heating in specified conditions may result in activation of the adsorbent. This
heightening in
adsorbing powers is attributed to an alteration in the nature of the adsorbing s
urfaces. For
example, chcoal gets)activated when heated in streaming steam and then in a clos
ed chamber
at about 800/ .
The molecules adsorbed on a surface show a distinct pattern. They are oriented a
arranged in a definite manner relative to the adsorbing surface as well as to th
emselves. In the
biological systems the patterned and orderly arrangement of the molecules of the
cell membrane
affords useful electrical properties. We shall discuss this aspect of adsorption
in the subsequent
The molecules in the bulk of a liquid are randomly distributed relative to each
whereas they are arranged in more or less orderly fashion at surfaces or interfa
ces. This orderly
arrangement of molecules in surface films or at interfaces is called molecular o
rientation. The

of molecular orientation was In-st introduced by Hardy and further developed by
Adam and their co-workers.
Molecular orientation results due to the differences between the forces of attra
ction of the
semipolar, and non-polar groups in a substance for another substance which may b
e the
or ariother phase. The polar groups like -OH, -SO3H, -NH2, -COOH, -CN, -CHO,
-NO2, etc., contain atoms which do.not have identical eectronegativities. As a r
esult, a net
of positive and negative chmges occurs. The atoms that possess free pairs of ele
a tendency to form co-ordinate linkages. Because of the free pairs of electrons
s are surrounded by rather strong forces of attraction. On the other hand, nonlike hydrocarbon radicals have weak forces of attraction around them. This is so
they contain atoms that have nearly equal attraction for the electrons and thus
there is
any difference in the electronegativities. When a molecule containing one of the
polar groups and a non-polar hydrocarbon radical comes in contact with a
it will tend to orient itself in a definite fashion.
Hydrocarbons are characteristically insoluble in water but soluble in organic so
if one of the earlier mentioned polar groups are introduced into a hydrocarbon m
When such a substituted molecule is added to water it
surface in a characteristic manner. Consider, for example, a solution
acid [CHc(CH)4-COOH] in benzene which is added to water. An emulsion soon
with benzene droplets surrounded by water. The benzene droplets thus form one ph
ase water forms the other. The acid molecules being freely soluble in benzene wh
ile less
: in water are retained in the benzene phase. But at the interface between the t
wo liquids
of caproic acid molecules takes place. The arrangement is interesting. The
,. acid molecules are attracted towards water and therefore they orient towards
water through hydrogen bonds. On the other hand, the C5HI group
acid, a non-polar group, has greater affinity for the organic solvent benzene an
d is
towards it. The acid molecules thUS concentrate at the-interface of the two liqu
and benzene, with their polar heads toward water and the hydrocarbon tails towar
(see Figure 7.7).
Figure 7.7 Orientation of caproic acid molecules across a benzene-water interfac
Acids with short hydrocarbon chains like acetic acid (CH3.COOH) and propionic ac
are freely soluble in water. Nevertheless, they do orient themselves at the wate

with their polar groups adhering into the water while the hydrocarbon radicals a

Biophysical Chemistry
directed above the surface towards the air vertically in a more or less parallel
fashion (see
Figure 7.8).
Solution of propionic
acid CHCOOH in
Figure 7.8 Orientation of propionic acid molecules across a water-air-surface
The living membranes have various kinds of molecules embedded in them. Some are
polar while some*fire non-polar. There also exist macromolecules like proteins a
nd compound
which are polar at some of their atomic groupings but are non-pglar at o
thers. This
difference in size, shape and arrangement of atoms in the different molecules in
fluences their
orientation. For example, lecithins and cephalins have been seen to orient thems
elves at a
water-lipid interface at an angle of 30 to the water surface, while the similarl
y shaped molecules
of sphingomyetins and glycolipids tend to orient with their long axis perpendicu
lar to the water
surface. Also, the molecular pattern due to orientation is constantly under chan
ge, as influenced
by environmental and intracellular conditions.
The arrangement of macromolecules relative to each other in the protoplasmic mem
is worth mentioning. According to the Singer and Nicolson model proposed in 1972
, the lipid
molecules are arranged in two layers with their hydrophllic heads to the exterio
r while the
hydrophobic hydrocarbon tails face each other. On the hydrophilic heads are adso
rbed the
protein molecules. Protein molecules may also be an integral part of the bilayer
(see Chapter 6
for diagrams). The protein molecules are so arranged because they are more hydro
philic than
the lipids and major part of the water of the membrane tends to be associated wi
th the protein.

The protein molecules are capable of translation or rotation. The long hydrocarb
on chains of
the lipid molecules are bound together at many points along their long axis by h
bonds. The membrane is dynamic and this poised arrangement of molecules may beco
disordered under certain conditions and a transition may occur from the gel-like
ordered phase
of the bilayer to the sol-like disordered phase.
Any two immiscible liquids normally forti a two-phase system when mixed
together. But
by vigorous shaking a colloidal dispe,rsion odroplets of one liquid in a
nother may form. This is
an emulsion. As soon as the mechanicai-ffispersive action ceases, the dr
oplets come in contact
with each other and merge to form larger particles in order that the tot
al surface free energy
may be reduced. The coalescence process is rapid and within a few minute
s the droplets merge
to revert to a two-phase system. Usually, one of the liquids is water an
d the other liquid Immiscible
with water can be designated as 'oil' for theoretical purposes. Accordin
gly, we come across

emulsions belonging to either of the two classes water-in-oil type (W/O) or oilin-water type
We have just mentioned that emulsions are usually unstable. But there are agents
when added to such 'temporary' dispersions convert them into stable ones. Such a
components are called emulsifiers or stabilizers. Milk is an excellent example o
f an emulsion of
butter fat in water stabilized by casein, a protein. We frequently come across m
any other
stabilizing agents such as gums, soaps, bile salts, and saponins. Most of the su
(those possessing surface tension lowering ability) act as good emulsifiers. The
eiliciency lies in their preferential adsorption for one of the two interfaces,
i.e., oil-air or water-This is because the emulsifier is adsorbed on the drops d
uring the formation of the emulsion
reduces their degree of coalescence though it may later on go and lodge itself a
t the oilwater interface. Surface-active substances can be put into two categories depend
ing upon their
number (hydrophile-lipophile balance number). The HLB number is calculated addit
composition of their chemical structure. The ones which show a low HLB number, i
to six, lead to 'W/O' emulsions while those with a high HLB number, i.e., betwee
lead to 'OfvV' emulsions. Ross and co-workers have shown that the HLB number
to the spreading coefficient and hence in the case of O/W emulsions it is linear
to the tendency of an oil drop to spread over the surface of an aqueous solution
of the
The most important aspect of the emulsifier action appears to be its orientation
at the
between the two liquids. A soa consists of a long hydrophobic hydrocarbon chain
and a hydrophilic polar end (head). In a oil-soap-water system, the polar head b
attracted to water will orient itself towards water and the non-polar tail will
the oil. By obeying the principle of minimal surfaces, the liquid which has a hi
tension will tend to draw itself into spheres and will be surrounded by the liqu
id whose
tension was more markedly lowered (see Figure 7.9).
Soap molecules
Figure 7.9 Orientation of molecules in an oil-soap-wter system

Thus the emulsifier which is. added tends to collectt the interface between the
phase (oil in this case) and the continuous-plse (water, in this case) to form a
of coating on the surface of the droplet, making it difficult for the surface of
one droplet to
the surface of another, thus preventing coalescence. Harkins pointed out that if
of the two parts of the stabilizing soap molecules is such that the polar end is
chain, then a stable emulsion will be obtained in which the area of
of the soap film is greater than that of the oil side. In other words, it will b
e an oill (Figure 7.10). On the other hand, if the polar group of the soap ha a smaller

(1) Abundance ofsodlum soap in
a off-soap-water system
resulting in a oil-in-water
Biophysical Chemistry
cross-section than the hydrocarbon portion, then a water-in-oil emulsion will be
{Figure 7.11).

Soap molecules with a large

polar head and a smaller
hydrocarbon tail
Figure 7. I0 An oil-in-water emulsion
Soap molecules with a
small polar head and a
long hydrocarbon tail
F/gure 7. / 1 A water-in-oil emulsion

It was observed that ffan oil was emulsified with water containing a sodium soap
, emulsions
of the oil-in-water type resulted; but when calcium soaps were used, the water-i
n-oil type of
emulsion was formed. Harkins forwarded the theory of oriented molecular wedge to
explain this
phenomenon. According to this, in the case of univalent metal soap, each metal i
on is attached
to only one hydrocarbon chain, but with the soaps of multivalent metals there wi

ll be several
chains for each cation depending on the individual valencies of the metal long.
The hydrocarbon
chains thus have a larger cross-section than the multivalent cation and this acc
ounts for the
stability ofwater-in-tl emulsions. This theory has been tested experimentally an
d proved to be
true with various oleates and stearates by J.H. Hildebrand et. al. However, ther
e are exceptions
to this theory as can be pointed out by the emulsions stabilized by silver soaps
. By this orientation
wedge theory, silver soaps ought to stabilize off-in-water emulsions but these s
oaps have been
seen to actually stabilize the emulsions of the reverse type. Bancraft offered a
different explanation
for the formation of two types of emulsions stabilized by soaps carrying differe
nt cations. As per
his suggestions, whereas a sodium soap is more soluble in water than in oil, cal
cium soaps are
more soluble in oil than in water. Therefore, sodium soaps lower the surface ten
sion of water
sufficiently to enable it to emulsify fat, while calcium soaps decrease the surf
ace tension of oil
and stabilize water-in-oil emulsions (see Figure 7.12).

Critical rail; sin soap

to calcium soap producing no
Abundance of calcium s o a p
in a oil-soap-water system
resulting in awater-in-oil

Adsorption 16
If in an off-soap-water system, the proportion of calcium soap to sodium soap is
the emulsifying action of the combination of soaps will depend upon the ratio of
metal long.
Clowes found out a critical ratio of calcium ion to sodium ion experimentally wh
ich produced
no emulsion, This critical ratio was Ca : Na = 1 : 4. If calcium is preponderant a
bove this
ratio, an emulsion with oil as the continuous
any preponderance
soap yields emulsions of off-in-water type.
Further work of Clowes on emulsions of both types gave interesting imdings. For
it was observed that an off-in-water type emulsion with a sodium or potassium so
ap as emulsifier
may be converted into a water-in-oil system by the addition of salts ofbi-and te
r-valent cations,
e.g., calcium, iron, aluminium, etc. This inversion is due to a phenomenon known
as /on
antagonsrr Long frequently exhibit an antagonistic action. Various long have ant
plysiologlca2 actlons upon p'otoplasm. For example, calcium is antagonistic to s
magnesium to calcium and sodium to potassium. Sodium in hgh concentration s toxi
c to the
living cell, but toxicity is reduced considerably if the increased concentration
is accompanied
by a corresponding increase in the concentration of other long, like potassium I
n thls case.
Magnesium in high concentration in blood leads to p'ofound anaesthesia, but Intr
oduction of

small amounts of calcium may result in prompt awakening and return to sensitivit
y. Calcium
long have a stimulating effect while potassium long have an inhibiting action on
the heart.
Sodium long increase the permeability of cell membranes to water soluble substan
ces while i calcium long decrease permeability. These interactions of Na, K, Ca
and Mg long in living
organisms take an essential part in vital activities. The concentrations of thes
e long and their
relative proportions in tissues and fluids are of such fundamental importance th
at slight
variations in their content or composition produce profound changes in physlolog
lcal behaviour.
Lastly, molecules in an oriented layer at an interface are in a dynamic conditio
n. Molecules
continuously leaving and entering it. An increase in temperature disrupts orient
ation by
increasing the kinetic motion of molecules.
A monomolecular layer, or m0nolayer, can exist only at interfaces. Interfaces be
tween two
hases of the same compound (ice in water, water in contact with water vapour, et
c.) are highly
dynamic and are continuously changing in molecular dimensions. A much less distu
rbed interface
is that between a solid and liquid or between two liquids which are usually inso
luble. However,
most of the data available to date have been recorded either on unimolecular fil
ms spread on
liquid surfaces (liquid-air interfaces) or films transferred on to solid surface
A monomolecular layer can be formed on the surface of water by dropping onto the
surface a solution of the substance in some volatile solvent such as benzene or
petroleum ether. The added solution spreads, the solvent evaporates and the subs
tance is left on the
urface of the liquid (water, in this case} as an insoluble unimolecular film. Ir
ving Langmuir,
the American physical chemist in 1916 introduced new techniques and made some va
and ingenious theoretical and experimental contributions to this field. He evelo
ped a device by
which the two-dimensional pressure due to the spreading tendency of the hsoluble
could be measured. This-device is named after him as the Langmuir trough. It con
sists of a
rectangular shallow trough, one centimeter to a few millimeters deep. The trugh
is coated with
some material (Lucite, Teflon or Nylon)which is not wetted by the solutio/n. A c
oating of Teflon
is preferable as it is very hydrophobic and permits the study of flls under high

without leaks developing. Quarter troughs may be used for study of protein films
and metallic troughs avoided since small amounts of metallic salts have a stron
g influence on the properties
of films. The trough is filled to the brim with the liquid upon which the films
are going to be

Biophysical Chemtstnj
formed. The surface of the liquid is cleaned by a movable barrier A, which is al
so non-wettable
(see Figure 7.13).
F/gure 7.13 Schematic view of a simple.film trough
A and B
are movable barriers,
is the compression bar,
TI and T2
are barrier ribbons,
is the torsion wire.
is the.loat.
The barrier is left a few centimeters away from the end of the trough. This oper
ation is
repeated with another barrier B from the other end of the trough. A third barrie
r C, also called
a "compression bar" is then placed in position. It can be moved horizontally to
decrease or
increase the film covered ea {Figure 7.14). The surface of the solution is separ
ated into two
parts by means of a teflon-coated aluminium or mica float, F. A torsion wire W,
is connected to
the float. The float also has two non-wettable ribbons T1 and T connected to the
sides of the
Figure 7.14 Side-view of a Langmuir trough.
The movable barrier can be moved n either direction (indicated by arrows
) to increase or decrease the
.film covered area.
Once the surface of the liquid is cleaned, a film can be formed on its surface i

n different
ways. The material to be spread in the solid, dissolved, or liquid state, is bro
ught into contact
with the surface and will then spontaneously form a film. Oleic acid, for exampl
e, which is only
slightly soluble in water spreads spontaneously In water. Others, like higher sa
turated fatty
acids have to be first dissolved in organic solvents and then a drop of the solu
tion is placed on

water surface to form a film. The choice of solvent is important. One should cho
ose a
solvent which does not dissolve in water, is very volatile and lighter than wate
The spreading of proteins should be carefully attempted. Certain proteins can be
the water surface from the solid state, but, it is preferable to spread them fro
m a dilute
(0.05% or less} with the help of micropipette. The spreading of globulins poses
problems, as in their native state the molecules are water-soluble but on unfold
ing they
' insoluble. This difficulty can be circumvented by adding a small amount of amy
the protein solution. This reduces the surface tension of the solution considera
it to spread rapidly on the water.surface.
It is also possible to transfer a monolayer or a system of stacked monolayers fr
om one
another surface. For certain studies, especially the determination of film thick
methods, it is advantageous to transfer the films from the liquid {water) surfac
e to
and has enabled a variety of studies on properties of deposited
polished clean glass slide is first conditioned with a layer of calcium or bariu
m stearate.
then dipped down vertically into a protein film-covered water surface. A protein
deposited on the slide. Because the test slide has a hydrophobic surface due to
a layer will be deposited during the first downtrip of the dipping process, agai
layer will be deposited on the uptrip and so on. In this way a number of protein
stacked one above another.
It is not always necessary for the slide to remain vertical during the transfer
of undenatured protein molecules can be deposited on slides by adsorption. In th
is, a
(coated with calcium stearate/barium stearatel can be stml,] l, tk
i trough containing the protein solution for a minute or so. It is then removed,
washed with
water, and dried. A monolayer ofundenatured protein molecules can be found adher
the slide. The complete process can be followed iran ellipsometer. The ellipsome
ter is a
designed by Rothen which is capable of measuring a film thickness within + 0.3/.
measures the change that takes place in ellipticity of reflected light produced
by a deposited
film. The ellipticity and azimuthal position in space of the reflected beam is a
very sensitive and
(over a certain range} function of film thickness.

A monolayer of matter behaves thermodynamically in two dimensions very similar t

three dimensional matter. If the surface concentration is small enough, the rela
film area (surface area} and film pressure {surface pressure} at a given tempera
same dimensions of energy just as does the product of pressure and volume and ca
n be
to the thermal energy term nRT where 'n' is the number of moles, 'R' the gas con
T the absolute temperature. If the area available on the water surface to a cert
ain number
s of the film is reduced, the film pressure increases. Deviations from this law
of both the distribution of the molecules and the orientation of the molecules i
n the
film. Accordingly, experiments on monomolecular layers can yield valuable result
s for
of molecular cross-sections and for the magnitude of molecular interactions,
both with each other and with the molecules of the underlying liquid. The above
dimension to
the use of monolayers was provided by the pioneering experiments of Langmuir in
1916. By
using one of the troughs, described earlier, he prepared a mono!ayer of stearic/
[CH3{CH2}6COOH] on water. He found the tension to increase markedly when ttl.ogl
were pushed together in the stacking position {see Figure 7.15}. The molecules i
n this position
stood upright with their polar heads touching the water surface while the non-po
lar hydrocarbon
chains lay parallel to each other at right angles to the water layer. All the th
ree quantities, /.e.,
the precise number of molecules on the surface, the area of and the forces per u
nit length are
directly measurable. This data is enough to derive the value of the cross-sectio
nal area of the
molecules when held in the upright position.

Biophysical Chemistry
Figure 7.15 Monolayer of stearlc acid molecules formed on water n a Langrnulr tr
A and B are movable bah'lets for cleann9 purpose,
C is the movable barrier used for compression ofthefdm,
F is thefloat.
As for example, stearic acid was found to have a cross-sectional area of 20.5 A
per molecule
by this technique. Knowing the molecular volume of stearic acid (556 A), it was
possible to
calculate the length of stearic acid molecule, i.e.. 556/20.5 = 27.1
The monolayer technique is extremely significant and has numerous applications.
With a
system such as a monolayer, we have the realization of a simple molecular functi
onal unit. In
other words, it is a system whoseroperties are determined by an orderly arrangem
ent of
molecules, i.e., the molecules form a team and the system behaves differently fr
om an independent
molecule. Such functional systems are often encountered in biological structures
, for example,
the proteins interact with lipid, polysaccharides and with other interfacially-b
ound compounds.
In fact, the whole living body is a functional unit where varied molecules inter
act and co
operate with each other.
Many immunological and enzymatic reactions have been studied by surface film tec
In addition, various aspects of protein structure can be deduced by investigatio
n of spread
protein films, for example, the study of compressibility of a protein film permi
ts the determination
of the molecular weight of the protein molecules forming the film. Tumit in 1954
has described
a method for obtaining protein diffusion coefficient (D) by monolayer technique
which is less
cumbersome and is speedy too. Lastly, surface films have also been used to study
the effect of
irradiation of proteins and the results supplement the information obtained by m
re conventional
Adsorption and Surface Tension : The Gibbs' Msorpflon Equation
Surface tension is regarded as one of the different forms of energy acttfig at s
urfaces giving

rise to adsorption. This is more evident at the liquid air interface. Consider f
or example a
solution where the solute components exhibit positive surface activity (lowers s
urface tension
of the solvent). In the course of ordinary thermal agitation, the solute molecul
es are brought to
the surface. As they concentrate in the surface film, they lower the surface ten
sion of the
solvent. In the process, they are restricted in their movement because their esc
ape would cause
an increase in free energy and then work would have to be performed. But the com
replacement of the solvent by solute molecules in the surface will be prevented
by thermal
agitation and forces of molecular attraction. On the other hand, in a solution w
here the solute

... (3)
... (4)
component exhibits negative surface activity (increases surface tension
of the solvent), no such
of solute molecules in the surface layer is seen. This is a feature particularly
observed with solutions of inorganic salts. The solute molecules, in thi case, a
re rejected from
the surface and thus have to be content with remaining in the bulk of the soluti
The exact thermodynamic relationship between adsorption and surface tension was
derived by J.W. Gibbs in 1872 and later independently by J.J. Thompson in 1888.
It is known
as the Gibbs' adsorption equation which can be derived as .follows.
Let us consider a solution which has attained equilibrium between its bulk phase
surface phase. The surface phase consists of those molecules which are close eno
ugh to the
surface to be acted upon fully by the surface forces. We shall designate the the
properties of the surface phase by a symbol '' and place it as a superscript. A
surface phase
defined in. this manner has an area but no thickness. In other words, it is a st
rictly twodimensional phase. The area of this surface phase will be denoted A. We
L system at constant temperature and pressure and constant composition of the bu
lk phase. The
i., free energy, G, of the surface layer is made up of three factors : (/) the fr
ee energy due to surface
Ltension (?A), (//) the free energy of the solute (n), and (///) the free energy o
f the solvent (2n ). DI and 2 are the chemical potentials of the solute and solv
ent respectively while n and n2
Ddepict the number of moles of solute and solvent respectively. The superscripts
indicate that

the functions apply to the surface. Thus, for the surface phase we can write
G o
. where S is the surface entropy and T is temperature.
Equation (1) can be obtained from the thermodynamic relationship at cons
tant pressure
,I [)\ ---S, at constant temperature and pressure G = Eiani and the equation dG
= ?dA
i! relating change in free energy with the surface tension (y) and change in sur
face area (dA).
At constant temperature the equation becomes
G = yA + Bn + B2n
... (2)
If a change in free energy of the surface phase is desired, it can be brought ab
out by
(/) varying the surface area which will cause the change ?dA, (ii) varying the am
ount of solute
which will cause the change Bdn or (//0 varying the amount of solvent, which will
cause the
change B2dn. Thus the differential form of the surface free energy becomes
dG = ydAa + Bdn + l2dn2
But the complete differentil of G is
dG =ydA +A*dy +t,dn' +n'dl +dn;
Comparing Equation (3) and (4) we get

... (6)
... (7)
... (9)
... {io)
... (11)
... (13)
Biophysical Chemistry
Now the surface concentration, Ci, in moles per unit area is defined by
Therefore, division of Eqn. (5) by A gives
The number of moles of solute present in the surface in excess of the number of
moles of
the same solute in the interior is taken to be the molar excess of solute. This
molar excess of
solute is the amount of solute adsorbed at the surface. If the concentration of
the solute is
small, a change in concentration will not affect the free energy of the solvent.
In such a case, the
excess C of the solvent vanishes. Then
dy = - P dt
... (8)
where F is the concentration of the solute in the surface phase. Since the chemi
cal potential is
related to the activity by
.= o + RT In a
where 'a' is the activity of the solute, fin
dt= RT dln a

Substituting equation (10) in equation (8), we have

dy = - F RT din al
For an ideal solution, a = X, the moIe.fractlon, so that
dy = - F RT dln X
1 d7
or r - .
... (12}
RT dlnX
and for dilute solutions where the activity is very nearly equal to the concentr
ation, X becomes I
proportional to C, the molar concentration, and
I dy
Ci .dy
RT dlnC
This expression is called the Gibbs' adsorption equation. The equation provides
mathematical basis for the generalization that if a substance tends to reduce su
rface tension it
will collect in the surface phase while those that tend to increase surface tens
ion will be retained
in-the bulk phase. We can also see from equation (13) that when the surface tens
ion of a
solution decreases with concentration, dy/dC is negative, I is positive and the
of the solute in the surface is greater than the bulk phase. The surface active
agents exhibit this
type of behaviour. On the other hand, when the surface tension of a solution inc
reases with
concentration, dy/dC is positive, I is negative and the body of the solution is
richer in the
solute than the surface. This is observed in solutions of many electrolytes. The
above equation
has also been experimentally verified by McBain and Humphrey. They employed an a

resembling a microtome to slice off the top layer (0.05 mm approx,) of the surfa
ce from a
was later collected in a sample tube for analysis. The experimental F obtained
satisfactory agreement with that calculated via the Gibbs' adsorption equation.
A solution is made up of two basic components : solute, which may be one or more
and, solvent. When an adsorbent is dropped into a solution either the solute or
may become adsorbed. Adsorpti6n of the solvent is xery rare. When the solute is
from the solution by an adsorbent, it is calledposit/ve adsorpt/or In this case
the concentration the solution decreases after treatment with the adsorbing agen
t. As an example, when a
blue in water is shaken with solid carbon, a part of the dye is removed by
solid carbon and the solution becomes more dilute. Similarly, activated carbon c
an be used
remove acetic acid from a solution of acetic acid in water. Conversely, when the
solvent is preference to the solute, the concentration of the solution actually
increases after
with the adsorbing agent. This phenomenon is known as negative adsorption. When
solvent and solute are adsorbed, the concentration of the solution after the ads
orbent has
will depend on the relative extent of adsorption, whether positive or negative.
Adsorption from solution is very similar to adsorption of gases and is governed
by the
i.e., the mechanism of adsorption is by virtue of electrostatic forces of attrac
surface tension are the factors resjonsible for an increase or decrease in
The Gibbs - Thompson princle states that "those substances which
urface energy tend to concentrate at a liquid-air interface (in the surface), an
d those
which decrease interracil energy tend to concentrate at a liquid-solid or liquid
interface". It follows from this principle that the lower the surface tension of
the solvdnt,
conditions being uniform, the less will be the amount of adsorption. On the othe
r hand,
is best from solvents of high surface tension, because here the solute causes th
decrease in surface energy at the solid-liquid interface. For example, picric ac
id is
adsorbed upon charcoal from aqueous solution than.from an alcoholic one. The
I adsorbed upon charcoal from water may be readily recovered by washing with alc
ohol. The
for this behaviour is that water has a much higher air-liquid surface tension
has alcohol, and so the decrease of the surface tension of the aqueous solution
concentration of picric acid is likely to be greater in aqueous than in alcoholi

c solution.
same is observed at the interface of adsorbing solid and liquid solvent.
When various inorganic salts are dissolved in water, the surface tension of the
solution is
r increased. Therefore, solid adsorbents like powdered silica, activated carbon,
or powdered
are raore effective in adsorbing non-eleCtrolytes from a solution than electroly
The effect of temperature on adsorption equilibrium is worth mentioning. Rise of
of adsorption. This is- in spite of the fact that surface tension
with a rise in temperature. The reason behind this bservation is that molecular
a fundamental cause of adsorption, is disrupted by thermal agitation. For exampl
iodine is added to starch solution, a blue colour appears due to formation of st
However, upon heating, the blue colour disappears due to the failure ofi0dine th
on the starch particles at higher temperatures.
Adsorption from solutions on the surface of solid adsorbents differs from the ad
sorption of
substances like gases, vapours, pure liquids, etc., in that the solution contain
s two
and solvent) forming a closely packed layer on the surface. Upon a change
the concentration, these two components displace each other in the surface layer
, a
observed only during adsorption from solutions. Thus, neither the surface soluti
the bulk of the solution has any free sites and only displacement of molecules o
f one
by molecules of the other takes place.

Biophysical Chemistry
The amount adsorbed from solutions depends on the properties of the adsorbent, t
hose of
the solution, and of its constituents. Polar molecules that are capable of formi
ng H-bonds with
the hydroxyl groups of the surface of the adsorbent are especially greatly adsor
bed. It is for this
reason that silica which has a hydroxylated surface can smoothly adsorb phenols,
water and amines. The adsorption of organic compounds from solutions of highly p
olar solvents
on the surfaces of polar adsorbents is negligible but adsorption of such substan
ces is strong on
non-polar or weakly polar activated carbons.
An increase in surface area of the adsorbent greatly enhances the adsorption of
from solution. This is clearly evident in the case of porous material like charc
oal, fuller's earth,
and powdered substance like silica.
Adsorption is associated with many of the reactions taking place in the living b
ody. It also
has numerous laboratory applications, industrial applications as well as various
applications. In the following text we shall discuss some of the uses of adsorpt
The velocity of any chemical reaction depends to a great extent on the active ma
sses of the
reactants, provided other factors are in optimum conditions. Practically, active
mass and
concentration are synonymous and an increase in concentration of the components
of the
reaction facilitates the reaction. In the reactions taking place in the protopla
sm, adsorption
plays a very important role. By this process, substances ordinarily present in l
ow concentration
may have their effective concentrations lncreased tremendously by being accumula
ted at the
interfaces, thus speeding up many chelIfl'cal reactions. Enzyme action also invo
lves adsorption.
The enzymes, being colloidal in nature, have large surfaces and surface adsorpti
on of reactants
is a requisite for the enzymatic reaction to proceed smoothly. The colloidal mol
ecules are
interspersed with a network of membranes which possess enormous surfaces. Adsorp
tion taking

place at these membranes promotes several vital chemical reactions.

Action of Drugs and Poisons
Substances capable of reducing interracial tension tend to accumulate at the int
To this class of surface-active agents belong varied. "ous drugs andpoisons. The
se substances, as
consequence of reducing interracial tension,' are concentrated at the interfaces
and exert thei
effect from that location. Selective adsorption of drugs may thus be responsible
for specc
Macromolecular Association and Dissociation
Various types of molecular associations seen in the living body are as a result
of adsorption.
These molecular associations between proteins and proteins, proteins and carbohy
proteins and lipids, and proteins and salts continuously take place in the cll p
rotoplasm and
are vital for the structural integration and function of the living cell. Likewi
se, dissociation of
macromolecules could be dictated by their desorption behaviours.
Histological Studies
Though adsorption need not be followed by absorption, absorption depends upon th
concentration of the molecules at the surface or interface. Acidic and basic dye
s which can be
distinguished by their staining power are important tools not only in histologic
al studies, but
also in experimental physiology, where they serve to trace the pathway and distr
ibution of
dissolved substances across cells and tissues. The rate of their entrance into c
ells depends to
some extent on their accumulation on cell surfaces prior to penetration. The cel
l colloids contain

their large surface a number of cationic and anionic centers which are the sites
of electrostatic
of the basic and acidic molecules respectively.
in Safety Devices
A bacterial toxin, hormone, or a mineral poison may be inactivated by adsorption
. Ferric
a good adsorbent Is often used as an antidote in cases of poisoning by arsenic.
are devices containing an adsorbent or a series of adsorbents which purify the a
ir for
r adsorbing the poisonous gases and vapours from the atmosphere.
Applications of adsorption from solution include the clarification of sugar liqu
ors by
removal of Impurities from petroleum oils and motor spirits by colloidal silica
of dyes from dilute solutions In a number of solvents,
Charcoal can also be used to remove odours from gases. CO, evolved durin
g the
process, often has objectionable odours. These odours can be effectively removed
t adsorption on charcoal. Thus, carbonated beverages can be made fit for consump
tion. Purifiers
used in toilets, refrigerators, etc., are generally adsorbents for gases which e
asily remove the
thus freshening the air.
One of the most impoFtant laboratory applications of adsorption is the recovery
of vitamins, proteins, and other biological substans by the method of
analysis, the details of which are discussed in one of the subsequent chapters,
title "Adsorption Chromatography".
in Research and Industry
Lastly, adsorbing agents have found wide use in industry and laboratory for puri

Adsorption has been used for purification of enzymes. The impure solution contai
enzyme at a parti..cular pH is brought in contact with an adsorbent such as alum
After the enzyme has been adsorbed, the adsorbent is washed and then the enzyme
(desorbed) by washing the adsorbent with a solution of another pH. This elution
is also employed in the separation and purification of plant alkaloids, vitamins
substances which are difficult to Isolate by ordinary methods. For example, vita
min B
vitamin B extracted from yeast are separated from each other by adsorbing vitami
n B on
gel in acid conditions (pH 3). Under these conditions, While vitamin B is mostly
is not. Elution of vitamin B from silica is carried out by using an alkaline sol
For adsorption of positive and negative long from solutions, ion exchange resins
used in the laboratories and industries. These resins have also found use in med
such purposes as reducing the acidity of gastric juice in cases of peptic ulcer,
reduction of
' and K concentration in body fluids in cases of congestive heart failure and ren
al failure.
also serve to adsorb toxic products of bacterial action in cases of diarrhoea. I
have made good utilization of ion-exchange resins for water softening and
purposes, removal of electrolytes from food material and other products and
purification of metals.

Biophysical Chemistry
Suggestions For Further Reading
1. Adamson, A.W., Physical Chemistry fSurfaces, John Wiley and Sons Inc., New Yo
rk, 1967.
2. Garner, W.E., Chemisorptior Butterworths, London, 1957.
3. Sherman, P. (ed.), Emulsion Science, Academic, New York, 1967.
4. Gregg, S.J. and Sing, S.W., Adsorption, Surface Area and Porosity, Academic,
New York, 1967.
5. Shaw, D.J., Introduction to Colloid and Surface Chemistry, Butterworths, Lond
on, 1966.

In this chapter an attempt has been made to describe certain relationships among
optical phenomena which produce signals conveying chemical information
either to the concentration of the chemical in a given solution, and/or its stru
information afforded by different optical signal source is so distinctive and va
each has spawned its own specialized instrumentation, In the following pages the
and applications of each of the optical signal sources has been discussed
Light is supposed to have dual characteristics, corpuscular and waveform. Thus,
of light may be understood as an electromagnetic wave-form disturbance or photon
propagated at 3.0 108 m/sec, i.e., at the speed of light. The term. electromagne
description of the radiation in that the radiation is made up of an electrical
a magnetic wave which are in phase and perpendicular to each other and to the
of propagation (Figure 8.1A). The magnitude of electrical vector is denoted by
symbol E and that of magnetic vector is denoted by the symbol H. Figure 8-1A den
otes one
of plane polarized light. A beam of light from a bulb consists of many randomly
polarized components being propagated in the same direction. The distance along
of propagation for one complete cycle is known as wavelength, (Figure 8.1A).
may be measured in centimeters (cm), micrometers (m), nanometers (nm), or
units (/), where Inm = 10-3 tm = 10-6 mm = 10- cm = 10-9 m, and 1A = 10-8 cm.
Electric field, E
Direction of
propogation q 1 IIIII III I=:Jllll I I
Magnetic Field,
8. I {A) The electromagnetic wave. The magnetic vector (unshaded) and electric v
ector (shaded) are perpendicular
to each other and to the direction of propagation. Wavelength ()) is the distanc
e between two crests or
Sometimes a term, frequency, v, is used rather than wavelength to describe a par
To understand this term it will be helpful to see Figure 8. IB denoting variatio
n in the
and magnetic field with respect to time at any given location in a plane polariz
ed ray;

number of waves passing through a fixed point on the time axis per second is kno
wn as the

Biophysical Chemistry
frequency, v, of the radiation (usually expressed in Hertz or cycles per second)
. Frequency
shares an inverse relationship with the wave, length so that
V = c/X
where c is the velocity of light, 3 x 108 m/sec.
EIectrlc field, E
Magnetic Field, H
Figure 8. I (B) The dependence of electric (shaded) and magnetic (unshaded} vect
ors at a particular location tn a
plane polarized electromagnetic wave.
Sometimes radiat ion, mostly in the infrared region (see later), is characterize
d by another
term known as the w<'e number and denoted by the symbol , Wave number means the
of complete cycles occurring per centimeter
The energy E, of a photon can be related to its wavelength and frequency with th
e help of
Planck's constant, h
where c is the velocity of light in vacuum. Remember that wavelength and frequen
cy share an
inverse relationship; this means that as the wavelength increases, the energy of
the radiation
decreases, while the energy increases with the increase in frequency.
A beam of radiation from an electric bulb consists of several wavelengths and is
known as
polychromatic. A beam in which all the rays have the same wavelength is known as
Electromagnetic radiation is produced by events at the molecular, atomic, or
level. Oscillations of nuclei and electrons in electrical or magnetic fields, mo
lecular bending and
vibration, excitation of orbital electrons, ejection of an inner orbital electro

n and rearrangement
of the other electrons, and nuclear break-up are some of the events which give r
ise to
electromagnetic radiation. Since each of these events differ in terms of the ene
rgy involved, the
radiation they emit will have different wavelengths. Thus, a complete spectrum o
f electromagnetic
radiation will be produced. This spectrum is depicted in Figure 8.2. The events
leading to each
component of this spectrum are also described in Figure 8.2.


Valence electron
& rotation
Oscillations of
nuclei and
electrons in
magnetic field

Vacuum I I INear

2-180 1400-'780 ] 25,000-125,000 0.005-30 300

Figure 8.2 The electromagnetic spectrum -- the main regions and their wavelength
s. Physical events involved in
their production are also indicated.

One of the earliest studied characteristics of chemical compounds was theicolor.

color intensity should form the basis of most widely used set of chemical assay
procedures is
then but natural. Things are colored because of their ability to absorb certain
components of
the electromagneticietrum with hich they interact. Consider a substance which ap
green in color. The substance in question here is absorbing most other component
s of the
electromagnetic spectrum except green, which is being reflected giving it a gree
n appearance. If
one can calculate the amount of light absorbed by this substance, one can arrive
at a fair
judgement about the concentration of the substance.
The absorption of light by any absorbing material is governed by two laws. The f
irst of
these laws is known as the Bouger-Lambert law. It states that the amount of ligh
t absorbed is
proportional to the thickness of the absorbing material and is independent of th
e intensity of the
incident light. To understand the above statement let us assume that a thickness
b has the
ability to absorb 50% of the incident intensity of the light passing through it.
If the intensity of
the radiation incident upon such a thickness is assigned a value of 1.0, the out
coming, i.e., he
transmitted beam will have a value of 0.5. If we now place a second equal thickn
ess b, it will
absorb 50% of the transmitted beam, i.e., 50% of 0.5. The second transmitted bea
m will then
have a value of 0.25. This process is illustrated in Figure 8.3 and may well ass
ume the graphical
Figure 8.3 The pattern of light absorption by successive equal path-lengths (b)
of absorbing solution.
form as in Figure 8.4. The successive light intensities are the sequence (0,5)I,
(0.5)2, (0.5)3 etc.
This is clearly an exponential function and may be expressed as
e -kb
I = the intensity of the transmitted light,
Io = the intensity of the incident light,

b = the absorbing thickness, better known by the term path-length

100% Transmission
Path length
Figure 8.4 Data of "igure 8.3 expressed graphically by plotting % trmlsslon agal
nt the path lenjth (thickness]
and k = the linear absorption coefficient of the absorbing material. The power t
erm in the
above relationship can be removed by converting to the logarithmic form. Thus,
In I-- = -kb, or In I--?- = kb,
changing to common logarithms we get,
2.303 log lo-- = kb
The second law of absorption is known as the Beer's law. This law states that th
e amount
of light absorbed by a material is proportional to the number of absorbing molec
ules i.e., the
concentration of absorbing solution. This can be mathematically expressed in the
form of an
equation similar to the one above.
2.303 log,o -- = k'C
where k' = absorptivity constant, and
C = the concentration Of the absorbing material.
We can now combine the two equations for the Bouger-Lambert law and the Beer's l

Here, k and k' merge to become a single constant a (see Box 8.1). The combined e
quation is
written as
lg,o-Io = abC
This equation has been alternately referred to as the Beer-Lambert law, the Boug
/aw, or more simply, Beer's law. This combined law states that the amount of lig
ht absorbed
(absorbance or extinction) is proportional to the concentration of the absorbing
substance and to
the thickness of the absorbing material (path-length). The quantity Io/I is know
n as the absorbance
or the optical density (O.D.). The reverse, I/Io is known as the transmittance,
T (the amount of
llght which escapes absorption and is transmitted).
Absorbance shares a linear relationship with sample concentration. On the other
the relationship between transmittance and sample concentration is a non-linear
one. It is

Box 8.1
is :the
Mo!ar abso
therefore easier to use absorbance as an index of sample concentration. This rel
ationship between
absorbance and transmittance is shown in Figure 8.5.
Percent. transmittmce
- Absorbance
p'igure 8.5 The relationship, between percentage transmission and absorbance.
The two terms are mathematically commutable and so one can be calculated from th
other. For this purpose we rewrite the equation so that
A [absorbance) = log Io - log I
but Io is always set at 100% and log 100 = 2, so
A 2-1ogl
In the equation

Biophysical Chemistry

Biophysical Chemistry
Stating Beer's law a
ional to the
sample concentration
e optical density of
standard solution is
ed from its
optical density. The

bit differently, we can say that optical density is proport

If the path-length is constant. It follows then, that if th
known, then an unknown sample concentration can be calculat
formula used for such calculations is

concentration of the unknown

O.D. of the unknown x conc. of a standard
O.D. of the standard

The standard chosen should have an optical density nearer to the O.D. of the unk
Before we go ahead, it is necessary to instill the concept of what is known as t
he "blank" or
the *reference" solution. To measure the O.D. of any given substance, one dissol
ves it in a
solvent. If the substance does not absorb in the visible region, many times one
adds other
reagents so that the compound becomes colored and absorbs in the visible region.
The solvent
and the other reagents might also absorb in the region in which the absorbance d
ue to the
substance of interest is being measured. The resulting O.D. will then be a sum o
f the individual
absorbances due to the substance and the solvent and the reagents. In order to c
ancel out the
O.D. contributed by the solvent and the reagents, we prepare what is known as th
e blank, which
consists of all reagents used in the solvent but not the substance of interest.
When this solution is
read in a spectrophotometer, a particular reading is obtained on the O.D. scale.
This O,D. is
due to the absorbance due to the solvent and the reagents. This reading is now m
ade zero with
the help of a knob in the instrument. When, subsequently, standards will be read
, the O.D.
observed will be due to the substance only, since the O.D. due to other regents
(which are
added in equal quantities in all the standards and the unknown) has already been
The most accurate way of measuring the concentration in the unknown sample is th
preparation of a calibration curve from a number of standards. The whole process
is described

in Box 8.2.

A standard curve should always be prepared to check that Beer's law applies to t
he analysis
performed (in which case the curve would be straight). This is necessary since t
here are
factors that may cause deviations from linearity. The most common factor causing
from linearity is the use of a band of wavelengths to measure absorbance in most
In the strictest sense, laws of absorption apply to monochromatic radiation and
The deviation from linearity in this case, however, is not so severe as
in such experiments. Other factors which cause deviations
are given below.
From Beer's Law
Following factors may cause deviations from Beer's law.
I. Deviations from Beer's law occur usually when hlgh sample concentrations are
One effect of high concentration is that the molecules may dimerlze. It is not n

Biophysical Chernistnj
that the absorpUon spectra of the dimers are the same as that of the monomers. I
f the spectra
differ, the absorpUon coefficient will also undergo a change (Figure 8.6) leadin
g to a positive or
negative deviaUon.
The spectral shift is normally due to polymerizaUon. There Is JUSt one wavelengt
h here
where the molar absorpUon coefficient has not changed. This wavelength (2) is .c
alled the
IsobesUc point. At there will be negative deviaUon and at 3 there will be a posI
Uve deviaUon.
High concenaUon may also lead to aggregaUon. Large aggregates then scatter light
. The
intensity of the radiaUon reaching the.detector Is thus lessened. Thus two diffe
rent phenomena
are contributing to the reduction in the transmitted intensity m absorpUon, and
scattering. In
such a case a positive deviation will be seen. A particularly interesting .manif
estaUon of this
phenomenon occurs in the formaUon of micelles (see Chapter 3; Box 3.3, and discu
ssion under
'Asoclatlon Colloids'). Over an extremely small concentration range known as the
critical micelle
concentration (cmc), certain kinds of solute molecules cooperatively associate i
nto large particles,
called micelles, The micelles are huge particles by comparison since each micell
e may co.ntain
more than 100 molecules per particle, The micelles cause appreciable scattering
of radiation in
the X-ray to visible region. Micelles are usually formed by those molecules whic
h have one of
the ends 'phillc' to the solvent while the other is 'phobic.' Examples are fatty
acids, hospholipids,
ionic lipids, etc.
Figure 8.6. (A)A schematlc of absorptWn spectra of the same substance at two dif
Figure 8.6 (B) Schematic representation.of how negative

and positive deviations appear on the chart

Aggregation, on the other hand, can lead to electronic interactions that can eit
her lessen
or enhance the absorption coefficient.
High concentrations can also lead to chemical reactions which will lead to a cha
nge in the
chemical composition of the solution. Naturally, a deviation from linearity will
- Deviations may also occur at low concentrations. The most significant point to
note here is
about proteins. Proteins are known to denature at low concentrations and the den
atured product
has an absorption spectrum that is different from the native protein.
2. Instrumentation limitations may also result in deviations from Beer's law. On
e of the
main causes here is imperfect rnonochromacy. Let us see what this means.
The calibration series for a red solution is measured using monochromatic light
wavelength 492 rim, i.e., at the maximum, and of 546 nm, i.e., on the flank. The
plots obtained are two straight lines having different Slopes. Ife were to make
a third series of
measurements now using a large half-bandwidth filter (20 m) with a maximum of 52
0 nm, the
resulting calibratiu, plot will be a curved line.

This is only an apparent deviation. The reason is not far to seek. Let us, for t
he sake of
understanding, assume that the filter is passing only two wavelengths. One of th
e wavelengths
is the 'm for the sample and the other wavelength is at the periphery of its abs
orption spectrum
in the red region. Let us say that a given unit of concentration has the. abilit
y to absorb 50% of
the 'm" However, the same concentration absorbs only 25% of the .wavelength at t
he periphery.
From our consideration of the Beer's law in the earlier pages we can say that th
e transmittance
series with every unit rise in concentraon for the .. will be. 1/2, 1/4, 1/8, an
d so on. For the
it will be 3/4, 3/8, 3/16, and so on, It is not difficult to see that if the
absorptions are plotted for both these series against increase in concentration,
result will be a straight llne for each. However, for the whole filter the compo
site transmittance
k i + 2. The series will not rise in an exponential manner as for the previous t
wo individual 2
Thus absorbance plotted for these composite transmittances will give rise to a
(Figure 8.6 (C)). When we think that there are many more wavelengths passing th.
than we have just assumed, it is easy to see why measurement using filters .will
in straight lines though there are no other conditions for violation of the Beer
's law.
2 4 6 8
Fgure 8.6 (C) Effect of imperfect monochromacy
imperfect monochr'omacy, other indeterminate instrumentation variations which
include (A) stray radiation reaching the detector, (B) sensitivity changes
, and power fluctuations of the radiation source and detector amplification syst
operation {to be discussed later) tends to cancel out most of the random causes
Apart from the factors mentioned above, the following factors can cause deviatio
ns from
i Beer's law.

Most experimental protocols insist that i heating is requied for color developme
nt, the
be cooled to room temperature before its absorbance is read. This insistence is
aqueous as well as other solu/ons expand upon heating. The absorbance in
is always different. Moreover, change in temperature results in a change in the
of solubility, dissociation/association properties of the solute, hydration, and
is also reflected in the absorbance. Thus, absorbance measurements always be don
e at a constant temperature.

Bophyscal Chemistry
Sample Instability
Experimental protocols for absorbance measurements of a few substances insist th
at the
measurement be done within a very short time of color development. One good exam
ple is the
Fiske Subbarow method of phosphate estimation by the ANSA method. The reason for
insistence is simple -- some colored compounds are unstable and undergo changes
quite short times. In such cases the color could increase, or decrease. Even mor
e detrimental is
the fact that for some such unstable compountis, even the X, may change.
Some solutes fluoresce (drugs and drug intermediates often do). For such substan
deviations occur because apart from the transmitted intensity, fluorescent inten
sity also reaches
the detector.
Turbid solutions always end up giving higher absorbance than what is determined
by the
The pattern of energy absorption by a substance when light of varying wavelength
through it is uniquely characteristic of the substance. This pattern is known as
an absorption
To establish the absorption spectrum for a given substance, transmittancy or opt
ical density
of a particular concentration of the substance is measured at different waveleng
ths (the path
length is kept constant throughout}. The data so obtained is plotted in the form
of a curve
relating transmittance or optical density (the latter is preferred) to wavelengt
h. An example of a
relatively simple absorption spectrum is shown in Figure 8.7; generally more com
plex curves
are found, Since the absorption spectrum of a substance is usually characteristi
c for it, it may
serve for its identification and may furnish information of analytical value. Th
e application of
absorption spectra is not limited to the visible region of the spectrum but may
be applied
equally wen to characterization of the ultraviolet or infrared absorption of man
y substances.

Wawength (nm)
Figure 8.7 A simpl/ged absorption spectnan curve. ), represents a concentration
twice as much as that of x. The
dotted//he cated the wave/ejth of maxm sens/ttvfor spectrophotometrc measurement
Absorption curves of a particular substance vary along the absorbance axis with
in the concentration of the substance; they do not vary along the wavelength axi
s (curve x and
y in Figure 8,7). It becomes clear from Figure 8.7 that although a particular su
bstance absorbs
at numerous wavelengths, there are regions where it absorbs more than in other r
egions. The
wavelength at which the compound absorbs most is known as its absorption maxima,
,.. If
one increases the concentration of a substance, it will be observed that absorba
nce at all

Energy, J
13.6- ground state
has increased; however, there is a greater change in absorbance per unit change
.concentration at the wavelength of maximum absorption. This is the reason why o
ne chooses
the absorbance of a compound at its )m, during a quantitative experiment. At thi
maximum sensitivity will be obtained in a photometric measurement. Occasionally,
as for example in a procedure where the absorbance curves for reagents and color
overlap considerably, the highest sensitivity may be obtained at a wavelength on
absorption maximum. Thus a knowledge of the absorption spectrum of both, the
compound is essential for the proper selection of an optimum wavelength.
is Absorption Spectrum Specific for a Substance?
How is it that a compound absorbs maximally at one wavelength and does not absor
b at
mother?. Let us assume that a substance S absorbs maximally between 270 and 280
| does not absorb at all at wavelengths beyond 300 nm or below 270 nm. The theor
y of
suggests that absorption o radiation means acceptance of energy embodied in the
to catapult electrons of the absorbing substance to higher energy levels. So why
is it
substance'S accepts energy from radiation of wavelength 270-280 nm to catapult i
levels, but does not accept energy from radiations of other wavelengths?
The answer is provided by the concept of quantized energy. As per quantum theory
, the
of m atom can exist only in certain orbitals which involve different electron en
the lone electron of hydrogen can exist in six different energy levels (Figure 8
lowest level being the ground state. These energy levels are signified by n, whe
re n has
of 1,2,3 etc. Quantum concept forbids intermediate energy levels like 1.2, 1.5 .
.. etc.
to become excited the electron has to Jump from n =1 to n = 2, or n = 3 etc. Qua
energy of light is not continuous, but is concentrated into packets
energy or quanta. In a low frequency (high wavelength) light each quantum will h
ave a small
T while, in light of higher frequency quanta will have greater energy. Quantum t
heory also
that in order to be excited the electron will accept only that radiation which h
as the

energy to push it into a permitted energy level. In other words it can absorb
wavelength or frequency which provides it with its exact requirement.
to the energy level n = 2 from the level n = 1, hydrogen electron needs a partic
which is provided only by radiation of the wavelength 1,217/i,. Consequently
Energy, eV
0.87 x 10-19
- 0.54
1.36 x 10-19
- 0.85
2.42 x I0-19
- 1.51
Excited states

5.43 x 10-19
- 3.40
Absorption of radiation of
wavelength 1217 X lifts
electron from n = 1 to n = 2
Ground state and excited state energy levels of hydrogen atom. Associate
d energies for each level are
whiten in Joules and V.

hydrogen absorbs light of this particulkr wavelength. Going by the example of hy

drogen we can
easily explain why the substance S does not absorb at 300 nm but absorbs at 280
nm. Quantum
theory, thus, explains why absorption spectrum is specific for a given substance
. Hydrogen is a
small atom. The very few energy levels available for its lone electron transitio
n give a sharply
defined absorption spectrum (line spectra) for this element. In complex molecule
s, the multlplicity
of energy levels available to electrons belonging to different atoms result in t
he discrete bands
to coalesce and thus, broad bands are observed, which are nevertheless specific
for the given
molecule. Moreover, vibrational and rotational energy levels are also associated
with each energy
level of electronic transition. Excitation of an electron and its promotion to a
higher energy level
is also accompanied by changes in the vibrational and rotational levels. This is
an additional
factor responsible for the broad bands of absorption spectrum of a given compoun
Let us now briefly deal with the types of electronic transitions which t.ake pla
ce when a
given substance absorbs light energy. The following types of orbitals are genera
lly found in the
ground states of organic molecules (see Figure 8.8(B) and Table 8. I),
Bonding morbttals: These are extremely strong and constitute single bonds betwee
n atoms,
The electrons are not at all delocallzed and the distribution of electrons is cy
lindrically symmetrical
about the bond [Table 8.1).
Table 8. I A few examples of some bond types, transitions, and molecular orbital
Type of bond
Transition of lowest
Shapq of molecular orbitals
Ground state
Excited state

g eon system
perpendicular to the
plane of the page.

Note :
Special distribution and sign of wave function of the molecular orbitals
has also
been provided.
Bonding -orbitals: These constitute multiple bonds between atoms and are based o
n a
combination of atomic p-orbitals. The electrons are strongly delocalized and int
eract with the
surrounding environment with relative ease.
n-orbitals : Certain molecules contain heteroatoms (e.g., oxygen, nitrogen). The
orbitals with highest energy in such molecules are those of lone pairs. These lo
ne pairs are not
involved in bonds (non-bonding) and thus retain their atomic character.
All the above three types are illustrated beautifully by formaldehyde as shown b
elow :
H/ .-------n
According to the molecular orbital theory, when a molecule is excited by the abs
orption of
energy (UV or visible light), its electrons are promgted from a bonding to an an
tibonding orbital
(higher energy sates). The antibonding orbital associated with the bond is calle
d " orbital
and that associated with the g bond is known as the ' orbital. Since non-bonding
electrons are
not decfly involved in bonding, there is no corresponding antibonding orbital fo
r them. The

Spectrophotometry 189
major electronic transitions within the ultraviolet a'Kd visible regions are:
---> o. n ---> a', n ----> =, and n----> x. These transitions are also shown in Fig
ure 8.8(B). The
with these transitions are given below in the decreasing order.
a ----> o > n ---> o* > ---> '> n ---> "
It is clear that the energy required for ----> transition is of a very high orde
r and ' short wavelengths are absorbed for these transitions. The organic compou
which all the valence shell electrons are involved in formation of sigma bond, t
herefore, do
the normal Ultraviolet region (180-400 nm). The usual spectroscopic
ues cannot be used below 200 nm because oxygen absorbs strongly at this range. T
these transitions, the entire path-length is to be evacuated. It is because of t
his that
below 200 nm is known as the vacuum ultraviolet region.
Energy required for n ----> * transition is lower than that of ----> a transition
. This type
transition usually takes place in saturated compounds containing one heteroatom
pair of electrons. Several molecules, including water, ether, saturated alcohols
, and
show absorption attributed to n * transitions.
Even lower energy is required for ----> n" transitions. These transitions take p
lace in the centres of molecules. These transitions are shown by alkenes, alkyne
s, carbonyl
cyanides, and azo compounds etc. Since these transitions are associated with a
energy, they take place at comparatively longer wavelengths easily obtained in a
spectrophotometer, n ----> n transitions usually have very high extinction coeffI
= 104 - 105 M-cm-) ff not forbidden by spin or symmetry selection rules.
n ---> * requires the least amount of energy. Therefore, these transitions frequ
ently appear
shoulders on the long-wavelength side of an absorption spectrum.
the above orbitals with ordering of their energies relative to each othe
r along with the
transitions are shown in Figure 8.8(B).
Anti-bonding electrons
Anti-bonding electrons
Non-bonding electrons
Bonding electrons
Bonding electrons
Figure 8.8(B) Schematic rnolecular orbital energy level diagram depicting relati

ve energy levels and allowed

By way of generalizing, it may be said that the absorption bands of almost all o
normally found in the near ultraviolet and visible regions are due to either n ---> "
n ----> * transitions. One can distinguish between n ----> n* and n ------> n* t
ransitions by
fat the extinction co-efflcients of the peaks at Xm. The n transitions are usual
ly symmetrical considerations and therefore have extinction coefficients of the
ust 10, whereas n ---> * transition which are rarely forbidden, have extinction
generally in the magnitude range of 103 - 104.
The transitions just discussed have been summarized in Table 8.2 along with info
the region of the spectrum in which they absorb.

Table 8.2
Types of electronic transitions

Region of electronic spectra

From a bonding orbital in the. ground state

to an antlbonding orbital of higher energy.
(a) o ----> (between orbitals)
(b) . g* (between orhitals)
Vacuum UV (e.g., ethane at 135 nm)
UV (e.g., ethylene at 180 nm, benzene
at 230 nm).

From a nonbonding orbital to an antlbonding

orbital of higher energy
(a) n ----> *
Near UV and visible (e.g., acetaldehyde
at 293 nm. nltrosobutane at 665 nm).
Far UV, or sometlme near UV (e.g.,
methyl alcohol at 174 nm, methyl
iodide at 258 nm).

From an orbital in the ground state to a very

high energy orbital (towards ionization)
Vacuum UV

Lastly, the structural character and the position of absorption maxima depend no
t only
upon the structure of the compound, but also on the nature of the solvent in whi
ch they exist.
The environmental factors that can cause detectable changes in the absorption sp
ectra are pH,
the polarity of the solvent or of neighboring molecules, and the relative orient
ation of ne/ghboring
absorbing groups.

Effects due to pH : It is the pH of the solvent which determines the ionization

state of a
molecule (see Box 1.8 and Tabie 1.7 for clear understanding). With a change in i
/ \ A
240 260 280 300
Wavelength (rim)

Figure 8.9. travlolet absorption spectra of 3'-CMP. The nucleotlde was obtained
by enzymatlc degradation of
tRNA. See the difference between the absorption at neutral and acidic pH. Also n
ote the ral
change In the absorption spectra at reglons other than the absorption maxOn

status, the absorption spectra may also change. Given below are the absorption s
pectra (Figure
8.9) of the pyrimidine nucle.otide CMP at neutral and acidic pH. Mark the differ
ence in the
absorption spectra of the same compound in the two states of ionization.
Polarity effects : In general, polar solvents shift the n =" transitions to shor
ter wavelengths and ----> transitions to longer wavelengths as compared to the g
as phase spectra (Figure 8.10). This is true for polar chromophores. For this re
ason polar solvents have
been used to distinguish between n n" and ---> =" transitions. Non-polar solvent
s, on the other hand, produce no such change.
260 270 280 290 300 310
Wavelength (nm)
Fure 8.10. Effect of solvent polarlty on the absorption spectrum of tyroslne. So
lid line represents absorption spectrum
in water while the dashed llne corresponds to 20% ethylene glycol The transition
here is n -- and
therefore the spectrum is shifted towards shorter wavelengths when water, which
is more polar, is used
s a solvenL
Orientation effects: The best example to understand orientation effect is theDNA
. Absorption
coefficient of a single nucleotide is greater than when the nucleotides are arra
nged in a singlestranded polynucleotide. The effect occurs because in a polynucleotide, the base
s are in close
proximity. The absorption coefficient decreases even further with a double-stran
polynucleotide because in this structure the bases are arranged in an even more
ordered manner.
The old definition of chromophore regards it as any system which is responsible
for imparting
color to the compound. Most of the nitro compounds are yellow in color. Clearly,
nitro group is
a chromophore which imparts yellow color. The modem day definition of chromophor
e, however,
akes use of the term in a broader scope. The chromophore is dejlned as any isola
ted covalently
bonded group that shows a characteristic absorption in the ultraviolet or the vl
s.lble region. Some of

the important chromophores are carbonyls, acids, esters, nitrile group of ethyle
nic or acetylenic
groups. Chromophores are known to be of twotypes.
(1) Chromophores containlng electrons and involved in ---> " transitions. For ex
ample, acetylenes and ethylenes (Table 8.3).
(//) Chromophores containing both and n electrons and involved in ---> " and n--> n" transitions. For example, carbonyls, nitrfles and azo compounds (Table 8.3

Awcochromes are groups which by themselves do not act as chromophores but whose
brings about a shift of the absorption band towards the red end of the spectrum
(longer wavelength).
Auxochrome is thus also known as a color enhancer. Important examples are -OH, OR,
-NH2, -NHR, -NR2, -SH etc. Auxochrome exerts its effects by virtue of its abilit
y to extend the
conjugation of a chromophore by sharing of the non-bonding electrons. This resul
ts in a new
chromophore which has a different absorption maximum and probably an enhancedext
In many instances the absorption and absorbance change either due to interaction
an auxochrome or due to change of the solvent. Four uch absorption and intensity
shifts are
known and are detailed below.
Bathochrom/c sh/Jt : This shift is due to the presence of an auxochr0me by virtu
e of which
the absorption maximum shifts towards higher wavelengths. Figure 8. I .YSuch an
shift is known as the red shift, or the bathochromic shift. Sometimes decreasing
polarity of the
solvent may also cause bathochromic shift
Hypsochromic Bathochrom/c
Wavelength {rim)
Figure 8.11 Different types of absorption and intensity shIjs
Hypsochromic shift :This is opposite of the bathochromic shift. This shift is du
e to removal
of conjugation and a change in the polarity of the solvent due to which the abso
rption maximum
is shifted towards shorter wavelengths (b/ue shift). See Figure 8.11.
Hyperchromic effect : This effect signifies an increase in the intensity of the.
maximum, or a change in the extinction coefficient to a higher value at the same
maximum. This effect is mostly due to the presence of an auxochrome {Figure 8.1

Hypochromic effect : This is the opposite of hyperchromic effect and is caused d

ue to
introduction of groups which cause distortion in the geometry of absorbing molec
ules. This
effect signifies that the intensity of the absorption maximum is lowered {Figure
8.1 I}.
In order to obtain an absorption spectrum it is necessary to measure the absorba
nce of a
substance at a known series of wavelengths. The instruments that are used to stu
dy the
absdrption or emission of electromagnetic radiation as a function of wavelength
are called

or spectrophotometers (colorimeters, if the instrument applies wavelengths only
visible range). More or less similar optical principles are employed in these in
are, however, some important differences in the specific components used in the
The essential components of a spectrophotometer include: (/) a stable and cheap
source, (tO a monochromator to break the polychromatic radiation into component
or "bands" of wavelengths, (///) transparent vessels {cuvettes) to' hold the sam
(/v) a photosensitive detector and an associated readout system (meter or record
available commercially involve quite a bit of complex arrangements, but all
represent variations of the block diagram in Figure 8.12.
Sample --- Detectr Amplifier &1
Holder " [ Recorder
Figure 8.12 Block diagram of a spectrometer
,adiant Energy Sources
Materials whlcL can be excited to h/gh energy states by a gh voltage electric di
scharge or
,by electric heating serve as excellent radiant energy sources. As the electrons
of these materials
return to the/r ground state, they em/t radiation of characteristic energies cor
responding to AE,
the energy difference between the excited and the ground energy levels. Some mat
erials have
numerous energy levels very close to each other. Consequently the wavelengths of
era/tied by these substances take the form of a continuum of radiation over a ve
ry broad region.
These materials would constitute an ideal source for absorption measurements if
the intensity
of all the wavelengths is alike. However, inpractice, this is not so and so we h
ave different
sources for different regions of the spectrum.
Sources of ultraviolet radton : Most commonly used sources of ultraviolet radiat
ion are
the hydrogen lamp and the deuterium lamp. Both the systems. :consist of a pair o
f electrodes
enclosed in a glass tube provided with a qumz window, Te glass tube is tflled wi
th hydrogen
or deuterium gas at low pressure. When a stabilized high voltage is applied they
ernit radiation
which is continuous in the region roughly between 180 and 350 nm. Xenon lamp may
also be
used for ultraviolet radiation, but the radiation produced is not as stable as t

he hydrogen ]amp.
Sources of visible radon :'lngsten filament Imp is the most commonly used source
visible radiation. It is inexpensive and emits continuous radiation in the regio
n between
and 2500 nm. Carbon. arc, which prov/des more intense v/sible radiation is used
in a small
number of commercially available instruments.
Sources ofnfrared radton : Nemst Glower and Globar are the most satisfactory sou
o infrared radiation. The Globar consists o a s/I/con carbide rod which when hea
ted to
approxLrnate]y 1200C, emits radiation in the 1-40 region. emst Glower employs a h
ollow rod of zh-'con/um and yttrium. It requires to be heated up to 1500C before
it emits radiation in
the range of 0.4-20 . Globar is more stable than the Nemst Glower.
Wavelength Selectors
All the sources discussed so far em/t continuous radiation over w/de range of wa
However, as pe/nted out earl/er in the chapter, the laws of absorption in the st
rictest sense
apply only to monochromatic radiation. Thus, absorption of nrrow band width will
show greater
adherence to Beer's law. Moreover, narrow band radiation will allow the resoluti
on of absorption
bands which are quite close to each other. Therefore, a narrow band width will g
o a long way in
increasing the sensitivity of absorbance measurement. Narrow band widths are mad
e possible
by using wavelength selector(s).

Biophysical Chemistry
'fffYgl'tlg'ffi sel'ecfors are of'two types, filters and mon0chromators.
lailters : Filters operate by absorbing light in all other regions except for on
e, whlch they
reflect. Gelatin filters are made of a layer of gelatin, colored with organic dy
es and sealed
between glass plates. Most modern filter instruments, however, use tinted-glass
filters. Filters
resolve polychromatic light into a relatively wide bandwidth of about 40 nm and
are used only
in coldrimeters. One disadvantage of glass filters is their low transmittance (5
Monohromators : As the name suggests, a monochromator resolves polychromatic rad
into Its individual wavelengths and isolates these wavelengths into very narrow
bands. The
essential components of a monochromator are: (i) an entrance slit whlch admits p
light from the source, (tO a collimating device such as a lens or a mirror whlch
collimates the
polychromattc light on to the dispersion device, (No a wavelength resolving devi
ce like a prism or
a grating which breaks the radiation into component wavelengths, (iv) a focussin
g lens or a
mirror, and (v) an exit slit which allows the monochromatic beam to escape. The
entire assembly
is mounted in a light-tight box. For obvious reasons, all the components in a mo
assembly must not absorb in the range of wavelengths which are to be studied. A
employing a prism for dispersion is shown schematically in Figure 8.13. The effe
ctive band
width of the light emerging from the monochromator depends mostly upon the dispe
rsing element
(prism or diffraction grating) and the slit widths of both the entrance and the
exit slits. Narrow
slit widths isolate narrow bands. However, the slit width also limits the radian
t power which
reaches the detector. Since the effectiveness of the resolving element is of pri
mary importance,
the two kinds most widely used, namely, prlsms and diffraction gratings are cons
idered below.
.... lens

Entrance slit
Exit slit
l%3ure 8.13 Pasta monochromator
Prisrr" A prism disperses polychromatic light from the source into its constitue
nt wavelengths
by virtue of its ability to refract different wavelengths to a different extent;
, the shorter wavelengths
are diffracted most. The degree of dispersion by the prism depends upon (/) the
apical angle of
the prisln (usually 60), and (it) the material of which It is made. Since it disp
erses the short
wavelengths more and long wavelengths less, the wavelengths at the red end of th
e spectrum
are not fully resolved; they are said to be crowded. This is a major disadvantag
e of a prism.
Two types of prisms, namely 60 Cornu quartz prism and 30 Littrow prism are usually
employed in commercial instruments. The latter is preferred, Simple glass prisms
are used for
visible range. For ultraviolet region silica, fused silica or quartz prism are u
sed. F1ourlte is used
in vacuum ultraviolet range. Ionic crystalline materials are used in the infrare
d region. Some
examples are NaCI, KBr, CsBr, and the mixed crystalline material commonly called

Figure 8.14 Diffraction grating and the dispersion of polychromatic radiation
Gratings : Gratings (Figure 8.14) are often used in the monochromators of
spectrophotometers operating in ultraviolet, visible, and infrared regions. The
grating possesses
a highly aluminized surface etched with a large number of parallel grooves which
are equally
spaced. These grooves are also known as lines. A grating may have anywhere betwe
en 600 to
2000 lines per mm on the surface depending on the region of the spectrum in whic
h it is
intended to operate it. The principle behind dispersion of radiation by a gratin
g is that it resolves
light into its component wavelength by virtue of constructive reinforcement and
interference of radiation reflected.
Very often, the monochromator consists of both, a prism and a grating. The prism
, placed
before the grating is known as the foreprism. It preselects a portion of the spe
ctrum which is
then allowed to be diffracted by the grating. This arrangement allows resolution
of a single
wavelength. The major advantage of diffraction grating monochromators is that th
eir resolving
power is far superior to that of prisms. In addition they.yield a linear resolut
ion of spectrum
which is not possible when prisms are used.
Sample Containers
Samples to be studied in the ultraviolet or visible regionare usually gases or s
olutions and
are put in cells known as cuvettes. Spectra of gases are taken using enclosed ce
lls, with an
evacuated cell as a reference. Standard path-length of gas cells is usually 1 mm
but cells with
path-length of 0.1 to 100 mm are available for special cases. Sometimes spectra
of solids may
be taken directly. For this purpose, the solids are generally in the form of pel
lets. The pellets are
kept in pellet holders for absorption measurements.
Most of the spectrophotometric studies are made in solution. The solutions are d
in cells known as cuvettes. Cuvettes meant for the visible region are made up of
either ordinary
glass or sometimes quartz. Since glass absorbs in the ultraviolet region, quartz
or fused silica
cells are used in this region. Standard path length of these cuvettes is usually
1 cm. However,
cuvettes of path-length of I mm to 10 cm are available for special purposes. The
surface of the
cuvettes must be kept scrupulously clean; fingerprint smudges and traces ofprevi
ous samples,

by causing interference in the optical path, might cause serious errors in quant
itative measurements. Rinsing with water should normally clean quartz or glass c
uvettes. If, however,
the dirt is abnormally tenacious, sulfonic detergents or nitric acid may be used
. The use of
rectangular cuvettes in spectrophotometers effectively curtails the chances of d
irt being
transferred during handling. The two sides of such ceils through which the light
passes are
precision ground and polished to be optically flat The other two sides are rough
ground glass
and the cell may be handled by these.
Since most of the spectrophotometric studies are made in solutions, the solvents
prime importance. The most important factor in choosing the solvent is that the
solvent should
not absorb (opt/ca//y transparent) in the same region as the solute. However, as
we have discussed
earlier, one should also take into consideration the effect that the solvent may
have on the

Bophysical Chemistry
absorption spectrum of the solute. The solvents which can be used in the UV and
visible region
are water, methyl-, ethyl-, isopropyl-alcohols, chloroform, hexane etc. Some oft
en used solvents
with their upper wavelength limit of absorption are given in Table 8.4.
Table 8.4 Upper wavelength absorption limits of some solvents
Upper wavelength limit (nm)

Carbon tetrachloride


Infrared gas cells are made up of glass. These glass tubes possess NaCl, KBr, or
windows for the passage of infrared radiation. The cells have varying path lengt
h; from a few
centimeters to several meters, The latter is achieved by multiple reflections wi
thin the cell.
Liquids are studied as thin films or solutions between NaCI, KBr, or CaF2 plates
. The distance
between the plates (path length) is usually 0.005 to 1 mm. Solids are examined i
n the infrared
as pressed KBr discs or as suspensions in high molecular weight liquids ("mulls"
Detection Devices
Most detectors depend on the photoelectric effect, where incident light (photons
) liberates
electrons from a metal or other material surface. Some sort of external circuitr
y collects these
electrons and measures their number as current. The current is then proportional
to the light
intensity and therefore a measure of it. Important requirements for a detector i
nclude (i high
sensitivity to allow the detection of low levels of radiant energy, (ii) short r
esponse time, (iii) long
term stability, and (/v) an electronic signal which is easily amplified for typi
cal readout apparatus.
Change in thermal energy, however, is the basis of detection for infrared radiat
Consequently detection devices used for this region are different than those ope
rating in the
ultraviolet and visible regions.
Ultraviolet and visible radiation detectors : There are three basic kinds of det
ectors in this
region. Photocells, phototubes, and photomultiplier tubes.
(i) Photovoltaic or barrier layer cells : It employs semiconductor materials.
Semiconductors are crystalline, and the bonding electrons between the crystals o
f some
semiconductors can be knocked out of their positions by incident radiation. Alth
ough a number

of materials are used in photocells (cadmium sulphide, silicon, selenium) seleni

um based
photocells are most common. A typical photocell consists of a thin coating of se
lenium over a

thin transparent silver film on a steel base. This arrangement ensures that elec
trons pass
easily from selenium to silver but not in the reverse direction. Due to the inab
ility of electro ,ns to
move away from the silver film, the silver acts as the collecting electrode for
electrons liberated
from selenium by the incident radiation. The steel plate functions as the other
electrode. The
current flowing between the two electrodes is then measured by a microammeter. A
diagram of the cell is given in Figure 8.15.
Steel back-plate
Figure 8.15 Selenium based photovoltalc cell
Photocells have a long life and are inexpensive and reliable. They are widely us
ed in
colorimeters but their use in spectrophotometers is becoming limited.
(ll) Phototubes or photoemiasive tubes : The components Of a phototube include(A
} an
evacuated glass envelope (with a quartz window), (B) a semi-eylindrical cathode
whose inner
surface is coated with alkali or alkaline earth oxide, and (C) a centrally locat
ed metal wire
mode. A potential difference of approximately 90 volts is applied across the ele
ctrodes. The
quartz window allows the passage of radiation which strikes the photoemissive su
rface of the
cathode. The energy of the photon is transferred to the loosely bound electrons
of the cathode
surface. The electrons become excited and finally leave the surface and travel t
owards the
anode causing current to flow in the circuit, If the electron collection is 100%
efficient, the
phototube current should be proportional to the light intensity. A schematic dia
gram of a
phototube and the associated circuitry is provided in Figure 8.16.

Evacuated glass
I Anode
lgure 8.16 Dlram of a photoemislve the. R stands for res/stance
Phototube currents are quite small and require amplification.This is usually acc
by placing a high resistance (R in Figure 8.16) in the phototube circuit.
(|iI) Pht.multl[r : These detectors are designed to amplify the initial photoele
effect and are suitable for use at very low light intensities. A photomultiplier
consists of (A) an
evacuated glass tube into whlch are sealed the cathode and the anode, and (B) ad

Biophysical Chemtstr
intervening electrodes known as dynodes. The arrangement is shown in Figure 8,17
. The external
circuitry is arranged so that a high voltage (1000 volts) exists between the ano
de and the
cathode. As the radiation strikes the photocathode, electrons are liberated and
the applied
potential difference accelerates the electrons towards the first dynode. Each su
ccessive dynode
is at a higher electrical potential and thus acts as an amplification stage for
the original photon.
The applied voltage causes sufficient electron acceleration to knock out other e
lectrons from
each dynode surface. The liberated electrons are dragged onto the next dynode wh
ere more
electrons are released and this process goes on as a cascade till the last dynod
e. By the time the
electrons arrive at the collecting anode, the initial photoelectric current is a
mplified by a factor
of approximately 106. In practice, photomultiplier tubes are used only for low l
ight intensities.
At higher light intensities, due to their great amplification power, photomultip
liers exhibit great
instability. Inspire of this tendency to be unstable, photomultipliers are the d
etectors of choice
in all modern spectrophotqmeters.
High voltage
Figure. 8.17 A photomultiplier tube
(iVl Phottditdes : Photodlodes are semiconductors that change their charged volt
(usually 5 VI upon being struck by Light. The voltage change is converted to cur
rent and is
measured. A photodiode array is a two-dimensional matrix composed of hundreds of
semiconductors spaced very closely together. Light from the instrument is disper
sed by either
a grating or a prism onto the photodiode array. Each position of diode on the ar
ray is calibrated
to correspond to a specific wavelength. Each diode is scanned, and the resultant
change is calculated to be proportional to absorption. The entire spectrum is es

sentially recorded
within milliseconds.
Near infrared detectors : These are usually photoconductive ceLls which detect i
radiation in the range 0.8- 3.0 . The sensing element is a semiconductor (german
lead sulphide, or lead teLlurlde). Upon illumination with radiation of appropria
te wavelength,
the electrons of the semiconductor are raised to conduction bands. This causes a
drop in
electrical resistance. Consequently, if a small voltage is applied, a large incr
ease in current can
be noted. The resistance of the system is such that the current may be amplified
and finally
indicated on a meter is recorded.
Middle and far infrared detectors : When middle and far infrared photons are abs
their energies are convened to thermal energy leading to a rise in temperature.
Obviously then,
rapid response thermometers such as thermocouples, resistance thermometers (bolo
and gas thermometers (pneumatic or Golay ceils) are used as detectors in this re
Thermocouples used in the infrared receivers typically consist of a blackened go
ld lead-teLlurium
metal pin junction which develops a voltage that is temperature dependent. To av
oid heat loss,
the the.rmocoupl is usually enclosed in a shielded evacuated housing. This preven
ts error
causing temperature fluctuations.

Wave number (cm-1)
Source of radiation
Amplification and Readout
Radiation detectors generate electronic signals which are proportional to the tr
light. These signals need to be translated into a form that is easy to interpret
. This is accomplished
by using amplifiers, ammeters, potentiometers, and potentiometric recorders.
Components of UV-visible and i.nfrared spectrophoometers have been summarized in
Tables 8.5 and 8.6 respectively.
Table 8.5 A summary of components of spectrophotometers and colorimeters
Region of electromagnetic spectrum

Radiation source
Optical system
Material used in the
Optical system
Hydrogen or deuterium lamp
Prism or diffraction grating, or
a foreprism grating double
Quartz or fused silica,
Tungsten filament lamp,

carbon arc (less used)

Tinted glass filters or interference

Sample holders
Quartz or fused silica, rectangular
Round glass cells.
Photovoltaic cell.

Table 8.6 A summary of the components of infrared spectrophotometers
Region of electromagnetic spectrum
4000 200 ,

Tungsten filament
Coil of Nichrome
wire, or Nernst
Glower, or Globar.
High pressure
mercury arc lamp.

Optical system
Quartz prisms or prism
grating double monochromator
Diffraction gratings


with a fore-prism
diffraction gratings.

Optical elements are made up of ionic crystalline materials like NaCI,

KBr, CsBr, or KRS-5.

Lead sulphide, or
lead telluride photoconductive
Thermocouple, ther- Pneumatic or Golay
mistor, or pyroele- cells, pr bolometers.

Bphysol Chemtry
Double Beam Operation
Voltage fluctuations inducing fluctuations in the source intensity can cause lar
ge scale
errors in spectrophotometer operation. To obviate this situation, double beam sp
ectrophotometers have been designed (Figure 8.18}. Double beam instruments employ som
e type of
beam splitter prior to the sample containers. One of the split beams passes thro
ugh the "blank"
or reference cell while the other passes through the sample cell. The two transm
itted beams are
then compared either continuously or alternately several times in a second. The
double beam
device, therefore, compensates for fluctuations in the source intensity, the det
ector signal, and
amplifier gain by observing the differences in signal between reference and samp
le at virtually
the same time. The modifications described above make the double beam devices mo
sophisticated mechanically and electronicaliy as compared to the single beam dev
ices. Obviously,
the double beam devices are expensive.

Mirror .,

,,. Mirror

Chopper ple
Open sector
Rotating sector

Figure 8,18 Optical arrangement of a double-beam instrument. A rotaW sector chop

per s also shown.

The beam splitting usually occurs after the monochromator. Rotatingsector mirror
s are
commonly used for splitting or *chopping" the beam (Figure 8,18). The chopped be
ams reach
sample and reference and subsequently to the detector at intervals which depend
upon the
rotational frequency of the chopper. The device then records the ratio of the re
ference and
sample signals.
Dual Wavelength Spectrophotometer
Some metal chelators absorb at One wavelength before chelating the metal ion and
at a completely different wavelength after the chelation has taken place. An exa
mple is that of
arsenazo III, a calcium chelator. This chelator absorbs at 675 nm before binding
to calcium and
at 685 nm after the binding has taken place. If this chelator is incubated with
a biological
system and the absorbance of the chelator is measured simultaneously at the wave
length pair
675 nm. 685 nm, the ratio of the two absorbances can provide an idea of the calc
concentration in the given biological system. Similarly, in many reaction kineti
c studies it is
necessary to monitor the absorbance changes of two chemical species simultaneous
ly. In many
experiments it is necessary to measure the relative absorbances of proteins {280
nm} and
nucleic acids (254 nm} simultaneously. For all these experiments it is necessary
to use dual
wavelength spectrophotometer.

Dual wavelength spectrophotometry refers to the photometric measurement of a mat
by passing radiation of two different wavelengths through the same sample before
reaching the
detector. Light from two different sources is allowed to be resolved into two di
fferent wavelength
with the help of a pair of diffraction gratings. Subsequently the two beams of d
ifferent wavelengths
are made to pass through the same sample by a complex arrangement of a large num
ber of
mirrors (Figure 8.19). Only a single detector, which is always a photomultiplier
tube, is used.
Light source

Figure 8.19 Optical arrangement of a dual wavelength spectrophotometer
From the above it is clear that dual wavelength spectrophotometry provides infor
from two wavelengths per unit time. All other factors being equal, the resultant
data should be
more useful than data from a double beam spectrophotometer.
Photometry being a very versatile technique, has diverse applications, only a fe
w of which
are summarized below.
Qualitative Analysis
Visible and ultraviolet spectra may be used to identify classes of compounds in
both the
pure state and in biological preparations. This is usually done by plotting abso
rption spectrum
curves. Since these curves are specific for a class of compounds, a knowledge of
the absorption
spectrum can help in identification of a substance in biological milieu. Table 8

.3 provides
information about the absorption ranges of the most commonly occurring functiona
l groups of
It is quite beyond the scope of this book to deal with the details of identifica
tion of an
unknown compound or the assignment of structure on the basis of its absorption s
pectrum (for
details the student is referred to literature cited at the end of this chapter).
However, a brief
discussion is possible. Before attempting to interpret the absorption spectrum o
f a given
compound, suffioient chemical information about the substance such as the elemen
ts present
should be known. Absorption by a compound in different regions gives some hints
of its structure.
Thus, compounds which do not absorb in 220-280 nm region are usually aliphatic o
r alicyclic
hydrocarbons or their derivatives. Sometimes they might be simple olefinic compo
unds. If the

Biophysical Chemistry
compound absorbs between 220-250 nm range, it will usually contain two unsaturat
ed linkages
in conjugation. Absorption in this range could also be due to benzene derivative
s. Presence of
more than two conjugated double bonds usually gives rise to absorption in the ra
nge 250-330
nm. It is a fact that as the number of conjugated double bonds increases, the ab
sorption range
is shifted more and more to higher wavelengths. Thus, -carotene, a precursor of
vitamin A has
eleven double bonds in a conjugated system and appears yellow because the light
in visible
region (450-500 nm) is being absorbed by it. Complex systems will give rise to a
curves with several maxima, each of them possessing a characteristic shape and r
ange indicating
the presence of the particular functional group.
As an example to prove how valuable absorption data can be, one can cite the exa
mple of
vitamin K whose structure was determined by the use of its spectral data. The ab
spectrum of vitamin K has the following absorption maxima: 249 nm, 260 nm, and 3
25 nm.
The maxima around 250-330 nm are characteristic ofa naphthaquinone. Chemical man
and comparison of K spectra with several model compounds indicated that the posi
tions of the
absorption maxima were similar to those of 2,3-dialkyl- 1, 4-naphthaquinone. The
structure of
vitamin K determined later is as below:
Also see Box 8.3 for further discussion.
Abetter example, perhaps, is afforded by the four nucleotides (Figure 8.20). If
you dissolve
the four nucleotides GMP, CMP, AMP, and UMP in aqueous solution at neutral pH, t
he absorption
maximum at highest wavelength for GMP occurs at 255 nm, for CMP at 271 nm, for U
MP at
262 nm, and for AMP at 259 nm. With just these absorption maxima, one can tentat
identify GMP from CMP since their absorption maxima are quite removed from each
However, it would be difficult to distinguish between AMP and UMP owing to their
spectra being quite close. However, one can resort to changes in pH of these sol
utions and the
data so obtained can help us in identification. A look at Figure 8.20 and the te
xt therein will
explain the point.

pounds o
wv - , .7 6"0

Biophysical Chemistry

behavior of
be ,zero
fthe pH is now raisedbeyondt 0.0, what do you
are rosine.
rise in absorption at295 nm will be seen because these tyros nes w I be sh elded
, f only two
tyrosines an; On the surface and two buried in the folds, riein absorpt on at 29
5nm w I only
be hail of what is expected for four tyrosines. Inthe last Case if the pH is rai
sed tosay 13.(,
all tyrosines wi be available for titri0n becausethe protein is now denatured.
largescale unfold ng of the protein
were buried when the protein was in the
surface brings about, a change n the
proteins: Whenever the substrate orthe competitive inhibitor
region or makes certain aminc acid residues
In doing so, it might quite frequ
spectral changes are
obtained with other stud es such as the so vent
quite a bit of information about the structure of the active stem ght be
studies. Solvent
of lysozyme, one observes
maximum of tryptophan is shifted to a longer wavelength.
pectral change corresponds with only one tryptophan residue.. If the
solution of the enzyme with the substrate is again studied by solvent perturbati
on method,
only'three tryptophan residues seem to be on the surface. The conclusion is quit
e Obvious
really. It seems that the e.nzyme has one tryptophan residue in the active site
which might be
involved in the binding. Studies with x-ray diffraction confirm this conclusion.
text, can you answer the followingquestions?

A protein solution is being heated and its spectral characteristics are
being determined at
250 nm (., for cysteine). At:45oc the extinction of the system suddenly increase
s. This
increase plateaus Out at 55oc. What conclusion should you draw?
A DNAsolution is being cooled after it was heated..Tle ext nction at 260
nm shows sudden
drop. What happened?

Bophystcal Chemistry
Quantitative Analysis
In developing a quantitative method for determining an unknown concentration of
a given
species by absorption spectrometry, the first step is the choice of the absorpti
on band at which
the absorbance measurements are to be made. If the chemical species of interest
has already
been researched upon, its .ultravlolet/vlsible absorption spectrum would be avai
lable in the
literature. If this is not the case, the absorption spectrum of the chemical spe
cie can be dctermcd
experimentally by means of a scanning double beam spectro-photometer. A suitable
band is then selected from within the absorption spectrum for quantitative measu
Absorptivity at any given wavelength is constant and is an inherent characterist
ic of the absorbing
substance. Most of the organic compounds of biological interest absorb in the UV
-visible range
of the spectrum. Thus, a number oflmportant classes of biological compounds may
be measured
semi-quantitatively using UV-visible spectro-photometers. Nucleic acids at 254 r
un and prote/n
at 280 nm provide good examples of such use. The absorbance at 280 um by protein
s depends
on their tyrosine and tryptophan content. All proteins will therefore have a dif
ferent absorbance
at 280 nm and may be only accurately assayed if a calibration curve {see Box 8.2
} is plotted for
the pure protein.
What do we mean by selecting a suitable wavelength or alsorption band? There are
rules for the choice. These may be summarized as under (Figure 8.21).
1. Choose an absorption peak with the greatest possible molar absorptivity.
2. Choose a relatively broad peak.
Choose a peak that is as far as possible from the absorption peaks of co
interfering chromogens. The same is true for solvents and other reagents used the
absorption band chosen should be as far away as possible from the absorption pea
of the solvent and the reagents.
Figure 8.21. Choice of the absorption band for quantitative analysts.

X has a small absorption coefficient. Quantitative analysis should normally not

be carried
out here. X has the highest absorption coefficient but the peak is too sharp. '3
has a sufficiently
high absorption coefficient (though lower than .) and the peak is broader than .
. k3 then
becomes the best choice. Of course, this must not correspond to absorption peaks
of other
interfering chromogens or the solvent.

The quantitative assay of enzyme activity is carried out most quickly and conven
the substrate or the product is colored or absorbs light in the ultraviolet rang
e because
or disappearance of a light absorbing product or substrate can be followed
which gives a continuous record of the progress of the reaction on a
chart recorder. Other light absorbing or light scattering substances must either
be absent
by appropriate blank measurements. Example can be cited of the measurement
of the enzyme lactate dehydrogenase, which is engaged in the transfer of electro
ns lactate to NAD*. The products of the reaction are pyruvate, NADH, and a proto
Lactate + NAD - Pyruvate + NADH + H
One of products, NADH, absorbs radiation in the ultraviolet range at 340 nm whil
e its
NAD, does not. No other component of the reaction, either substrate or
tbsorbs at 340 rim. It is thus very obvious that the progress of the reaction in
llrection can be followed by measuring the increment in light absorption of the
nm in a spectrophotometer.
simplicity and convenience of optical assays prompts their use in following the
of an enzymatic reaction in which neither the substrate(s) nor product(s) have a
absorption maxima. Such type of enzyme reactions are coupled to some other
reaction which has an easily measured optical change. An example of the reaction
hosphoenolpyruvate and ADP yielding pyruvate and ATP catalyzed by pyruvate kinas
Phosphoenolpyruvate + ADP v- Pyruvate + ATP
Although neither the substrates nor products of this reaction absorb light in th
e 300-400
the reaction is easily measured if lactate dehydrogenase and NADH are added to t
large excess. By manipulating the system in such a manner we obtain the followin
I reactions, which have the common intermediate pyruvate:

Phosphoenolpyruvate + ADP Pyruvate + ATP

Pyruvate + NA{)H + H -- Lactate + NAD
Since we have added a large excess of NADH to the system, the system now absorbs
at 340
But from the reactions written above it is clear that for each molecule of pyruv
ate formed
first reaction, a molecule of NADH is oxidized to NAD in the second reaction when
converts pyruvate to lactate. Since NAD does not absorb at 340 nm the absorbance
on decreasing with increased pyruvate generation. Such measurements are known as
assays and are fairly routinely used.
Weight Determination
If a compound forms a derivative ith a reagent which has a characteristic absorpt
' at a wavelength where the compound does not absorb, then the extinction
f the derivative is usually the same as that of the reagent. Although the extinc
of the absorption band remains constant in all the derivatives, the optical dens
is different for compounds of different molecular weights. The molecular weight,
M, of the
be readily calculated on the basis of its absorption data.
M = awb/OD
or M= 10a/E IL

Biophysical Chemistry
where w is the weight of the compound in grams per litre, and b is the pathlengt
Molecular weights of amine picrates, sugars, and many aldehyde and ketone compou
have been determined by this method. The method has an accuracy of+ 2%. Molecula
r weights i
of only small molecules may be determined by this method'.
Study of Cis-Trans Isomerism
Sine geometrical isomers differ in spatial arrangement of groups ab.out a plane,
absorption spectra of the isomers also differs. The trans-isomer is usually more
elongated than
its cis counterpart. It is usual therefore, for the trans-isomer to have a highe
r wavelength of
maximum absorption and also to have a higher ema' Absorption spectrometry can th
us be
utilized (indeed it has been) to study cis-trans isomerism.
Other Physicochemical Studies
Over the years, spectrophotometry (UV-VIS) has been used to study such physicoch
phenomena as heats of formation of molecular addition compounds and complexes in
determination of empirical formulas, formation constants of complexes in solutio
n, hydration
equilibria of carbonyl compounds, association constants of weak acids and bases
in organic
solvents, tautomeric equilibria involving acid base systems, protein-dye interac
tions, chlorophyllprotein complexes, vitamin A aldehyde-protein complex, association of cyanine-dy
determination of reaction rates, determination of labile intermediates, and diss
ociation constants
of acids and bases.
Control of Purification
This is one of the most important uses of UV-VIS spectrophotometry. Impurities i
n a
compound can be detected very easily by spectrophotometric studies by experiment
ally verifying
whether the given compound shows an absorption maxima not characteristic of it.
Thus carbon
disulphide impurity in carbon tetrac, hloride can be detected easily by measurin
g absorbance at
318 nm where carbon disulphide absorbs. Similarly benzene impurity in commercial
alcohol can be detected by measuring absorbance at 280 nm where alcohol (210 nm)

does not
absorb. A lot many commercial solutions are routinely tested for purity spectrop
Difference Spectroscopy
Difference spectroscopy provides a sensitive method for detecting small changes
in the
environment of a chromophore. It may also be used to demonstrate ionization of a
leading to identification and quantitation of various components in a mixture. D
spectroscopy involves comparison of absorption spectra of two samples which diff
er only slightly
in their physical states. The common features in the spectra cancel out and the
bands which
are recorded can be interpreted in terms of known differences between the sample
Difference spectroscopy was developed by Chance and Williams in course of their
on electron transport chain proteins in the mitochondria. The technique subseque
ntly provided
much needed information about the state and sequence of the electron transport p
Difference spectroscopy has also been utilized in toxicology laboratories for an
alysis of many
toxic drugs. Example can be cited of barbiturates which show characteristic chan
ges in absorption
spectra between their keto and enol forms. Moreover, difference spectroscopy is
a necess.ary
tool to study globular protein conformation.
Turbiflimetry and Nepheloraetry
Bacterial Or any other particulate suspension makes the liquid turbid. This is d
ue to
Tyndall effect which addresses itself to light scattering by colloidal particles
(see chapter 3).
While. the liquid in this system might absorb at a particular wavelength, the pa
rticles scatter

the incident light. If, then, radiation of a wavelength which is not absorbed by
the liquid is
made to pass through this suspension, the apparent absorption will be solely due
to light scattering
by the particles. The light transmitted by the suspension will have lesser inten
sity than the
light which was incident. Measurement of the intensity of this transmiR, ed ligh
t will allow one to
have an idea of the number of particles in the suspension. Using this technique,
known as
turb/d/metry, one can arrive at a fair approximation of the number of particles
in a given
suspension. This technique is routinely used to measure the number of bacteria i
n a given
suspension. The wavelength used for this purpose is 600 nm. The technique, howev
er, is very
tedious to standardize as the particle size is critical for accuracy (larger par
ticles scatter more
light as compared to smaller particles; thus contamination of small particle sus
pension by a
small number of large particles will give a value far in excess of the number of
small particles
actually present). The principle of turbidimetry is shown diagrammatically in Fi
gure 8.22(A).
Nephelometry is a term many times used synonymously with turbidimetry probably b
the two techniques are based on a common principle. The major difference between
and nephelometry is that while the former measures the intensity of transmitted
light coming
out of a suspension, the latter measure the intensity of the light scattered by
the particles in
suspension. The scattered intensity is usually measured at right angles to the d
irection of
incident light. For low concentration this method is more sensitive since zero c
oncentration is
represented by a dark background. On the other hand zero concentration in turbid
imetry means
full illumination. The principle of nephelometry is diagrammatically shown in Fi
gure 8.22(B).
Nephelometry is commonly used for estimating the concentration of microorganisms
. It is also
used for waste-water analysis as well as in the beverages and pharmaceutical ind
ustries to
evaluate the amount of haze present in the preparations.
Sample cell
containing suspension
[ (A) f ,Photocell

Light Slit
Photocell detector
Figure 8.22 Principle of turbidimetry and nephelometry.
(A) Light is scattered by particles in the suspension in sample cell. The transm
itted light is therefore of
a weaker intensity. A turbidimeter measures the intensity of this transmitted li
ght and a calibration
cw' beaueen transmitted intensity and particle concentration can be drawn.
(B) Nepheiometry measures the intensity of scattered light rather than transmitt
ed light.
As evident from the electromagnetic spectrum diagram, infrared radiation is of m
higher wavelength as compared to the ultraviolet and the visible region. Consequ
electromagnetic radiation of this region has considerably lower energy. Infrared
radiation is,
therefore, not associated with electronic transitions; rather, it is associated
with vibrational
transitions of molecules as we will see below.

In-plane deformations
Scissor and Rock
Out-of-plane deformations
and Wag
Figure 8.23 Types of vibrations : (A) Stretching, (B) Bending
All the molecules are continually vibrating. These vibrations are of two types.
The bond
distances between the atoms in a molecule fluctuate to about 0.5A. It should be r
that while this increase or decrease in bond length is occurring, the atoms rema
in in the same
bond axis. These vibrations are known as stretching vibrations (Figure 8.23{A)).
The other type
of molecular vibration, known as bending vibration (Figure 8.23(B)) involves cha
nges in the
positions of the atoms with respect to the original bond axis. Such variations i
n bond angles
may be about 0.5. Vibrational transitions are low energy transitions and these ene
rgy levels
correspond to the energies of electromagnetic radiation in the infrared region o
f the spectrum.
Consequently, a molecule can absorb infrared radiation of an appropriate frequen
cy, accompanied
by promotion of the molecule to an excited vibrational state. The presentation o
f infrared spectra
differs from UV-visible spectra in that wave number is used in this region rathe
r than wavelength;
infrared spectra are typically presented as percent transmission (transmittance
x 100) versus
wave number.
Cslculatlon of Vibrational Frequencies
The vibrational frequency of a bond can be calculated with the help of Hooke's l

which correlates frequency with bond strength and atomic masses.
2n mim2/(m, +rni)
where v is the frequency, k is the force constant of the bond and m and m2 are t
he masses of
the two atoms involved in bond formation. The quantity mrn/(m+ m2) is often expr
essed as m,..
the reduced mass of the system.
Let's try and calculate the approximate frequency of the C--H stretching vibrati
on from
the data given below.
k=5.0 x 10Sgs-2
mass of carbon atom = 20 x 10-24.g


= 9.3x10asDividing the above value with the speed of light we get the value in wave number
which is
3100 cm-L When you experimentally determine the vibrational frequency for C--H s
you find it ranging from 2800 to 3100 depending on the compound you choose. This
observation tells us that the vibration of any given bond will be affected by th
e other atoms and
their bonds that it coexists with.
If you look at the above equation, it should be easy to surmise that the vibrati
onal frequency
of a bond should increase with the strength of the bond. Also when the reduced m
ass of the
system decreases, the frequency should increase.
The foregoing may make us think that we can predict the frequencies of vibration
for a
given bond. To an extent we can. For example, double bonds are stronger than the
single. So we
can safely say that C--C should have a frequency lower than that of C---C. This
we predicted on
the basis of the bond strength. On the basis of mass we may hazard a guess that
C--H should
absorb at a higher frequency as compared to CmC since the latter has a higher re
duced mass.
However, we are stepping onto treacherous territory if we start predicting frequ
encies on the
basis of masses without knowing the force constant. One example will prove this.
Given below
are a few bonds. Guess which of these bonds will absorb at the highest frequency
solely on the
basis of the reduced masses.
C--H ,. N--H, O--H, and F--H.
Solely on the basis of masses your answer must have been that the absorption fre
falls along the series given. The actual observation is quite to the contrary. T
he frequencies rise
along the series. They rise because all along the series the electronegativity r

ises and with it

rises the force constant.
Thus, although it is possible to predict the frequencies in a general manner tak
ing the
help of Hooke's law, some caution .must be exercised in doing so.
Modes of Vibration
The theory of molecular vibrations predicts that an asymmetrical molecule which
n atoms will have 3n - 6 modes of fundamental vibrations. This means that a mole
cule like CO2
o should possess (3 x 3) - 6, i.e., 3 fundamental modes of vibrations. Likewise,
methane should
have 9 and ethane 18.
Figure 8.23 shows vibrational modes available for AX systems (any atom joined to
other atoms, e.g., NH2, NO2, CH2 , etc.). Normally each vibration mode absorbs a
t a different
frequency. Thus a CH group may give rise to two C--H stretch bands, symmetric an
d asymmetric.
However, this is not always true. There will be some vibrations which may absorb
at the same
frequency. Naturally their absorption bands will overlap. Such vibrations are ca
lled degenerate.
Also, there are vibrations whose absorption frequency may lie outside the normal
region examined.
So far we have been talking about vibrations which are dubbed fundamental. There
other frequencies at which bands appear in.an infrared absorption spectrum. Some
of these
bands are called overtone bands. These bands are generated by modulation of fund

Biophysical Chemistry
vibrations, Thus, strong absorption at 800 cm-I may give rise to a weaker absorp
tion at 1600
cm-; a strong absorption at 1700 cm- may give rise to a weaker absorption at 340
0 cm-I. Another kind of modulation is when two different frequencies, x and y, i
nteract with each other
(combinations). Such interactions may take place either as x + y, or as x - y. T
he resulting
weaker absorptions are called beats.
You would agree that combination bands are unique to a compound. Since each comp
has a particular arrangement of atoms, a particular kind of combination can only
occur in that
compound and in none other. The combination bands, therefore, assume extreme imp
because they may be the signature or the fingerprint of a given compound. A larg
e number of
these combination bands fall in the region between 900 cm- and 1400 cm-. For thi
s reason, this region is dubbed the fingerprint region.
In summary we can say as under.
Any given bond in a molecule does not exist in isolation. Thus if we refer to C-H stretch
frequency, we cannot hope that this particular bond is in isolation from the res
t of the molecule.
If this bond exists within a given molecule, the other bonds in that molecule, t
he other atoms
present in that molecule are bound to have an effect on the way this bond behave
s. They are
going to have an effect on the exact frequency it absorbs. Thus a C--H bond in o
ne compound
may vibrate at a slightly different frequency when compared to a C--H bond in a
molecule. We may therefore say that the frequencies of molecular vibrations do n
ot depend just
on the masses of the atoms concerned and the strength of their bonds, but also o
n the
arrangement of atoms. The vibrational frequencies therefore reflect the structur
e and
conformation of a molecule. Since the atoms involved and therefore their masses,
the strength
of their bonds, and the arrangement of atoms differ from compound to compound (u
nless the
compounds are enantiomers),it may be said that the infrared spectra of no two co
mpounds are
alike. Conversely, substances that give-the same infrared spectra are identical.
The infrared
spectrum of any molecule is thus absolutely specific and is therefore known as t
he 'fingerprint'
of the compound. -..
The molecules in which biochemists are more interested are the biological macrom
(proteins, nucleic acids, polysaccharides). Since these molecules have a very la

rge number of
atoms, they will have an enormous number of possible modes of vibration. Conside
r a molecule
which has 100 atoms; it will have (3 x 100) - 6 = 294 fundamental modes of vibra
tion not to say
anything about the bands that will appear out of combinations and other modulati
ons. Biological
macromolecules have much more than 100 atoms. These macromolecules will possess
such an
enormous number of fundamental modes of vibration, that a rigorous explanation o
f their
infrared spectra will be unattainable. And yet the infrared spectra of even thes
e compounds will
provide information about the various functional groups which absorb at characte
ristic infrared
regions regardless of whether they are present in a large or a small molecule (
later we will see
that even conformational studies on macromolecules are done with the help of inf
rared spectra).
The importance of infrared spectroscopy to the study of the functional groups ca
nnot therefore
be overemphasized. It will be apt for us to spend some time discussing the vibra
tions of dlfferent
functional groups of.ubiquitous occurrence.
Infrared Spectra of Common Functional Groups
The regions in which functional groups absorb are summarized in Figure 8.24. The
also illustrates a very simple spectrum belonging to the liquid paraffin Nujol,
a substance often
used for taking infrared spectra of solids.

tching I

4000 3500 3000 2500 2000

C "--O
1 | bending and corn-|
|bination bands.
Stetc I'll | The fingerprint
Bending [ region

Figure 8.24. A summary of the regions of absorptlon correspondgng to the stretch

ing and bending vibrations of the
ma functlonal groups and carbon skeleton bonds. IR spectrum of the Iklukl hydrcx
:oybon, NuJol, is olso

Obvious from the figure are some rules that must be borne in mind.
Owing to their low mass, the stretching vibrationsf single bonds involvi
ng hydrogen
give rise to absorption at the high frequency end of the spectrum.
The greater the steength of the bond between two similar atoms, the high
er the frequency
of the vibration. Thus, stretching vibrations of triple bonds between carbon ato
and carbon and nitrogen absorb just below the region where single bond stretchin
involving hydrogen absorb.
Below this is the region where stretching vibrations of double bonds bet
ween carboncarbon, carbon-oxygen, carbon-nitrogen, and nitrogen-oxygen absorb. N--H bending
vibrations also absorb in this region.
Bending vibrations are of much lower frequency and usually appear in the
region below 1500 cm-'. N.--H bending is an exception to the rule.
In a book of this size and generality, it is not possible to discuss the vibrati
ons assignable
to each and every functional group. However, a cursory discussion of major funct
ional groups
in structures that may be encountered frequently-in biochemistry follows.
The Carbon Skeleton
Aromatics: C--H str, C=-'C str, C--H def and a group of overtone combination bon
ds are
seen in infrared spectra of aromatics. C--H sir occurs Just above 3000 cm-. Thes
e bands may
be quite weak.
Most aromatic compounds show three of the four possible OC str bands. Of these,
band at 1450 cm- may not be seen frequently, and the two bands around 1600 cm-I
may coalesce. Thus, two, three, or four bands may be expected for C'-C sir.
The number of hydrogen atoms on the ring may be characterized by out'of-plane
C--H deformations. Thus these bands are characteristic of the substitution patte
rn on the ring.
The p-substituted benzenes present a strong band above 800 cm

Bophyscal Chemistry
Alkanes and Allcyl Groups: Most commonly C--H str absorptions appear Just below
cm-. Out of these .two, the band with the higher frequency is the one assignable
to the
antisymmetric stretch. For the alkyl groups the antisymmetric CH3 def occurs aro
1390 cm-.
Alkenes: These skeletons give absorptions quite singular to that of aromatics an
d as such
if an alkene occurs within an aromatic molecule, it is all but impossible to det
ect it.
The most. characteristic feature of alkenes may be the strong overtone bands for
out-ofplane C--H def vibrations. The combination vibration occurs around 1800 - 2000 c
m-, where
few other absorption appear. Trans-alkenes and cis-alkenes are easily detectable
from each
other: the former gives a C--H def band around 970 cm-] while the latter gives i
t around
700 cm-.
Cumulative double bonds give rise to strong absorptions around 2000 cm-. Thus,
C--C-C (allenes) absorb around 1950 cm-I, O-CO absorb at 2350 cm-, C-C---O (kete
absorb at 2150 crn-, --N--C-O (isocyanates) absorb at 2250 cm-, --N---C-S (isoth
absorb at 2100 cm-!, and --N3 (azides| absorb at 2140 cm-.
Alkynes: Out of terminal and nonterminal alkynes, the former are easily detectab
le. A
strong C--H str band occurs near 3300 cm-. The weaker CC sir band occurs near 22
00 cm-i.
The nonterminal alkynes have an extremely weak C-=C str and they lack the C--H s
r absorption.
Cas4nyl Group
The stretching absorption of this group has probably been studied more than any
group. The CO stretch band is always strong and so the overtone is almost always
around 3400 cm-.
In enols theCO stretch frequency occurs very low at 1580 cm-.
In aldehydes, two C--O stretch bands occur. Just below 1800 and Just above 1800
The latter is for antisymmetric stretch.
In saturated esters the C---O stretch band occurs around 1740 cm-. If the carbon

yl group
is in conjugation with a double bond or an aromatic ring, the band occurs lower
1720 cm-. Chelation with a nearby OH group weakens the C--O bond even further an
consequently the band is lowered even more around 1880 cm-.
If the CO stretch bands occur around 1700 cm- along with a broad band around 300
0 cm- |O--H stretch), the possibility is that we are seeing a carboxylic group.
C-O stretch bands for carboxylic acid anhydrides occur near 1800 cm:.
Hydroxy Compounds
For the primary alcohols C--O sir band is centred around 1300 cm-, and the O--H
between I000 and 1100 cm-.
For secondary alcohols the C--) sir is situated more or less as for primary alco
hols, but
the O--H def is centred around I I00 cm-].
For tertiary alcohols the former occurs between 1300 and 1410 cm- while the latt
er also is sh/fted towards higher frequencies and occurs between I I00 to 1200 c
For the carbohydrates the detection is made simple by the presence of an extreme
ly intense
OH sir centred on 3300 cm- and a C---O str entred at around 980 cm-.

Nitrogen Compounds
Hydrogen bonding in amines modifies both symmetric and antisymmetric N--H str
bands. In dilute solutions free NmH sir can be seen near 3500 cm-. NmH def occur
s around
1600 cm-.
For nitro compounds two NcD str bands occur, one ranging from 1500 to 1600 cm-.
the other ranging from 1300 to 1400 cm-.
For nitriles the C eN.str occurs just above 2200 cm- and for isonitriles this ba
nd occurs. just below 2200 cm-.
The spectrometer consists of a source of infrared light, emitting radiation thro
ughout the
whole frequency range of the instrument. Light from the source is split into two
beams of equal
intensity. One beam is made to pass through the sample while the other is allowe
d to behave as
the reference beam. The function of such a double beam operation is to measure t
he difference
in intensities between the two beams at each wavelength.
Now the two beams are reflected to a chopper which is rotating at a speed of 10
per second. The chopper makes the reference and the sample beam to fall on the m
grating alternately. The grating also rotates, albeit slowly. This rotation send
s individual
frequencies to the detector. It is the function of the detector to convert infra
red thermal energy
to electrical energy.
At the wavelength where the sample has absorbed, the detector will receive a wea
k beam
from the sample while the reference beam will retain full intensity. This will l
ead to a pulsating, or alternating current to flow from the detector to the ampl
ifier. On the other hand,, at the
frequencies where the sample doesn't absorb, both the beams will have equal inte
nsities and
the current flowing from detector to amplifier will be direct,, not alternating.
The amplifier is
designed to amplify only the alternating current. The amplified signal is record
ed by a penrecorder.
This instrument optically balances out the differential between the two beams. T

this kind of instrument is called optical null recording spectrometer. More soph
instruments are called ratio-recording instruments. In these instruments the int
ensities of
both sample and reference beams are measured and ratioed.
Samplin Technique
The sampling techniques depend on whether the sample is in vapor phase, a liquid
, or a
solid. In these three phases the intermolecular forces differ significantly and
thus it is imperative.
that the data obtained be specified for the sampling technique used.
Vapor phase : The vapor or gas is introduced into gas ce//s which are either abo
ut I0 cm
long or shorter with a series of internal mirrors (multi-pass cells} which refle
ct the infrared
beam back and forth lengthening the path-length. The gas cell has NaCl windows a
t the ends
(NaCI is transparent to infrared).
Most organic compounds have too low a vapor pressure for this phase to be useful
L/quids : Liquids are usually observed as a thin film between two infrared-trans
windows, This is done by squeezing a drop of liquid between NaCl flats.
The flats must be kept cle.an by washing them in toluene or chloroform and they
must be
optically polished using jewellers' rouge. The flats must be.kept dry and they m
ust be handied
by the edges only.

Biophysical Chemistry
The thickness of the liquid film varies between 0.01 to 0.1 mm. Pressure is appl
ied to the
flats to achieve the desired thickness.
NaCI flats are used almost throughout the infrared region. However, if the sampl
e contains
water, they become useless. In such cases CaF2 flats are used.
Solids: Solid spectra are recorded in three different ways, mu//s, KBr d
/sks, and deposited
Mulls are prepared by grinding about 1 mg of a solid in a small agate mortar wit
h a liquid
hydrocarbon (Nujol, Kaydol, etc.). Nujol is transparent to infrared over a very
wide range and
for this reason Nujol mulls are very widely used. One disadvantage with Nujol is
that it gives
C--H str and C--H def bands. Thus if C--H vibrations are to be studied, Nujol ma
y not be a
good choice. For these purposes hexachlorobutadiene, or chlorofluorocarbon oils
are used.
Once the mull has been prepared, it is squeezed between flat plates of NaCI and
for spectroscopy.
To avoid bands due to mulling agents altogether, the sample may be ground with p
KBr (0.1 to 2.0 per cent sample by weight). The KBr must be dry and the grinding
must be
conducted under infrared lamp to not to allow the moisture to condense. With all
precautions, however, slight moisture does get in and that results in a band at
3450 cm- due to OH group. Another precaution that should be taken with this meth
od is that the grinding
must be done well. The particle size should be lower than the infrared wavelengt
h, i.e., less
than 2 turn. Poorly ground mixtures tend to scatter more light and lead to erron
eously low
transmissions. Mechanical ball mills are available for the purpose. Once the gri
nding is done
the sample is squeezed, as before, between optical flats.
For solid films, the sample is dissolved in a volatile solvent and then the solu
tion is allowed
to evaporate drop by drop on an NaCI plate. Polymers and fatty materials often g
ive excellent
results as solid films. Solid films are also used for infrared dichroism study.
It must be kept in mind that intermolecular forces are different in solids as co
mpared to
solutions. This is particularly true of those functional groups which take part

in hydrogen
bonding. Thus solid state spectra are different from solution spectra. However,
the number of
resolved lines are far greater in solid state spectra. Many organic compounds ex
ist as polymorphic
variations. These different crystalline forms lead to differences in infrared sp
ectra. It is better to
measure such substances in solution, since all polymorphism is lost in that stat
So/ut/ons : The principal complication here for biochemists is that aqueous solu
cannot be used for infrared spectra. This is because water absorbs infrared powe
rfully owing to
its high absorption coefficient and a high concentration (55 M). This problem is
addressed by
dissolving the sample in DO or D20 -- H20 mixture. Another alternative is to use
This solvent dissolves quite a few polar molecules. However, it suffers from the
disadvantage of
inducing severe conformational changes in macromolecules.
The sample is dissolved in an appropriate solvent to give a 1-5 per cent solutio
n. This
solution is then introduced into a solution cell made of NaCI. The pathlength of
the cell varies
between 0.1 to 1.0 mm. A second cell containing pure solvent is placed in the re
ference beam to
cancel out absorption due to the solvent only. For true compensation, however, t
he pathlength
of the reference cell should be 95 per cent of the pathlength of the sample cell
if the solution
concentration is 5 per cent; it should be 96 per cent if the solution concentrat
ion is 4 per cent
and so on.
Applications of Infrared Spectroscopy
Mainly four types of problems have been addressed by the life scientists employi
ng infrared
spectroscopy. These are : identification of compounds, assaying the rate of reac
tions, studying
the conformation of molecules, and understanding interactions between molecules.

Ider.]ation of : Macromoleees ssess a lge number of atoms d as have numerous fde
n braons. s seeg disadvge c be actuy
adve c nse at tt pruces a deed red spec which secs as c et of e concerned mole.
Sups we susct at a ven comund is idcnc
to a o ple, we have to do is to te r sa ofbo csc compounds under flenfl confions
. If e d speca match, e comunds e idenc.
oer approach to idencaflon cs rccose to idencafion of funcon oups.
Here, oaon about vous ncn oups of uo compound is obted nog e ons wch e abon bds
appe. t us usatc s approach the help of example. Consider a substance which has
the elemental foula CHO. See ere c o protons for each cn atom, c compound posses
ses elthcr one
or one double nd. If a double bond volg cn Is present, e icd spectm must show a
sh bd bceen 16 -18 cm-. e elcment foula shows at c
md has a lone ogen atom wch maybe present as a cbonyl oup or as a hydrol
or as cer. If it a hyl oup, e compound must show a sh bd beccn cm. e mpound sho ese bds d us crc Is a double bond n d e lone ogen Is pnt as a hyo
l oup. We c erefore role out
t re ven to e elemen fo. entuy, when e scte lete completely it was fod to be CHa
(CHz)3CH=CH(CHz)7CHzOH; it ssesses go,
e hyl oup d e cbon-cbon double bond as predicted by e red data.
R ofr: Ied speca we wonderful dicaflon for my funcon oups.
eflc acflons volg ese funcon oups eider ese oups e consum or generated e eaflc reacon c be assayed e help of red specoscopy. us, ff e subsate possesses a hydrol oup d
e product doesn't, e rate of e
cflon med by measg e rate of sappece of e H setcg bmflon. Or ff e subsate ds not
possess a cnyl oup d e product does, e rate
ofe rcflon c meased by measg e rate of appece ofe cbonyl setcg bmflon.
e loss or appellee of or en sg of bds has been of oer benefit to e
bihet. My cflon oups bioloc (cro)molecules exchge eff protons e protons of water
. us, when a molecule le prote is dissolved water, e protons
to 0gen, ogen, d su atoms exchge eff protons e protons of ter. enfls we sply ide
n ese oups e help of ed scoscopy. If a prot is sIv DaO, e ae sd protons be exche
d for deuterons.
NH + DzO
@H + DzO
D .+ HDO
What is happening in the above reactions is that an atom of mass number 1 is bei
for an atom of mass number 2. From our discussion above we know that as the

reduced mass increases the frequency of absorption should decrease. Thus the ban
ds of
for the groups which have exchanged their protons shift to a lower wavenumber. A
shift tells us about the groups that exchange slowly and a fast shift tells us a
which exchange faster.
For the peptide group, the rate of exchange can be studied by obse -rving the am
ide II band. located at !550 cm- for --CONH-- and at 1450 cm- for COND--.

Biophysical Cherntstry
Why should these exchanges be of interest to us? They are of interest because th
ey tell us
much more about the protein than just the exchange. Consider this completely den
proteins and small peptides exchange their protons fast; this is a first order r
eaction with a half
life of about 0.1 to. 1.0 minute; in comparison, proteins in their native state
exchange very
slowly with half lives extending into hours or days for complete exchange. Thus
if we study the
kinetics of such exchanges, it gives us information about the kinetics and therm
odynamics of
the conformational transitions of the proteins concerned.
Study ofconformatlon : Proteins (and for that matter, any macromolecule) contain
a huge
number of atoms. This would mean that their infrared spectra will contain a huge
number of
vibrations, This surely seems like a disadvantage as far as studying conformatio
n of proteins
with the help of infrared spectroscopy is concerned. And yet, infrared spectrosc
opy is of
considerable use in studies of protein conformation. The reason for this is not
far to seek. The
chemical polypeptide repeat unit gives rise to nine characteristic infrared abso
rption bands.
The generally accepted nomenclature, the approximate frequencies, and the approx
description of each mode is given in Table 8.7. Some bands are more useful for c
studies than the others. The amide A, amide I, and amide II and amide V have bee
n most
frequently used for such investigations.
The amide A and B bands arise from the NH stretching vibration in resonance with
first overtone of amide II (essentially NH bending) vibration. These bands are v
ery sensitive to
hydrogen bonding and have been extensively utilized for hydrogen bonding in biol
macromolecules and pertJnent model compounds. In oriented samples these bands sh
ow marked
dichroism and can be utilized to study the direction of N--H bonds.
Table 8.7 Characteristic Infrared Bands of the Peptide Linkage
App frequency(cm-}
Description A

-33O0 }
-3100 }
NH stretching in resonance
with NH bending
C-O tretching
C--N stretching, NwH bending
NH bending
OCN bending
out of plane NH bending
out of place C-----O bending
skeletal torsion.

The amide I band is of great value as far as the study of secondary structure of
a given
polypeptide is concerned. The reason for this importance is that the frequency o
f this band
depends upon the environment of the bond. Thus, when the given bond is a part of
the a-helix,
the band appears at 1650 cm-, when it is part ofa [-structure, the band appears
at 1632 and
1685 cm:, and ff the bond happens to be present in a random coil, the band appea
rs at
1658 cm-. In addition, the amide V band appears at 600 for alpha-helix, 700 for
beta structure,
and at 650 cm- for the unordered structure. These bands are all well resolved. A
nd if a protein contains all the three structures, all three bands will appear.
In such a case, measuring the

intensities of these bands, will give an idea about the proportion of amino acid
s which are in a
given configuration. Of course, since D20 is the solvent which is used, one can
never be sure
whether the same proportion of the configurations also occurs naturally in the a
queous medium.

There is a totally different mariner in which infrared spectroscopy is applied t
o study
conformations. Here, researchers make use of what is known as infrared
In the next chapter we will be discussing the phenomenon called circular dichrol
dichroism means the difference in the absorption of right- and left-handed circu
by an optically active compound. The phenomenon used in infrared dichroism is
One can refer to this as linear dichroism. This phenomenon means that
in one direction will absorb plane polarized light differently when the electric
of the light is parallel to the orientation of the molecule and when it is perpe
ndicular to
Whether the compound is optically active or not is of no consequence to this
; even optically inactive compounds will show linear dichroism.
Let's try and understand this application without going into the mathematics of
simple fact is that absorption by an oriented sample will be maximum when the
is parallel to the transition dipole moment of that vibration
is to be excited. Absorption will be zero when the dipole moment of the vibratio
n is
to the electric vector.
If molecules in a sample are randomly oriented, for every molecule which is para
llel to the
a molecule which is perpendicular to it. Also, there will be molecules
all degree of angles with the electric vector. In such a situation there will no
t be any
Thus the trick of studying infrared dichroism is to orient the sample. This can
the sample is prepared in the form of a thin film. This film then can be attache
d to
drums which are gently rotated stretching the film slightly. This stretching of
the film
the sample in the direction of the stretching. Such studies can also be done on
solutions provided the liquid is placed in the space between the two cylinders a
nd the
rotated. The molecules then orient themselves with their long axes in the direct
The importance of infrared dichroism studies can bdst be demonstrated with the h
elp of
following examples.
The conformation of fibrous proteins has been studied by infrared dichroism. Thu
s rat tail
tendons, porcupine quills, silk fibre etc. have been studied. In these proteins
the absorptions at
1640 cm-I and 3300 cm-I are maximum when the electric vector of infrared light i
s perpendicular
to the fibre axis. These two frequencies are for C--O and N--H stretching respec

tively. This
observation can only be interpreted one way - these two bonds in the peptide bac
kbone must be
oriented perpendicular to the fibre axis (Figure 8.25). This inference is backed
up by other
studies on fibrous protein structure as well.
H N/ --T
Fibre axis
-- --R
of the po/ypept/de dm/n 0t st/k (otherflbrous prote/ns may have s/m//ar arrangem
Note than the C-O and N--H groups of the peptide backbone lie perpendicular to t
he fibre axis.
What is true for these two groups is true for the bases in the DNA structure too
. The bands
1600 and 1750 cm{stretching vibrations for aromatic rings) show greater intensities

Biophysical Chemistry
when the electric vector of infrared light is perpendicular to the axis of DNA f
ibre. This again
automatically means that the bases are arranged perpendicular to the axis of the
fibre. This is
borne out by other studies as well is predicted by the Watson-Crick structure.
Iateration between molecules : Polypeptide chains form interchain hydrogen bonds
. So do
the two stands of DNA. Hydrogen bonds have been studied very profitably using.in
The reason that hydrogen bonds can be studied with the help of infrared spectros
copy is
that the strength of the bonds of functional groups involved in hydrogen bonding
is altered.
Once the strength, or to put it in more technical terms, the force constant is a
ltered, the-bands
due to the vibrations of these functional groups also shift. This shift gives ev
idence of the
presence of hydrogen bonds and is studied by infrared spectroscopy.
As an example let's consider the hydrogen bond between an NH and a C-O group. Th
presence of hydrogen bond here lowers the force constant of both these bonds to
stretching. In
the Hooke's equation, force constant occurs in the numerator. It is obvious that
the frequency
of these stretching vibrations will be reduced.
What about the bending vibrations? Hydrogen bonding places restrictions on the b
of these bonds. Consequently, the bands attributable to bending will occur at hi
gher frequencies.
Apart from hydrogen bonding, other molecular interactions such as the protein- l
binding, enzyme-coenzyme interactions etc. are also studied by infrared spectros
Disadvantages of Infrared Spectrophotometry
With all the numerous applications listed above, infrared spectrophotometry suff
ers from
two major disadvantages -- the first one of them specifically for the biochemist
The best solvent for many biological works is water. Yet, as we have said earlie
r, water
absorbs intensely in the infrared. Thus, biologists are forced to use other solv
ents such as the
DO, D20--H20 mixtures, chloroform, or even CCI4. The problem is that the data ob
about any molecule or situation in such solvents may not necessarily be true for

It is very difficult to obtain quantitative data with infrared spectrophotometry

. This is
again a problem related to the solvent. There isn't possibly a solvent that is c
ompletely transparent
to infrared. In order to minimize absorption due to any solvent that is used, sc
ientists use very
small pathlengths. This too is not desirable as far as quantitative results are
concerned because
short pathlength would require higher solute concentration. At high concentratio
n, Beer's law
may not be obeyed.
An alternative is to do away with the solvent and to read the sample in the soli
d state. For
this the sample may be ground with KBr. First of all this method requires very p
ainstaking and
fine grinding because large crystal size would give rise to scattering. Even if
this is done and the
solid is prepared, the problem is of accurately measuring the pathlength of such
a solid sample.
When incident light is scattered by intervening sample molecules, the frequency
of light
scattered is the same as that of the frequency of the incident photon. Such osci
llations are said
to be elastic. However, during scattering of monochromatic light by molecules, a
small fraction
of the scattered light is observed to have a different frequency from that of th
e incident photon.
This phenomenon is known as the Raman effect. Since its discovery in 1928 by Sir
C.V. Raman,
the Raman effect has been an indispensable tool for the elucidation of molecular
structure. It
has been of immense use in locating various functional groups or chemical bonds
in molecules
and also for quantitative analysis of complex mixtrares. Only those vibrations w
hich cause a

change in dipole moment. Le., a charge displacement, are observed in the infrare
d region. Those
vibrations which do not cause a change in dipole moment and are consequently ina
ctive in the
are observed in Raman spectrn Thus, although the origins of Raman and infrared
are quite different, the two techniques provide complementary informations about
of molecular vibrations and therefore about the structure and conformation of a
Rayleigh scattering results when the .sample molecules scatter light which is of
the same
as that of the incident photon. Naturally we should infer that collision of the
such molecules in not resulting in any energy exchange between them. Some molecu
les (a
less than 1 are capable ofindulglng in energy exchange before scattering
These molecules give rise to Raman effect. A collision between a molecule and a
(in case of light scattering) does not lift the molecule to any quantized level;
rather the
molecule can be thought to be virtually excited (see Figure 8.26). If now, the m
absorbed the radiation while it was in the lowest vibrational state does not ret
urn to the
level, but to a level which is slightly higher, the emitted or the scattered
will be of a lower frequency as compared to the incident radiation. The differen
ce in
equal to the natural vibration frequency of the molecule's ground electronic sta
such shifted lines, known as Stokes lines are observed in the Raman spectrum and
to a different vibration in the molecule. The Raman spectrum, thus, provides
detailed information about the vibrational spectrum of a given molecules. There
can be other
present in the Raman spectrum. These lines are known as anti-Stokes lines. These
when some molecules absorb incident radiation when they are in a lower state. Th
may subsequently decay to their ground state (which is lower than the state at w
absorbed radiation) and consequently emit radiation which has a higher frequency
. anti-Stokes lines may not usually be considered for chemical analysis.
Since most of the molecules indulge in lyleigh scattering, radiation due to it i
s cosiderably
intense than the radiation due to Raman-shifted components. The primary function
of a
spectrometer is to reject totally radiation due to Rayleigh scattering and to de
tect the
Raman-shifted components. The Raman spectrometer should have (i) an intense
light source, (t/) sensitive detection, and (///) high light gathering power. A
unit serves as a good light source and the detection is usually performed by

The phenomenon whereby a molecule, after absorbing radiations, emits radiation o

f a
as fluorescence. Thus a compound which absorbs in the ultraviolet
range. This shift toward a longer wavelength is known
Stoke' s shift [Figure 8.26).
When an atom or molecule absorbs light, the energy of photon absorbed lifts an e
higher orbital. The excited electron can now return to the ground state in eithe
r of the two
It might do so in one single step in which case it will emit light of the same w
Fhe electron might, however, return to the ground state in a step-wise manner
energy levels, emitting quanta of radiation corresponding to each energy
. Since each quantum will have a smaller amount of energy, the radiation emitted
will have
the original exciting radiation. It is obvious that the emitted light will
T different wavelengths corresponding to each intermediate energy level the elec
on its Journey to the ground state. Therefore, fluorescence spectra are band spe
' are usually independent of the wavelength of the radiation absorbed.

Biophysical Chemistry
First excited electronic state

Virtual excited state {Laser frequency)

..... "

I 'l -[ .
' ........

Excited vibrational
energy levels

Figure 8.26Diagrammatic representation of Rayleigh and Raman scattering. Note th

at no energy exchange takes
place in Raman scattering (B and C).
Fluorescence is an extremely short lived phenomenon (10- seconds or less, see Bo
x 8.3) and therefore can provide information about events which take less than 1
0- seconds to Occur.
Structural Factors Which Give Rise to Fluorescence
Aromatic molecules or the molecules having multiple conjugated double bonds with
high degree of resonance stability generally fluoresce. Both classes of substanc
es possess
delocalized n-electrons which can be placed in low-lying excitec single states.
The higher the
number of n-electrons, the higher is the fluorescence. Thus polycyclic aromatic
compounds are
more fluorescent than benzene derivatives. Substituents strongly affect fluoresc
ence. Electron
withdrawing substituents (hCl, --I, .--Br, --NO2, --NHCOCH, hCOOH, etc.) decreas
fluorescence. On the other hand substituents which delocalize the n-electron [-NH, OH, --F,
--NHCH, N(CH)2, OCH, etc.] enhance the fluorescence. Fluorescence is often given
molecules containing a nonbonding pair of valence electrons. Examples are amines
with a lone
pair on their nitrogen atom.

Molecular rigidity is conducive to fluorescence. Thus among the aromatic compoun

those that are most planar, rigid and sterically uncrowded are the most fluoresc
ent. Chelation
of aromatic compounds with metal long often promotes rigidity and reduces intern
al vibrations.
Chelation thus promotes fluores, cence (this principle is exploited in measuring
the concentration
of many metal long). Low temperature, glassy state and high viscosity are all pr
omoters of
Intensity and wavelength of fluorescence of the same compound may vary with the
used. Solvents exhibiting strong van der Waal's binding forces and solvents poss
essing electron
withdrawing groups diminish fluorescence. "
Drastic changes in pH, especially those changes which affect the charge status o
f the
chromophore influence fluorescence. Thus aniline fluoresces at neutral and alkal
ine pH but
becomes non-fluorescent at acidic pH. Aniso!e which fluoresces at neutral pH is
at alkaline pHs.

Fluorometry : Theory and Instrumentation
Fluorometry is an important analytical tool for the det6rmination of extremely s
concentrations of substances which exhibit fluorescence. Beer-Lambert law, which
we have
considered previously, is also applied to fluorometry in the following form
log ISOL'ElCr -- Ef Cb
where ef is the absorptivity of the fluorescent material. C is the concentration
of the substance
and b is the path length. The values of intensities of the incident radiant ener
gy and the
transmitted energy are indicated by ISOLVEr and ISLE respectively. The intensity
of radiation
absorbed is therefore given by ISOLVET -- ISAMPLE. The intensity of fluorescence
is given by
F = k (IsoLV.Z/cr -- ISMPL)
where k is the proportionality constant (< I). Thus,

F = kIso.VET (I -- I0Cb}
f k[SOLVENTIS written as Fn the relationship becomes
F = Fn (I - 10fcb)
F-Fn = 10fCb
log = fCb
For Cb < 0.01, F= 2.303 kIso..t eCb. This equation holds good for concentrations
as low as a
few p,p.m.
The instrumentation of a spectrofluorimeter differs from that of the spectrophot
ometer in
two important respects besides other minor variations.
There are two monochromators instead of one as in a spectrophotometer; o
monochromator is placed before the sample holder and one after it, and
As fluorescence is maximum between 25-30C, the sampleholder has a device
maintain the temperature.
The main components of a spectrofluorimeter, indicated in Figure 8.27 are :

- ----- Gt
Source Collimator
or I

..Monochromator 2

a continuous source of radiant energy (mercury lamp or xenon arc);
a monochromator usually a prism (P), to choose the wavelength with which the sam
is to be irradiated;
a second monochromator (P2) which, placed aider the sample, enables the
of the fluorescent spectrum of the sample;
(/v) a detector, usually a photomultiplier suited for wavelengths greater than 5
00 nm; and
(v) an amplifier.
The fluorescent radiation emitted ly the sample is given off in all directions,
but in most
instruments the sample is viewed at right angles to the incident beam.
Spectrofluorimetry vs. Absorption Spectrophotometry Advantages
Spectrofluorimetry gives extremely accurate results when very low concen
trations are
used. At very low concentrations, absorption spectrophotometry is not at all acc
To cite an example, sensitivityof absorption spectrophotometry is taxed when I00
of serotonln is to be detected; spectrofluorimetry on the other hand can determi
ne 100
pg of serotcnin with relative ease.
The 'Stokes' shift enables use of two monochromators in spectrofluorimet
ry; one selects
the activating wavelength while the other selects the fluorescent wavelength. Th
arrangement imparts great spectral selectivity to spectrofluorometers.
Since there is a direct relationship between sample concentration and th
e intensity of
fluorescence, spectrofluorimeters can make do with quite simple electronics. Thi
s is
generally not possible with absorption spectrophotometers.
Speetrofluorimetry vs. Absorption Spectrophotometry; Disadvantages
A drawback of spectrofluorimetry is a high degree of absorption of fluor

escent radiation
by the emitting sample itself. This is known as quench/ng. Quenching also occurs
to impurities. Dissolved oxygen is a very effective quencher. Thus, if precise w
ork is
required, nitrogen is bubbled through the sample to remove oxygen. In old instru
the problem of quenching is obviated by measuring a low concentration of the
sample. The modem instruments use microcells.
A note of caution : Detergents, filter paper and many laboratory tissues
interference in fluorimetric assays because they can release strong fluorescing
The cuvettes used for fluorimetry should, therefore, never be washed with a dete
solution. The cuvettes may also not be dried by wiping them with tissue paper.
The more common applications of spectrofluorimetry include qualitative analysis
spectra and absorption spectra gives a fair idea about the identity
a compound); quantitative analysis (applications include assay of riboflavin, th
such as cortisol, oestrogen, serotonin and dopamine, 'organophosphorus pesticide
smoke carcinogens, drugs such as lysergic acid and barbiturates, porphyrins, cho
some metal long); and studies on protein structure (FAD containing proteins). Ta
lists fluorescence maxima of some biologically important compounds. However, mor
of spectrofluorimetry are given below.

Biophysical Chemistry
Table 8.8 Characteristic fluorescence maxima of some compounds of biological int

Chlorophyll a
Chlorophyll b
Rhodamin B
Water, pH 7.0
Water, pH 7.0
Water, pH 7.0
Water, pH 7.0
Water, pH 7.0
Water, pH 7.0
0. i N NaOH
0.1 N NaOH
Water, pH





(i) Intracellular free calcium concentration assay : Quin-2 (an EGTA derivative)
, Quin-2 AM,
and Fura-2 are three fluorescent probes which allow us to assay intracellular fr
ee calcium
concentration. These probes are permeable to the plasma membrane and upon enteri
ng the
cytosol combine with calcium (chelation). This chelation gives rise to fluoresce
nce whose
magnitude is directly proportional to the free Ca2 concentration in the cytosol.
These studies
assume importance because of the role of calcium in controlling cellular metabol
(ii) Fluorescent probes and studies on membrane structure : Fluorescent probes s
uch as
anilinonaphthalene-8-sulphonate (ANS) and N-methyl-2-anilino-6-naphthalene sulph
(MNS), contain both charged and hydrophobic areas and therefore locate at the wa
ter lipid
interface of the membrane. Such compoinds afford important information about thi
s interface.
This is especially so since the fluorescent properties of a molecule, as pointed
out earlier, vary
with its mobility and also with the polarity of the environment. Studies with AN
S have shown
that structural changes occur in mitochondrial membrane during oxidative phospho
The probes have also yielded much information about the structural features of t

he plasma
(No Assay of membrane potential : Membrane potential of excitable cells is regul
ated within
strict limits. Changes in this potential regulate ion entry into the ceils; Thes
e membrane potential
changes can be monitored by using fluorescent probes such as Di-S-C3-(5),. and m
540 (the latter is not so satisfactory).
(iv) Fluorescent microscopy : Spectrofluorimeter when combined with a microscope
the determination of subcellular location of fluorescent compounds or of materia
ls which bind
fluorescent dyes. This technique has given very important information in the fie
ld of immunology
and pharmacology. Thus, presence of pathological immune complexes may be detecte
d with
the help of FITC conjugates. The presence of an antigen on the cell surface may
be detected by

a fluorescence labelled antibody. By using acridine orange, this technique allow
s visualization
of nucleic acids within subcellular organelles. Since this technique alS allows v
isualization of
chromosomes, it is being exploited in genetic counselling specifically to determ
ine whether the
fetus is genetically normal.
(v) Since fluorescent emission is extremely sensitive tolocal environment, it ca
n be used to
mom'tor the kinetics and thermodynamics of the incorporation of a particular sub
unit or substrate
into a macromolecular assembly. It is being used to obtain definitive informatio
n about the
between pairs of loci in a macromolecular assembly. Spectra and the StudF of Protein Structure
As with absorption spectrophotometry, a great deal of information about the stru
cture of
,ven protein can be found out with the help of fluorescence studies. Here too, f
changes under different conditions provide the necessary clues about the positio
ns of
amino acids residues in the protein, the composition of the active site, protein
interaction, denaturation etc.
A few important empirical rules for interpreting fluorescence spectra of protein
s are listed
i. The fluorescence of a protein is solely due to the amino acids typtophar., ty
rosine, and
This rule holds true in all cases except where the protein is known to contain
2. Usually it is the tryptophan fluorescence which is studied most often. This i
s so because
weak fluorescence, mostly due to quenching. Such quenching can be due
proximity to tryptophan, a carboxylic group, or an amino group. Quenching also t
if tyrosine is ionized. Phenylalanine has the smallest of quantum potential of t

he three
amino acids.
3. Decrease in polarity of the solvent pushes . max of tryptophan to shorter wav
such a situation increases the intensity of the . max.
4. If a shift in . max occurs towards shorter wavelength when the protein has be
en dissolved
solvent, one may conclude that the tryptophan is internal as well as existing in
a nonenvironment.
5. If a shift in . max occurs towards shorter wavelength when the protein has be
en dissolved
non-polar solvent, one may conclude that the tryptophan is on the surface of the
unless the solvent is such that it has brought about large-scale conformational
change in
6. Quenching of fluorescence by known quenchers (iodide, nitrate, cesium ion, ac
provides relevant information. Fluorescence due to whichever of the fluorescing
is quenched, that amino acid should be on the surface.
If a known quencher fails to quench the fluorescence of an amino acid, t
he following
may be considered :
(a) The amino acid is internal.
(b) The amino acid is hidden in a crevice which is too small for the quencher to
The surroundings of the amino acid might be highly'charged so that the q
uencher is
being repelled.

Biophysical Chemistry
The last case may be verified by trying to quench through a neutral quencher lik
e acrylamide.
If it is able to quench, the existence of the amino acid in a charged environmen
t is confirmed.
Even the type of charge may be determined. If positively charged quencher fails
to quench, the
amino acid is in a positive environment. Ditto with the negatively charged quenc
8. If the substrate quenches the fluorescence due to tryptophan in a given enzym
e, the
tryptophan might be present in the active site, or quite near it.
Extrinsic Fluorescence
There are macromolecules where no fluorescent group is present in the location w
here it is
desired, in such cases biochemists introduce a fluorescent group into the molecu
le. Such a
method is given the name - extrinsic fluorescence. The groups which are introduc
ed in such a
way are catled fluors. To be used as a fluor, the chemical group must saUsfy cer
tain requirements.
(/) It should have the ability to bind tightly at a unique location; (it) its fl
uorescence should be
susceptible to changes in the environmental conditions, and (iti) the group shou
ld itself not
bring eonformational changes in the maeromoleeule in which it is introduced.
The most commonly used fluors for the studies on nucleic acids are ethidium brom
proflavin, acriflavin and acridine orange. Those preferred for use in protein st
udies are ANS,
1-dimethylaminonaphthalene sulfonate (DNS), 2-p-toluidylnaphthalene-6-sulfonate
fluorescein, rhodamine, and dansyl chloride.
All the above named naphthalene sulfonates (ANS, DNS and TNS) have a peculiar pr
of fluorescing quite weakly In the aqueous medium. But in non-polar surroundings
, the strength
of their fluorescence increases while the florescence maxima shift to shorter wa
velengths. These
compounds are therefore, naturally, used to detect non-polar regions of a given
To illustrate just how extrinsic fluorescence may be of help in studying maeromo

two examples have been cited below.

I. Acridine orange has a property of an increase in fluorescent intensity as wel
l as a shift
in fluorescent maximum to shorter wavelengths when bound to nucleic acids. All t
he more
important is the fact that the fluorescent maxima are different for different nu
cleic acids. Bound
to single stranded nucleic acids (RNA, or single strands of DNA) it gives a red
Association with double stranded DNA causes it to fluoresce green. Naturally, wi
th the help of
acridine orange you may detect whether the sample contains single or double stra
nded nucleic
aeid, and If the sarple contains both, how much of each type is there.
2. Haemoglobin molecule has two components -- the prosthetic group which is a po
and the protein, known as apohaemoglobin. ANS has a property of giving no fluore
scence when
it is bound to haemoglobin. But an association with apohaemoglobin causes it to
That it fluoresces when bound to apohaemoglobin indicates that it is binding at
a region which
is .non-polar.
If the porphyrin prosthetic group is now added, the fluorescence vanishes and AN
S is
removed from binding. This indicates that ANS binds at the same site where the p
orphyrin is.
And that the site where the porphyrln binds to apohaemoglobin is highly non-pola
Fluorescence and Energy Transfer
Given below are the excitation and the emission spectra of two different fluors,
and y.

Spectra for (A N. Abson s d by s esn s
d is. N sn s of A os t son s ofB. (C) sn s w n sWn . y fer een 1 2.
Note at e esston sc ofx oveHaps e excitaon spec ofy.
excitation spec we me e rge of wavelens at a fluor must absorb
to fluoresce. f, ou lack of pointed discussion on e pot you e ven to
at e excision specm is sonous e absoon specm for a fluor.
s is deed e case. Howler, somees ngs turn out derenfly,.
Consider a system where go e fluors x, d y e e se soluon. In such a it may we we
be at e luflon is adiated e of e cion of x, e fluorescence due to y be obted. I
n such a case we c say at dion specm for y is derent from its usu abon specm. To
be ct,
was produced by absoflon of much smer wavelens. at happened?
A loc reason for e phenomenon may be as foows: en x s excited, it fluoresce.
e ession specm of x oveHaps e cition specm for y. So, e
, x ab by y, wch en etted oer photon d alonger ve!en espong to its ession specm.
In s laon e ener absorbed by e t
fluor is sfeed.to e.oer raaflon as a mediator. is detely is a possib but s is no
t e reason for e ave phenomenon.
ely as 1928 Wbg d Negele showed at t abrbed by e oflc o ads of a heme prote yeas
t wch were poisoned by cbon monode pcipat sptg off e cbon monode radlc attached
to e heme moie. e efficien of s
press w later sho to 1 %. ere were oer studies about acaflon of ees e help of t.
In ese studies too it could demonsated at ener absorbed at ous ps of e prote mo
lecules could ate to e locaon whe e acflvaon
ced. er oer ents so demonst e fact at abflon of t me comophores cod result fluor
escence etted by oer comophores which we not cit dfly by e t.

Biophysical Chemistry
Several mechanisms were proposed for the transfer of energy in protein molecules
. Some
of these were (1) transfer by electron migra.tion in conductivity bands, (2) tra
nsfer by exciton
migration, (3) transfer by proton, hydrogen radical, or hydride ion migration th
rough an ordered
array of water molecules surrounding the macromolecule, or (4) transfer by reson
ance interaction
between chromophores. Since the experimental data fit the last mechanism, this p
has come to be known as resonance energy transfer.
Three Conditions must. be Satisfied for resonance energy transfer to occur. Thes
e are
The energy donor must be fluorescent. In fact the efficiency of energy t
ransfer increases
with the fluorescence quantum yield of the donor.
The absorption spectrum of the acceptor must overlap with the emission s
pectrum of
the donor. The more they overlap, the higher is the efficiency of transfer.
The distance between the donor and the acceptor must not exceed 50-100 A
. In fact,
70/ seems to be the upper limit for efficient energy transfer.
It is the last condition that makes this phenomenon of such large interest to a
Let us See why.
If the two molecules engaging in energy-transfer are nearby, the transfer may ta
ke place
at a very high efficiency. However, as the distance between the molecules increa
ses, the efficiency
of energy-transfer may decrease. We may then say that the eJficiency of transfer
is a function of
molecular distances. And this is exactly what makes the phenomenon of interest t
o a biochemist.
Because, then by measuring the efficiency of energy-transfer, a biochemist can p
redict the
distance that may be there between two fluors lying within the same macromolecul
e. Fluorescence
energy-transfer is then some kind of a molecular ruler or a scale.
In 1948 Forster proposed a theory for the resonance energy transfer. He postulat
ed that
the rate of transfer depends on the inverse sixth power of the distance between
the donor and
the acceptor. Thispredicted distance dependence was verified later by experiment
al studies of
fluorescent donor-acceptor pairs separated by a known distance in defined system

The mathematical equation that describes the eciency of transfer as a function o

f molecular
distance is as follows
where E, is the efficiency, R is the distance between the donor-acceptor pair, a
nd R is a constant
related to each donor-acceptor pair.
The above equation may be rewritten for R as follows
= Ro(1-Ej
Let us see how E is measured. There are mainly two methods to measure E, Both th
methods utilize three wavelengtths, )h' 12, and )a" The characteristics which th
ese three
wavelengths must possess are as follows : it must be absorbed by the donor effic
iently but not
by the aeeeptor: t2 should be a wavelength emitted by the donor but not by the a
ecelStor; la
should be a wavelength emitted by the aeceptor and not by the donor.

It stands to reason that if energy transfer is taking place, the emission ate, t
he wavelength
at which the donor emits, should be quenched. The first method excites the donor
by using ,
and then measures quenching at 2" Let f be the fluorescent intensity at 2 if the
donor was
excited using . Let iv be the fluorescent intensity when the acceptor is absent
and let fv.^ be
the intensity in the presence of the acceptor. The fraction of the donors that r
emain excited is
written as loE. Then
The second method deals with measuring the fluorescent intensity of the acceptor
at 3" The mathematical expression in this case is
(^ V
the fluorescence of the acceptor at 3 when the donor and acceptor both are prese
nt, while f
is the fluorescence of acceptor at X when only the acceptor is present. The exci
tation wavelength
From E one can measure R if To is known. To determine To one has to measure (1)
fluorescent intensity of the aceptor as a function of , (2) extinction coefficie
nt of the donor,
and (3) the value of Q (photons emitted divided by the photons absorbed) of the
donor when the
acceptor is absent. There is another factor that must be considered but which is
beyond the
scope of this book. This is the orientation factor. A consideration of the orien
tation factor is
important owing to the fact that the fluorescence from the donor is polarized an
d the acceptor
may be at an angle with respect to the. plane of polarization such that maximum
may not take place. However, the donor and acceptor groups are in rapid motion w
ith respect
to each other and the orientation factor is hardly ever higher than 1.20.
Before energy-transfer experiments are performed, the following conditions must
be met:
(I) if a fluorescent group is to be attached, it should be attached in a manner
that it doesn't
alter the structure of the macromolecule; apart from the manner of attachment, t
he group itself
should be inert so as to cause minimal perturbations in the macromolecular struc
ture; (2)
There should only be one donor and one acceptor; moreover, both should be at kno
wn chemical

.sites;. and (3) The To value for the donor-acceptor pair must be known and shou
ld be in close
agreement with the distance between the donor and acceptor. Once these condition
s have been
considered, the experiment can be carried out.
The first step in identifying a donor-acceptor pair is to ascertain whether the
has an intrinsic chromophore that can serve as a donor or an acceptor. Tryptopha
n residue in
proteins serves as an excellent donor owing to the fact that its emission center
ed at around 330
nm overlaps the absorption spectrum of many potential acceptors. The galactose b
protein from Salmonella possesses Just one tryptophan residue and this is wonder
ful for energy
transfer measurements. Fluorescent coenzymes such as NAD, FMN (oxidized), and pyr
phosphate are dlso attractive potential donors and acceptors. The heme group in
heme proteins
is a very good acceptor since it has an absorption spectrum covering the entire
visible range.
This group is no good as an acceptor since it does not fluoresce.

Biophysical Chemistry
If a good donor or acceptor is not naturally
analogues are available. Thus benzoadenoslne
nucieotides. Protoporphyrin and its zinc and
for heine. Several
fluorescent analogues are now available. The

available in the macromolecule, flu

derivatives are good analogues for
tin derivatives are good analogues
following table lists a few.

Table 8.9 Florescent analogues of a few biomolecules. These analogues can be use
d as
labels or energy transfer experiments
Fluorescent analogue

ATP, NAD, FAD, CoA, and other

adenine nucleotides
Thiamine diphosphate
Fatty acids
ethenoadenosine derivatives
benzoadenosine derivatives
protoporphyrin, zinc and tin porphyrin
thiochrome diphosphate
a- and -parinarlc acid
phospholipids containing parinaric acid,
dialkyl cyanine dyes, derivatives of
phosphatidyl ethanolamtne
Th, Eu

A few examples of the application of the energy-transfer technique to structure

are given below.
Three-Dimensional Structure of tRNA
In the crystalline state the tRNA exists in clover-leaf structure. What is its s
hape when it
is in solution? Is it different or is it the same?
Yang and Soll tackled this problem using energy-transfer studies. They prepared
five species
of tRNA (either fmet or glutamate tRNA from E.co/0 labeled with acridine, dansyl
, anthranilamlde,
or coumarin derivatives at two of the following sites :
(a) the 5'-end,
(b) 4-thlouridine,
(c) dihydrouridine,
(d) 2-thiouridine at the anticodon,
(e) pseudouridine, and
(i) 3"-termlnal adenosine.
- The distances that they calculated from observed transfer efflciencles were as
follows: a
was separated from F by 24, b from fby 38, c from e by 36, d from fby more than
65, and e from
f by 55 amstrong units. The distances that were determined crystallographlcally
are 25, 41,
23, 74, and 53 amstrong units respectively. Thus, except for the distance betwee
n c and e
where the two data do not agree well, all other distances are very close. The co
nclusion that
Yang and Soll reached was that even in solutions tRNA adopts a cloverleaf struct
ure. (see
Figure 8.29).

8.29 .Clover leaf structure of tRNA. The diagram shows the. positions at which j
'luorescent labels were
introduced as well as the positions of unusual bases on the basis of which each
arm is given a name.
pyntvate dehydrogenase complex -.
Pyruvate dehydrogenase complex is a multienzyme complex which converts pyruvate
It consists of three enzymes : pyruvate dehydrogenase, dihydrolipoyl transacetyl
dihydrolipoyl dehydrogenase. It has five coenzymes : NAD, CoA, "lipoic acid, thia
and FAD. The enzyme dihydrolipoyl dehydrogenase is centrally placed in the
a lipoic acid moiety attached to a lysine and it is hypothesized that it is this
t moves around the crystal of the enzyme as a swinging arm bringing successive
to the other enzymes in order that the reaction proceeds. Do we have any
support for this hypothesis?
The length of the lipoyllysine arm is known to be 14A. Now if the swinging arm h
the distance between the active sites of any two enzymes within the crystal must
28]. This can be more easily understood from the figure given below (Figure
i. However. the energy transfer studies indicate that the distance between the a
ctive sites of
dehydrogenase and dihydrolipoyl dehydrogenase is at least 45A.
The lack of evidence does not mean that the hypothesis is wrong. However, energy
have spurred proposition of alternative models. Two of the main alternative mode
are (I) substrate diffusion within the complex, and (2) acyl transfer between ad

Biophysical Chemistry
Lipolysme arm
-< 28A

Figure 8.30. (A) The lipoyllystne ann s 14 in length. Thus if the active sites o
f the two other enzymes core placed a maximum of 28 A from each other, the arm c
an reach them. (B) If the distance becomes.greater than

28 , the arm cannot reach the actlve sltes.

Ill +Ix
p - Ill - Ix
Changes in the Enzyme Conformation When Substrate Binds
It was Emil Fischer who had, in order to explain the great specificity of an enz
yme for a
group of substrates, proposed the 'lock and key model." The model proposed that
the active
sites of the enzymes are like the key-space of a lock. The substrate behaves lik
e a key. The
correct substrate is like the correct key for a given lock which fits snugly int
o it. The wrong
substrate has the wrong shape and doesn't fit snugly. D. E. Koshland improved up
on this
model when he suggested the 'induced-fit model.' The model suggests that when a
approaches a given enzyme, both undergo a change in their three-dimensional stru
cture. If the
substrate is true, the change is such that they will fit snugly.
This hypothesis can be tasted by energy-transfer studies. Donor and acceptor gro
ups are
bound to an enzyme and the distance between them is measured when no substrate i
s present.
Then the substrate is added and the distance is measured again. When such studie
s are
performed, a large change in the distance between the donor and the acceptor gro
ups takes
place upon addition of the substrate. This is ample proof for the induced-fit mo
Rhodopsin Serves as a Light-Sensitive Gate
Rhodopsin is the main light absorbing component in the discs of rod cells in the
eye. There
are two parts to it: the protein, opsin and a fluor, cis-retinal. It is the latt
er which absorbs light.
The molecular weight of rhodopsin is 40 KD. A spherical molecule
roughly have a diameter of about 45.. To check whether rhodopsin
experiments were performed. The protein already has a good donor
Another fluor
was tied to a sulfhydryl group in opsin. This fluor acted as the

of this size wo
is spherical, e
in cis-retinal.

The efficiency of transfer showed that the two fluors must be about 75A away fro
m each
other. This means that rhodopsin cannot be spherical and, indeed, must possess a
n elongated
protein. In fact, 75,. is a distance big enough to make this protein traverse th

e retinal disc
The above data encouraged researchers to hypothesize that rhodopsin may actually
serving as a light-sensitive gate controlling the ion flow across retinal disc m
embrane. Subsequent
X-ray-scattering experiments confirmed the dimensions of rhodopsin to be just th
ose found
with energy transfer experiments. And several lines of evidence suggest that rho
dopsin indeed
may be acting as a light-sensitive ion-flow gate.
If the orientation of the polarizer is parallel to the plane of polarization of
light, the intensity
o.f the transmitted polarized light will be maximum. This intensity will be zero
if the polarizer
orientation is perpendicular to the plane of polarized light (Figure 8.31). Ther
efore, for a partially
polarized light, the polarization P, may be given by the relationship
Where I and Ii are the intensities observed parallel and perpendicular to an arb
itrary axis.
The value for P varies between +1 and -1. A value of zero means that light is un
Other values mean that the light is partially polarized.

le holder
Direction of
Figure 8,31. Production of plane-polarized light. Waves of all orientations fall
on the polarizer, which allows only
those waves to pass whose electrical vector is parallel to the axis of the polar
Fluorescence polarization can be determined using the instrument shown in Figure
8.32. The sample is ecited with polarized light. In order to do sol a polarizer
is placed between
the monochromator)and the sample. A second polarizer is placed between the sampl
e and the
detector. The axis 9f this polarizer can be varied from being parallel to the fi
rst polarizer to
being perpendicular. By Varying the axis of the second polarizer, both 11] and Ic
an be determined.
Thus P can be measured. Usually, if the exciting light is polarized, the fluores
cence is found to
be only partially polarized or even unpolarized. The factors leading to this los
s of polarization
are explained below.

A chromophore absorbs polarized light maximally if the direction of the electric
vector of
is parallel to the electric dipole moment of the chromophore. In a solution, the
randomly oriented. Only a few of them will satisfy the above condition. Others w
ill have
electric dipole moment at various angles to the plane of polarized light. If thi
s angle is O,
the probability of absorption of polarized light is cos20.
What if the molecule, that is absorbing the plane polarz, ed light a fluor? Will
it emit the
in the same plane as it absorbed? Not necessarily. This is so because the polari
light is not determined by the electric dipole moment, but by the transition dip
The latter is not generally parallel to the former. The probability of emission
with the plane of polarization at an angle with respect to the transition dipole
is proportional to sin2.
Note the fact that the transition dipole moment is not generally parallel to the
This is the major factor for the loss of polarization. This non-parallel relatio
the two dipoles ensures that even if the absorbing molecules are perfectly align
ed with
of polarization of the light being absorbed, there would still be loss of polari
zation; P
be less than 1. In-a solution then where the molecules are randomly oriented, th
will be even more true. This loss of polarization ( Pvalue being less than 1) is
So far we have seen that fluorescence polarization, its value, is a result of th
e fact that the
are not parallel. This value of polarization is called the intrinsic polarizatio
n, Po.
there are other factors that affect polarization and therefore intrinsic polariz
ation is
the value that is observed experimentally.
Consider a molecule. It has absorbed polarized light. In a very short time, it w
ill be emitting
But in the short time between absorption and fluorescence, it moves. This motion
transition dipole orientation and will cause loss of polarization. The motion we

about here is rotational motion and not translational motion because translation
is unable to change the orientation of the dipole. Rotational motion is therefor
e one of
that affect fluorescence polarization. The other factor that affects polarizatio
r is the energy transfer that may occur between the molecules. .
In fact both the above factors are complex. The rotational motion of a molecule
is a function
only its own size and shape, but also depends upon the viscosity of the solution
, as well
!the temperature. The larger the molecule, the less will be its rotational mobil
ity, the lesser
be the loss of polarization. Thus macromolecules show substantial polarization o
wing to
really decreased mobility. The higher the viscosity, the lower the rotational mo
tion, the
be the extent of loss of polarization (in fact at very high viscosity, the polar
may be very near that of the intrinsic polarization since the molecule will elic
it very
r rotational motion). The higher the temperature, the more will be the rotationa
l motion, the
will be the loss of polarization.
The second factor is that of energy transfer between identical molecules. Althou
gh resonance
transfer takes place with highest probability between molecules having parallel
take place when the dipoles are not parallel. When this occurs, naturally there
In the previous pages we have seen that resonance energy transfer is a
of distance between molecules. As the distance increases, the efficiency of tran
sfer "
, energy transfer is also affected by concentration. The more the concentration,
less the distance between the molecules, the more the energy transfer, the more
the loss of
But concentration here is a complex term. To explain with the help of an example

let's conjure an image of a fluor bound to a macromolecule. Concentration in suc
refer to a low concentration of the macromolecule-fluor complex in the solution.
refer to the distance between the fluors on the macromolecule. The higher this d
lower we will say the concentration is.
" After having considered energy transfer as the second factor affecting
arrive at a good relationship. Even if we completely immobilize a molecule by in
of the solution to a very high level, loss of polarizition will take place - in
these conditions it
be due to energy transfer. On the other hand, if the viscosity of solution is ve
ry low, the loss
polarization will mainly result from rotational motion of the molecules.
The major conclusion that derives from the above discussion is as
rotational motion, polarization decreases. We need to understand the consequence
s of this
rule as well as understand truly what we mean by rotational motion.
I. Small molecules rotate freely and thus do not give any polarization (P value
is zero)
If these small fluors are attached to another molecule (which may itself
polarization will increase owing to the larger combined size and reduced
The higher the size of the molecule, the lower will be the rotational mo
attached fluor, the higher will be the polarization.
A fluor bound to a macromolecule shows good polarization because its mob
greatly reduced by such binding owing to the large size of the macromolecule*.
The nature of binding of the fluor to the larger molecule also affects t
he extent,
polarization. If the binding is rigid (intercalation between bases of DNA) the m
the fluor effectively means the mobility of the whole molecule. In this case
polarization is quite high. On the other hand, if the binding is such that the f

luor move without the whole macromolecule moving ( binding to an amino acid side
which can move with respect to the polypeptide chain) the polarization may not
high as in the first case.
If the macromolecules undergo polymerization, the larger structure will
lesser rotational movement. If the fluor is bound to such an associating system,
polarization will increase with association.
7. If the fluor is bound to a macromolecule which changes its conformation, its
will be affected: If the change in conformation leads to the macromolecule assum
ing more ordered structure, it will result in reduced rotational mobility and
higher polarization. On the contrary, if the conformational change leads to diso
the rotational motion is slated to increase and the polarization will decrease.
We have consistently talked about the polarization of a fluor bound to a macromo
lecule. What
the intrinsic fluorescence of the macromolecules and its polarization? For examp
le the
fluorescence of tryptophan in a protein and utilization of its polarization in s
tudying the
There is a problem here. Large proteins move very slowly on a molecular scale. T
hus, to observe
depolarlzation due to motion, the lifetime of the excited state should be suffic
iently long, i.e. , there
should be a good time lag between excitation and emission so that the molecule m
movement in that time and depolarization may occur. For very sma]l proteins, int
may be of some use, but for larger proteins, extrinsic fluorescence has to be ma
de use of.

Given below a,.e a few examples of use of fluorescence polarization to biochemis
Studies on Proteins
The enzyme lactate dehydrogenase is a tetramer. The association/dissociation pro
been studied using fluorescence polarization. The trick is in tagging dansyl
to the polypeptides. When the monomers associate to form tetramers, the resultin
is large. Thus polarization increases as association occurs. When the tetramer
depolarization occurs. It is also seen that depolarization and loss of activity
in hand meaning that the tetramer is the active form while the monomer is inacti
The effect of various environmental factors, such as the pH, the ionic strength,
and the
the association kinetics has also been studied using the fluorescence
Tag an extrinsic fluor to an antigen. Incubate the antigen with a mixture of ant
ibodies. If
antibody specific for the antigen is present in the mixture, binding will occur.
This binding
rise to the antigen-antibody complex which will be large. Naturally, the polariz
to the extrinsic fluor should increase owing to lesser rotational motion of the
complex. This
can be used to detect the presence of specific antibodies in a given mixture. No
t just
Even the kinetics of binding can be assayed with the help of polarization.
What is true for the antigen-antibody interaction is true for receptor-ligand in
teraction, as
as for the substrate enzyme interaction. These systems too have been studied usi
in Proteins
If one can tag an extrinsic fluor to a protein without changing its conformation
, then
in protein conformation can be studied using fluorescence polarization. Conditio
flexibility of a protein will decrease polarization by giving rise to higher rot

of different proteins and the different conditions that contribute
can be studied.
Presence of disulfide linkages can also be studied with the help of this techniq
ue. If treatment
protein with 2-mercaptoethanol reduces its fluorescence polarization, disulfide
be present (2-mercaptoethanol destabilizes disulfide linkages and will thus incr
ease the
protein concerned). The method may even be made quantitative for measurement

Luminescence may be described as the emission of light from a chemical
the temperature of incandescence. The phenomenon is usually ascribed to
taking place in solution producing molecules in an excited state. While some
release energy in the form of heat, some others release it in the form of photon
of luminescent compounds are luciferin, acridinium salts and luminol.
Luminescence has been classified into two categories. Luminescence produced by
chemical means is known as chemiluminescence. Example can be cited of oxidation
luminescent compound (e.g., luminol) with hydrogen peroxide in the presence of m
which act as catalyst. Luminescence produced by the intervention of an enzyme is
bioluminescence. As compared to chemiluminescence, bioluminescent systems conver
t and
a higher proportion of energy as photons.
Luminescent Measurements
Luminescent measurements have several advantages over spectrophotometry. First o
f they are more sensitive as compared to spectrophotometry. Theoretically as lit
tle as one
(I0-8 mole) of the analyte may be assayed. Although this limit is not achieved i
than femtomole quantities are measurable. The second advantage concerns
instrumentation of luminometers. Since luminescent light is virtually monochroma
tic as
result of its emission through a specific reaction, elaborate wavelength selecto
rs, so
for spectrophotometers, are not required in luminometers.
The basic featm-es of luminometers are (i) a light tight chamber in which the
containing the sample can be placed. The chamber is also thermostatically contro
facility for addition of luminescent reagents in a llght-tight fashion, and (iii
) a detector which
usually a photomultiplier along with suitable amplifier and a recorder. The li
reaction taking place in the cuvette is measured either as a peak value or as th
e rate of chan
in the intensity. While the former method serves to measure the
of interest, the latter is suited for measuring enzyme activities.
The awareness of the advantages of luminometry have prompted improvement in,
commercial availability of luminometers. Three systems in frequent use are firef

luminescence and luminol chemiluminescence. The principles and applications of e

systems are described below.
(i) Firefly luminescence and ATP measurement : Luciferase, in the presence of ma
catalyzes the following reaction.
Luciferin + ATP + 02
Oxyluciferin + AMP + CO2 + Photon (562 nm)

The reaction stoichiometry is such that for each molecule of ATP reacting, one p
of maximal intensity at 562 nm is prodiced. The method, therefore, is the most s
method for ATP measurement and much less than one f mol (10-s tool) of ATP can b
e measured.
The system becomes absolutely specific for ATP if all the reagents are purified.
By linkage to
another reaction, this method has been used to assay numerous ATP-specific enzym
es and
their substrates such as creatine kinase, creatine phosphate and triglycerides.

(tl} Bacterial luminescence and measurement of coenzymes : The coenzymes that ca
n be
measured by this system are NADH and NADPH. The system utilizes a purified oxido
(specific either for NADH or NADPH) obtained from the bacterium Beneckea harveyL
The sequence
of the oxidoreductase reaction coupled to a bacterial luciferase is as follows
NAD{P]H + H+ + FMN
FMNH2 + R.CHO + 02
FMN + R.COOH + H20+ Photon {495 nm)

A photon of maximal intensity at 495 nm is produced in the reaction in which the

bacterial luciferase catalyzes the oxidation of an aldehyde by oxygen in the pre
sence of
FMNH2. The method allows about 100 fmol of NADH to be assayed. The system can be
utilized to measure numerous oxidoreductases which utilize NADH or NADPH. The
substrates of such enzymes can also be assayed by this system.
(ili) Chemiluminescent assays using luminol : Several compounds have been used f
;hemiluminescent systems, but luminol has been the most popular. Luminol is oxid
by hydrogen peroxide at pH 10-11 if copper, chromium, iron or haemin compounds a
used as catalysts. Luminol may be oxidized at neutral pH if peroxidases or vario
us other
oxidases are used as catalysts.
CO0+ 2HO + 20H[ "COONH2 O

+ N2 + 4H20 + Photon
{430 lu)

Photons with maximal intensity at 430 nm are produced. However, the photon
efficiency is only 1% and the method is capable of assaying 1 pg of hydrogen per
oxide or
0.1 pg of peroxidase per ml solution. The system lends itself to measurement of
peroxide produced by specific enzyme methods from such substrates as glucose or
Additionally, luminol has been much used as a marker in luminescent immunoassays
Use of Genetic Engineering in Blosensors
Various laboratories world over are trying to develop biosensors that are based
on the
ability of genetically engineered bacteria to emit visible light in response to
compounds. The ease of measuring light makes this type of biosensor especially a
The following example will make the understanding of the above approach easier.
Vibrio Jischeri, a marine bacterium possesses lux genes which are involved in th
emission of light. The lux operon consists of five structural and two regulator)
, genes. Lux
A and the lux B gene code for two subunits of a heterodimer flavin manoo-ygeis-e
luciferase which catalyzes light production by oxidation of a reduced aldehyde.
production is catalyzed by enzymes encoded by lux C, D, and E genes.

regulatory C D A B E

Biophysical Chemistry
Another bacterium, Serratia marcescens, possesses the mer genes, which are invol
ved in
mercury detoxification. These genes are inducible genes and are transcribed only
when mercury
is present in the medium.
Geiselhardt et. a/. of ClarksonUniversity, New York, have recently fused these t
wo operons
into a plasrnld so that the lux genes are situated downstream of the mer genes a
nd are therefore
placed under the mer promoter. Naturally, whenever mercury is present in the med
ium, not
only are the mer genes, but also the/uxgenes are induced owing to the mer promot
er controlling
the expression of both.
E. coli cells were transformed with this plasmid. These E.colicells, when placed
in a medium
containing mercury, emitted light which was easily measurable. This is then an i
deal biosensor
to measure mercury in any given medium.
Like the mer gene system, genes for detoxification of other elements are also fo
und in
certain bacteria. Bringing the lux genes under the control of the promoters of t
hese gene systems
may give rise to biosensors for other elements as well.
The flame photometric analysis method is more or less similar to that of spectro
with the exception that the place of the sample cell is taken by a flame. Conseq
uently, it is the
absorption or emission of specific wavelengths by excited atoms that iS studied
by this technique.
The-optical system and even the photo-detectors used in spectrophotometry and fl
spectrophotometry are identical.
The general method of flame photometry can be applied in two complementary ways:
emission flame photometry and atomic absorption spectrophotometry. Both the vari
ations will
be dealt with simultaneously.
Volatilization of molecules in a flame produces free atoms and then excites them
to higher
energy levels. The characteristic emission spectrum of the element is produced w

hen the excited

atoms return to their ground state. This is the principle of emtssionflame photo
metry. Atomic
absorption spectrophotometry, on the other hand, measures the absorption of a be
am of
monochromatic light by atoms in a flame. Since the transitions available to the
electrons in any
given atom are specified by the available energy levels, atomic spectra are abso
lutely specific for
the element involved. Moreover, the energy absorbed or emitted is proportional t
o the number
of atoms present in the optical path. Thus, apart from giving the identity of th
e element(s)
present in a sample, flame photometry also provides information about the quanti
ty of the
element(s] present.
The amount ofenergy emitted also depends upon the (t) temperature and (ii) compo
of the flame. It is therefore very necessary that the two flame variables must b
e maintained
constant and that standard solutions be used to calibrate the system. The need t
o maintain
flame composition constant also dictates which element should be determined firs
t. Thus, sodium which gives a very high background emission is measured first an
d the quantity of sodium
determined is added to all the standards. Certain elements, such as the alkali m
etals, enhance
the emission of other elements. On the other hand, some substances like aluminat
e and silicate
cause a decrease in emission of other elements. To relieve this deleterious effe
ct certain other
elements known as the releasing agents (strontium or lanthanum) must be added.
Another way to deal with interferences is to measure all interfering components
in a given
sample. After this, standards for each of the components are prepared which cont
ain the
previously determined concentration of interfering components. This is known as
cyclical analysis.

Spectrophotometry 243
About two to three such cycles are necessary before an accurate idea of the quan
tities of all
sample components can be deermed
Organic material in biological samples (which might cause interference) is usual
ly removed
by ashing. To prevent more volatile elements from getting sublimated, the ashing
is usually
carried out under low temperatures in the presence of oxygen. Alternatively, liq
uid ashing, i.e.,
oxidative digestion of the sample in hydrogen peroxide/concentrated sulphuric ac
id solution
may be carried out. A small amount of selenium sulphate, if added, acts as a cat
alyst, while
lithium sulphate is sometimes added to raise the boiling point.
It is advisable to store samples md standards in polythene bottles. This is so s
ince even
the good quality glass containers release metal long.
Flame instability c.an cause large errors in flame photometric analysis. It is,
essential that all assays be carried out in triplicate. Calibration cues should
be checked
or reconstructed when the assays are carried out. If high accuracy is desired, a
solution containing more or less the same concentration of the element as the sa
solution, is assayed immediately before and after the sample solution. This meth
od is
known as bracketting. Very frequently, internal standards are used and the choic
e element
for this purpose is usually lithium.
Instrumentation for Emission Flame Photometry
The basic components of a flame emission spectrophotometer are shown in Figure
8.33. The individual components are discussed below.

Air from -- ....
Detector Recorder

Figure 8.33 Basic components of an emtssion Jlame photometer

(i) Nebultzers or atomizers : Samples, before they get into the flame, must be c
onverted into
a fine spray, i.e., nebulized. This is necessary because large drops do not rema
in in the hottest
part of the flame for a long time and therefore may not become volatilized and e
xcited.. Because
of this reason, the nebulizer becomes the most critical part of a flame photomet
er so much so
that the efficiency of an analysis depends on the efficiency of the nebulizer.
nebulizers are essentially of the 'scent spray' type whereby a forced stream of
at nearly the speed of sound) passes over a capillary tube dipping into the test
solution. This leads to a considerable drop in pressure leading to a suction of
the sample
through the capillary. As the sample emerges from the tip of the capillary it is
broken into a
mist of fine droplets by the flow of air. To eliminate large drops, a cloud cham
ber is placed
between the flame and-the nebulizer where the large drops condense and drain awa
y. The
design of a simple nebulizer is shown in Figure 8.34(A).

Compressed Sample
Figure 8.34 (A) Design of a simple nebulizer
Since large droplets condense and drain away, there is a large loss of sample (9
0% is lost,
only 10% reaches the flame) and if one has only a small amount of sample to star
t with, this
poses a big problem. To alleviate this problem, an improvement on the basic desi
gn of the
nebIzer has been achieved by placiv an impact bead a few millimeters away from t
he nebulizer
tip. The large droplet, when they emerge from the tip, collide with the bead and
are broken into
smaller droplets. This design lowers the average droplet size and thus improves
the efficiency of
the analysis besides reducing the loss of sample. The design of this nebulizer i
n shown in
Figure 8.34 (B). "

Impact bead

Figure 8.34 (13) Nebulizer with an b'npact bead

(it) The flame (Also see Box 8.5): Various gas mixtures producing different flam
differing in their temperatures are used in flame photometry. Table 8.10 lists s
ome of the
often used combinations.
consuming. Moreover, atleast 2-3 ml of sample are required

Table 8.10 Fuels. gases and temperatures used in flame spectrophotometry
Gas (oxidant}
Temperature (C}
Elements assayed
Propane ,
Natural gas
Nitrous oxide
Na, K

(it0 Monochromators: In sophisticated instruments prisms or sometimes even diffr

gratings are used. However, for routine analysis of such elements as calcium, so
dium, and
potassium a simple filter might suffice.
(iv) Photocells: These are the usual detectors in a flame photometer. Unfortunat
ely the
flame instability reduces their accuracy. Therefore a multi-channel polychromato

r is used in
some routine procedures to allow measurement of up to six elements simultaneousl
Instrumentation for Atomic Absorption Spectrophotometry
This is practically similar to that of emission flame photometry. An important p
oint of
difference is the need to have a radiation source. It is practically impossible
to isolate a particular
.resonance wavelength from a continuous source by using a prism or a diffraction
grating or
both simultaneously. This problem was solved with the development of hollow-cath
ode discharge
lamps. Such lamps produce monochromatic radiation characteristic of the element
In these lamps the cathode is a hollow tube which is lined by the element in que
stion. The lamp
will thus emit monochromatic radiation characteristic of the emission spectrum o
f the element
involved. Such lamps ha,e now become commercially available for a long range of
elements. In
less sophisticated instruments, a continuous discharge lamp with double monochro
mators is
Instruments with single and double beam optics are available. The double beam op
arrangement is more or less similar to that of double beam apparatus in absorpti

Bophyscal Cherrtr
The primary use of flame photometry and atomic absorption spectrophotometry is i
n the
assay of elements in biological samples such as blood, plasma, other body fluids
such as urine,
saliva, cerebrospinal fluid and milk, tissues, cells, organelles, soils, plants
and even in the
macromolecules. Flame photometry is used in routine estimation of sodium, potass
ium, calcium,
magnesium, mhnganese, indium and thallium in a host of biological samples. Flame
is very sensitive to the estimation of alkali, alkallne-earth and rare earth ele
ments. It also
permits estimation of silver, aluminium, gold, bismuth, cadmium, copper, mercury
, lead,
selenium, iron and zinc. Although most elemental analysis is possible directly,
copper, iron,
lead and mercury need to be 6xtracted from the biological fluids before they can
be assayed.
Atomic absorption spectrophotometry (AAS) is a more sensitive technique and can
detect presence of much less quantities of elements with the exception of alkali
and alkali
earth metals for which flame photometry is preferred. AAS can detect quantities
less than
1 part 10-e of more than twenty elements.
Except for minor differences, the performance of both the techniques is more or
comparable. Flame photometry, however, has a very important advantage over AAS i
that it allows simultaneous quantitative multielement analysis to be performed.
A list of wavelengths used and detection limits for various elemerts in emission
absorption flame spectrophotometry is given in Table 8.11.
Table 8.11 Measurement various elements by emission and absorption flame
spectrophotomet r: Detection limits and wavelengths used
Absor tion
Wavelength Detection
- limit

(parts 10}
(parts 10)
0. I



24 7
Atomic Fluorescence
We have seen the relationship between absorption spectrophotometr" and
spectrofluorometry. A similar relationship exists between atomic absorption
spectrophotometry and atomic fluorescence spectrophotometry. In atomic fluoresce
the flame retains its role as a source of atoms; these atoms, however, are excit
ed by an
intense source of radiation and their fluorescent emission is assayed at an angl
e of 90
in a manner similar to that of spectrofluorimetry. Lack of sufficiently intense
source for
many elements has been the limitation of this technique, however, with time
instrumental developments are overcoming this problem. High intensity hollow-cat
lamps, or xenon or mercury discharge lamps are used.
Perhaps the greatest advantage of atomic fluorescence is its extreme specificity
complete freedom from many forms of interference. Moreover, the sensitivity of t
technique is much better than that of the absorption method. We may cite the exa
mple of
zinc and even cadmium where the levels detected are as low as 1 and 2 parts 10-I
Developments in the field of instrumentation will surely make available this
technique for use in biology.
The use of nuclear magnetic resonance (NMR) in the determination of molecular
structure has been a major growth point in biochemistry. Until recently technica
l and
theoretical difficulties were major inhibitory factors for the application of NM
R. In recent
times, however, developments in instrumentation and accumulation of basic data h
allowed this technique to be applied to determine macromolecular structure and
Many physical methods are comparatively uninformative when applied to aqueous
solutions, and those which can be readily applied often depend on alterations of
properties and therefore cannot reflect much of the detailed structural informat
ion of
interest. Figure 8.35 provides a comparison of the magnitude of energies and the
frequencies of
transitions over the entire spectroscopic range. It will be observed that a char
acteristic feature

of NMR spectroscopy is the very small value of the energy absorbed in the transi
tion of nuclei to
the excited state. It is natural then, that the appearance of the spectra is dep
endent on slight
variations in electronic configuration. Such spectra can be expected to reflect
the more or less
unaltered structure and conformation of macromolecules in solution.
Frequency 3 x 1015
5 1012

4 1014

UV & visible ----Infrared -Microwave - -- Radio---EnergyA , 260

Electronic &
Transitions------ Vibrational
9.5 xl0-4 9.5 x 10-7

Biophys,.al Chemistry
Most nuclei, the protons, and the electrons possess inherent magnetic fields. Th
e effect of
nuclear fields are, however, too small to be observed in the ambient magnetic fi
eld of the earth.
Artificially created intense magnetic fields can, however, make the nuclei assum
e specific
orientations with corresponding potential energy levels. Nuclear magnetic resona
spectrometry addresses itself towards detecting the minute amount of energy abso
rbed or emitted
as the nuclei jump from one energy level to another.
Magnetic Properties of the Nucleus
In order to explain the magnetic properties of certain nuclei it is necessary to
assume that
the nuclear charge is spinning around an axis. Such a nucleus is then supposed t
o possess an
angular momentum represented by a spin quantum number, I, which is assigned half
values, 0, 1/2, 1, 3/2 ........ 9/2 depending on the particular nucleus. Nuclei
possessing anodd
mass number {either the number of neutrons or the number of protons should be od
d, but
never both odd) are assigned half-integral spin quantum numbers; for example H,
gF, P()
and B(3/2). Figure 8.36 (A) illustrates a nuclei as a spinning sphere. This spin
ning charge
gives rise to a magnetic field. There is an associated nuclear magnetic moment,
, along the
axis of the spin. Nuclei possessing odd numbers of both neutrons and protons hav
e an integral
spin number of I = 1. Thus, the charge on them is distributed non-symmetrically
(e.g., 2H, N).
Nuclei possessing even numbers of both protons and neutrons (2C, O, 3S, etc.) ar
e not measured
in n.m.r, experiments because they do not possess an angular momentum (I = 0) an
d do not
exhibit magnetic properties.
North magnet pole
---- Nuclear magnetic
(Magnetic component of I7'

Precessional axis
South magnet pole
lgure 8.36 (A) Spinning charge in nuclei generates a magnetlc fleld with a rnagn
etc moment p. When placed in a
powerful unorm magnetlc fleld the spin axes of these nuclei align themselves in
an manner with respect to the fleld and, like the top of a gyroscope, precess ab
out the fleld direction in such a
way that each pole of the nuclear axis sweeps out a c'cular path in the XY-plane
, When a second,
weaker.field of rad frequency (RF} is applted at right angles to the uniform mag
netic fleld, the nuclei
may undergo a transttion to a higher energy level by absorbing the RF energy. On
ly that RF whose
sense of rotatlon is e.mctly equal to the rate of precesslon of nuclear dpole re
quency of RF equal to
precesslon frequency) will be absorbed.

Magnetic nuclei assume discrete orientations with corresponding energy levels un
der the
influence of external magnetic fields. The value of I determines the number of q
uantized energy
levels available. This is given by the series :
l,I- 1, I-2


Any given nucleus can have 2I + 1 possible levels or orientationsl Thus

for IH, 15N, gF and
sip, with I = V2, only two orientations are available. These levels are
described as
(0 aligned with the applied field (lower. energy); and (tO antiparallel
to the field (higher
energy). These two levels (Figure 8.36(B)) will have the energy of -Ho a
nd +Ho for low
and high energy respectively, where Ho is the intensity of the applied m
agnetic field and
is the nuclear magnetic moment. The difference in energy, E, is then equ
al to 2Ho.
The general relationship is as follows :
E -- Ho/I
Alignment against
the field
External field, Ho
I= +V2
No field
<.zE = hv = HoI
I = -V2
Alignment with the field
Figure 8,36 (B) Energy states for nuclei in a magnetic fleld
In order to change from low energy state to high energy state, such nuclei must
absorb the
appropriate quantum of energy. In a magnetic field of several hundred millitesla

(several thousadd
gauss} such nuclei absorb radiation in the radiowave region of the electromagnet
ic spectrum.
This phenomenon is known as nuclear resonance or nuclear magnetic resonance. The
equation can, thus, also be written as
AE = hv -- 2Ho (for cases where I =
If we combine the two equations, we get
2rv - 2 ]Ho YHo
here 2 serves to convert linear frequency to angular units of frequency. , which
is obviously
equal to 2r/hI is known as the gyromagnetic ratW and is a characteristic propert
y of the
nucleus. Another mathematical expression for can be derived from the above relat
ionships :
Gyromagnetic ratio =y This relationship is a fundamental equation for n.m.r. The relationship obviousl
y describes
the ratio between the frequency and the field. The ratio is sometimes termed *re

Btophyslcal Chemistry
The frequency of the radiowave absorbed during n.m.r, is dictated by () the isot
ope being
studied, and (tO the intensity of the magnetic field.
Figure 8.37 The n.m.r, spectrum of
methanol (CHaOH)
Obviously all nuclei do not absorb at the
same applied field but the absorption depends
upon the magnetic field which a particular
nucleus, feels. Clearly, the effective field
strength is different for different nuclei as
one nucleus will have slightly different
environment from any other nucleus, Thus,
at a g,ven radio frequency', dlfferent nuclei
will require slightly different magnetic field
strength to give rise to the same effective
magnetic strength which causes absorption.
It is, therefore, a normal practice to measure
the absorbance of a sample at a
monochromatic radiowave frequency while
varying the magnetic field intensity.

n.m.r, spectra are thus a plot of energy absorbed against the magnetic field str
ength, applied.
Such a plot is shown in Figure 8.37. The number of signals obtained on such a pl
ot are indicative
of the different sets of equivalent nuclei or protons. For example, in Figure 8.
37 there are two
signals which are indicative of two sets of protons existing in different enviro
nment, viz., CH3,
and --OH. The area under the peak in such plots is directly proportional to the
number of
nuclei or protons which are responsible for the resonance. For an example one ca
n refer to
Figure 8.37 again; the peak corresponding to CH3 is much higher than the peak co
to ---OH.
For a clearer understanding, let us consider the number of signals generated by
compounds as examples. Acetone andcyclobutane are considered first. The structur
al formulae
are given below.

Hsc/C ---0
It is easy to see that all six protons of acetone and all eight protons of cyclo
butane exist in
the same environment. Therefore, in an n.m.r, experiment, only one signal will b
e observed for
each of these compounds. The area under the peak of cyclobutane will be more tha
n that under
acetone peak owing to a larger number of protons in the former.
We have already seen how CH3OH gives two n.m.r, signals owing to two different s
ets of
proton equivalents, i.e., sets of protons existing in two different environments
. Another compound
Which gives two n.m.r, signals is 1, l-dibromomethne, CH3CHBr2. Propanal. CH3CH2
CHO, on
the other hand has three sets of equivalent protons existing in three different
(CH3, --CH, and --CHO); this compound gives three n.m.r, signals.
Chemically equivalent protons should also be stereochemically equivalent. Thus,
a given
set of protons is chemically equivalent only if all the protons exist in identic
al environment even
when stereochemical formula of the molecule is written. This principle can be gr
asped better
with the help of an example. The compound 1,2-dichloropropane is expected to giv
e three
n,m,r, signals in the following manner:

Heft : Ho - oH
3 2 i
In an n.m.r, experiment, this compound gives four signals. To understand this le
t us take
a look at the stereochemlcal formula of the compound.
It is evident from the above formula that the two protons attached to C do not e
xist in
exactly identical environments. Consequently these two protons will give rise to
two different
signals rather than one.
Chemical : Position of Signals
We have seen that the number of signals in an n.m.r, spectrum gives information
about the number of equivalent sets of protons/nuclei that the compound possesse
s. The
position of these signals is indicative of the nature of the environment surroun
the protons/nuclei. For example, the position of the signals can reveal whether
the environment
of proton is aromatic, aliphatic, acetyleni.c, vinylic, or whether the proton ex
ists near an electron
withdrawing group or an electron releasing group. Each o the above named sets of
have electronic environment characteristic of the type: These proton sets theref
ore absorb at
different applied field strengths. It may be said that the electronic environmen
t of the protons
dictates where the proton will absorb in the spectrum.
The electrons involved in covalent bonding are paired and usually do not have a
magnetic field. An applied magnetic field, however creates additional modes of c
irculation of these electrons
thereby generating a small localized magnetic field. This magnetic field is prop
ortional to the
applied magnetic field. Such nuclei, circulation of electrons around which has g
iven rise to a
magnetic field, might not resonate. The phenomenon is known as d/amagnet/c shie

8.38), and the nuclei are said to be shie/ded. Such nuclei are not resonating be
cause rather
"than experiencing the fuji magnetic field applied, H0, they are experiencing a
smaller magnetic
field due to the oppeelflon created by the field of electrons.
where is the shielding constant whose Caue depends upon the density of electrons
around a proton or nucleus. It is thus a function of the structure of the compou
nd. For the
above situation, a higher magnetic field will be needed to make the nuclei reson
Thus, shielding of nucleus proton shifts the position of the signal, Le., absorp
tion upfle.kL

Ho -.-..-: :..
""" ?...F:.'.i

Figure 8.38 Diamagnetic shielding. Local magneticJlelds opposing Ho generated by

uuced electronic drculatlon
Magnitude of shielding decreases with increasing electron withdrawing power of t
he nearby
substituents (strongly electronegative substituents such as oxygen). Sometimes t
he induced
field augments the applied field. The nucleus is then said to be deshlelded and
a smaller applied
field is required to make such nuclei resonate. Thus. deshielding shifts the abs
orption downfleld.
The above discussion can be understood better with the help of an example. Let u
s again
consider the n.m.r, spectrum of CH30H given in Figure 8.37. One can see that the
due to --OH is occurring at an applied field lesser than that required for --CH3
. This iS because
in the former, the proton is adjacent to the strongly electron withdrawing oxyge
n atom. The
proton is therefore deshielded and requires lesser magnetic field to resonate; P
rotons in CH3 are
more shielded and therefore absorb at a higher magnetic field. The signal due to
CH is therefore
shifted upfield.
It is usual, just as we didin case of absorption spectrophotometry, to compare t
he positions
of n.m.r, absorptions arising out of shielding and deshielding with a standard r
The shifts in positions of n.m.r, absorptions as compared to the standard refere
nce are
known as chem/ca/sh/fls. For proton spectra in nonaqueous media, the reference m
is tetramethyl sflane (CH3)4Si, abbreviated as TMS. TMS contains 12 protons and
all these
protons are chemically equivalent. Therefore, TMS gives a single sharp signal in

n.m.r, experiment.
Silicon has a very low electronegativity and therefore equivalent protons of tet
ramethyl sflane
are deshielded very little; it may be said that shielding of equivalent protons
of TMS is greater
than most of the organic compounds, Therefore, n.m.r, signal for tetramethylsfla
ne is taken as
a reference and chemical shifts for different sets of protons is determined rela
tive to it. In
comparison to this reference TMS signal, signals for different types of protons
will appear at
different field strengths. This difference in the absorption posttlon of tte pro
ton with respect to
TMS signal is called chemical shift. The magnitude of the chemical shift Is expr
essed as 8-value
which is calculated as follows:
8 = HSAMPUS --HTMS X 10e
where HSAMPLE and HTMs are ,tl e positions of the absorption lines for the sampl
e and
reference respectlvcly, expressed in frequency units {hertz}, and i is the opera
frequency of the spectrometer. is usually expressed in parts per million {ppm}.
Most chemical shifts have values between 0 to 10.

Another scale used for measurement of chemical shift is known as the x (tau) sca
le. It is
related to scale by the following s.imple relationship:
= 10- "
It is usual to plot n.m.r, signals with magnetic field strength increasing to th
e right. TMS
is assigned a value of 0 ppm and its signal appears at the extreme right (Figure
8.39}. Protons
which experience greater deshielding have larger values. This is so with most of
the organic compounds. A list of values for chemical shifts for protons in diff
erent environments is provided
in Table 8.12.

Highly shielded signals
of protons

Chemical shift in ppm

9.0 10.0

to -0.5
to +6.0
to -5.O
- 12,0
- 12.0
- 17.0


Biophysical Chemistry
S Uttlng ,
We have dy seen how elg d deselg ect posion of n.m.r. specWa. e n.m.r, speca bec
ome fuer compcated what Is o as spin-sp coup. We m dersd s phenomenon fly e foHo
Consider eyl brode, CHCHBr: from what we have considered so f, we ow at
s molece cons o ds of protons denot as a d b low.
It Is erefore et at e n.m,r, s of s md Ist of is, We so eect t e o sis be smets,
i,e., e sis each have one peak. e n.m.r, spectm of this compound, however, show
s two sisals
compos of mple, i.e., a cluster of pes. (re 8.). For a up of ptons we
obsee a slgn consisting of a cluster of three pes (plet) whereas e s for b
oup of protons consis of a cluster of fo ps (quiet). y have e ss spt? e molece o
f eyl brode, e sp of (HO c couple e ney meylene oup ee disct ways reon to e e fi
eld. ese ee ways of coup e
8.0 7.0 6,0 5.0 4.0 3.0. 2,0 1.0.



Signal from -

{B) (Not effectlng)

'a' protons



Spin influence of
protons 'b'
This is the reason why a triplet signal is given by --CHs.
Let us now consider the reason for a quartet signal for the-CH2 group. The three
protons of the methyl group couple with the adjacent methylene group in four di
fferent,ways in relation
to the external field as outlined below.

i Spectrophotometry
/(A) ,
(ReinforcLng : Strong)

(B} l (Reinforcing : Weak) External

Slgnal from
(C} 6' 4% (Opposing : Weakl field
'b' protons
(Opposing : Strong)
Spin influence of protons 'a'
From the above, it is clear that the slittLng of the signals into multlplets has
been because
'the different environments of two sets of protons with respect to the nearby pr
otons. It is
that this mutual magnetic influence between the two sets of protons is not trans
but through the electrons of the chemlcal bond between the two groups. This
which involves interaction between like and different spins of nearby nuclel is
Analysis of the n,m.r, spectrum of a compound, only the empirical formula for wh
ich is
beyond the scope of thls book. We are, however, at a stage where me e.aa y to
a given compound gives a partlcular n.m.r, spectrum. We again take up the
the first example. From its formula we can deduce that the compound
two signals. It does; but both the signals are multiplets. One signal is a quart
We have already seen the particular spin-spin coupling by which we
that the quartet belongs to the methylene group while the triplet belongs
the methyl group. Since the methylene group is nearer to the bromine atom, we ex
pect its to be deshielded more than that of the methyl group. Consequently we ex
pect the
due to the methylene group at a lower applied field as compared to the methyl gr
figure it can be seen that the signal for methylene group occurs at 6.6 as compa
red | that for the methyl group which occurs at 8,35 .
b a
As a second example let us consider Lelchloroethane, CI2CHCH2CI.As indlctted, tw
o sets
and we might expect two signals. Figure 8.41 shows two signals indeed,
a triplet while the other is a doublet. Which of the slgnal belongs to aand

0 ppm (6)
Hgu 8.41 N'MR specan of bdoroethane. See text for descr/pKon (taken from cata/og
to b? The proton set b has two chlorine atoms (electron withdrawing) near it
proton set ahas only one such atom near to it. We, therefore, rnlght expect prot
on set
more d6shielded as compared to o. If this is so, the triplet which is present at
a lower
should belong to group b and the doublet should be due to a. Let us also confirm
this by

Bophus.co Chrrtrv
consideng the spin-spin coupling. Splitting of signals from proton set aby the p
roton b should
as follows
(A) ' (Reinforcing)
T External
(B) (Opposing) I field
Thus coupling of proton set a with a single proton b will give rise to a doublet
. On the other
hand signal from proton b will be split by proton set into a triplet in the foll
owing manner.
(Non effecting)
[ External
| field
Thus from spin-spin coupling also we can see that the triplet belongs to b while
the doublet
belongs to o.
Due to all the complications which split and shift the peaks, it is a difficult
Job to
interpret n.m.r, spectra. Usually services of an expert are required. Sensitivit
y of the old
generation n.m.r. Instruments was much less as compared to other optical techniq
and such other techniques as gas chromatography, and mass spectrometry. The mode
day n.m.r, instruments, called the Fourier transform n.m.r, are butt around a sm
high speed digital computer. These instruments have revolutionized the practice
of n.m.r.
in organic chemistry.
Figure 8.42 shows the basic components of an n.m.r, spectrometer. It would not b
wrong to say that the magnets are the heart of an n.m.r, spectrometer. In compar
old instruments extremely heavy electromagnets (103 104 kg) produced fields ranging
from 1-10 tesla. The newer gendration spectrometers, however, use superconductin
solenoids which generate fields above 3.5 teslas. The magnetic field can be vari
ed by

about 10-2 tesla by using an auxiliary sweep generator. Since the nuclei absorb
in the
radiowave region, the source of radiation is a radio frequency transmitter. The
must be dissolved to a relatively high concentration in a solvent which is proto
or CDCI3). Sample is usually placed n a high precision diameter tube (this minim
izes the
variations in the magnetic field) and is rotated at high speed by an air turbine
. The
absorption signal is then detected by a radio receiver..The signal is amplified
and recorded.
. ,/ Radio receiver
/weep coils
Figure 8.42 Main components of a nuclear magnetic resonance spectrometer
"(0 Structural diagnosis: The n.m.r, spectroscopy is mainly applied to study the
of small organic molecules and small globular proteins. Thus, structural informa
tion which

25 7
relates to the biological functions of the antibiotics such as valinomycin and g
have been obtained from n.m.r, studies. Structural information about small prote
ins such
as some neurotoxins, various cytochromes, hen egg-white lysozyme, and calcium bi
proteins have been obtained using n.m.r, spectroscopy. For protein studies, howe
ver, the
technique is combined with X-ray tudy for better information.
(ii) Study of dynamic-characteristics of protein structure: Processes which modu
intemuclear distances, e.g., .the internal motions of macromolecules or chemical
affect the intrinsic properties of n.m.r, resonances and make it possible to pro
be the
dynamic aspect of molecular structure by this technique. Thus, internal motions
proteins such as the opening of secondary structure, aromatic side chain rotatio
segmental motion of the main chain, and overall tumbling of protein have been st
using n.m.r, spectroscopy. The proteins which have been studied for their dynami
characteristics include histones, cytochrome b5, prothrombin, plasminogen and
chromogranin A.
(iii) Studies on complex formation : Using n.m.r., it is possible to detect very
conformati0nal changes. Thus, n.m.r, has been used to study complex formation su
ch as
the binding of a ligand to an enzyme, a drug to DNA, an agonist to the receptor,
or an
antigen to an antibody.
(iv) Biological structures and compartments : Compartmentation is an essential p
art of
the organization that characterizes living systems. In the recent past n.m.r, ha
s been
increasingly used to study this biological structure. Extensive use of n.m.r, ha
s been
made to study the conformation of the lipid headgroups of the biological membran
es and
their interaction with integral proteins of the membrane, n.m.r, has also been u
sed to
measure intracellular pH, membrane transport phenomena, and metabolite
concentrations, interconversions and fluxes.
(v) Quant/tat/ve stud/es : Over the years n.m.r, has been used to determine the
of metabolites. As a direct method n.m.r, has an undoubted advantage over freeze
analysis. Measurement of the phosphocreatine concentration in muscle can be cite
d as a
representative example. Another example can be given of the measurement of
hexakisphosphatephytic acid which accumulates in the pith tissue of plants.

(vi) Thermodynamic studies : In the general case of an equilibrium between two s

n.m.r, can be used to measure the associated thermodynamic quantities, if the n.
response of the two states is different, n.m.r, has been used to measure quantit
ies such
as binding constants, heats and entropies of binding, pKa values, and partition
for the distribution of a molecule between different compartments. Examples can
be cited
.of studies made on folding and unfolding of proteins and tRNAs, and the interac
tion between
actinomycin D and deoxy-pGpC, pKa of histidine residues in proteins (e.g. haemog
has been determined using n.m.r. The techniques has also shed welcome light' on
mechanism of action of proteases and on the mechanism of their inhibition by som
(vii) Membrane transport: Membrane transport either in in vivo systems or using
synthetic membranes has been studied using n.m.r. The technique has been used to
study alanine and lactate transport in the human erythrocyte by exploiting the d
in the magnetic susceptibility between the inside and outside of the cells; Very
Na transport in human erythrocytes has also been studied using n.m.r.
(viii) Intact organ studies with n.m.r.: In one of the most intriguing new areas
biochemical n.m.r., 31p has been applied to the study of such intact biological
as heart, kidney, and skelet.al muscle. This has been possible largely because o
f the
development of instrumentation capable of resolving 31p resonances of small mole

such as adenosine triphosphate, adenosine diosphe, .eae phosphate, d orgc
phosphate -- e moles most pot ceHul physiolo. e pK's of er sin molecules of phys
ioloc impoce e ound 7. us their 3p chemlc shifts e
sensive to pH d c be used to mease WaceH pH.
() : Bioloc objects such as its, nuts d ce have n ed proton n.m.r, zeuatoaphy. P
resonce stues of ceH metates is now prodg
sit to ceHul compenflon.
A chec species odd number of elecons ibits chactesc meflc propees much e e nucle
us. e spng acon of unped elecon generates a maec moment, g. If an intense magnet
ic field is applied, the electron assumes
oenmons ower ener, HJ or st (er ener, + HJ e rid& e ener derence, AE, be 2 Ho. In a mer si to e ato
c nucleus, elecon a ec field is able to absorb ener of e proper frequent, = wch
catapult it from e lower to a hier ener level. is phenomenon is o as ecn reso, d
e tecque wch is employed to study s e of behaor is ced eon sp reso
(e.s.r.) s. a mec field of e oer of gauss (i for e.s.r.) e appropte qut of ener
is obned from radiaon e crowave re,on of e elecoec
has en seen respect to n.m.r., It is coon practice to subject e sple to deg male
fic tensies keepg e crowave frequen const. e mec field is
ved e resonce occas. e ea of e.s.r, pe is fly propoon to e numr of ped elecons e
sple vesflgated d us to e concenWaon ofe ple. In qumflve ysis, pe eas of e sple
e comped to e pe ea of a said
wch conts a o quflW of unped elecWons.
Le n.m.r;, e e.s.r, speca do ebit he sptg wch is caused by temons
een e sg elecWons d adjacent spg malefic nuclei. e e.s.r, specWa,
howler, show no phenomenon wch is pel to e chec s seen n.m.r, sc.
from e above it t en at n.m.r. d e.s.r. e complemen tecques.
ure 8,43 usates e basic components of e.s.r, specometer. elds of 0 llltesla, required for accurate ork, are enerated by elecomaets. A sweep
enerors a capacl of I0-I00 tesla e so prodded. Monocomac owave radiaon t be read
y obted y us a yson oscator.
p cs
Oaor Met

Saml)les for e.s.r, mxst be soids. Biological samples which cort laxi[e mouv.t o
i water are therefore frozen in liquid nitrogen before e.s.r, experiment.
Electron spin resonance spectrometry has proven most helpful in studying mechani
of reactions which proceed through free radical intermediates.
Electron spin resonance spectrometry is one of the main methods to study transit
metal containing metalloproteins, i.e., copper (cytochrome oxidase, superoxide d
molybdenum (xanthine oxidase), and iron (cytochromes, ferredoxin, haemoglobin, e
Normally, biological macromolecules which lack unpaired electrons can not be stu
died by
e.s.r, because they do not resonate. These macromolecules can however be "spin l
abelled" (spin
labelling involves the attachment of a stable and unreactive free radical to the
and studied. Thus, lateral diffusion of glycerophosphatides in plasma membranes
has been
studied by labelling glycerophosphaUdes with a stable nitroxide free radical.
While some proteins or enzymes contain intrinsic functional groups with unpaired
there are many which do not. Much information can be gamered about these macromo
by incorporating in them an extrinsic functional group with unpaired electrons.
Spin labelling
refers to the use of stable free radicals as reporter groups or labels. The term
"spin label" was
first coined by McConnell and co-workers in 1965. Spin labels (stable free radic
als) are usually
molecules containing the nitroxlde molety that contains an unpaired electron loc
alized on the
i: nitrogen and oxygen atoms (Figure 8.44). Adjacent methyl radicals (Figure 8.4
4(A)) were developed
between 1960-65. In addition to the nitroxlde moiety, these labels contain a fun
ctional group
useful in covalent attachment of the nitroxide moiety to a larger molecule throu
gh a C--O,
C--S, or C--N bond. Another class of nitroxides developed in 1967 (Figure 8.44(B
)), known as
*doxyl" are usefu. I for studies with steroids, fatty acids and phospholipids.
Figure 8.44 Tgpa:al spia labels

The biochemical methodology behind designing a spin-label experiment is analogou

s to
for any other reporter group study (e.g., affinity label study, substrate-inhibi
tor analog
spin labels carry those functional groups which have been deliberately designed
L at specific high affinity site(s) on the macromolecule and/or covalenfly bind
with hyperreactlve
group in the macromolecule structure. The bound labels, ff they bind covalenfly
spin/abe/s; other labels, binding noncovalenfly are known as spin probes. For pr
a large number of covalenfly binding labels with specificity for distinct amino
become available lately. These labels might be classified as alkylaing, acylatin
(Figure 8.45 (A)), and phosphonylating (Figure 8.45 (B)).

Biophysicat Chemistry
llure 8.45 {A) Sulfonylattng spin labels. {B) Phosphonylating spin labels.
A brief list of the kind of information that spin labels can provide in an e.s.r
, experiment is
given below (also see Box 8.6).
Rates of catalysis: The rate of some step in an enzyme catalyzed reactio
n can be
under circumstances where a change in motional state of the spin label is exhibi
before and after the reaction. This is possible when (i) the conformational
of the spin label on the protein is sensitive to steps in catalytic mechanism, a
when the spin label is (one oi) the substrate.
Active site geometry: Use of spin labels has provided much information a
bout the
depth or width of the substrate binding region of various enzymes, One of the ve
important applications has involved the use of spin labels to compare the active
conformations of families of related enzymes.
Denaturation and protein folding: If a spin label is present in an envir
onment which is
sensitive to the degree of folding or unfolding of the overall protein structure
, much
information is reported by it about the denaturation and renaturation process. O
the years these studies have yielded much important information about the struct
features of these conformational states.
Enzyme-ligand interactions: Depending on the environment of placement, s
pin labels
have been shown to be excellent reporters of conformational changes, even subtle
ones. ThuS, spin labels bound at the active slte provide much information about
enzyme-ligand interactions. In addition, these labels provide information about
pH, salt, or temperature-induced structural changes. These strategically placed
also yield information about protein-protein interactions. In fact, e.s.r, spect

rum of a
spin labeled protein easily detects the narrow line spectra exhibited by proteol
damaged species comprising a few percent of the total protein.
Symmetry and orientation studies: Studies of proteins by spin labeling m
ay be applied
to crystalline proteins as well. Spin labeled enzyme crystals provide informatio
n about
their symmetry and orientation.
Spin labels have provided insight into the kinetics and mechanism of str
uctural changes
of a variety of condensed phases of DNA.
Studies of hydrocarbon and phospholipid motion in lipid bflayers have be
en performed
with the aid of spin labels. Such studies are currently in progress and are expe
cted to

provide much Information about the domains of phosphollplds involved in these
Myotonic dystrophy: Roses eL a/. have studied erythrocyte membranes from human
patients affected with myotonic dystrophy using fatty acid spin labels as probes
. As
compared to controls, the label was found to reside in a more fluid less polar l
ocus in
patients. It has thus been concluded that myotonic dystrophy is a diffuse membra
Other muscle diseases: Work with spin labels is helping in providing ins
ight about the
molecular nature of many muscle diseases. Studies with spin labels, when taken
together with other measurements, suggest abnormal calcium pumping in diseased
membranes and altered interactions with primary membrane proteins such as the
calcium ATPase.
The Mossbauer effect is based on the resonant absorption of nuclear gamma radiat
by certain stable nuclear isotopes. Discovered by Rudolph Mossbauer in 1957, the
a technique which has since had numerous applications in biophysics. With the
which is about 2.2% in abundance in the natural isotopic mixture of iron
isotopes occur in high proportion in biom01ecules. However, some
may be introduced into biological macromolecules by the so called enrich
Mossbauer isotopes most often used for biological applications are 5rFe, and 2I.
It is
present a complete analysis of this phenomenon in this sectlon; a brief explanat
and a brief idea about the applications of this technique is given below.
We have seen that atoms can transit between excited and ground states by absorbi
ng or
emitting electromagnetic radiations in a manner dictated by their electronic str
ucture. Similarly,
nuclei also are capable of transitlons between certain nuclear energy levels as
a consequence of

absorption or emission of electromagnetic radiations such as -rays. In order tha

t momentum
be conserved, whenever a T-ray is emitted form a nucleus, the nucleus recoils. T
he recoil of
nucleus is an energy requiring process and is defined by the following relations
RE = E/2Mca
where M is the nuclear mass, c is the velocity of light, E, is the energy of the
emitted photon,
and RE is the recoil energy. Since both E and RE are derived from the energy of
transition, E is
less than the transition energy AE.

Biophysical Cherrdstry
If the nucleus had not lost some of the transition energy in the recoil, the emi
tted photon
would have possessed exactly the same quantum of energy wch could be absorbed by
nucleus of the same type. However, due to the energy loss, the emitted photon ha
s less energy,
and it can not be further absorbed by another nucleus. Mossbauer discovered exce
ptions to the
above phenomenon when he found that certain low energy y-emisslons took place wi
thout any
recoil. This became possible because the recoil energy in these cases was not su
fficient to make
the nucleus move as a free particle. The momentum of recoil in these cases was t
ransferred to
the entire molecule in which the nucleus was bound, and the large mass of the mo
lecule protected
any energy loss. In such cases, the emitted y-ray will have roughly the same ene
rgy as the.
energy of transition and therefore will be absorbed by another atom of the same
type: Thus,
when y-absorption is measured as a function of energy of the incident radiation,
a very sharp
resonance absorption line is seen at the transition energy of Mossbauer transiti
on. This
phenomenon is known as the Mossbauer effect and the technique based on this is .
Mossbauer spectroscopy.
57Fe is the Mossbauer isotope of keen biological interest because of the natural
of iron in a number of proteins such as cytochromes, haemoglobin, myoglobin, fer
redoxin etc.
We will therefore discuss Mossbauer spectroscopy with respect to this isotope. S
Co is the parent
nucleus of Fe, and the former is used as a radiation source in studies of latter
. As shown In.
Figure 8.46; 5C0 decays in two steps.
14.4 KeV EI y-ray
---------G 14.4 KeV
Figure 8.46 Schematic representation of EC decay ofTCo toTFe. Probabflttles of t
he steps aregen tnpercentaBes.
G and E are the.ground and first excited nuclear states respectively. E to G tra
nsition results in the
emission of 14.4 KeV y-ray. Absorption of this energy raises another Fe nucleus

from G E state.
Through EC decay (see chapter 13), it gets converted, in the first step, to the
stable daughter
nucleus Fe. However, the EC decay does not lead directly into the ground state o
f SFe; rather
it proceeds through the first excited state of TFe which is located 14.4 KeV abo
ve the ground
state. This state has a mean life of just 140 nanoseconds from which it descends
to the ground
state by recoil-free emission of gamma ray photon of 14.4 KeV. Since this is the
exact quantum
o.f energy that ground state SFe can absorb, Co is used as the radiation source.
The absorption
of gamma radiation produced by cobalt-57 source by Fe in the sample being studie
d is then
measured at various temperatures, and over a small range of energies on either s
ide of the
transition energy. It is interesting to note how the range of energies is produc
ed. The source,
which emits 14.4 KeV energy is moved by an electromagnetic drive system at const
ant velocity,
O, toward and away from the sample (absorber}. This movement results in a Dopple
r effect, the
energy E of the y-ray varying by a small amountAE according to the relation
AE - (0tc] E
where cs the velocity of lght. The velocity, #, is.positive when the source is m
oved toward the
sample and negative when moved away. A typical measurement requires velocities o
f the order

of some mm/s. The y-ray intensity transmitted by the sample is recorded in a pro
counter placed behind the sample (Figure 8.47) and this as a function of the Dop
pler velocity/)
is called the Mossbauer spectrum. As an example, Mossbauer spectrum for methemog
lobin is
shown in Figure 8.48. It should be noted that the energy of incident radiation u
sed in a Mossbauer
spectrum is not expressed in terms of wavelength or frequency; rather, Doppler s
hift velocity is
used for this purpose,
Figure 8.47 Principle of Mossbauer spectroscopy. An electromagnetic drive system
(EDS) moves the energy source
(S) towards and away.from the absorber (A) with a constant velocity i. Ttansmltt
ed radiation is measured
by the proponal counter (Z. Lead collimators (C) dej'be beam geometry.
In the discussion above we have said that 'a very sharp resonance line is seen a
t the
transition energy of Mossbauer transition'. From Figure 8.48, however, it become
s clear that
this is not so and in effect quite a few bands are seen. This is so because the
features of a Mossbauer spectrum are affected by the local environment in which
the nucleus
giving rise to Mossbauer effect exists. This local environment is responsible fo
r broadening the
absorption line into a band of variable line width. The band may become further
split by what
is known as hyperflne or quadrupole splitting. Moreover, the band may be shifted
slightly in
energy relative to the standard energy source. This is known as isomer shift. Al
l these effects
depend on temperature and just like in NMR (where different kinds of splitting p
information about the environment) these effects, since they are produced by the
environment, provide much information about the local environment itself. For ex
ample, these
effects tell us quite a good deal about the interactions taking place not only w
ithin the nucleus
itself, but also in the lattice around it.
-I.0 -0.5 0 0.5
1.0 1.5
Doppler velocity (cm/sec)
Figure 8.48 Mossbauer spectrum of human methemoglobln cyanide

Most of the applications of Mossbauer spectroscopy to biology have been with res
pect to
the iron containing proteins. For instance, such studies have proved very sensit
ive in
distinguishing different Classes of cytochromes. However, the most studied iron
protein has been haemoglobin and some results of such studies are cited here. Nu
publications discuss the mechanism of reversible binding of an O2 molecule to th
e iron in
haemoglobin. Yet, the mechanism is not understood in detail. Mossbauer studies o
oxygenated haemoglobin have provided some evidence that duing the binding of oxy
gen to
iron, one electron is transferred to the oxygen molecule. Therefore, the electro
n configuration of
better described as an Fe3+O configuration, rather than as Fe2+O2.

Biophysical Chemistry
Mossbauer studies have also provided some data on the Bohr effect (chapter 1) wh
speaks about the regulation of oxygen affinity of human haemoglobin via pH chang
es in its
surroundings. Although the inference drawn by such studies is negative, it never
theless will be
helpful in the ultimate explanation. What Mossbauer studies tell us is that the
Bohr effect may
not be due to any change in the immediate surroundings of the iron; the change i
n the affinity
of haemoglobin for oxygen consequent to pH changes must be due to changes in the
occurring at greater distances, from the iron. Such changes are probably alloste
ric in nature.
Mossbauer studies have provided quite a lot of information about the dynamic pro
of biomolecules. Let us again take the example of haemoglobin. Iron, to which ox
ygen binds is
not situated at the surface of haemoglobin; rather, it is situated in a pocket a
nd oxygen reaches
the iron via a channel which leads from the molecular surface to the heme pocket
X-ray diffraction studies tell us that this channel is too narrow for the passag
e of oxygen. How
does the oxygen reach iron? Recent Mossbauer experiments give direct evidence th
at the protein
molecule indulges in a sort of breathing motion which opens the channel momentar
ily wide
enough for the oxygen molecule to pass through.
Mossbauer spectroscopy is now being used along with X-ray diffraction for struct
determination of proteins. The details of the process are beyond the scope of th
is book and it
will suffice to say that the technique is used to solve phase problems in X-ray
determination of proteins.
Apart from these studies, Mossbauer spectroscopy has provided a good deal of inf
about the electron structure of bacterial ferredoxin.
Some Solved Problems
A tube containing NADH in solution was exposed to. oxidizing atmosphere
by mistake. Now
the solution contains.both NAD+ and NADH. This solution gives an O.D. of 0.5 at
340 nm and
1.4 at 260 nm. Can you find out how much oxidized and how much reduced form of t
coenzyme is currently present in the tube? Let us tell you that only NADH absorb

s at 340 nm,
but both NAD and NADH absorb at 260 nm. The extinction coefficients of NADH are 1
at 260 nm and 6220 at 340 nm. The extinction coefficient of NAD at 260 nm is 18,0
00. Also
assume that the cuvette used has a standard path length.
Calculating NADH concentration from O.D. at 340 nm is uncomplicated sinc
e NAD does not
absorb here.
A = abC
0.5 = (6.22 x 103) (1)(C)
C =0.8x10
6.22 x 103
Thus concentration of NADH is 8 10-5 M
The O.D. at 260 nm is due to both NAD and NADH..Let us find out just how much abs
is due to NADH.
A = ambC
am for NADH at 260 nm is 15 103
= [!5x I0){I)[8 10)
= 120 10-2

0.225 =
A4o,m =
(am 450(G} x Co) + (am 450(Z) + C}
0.36 =
(15 x l0s Co)+(7 x 103Cz)
Aoo,m =
{am 600(G) Co) + (am 600 (Z) Cz)
0.225 =
(3 10Co)+(6.5 x 10Cz)
Solving for Co in terms of Cz (You may do the opposite and yet solve the problem
0.225 =
Thus, out of the total O.D. of 1.4 at 260 nm, 1.2 is due to NADH. O.D. of only 0
.2 is due to
NAD. It is now easier to find out the concentration of NAD.
= am be
0.2 = (18 x 10s)(1){C)
C = 2xI0-1
= 0.11x10-4
Therefore, concentration of NAD is 1.1 10-s M.
The solution contains two substances G and Z. Both the substances absorb at 450
nm and
600 nm. The absorbance at 450 nm is 0.36 and at 600 nm is 0.225. The molar absor
coefficients of G are 15,000 and 3000 at 450 nm and 600 nm respectively. The mol
ar absorption
coefficients for Z are 7000 and 6500 at the two wavelengths. Can you calculate t
concentration of the two substances? Assume that you are using :a standard pathlength
Let us write equations for O.Ds at both the wavelengths first.
0.36 = 15 x I03C+7 x l0sCz

0.36-7 103Cz =
15 I03Ca
0.36- 7 x I03C
Substituting the above value of CQ in the equation for O.D. at 600 nm
0.225 = (3 x 10CG)+(6.5 x 10sCz)
0,225 -- (3x103) 0"36-7xi03 Cz +6.5x103Cz

1.08xI0 -21x108Cz
0,225 -15x103
Multiplying the right hand term with 15 x 103

1.08103 - 21x lOaCz + 97.5x 108Cz

3.38 x l03= 1.08 x 103-21 x 10sCz + 97.5 x 108Cz
2.3 x103 =76:5x 103Cz
- 3xI0-SM
Cz 76.5x10s
Therefore concentration of Z is 3 x 10-5 M.
We may now substitute the concentration of Z in the equation of O.D.450 or 600 r
0.36 = (15 x 103C) + (7 x 103Cz)
0.36 =
15 x 103 Ca + (7 x 103) (3 x 10-)
0.36 =
15 x 10CG + 0.21
0.15 =
15 X 103 CG
C =
0.15/15 x 103 = 1 x 10-SM
Therefore the concentration of G is 1 x 10-5 M.
To a 4.0 ml solution of glucose was added 2.0 ml of solution containing excess A
MgCI2, hexokinase, and glucose-6-phosphate dchydrogenase. The absorbance at 340
due to NADPH was found to be 0.91 after a considerable amount of time had elapse
d. Can
you calculate the concentration of glucose in (i) the final, and (ii) the origin
al solution. Given
that K values for hexokinase and glucose-6-phosphate dehydrogenase lie far to th
e right.
Assume that you are using 1 cm path-length. The molar absorption coefficient of
Assumption : The two enzymes added to the tube will carry out the ollowing react
ions :
Hexokinase reactions :
. .
Glucose + ATP Glucose-6-phosphate + ATP
Glucose-6-phosphate dehydrogenase reaction :

Glucose-6-phosphate + NADP*
6-phosphogluconic acid--lactone + NADPH + H
The Kq values are far to the right and ATP and NADP* are in exdess. Therefore it
can be safely
assumed that for every mole of glucose consumed, one mole of NADPH will be gener
ated. The
absorption at 340 nm is solely due toNADPH and glucose and other components of t
he reaction
mixture do not absorb at this wavelength. However, since one mole of NADPH is be
ing generated
for one mole of glucose consumed, measuring NADPH will mean measuring glucose.
= ambC
= (6.22 103)(I)(C)
6.22 103
CNDpH = 1.463 10- M NADPH
Since we are taking NADPH as an index of glucose concentration, the above is als
o the
concentration of glucose in the final solution. For finding out the concentratio
n of glucose in
the original solution, we will have to take into cognizance the dilution factor.
C (original) = C (final) x dilution factor
The dflutlon factor of the solution will be 6/4, or 3/2.

Therefore, C (original) = (1.463 x I0-) x 3/2
C (origlnal) = 2.2 10-4 M.
Instead of glucose, if one has to measure glucose-6-phosphate, can the s
scheme of things operate? Also, study the metabolic fate of glucosc-lphosphate. What reaction mixture can you prepare for measuring the
concentration of glucose-l-phosphate?
4. Lactate dehydrogenase was assayed by measuring the. generation of NADH in a 1
cm cuvette
spectrophotometrically. The assay mixture of a total volume of 1.0 ml contained
excess lactate,
buffer, 0.1 ml of enzyme preparation. Semicarbazide is also added to the solutio
n with a view
of capturing pyruvate and carrying the reaction to completion. The absorbance at
340 nm
increased at a rate of 0.04/min. The enzyme preparation contained 50 mg protein/
ml. Calculate
(i} the units of the enzyme present in 1 ml enzyme preparation, and (ii) the spe
cific activity of
the enzyme.
Activity = aA/min = 0.04/min
A = (am) (aC} {b}
= 6.43 I0- M = 6.43 IX moles/litre
Activity = 6.43 IX moles/lit/min = 6.43 10- Ix moles/ml/min. 6.43 10-3 units of
the enzyme are present in 0. I ml of the preparation. Therefore 10 times the amo
unt will be
present in 1 ml of the preparation. Thus 1 ml will contain 6.43x 10- units.
The enzyme preparation contains 50 mg protein/ml. However, only 0.1 ml of enzyme
present in I ml of the assay mixture. Thus the effective concentration of protei
n was reduced
to 5 mg/ml.
Therefore the specific activity of the enzyme here was
6,43 I 0-2
S.A. =

= 0.013 units/mg protein.

Suggestions For Further Reading
Ultraviolet and Visible Spectrophotometry
I. O]sen, E.D., Modem Optical Methods of Analysls, McGraw-Hill, New York, 1975.
Willard, H.H., Merr/tt, L.L., Dean, J.A. and Settle, F.A., Instrumental
Methods of Analysls,
Wadsworth Publishing Company, USA, 1986.
3. Brown, S.B., An Introduction to Spectroscopy for Biochemists, Academic Press,
London, 1980.
4. Rao, C.N.R., Ultraviolet and Visible Spectroscopy, Butterworths, London, 1975

Biophysical Chemistry
1. Udenfr/en, S., Fluorescence Assay in B{ology and Medicine, Academic Press, Ne
w York, 1969.
Willard, H.H., Merritt, L.L., Dean, J.A. and Settle, F,A., Instrumental
Methods of Analysis,
Wadsworth Publishing Company, USA, 1986.
Konev, S.V.0 Fluorescence and Phosphorescence of Proteins and Nucleic Ac
ids, Plenum Press,
New York, 1967.
Infrared Spectrophotometry
Wood, D.L., Infrared Spectrophotometry in Methods in Enzymology, Vol. IV
, Academic Press,
London, 1957.
2. Rao, "C.N., Chemical Applications oflnfrured Spectroscopy, ,cademic Press, Ne
w York, 1963.
Colthup, N.B., Daly, L.H. and Wiberley, S.E., Introduction to Infrared a
nd Raman Spectroscopy,
Academic Press, New York, 1975.
Flame Emission and Atomic Absorption Spectrophotometry
1. Alkemade, C. and Herrmann, R., Fundamentals of Analytical lame Spectroscopy,
Hflger, Bristol,
Pinta, M., Atomic Absorption Spectrometry, Hilger, London, 1975.

Metcalfe, J.C., Nuclear Magnetic Resonance Spectroscopy in Physical Prtnc/ples a
nd Techniques
of Protein Chemistry, Part B, Academic Press, New York, 1970.
Haschemeyer, R.H. and Haschemeyer, A.E., Prote/ns, John Wiley, New York, 1973.
Opella, S.J., BiologicaI Nuclear Magnetic Resonanc Spectroscopy, Science, 198 :
158-165, 1977.
Moore, G.R., Ratcliffe, R.G. ad Williams, R.J.P., NMR and the Biochemist in Essa
ys in
Biochemistry (P.N, Campbell and R.D. Marshall, Eds.], Academic Press, London, 19

Willard, H.H., Meritt, L.L., Dean, J.A. and Settle, F.A., Instrumental Methods o
f Analysis,
Wadsworth Publishing Company, USA, i986,
Jost, P.C. and GriiTith, O.H., The Spin-Labeling Technique in Methods in Enzyrno
logy, Vol.
XLIX, Academic Press, London, 1978.
Berliner, L.J., Spin Labeling in Enzymology : Spin-Labeled Enzymes and Proteins
in Methods
in Enzymology, Vol. XLIX, Academic Press, London, 1978.
Campbell, A.K., Holt, M.E. and Patel, A. (1985) in Recent Advances in Cl
inical Biochemistry,
Vol. 3, p. 1. Edinburgh : Churchill Livingstone.
Geiselhart, L., Osgood, M. and Holmes, D.S., Construction and Evaluatlon
of aSelf-Luminescent
Biosensor, Ann. N.Y. Acad. Sci., Vol. 646 : 53-59, 1992.
3 King., J.M.H., eL al., Science, Vol. 227 : 778-781, 1990.
4, Rechnitz, G,A,, Chem, Eng. News, Vol. 66 : 24-36, 1988,
Substances A and B absorb at both 475 nm and 500 nm. These substances ar
e given to you
in a single solution which shows an O.D. of 0.62 at 475 nm and 0.54 at 500 nm. T
he a of
" compound A at 475 nm is 12000 and at 500 nm is 4000, Compound B has an a of 50

00 at
475 nm and 11600 at 500 nm. Calculate the concentrations of the two substances i
f the.
cuvette used to take the reading has a path length of I cm.

[A] =0.42 x I0-aM,[B] = 0.37 x I0-M
To a 1.5 ml of a solution containing the enzyme glutathione reductase and an unk
concentration of oxidized glutathione, was added an equal volume of a solution w
hich was
2x 10 M with respect to NADPH. The O.D. at 340 nm stabilized at 0.25 in a 1 cm c
Given that the glutathione reductase reaction is as under
Oxidized glutathion + NADPH + H reduced glutathione + NADP*
and that the reaction proceeds completely to the right hand side, can you calcul
ate the
concentration of oxidized glutathione In 1.5 ml of the solution? a of NADPH at 3
40 nm
is 6220. (Hint. First calculate the O.D. of NADPH due to the given concentration
Concentration of oxidized glutathione = 0.196 x 10- M in the original solution.
The enzymes glutamate-oxaloacetate transminase (GOT) is assayed by a cou
pled system,
having the following reactions.
(a) aspartate + a-ketoglutarate----- glutamate + oloacetate
(b} oxaloacetate + NADH malate + NAD
(the first reaction is catalyzed by GOT and the second by malate dehydrogenase).
Large excess of NADH is added which gives a good O,D. at 340 nm. The second reac
depletes NADH depending upon the concentration of oxaloacetate generated in the
first reaction. Since both the reactions are going on simultaneously, the rate o
f decrease
of O.D. is driven by the rate of appearance of .oxaloacetate and is therefore th
e index of
GOT activity.
On the basis of the above solve the following problem.
A reacUon mixture containing excess asparate, 0.1 ml serum (which contains GOT).
0.3 }
mole of NADH, and an excess of malic dehydrogenase in a total volume of 0,9 ml.
reaction is started by adding excess of a-ketoglutarate in 0.1 ml. The absorbanc
e decreases at the rate of 0.04 unit/rain. The cuvette has a path length of 2 cm
. Calculate
the concentration of GOT in the serum as unltsml.
3.21 x 10-2 units/ml
Calculate the O.D. of the following soluUons at 340 nm in a 2 cm cuvette.
(a) 7.3 x 10-MNADH (b) 9 x 10-2MNADPH (c) 2.2 x 10-MNADH
(a) 0.91 (b) 0.11 (c) 0.27
Make a study of glucose metabolism and on the basis of your study describe a pro

method for spectrophotometric measurement of giucoose-l-phosphate based on light

absorption at 340 nm.
You have prepared two concentrated solutions adenine and guanine. Inadve
rtantly. you have
forgotten to label the flasks and now you are not sure which flask contains what
. Can
spectrophotometry resolve the confusion?
You have two samples of DNA derived from different organisms, A and B, D
NA from A shows
an increase in optical density beginning at 70C and a plateau at 80C. DNA from B s
hows a
corresponding increase in O.D. beginning at 65C and plateaus out at 76C. What is y
There is Just one phenylalantne residue in a given protein which is abso
rbing maximally at
259 nm with an a, of 206 (both of which are very near the normal values) if the p
rotein has
been dissolved in 100% water. If the protein is now dissolved in 70% water and 3
0% glycerol
the wavelength of maximal absorpUon changes to 265 nm and extlncUon goes up to 2
17. If
the protein is brought b.ack to 100% water, the values also return to the origin
al values. What
is your conclusion?

Biolhysica Cherrstnj
A protein is o to possess a se oph d a se phenyle residue, At a
concenton of 55 mg/ml ff eylene #ycol is added to e soluon to a level of 3/0 go
mmum absoflon velen d e ecflon increase as eomped to what ey were
in 0. I M NaCI. If the concenaflon ofe protein is cased to 5 mg/ml 0.1 M NaCI, g
o e X d e encflon increase Howler, if eylene glycol Is added now at is hi
ptein concentration, no fuer specM chges e seen. at conclusions may you draw
about e prote ?
at is absoflon mum ? Does e sctur chmcter d the posion of absoflon
mum depends sole upon e scture of e compound ? Discuss.
at mgement may be present some specophotometers If e eors due to voltage
fluctuaons e to avoided togethe Discuss.
12. Discuss factors which give flse to fluorescence. y e fluorescence spec bd sp
ec ?
A given protein is o to con 12 tophs. If cesium long quench 25% of e
fluorescence, is it vd to conclude at ree of e tophan residues e on e surface,
If not. what consideraOons me e conclusion invMid?
A ven protein conns oy one toph which is shong a fluorescence mum as
at for flee toph. Yet, e intensi of fluorescence is inordinately low. at do you
conclude? er, acid flaflon of e protein tes you at e pK of sion is due to a
cbol. so e acid titration er decreases tenai. at do you ow about is
toph no -- 15.
en S Is bound to a ven prote, fluorescence is obned. However, ff e prote
concenaflon is incased fore addg S, fluoence decreases. Your coen? (Note.
More th one elaon is possible).
Descb briefly e eo of n specome. at foaon c be obned from e
n absoflon s?
at is met by e te chec sh? WHte eples, e shielding d deshieldg effects i
nvolved n specome.
at foaflon is prodded by e positions of sign.s specm? How my sign.s e ee
cted. each of e foOt.g:

(a) prope, ) eol, (c) buol d (d} eyl acetate?

Natural unrefle.cted light from any light source behaves as if it consisted of a
large number
of electromagnetic waves vibrating in all possible orientations around the direc
tion of propagation.
This unpolarized light can be resolved by Nicol prism into two beams in which al
l the rays
vibrate in only one particular plane. These beams are known as plane polarized (
of course,
since a light wave consists of an electric and a magnetic component vibrating at
right angles to
each other, the term 'plane' in not so right, but the ray can be said to be plan
ar if the meaning
is restricted to convey the position of the electrical component only). Each one
of the plane
polarized beams emerging out of the Nicol prism can be further resolved into two
beams of
circularly polarized rays by a device known as Pockels cell. A plane polarized b
eam is, therefore,
considered to be a sum of two circularly polarized components (Figure 9.1), the
right and the
left circularly polarized components.
If we pass these circularly polarized rays of light through an anisotropic mediu
m, it would
be seen that the plane of polarization has been rotated (Figure 9.1). This rotat
ion of the plane of
polarization might be due to either of the two phenomena considered below.
An anisotropic medium can refract the right (R) and left (L) components
of the plane
polarized light to a different extent so that I'll nR, where n = the refractive
index. This difference between the indices of refraction of the medium for the r
ight-hand and the
left-hand ray results in retardation of one component more than the other. The
observable result of this preferential refraction is a rotation of the plane of
since the angle a and no longer remain identical. If the medium preferentially r
efracts the left circularly polarized component the resultant would be a plane p
olarized ray
i'otated somewhat to the right from its original position (Figure 9.1), and vice
This phenomenon is known as optical rotation, The extent and even the sign of op
rotation differs at different wavelengths. This wavelength dependence, of the op
rotation is known as optical rotatory dispersion.
If the plane polarized ray has the wavelength falling within the range o

f the absorption
maxima of the anisotropic medium, the medium will absorb it. The optically activ
medium, however, shows a preference for absorbing either the left or the right c
polarized component.

Figure 9.1 (A) Representation of a plane-polar&ed ray as a sum of two clrcularly
polarlzed rays. EL (s the left and
Result of the passage of plane-polarlzed light through an optically acti
ve meal:lure. The plane of
polarized l@ has been rotated due to retardation of one of the ciradar component
s, a denotes
optical rotation.
In the previous case of optical rotation due to refraction both the refracted co
had equal intensity. In this case, however, since one of the components is being
absorbed, its transmitted portion will have less intensity than the incident ray
. Thus; in this
case, not only will the plane of polarization be rotated, but the two transmitte
d components will
also differ in intensity. The resultant light is said to be e///pt/ca//y po/ar/z
ed (Figure 9.2]. The
dierential absorbance of the circularly polarized light resultlng from a differe
nce in absorpttvtty
of the two rays is called circular dichroism (CD).
Figure 9.2 Elliptlcalpolarlzatn oftlght upon leaving an optically active medium
in the absorption range of an optleally
active troJitWn` Note that E is shorter than E. 8 describes the CD ellpiaj. It i
s coJculated from the
following relatlonshtp:

Other Optical Techniques for Molecular CharacterizatWn

We will now discuss the theory behind circular dichrolsm and optical rotatory di
individually (as we will see in subsequent pages, optical rotatory dispersion an
d circular dichrolsm
are mathematically commutable so that one can be known from the value of other;
it is only for
the sake of understanding that they are being discussed independently).
The circular dlchrolsm spectrmn may be thought of as the difference between two
spectra, one obtained using the left while the other using the right circularly
polarized component.
If this s so, one can apply Beer's law to circular dichrosm.
AL = aLCb
A = aCb
where the two subscripts L and R indicate the results obtained employing the lef
t and right
circular components, respectively. Taking the difference, we get
AL-A = (aL--aR) Cb,
... a = -aR = -AICb
extinction coeffcients. The usual representation
spectrum is to demonstrate Aa as a function of wavelength. As circular dichroism
only in those spectral regions where absorption occurs
will not be observed in the regions where no absorption occurs. In the latter sp
aL and a will be zero.
There are two major differences between CD spectra and absorption spectr
Extinction coeffcients are always positive. However, Aa can assume eithe
r a positive
or a negative sign depending on the relative sizes of aL and aR. Thus. optical i
somers of
any given compound at a given wavelength will give rise to CD spectra of opposit
signs, that is
aa isomer = - a isomer

CD spectra and the absorption spectra differ in the relative size of a a

nd the average
extinction coefficient, (aL + a/2. aa for most of the molecules of biol0gical in
terest are
less than I% of (aL +
From the second point above, we can understand that the value of Aa is very smal
l. How
do we measure it to get the CD spectrum? Ideal situation would be to fill a cons
tant pathcell with a solution of particular concentration C and then measure absorbance d
ue to
left and right components (AL and A) individually and then arrive at the differe
one from another. In actual practice a plane polarized beam is passed through
quarter-wave plate which is rotated from +45 to -45 producing first d and then I c
measures the periodicvariation in the transmittance
: when the incident radiation experiences periodic changes in the handedness, ff
we use the
relationship between A and.T,
(A = -log T), we get
a = (-log TL + log TICb
= l/Cb log TR = log Is/I
T. Cb
= log Iz

Biophysical Chemistry
where I,. and IR are the intensities transmitted. If the sample does not exhibit
circular dichroism,
TR and TL will be the same and log (TR/TL) will be zero. On the other hand, if t
he sample shows
circular dichroism, the oscillation frequency of the transmittance will be same
as the oscfllaUon
for the handedness of the incident beam. The circular dichroism of the sample is
from the magnitude of the oscillation in the intensity of the transmitted beam s
triking the
Since the projections of the electric vectors in circular dichroism differ not o
nly in their
angular velocity but also in length (Figure 9.2), the polarization of light leav
ing the medium is
elliptical. Due to this, circular dichroism is also expressed in terms of molar
ellipticity [0]. The
units of [0] are degree-centimeter squared per decimole (deg-cm21dmole). Those o
f ha on the
other hand are centimeter squared per mfllimole (cm21mmole). The following equat
ion relates
and Aa.
[0] -- (3300 deg mmole/dmole) Aa
Optical Rotatory Dispersion
In contrast to circular dichroism, an optically active sample gives rise to opti
cal rotation
even at wavelengths which do not fall within the region(s) in which the sample a
bsorbs. This is
so since refractive indices are never zero even in regions where the sample is t
ransparent (does
not absorb). Thus even those solutions which do not absorb in the ultraviolet re
gion wig glve
optical rotation in these regions.
Optical rotation, a, is given by
a = 180 -(I'll - nR)
However, the common form in which optical rotation is reported is either the spe
rotation [a], where [(] = 100 alCb, or the molar rotation (m'), where(m) = [a] M
The units for the specific rotation are deg-cm/decagram. The light path b is exp
ressed in
decimeters and the concentration C is expressed in grams/100 cm3. If the specifi

c rotation is
multiplied by molecular weight M and divided by 100, it gives rise to molar rota
tion whose units
are deg-cm/decimole. Note that the units for [M'] and [0] are identical. Experim
determination of [M'] at different wavelengths would give rise to optical rotato
ry dispersion
CD and ORD Spectra
Figure 9.3 depicts absorption, circular dichroism and optical rotatory dispersio
n spectra
for a hypothetical optically active substance which has a single absorption band
. The wavelength
at which the maximum absorption takes place, ,=, is denoted by a dashed line. Th
e similarity
between the absorption and CD spectra wig become obvious from the figure. On the
hand, the ORD spectnzm shows a more complicated pattern; no optical rotation is
observed at
X,, but maximum optical rotation is obtained at wavelengths slightly away from ,
=. Even
those regions which are far removed from Zm, x exhibit some optical rotation. Th
is property of
opUcal rotatory dispersion is very useful for compounds which absorb maximally a
t vacuum
UV where determination of CD is tedious; for such compounds optical rotatory dis
persion can
be measured at wavelengths far removed from the vacuum UV. If measurements of op
rotation are limited to these regions which are far removed from the absorption
bands, the
molar rotaUon is described by the Drude Equation.

Other Optical Techniques for Molecular Character/zat/on
9.3 Idealized absorption, clrcular dichrolsm and optical rotatory dispersion spe
ctra for a hypothetical compotmd
which s optk:ally active. It s assumed that the compound has only one absorption
band. Absorption
maxlmo are denoted by the dashed vertical lines. (A) and (B) denote spectra of c
ompounds which are
rrdrror brcu3es of each other. Further dLscusskm n the text.
where K and o are constants. Rearranging the above equation we get
.2 [m'] -- . [m'] + K
It would seem from the above equation that a plot oD.:[m']versus[m'] will be a s
llne. In fact the above equation fits optical rotation of transparent aqueous so
lutions of numerous
biological compounds in the visible region of the spectrum. If the equation does
not make a fit,
the inference usually is that the visible optical rotation of the biological sam
ple is due to
contribution from more than one optically active absorption band.
Figure 9.3(B) depicts the absorption, circular dichroism and optical rot
atory dispersion
spectra of the mirror image of the hypothetical molecule considered in F
igure 9.3(/I). Note that
while the absorption spectra in both cases are identical, the circular d
ichroism and optical
rotatory dispersion spectra have changed signs If a racemic mixture of t
his hypothetical
compound is subjected to the above experiment, the absorption spectnm wo
uld still be identical
but the circular dichroism and optical rotatory dispersion spectra would
cancel out.
It is interesting to note that the ORD curve resembles the first derivative of t
he CD curve.
ORD and CD are therefore coupled phenomena which in principle are mathematically

commutable. It is possible to calculate CD spectrum of a given compound from its

ORD spectrum
by applying the mathematical relationship known as Kronig-Kramer transform. Inte

BiophysPzd ChemLstry
of ORD spectrum is made difficult by the fact that it is complicated and extends
to regions far
removed from ,,. This is especially so for those molecules which have multiple o
ptically active
absorption bands. For this reason circular dichroism, which is easier to interpr
et, is preferred.
(1) CD/ORD of Proteins ,
Optical ativity of a macromolecule is usually a resultant of three factors. In t
he first
place, the constituents of the macromolecule; for example proteins are made up o
f L-amino
acids and these residues would contribute to optical activity. Secondly, these r
esidues might be
arranged in an ordered fashion such as the DNA double helix or the a-helices of
proteins, and
this arrangement is also a basis for optical activity, Thirdly, an asymmetric di
stribution of
charges or dipoles about a chromophore, as prevalent in a rigid tertiary structu
re, will also give
rise to optical activity.
Obviously, if one determines the optical activity of a given macromolecule, an a
nalysis will
provide good information about the general structure of that macromolecule. ORD
and more
preferably in modem days, CD spectra are used to deduce the chain conformation o
macromolecules. Although, by modem standards, X-ray diffraction crystallography
is the method
of choice for structure determination of biopolymers, spectropolarimetry continu
es to make
important specific and complementary contributions. X-ray analysis might be virt
ually impossible
if sufficient quantity of the material is not available or if the molecular weig
ht is too high or if
crystallization is a problem. In all these cases spectropolarimetry comes handy.
Besides, this
method consumes very little time as compared to X-ray analysis which is an extre
mely lengthy
To understand how measurement of optical activity can provide us an idea about t
conformation of a macromolecule, we will consider an example of synthetic polype
ptide poly-Llysine. This synthetic polymer is readily soluble in water at pH 5.7. At this pH
the e-amino
groups are protonated. Consequently the polymer can exist in a variety of confor
mations. The

polymer may then be thought as existing in a random cot state in solution. Obser
ve the CD
(Figure 9.4(B)) and ORD (Figure 9.4(A)) of this random cot (only CD is discussed
; observe,
however, that wherever extinction is maximum for CD, ORD is zero). There is a we
ak positive
circular dichroism at 217 nm and a strong negative circular dichroism at 197 nm.
If one removes the positive charge of z-amino groups by raising the pH of the so
lution to
1 I. 1, the polymer adopts an ordered structure known as the a-helix. Observe th
e drastic change
in the CD and ORD as a consequence to this confo.rmational change. Negative circ
ular dichroism
is now seen at 208 and 222 nm and a strong positive circular dichroism is seen a
t 191 nm. The
synthetic polypeptide can be converted to the -pleat sheet structure by heating
at 52C for 15
minutes and then cooling. Again, the CD and ORD undergo drastic change. A positi
ve circular
dichroism is now seen at 195 nm and a negative band is seen at 217 nm. It may be
that while all these drastic changes take place in the optical activity as a con
sequence of changes
in conformation, not much change in the absorption spectrum is observed which ex
hibits only
one absorption maximum for all conformations at i90-200 urn.

Other Optical Techniques for Molecular Characterization
[m'] x 10
I I. I00% a Helix
Rdom coil
190200 210 220 230240250
I. 100% a Helix
2. ioo%
3. 100% Random
19o 200 'i0 220 230 240,250

9.40pti6al rotatory dispersn (A) and circular dichroism (B) of poly-L-lysine in

the a-helicczi random coil, and
-conformatins. Descriptn in text. (Adapted from. Greenfield. N.. and Fasman. G.D
., Biochemistry, 8:4
108, 1969.)
Let us see whether the same pattern of optical activity is found for other prote
ins of
conformation. Figure 9.5 depicts CD spectra of two proteins, sperm whale myoglob
phosphate buffer pH 6.86. From X-ray diffraction studies we know that
whale myoglobin exists largely as an a-helix (about 80% of the amino acids are p
eight segments of a-helix).

240 .-0 220


C'radar dhrolsm spectra for (A) sperm whale myoglobln, and (B) eoneanava
lm A,
(A) Sperm whale myoglobin in phosphate buffer, pH 6,86.
(B) Concanavaltn A n phosphate buffer (curve I) and concanavaln A n phosphate bu
ffer + 0.018 M
sodan d.ajl sulphate (coe 2). Descrtn m tex (Adapted from. Maitre, W.L et. oi.,
15 : 4264, 1976)

Bophysk Cherrrlstrg
Observe that its CD spectrum shows the same qualitative features as observed for
poly-L-lysine. The CD spectrum for concanavalin A has the same qualitative featu
res as that of
poly-L-lysine -pleat sheet structure (Figure 9.5(B)). X-ray diffraction studies
confirm that there
is no a-helix in concanavalLn A and about 50% of the amino acids adopt the -plea
t sheet
structure. Figure 9.5 also depicts CD spectrum of cocanavalin A upon addition of
dodecyl sulphate. The spectrum shows the same pattern.as expected of an a-helix.
We can infer
that the detergent sodium dodecyl sulphate has induced formaUon of a-helix in co
ConformaUonal changes in the enzyme do take place when a substrate interacts wit
h it.
We have already seen that CD and ORD are responsive to conformational changes. T
CD and ORD measurements provide a sensitive method of studying enzyme substrate
A case in point is the study carried out by Teng et.al, on the enzyme p-hydroxyb
hydroxylase. The CD of pure enzyme is shown in Figure 9.6. It was known that the
enzyme has
a tightly bound FAD moiety. One of the substrate for it was p-hydroxybenzoate. H
owever, it was
not definite whether NADH, or NADPH was the other coenzyme needed. A CD.spectra
obtained for the enzyme in the presence of NADH and NADPH, The results of the ex
are shown in Figure 9.6. From the results it is clear that upon NADH addition th
e CD spectrmn
of the enzyme solution does not change significantly, whereas upon NADPH additio
n the CD
spectrum of the enzyme solution undergoes significant alteration. It can therefo
re be concluded
that the enzyme specifically binds NADPH which must be the coenzyme used in" the
Figure 9.6 Effect of NADPH on CD spectrum of the enzyme p-hydroxybenzoate tujdro
lase. Description tn text
(Adopted from Teng, N., eL al,, J. BioL Chem.. 246 : 5448-5453, 1971).

Figures 9.4, 9.5 and 9.6 show that CD and ORD are responsive to conformational c
of proteins. This is the reasonwhy CD and ORD are extensively used to study conf
changes in proteins and polypeptides. It might, however, be pointed Out that rel
ationship between
ORD, CO, and chain conformation is not as simple as we hope it tobe. Many protei
ns which
have been shown to exist largely as a-helices do not show the qualitative featur
es of a-helix
shown in Figures 9.4 and 9.5. Moreover, changes in optical activity may not be t
otally assignable
to conformational changes; solvent effects might also play a large role. With al
l these ambiguities,
CD and ORD remain important methods to study the structure of proteins.

220 240
Other Optical Techniques for Molecular Characterization
(2 CDORD of Carbhydrate
CD and ORD are also frequently used in studies on carbohydrates. CD can indicate
nature, extent, and position of substitution in carbohydrates. Perhaps the best
example of
such studies is afforded by studies on oligosaccharides from blood-group substan
ces and human
Chain conformations of a-and -llnked glycan derivatives have been studied throug
h CO.
The studies suggested that x-linked amylose tricarbanilate adopted a hellcal con
whereas the -linkedcellulose derivative did not. The CD spectra of these derivat
ives is shown
in Figure 9.7. Frequent use of CD has been made to study not only the conformati
on of other
polysaccharides but also their association in certain polysaccharide gels like a
lginate and pectin.
IAI 6-1,4
OR "
(B) a- 1,4
G.R., in New Techniques n Bphys.s Cell Biology, Vol. I, Wtly, 1973).
An extremely important application of CD is its use as a 'finger-printlng' techn
ique for
qualitative analysis of trace amounts of carbohydrate materials such as mucopoly
9.8 shows the CD spectra of dermatan sulphate (a mucopolysaccharide containing 1
,3sugar) and heparitin sulphate (a mucopolysaccharlde containing 1,4-1inked
sugar). The s ctra for these two mucopolysaccharides differ from each other

----Dermatan Sulphate
Heparifln Sulphate
Fre. 9.8CD spectra of two mv.copolyso.ccharldes. (Adapted from Morris, E.R., and
Sanderson, G.R., in New
in Bhyslcs md Cell BWlogy, Vol. I, Wiley, 1973)

4x I0"
2x 10
-4x I0
BphsP.al Chemtry
significantly and this difference lends itself to an important clinical applicat
ion. An accumulation
of these two polysaccharides occurs in the urine of patients with the Hurler syn
drome. The
syndrome has two variants: the Sanfllippo variant where the primary polysaechari
de accumulated
is heparitin sulphate and the Hurler variant where a mixture of dermatan and hep
aritin sulphate
is excreted. Through chemical means it is very difficult to identify the two muc
as separate from each other. However, if after some preparation the urine is sub
jected to CD,
an identification is readily made. CD has also been used as a quantitative metho
d for estimating
optically active polysaccharides such as mucopolysaccharides. Here it is extreme
ly useful because
it can measure a very small amount of optically active polysaccharide present in
a large excess
of optically inactive substances (e.g., pectin in the presence of citric acid an
d sucrose).
(3) CD/ORD of Nucleic Acids
Over the years, CD and ORD have also been extensively used in the study of nucle
ic acids.
The ribose phospIiate backbone of nucleic acids does not absorb significantly ab
ove 180
nm. Therefore when we measure CD of nucleic acids, the most important contributo
rs are the
bases : the purines and the pyrimidines. In themselves, both these kinds of base
s are symmetrical
chromophores. However, they become optically active when attached to a ribose su
gar by means
of an N-glycosidic bond. Their optical activity increases further when they assu
me helical
At 270 nm, the purine bases have. a negative signal whereas the pyrimidine bases
have a
positive signal. Since the bases contribute to the CD signal owing to the chiral
ity induced by
their attachment to ribose, the base composition of a given nucleic acid should

contribute to
the CD spectrum. It does also. However, this contribution is almost insignifican
t when compared
to the contribution made by the orientation of the bases. We know that the bases
are stacked
over each other. It is this stacking that contributes most to the CD spectrum of
the nucleic
acids. CD spectra therefore give us more information about the conformation of n
ucleic acids
rather than their composition.
-2 x I0
..Ac acid
poly (A)

240 260 .280 300

Figure 9.9 CD spectrum of adenylc acid, polyadenyl(c add [poly (A)] and denature
d poly (A). Explanation n the text.
CD (and of course ORD) is therefore an extremely sensitive probe of conformation
al changes
in polynucleotides. How sensitive this probe is will become clear ff one compare
s it with simple

Other Optical Techniques for Molecular Characterization
absorption spectrometric studies. If we study the absorption of light of 258 nm
by adenylic acid
and by polyadcnylic acid, we find that the latter absorbs 26% less than the form
er. The
hypochromicity is due to the formation of an ordered structure by the polymer. N
ow take a look
at the CD spectrum {Figure 9.9} of adenylic acid and polyadcnylic acid. The diff
erence between
the CD spectra of the two is much larger than the 26% decrease in absorption. Al
so shown in
the same figure is the change that occurs in the CD spectrum of polyadenylic aci
d upon
denaturation. Again note the large difference in the native and the denatured sp
ectra. It is
exactly due to such extreme differences that CD is such a sensitive probe of cha
nges in nucleic
acid conformation. Since it is such a fine probe, CD/ORD is used to study (1) si
ngle-doublestrand transition of nucleic acids, (2) denaturation of nucleic acids due to var
ious agents such
as temperature, pH, ionic strength, etc., and (3) binding of proteins, other sma
ll organic
compounds as well as cations.
A few examples of the use of CD/ORD in studying nucleic acids are provided below
of B-DNA is D/fferent as Compared to A-DNA
B-DNA is the native form of DNA; what this means is that the DNA in our cells is
in this
Outside the cell, we can obtain B-DNA when the humidity is 92% and the
is an alkali metal such as Na. This is a right handed helix with a diameter o{20A
helical twist per base pair is 36 and the pitch is 34. There are I0 bases per turn
of the
spectrum of B-DNA is shown in Figure 9.10. Note the negative band centered aroun
nm and a positive band around 275 nm. The zero occurs at about 258 nm.


Wavelength (nm)

Figure 9. I0 CD of B-DNA. Explanation in the text

this with the CD of A-DNA (not shown in the Figure 9. I0). A-DNA is 26 ,/ in
has 11 bases per turn of helix, has a helical twist of 33 per base pair, and a pi
tch of
This DNA shows an intense positive band at 190 nm, a good negative band at 210 n
m, and
positive band at 260 nm.
Curiously, the samecharacteristlc is given by duplex RNA. It may therefore be as
duplex RNA assume the A-form.
ORD spectrum of polycytidylic acid shows that the [m]292 is 35,160 deg M-Icm-. T
his high
value means that poly(C) is very asymmetric. In other words this means that it i
s helical. The
that suplort this helicity can also be determined easily.. Addition of formaldeh
yde does
change [m]29 significantly. Formaldehyde is a compound that disrupts hydrogen bo
were a function of hydrogen bonding between bases, formaldehyde addition should

Biophysical Chemistry
have reduced [rn]292 considerably. Since this did not happen we believe that hyd
rogen bonding
does not contribute significantly to the helicity of the polynucleotide.
On the other hand, when ORD spectrum is determined when poly(C) is suspended in
ethylene glycol, the [m]29 is found to be 7223 deg M-cm-. This is a huge reducti
on and it
means loss of asymmetry or of helicity. Ethylene glycol disrupts interaction bet
ween hydrophobic
groups. A reduction by such a substance means that the helix was mainly supporte
d by
hydrophobic associations between the bases. ORD spectra therefore provide a very
good support
for base stacking.
DNA has a Different Conformation in Chromatin
Does DNA have a different conformation in chromatin as compared to the conformat
ion in
the free state? It would appear so from the X-ray diffraction studies and the CD
studies. When
bound to histones, the CD band for DNA shows about half the maximum ellipticity
and half the
area of the spectrum for free DNA. From the example about base stacking given ab
ove, we know
that the DNA CD spectrum is mainly due to base stacking. Therefore, the chromati
n spectrum
may be telling us that the bases .are less stacked in chromatin. The point is co
nfirmed by X-ray
diffraction studies which give the same result.
X-ray diffraction is a far better tool to obtain detailed structural information
. However, CD
scores over the former in that it is rapid and can give reliable information abo
ut DNA-histone
interaction as well as about the parameters that affect this interaction. X-ray
diffraction studies
are not such a good idea when we want to study the DNA-histone interaction depen
dence upon
such factors as the pH, ionic strength, and the concentrations of the interactin
g species. As a
result of CD studies we know that DNA interacts with different histones differen
tly and with
different conformational changes in each case.
Instrumentation for Measuring Optical Rotatory Dispersion
Optical rotatory dispersion is measured by a spectropolarimeter. The instrument
the following basic parts:
(i) A light source

(ii) A monochromator
(///) A polarizer
(iv) An analyzer
(v) Sample tubes
(vt) A photomultiplier
The light source can be a tungsten filament lamp, if a continuous light source i
s desired.
For specific wavelengths xenon-or mercury-vapor lamps are used. If tungsten fila
ment lamp is
used, the monochromator has to be sophisticated. However, with either sodium vap
or or mercury
Vapor lamps, simple filters are required (this is because these two lamps emit l
ight of a limited
number of wavelengths, for example sodium lamp emits only two-589, and 589.6 nm)
Polarizer can be any of the three types: a Nicol prism, Glan-Thompson prism, or
a polaroid
filter. The last is the least desirable as it never gives 100% polarization. The
prism is the best and used in most spectropolarimeters.
When the sample is introduced between the polarizer and analyzer prism, optical
is produced, i.e., the plane polarized light emitted by the polarizer is rotated
. The extent of
rotation can be measured by rotating the analyzer with respect to the polarizer
till the rotation
is fully compensated. In more sophisticated instruments, a quartz-wave compensat
or is
introduced. In these instruments, the polarizer and the analyzer are left perman
ently crossed

Other Optical Technkltes for Molecular Characterization

with respect to each other. The optical rotation produced is then compensated by
a piece of
quartz which rotates light in the opposite direction to that of the sample. The
two quartz pieces
are laevo-and dextrorotatory.
Instrumentation for Circular Dichroism
Even an ordinary spectrophotometer can be adapted to measure circular dichroism.
only necessity is to provide some means of producing d and I circularly polarize
d radiation. The
usual arrangement for this is to pass a plane polarized beam (obtained through a
ny of the
polarizers listed above for polarimeters) through a quarter wave plate. A rotati
on of this plate
from +45 to -45 produces respectively, d and l circularly polarized radiation. If
a large
wavelength region is to be covered, several such quarter-wavelength plates would
be required,
each catering for a particular band-width. The absorption by the sample of the r
ight and the left
circular components is then alternately measured to arrive at the CD spectrum.
Specialized instruments measuring circular dichroism are also available and have
wavelength range of 185-600 nm. Recently composite CD/ORD measuring instruments
also become available and offer a wavelength range of 185-800 nm.
Light of changing
circular polarization

Figure 9.11 Depicts the schemat/c diagram of specialized CD instruments

CD measurements would, in principle, require two light sources: one for L and th
e other
R circularly polarized light. Each would have a monochromator for wavelength sel
commercial instruments have just the once source from which L and R circularly
light is generated. The trick here is to pass the plane-polarized light through
a crystal

is subjected to an alternating electric field. The crystal is called an electroo

ptic modulator
a photoelastic modulator (the older CD instruments have a Pockels cell in place
of this
It has a remarkable property in that the polarity of the field determines which
component will be transmitted. The current is alternating and therefore the L an
d R
are transmitted alternately. The beam is then allowed to pass through the sample
it is transmitted to the photomultiplier. The output of photomultiplier is then
processed to give the final result. CD instruments normally operate in the
range of 185-600 nm. Recently composite CD/ORD measuring instruments have
also become available and offer a wavelength range of 185-800 nm.
We have seen that molecules in solution show translational movement caused by th
of the solvent. In addition to this translational movement, each solute molecule
to its centre of mass. This motion is known as rotational diffusion and is descr
diffusion coefficient O. It has the units of reciprocal seconds and expresses

Biophysical Chemistry
the average angle of rotation per unit time. Rotational diffusion coefficient, w
hich is a constant
for a given solute, can be expressed in terms of frictional coefficient
e ' KTI frot
Rotational diffusion coefficient is related to the dimensions of the solute part
icle. Consequently
its measurement assumes importance since it can provide an idea about the dimens
ions of the
solute particle. Its measurement is particularly valuable in case of molecules o
f high axial ratio
(length/width; for example long thin rods) where it can provide a precise measur
e of the length
of the solute particle in solution.
Three methods are mainly used to determine rotational diffusion coefficient. The
y are
(1) flow birefringence, (2) electric birefringence, and (3) polarization of fluo
rescence. Of these,
although electric birefringence can yield 0, its main use is in the study of dip
ole moments. All
the three methods of determining 0 are discussed in the following pages.
(1) Flow birefr/ngence
Birefringence means double refract/on. The double refraction can be given rise t
o by the
mIsotropy of molecular arrangement which causes I/ght to travel along one ax/s o
f the crystal
with a different velocity as compared to the velocity at which it t.ravels along
the second s,
Many Crystalline substances are b/refringent since they possess two indices of r
efraction along
different es. Such substances m/ght give rise to certain recognizable optical ch
when studied under polar/zing light microscope. Solution of m/sotropic molecules
, on the other
hand, does not give rise to b/refringence. This is so since, at rest, the molecu
les in e solution are randomly oriented. If however, the molecules are forced to
zltgn themselves in a
uniform way either by imposing an electrical field (electr/cal btrefringence, el
ectr/cal double
refraction) or by means of hydrodynmIc shear (flow b/refrlngence, stremng btrefr
double refraction of flow), btrefringence will be observed (F/gure 9.12).
Fure 9.12(AJ Situation at rest. Particles are randomly oriented. At this stage n
o birefringence will occur.
Hydrodynamic shear applied. This gives rise to a velocity gradient. The
particles become aligned to

the stream line. Birefrlngence may occur in this state.

Microscpic situatin f a prlate ellipsoid particle in a velcity gradienL
Arrows indicate stream line.
FIw birefringence can be understood properly with the help of a commonplace exam
A curious thing happens when an aged colloidal dispersion of vanadium pentoxide
is stirred
slowly; the path of the stirring rod lights up since the colloidal particles ori
ent themselves along
the stream lines. This effect is observed because of the difference in the amoun
t of light reflected
by the symmetrically oriented particles as compared to the randomly oriented one
s. In a similar

Other Optical Techniques for Molecular Characterization
way, when a solution of nonspherical solute particles is subjected to hydrodynam
ic shear, the
fleld of polarizing microscope will light up due to birefringence; the brightnes
s of the field will be
directly proportional to the birefrlngence. "
Theoretical considerations indicate that the double refraction of the system app
ears as a
result of the equilibrium between the orienting effect of the applied field and
the disorienting
effect of the Brownian motion. The intensity of the birefrlngence depends on the
flow rate and
the shape of the particles, but is independent of the birefrigence of the indivi
dual particles. In
fact even Optically isotropic particles will give rise to birefringence provided
that they have an
anisotropy of the system as a whole and not the individual ansotropy
i. tlmt gives rise to flow birefringence.
The direction of the optical axis of the solution which is determined by the ave
rage orientation
macromolecules, as a function of shearing force, gives the rotary diffusion cons
tant of the
from which their size and shape are estimated by applying an appropriate
Hydrodynamic shear : Flow birefringence is usually measured in an apparatus whic
concentric cylinders (Figure 9.13). Two types of apparatus are available dependi
whether the inner or the outer cylinder is rotated. For various reasons the oute
r cylinder
------- Light source
>Condensing lens
C Y Diaphragm
).t Condensing lens
Po r

Concentric cylinde
Liquid between the
( Quarter wave plate
Half-shadow wedge
- Condensing lens


9.11t AI Iommr representon oft/w.flow birefrtnnee Olm. Inddent lht is conjed by

condenser on to the opening in the dW.phragm. The diaphragm now acts as lht sour
ce. The light
now falls into the lluld between the on,ntc cylinders aJter Imssing through a con
denser and
nlcol polarizer. For measurement of the extinction angle, quarter wave plate and
are removed. They are required only for measuring birefrirjence. Light now passe
s through the
analyzer nlcol and is then focussed by the condenser on to the observirj telesco
pe through which
optical patterns are observed.
Cross-sectlon of the concentric cylinders, o is the angular velocity of
rotation. Rz and d are radius of
the fixed cylinder, space between the flxed and the rotating cylinders respectWe
ly. R is the sum of
Rz and d. It is on these factors that the shear gradient G is dependent. G is gi
ven by the relatWnshtp.

Biophysical Chemistj
rotating model is more preferable, although its design is a bit complicated. The
outer cylinder is
connected through a pulley system with a motor, the rotating speed of which can
be changed by
voltage control. The macromolecular solution is placed in the space between the
two concentric
cylinders. As the outer cylinder rotates, while the inner cylinder is stationary
, a velocity gradient
is set up. This velocity gradient produces a torque on the molecules tending to
align their long
axis tangential to the direction of the flow. The higher the axial ratio of the
particle (length/
width), the greater the degree of alignment will be. As the velocity gradient is
increased, the
angle between the long axis of the particle and the direction of flow (stream li
nes) decreases; in
short, the particles align themselves in a manner which offers least resistance
to the flow.
Anyone who has observed a small wooden stick floating on water would be able to
visualize the
alignment of the particles. Wherever the current of water is strong, the stick d
oes not rotate but
aligns its long axis in the direction of flow (the molecules, however, turn very
slowly, depending
on their rotational diffusion coefficient).
The optical system : The alignment of the molecules is determined by passing par
light from a polarizing prism, called the polarizer, through the solution, and t
hen through
another polarizing prism, called the analyzer, placed at right angles to the fir
st. The optical
system for the measurement of birefringence consists of a light source, a collim
ator lens, a
filter, a polarizer, a quarter wavelength plate, and an analyzer, The sample sol
ution enclosed
between the two concentric cylinders is located between the polarizer and the qu
arter wavelength
plate (Figure 9.13). The polarizer and analyzer are usually Nicol prisms or occa
sionally polaroids.
Calculation of Rotational Diffusion Coefficient
When the outer cylinder is not rotating, i,e., when the solution is at rest, it
is isotropic. The
incident light coming through the polarizer, therefore, remains linearly polariz
ed when it comes
out of the solution and is blocked by the analyzer which is placed at right angl
es to the polarizer.
The field appears totally dark. However, when the outer cylinder is rotated, the
particles align
themselves along stream lines and the solution becomes anisotropic and birefring
ent. The
refractive index of this solution is no more the same in all directions. The lig
ht transmitted no

more remains linearly polarized, but becomes elliptically polarized and passes t
hrough the
analyzer. As the orientation of the particles is increased by increasing the spe
ed of the outer
cylinder, more light passes through the analyzer. It would be seen that light pa
sses through
every point except for four positions. These four dark areas, which correspond t
o no birefringence,
form a cross known as the cross ofisocltne (Figure 9.14). This dark cross is see
n to form an

Figure 9.14 The cross of tsocline. The cross forms an angle with the polarizer a
xis (P-P). The same angle Is formed by the cross and the analyzer axis (A-A). Th
s ts the extinction angle 2. The intersection of the long axis of
the particle with the stream line also gives rise to the same angle. However, th
e former relationship utilized to measure .

Other Optical Techniques for Molecular Characterization
angle with analyzer axis and with the polarizer axis, both the angles being of t
he same extent.
This angle is known as the extinction angle, and is denoted by the symbol ;(i
The same angle, X, is made by the long axis of the particle with the stream line
9.14). The extinction angle depends upon the shear gradient G; the angle decreas
es as the
speed of the rotating cylinder increases. I,n fact G depends upon the speed of t
he rotating
cylinder and the distance between the two concentric cylinders.
Rotational diffusion coefficient can be calculated if G and are known. The follo
wing relationship is utilized for the purpose
tan 2X G
After some time the rotating system attains equilibrium. At this point the parti
cles for
remain aligned in a preferred orientation. This preferred orientation is denoted
symbol a. a is a function of the dimensions of the solute particle and is descri
bed by the
It is actually the rotary frictional coefficient from which the shape of the par
ticle in
of its axi.al lengths can be calculated. This rotary frictJ.on coefficient can b
e calculated
the following relationship
where is the rotary frictional coefficient, k, is the Boltzmann constant and T i
s the
once rotary diffusion coefficient has been experimentally determined,
can be calculated from it.
The relationshipbetween the rotary frictional coefficient and the shape of the p
article is

axial length. For a long prolate ellipsoid (Figure 9.15) with semiaxes
iand b where a> 5b
16 moa
The prolate ellipsoid model. The model is obtained by rotation of an ell
ipse of major axis a and minor
ax/s b about the a axis.
o is the viscosity of the solvent. The axial ratio (a/b) of the particle concern
ed can be
by intrinsic viscosity measurements.

32 ob3
Biophysical Chemistry
For oblate ellipsoids
Here b is longer than

Figure 9.16 A schematle representation of the plot to determine

Q. c is measured for different values of G and
dX I
is related to 0 by -- =
dG 12 @ "
Rotational diffusion
can be measured by another
Here, ; is measured for
of G by varying the
cylinder is rotated. The Values of X
obtained are then plotted against
(Figure 9.16). When a is less than
the relationship is as follows I
It is thus possible to relate
initial slope of the plot shown in
9.16 to G by


(Experimentally, the angle between the polarizer axis and the cross
two times, each time the cylinder.rotating in opposite directions. The differenc
e between
two positions is equal to 2).
Dimensions of several macromolecules have been determined using flow
For example, the length of the major axes of flbrinogen and serum albumin were f
ound to
670/ and 190/ respectively. Both these values are in agreement with values for t
macromolecules found by other hydrodynamic methods. Some other example
whose shape has been determined using flow birefringence are myosin, tropomyosin
tobacco mosaic virus etc.
Relationship Between Flow Birefringence and Molecular Weight
If is the angle of rotation of the analyzer in degrees, btrefringence of the sol
be calculated by the equation
where . is the wavelength of the incident light in vacuum and S is the path
Once the degree of birefringence has been calculated, it can be related to the w
average molecular weight of the macrom, olecules by the following equation
= BnM

Other Optical Techniques for Molecular Characterization

where Bn is a constant characteristic of the solute, C is the concentration of t
he solution and M
is the molecular weight.
Although fl0w birefringence has been used many times for determination of molecu
weight of macromolecules, the method depends upon assumptions regarding the mole
geometry which involves an appreciable degree of uncertainty. Moreover it requir
es evaluation
of empirical constants. These serious drawbacks have limited the application of
this method for
molecular weight determination.
2. Electric birefringence
Another technique to study the dimensions of macromolecules on the basis of thei
r charge
properties is electric birefringence. In flow blrefringence macromolecules were
aligned with the
help of hydrodynamic shear. In electric birefringence an electric field is used
to align the
macromolecules and the alignment is determined by the electrical.properties of t
he molecules.
Macromolecules are forced to align by application of electric field. The fiel is
applied as a short pulse of the order of microseconds. The degree of alignment i
s then determined
i from the birefringence produced. The measurement involves determination of int
ensity of light
passing through crossed polarizing lenses and falling on a photomultiplier tube
where it is
converted to an oscilloscope signal. The optical system is so desigrted that whe
n the molecules
align and the solution becomes birefringent, a tracing immediately appears on th
e oscilloscope
Inspite of providing a considerable amount of information about macromolecules,
method has a serious disadvantage which limits its application; it can be of uti
lity only when
in which the macromolecules are placed is relatively nonconducting.
The rise and decay of birefringence (Figure 9.17)
(2 e
provide two different informations about the
Rir-e "macromolecule. At the onset of the electric pulse, the

shape of the rise of birefringence provides information

about the orientation of the induced and permanent
dipole moments of the molecule. The decay of
, Time ( sec)

birefringence is due to rotational diffusion coefficient

of the macromolecule. The decay, then, provides a

9.17 Oscilloscope tracing showing the
precise measure of the rotational diffusion coefficient,
trans/ent e/ectrlc blrefr/ngence of
flbrtnogen in solution (0. I M
which as we have seen earlier can provide an idea
glyclne, pH 7.9)
about the shape of the macromolecule.
From the dipole moments one can determine the
pattern of distribution of charged groups on the
;. The method is of considerable utility to study reactions in which charge
take place on the protein molecule. For example, activation of a protein in whic
are cleaved from the protein can be studied with the help of electric birefringe
activation (where two peptides with a charge of-4 are cleaved by the action of t
thrombin) can be studied with the help of this technique. In a likewise manner,
protein can also be studied. For example, the technique is utilized to study
of a charged hapten to an antibody specific for it.
Polarization of fluorescence
Polarization of fluorescence has been often used to determine rotational diffusi
on coefficients
' macromolecules. Unlike other hydrodynamic methods, this technique is not limit
ed to

Biophysical Chemistry
In this technique the sample is irradiated with polarized light of the w
avelength of absorption.
The absorption of this light now depends on the orientation of the electric dipo
le of the solute
molecules. Those molecules whose electric dipoles are in closest alignment with
the field direction
will absorb the most. The lifetime of excited state of a solute molecule after a
bsorption of llght is
usually 'of the order of 10 nanoseconds (nsec). If the alignment of the solute m
olecules does not
change within this time, the resultant fluorescence will show the same extent of
polarization as
that represented by the absorption distribution. In this case a maximum value fo
r the fluorescence
polarization will be obtained. This, however, seldom takes place. In solutions,
Brownian motion
leads to rotational diffusion which randomizes the orientations of chromophores
during this
period (10 nsec). This results in fluorescence depolarization additional to that
caused by initial
random distribution of chromophores. Brownian motion has a large effect on small
(faster rate of rotational diffusion) whose alignment gets randomized fast and t
heir solution
shows complete depolarization of fluorescence. On the other hand, those chromoph
ores which
are tightly bound to macromolecules have a slower rate of rotational diffusion (
times for this process are of the order of 100 to 1000 nsec). Thus with these ch
romophores only
a partial depolariztion can occur during lifetime of the excited state (10 nsec)
. The rotational
diffusion coefficient of these chromophores ( and therefore the macromolecules t
o which they
are bound) can then be calculated by comparison of the resultant polarization wi
th that which
would be obtained if no diffusion took place. In practise this is done by measur
ement of
fluorescence polarization as a function of viscosity and subsequent extrapolatio
n of the data to
infinite viscosity. This is the simplest method by which rotational diffusion co
efficients of
macromolecules can be determined. Moreover, the method is free from those limita
tions suffered
by hydrodynamic methods and is sensitive to very small quantities of sample.
Fluorescence polarization may be characterized by emission anisotropy. When the
beam used is polarized, the emission anisotropy is given by the following expres
r+ 2I

where Ii and I, are the principal components of the polarized fluorescence vibra
ting in parallel
and perpendicular directions respectively (with respect to the direction of the
exciting beam).
Il and I are in practice determined by measuring fluorescence intensities at righ
t angles
to the exciting beam. This is made possible by using a rotating polarizeralterna
Uvely transmitting
the two directions of vibration (Figure 9.17). Normally the two polarized compon
ents are measured
using the same photomultiplier.
If a parallel beam of white light illuminates a colloidal solution, faint bluish
light can be
observed laterally. This phenomenon, caused by the scattering of light, is commo
nly known as
the Tyndall effect after its discoverer J. Tyndall. Although light scattering is
more pronounced
in colloidal solutions, it is observable in all transparent media like gas, any
pure liquid solution
and even in crystals. Lord Rayleigh formulated the fundamental laws of light sca
ttering in 1871
by calclflating the polarizability of individual gaseous molecules placed in an
electromagnetic field of a light beam. As per this theory the incident electroma
gnetic impulse of
a beam of light causes electrons of an isotropic particle to vibrate in unison w
ith it. An oscillating
electric moment is thus induced in the particle. The oscillating electrons now b
ecome sources
of scattered or diffracted light which will mostly have the same frequency as th
at of the incident
beam. The intensity of the transmitted beam is consequently lowered. The intensi
ty of the
transmitted beam, and therefore, the intensity of the scattered light can then b
e expressed as a

Other Optical Techniques for Molecular Characterization
function of the number of centres of scattering (i.e., particles or molecules) p
er unit volume.
Thus, if a value for Avogadro's number is adopted, quantitative measurement of l
ight scattering
can provide an idea of the molecular weight of the scattering specie. Smimov and
Bazenov of
U.S.S.R. and Putzeys and Borsteaux of France were the first to apply light scatt
ering toward the
calculation of molecular weight in 1935.
Ill I
Figure 9.18 A simple setup for Jluorescence polarization measurement. S
is the Ikjht source; we is the exciting
frequency; Pz .is the flxd polarizer; vf is the Jluorescence frequency;
P2 is the rotating polarlzer which
alternately transmits Ill and I ; D is the photomultlpler. Monochromator
s and collimators are not shown.
A mathematical relationship describing light scattering phenomenon can be writte
n in
much the same way as the Lambert's law
Io = intensity of the incident light,
= intensity of the transmitted light,
= turbidity,
= the path length.
Turbidity,, depends upon the number and size of the scattering particles. For li
scattered at 90 to the incident beam in ideal systems, the turbidity can be expre
ssed by the

following mathematical relationship

X4 a
where n = index of refraction of the solution, no = index of refraction of the s
, = the wavelength of light in vacuum,
and a = the number of solute particles per ml.
To introduce a term for molecular weight into the above mathematical relationshi
p, a is
replaced by its equivalent CN/M (where C is the concentration of the solute in g
ins per ml, M is

Biophysical Chemistry
the molecular weight, and N is Avogadro's number). The mathematical expression c
an now be
written as
where k is a proportionality constant defined by the relationship
The relationship /C = kill is for ideal system. For nonideal systems the relatio
nship takes the
following form ,
kC 1
where R is the interaction constant and is dependent upon the solvent used. This
equation can
be used to calculate molecular weight after obtaining light scattering data.
Molecular weights obtained by light scattering data are weight average molecular
(See Chapter 4). The method has a srious drawback in that it is very sensitive t
o the presence
of aggregates and large scale errors may creep, in molecular weight determinatio
n if formation
of aggregates is not guarded against. As it is, molecular weights obtained by li
ght scattering are
considerably higher than those obtained by other methods.
The apparatus used for measurement of light scattering is called light scatterin
g photometer.
Figure 9.19 is a schematic representatibn of a typical light-scattering experime
nt. The solutions
must essentially be dust free, Fine pore filtration or high speed centrffugation
might be performed
to get rid of the dust particles. Presence of aggregates must also be avoided at
all costs. The
presence of any of the two Impurities stated above will lead to false scattering
[ ser t
Figure 9..19 Schematic of a typical- apparatus for light scattering nts. Monochr
omatic light is obtained from
a laser.source. Lens. L focusses thecollimated beamofwavelength and intensiJloon
to thescattering
cell. D is the detector, usually a photomultiplier which records the scattered r
adiation, D is mounted on

a moveable support so that by chancjing its position around the scattering cell,
scattered intensity at
any angle 8 can be measured.
Although in the present text we have touched only the aspect of molecular weight
determination by light scattering measurement, it should be noted that the pheno
menon is
also useful in providing data on the size and shape of the dissolved macromolecu
les as well as
information on the thermodynamic properties of the system. Moreover, owing to th
e rapidity of
the method, light scattering offers unique possibilities of following the kineti
cs of macromolecular
reactions involving a change in the size or shape of the dissolved particles.

Other Optical Techniques for Molecular Characterization

It is very instructive to wonder as to where molecular biochemistry would be tod
ay if there
had been no X-ray analytical methods to discover the atomic architecture of biop
olymers such
as proteins and nucleic acids. The importance of this method of s.tructural anal
ysis can be
stated simply by saying that the structure of DNA was discovered largely due to
the availability
of X-ray crystallography data.
The wavelengths of X-rays are of the same order, viz., 10-s cm as the distance b
individual atoms in a crystal. This'similarity led Max yon Laue in 1912 to make
a brilliant
suggestion that crystals could act as natural and very fine three dimensional di
ffraction gratings
for X-rays. W. Friedrich and P. Knipping verified this idea by passing a beam of
X-rays through
a crystal of zinc blende. This resulted in a deflrdte diffraction pattern on the
exposed photographic
plate. A pattern of this type is generally referred to as the Laue pattern.
Previously this method was used to calculate the wavelengths of X-rays, the crys
tal playing
the part of a diffraction grating. W.H. and W.L. Bragg were the first to call at
tention to the fact
that, since a crystal is composed of a series of equally spaced atomic planes, i
t may be employed
not only as a transmission grating, but also as reflection grating. An X-ray bea
m striking these
atomic planes will be diffracted in such a manner as to cause either interferenc
e or reinforcement
of the beam diffracted from the outer plane. The whole beam would behave as if i
t has been
reflected from the outer surface of the crystal.
To understand the theory of this method better, consider Figure 9.20. A wave fro
nt, LP, of
X-rays is approaching a series of identical, parallel and equidistant lattice pl
anes, AA,. BB, CC,
which constitute the atomic planes of the crystal. Part of the beam, LM, will be
reflected at M
along RUN, at the angle of reflection, 9. Similarly, the beam PM'will be reflect
ed partly at M' along
RUN', and partly at Q on the second plane along QMN. To emerge along RUN, the se
cond beam
travels a longer distance than the first, the distance Plt QM as compared to the
distance LM.
If the length of the path LMN differs from that of PM" QMN by a whole number of
then the two beams will be in phase at-M, will reinforce each other and a maximu
m intensity
beam will result. However, if the two beams are out of phase, interference will

result, and the

intensity of the reflected beam will be less than maximum. It is thus clear that
the condition for
maximum intensity beam is that the distance
PQM-LM = n
where is the wavelength of the X-ray used and n is an integer equal to 1,2,3,4,
etc., and is known as the order of reflection.
Iure .0 ReJleetlon of X-foxes y l:u"lle[ loes
If we now draw a perpendicular from M to the extension of line PM" Q, and draw a
from M to Rerpendicular to AA, BB and CC, it becomes clear that

But, from the figure it is clear that QM = QR. Thus
LM -- PS
Biophysical Chemistry

Therefore, PQM = LM = PR - PS
= SR
SR = rv
From the figure it is also clear that angle SMR is (3. Now, since MS was drawn p
Sin(3 MR
SR = MR sin 0
= 2d sin (3
where d is taken as the distance between any two atomic planes in the crystal.
rvX = 2d sin (.
This relationship, known as the Bragg equation, is applicable to reflection from
planes parallel to AA and BB. This simple expression directly relates the wavele
ngth and order
of reflection of theX-rays to the interplanar distance d and the angle of maximu
m reflection, 0.
The relationship allows calculation of the ratio )Jd by measuring n, and (3. Mor
eover, if d is
known, the wavelength, Z, of the X-ray Can be calculated. More importantly, if t
he wavelength,
Z, of the X-ray being used is known, the distance between the successive lattice
s of the crystal,
d, can be calculated. X-ray diffraction can thus tell us a great deal about the
structure of the

Every atom in a crystal scatters an X-ray beam incident upon it in all direction
s. As all
crystals, even the smallest one, are made up of a very large number of atoms, th
e chance that
these scattered waves would constructively reinforce would be almost zero but fo
r the fact that
the atoms in a crystal are arranged in a regular repetitive manner. The Bragg eq
uation described
above states the condition for diffraction of a beam of X-rays from a crystal. W
hile maximum
contribution to the intensity of the diffracted beam is afforded by the atoms lo
cated exactly on
the crystal planes, maximum destructive interference is meted out by the atoms e
xactly halfway
between the planes. Atoms located at intermediate positions interfere constructi
vely or
destructively depending on their exact location, but with less than maximum effe
ct. The scattering
power of an atom increases as the number of electrons it possesses increases. Th
us, although
.the position of the diffracted beams depend only upon the size and shape of the
repetitive unit
of a crystal and the wavelength of the incident X-ray beam, the intensity of the
diffracted beams
depend also upon the type of atoms in the crystal and the location of the atoms
in the unit cell
(the fundamental repetitive unit). Therefore, if one considers the direction and
the intensity of
the diffracted beams, no two substances can have absolutely identical diffractio
n patterns. The
diffracUon pattern of a crystal can thus be compared to a 'fingerprint' and prov
ides identities of
the components of the crystal.
Reciprocal Lattice Concept
Diffraction phenomenon can be interpreted most conveniently with the aid of reci
lattice concept. A plane may be represented by a line drawn normal to the plane.
The orientation
of the plane would then be described by the spatial orientation of this line. Th
e length of the

Other Optical Techniques for Molecular Characterization

normal is usually fixed in an inverse proportion to the interplanar spacing of t
he plane it


/ ' I02
" (0|
Figure 9.21 A profde of several planes in the unit cell of a crystal. Norrnals t
o the planes are also shown.
When normal are drawn to all the planes in a crystal from a common origin, the t
points of these normals constitute a lattice array. However, since the distance
of each point
from the origin is an inverse or reciprocal of the interplanar spacings, this is
called a reciprocal
/att/ce. Figure 9.21 shows, near the origin, the traces of several planes in a u
nit cell of a crystal,
namely, the (I00}, (001}, (101L and (102} planes. The normals to these planes ar
e called the
reciprocal lattice vectors ha and are defined by
The lattice array is defined by three reciprocal lattice vectors in three dimens
ions. The
magnitudes of these three vectors are given by
b =oo = d
The directions of these vectors are defined by three interaxial angles a', [Y, y

The Bragg equation now might be rewritten in a form that will relate the glancin
g angle O,
with the other parameters described above.
In the above expression the numerator represents one side of a right triangle wi
th 0 as
another angle and the denominator represents the hypotenuse (Figure 9.22(A)). "l
-le construction
in Figure 9,22(A) can also be interpreted as shown in Figure 9.22(B}. ,e diamete
r of the circle. ABC represents the direction of the incident X-ray beam. The li
ne ,AD. drawn through the
origin of the circle and making an angle 0 with the incident beam defines a crys
tal plane which
satisfies Bragg diffraction condition. The llne BD forming an axgle 20, with the
incident beam
and an angle 0, while the crystal plane represents the diffracted beam's directi
on. Then the

Other Optical Techniques .for Molecular Characterization
line CD is the reciprocal lattice vector to the reciprocal lattice point Dh lyin
g on the circumference
of the circle. The vector h originates at the point on the circle where the dire
ct beam leaves the
circle. Now when a reciprocal lattice point lies on the "sphere of reflection" (
a sphere formed by
rotating the circle upon its diameter -'-), the Bragg equation is satisfied. Und
er no other
conditions will Bragg equation be satisfied.
. Diffracted

/ beam
Figure 9.22 Diagrammatic representation of the diffraction condition
In a diffraction experiment the crystal can now be pictured to be at the centre
of a sphere
of unit radius. The reciprocal lattice of this crystal will then be centred at a
point where the
direct beam leaves the sphere (Figure 9.23). It thus follows that with rotation
of the crystal, the
reciprocal lattice will also rotate. Whenever a reciprocal lattice point will in
tersect the sphere, a
reflection will emanate from the crystal at the sphere's centre and will pass th
rough the
intersecting reciprocal lattice point.
The Determination of Crystal Structure
"the. Bragg equation makes it clear that if the glancing angles 0 are measured f
or the
various orders of maximum reflection, and if the wavelength of the impinging X-r
ay is known,
the distance d between successive lattice planes of a crystal can be calculated.
Two methods
are most popular. The rotat/ng crystal method and the powder method.
Incident X-ray
Sphere of reflection


|/'-- .,


Crystal rotation axis

Bophgscel ChemLstn3
Rotating crystal method : As the name suggests, the experimental set up is such
that a
monochromatic X-radiation is Incident upon a crystal which is rotated about one
of its axis.
lgure 9.24 Diagrammatic representation of
Bragg X-ray spectrometer.
Description in the text
Thereflected beams lie as spots on the surface of cones
which are coaxial with the rotation axis. In order to
determine the positions of maximum reflection intensity,
use can be made.either of the Bragg X-ray spectrometer
(Figure 9.24) or a photographic film. In the X-ray
spectrometer a beam of X-ray of a definite wavelength
cming from the anticathode of an X-ray tube, X, is
allowed to escape through a slit S. The beam then falls
upon a known face of crystal C, mounted on a rotating
turn table. The position of the crystal at any given time
can be read on the scale L. The rays reflected by the
crystal are allowed to reach an ionizing detector D
through another sllt. The detector is usually a Geiger
cbunter. The apparatus is so designed that the reflected
ray always enters the detector D, and the Intensity of
such a ray is determined. The glancing angles, 8, which
satisfy the Bragg equation, give the strongest reflections.
The procedure is repeated for all the planes of the crystal.
This method necessitates the use of a large crystal
with well defined faces. Moreover, since reflections of

several orders must be examined for a large number of faces, the total labor Inv
olved is enormous.
This, however, is compensated by relatively simple Interpretation of the results
The Imwcler mthod : In 1916, P. Debye, P. Scherrer and A.W.Hull devised the powd
method of X-ray crystallography which went on to become a widely used method. A

Figure 9.25 Diagrammatic repre
sentation of the principle
of the powder method.
Description in the text.
beam of X-rays falls on the finely powdered substance
P. The powder is usually coated on a hair or inside a

thin walled glass tube. The diffracted rays collide with

the photographic film F which is arranged In a circular
arc with P at its centre. As crystals In the fine powder
are oriented in all directions, a large number will have
their lattice planes In the correct positions for maximum
X-ray reflection to occur. All crystalline particles whose
(100) planes are In proper angle with the Incident X-ray
beam will give rise to first order maxima In directions
lying on a circular cone (Figure 9.25). Other crystals
whose (I 10) planes are in proper angle with the Incident
X-ray beam will produce another circular cone. Circular
cones will be produced In a similar manner for other
planes. The distance between the powdered substances
P, and the spot of Intersection of undiffracted beam with
film, I, is fixed for a given X-ray camera system. Thus,
In order to measure 0, for a particular reflection, the

only necessity is to measure the distances such as/D or IE (Figure 9.25). The st
ructure of the
crystalline material can then be determined.
Chol of X-Radiation
Bragg's equation can be rearranged and written as follows:

Other Optical Techniques for Molecular Characterization
The resultant of the terms in the parenthesis never exceeds unity. Due to this u
se of long
wavelength radiation is not very useful as it limits the number of reflectlons t
hat can be observed.'
On the other hand, in case of a crystal having a very large unit cell, usage of
short wavelength
radiation results in a crowding of individual reflections making the interpretat
ion a tough job.
Clearly then, the choice of radiation has to be a compromise between the two. ex
Additionally, the chosen radiation should not fall Within the absorption range o
f the crystal
material. In such a case the crystal absorbs the radiation and emits fluorescent
radiation in all
directions. This radiation darkens the film making it difficult to locate the di
ffraction maxima
sought. Thus, the wavelength of the chosen radiation should be outside the absor
ption range of
the crystal material.
Specimen Preparation
Use of single crystal is preferred for structure determination because the data
so obtained
is easy to interpret. The crystal in this case should be of such a size as is co
mpletely bathed by
the incident radiation. The crystal is generally affixed to a glass capillary wh
ich, in turn, is
fastened to a brass pin (Figure 9.26). For protein crystals, however, it is nece
ssary to mount
Glass capillary
Picein wax
F@ure 9.26 TWo methods of specnen mounts for X-ray di.'actloru (A) Single crysta
l, and (B) Powdered sample.
the crystals in an enclosed space. This is so since the protein crystals contain

within themselves
a large amount of solvent from which they are grown. About half the volume of pr
otein crystals
is of solvent. If such crystals are exposed to air, liquid evaporates and the cr
ystals shrink
deteriorating the quality of the X-ray pattern obtained,. Therefore, protein cry
stals are placed in
[ thin wall capillary wliich is then sealed at both ends. Sometimes the interior
of the capillary
is coated with a hydrophobic film to make for a cleaner mount.
When a single crystal of sufllcient size is not available, a polycrystalline agg
regate is formed
into a cylinder whose diameter is smaller than the diameter of the incident X-ra
y beam. At
other times the powdered substance might be coated on to a hair and the assembly
is fixed to
a brass pin (Figure 9.26).
X-ray Diffraction and Molecular Weight
A unit cell might contain more than one asymmetric units. Prom the space group a
nd the
unit cell volume, the volume of the symmetric unit can be calculated. If the app
roximate molecular
(M) of the macromolecule is known from other methods, the number of molecules in
symmetric unit can be calculated. If we now denote the molecular weight of the a

1 V
Biophysical Chemistry
macromolecule by W, the volume of the dry unit cell by V, and the number of asym
metric units
per unit ceil by n, the following expression Can be written
where k is a constant.
From the above equation it is obvious that if one knows the number of asymmetric
in a unit cell, one can arrive at a fairly accurate value of the molecular weigh
t of the molecule.
There are, in fact, few other methods of molecular weight determination which wi
ll give a value
as accurate as this from a single simple experiment. It should however, be borne
in mind that
the molecular weight as determined from X-ray diffraction data of the crystal mi
ght be a multiple
or submultiple of the true molecular weight and might also differ from the value
of the molecular
weight determined by other methods. The molecular weight as determined by X-ray
data is
therefore termed as "crystal molecular weight".
Suggestions for Further Reading
Imahori, K. and Nicola, N.A., in Physical Prlnctples and Techniques of P
roten Chemistry, (S.J,
Leach, ed.) Part C, Academic Press, New York, 1973, p. 358.
Sears, D.W. and Beychok, S., in Physical PHnciples and Techniques of Pro
teln Chemistry, (S.J.
Leach, ed.) Part C, Academic Press, New York, 1973, p. 446.
3. Adler, A.J., Greenfield, N.J. and Fasman, G.D., Methods in Enzymology, 27 : 6
75, 1973.
Morris, E.R. and Sanderson, G.R., in New Techniques in Biophysics and Ce
ll Biology, Vol 1,
(R.H. Pain, and B.J. Smith, eds.)p.113, John Wiley, London, 1973.
Edsall, J.T., The Sze, Shape and.Hydration of Protein Molecules in the P
roteins, Vol.l, Part B,
(H. Neurath and K. Barley, eds), pp. 549-716, Academic Press, New York, 1953.
6. Beychok,-S., CircularDichroism of Biological Macromolecules, Science, 154 : 1
288 (1966).

Caldwell, D.J. and Eyring, H., The Theory of Optical Activity, Wfley-Int
erscience, New York,
Feeney, J., Fluorescence Nanosecond Pulse Fluorimetry, in New Techniques
in Biophysics &
Cell Biology, Vol. 2, pp. 233-287, (R.H. Pain and B.J. Smith, eds.), John Wiley,
London, 1975.
Yoshioka, K. and Watanabe, H., Dielectric Properties of Protelns II. Ele
ctric Brefrlngence and
Dichrolsm in Physical Principles and Techniques of Protein Chem/stry, Part A, (S
idney Leach,
ed.] Academic Press, New York, 1969.
I0. Stacey, K.A., L/ght Scatter/ng in Physlca/Chemistry, Academic Press, New Yor
k, 1956.
I I. Tlmasheff, S.N. and Tbwnend, R., /.jht Scatterb in Phy$1ca/Pr/nc/es and Tec
hniques of
Protein Chemistry, Part B, (S.J. Leach, ed.} Academic Press, New York, 1970.
Dickerson, R,E., X-ray Analysis and Protein Structure in The .ProteUs, 2
nd ed., Vol, 2,
(H, Neurath, ed,) Acadera/c Press, New York, 1964.
Willard, H,H,, Meritt, L,L., Dean, J,A. & Settle, F,A, Jr,, Instrumental
Method of AnoB,
8th ed, CB$, New Delhi, 1988,

Maeromolecules are almost insensitive tO gravitational settling. This is because
, for small
gravitational force is so minute that the random bombardment of the molecules of
;surrounding medium far outweighs the directing.force of gravity. Thus, only on
standing for
extended period of time will concentration gradients develop in undisturbed solu
sedimentation would then appear to be completely useless for separation or
of macromolecules in solution. This, however, is not completely true. A
solution to this difficulty is to increase the gravitational potential energy by
. the
in a vessel rotating at high speed. The particles in the solution will t
a centrifugal force is acting upon them in addition to the gravi
Rwas in 1923 that Svedberg and Nicols employed a centrifuge for the first time t
o increase
so as to speed up the rate of sedimentation for the purpose of measuring
sizes. This pioneering work was followed by gradual development of ultracentrifu
is probably the technique most responsible for our current understanding of cell
The applications of this technique range from collection and separation of cells
and molecules to the study of molecular weights of macromolecules.

A yplml rotor with holes to accomodate

vessels Jled wh suspension. The vessel
and the rotor Iki are also shown.
The basic components of a centrifuge
are (t) a metal rotor with holes in it to
accommodate a vessel of liquid (Figure
10 I{A} and (tO a motor or alternative means
of spinning the rotor at a selected speed.
All other parts that different centrifuges
consist of are accessories for maintaining
the environment within which the
centrifuge operates or for modifying the
working of the rotor itself during


An object moving in a circle at a steady angular velocity will eperience a force

, F, directed
This is the basis of centrliation. Angular velocity in radians, o), and the radi
us of
r, to cent/meters, collect/rely determine the magnitude of the force F.
F= ' r
.,, (I}
F might be expressed in terms of earth's gravitat/onal force if it is divided by
980. The
referred to as the relative centrifugal force, RCF. RCF is more frequently refer
red to
'number times

The speed of a centrifuge rotor might be expressed in terms of rlSm or RCF. Howe
centrifuges owing to their designs would have different radii (distances between
axls and the. middle of the sample tube) which would give rise to different RCFs
at the
is illustrated below. Consider two centrifuges operating at the same rpm, 12000.
two centrifuges, however, have different radii, 4,8 and 8.0 cms. Calculating for
the RCFs
both the centrifuges we get
(/) RCF = (1.119 x 10-5) (12,000)2 zt.8
= 7,734 x g.
(ii) RCF = {I.I19 x 10-5) (12,000) 8.0
= 12,891 x g.
In view of the above, and to avoid ambiguity in scientific work, it is better to
express the
acting upon a particle in terms of RCF rather than the rpm. A nomogram based, on
(4) relating RCF to rotor speed and r is given in Figure 10.2.
Rotor speed
(in cm)
centrifugal force
(rev rain-')
00.. SOoOOO
'00 .:',00
15O0 15,00O

310 "- I000

50, 5000
Relationship between radius, rotor speed and relative centrifugal force.
By aligninj the values of the
radius and rotor speed, one can.find out the value of the relative centrifugal f
orce. The right side and the
left side of the RCF scale correspond to the right and left side of the rotor sp
eed scale respectively.
Apart from RCF, the rate of sedimentation of a given particle would also depend
upon its
characteristics such as its density, and its radius. The characteristics of the
medium in
the particle is suspended -- its density, viscosity -- will also tend to affect
the rate of
of the given particle.
Consider that centrifugal force is being applied to a particle. As he particle s
ediments, it
have to displace some amount of the medium of suspension. This displacement will

4. The higher the viscosity of the medium, the slower will be the particle movem
A different way to look at the above mathematical expression is to consider the
required for a spherical particle to sediment to a given distance in a centrifug
al field as a
function of the variables listed above. An expression for sedimentation time can
be obtained by
integrating equation (8}.
t=-- x
t = sedimentation time in seconds,
rt = radial distance from the centre of rotation to the liquid meniscus,
rb = radial distance from the centre of rotation to the bottom of the tu
The above equation makes it clear that a mixture of heterogeneous particles ( fo
r example,
broken cells) can be separated by centrifugation on the basis of their densities
and/or size, This
can be achieved by two methods,
Letting the particles (different organdies in case of broken ceils) sediment to
the bottom
of the tube, 0rganelles differ in their size as well as their densities. Natural
ly, they will sediment
at different rates and thus some will reach the bottom before the others. Once a
particle reaches
the bottom and packs there (such a packed deposit under sedimentation is called
a pellet), we
can removethe supernatant (the suspension above the pellet) and resuspend the pe
lleted particles
in a suitable medium. We can repeat the procedure with the supernatant and pelle
t different
organelles differently. This is the principle of the so called dtfferent' centrl
fugatton and we will
discuss it later.
Letting the particle be sedimented for a fixed time at a fixed sedimentation vel

Since each particle sediments at a different rate, all the particles will be fou
nd at different zones
within the tube ailer sufficient time has been allowed to pass. This principle i
s exploited in
density gradient centrlfugation which, again will be discussed later.
We defer the theoretical discussion here to certain other sections where it will
be more
Many centrifuges of different designs are available in the market. However, all
can be roughly categorized into three different types on the basis of their oper
ating speed.
"Desk Top Centrifuges
These are very simple and small (can be placed atop a desk and hence the name) a
nd are
the least expensive. They are normally used to collect rapidly sedimentlng subst
ances such as
red blood cells, yeast cells or bulky precipitates of chemical reactions. These
are also known as
.clinical centrifuges since most of the clinical work is done by these models, T
heir maximum
speed is usually 3000 rpm and they do not have any temperature regulatory system
The main difference between the centrifuges of this category is the maximum carr
capacity. Separation can be carried out in 10, 50 or 100 cm tubes. Larger capaci
ty (4-6 dm)
centrifuges are also available and there are centrifuges whose rotors can accomm
odate bottles
of fairly large capacity. In all these centrifuges the rotors are mounted on a r
igid shaft. It is
therefore very important that the contents of the centrifuge tubes are balanced
accurately and
that they are never loaded with an odd number of tubes. Moreover, if the rotor i
s only partially
loaded, the tubes have to be placed diametrically opposite to each other to disp
erse the load
evenly. These precautions are true for all types of centrifuges discussed here.

Biophysical Chemistry
High Speed Centrifuges
High speed centrifuges can operate with maximum speed of up to 25,000 rpm provid
about 90,000 g centrifugal force in the process. They are usually equipped with
equipment to remove heat generated due to friction between the air and the spinn
ing rotor. The
temperature can easily be maintained in the range 0-4C by means of a thermocouple
. The
highest carrying capacity may be 1.5 dm3. These instruments are routinely used t
microorganisms, cell debris, cells,, large cellular organelles, precipitates of
chemical reactions
and immunoprecipitates. Although these centrifuges are useful in isolating sub-c
ellular organelles
such as the nuclei, mitochondria, lysosomes etc. they are of little use in isola
ting smaller
organelles such as the ribosomes, microsomes, etc. Neither are they useful in se
individual molecules for want of sufficient centrifugal force.
The Ultracentrifuge
The ultracentrifuge can operate at speeds up to 75,000 rpm providing centrifugal
force in
excess of 500,000 g. At such speed the friction between air and the spinning rot
or generates
significant amount of heat. To eliminate this source of heating, the rotor chamb
er is sealed and
evacuated by two pumps working in tandem making it possible to attain and hold v
acuums of
1 to 2 . Apart from this the ultracentrifuge has a refrigeration system which ca
n maintain the
temperature of the rotor between 0 and 4C. The drive shaft on which the rotor is m
ounted is
merely 1/16 inches in diameter. The small diameter allows the shaft to flex duri
ng rotation
accommodating a certain degree of rotor imbalance without spindle damage, The sh
aft is made
up of aluminium or titanium alloy of high tensile strength to withstand the grea
t forces generated
during centrifugation.
To prevent the rotor from operating at speeds which exceed its maximum rated spe
ed, all
centrifuges possess an overspeed device. Operation of rotor at excessive speeds
can result in an
explosion with the rotor being torn apart. To contain such explosions the rotor
chamber is
always enclosed in a heavy armor plate.
The resolution power of an ultracentrifuge can be gauged from the fact that it c
an resolve
two types of DNA molecules differing only in the fact that one of the two types
contains SN (the

heavier isotope) in place of the naturally occurring 4N isotope of nitrogen. Wit

h this backdrop it
is easier to understand how the ultracentrifuge has helped biochemists in partic
ular and the
biologists in general to not only isolate, but to study the structure-function r
elationship of
those subcellular organelles which could previously be only observed under an el
microscope. Over the years the ultra has been used to isolate viruses in pure fo
rm. This has
allowed careful analysis of their composition. Moreover, the ultra has also been
of much use in
such analytical applications as the characterization of macromolecules (proteins
not only with respect to their molecular weights, but to some extent their confo
rmations also.
Ultracentrffugation can be carried out either with a desire to obtain certain bi
material in isolation from the components that it associates with (e.g., isolati
ng a cell type away
from all other cell types, obtaining a sub-cellular organelle without any contam
ination from
other organelles or fractionation of a macromolecule) or with a purpose to chara
cterize a
macromolecule or sub-cellular particle with respect to its molecular weight or s
coefficient. Centrifugation for isolation and purification of components is know
n as preparatory
centrifugation, while that carried out with a desire for characterization is kno
wn as ana/yt/cal
centrifugation (we will discuss both these types in the subsequent pages).
The ultracentrifuges also are of two types -- the preparatory ultracentrifuge, a
nd the
analytical ultracentrifuge. All the description given above was that for prepara
tory ultracentrifuge.
Given below is a description of the analytical ultracentrifuge.
Analytical Ultracentrifuge
The analytical ultracentrifuge is more or less like the preparative ultracentrif
uge described
above in that it operates at almost the same maximum speed providing the same RC
F; it also Is

refrigerated and has an evacuated chamber; the alloy used in the rotor and the s
haft are the
same. It, however, differs from the preparative ultracentrifuge in having differ
ent type of rotor
and in possessing a specialized optical system to monitor the progress of centrf
fugation. The
rotor of an ultracentrlge is elliptical (Figure 10.3 A) and has two holes for ho
lding two centrifuge
cells. One cell is known as the analytical cell while the other is known as the
counterbalance or
the counterpoise cell. The rotor holds these cells vertically whether it is at r
est or rotating. The
main function of the counterpoise is to counterbalance the analytical cell. It i
s a precisionmachined block of metal with two holes drilled at calibrateddistances from the c
entre of rotation.
These holes serve as calibrations for measuring the distances in the analytical
cell. The analytical
cell is sector shaped and can hold a liquid column about 14 mm high. It has a ca
pacity to
accommodate about 1 cma of sample. The upper and lower planes of the analytical
cell are
transparent having quartz or synthetic sapphire windows. The windows are provide
d for the
passage of light to monitor the progress of centrifugation. The optics used in a
n analytical
centrifuge are either Schlieren optics or Rayleigh interference optics. The Rayl
eigh interference
operates on the basis that the region of the solution in analytical cell harbour
ing macromolecule
will have a refractive index higher than the rest of the solution. At the beginn
ing of sedimentation
this peak of refraction will be at the meniscus. With the progress of sedimentat
ion, however, as
the macromolecules move down the cell the )eak also shifts giving direct informa
tion about the
To vacuum
Lens Photographic plate
DriVe shaft
Analytical cell

Rotor chamber

Light source

14 40
Bphysat Cherrs
sedimentation characteristics of the macromolecules. The whole optical informati
continuously photographed. Figure I(.3 (B) provides diagrammatic representation
analytical ultracentrifuge system.
Analytical ultracentrlfugation has made it quite easy to measure the
coefficients and molecular weights of macromolecules. Molecular weights
species, even when they are in a gross mixture, have been measured by this techn
measuring molecular weights, it has several other applications discussed elsewhe
re in
One point must be made clear here. The name 'preparative ultracentrifuge' is a b
it of.
misnomer. This is so because apart from being used for preparative purposes, it
is used quite
frequently for analytical purposes too. This will become clearer when we
applications of this type of ultracentrifuge.
Basically, rotors come in four varieties : fixed-angle rotors, vertical tube rot
ors, swinging.
bucket rotors, and zonal rotors. The first three rotors are discussed below. Zon
al rotors will be l
discussed in a later section.
Fted-ang/e rotors: These rotors have holes within their body and one can slide t
he centrifuge
tubes within these holes. Since the holes are at an angle (between 14 and 40) to t
he vertical,
the tubes and the solution within also take the same angle (Figure 10.4). Under

Tube angle
Axis of rotation

Figure 10.4. The flxed-angle rotor. (A) CroSS section of a typical flxed-angle r
otor. (B] If the centrifuge tube {s fllled
with a gradient and placed in the rotor: no centrlfugal force ts applied. (C) Ap
plication of centrlfal fore
leads to reorientation of the sample and the gradient, (D) The sample components
separate. (E) Gradient
reorients as the rotor stops.

field, the particles move radially outwards, travel only a short distance before
they strike the
wail. The particles then slide down the wall and the pellet is formed at the out
ermost point of
the tube. This sliding down makes the sedimentation quicker (wall-effect). Howev
er, there is a
severe disadvantage - particles differing highly in their sedimentation characte
ristics can only
be resolved in these rotors; particles which do not differ much in their sedimen
tation behavior
are not resolved. (For more, see discussion under wall-effects).
Vertlcal-tube rotors: These rotors too have holes within their body in which one
can slide
the centrifuge tubes. However, these holes lle parallel to the rotor shaft and n
ot at an angle. As
the rotor accelerates and centrifugal field is applied, the solution within the
tube reorients
through 90. This reorientation makes it lie perpendicular to the axis of rotatio
n. As the rotor
decelerates, the solution orients back to the original position (Figure 10.5).
Centrifugal field
Axis ofrotation
Centrifugal field

Figure 10.5. The vertical tube rotor. (A) Cross-sectlon of a typical vertical tu
be rotor, (B) Tube.filled with gradient and
sample; no centrifugal force applied. (C) Application of centrifugal jeld leads
to reorientation of the
gradient and the sample. (D) The orientation that the gradient and the sample as
sume under ccmtrlfugal force. (E) The sample components separate. (F) As the rot
or decelerates, the gradient and
sample begin to reorienL (G) When the rotor stops, the original orientation is r
Sedimentation in these rotors occurs across the diameter of the tube. The partic
les thus
have to traverse the shortest possible distance and sedimentation is quicker tha
n the other
rotors. Moreover, the tubes lie at the edge of the rotor. This makes rm quite la

rge and the RCF,

at its minimum, is more than what is possible in any other rotor. This is anothe
r reason why
separation in these rotors is quicker.
The pellet in such- rotors will be deposited all along the outer wall of the tub
e. This can be
a disadvantage as the pellet may fall back into solution at the end of centrifug
ation. Even if it
doesn't fall back, it may not be easy to reconstitute the whole pellet and some
loss of yield may
be inevitable.
Swfnglng-bucketrotors: As against fixed hole type rotors we have seen above, the
se rotors
have buckets that swing out to a horizontal position when the rotor accelerates.
The solution in
the tube reorients to lie perpendicular to the axis of rotation and parallel to
the applied centrifugal
field. When the rotor decelerates, the tubes fall backto their original position
and the solution
too regains its original orientation (Figure 10.6).


Centrifugal field
Biophysical Chemistry
Centrifugal field

Tube at res
Tube during centrffugation
Axis of rotation
F3ure 10.6. The swLnfling-bucket rotor. (A) Cross section of a ttjpical swinging
-bucket rotor. (B) Centre tube fllled
with the gradlent and sample; no centrifugal force applied. (C) As the centrifug
al force is applied, the
tube swings out and orients at rjht angles to the axis of rotatlon. (D) The samp
le components separate.
(E) When the rotor stops, the bucket reorients to its original position.
Even in swinging bucket rotors, the particles strike the wails of the tube and s
lide down.
These rotors too suffer from wall-effects like the swinging bucket rotors. But t
hese rotors are
normally used for density-gradient centrffugation and the density gradient can c
ushion and
lessen the wall-effects.
Wall Effects or Trajectory of a Particle Inside the Rotor Tube
The centrifugal force acts on the particle in an outward direction. Thus, when p
centrifugation in a fixed angle rotor, the particle does not travel in a straigh
t line towards the
bottom of the tube. Rather it moves outward within the tube till it hits its wal
ls and then slides
down this wall to be pelleted at the bottom (Figure 10.7). This results in a rap
id sedimentation
of particles in a fixed angle rotor tube. This is known as the wall effect. This
behaviour, however,
gives rise to strong convection currents due to which it is not possible to reol

ve particles which
vary very little in their sedimentation characteristics. On the other hand, this
rotor design is
Axis of rotation
Cite: tee!e tube of fluid [I
Boundaxy of |
Descending layer ---./
(High eoneentration]/(
Thin layer of
Pellet Aseending layer
(Low concentration)
Figure 10.7 Schematic diagram of convectlon currents generated due to wall effec
ts. The diagram shows parles
descending along the wall of the tube (descending layer)

very helpful in separation of particles which vary in their sedimentation rates
by a significant
order of magnitude.
This particle behaviou is true for swinging bucket rotor tubes also, albeit to a
extent. This is because the particles in a centrifugal field, rather than sedime
nting in parallel
lines, fan out radially from the centre of rotation. Thus, in these cells also t
he particles hit the
wall and then .slide down them to the bottom. Since swinging bucket rotors are g
enerally used
for density gradient centrifugation, the gradient usually decreases these convec
tion currents
due to wall effects.
Attempts have been made to' minimize wall effects by using a sector shaped cell
in the
swinging-bucket rotor. However, the best way to minimize the wall effects is to
use a zonal
rotor. The discussion of zonal rotor is deferred to a later section as an unders
tanding of density
gradient centrifugation is essentiaJ to understand its working.
Preparative centrifugation is concerned with the actual isolation of biological
material for
subsequent biochemical investigations. Preparative centrifugation methods can be
divided into
two main techniques depending upon the medium of suspension in which the separat
ion is
carried out. Separations carried out in a suspending medium which is homogenous
are known
as differential centrifugation while those carried out in a suspending medium ha
ving density
gradients are known as dens/ty gradient centrifugations.
Recall equation (I0) from our previous discussion of basic principles of sedimen

The above equation makes it clear that a mixture of homogeneous partlclcs can be
by centrifugation on the basis of their densities and/or their size. This can be
achieved either by
the time required for their complete sedimentation in a fixed centrifugal field
or on the extent of
their sedimentation after a given time in a fixed centrifugal flcld.
If we now substitute in the above equation the approxlmatc data about the shape
densities of various intraccllular particles {we keep the mcdinm and therefore i
ts characteristics,
and the centrifugal field constant} we can arrive at a fair estimate about the t
ime requlrcd for
each of them to sediment completely in a given centrifugal field. In a similar m
anner we can
va the value of the centrifugal field applied for each intracellular organelle a
nd again find out
the time required for each of them to sediment completely under various centrifu
gal fields. If we
assemble all the data so generated we would find that under a flcld of roughly 1
000 g the cell
debris and the nuclei would sediment if the field-is applied for about 15 minute
s. Similarly,
upon subjecting the homogcnate to centrifugatlon for 15 minutes at 10,000 g, the
and lysosomcs would pellet out. Similar data would also be generated for other i
organelles {all the data represented here is approximate and it varies with tiss
ue and species
differences}. The best strategy that we can adapt now to separate the tissue hom
ogenate into
various organellcs is to centrifugally divide it into a number of fractions by i
ncreasing the
applied centrifugal field at each step. We can choose the centrifugal field in s
uch a manner that
a particular organcllc sediments during the already known time of centrifugation
to give a
pellet. The pellet and supernatant arc separated at the end of each step and the
reccntrifuged to sediment another lighte" intracellular organelle. This is the e
ssence of differcntlal
centrlfugation.,FIgure I0.8 provides an outllnc of a typical fractionatton proce
dure based on
differential centrifugation.

lO00'x g
I0,000 x g
I00,000 x g 100,000 x g
5-15 rain
15 mln
I-2 hr
Pellet of
(.. Pellet of
mitochondria +
some heavy
lgure 10.8 Outline of a typlcal fractwnatlon by differentW.l centratlon
Every pellet has to be washed several times. This is so since the pellet obtaine
d is never
pure, i.e,, apart from the desired particles, it consists of contamination from
the other pin.des
l.'.i.. Small sized particles
Large sized particles
Time of
centrifuUon .

Large sized particles

Medium sized particles
- Small sized particles

Resupenson ofthepellt and reeen yeld apellet which sfcdrly putw, Howwr,
th yidof

,contained in the homogenate. To understand the situation let us take a look at
Figure 10.9.
Before the centrifugation is initiated all the particles of the homogenate are h
distributed throughout the centrifuge tube (Fig. 10.9A, (i)). Centrifugation-res
ults in sedimentation
particles at their respective sedimentation rates till a pellet is formed at the
bottom of the
tube (Figure 10.9A (ii) and (iii)). This pellet, however, is not entirely made u
p of the large
some of the lighter particles, originally suspended near the bottom of the tube
and thus contaminated the pellet. Repeated resuspensions and recentrifugations
pellet (Figure 10.9 B and C) however, yield a fairly pure pellet of large partic
les. It
pointed out here that the repeated washings invariably reduce the yield of the f
Inspite of its reduced yield differential centrifugation remains probably the mo
st commonly
method for isolation of intracellular organelles from tissue homogenates because
of its
ease, convenience and time economy. The drawback of this method is ofcourse its
the fact that the preparations obtained are never pure. For experiments which st
absolute purity of preparations an alternative method known as density gradient
centrifugation (see below) is used.
As opposed to differential centrifugation, where a homogenous medium is used for
gradient centrifugation employs medium which has gradients, The separation
centrifugal field is therefore dependent upon the buoyant densities of the parti
gradients, apart from exerting their separating effect, eliminate mixing of sepa
due to convection and mechanical vibrations. This method gives a much better
than differential centrffugation. Density gradient centrifugation has two variat
centrffugation, and isopycnic centrifugation.
The gradient used here has maximum density below that of least dense sedimenting
gradient is reasonably shallow, The technique involves careful layering of a sam
on top of a preformed liquid density gradient whose density continuously increas

the bottom of the sample tube. Centrifugation is then performed at a comparative

speed for a short time. The sample particles travel through the steep gradient a
nd form
zones depending upon their sedimenting rate. For separation to be achieved b thi
it is necessary that centrifugation be terminated before any of the zone reaches
centrifuge tube. This method is useful for separating particles which differ in
Sample containing
particles of
different sizes
small particles
medium psrtlolss
;;: Imnll portloloe Medium eled pmrtleloe ..oLarOo pertleloe
| O. I 0 RaW.zonal centratton. (A) Sample layered over a continuous densWj gradi
ent. (B) Posgton of zones
due to dterent sze of parcles at the termlnaton of centrtton. Note that separati
on s due to
d{lerences in sze and shape,

Biophysical Chemistry
but not in density, Thus, while this method is extremely useful for separation o
f proteins
possessing nearly identical densities but differing only slightly in their molec
ular weights, it is
not at all useful for separation of organdies such as mitochondria, lysosomes an
d peroxisomes
which have different densities but similar sizes. The method has been very usefu
l for separation
of RNA-DNA hybrids and ribosomal subunits. Figure 10.10 illustrates the salient
features of
rate-zonal centrifugation.
Isopynic Centrlfugation
For better understanding of this technique, it would be good if equation (9) is
In the above equation if one substitutes identical values for the density of the
particle and
density of the medium, the rate of sedimentation, , will become zero. If a densi
ty gradient is
now prepared in a tube in such a manner that the density goes on increasing towa
rd the
bottom of the tube and a solution of different particles is centrifuged in this
medium, different
particles differing in their buoyant densities will travel different lengths and
become stationary
at a region where the density of the layer below them is greater than their own
buoyant density.
This is the essence of Lopycnlc centrg@atlon also known as the n eqW10rlum
The method differs from rate-zonal centrifugation in two significant ways. (i) A
s opposed
to rate-zonal centrifugation, where the grad/ents were shallow, isopycnic method
used gradients
which are reasonably steep so that at maximum, the gradient density is greater t
han the most
dense sedimenting species. (il) As opposed to rate-zonal method where centrifuga
tion is carried
out for a limited period of time, isopycnic method allows centrifugation for pro
longed periods at
relatively higher speeds to permit all species to seek their equilibrium densiti
es. Table 10. I
summarizes the differences between the two techniques.
Table 10.1 S--igniflcant differences between rate-zonal and iso.lcnic eenation

s-zonal, sedimentation veloc/ty,

Density equil/bration, sedimentation
Shallow, maximum gradient density
Steep, maximum gradient density
less than that of the least dense
greater than that of the most dense
sedimenting specie, gradient
sedimenting specie, continuous or
discontinuous gradients.
Centrifugation Incomplete sedimentation, low
Complete sedimentation till
speed, short time.
equilibrium is acheived, high speed,
long time.
RNA-DNA hybrids, ribosomal subDNA, plasmallpoproteins, lysosomes,
units etc.
mitochondria, peroxisomes etc.
There are two ways in which isopycnic centrifugation may be carried out. One way
is to
carry out a preliminary centrifugation of the sample at an RCF which will sedime
nt particles
heavier than the one desired. The supernatant is then layered over a medium whic
h has the
same density (isopycnlc) as the desired fraction. If centrifugation is now carri
ed out, the desired
fraction wiB-migrate to the middle of the liquid column. The fraction lighter th
an the desired
one will be at the meniscus, while the one that is heavier will be at the bottom
of the centrifuge

The alternate way is to prepare a continuous density gradient in a tube. The gra
should span the range of particle densities of interest. No pretreatment of the
sample is necessary
and it can directly be layered on top of the densitygradient column. Upon centri
fugation individual
particles will sediment down the tube till they encounter a gradient whose densi
ty is greater
than their own buoyant densiW. The particles will thus become stationary forming
zones (Figure I0.II).
Srnlde cont|inlng
clMere cleities

Centrifugal force acting

on the particle
Higher density : acts
as a cushion
The partles have formed d,rent zones n regions of the gradient havbg densities s
bnilar to their
Isopycnic separation depends solely on the buoyant densities of the particles to
be separated
and not on their shaPe or size. Thus, the method is not useful for separation of
proteins many
0fwhich have similar buoyant densities inspire of differences in molecular weigh
ts. It is however,
very useful for separation of such intracellular organelles as mitochondria, lys
osomes, and
perox/somes which do not differ in size but differ in their buoyant densities. T
he method is also
useful for nucleic acid fractionation.
Table 10.2 lists the densities of a few important organelles and other macromole
cules in
sucrose soluUons.
able 10.2 Approximate densitie of particles in sucrose solutions
Denai (n/cm

Golgl apparatus
1.06 1.10
Plasma Membranes
Smooth endoplasmlc reticulum
I. 16
Intact oncogenic viruses
I. 16 - I. 18
Plant viruses
Soluble proteins
Rhino- and enterov/ruses
Nucleic acids, ribosomes
1.30- 1.45
1.30- 1.45
1.60- 1.75

Biophysical Cherntstnd
Gradient Materials
Pickels (I 943), Brakke (I 95 I) and Kahler and Lloyd { 195 i) were the first fe
w scientists to
use stabilizing gradients. They used sucrose for these gradients. Sucrose still
remains the
materialin most general use.
A gradient material should meet several requirements. There is no ideal all-purp
ose gradient
material. Sucrose is used routinely for rate-zonal centrifugation, while cesium
chloride may be
the usual choice for isopycnic centrifugation. Apart from allowing the desired t
ype of separation,
the gradient material should have the following properties :
(0 it should not affect the biological activity of the sample being Separated,
(iO it should not interfere with the assay technique,
(tit) it should be easily removable from the purified product,
(iv) it should not absorb in the ultraviolet range,
(v) it should be non-corrosive to the rotor,
(vO it should be easily sterilizable,
(vii) it should be cheap and readily available, and
(viii) it should preferably be recoverable for reuse ....
Table 10.3 provides data about most commonly used gradient materials along with
maximum densities at 20C.
Table 10.3 Types of Gradient Materials
Maximum density
Sucrose (66%, .5C}
Silica sols
Cs acetate

Cs formate
K formate
Na formate