Physical Chemistry

Reference: Physical Chemistry

Principles and Applications in Biological Sciences
Tinoco and others
Fourth Edition-2002

By
Dr. Gehan Abdel Raouf

Principles of Physical Chemistry

Physical chemistry has been especially powerful
in understanding fundamental biological
processes.
Its principles are basic to the methods used to
determine the sequence of the human genome,
obtain atomic resolution structures of proteins
and nucleic acids, and learn how biochemicals
react and interact to make a cell function.

Course Portfolio
Thermodynamics
Intermolecular forces
Quantum mechanics and its biological
application
Chemistry of radiation

Principles of thermodynamics
Thermodynamics deals with interchanges
among different forms of energy {energy
conversion and conservation}.
It is the change in energy in which we are
interested.
The three laws of thermodynamics have
been summarized as:
You cant win, you cant break even, and you
cant get out of the game.
4

Thermodynamics
Thermodynamics originated as the study
of the relationship between mechanical
and thermal energy- the energy
associated with the disordered motions of
the atoms and molecules within a
substance
It is important whenever temperature play
a role.
5

Applications
How do you calculate the work done when
muscle contract or stretches?
How can chemical reactions be used to do
work or to produce heat?
How much heat can be generated by
burning 1 g of sugar or from heating and
digesting 1 g of sugar?

Systems
System
Surroundings
Boundaries
Systems:
-Closed system ex. Water in a beaker plus
evaporated water.
-Open system ex. Water in a beaker only.
7

Work and Heat

A system can do work on the
surroundings, or the surroundings can do
work on the system.
Work: is defined as the product of force
times a distance.
W= F.dX , F is the force in newtons (N)
X is the distance in meter (m)
W is the work done in joules (J)
9
also
1 erg=10-7J , 1cal= 4.184 J

Work and Heat

Work is positive if the surroundings are
doing work on the system.
Work is negative if the system is doing
work on the surroundings.
Work of extending spring (Hookes law)
Ex. DNA, muscle fiber
W= F(X2-X1) , F= - k.dx
10

 Work in gravitational field

W=mg(h2-h1)

Work in an electric field

Radiation energy= h

W=vIt

11

Work of increasing or decreasing

volume
P=F/A , F=PA
W= F.dX
= PA.dX ,A.dX= dV
=- P.dV
Compression a decrease in volume or a ve dV,
means the surroundings have done work on the
system and W is +ve.
Expansion an increase in volume or a +ve dV,
means the system dose work on the
surroundings and W is ve.
12

Ex. 2.2 P 22
Calculate the PV work done when a
system containing a gas expands from
1.0L to 2.0L against a constant external
pressure of 10 atm.{1L.1atm.= 101.325J}
W = -P(V2-V1)
=-10(2-1) = -10 L.atm
W =-10x101.325 = -1013 J
the system dose work; W is negative.
13

Heat
When two bodies are in contact with each
other, their temperatures tend to become
equal.
Energy is being exchanged. The hot body
will lose energy and cool down; the cold
body will gain energy and warm up. {heat
transfer}
Heat is +ve if it flows into the system
Heat is -ve if it flows out of the system
14

 For closed system, the transfer of a small quantity of

heat dq will result in a change dT in its temperature.
The ratio dq/dT is called heat capacity C
C = dq/dT q= C(T2-T1)
Heat capacity of every material: is a quantity that
characterizes how much heat is necessary to raise its
temperature by 1oC or 1 K.
It is usually determined by measuring the changes in
temperature when known amounts of electrical
energy are dissipated in this material.
Its units are
15

JK-1mol-1 or
cal K-1mol-1
K = oC + 273.15

- C is different for different materials, and for a

given material, C will vary with temperature.
- For a hot body in contact with cold body, the heat
capacity C of each body must be known and the
equation
q= C(T2-T1) must be applied
separately.
- C is increasing with the amount of materials in
the body.
- For a pure chemical substance
- C= nC , n is the number of moles
C is the molar heat capacity
16

 Ex. 2.5 p 26
Calculate the heat, in joules, necessary to
change the temperature of 100 g of liquid water
by 50oC at constant pressure. The heat capacity
of liquid water at constant pressure is 1 cal g -1
deg-1 and is nearly independent of temperature.
(1cal= 4.184J)
The heat absorbed by the system
q=C(T2-T1)
= 100g (1 cal g-1 deg-1 )x(50 deg)x4.184

=20.9 KJ
17

First law of thermodynamics

It states that energy is conserved; it can be
transferred between the system and surroundings, but
the total energy of the system plus surroundings is
constant
In open system: the change in energy E of the
system is equal to the amount of energy that entered
it( from the surroundings) minus the energy that went
out of it (into the surroundings)
In closed system:
E=q +W , q is the net heat transferred to the system
W is the net work done on the system (in)
E equals the change in energy of the system
18

Additional terms can be added to the equation if

there are energy exchanges other than heat and
work between the system and surroundings or if
the system is open one.
E= zero for an isolated system

Because E is a property of the system, it is

sometimes called the internal energy of the
system.
19

 Pressure P, volume V, and temperature T

can specify many other properties of liquid
for example, such as its density, surface
tension, refractive index, and so forth.
All these properties of the system together
with P,V, and T are called variables of
state.
Work and heat depend on the path
between states
Enthalpy H is a new variable of state
H= E+PV
20

 The energy or enthalpy change when the

teaspoon of sugar is converted to CO2 and H2O
is the same whether sugar is burned in a
reaction vessel or metabolized in human body,
as long as the final states for the reaction are
the same in the two cases.
It does not matter whether the conversion
involves a direct reaction with O2 (combustion)
or multiple enzyme-catalyzed steps inside a
human being
Table A.6
table 2.3
The bond dissociation energy is the enthalpy at
25oC and 1 atm, for the reaction.
A-B (g) A (g) + B(g)
21

22

23

Ex.2.13 p54
Calculate the heat of formation for gaseous cyclohexane using tble 2.3
and compare with the measured value in the appendix (table A.6).
The reaction for the formation of cyclohexane is

6C(graphite)+6H2(g) C6H12(g)
We can write it as a sum of bond-breaking and bond-forming reactions
16C(graphite)6C(g)
H1=6D(graphite) = 6x716.7=4300KJ
This is the enthalpy required to remove 6 mol of carbon atoms from the
crystalline lattice of graphite, which is the standard state for elemental
carbon.

2-

3- 6C(g) + 12H(g) {6(C-C)+12(C-H)}=C 6H12(g)

H3=-6D(C-C) -12D(C-H)= -6x344 -12x415
= -7044 KJ

6H2(g) 12H(g)
H2=6D(H2 )=6x436 = 2616 KJ

Note that bond formation energies are just the

24
negative of bond dissociation energies

 Hf = H1 + H2 + H3
= (4300+ 2616)- 7044= -128KJ
The value in table A.6 is -123.15KJ which is
in good agreement. (molecule with normal
bond)

25

Ex. 2.14
Calculate the heat formation for gaseous benzene using table 2.3 and
compare with the measured value in table A.6 in the appendix.
The reaction for benzene is
6C(graphite)+3H2(g) C6H6(g)
16C(graphite)6C(g)
H1=6D(graphite) = 6x716.7=4300KJ

2-

3- 6C(g) + 6H(g) {3(C-C)+3(C=C)+6(C-H)}=C6H6(g)

H3= - 3D(C-C) -3D(C=C) - 6(C-H)
= -3x344 - 3x615 6x415
= -5367 KJ

Hf = H1 + H2 + H3
= (4300+ 1308) - 5367= 241 KJ

3H2(g) 6H(g)
H2=3D(H2 )=3x436 = 1308 KJ

The value in table A.6 is 82.93 i.e is about 158 KJ lower in enthalpy than would
be expected.
This energy is what we call the resonance energy.
26

Chapter 3. The second law

The entropy of the universe increases

The second law of thermodynamics can be phrased in several ways.

In term of macroscopic description of a system, it states that a quantity
called the entropy [S] tends to increase in all processes.

Macroscopic variable such as temperature, pressure, and volume.

At the microscopic level, entropy is closely related to the randomness or

disorder of the constituents; all systems tend toward states of greater
disorder.

Example: every time we freeze an ice tray full of water in the freezer, we
are increasing the order in ice tray. However, the disorder caused by
the heat released outside the freezer compartment more than
balances the order created in the ice.

The total disorder in the universe has increased; the total entropy of the
universe has increased
27

Entropy
mol-1

Entropy
mol-1

H2O(s)

41

JK-1

H2O(l)

63.2

JK-1

H2O(g)

188.3 JK

28

-1

Carbon
(diamond)

2.4 JK-1 hard

Carbon
(graphite)

5.7JK-1

soft

 The greater the disorder the greater the

entropy i.e. entropy is a quantitative measure
of disorder and it is not conserved
Like the internal energy, the entropy of a system
depends only on its state and not on how that
state is achieved
All entropies increase as the temperature is
raised, because increasing molecular motion
increases disorder and thus increases the
entropy
29

Gibbs free energy

Gibbs free energy G, defined as the enthalpy H minus the
product of the absolute temperature [T] and the entropy [S]

G= H-ST

G is
G is

-ve the process occurs spontaneously

+ve the process can not occurs
spontaneously.
G = 0
the system is at equilibrium
Thermodynamics allows us to decide which reactions are
impossible under given conditions and how the conditions can be
changed to make impossible reactions probable
e.g.

30

graphite diamonds ????

Noncovalent reactions p97

If two points charge +e and -e are separated by a distance r, the dipole

moment= er

Types of Interactions:
1- Ion dipole interactions

A charged ion and a neutral molecule with a dipole moment (such as water
molecule) are called ion dipole interactions

2- charge-induced dipole moment

Ions can also interact with neutral molecule with zero dipole moment (such
as CCl4) causing the molecule to be polarized. We say that the molecule
has induced dipole moment and the interaction is called chargeinduced dipole moment

3- London interaction (only attractive force)

induced dipole-induced dipole interaction:

Also exist because the fluctuations in the electronic distributions in the
molecules.
An induced dipole moment molecule can induce a dipole in the neighboring
molecule

4- van der Waal interactions

31
Include
permanent-dipole permanent dipole interactions

Noncovalent reactions p97

The London-van der Waal forces can become specific when carful fitting
of molecules is involved.
Binding of a particular substrate to an enzyme, antigen-antibody binding,
and the function of specific membrane lipids may be dominated by
The London-van der Waal interactions
5- The hydrogen bond
Is one of the important bonds that determines the three dimentional
structure of proteins and nucleic acids. O-H..O, N-H..N, N-H..O
6- Hydrophobic interactions (fear of water)
It is important in aqueous solutions. Water molecules have a strong
attraction for each other (as a consequence of hydrogen-bond
formation)
The oxygen atom of most molecules of liquid water is hydrogen-bonded
to two hydrogen atoms of two hydrogen atoms of two other water
molecules and also the hydrogen atoms
Therefore, the molecules of liquid water form a mobile network. The
network is not a rigid one, and change in neighbors occurs rapidly
because of thermal motions
32

Noncovalent reactions
Water-soluble proteins, polar lipid molecules form bilayer
sheets or membranes in water, in which the
hydrocarbon proteins are buried inside and the polar
or charged proteins are on the surface exposed to
water. Such molecules are called amphiphilic
Hydrophobic interactions are characterized by low
enthalpy changes and are entropy driven
We should note that hydrophobic interaction is a
term that we use to describe the combined effects of
London, van der Waals, and hydrogen-bonding
interactions in certain processes in aqueous
solutions
33

34

Proteins and Nucleic Acids p101

Proteins are polypeptides of 20 naturally
occurring amino acids.
Amino acids are linked by amide bonds from the
carboxyl group of one amino acid to the amino
group of the next (fig. 3.4)
The sequence of amino acid residues in a
polypeptide is called primary structure
The polypeptides fold into different secondary
structures held together by hydrogen bonds
and other non covalent interactions
35

36

 The different folded conformations of a polypeptide

depend on rotation about the two single bonds
attached to the amide group, fig.3.4.
-helix is a common secondary structure
element in proteins.
Nucleic acids are polynucleotides of four naturally
occurring nucleotides. The nucleotides are
composed of a sugar group connected to one of
four bases and to a phosphate group.
Nucleotides are linked by phosphodiester bonds
(fig.3.6 b). The sequence of the bases in the
polynucleotide is the primary structure.

The stacking of the base pair, one above

the other, plus the hydrogen bonds
between bases provide the stabilizing
enthalpy and free energy of the helix
37

38

 Table 3.2 measured enthalpies for biochemical

reactions involving changes in shape
(conformation) of molecules.
By changes in conformation, we mean
changes in the secondary structure of the
molecule (the primary structure involves the
covalent bonds) e.g. change in a polypeptide
from a rigid helix to a flexible coil.
Denaturation of proteins involves this type of
change.
39

40

Chapter 4
Free energy and chemical equilibria
When a chemical reaction occurs in a closed
system, the amounts of the reactants decrease, and
the amounts of the products increase, until an
equilibrium position is reached.
At equilibrium, the reactant and products can
interconvert, but the composition of the system
remains unchanged.
We learned in the preceding chapter that at
constant temperature and pressure, the change in
the Gibbs free energy G of a system undergoing a
spontaneous reaction must be -ve. If G is +ve,
only the reverse reaction can spontaneously occur;
if it is zero, the system is at equilibrium.
41

Free energy and chemical equilibria

The Gibbs free energy G of an open system is dependent
on the temperature, pressure, and the amounts of
materials that make up the system (concentration).
When a very small amount of a substance is added to the
system at constant temperature and pressure without
changing any of the other composition variables, the
change in G per mole of the substance added is
termed the partial molar Gibbs free energy of the
added substance.
Thus, the partial molar Gibbs free energy of a
substance determines its chemical potential in a
reaction at constant temperature and pressure.
Temperature, pressure, composition variables (partial
pressures for gases in a gaseous mixture and
concentrations for solutes in a solution) influence the
chemical potential of a substance.
42

Applications in biological systems

1- Metabolic reactions in which chemical bonds
are broken and new ones formed.
2- Dissociation of H+ from acidic compounds and
binding H + to bases.
3- Oxidation-reduction reactions in which electrons
transfer occurs.
4-Interactions involving the aqueous medium in
which metabolites and ionic species occurs in
the cytoplasm or other biological fluids.
5- The assembly and disassembly of membranes
and other multicomponent cellular structures.
43

Chapter 5
Free energy and physical equilibria
Applications
Membrane and transport
Most biological membranes consist of a lipid bilayer that
contains proteins and other molecules that serve as
recognition sites, signal transmitters, or ports of entrance
and exit.
Membranes are so thin that they are often considered to
be two-dimensional phases.
The thermodynamic properties of the membrane are
then described in terms of surface properties, such as
the surface chemical potential and the surface tension or
pressure.
44

 Membranes permit the controlled transport of

molecules and signals between the inside and
outside.
Difference between the inside and outside of
a cell influence the exchange of metabolites and
electrical signals, the flow of heat, and changes
in shape.
1- Temperature differences causes heat flow.
2- Pressure differences cause changes in shape.
3- Electrochemical potential differences cause
molecular transport and electrical signals.
45

Ligand binding
p188
Noncovalent interactions that bind ligands like O2 to
hemoglobin, substrate to enzymes, and complementary
strands of DNA or RNA to one another underlie essential
dynamic processes in living cells.
Equilibrium dialysis provides a method of exploring
the binding between macromolecules and small
ligand molecules.
In equilibrium dialysis a semipermeable membrane
allows a ligand to reach equilibrium between two phases,
one of which contains a macromolecule. The difference
in concentrations of ligand on opposite sides of the
membrane depends on the interaction of ligands and
macromolecule.
46

Colligative properties
The chemical potential must be the same for each
component present in two or more phases at
equilibrium with one another.
The component can be the solvent or each of the
solutes in a solution. The phases are solids,
liquids, gases, or solution compartments separated
by a semipermeable membrane.
Any change in a property such as temperature,
pressure, or activity in one phase that results in a
change in chemical potential must be
accompanied by an equal change in chemical
potential in the other phase, for the for the system
to remain in equilibrium.
47

 This fundamental fact allows us to explain the

colligative properties, such as
1- the freezing point lowering
2- the boiling-point elevation
3- the vapor-pressure lowering
4- the increase of osmotic pressure when a solute is
dissolved in a solvent.
Colligative properties play essential roles in biological
cells.
Osmotic pressure that results from the activities of
components present in the cytoplasm needs to be
balanced by a suitable external pressure lest the cell
rupture and burst.
Colligative properties are used
1- To determine the concentrations and molecular
weights of solutes in solution
2- To measure association and dissociation equilibrium
constants of biopolymers.
48

49

Phase equilibria
The transfer of a chemical from one phase to another is
illustrated by :
1-the evaporation of liquid water into vapor phase
2- the heat removed from our bodies by evaporation of
sweat is essential to survival in hot climates.
3- the transport of ions from inside a cell to outside,
which is vital to nerve conduction.
(we can consider the inside and the outside of the cell as
two different phases).

 Equilibrium is a state where nothing seems to happennothing apparently changes with time.
For living system to exist, they must be out of
equilibrium; dynamic processes need to occur to
maintain the living state.
When an organism dies; it approaches closer to
equilibrium.
The usefulness of considering equilibrium in connection
with living organisms is that it helps define the direction
of dynamic processes.
One of the consequences of the second law of
thermodynamics is that spontaneous processes result in
the system moving toward a state of equilibrium.

For an open system, spontaneous processes

are accompanied by a decrease in chemical
potential,
0.
at equilibrium T,P =0
50

 Equilibrium dialysis
see p 197- p 200
If we had to rely only on normal saline solution flowing in
our veins and arteries, the amount of O2 transferred from
our lungs to muscle cells would be far too little to support
life as we know it.
The dissolved oxygen concentration is too low, even if we
breath pure O2.
Red blood cells (erythrocytes) solve this problem for us by
packaging hemoglobin (Hb) molecules, which are proteins
containing a heme that binds O2 strongly. Muscle cells
contain a related protein, myoglobin (Mb), that binds O 2
and stores it until needed.
Red blood cells are packed full of Hb and contained by a
plasma membrane boundary.
The plasma membrane is freely permeable to small,
neutral molecules like O2 but is impermeable to large
protein molecules like Hb and to many charged ions.
51

Equilibrium Dialysis

52

The operation of the red blood cell is illustrative of a technique

called equilibrium dialysis that is a laboratory method of
studying the binding of a ligand (small molecule like O 2) by a
macromolecule (protein, nucleic acid, etc.)
Fig 5.4 p 197
1- Control, where no macromolecule inside the dialysis bag
2- Another control, where albumin protein is inside (it does not bind
to O2).
3- If a protein like myoglobin is in the bag, then the total
concentration of O2 (in mol/L) inside will be significantly larger than
the concentration of O2 ouside, where myoglobin is absent.
The presence of the Mb inside serves to concentrate the O2 by
binding it.
By series of quantitative measurements, it is possible to determine
both the binding equilibrium constant K and the number of ligand
binding sites per macromolecule.

53

 M+A M.A ,M macromolecule

A single binding site for ligand A

K=[M.A] / [M][A] , K equilibrium constant
To relate these concentrations to the measurable
quantities,
CM = [M.A]+[M]
cA(outside)=[A]
cA(inside)=[A]+[M.A]
cA(bound)=[M.A]
At equilibrium the activity of A inside is the same inside.
54

K=cA(bound)/ {cM - cA(bound)} cA(outside)

The Scatchard equation

The equation of K can be simplified

The average number of ligand molecules bound per macromolecule at
equilibrium =
= cA(bound)/ cM
, cA(bound)=concentration of A bound
cM concentration of macromolecule

K= / (1- )[A]

/ [A] = K (1- )

The equilibrium constant was written with the assumption that only one
molecule of a was bound per macromolecule; i.e. can vary only
from 0(no ligand) to 1 (each macromolecule has bound an A).
However, many macromolecules have more than one binding site for
ligand. (Hb for example has four binding sites for O 2).

55

Now can vary from 0 to N, the number of binding

sites on each macromolecule.
/ [A] = K (N- )
The Scatchard equation
see Fig. 5.5
The slope = -K intersect the y-axis at NK
and x-axis at N
If there are N identical and independent binding sites
per macromolecule, this means that the N sites have
the same binding equilibrium constant K and that
binding at one site does not change the binding at
another site.

56

 The Scatchard equation is often used to study binding to

macromolecule.
The value of [A] (free cA), is the concentration on the solvent side of
the dialysis membrane at equilibrium.
The value of = cA(bound)/ cM is the concentration of A on the
macromolecule side at equilibrium.

If a Scatchard plot does not give a straight line, this

indicates that the binding sites are not identical or
not independent. (The four binding sites for O2 in Hb are neither

57

identical nor independent).

A macromolecule is made of monomer units, such as the peptide
units in a protein. A DNA molecule is a polynucleotide consisting of
nucleotides as its monomer building blocks.
Sometimes it is more convenient to define the binding parameters on
a per monomer unit basis.
r= number of bound A per monomer unit of the macromolecule
n=number of binding sites per monomer unit of the macromolecule
r / [A] = K (n- r)
The Scatchard equation

58

59

Cooperative binding and Anticooperative

Binding
Although the sites are identical, there is significant
interaction among them.
The binding of a ligand to one site affects the
binding of ligands to other sites.
The first ligand bound affects the binding of the
next one, which affects the binding of the next one,
and so on.
In cooperative binding, the first ligand bound
makes it easier for the next one to be bound. (case:
all- or- none binding)
In anticooperative binding, each succeeding
ligand is bound less strongly than the previous one.
60

Donnan Effect and Donnan potential

We use equilibrium dialysis to measure binding of a small molecule

ligand by a macromolecule.
The method becomes more complicated if the macromolecule and
ligand are charged.
The solutions on each side of the dialysis membrane must be
electrically neutral means that there can be an apparent
increase in binding of a ligand with the opposite charge to that of
the macromolecule and a decrease in binding of a ligand with the
same charge.
These effect depends on the net charge on the macromolecule.
When equilibrium (except for the macromolecule) is reached for
charged species, a voltage is developed across the membrane.

The asymmetric distribution of ions caused by the

charged macromolecules is called the Donnan
potential
61

Membrane p 213
Whenever there are two phases in contact, there
is also a surface, or interface between them.
This surface has different properties and
behavior than the phases.
The surface has thermodynamic properties
specified by its free energy, enthalpy and so on,
just as the bulk phases have.
62

Lipid molecules

Amphiphilic molecule consists of two parts, one of which interacts

primarily with the hydrophobic phase and the other with the aqueous
phase.
Surfactant, molecules that have a hydrocarbon tail and a polar head;
(surface active molecules)
Fig. 5.14

There is a large variety of hydrophilic head groups:

1- Some are polar owing to exposed OH or NH2
2- Others are negatively charged
3- Or zwitterionic, bearing both positive and negative charges at PH 7
There is variability in the number of hydrocarbon tails (usually one or two)
attached to a head group variations are important for defining the
properties of the surfaces, especially in membranes and vesicles.
They determine the :
1- Thermal stability,
2- Fluidity
3- Curvature of the membrane
4- The interactions with proteins and other molecules associated with or
embedded in the membrane}
Lipid
bilayers
p214
63

64

Phase Transitions in Lipids, Bilayers, and

Membranes
The lipid bilayers are thought to have a fluidity
something like that of olive oil.
The behavior is liquidlike in two dimensions.
As the temperature is decreased, transitions to
a solidlike membrane may occur.
Under these conditions, the two-dimensional
mobility is greatly decreased.
Liquid-phase transitions can be studied using
technique called differential thermal analysis
{DTA}, using differential scanning calorimeter
(DSC).
65

Phase Transitions in Lipids, Bilayers, and

Membranes
Heat is added to the sample electrically at a
constant rate, and the temperature is
continuously monitored using a small probe.
When the temperature reaches the melting
point of the lipid, extra heat is required to
induce the transition from solidlike to liquidlike
behavior.
Once the transition is completed, the
temperature once again rises smoothly in
proportion to heat capacity
Fig. 5.16
The peak of the curve at 41.55oC indicates the
transition temperature, Ttrans, for the lipid.
66

67

 Factors that influence the transition

temperatures for lipids include:
1- the length of the hydrocarbon tail (increased for
longer hydrocarbon tails)
2- the nature of the head group
3- the presence of unsaturation (double bonds) in
the hydrocarbons (decreased)
4- additional molecules like cholesterol that
incorporated into bilayer (increased)
Transition temperatures reflecting the
hydrocarbon fluidity that is important for
biological function (in the -30o to 100oC
temperature range)
68

Surface Tension
Molecules at the surface (exposed to air)
are attracted inward.
This creates a force in the surface that
tends to minimize the surface area.
If the surface is stretched, the free energy
of the system is increased.
The surface tension :
=The free energy per unit surface area
(J/m2)
= force per unit length (N/m)

69

Surface Tension
When a substance is dissolved in the liquid or
added to the surface, the surface tension either
decrease or does not change very much. (it
never increases greatly)
The size of the drop is directly proportional to the
surface tension.
Substance that tends to raise the surface tension
of a liquid raises the free energy of the surface;
they concentrate less at the surface.
Substances that lower the surface tension also
lower the free energy of the surface; they migrate
to the surface.
70

 The surface tension

= (G/A)T,P

,A=surface area

Surfactant Langmuir film balance fig.5.18

Fig. 5.19
Psurface(mNm-1) =o
, o is the surface tension of pure water
is the surface tension of coated water
As the film is compressed, the surface pressure rises.
In some cases, discontinuities appear in the plots owing to
phase transitions that occur in some surfactants.
The high surface pressures at low area per molecule (high
surface concentration) result from the low surface
tension produced by the surface-active molecules.
71

72

73

Biological membrane p225

The composition and orientation of the
molecules determine their function.
Lipid bilayer
The proteins may be
1-Intrinsic or integral proteins (in which they are
incorporated directly into the membrane
structure
2- extrinsic proteins (if they are attached to the
membrane surface or interact strongly with it.
Hydrophobic and hydrophilic sites are located in
different regions of the membrane proteins.
74

The variety of membrane composition results

in a range of physical properties.
For example
1- the mobility of the molecules in two dimensions
in a membrane may be that of a typical liquid or
that of a solid. (phase transition)
2- The transition temperature or melting point is
sensitive to the lipid composition.
3- Many proteins are amphiphilic and interact with
both the hydrophobic lipids and the polar
aqueous interface.
75

Active and Passive Transport

Passive flow (concentration-electric field)

{in equilibrium dialysis flow of ligand to bind with

the macromolecule}

Active transport (Na-K pump)

{the transport of a substance from a lower
to higher chemical potential}
F=kQQ/r2
V=E.L V=KQ/r
Electric field lines - direction
E= KQ/r2
76

77

A protein complex called the sodium-potassium pump uses the free

energy of hydrolysis of ATP to pump Na ions out of the cell and K ions
into the cell.

The free energy of the net reaction must be negative.

This means that the positive free energy of the actively transporting
ions against concentration and voltage gradient must be more than
balanced by the negative free energy of ATP hydrolysis

= RT ln aNa+ (outside) + ZFV

aNa+ (inside)
, R= gas constant =8.3145 J/K mol
T = temperature in Kelvin
aNa+ (outside)= concentration of sodium ions outside
aNa+ (inside)= concentration of sodium ions inside
Z = charge on ion 1, 2, 3,..
F= faraday constant =9.6485x 104 C/mol
V= 2 - 1 is the potential difference in volts between the two phases
78

79

80

81

82

Diffusion
The random motion of the liquid molecules can
be measured (fig.6.1). The diffusion depends
on the size and shape of the molecule and on
the properties (viscosity) of the solvent.
Diffusion occurs whenever their is a
concentration difference in a container; diffusion
will eventually make the concentration uniform.
Diffusion is a slow process compared to mixing
caused by stirring (transport molecules).
83

Ficks first law

The flux : the net amount of solute that diffuses through
this unit area, per unit time, in the x-direction.

Jx = -D {dc/dx}
, Jx = is the flux
D = the diffusion coefficient cm2s-1
c= the concentration
x= distance
The negative sign indicates that the net transport by
diffusion is in a direction opposite to the concentration
gradient.
dc/dx is called the concentration gradient in mol/cm -4
As time goes on the system gradually approaches
homogeneity and dc/dx approaches zero.
84 Ficks first law of diffusion is given the flux at any time

 It is also possible to describe how the

concentration in gradient changes with time.
The change of concentration with time (c/t) at
position x is proportional to the gradient in the
flux (J/ x) at that point.
Ficks second law:
It states that the change in concentration
with time at any position x, (c/t)x is proportional
to the second derivative of the concentration with
respect to x at time t, (2c/x2)
(c/t)x = D(2c/x2)t
Fig 6.5
85

86

Chapter 7
kinetics: Rate of chemical reactions
Kinetics: the study and understanding of
the rate of change of anything
It is useful in medicine, biology, and
biochemistry.
It is often, one or a few steps control the
rate of an extensive chain of reactions.

87

All the steps involved in

Metabolism
Cell division and replication
Molecular concentration,..
Are subject to the same basic principles, as
are the elementary reactions of chemist.
The rate or velocity, v, of a reaction or
process describes how fast it occurs.
88

 The rate of reaction : is the change in

concentration per unit time
v = dc/dt
It may be the change in population of cells
with time
Or decrease in the pressure of a gas with
time
Or a change in absorption of light by a
colored solution with time
89

 Rate law
The rate is a function of the concentrations
v= f(concentrations)
Substances that influence the rate of a reaction can
be grouped into two categories:
1- Those whose concentration changes with time
during the course of the reaction
Reactants- decrease with time
Product- increase with time
Intermediates- increase and then decrease during
the course of the reaction
Example: A CB
2- Those whose concentrations do not change with
time
Catalysts (both promoters and inhibitors), including
90
enzymes and active surfaces.

Order of reaction
We need to distinguish the:
Stoichiometric reaction
The order of the reaction
The mechanism of the reaction
1- Stoichiometric of the reaction: describes how many
moles of each reactant are needed to form each mole of
products. Only ratio of moles are significant. Example
H2 + O2 = H2 O
2H2 + O2 = 2H2 O
are both correct stoichiometric reactions
91

2- The mechanism of a reaction: describes how

the molecules react to form products.
(a set of elementary reactions + stoichiometric
reaction)
Example:
H2 2H
H+ O2 OH+ O
OH+ H2 H2 O + H
O + H2 = OH +H
Each step in the mechanism describes an
elementary reaction
92

3- The kinetic order of a reaction: describes the way in

which the rate of the reaction depends on the
concentration.
Example:
Consider a reaction whose stoichiometric is
A+B P
The rate law
v= k cAcBcP
cA , cB , cP are the concentrations and k is the rate constant
v= k[sucrose][H+][H2 O]
kinetic order 1
H+ is a catalyst and its concentration is constant during a
run, H2O is also little changed
The rate law for a reaction must be determined from
experimental data.
93

 Zero-Order Reaction
dc/dt = k0 , k0 is constant Ms-1 ----------c is the concentration mole
t is the time in second
c- c0 =k0t ----------------------------,c0 is the initial concentration at zero time
c is the concentration after time t
This is a straight line equation, the slope is
the rate constant k0.
Fig. 7.1 p322
94

95

First-Order Reaction
dc/dt=k1c , k has unit s-1 ---------------- We need to know only the elementary step in a reaction
of the form
AB
Has a rate law of the form
v= - d[A]/dt= d[B]/dt= k1[A] ---------------------------The rate of the reaction can be expressed in terms of either
the rate of disappearance of reactant,
-d[A]/dt, or the rate of formation of product,d[B]/dt.
-d[A]/dt= k1[A]------------ d[A]/[A]= - k1dt

Ln[A]/[A]0 = -k1t

-------------------------------------, [A]0 the value of initial concentration at t=zero

Fig.7.2 the slope = - k1
96

97

Chapter 10
Molecular structure
and interactions: Spectroscopy
Light and transitions
Light is considered to be a wave with an
electric field component and a magnetic
field component.
In the quantum mechanical view, light also
has particle properties and the energy of
these particles or photons depends on
frequency through Planks law.
98

E= h , =c/
= hc/ , h= Planks constant (6.626x10-34 Js)
= frequency of the radiation
= wavelength of the radiation
c= speed of light (3x 108 ms-1)
Wavelength : the distance between to
successive peaks (nm=10-9m).
Frequency :the number of successive peaks
passing a given point in 1 second (hertz or s -1).

99

 Atoms and molecules exist only in discrete

energy levels.
Light may be absorbed or emitted for
photons with an energy that matches the
energy difference between occupied and
unoccupied levels fig.8.2.

100

Color and refractive index

The green color of leaves is due to chlorophyll
absorption, the orange of a carrot or tomato
arises from carotenes, and the red of blood
results from hemoglobin.
The color is characteristic of the spectrum of
light in the visible region transmitted by the
substance when white light (sunlight) shines
through it or when light is reflected from it.

101

 The quantitative measure of color that we

use is the absorption spectrum. Fig.10.2
Note that the spectra of the three different
molecules have both similarities and
differences; the spectra are much richer
in information than the colors would
indicate.

102

103

 Refraction (e.g. the bent of a pencil partly

immersed in a glass of water results from the
difference in refractive index of light in air and in
water)
The refractive index n: is a measure of the
ratio of the velocity of light in vacuum c to the
velocity in the medium v.
n= c / v
, c velocity of light in vacuum = 3x108 ms-1
v is the velocity of light in the medium
The refractive index of air for visible light is about
1.0023 at 15oc and 1 atm pressure
104

105

 The reason that we are able to see objects that

are not colored is because the changes of
refractive index at the boundaries resulting in
bending of the light rays.
Techniques such as phase contrast have been
used in microscopy to increase the contrast
between different regions of biological
organelles.
The appearance of detailed internal structure in
such organelles occurs because their refractive
index differs in the different regions.
Because refractive index is an intrinsic property
of a material that is related to its composition, a
measurement in refractometer can be used
to characterize the absorbance.
106

Absorption and Emission Radiation

Light that is incident on a colored sample is partly absorbed
by it.
This means that at certain wavelengths there is less intensity
transmitted.
There is no breakdown in the law of conservation of energy.
The result of absorption may appear as
1- heat
2- luminescence (in which a photon of the same or lower
energy is emitted).
3- chemistry (energy may alter the bonding structure)
4- combination of these.
The total energy change of the processes is always exactly
equal to the energy of the photon that was absorbed
107

108

 E.g. UV or visible light

The interaction of electromagnetic radiation with
matter leads to the absorption of light.
Results in a change in the arrangement of the
electrons in a molecule [transition to a new
electronic state ]
The new state will be of higher energy if
radiation is absorbed (fig 10.3)
The excited electronic state has a rearranged
electron distribution. [as a result of a promotion
of one of the ground-state electrons to an orbital
of higher energy]
This completes the absorption process, which
usually occurs very rapidly (within 10-15s)
109

 But the excited state is usually not stable

for very long.
Typically, within 10-8 s, it has disappeared
by fluorescence emission, the dissipation
of heat, or the initiation of photochemistry.
Fluorescence and heat conversion result
in the return of the molecule to the ground
state [time dependent], results a photon of
lower energy (fig 10.4)****

110

111

Radiation-Induced Transitions
Fig.10.3a p536
The states of a molecule will differ in
energy by an amount EE-EG= h
All molecules will be in the ground state in
the dark at ordinary temperatures.
In the presence of radiation field, this
population distribution will be slightly
disturbed.
112

Role of environment in electronic

absorption spectra
P 541
Fig 10.6
Vibronic transition {the energies of the different
vibrations are added to the energy of the
electronic transition as a result of photon
absorption}.
A details vibrational analysis may be needed to
locate this energy precisely [fig. 10.7].
Because there are many ways in which large
molecules can vibrate (many normal modes of
vibrations)
113

114

Beer-Lambert law p543

Bear-Lambert law describes the quantitative relationship
between the absorption of radiation and the concentration of
the absorbing substance.
Lamberts law states that the proportion of energy absorbed
by a substance is independent of the intensity of the incident
radiation.
Beers law states that the absorption of energy is
proportional to the total number of molecules in the
light path.
log10 Io/I = cl , Io incident radiation
I transmitted radiation
molar absorption coefficient [L mol-1 cm-1]
c is the concentration
l length of the light path
115

116

 The beer-Lambert law expresses the amount of

light absorbed by a sample in terms of the
concentration of the sample and the length of
the light path.
The values for I and Io cannot be measured in
absolute terms and the measurements are made
by expressing I as a percentage of Io.
Percentage transmittance (T) = I/ Io x 100
A = log10 100/ T
A = cl [at particular wavelength]
117

Quantitative determinations using

Beers law
One of the most widely used applications
of spectroscopy is for the quantitative
determination of the concentration of
substances in solution.

118

 Absolute methods
ADP shows absorbance of
0.22 at 258nm
Molar absorption coefficient
of ADP at this wavelength
=1.54x104

A = cl
C= A/ = 0.22/1.54x104
= 1.42x 10-5 mol/L
119

120

121

Deviation from the Beer-Lambert law

The assumption that the difference between the incident and the
transmitted radiation is a measure of the radiation absorbed by the
analyte is not completely true because this may not be the only
reason why the incident radiation does not appear in the transmitted
form.
A certain amount of radiation will be:
1- Reflected from the surface of the sample holder, usually a glass or
plastic cell.
2- Absorbed by the material of which the cell is composed.
3- The sample may also be dissolved in a solvent which itself may
also absorb or reflect radiation
Incident (Io)= absorbed + transmitted (I) + other losses
For this reason the radiation transmitted by a blank sample is
measured and taken to be the effective incident radiation.
This blank should be identical to the test sample in all aspects
except the presence of the test substance.
122

Absorbed = blank- transmitted (I)

 An important factors
which influences the beer-Lambert relationship is
1- the wavelength range of the incident radiation.
The incident radiation should be monochromatic
radiation
The monochromatic radiation is radiation of only one
wavelength.
If the incident radiation contains wavelengths that will not
be absorbed by the test substance, a nonlinear
relationship will exist as illustrated in fig. 2.13
This problem is particularly relevant to instruments that
use simple glass filters rather than monochromating
systems such as prisms or diffraction gratings.
2- Molecules may tend to associate with one another when
the concentration is high or, complexes may tend to
dissociate in low concentrations
These lead also to non-linear graph.
123

Vibrational Spectra, Infrared Absorption, and

Raman Scattering
Vibrational spectra arise from transitions
between vibrational energy levels.
These energy levels correspond to bond
stretching and bond bending.
Some vibrational frequencies identify particular
groups in the molecule, such as a C-H bond, a
C=C double bond, or phenyl group.
Other frequencies characterize conformations
such as amide frequencies in proteins or
phosphate ester frequencies in nucleic acids.
IR region 103nm to 105 nm or 10,000 to 100 cm-1
124

 For harmonic oscillator (for a molecule),

the vibration frequency equal to
f=1/2. [k/]
, f is the frequency in Hertz
k is the force constant for the oscillator
is the reduced mass.
Stronger bonds with larger force constants
have higher vibrational frequencies
125

 If a proton attached to a heavy atoms, the

frequency will decrease by a factor of
approximately 2 on substitution of
hydrogen (mH) by deuterium (mD):
f(H)/f(D)= mD/mH =2
Smaller isotope shifts for heavier atoms
involved in vibrations are also easily
detectable.
126

Infrared Absorption
Fig 10.27
There are selection rules that describe the allowed
transitions.
A vibration must cause a change of electric-dipole moment
of a molecule for there to be absorbed of light.
Thus N2 and O2 do not absorb in the IR range.
CO2 has no electric-dipole moment, but an asymmetric
stretch of its C=O bonds or an O=C=O bend will break its
symmetry and lead to IR absorption.
IR is used in the identification and characterization of
organic molecules [proteins and nucleic acids].
One disadvantage for studying biological macromolecules
is the strong and broad absorption of liquid H 2O in the IR
range.
127

Raman Scattering
All molecules scatter light.
Elastic scattering occurs when a photon interact
with a molecule, but no absorbance occurs.
The electric field of the light perturbs the electron
distribution of the molecule momentarily, but no
transition occurs.
Because the molecule does not go from one
stationary state (ground-state energy level) to
another (excited-state energy level), there is no
selection rule

128

129

 Fig.10.27 indicates scattering occurring by a transition to

a virtual state; molecules immediately returns to the
ground electronic state, and the photon is scattered.
If there is no change in the energy of the scattered
photon, the scattering is elastic; it is called Rayleigh
scattering.
In Raman scattering, the molecule returns to a different
energy level after interaction with light [inelastic
scattering].
The final state is an excited vibrational level of the
ground electronic state.
The scattered photon has lower energy than does
the incident photon.
The difference in frequencies between the incident and
scattered is the frequency of the vibrational transition
being measured
130

 The selection rule for Raman scattering is that the

polarizability of the molecule must change with vibration in
order to have a transition to different energy level.
[The polarizability : is a measure of how easy it is to
induce a dipole in a molecule by applying an electric field]
ind= 4oE
, ind is the dipole induced in Coulomb.m
o is the permittivity of vacuum = 8.854x10-12 C2/Nm2
is the polarizability in m3
E is the electric field in volt.m-1
Thus, N2 and O2 will show vibrational Raman spectra
because their vibrations cause a change in polarizability.
For CO2, its asymmetric stretch will cause no change in
polarizability, but its symmetric stretch and its bend will.

131

 Resonance Raman spectra occur when

the exciting light is in an electronic
absorption band of the molecule.
Fig.10.27
Comparison between IR spectrum and
Raman spectrum fig.10.28

132

133

Nuclear Magnetic Resonance NMR

The absorption of microwaves and radiowaves
can result in molecular transitions.
Nuclear magnetic resonance (NMR)
spectroscopy and electron spin resonance
(ESR) spectroscopy are examples of techniques
that depend upon the magnetic properties
exhibited by nuclei and electrons in certain
molecular situations.
They are useful tools in the study of molecular
structures and biochemical reactions such as
enzyme catalysis.
134

H, 13C, 31P, 15N

NMR

Magnetic properties are only exhibited by molecules

that have atoms with an odd mass number.
Nuclei with an equal number of protons and neutrons
will have an even distribution of charge.
An imbalance in this number will give the atom a
magnetic moment, i.e. it will have a positively charged
section and a negatively charged section.
If the molecule is placed in a magnetic field it will tend to
occupy a position involving the least energy and will, like
a compass needle, align itself with the magnetic field.
(or opposite to the magnetic field)
The energy for the transition is produced by a radiofrequency generator (frequency of MHz called the
resonance frequency).
135

The spectrum
It is very difficult to measure the exact frequency of radio
signal, in practice the frequency of the energy absorbed
by a test compound (the resonance frequency) is
measured relative to that of a reference compound.
Reference either TMS (tetra-methyl silane)
Or its water soluble derivative DSS (2,2dimethylsilapentane 5-sulphonic acid).
These compounds give a sharp proton peak at the righthand side of a typical NMR spectrum (fig. 2.39).
The difference between the test peak and the reference
peak is known as chemical shift of the test. This scale
of frequency normalized to give the reference peak a
value of zero.

136

Chemical shift = sample frequency reference frequency/reference

frequency x106

 The absorption property of a nucleus is affected

by the magnetic effects of adjacent nuclei.
This results in what is known as spin-spin
splitting of the initial resonance peak.
In general, if there are n adjacent similar nuclei,
the peak will be split into n+1 components
and this can give information about the manner
in which the nuclei are arranged in the molecule.
Fig.2.39
137

138

Applications
The study of the structure of macromolecules such
as proteins and nucleic acids
2- The study of membranes, enzymic reactions.
3- Analysis of body fluids, determination of both
the content and the concentration of many
metabolites in urine and plasma.
NMR is not a very sensitive technique and it is
often necessary to concentrate the sample.
139

Macromolecular structure and Xray diffraction

There is no better way to understand how
macromolecules function in a cell than to have a
visual image of their parts and how they interact.
In light microscope, light is either reflected from
the surface of an object or transmitted through
the object
In both cases, the scattered light is focused by a
series of lenses to form an image of the object
fig.6.1------------p 242
140

141

Structures at Atomic resolution

The only method that currently yields reliable
structures of macromolecules at atomic
resolution is X-ray diffraction from single crystals
This technique requires three distinct steps:
1- Growing a crystal
2- Collecting the X-ray diffraction pattern from the
crystal
3- Constructing and refining a structural model to
fit the X-ray diffraction pattern
All three steps must be completed to determine the
structure of a macromolecule
142

143

Structures at Atomic resolution

A molecular structure solved to atomic resolution means
that the positions of each atom can be distinguished
from those of all other atoms in three-dimensional space,
without the need to apply additional assumptions
concerning the structure of the molecule
The closet distance between two atoms in space is the
length of covalent bond
Since the typical covalent bond is approximately 0.12nm
we need to see two atoms separated by this distance as
distinct particles
Fig. 6.2-----------------p245
144

145

Limitations:
The system must have the atoms of its
molecules must held rigidly
Each molecule or group of molecules in the
system must have identical conformations
[single crystal]
Fig 6.1-------------atomic force microscope
The limit of resolution (LR) of any optical
method is defined by the wave length of the
incident radiation
LR /2
146

147

 If we require the resolution of the

technique to be about 0.12nm to resolve
the atoms of macromolecule, the wave
length of light required for our atomic
microscope would necessarily be <0.24nm
This falls into the X-ray range of the
electromagnetic spectrum
Fig. ------------6.3
148

149

 X-ray can not be focused and thus can not

form an image of an object in the same
manner as light microscope
Interference [constructive and destructive]
caused by scattering radiation from the
regular and repeating lattice of a single
crystal to determine the structure of
macromolecules
Fig 6.4 ,
150

151

152

Ch. 12 Macromolecular structure

and X-ray diffraction
X-ray is emitted from electron transition
between the inner shells
The wavelength of X-ray radiation is well suited
for resolving atoms separated by the distance of
a covalent bond
The energy of a quantum of this radiation is
approximately 8000eV, which is approximately
the energy of electrons in their orbitals
Electrons of an atom will primarily be
responsible for the scattering of X-rays.
153

 The number of electrons in a given volume of space

(electron density) determines how strongly an atom
scatters X-rays
The interference of the scattered X-rays leads to general
phenomenon of diffraction
X-ray diffraction to single crystal can learn the crystal
morphology and how we can transform the diffraction
data into the structure of the molecules in the crystal.
- Diffraction
- Scattering
- interference
154

 Scattering: the ability of objects to

change the direction of a wave (e.g.
reflection from a mirror)
Fig.6.8 Huygens principle p 259
Fig. 6.9 constructive and destructive
interference
Fig 6.10 Braggs Law
2d sin= n
155

156

157

158