Proteins

Proteins
 Next to water, PROTEINS are the most
abundant substances in most cells.
 Important class of food molecules because
they provide an organism not only with C and
H, but also with N and S, elements which are
unavailable from fats and carbohydrates.
 Protein Functions
 Catalysis: Alcohol
Almost all chemical dehydrogenase
oxidizes alcohols
reactions in a living cell to aldehydes or
are catalyzed by protein ketones
enzymes.
 Transport: Hemoglobin
Some proteins carries
transports various oxygen
substances, such as
oxygen, ions, and so on.
Insulin controls
 Information transfer: the amount of
For example, hormones. sugar in the
blood
 Proteins
 Contractile proteins in muscle permit movement
 In bone, the protein collagen forms a framework
for the deposition of calcium phosphate crystals,
acting like the steel cables in reinforced concrete.
 Immuno globulins fight infectious bacteria and
viruses.
 Some functions of proteins

 The light produced by fireflies is the result of a reaction involving

the protein luciferin and ATP, catalyzed by the enzyme luciferase.
 Erythrocytes contain large amounts of the oxygen-transporting
protein hemoglobin.
 The protein keratin, formed by all vertebrates, is the chief
structural component of hair, scales, horn, wool, nails, and
feathers.
 Proteins
 Proteins are polymers of amino acids.
 Among all the possible amino acids>300
amino acid), only 20 are commonly found as
constituents of mammalian proteins.
 These 20 amino acids are the only amino
acids that are coded for by DNA, the genetic
material in the cell.
 Amino acid: Basic unit of protein

R Different side chains,

R, determine the
NH3+ C COO- properties of 20
amino acids.
Amino group H Carboxylic
acid group

An amino acid
Video presentation 1
Amino acid
 Amino Acids
 Each amino acid has the following
components which are bonded to the
α-carbon atom
• carboxyl group
• primary amino group
• distinctive side chain (“R-group”)
 Exception: proline, which has a
secondary amino group
 Amino Acids
• For all the common amino acids except glycine, the α-
carbon is bonded to four different groups (The α-carbon
atom is a chiral center.)
• The amino acid residues in protein molecules are
exclusively L-stereoisomers.
• Only the L-form of amino acids is found in proteins
synthesized by the human body.
 Amino Acids
Amino acids can occur in L- and D-forms, but
only L-forms are used by cells.
Every amino acid (except glycine) can occur in two
isomeric forms, because of the possibility of
forming two different stereoisomers around the
central carbon atom.
 Amino Acids
• All the amino acids have trivial or common names,
in some cases derived from the source from which
they were first isolated.
• Asparagine was first found in asparagus, and
glutamate in wheat gluten.
• Tyrosine was first isolated from cheese (its name is
derived from the Greek tyros, “cheese”);
• Glycine (Greek glykos, “sweet”) was so named
because of its sweet taste.
Why are amino acid side chains so important?
 The side chains that ultimately dictates the role an amino
acid plays in a protein.
 The R groups, and thus the individual amino acids, are
classified according to several criteria:
• Polarity nature of the side chain
• Presence of an acidic or basic group in the side chain
 AMINO ACIDS with NONPOLAR SIDE CHAINS
Each amino acid is shown in its fully protonated form, with dissociable hydrogen ions
represented in red print. The pK values for the α-carboxyl and α-amino groups of the
nonpolar amino acids are similar to those shown for glycine.
Charge and polarity of the side chain at acidic pH.
 AMINO ACIDS with
NONPOLAR SIDE CHAINS
 Each of these amino acids has
a nonpolar side chain that
does not gain or lose protons
or participate in hydrogen or
ionic bonds
 The side chains of these amino
acids can be thought of as
“oily” or lipid-like, a property
that promotes hydrophobic
interactions (induced dipole-
induced dipole London
Dispersion forces)
 AMINO ACIDS with NONPOLAR SIDE CHAINS
Location of nonpolar amino acids in proteins
• In proteins found in aqueous
solutions––a polar environment––
the side chains of the nonpolar
amino acids tend to cluster together
in the interior of the protein
(HYDROPHOBIC EFFECT) interacting
with the lipid environment.
• The nonpolar R-groups thus fill up
the interior of the folded protein and
help give it its three-dimensional
shape.
• The importance of these Location of nonpolar amino acids
hydrophobic interactions in in soluble and membrane proteins.
stabilizing protein structure.
Proline
 Proline differs from other
amino acids in that
proline’s side chain and α-
amino N form a rigid, five
membered ring structure.
 Proline has a secondary
(rather than a primary)
amino group.
 It is frequently referred to
as an imino acid.
 Proline

 Proline gives the

fibrous structure of
collagen, and
interrupts the α-
helices found in
globular proteins.
AMINO ACIDS with UNCHARGED
POLAR SIDE CHAINS

Charge and polarity of the side chain at acidic pH

 Uncharged Polar Side Chains
• More hydrophilic because they form hydrogen bonds
with water.
• Includes serine, threonine, cysteine, asparagine, and
glutamine.
• Serine, threonine, and
tyrosine each contain a
polar hydroxyl group that
can participate in hydrogen
bond formation.
Hydrogen bond between the
phenolic hydroxyl group of tyrosine and
another molecule containing a carbonyl group.
Uncharged Polar Side Chains
 Uncharged Polar Side Chains
 The side chains of asparagine and glutamine each
contain a carbonyl group and an amide group, both of
which can also participate in hydrogen bonds.
Disulfide bond  The side chain of cysteine
contains a sulfahydryl group
(–SH), which is an important
component of the active site
of many enzymes.
 In proteins, the –SH groups of two
cysteines can become oxidized to
form a dimer, cystine, which
contains a covalent cross-link
called a disulfide bond (–S–S–).
 SIDE CHAINS AS SITES OF ATTACHMENT FOR
OTHER COMPOUNDS

 The amide group of asparagine, as well as the

hydroxyl group of serine or threonine, can serve as
a site of attachment for oligosaccharide chains in
glycoproteins.

N-linked glycosylation O-linked glycosylation

 AMINO ACIDS with ACIDIC SIDE CHAINS

 The amino acids aspartic and glutamic acid are proton donors.
 At physiologic pH, the side chains of these amino acids are fully
ionized, containing a negatively charged carboxylate group (–COO–).
 They are, therefore, called aspartate or glutamate to emphasize that
these amino acids are negatively charged at physiologic pH.
AMINO ACIDS with BASIC SIDE CHAINS
Charge and
polarity of
the side
chain at
acidic pH

• The R groups have significant positive charge.

• Lysine has a second positive amino group on its (R) chain.
• Arginine has a positively charged guanidino group.
• Histidine has a positive imidazole group.
Amino acids with basic side chains
 The side chains of the basic amino acids accept
protons.
 At physiologic pH the side chains of lysine and
arginine are fully ionized and positively charged.
 Histidine is weakly basic, and the free amino acid
is largely uncharged at physiologic pH.
 When histidine is incorporated into a protein, its
side chain can be either positively charged or
neutral, depending on the ionic environment
provided by the polypeptide chains of the
protein.
 This is an important property of histidine that
contributes to the role it plays in the functioning
of proteins such as hemoglobin.
20 Amino Acids

Nonpolar,
hydrophobic

Polar, uncharged

Polar, charged
 Abbreviations and symbols for
commonly occurring amino acids
• Each amino acid name has an associated three-letter
abbreviation and a one-letter symbol.

• The one-letter codes are determined by the following rules:

1. Unique first letter:

If only one amino acid begins
with a particular letter, then
that letter is used as its
symbol.
For example, I = isoleucine.
 Abbreviations and symbols for
commonly occurring amino acids
2. Most commonly occurring amino acids have priority:
If more than one amino acid begins with a particular
letter, the most common of these amino acids receives
this letter as its symbol.
For example, glycine is more common than glutamate,
so G = glycine.
 Abbreviations and symbols for
commonly occurring amino acids
3. Similar sounding names: Some one-letter symbols sound
like the amino acid they represent.
 Abbreviations and symbols for
commonly occurring amino acids
4. Letter close to initial letter: For the remaining amino acids, a
one letter symbol is assigned that is as close in the alphabet
as possible to the initial letter of the amino acid.
Optical properties of amino acids

• The α-carbon of an amino acid is

attached to four different chemical
groups and is, therefore, a chiral or
optically active carbon atom.

• Glycine is the exception because its α-carbon has two hydrogen

substituents and, therefore, is optically inactive.
• Amino acids that have an asymmetric center at the α-carbon can
exist in two forms, designated D and L, that are mirror images of
each other.
• The two forms in each pair are termed stereoisomers, optical
isomers, or enantiomers.
• All amino acids found in proteins are of the L-configuration.
• D-amino acids are found in some antibiotics and in plant and
bacterial cell walls.
Dipolar nature of amino acids
- when an amino acid is in aqueous solution, it exists in various ionic
forms, the predominant form depends on the pH of the medium

- the COOH group can easily lose H+ in solution leaving COO-

- the NH2 group can easily accept H+ in solution forming +NH3
- so the acidic and basic groups of amino acid react to form an
internal salt or “zwitterion” which has no net charge for it contains
one positive and one negative charge.
- The zwitterion form exists at a pH value called the isoelectric pH.
At this pH, the molecule is electrically neutral and would not
move toward positive or negative electrode.

- Any amino acid in which the positive and negative charges are
balanced, is at its isoelectric point and the pH at which this
balancing occurs is the isoelectric pH (pI)

- The pI of an amino acid can be calculated by the following

equation:
 BUFFER
 A buffer is a solution that resists change
in pH following the addition of an acid or
base.
 A buffer can be created by mixing a weak
acid (HA) with its conjugate base (A–).
 If an acid such as HCl is then added to
such a solution, A– can neutralize it, in
the process being converted to HA.
 If a base is added, HA can neutralize it, in
the process being converted to A–.
 Maximum buffering capacity occurs at a
pH equal to the pKa, but a conjugate
acid/base pair can still serve as an
effective buffer when the pH of a
solution is within approximately  1 unit
of the pKa.
 ACIDIC AND BASIC PROPERTIES OF AMINO ACIDS
• Amino acids in aqueous solution contain weakly acidic α-
carboxyl groups and weakly basic α-amino groups.
• Each of the acidic and basic amino acids contains an ionizable
group in its side chain.
• Thus, both free and some of the combined amino acids in
peptide linkages can act as buffers.
• The concentration of a weak acid (HA) and its conjugate
base(A-) is described by the Henderson-Hasselbalch equation.
Buffer pairs:
 The – COOH/– COO– pair can serve as a
buffer in the pH region around pK1, and
the – NH3+/– NH2 pair can buffer in the
region around pK2.
 When pH = pK: When the pH is equal to
pK1 (2.3), equal amounts of Forms I and II
of alanine exist in solution. When the pH
is equal to pK2 (9.1), equal amounts of
Forms II and III are present in solution.
Isoelectric point:
 At neutral pH, alanine exists predominantly
as the dipolar Form II in which the amino
and carboxyl groups are ionized, but the net
charge is zero.
 The isoelectric point (pI) is the pH at which
an amino acid is electrically neutral.
 For an amino acid, such as alanine, that has
only two dissociable hydrogens (one from
the α-carboxyl and one from the α-amino
group), the pI is the average of pK1 and pK2:
pI = [2.3 + 9.1]/2 = 5.7.
 The pI corresponds to the pH at which the
Form II (with a net charge of zero)
predominates, and at which there are also
equal amounts of Forms I (net charge of +1)
and III (net charge of –1).
TABLE3–2 Properties and Conventions Associated with the Common Amino Acids
Found in Proteins
Aspartic acid
 Classification of Amino Acid According
to Nutritional Value
 Essential amino acids
- These amino acids cannot be synthesized or
formed in the body. These are essential to be
taken in diet. Their deficiency affects growth,
health and protein synthesis.
 Semi-essential amino acids
- These are synthesized or formed in the body
but not in sufficient amount for body
requirements especially in children.
 Classification of Amino Acid According
to Nutritional Value
E

 Essential and Non-essential amino acids

Summary of essential and semiessential amino acids
Villa HM = Ten Thousand Pound
V= valine i= isoleucine l= lysine l= leucine a = arginine*
H= histidine* M= methionine
T= tryptophan Th= threonine P= phenylalanine
*= arginine and histidine are semiessential

 Non-essential amino acids

- These are the rest of amino acids that are formed in the
body in amount enough for adults and children. They are
the remaining 10 amino acids.
 COMPLETE PROTEIN
• A complete protein contains all the essential amino
acids in the proper amounts.

• An incomplete protein is low in one or more of the

essential amino acids, usually lysine, tryptophan, or
methionine.

• Except for gelatin, proteins from animal sources are

complete, whereas proteins from vegetable sources are
incomplete.
 Summary
• Each aa has an α-carboxyl and an α-amino group (except Pro,
has an imino group)
• At physiologic pH: α-carboxyl  COO-, α-amino  NH3+
• Each aa contains one of 20 side chains
• The chemical nature of side chain determines function of aa in
a protein, and classifies aa as nonpolar, uncharged polar,
acidic, or basic
• All free aa’s plus charged aa’s in peptide chains serve as buffers
• Relation b/w the conc. of weak acid and its conjugate base is
described by Henderson-Hasselbalch eq.
• Buffering occurs within ±1 pH, and max when pH = pKa at
which [HA] = [A-]
• The α-carbon of each aa (except Gly) is attached to 4 different
chemical groups i.e., a chiral or optically active carbon atom
• Only L-form of amino acids is found in proteins synthesized by
human body
Formation of Peptide Bond
 Peptide bonds
have double bond
character resulting
from resonance
stabilization (C-N
bond has 40%
double bond
character) C-N and
C-O have partial
double bond
character.

 The peptide bond has a partial double-bond character,

that is, it is shorter than a single bond (stronger).
 Partial double-bond character prevents  However, the bonds
free rotation around the bond between the between the α-
carbonyl carbon and the nitrogen of the carbons and the α-
peptide bond. amino or α-carboxyl
groups can be freely
rotated (although they
are limited by the size
and character of the
R-groups).
 This allows the
polypeptide chain to
assume a variety of
possible
configurations.
• The peptide bond is planar, and the two adjacent α-
carbons lie trans to it.

 The peptide bond is generally a trans bond (instead

of cis), in large part because of steric interference
of the R-groups when in the cis position.
• Almost all of the peptide bonds in proteins are planar and have a
trans configuration.
• This is quite important physiologically because it makes protein
structure relatively rigid.
• The peptide bonds are covalent and quite stable – can be
disrupted by chemical or enzymatic hydrolysis but are not directly
influenced by salt concentration, change in pH, or solvent
Naming the Peptide
• Each component amino acid
in a polypeptide is called a
“residue” because it is the
portion of the amino acid
remaining after the atoms of
water are lost in the
formation of the peptide
bond.
 Naming the Peptide
• By convention, the free amino end (N-terminal) of the peptide
chain is written to the left and the free carboxyl end (C-terminal) to
the right.
• Therefore, all amino acid sequences are read from the N- to the C-
terminal end of the peptide.
• Linkage of many amino acids through peptide bonds results in an
unbranched chain called a polypeptide.
 Naming the Peptide

• When a polypeptide is named, all amino acid residues

have their suffixes (-ine, -an, -ic, or -ate) changed to -yl,
with the exception of the C-terminal amino acid.

• For example, a tripeptide composed of an N-terminal

valine, a glycine, and a C-terminal leucine is called valyl
glycyl leucine.
 The pentapeptide serylglycyltyrosylalanylleucine, or
 Ser–Gly–Tyr–Ala–Leu.
 Peptides are named beginning with the amino terminal
residue, which by convention is placed at the left.
 The peptide bonds are shaded in yellow.
 The R groups are in red.
Small Peptides with Physiological Activity
1. Aspartame (Asp-Phe)
• Sold under the trade names Nutrasweet and Equal.
• aspartame is the artificial sweetener used in almost every diet
food on the market today. Its caloric content is the same as
sucrose but is ~ 180 times as sweet .
• Both aa’s present in the dipeptide must be in the L- form for the
sweet taste to occur; The L-D, D-L, and D-D forms have a bitter
taste.
Small Peptides with Physiological Activity

2. Glutathione, GSH (Glu-Cys-Gly)

• The tripeptide, produced by the body itself, is present in
significant concentrations in most cells and is of considerable
physiological importance as a regulator of oxidation-reduction
reactions.
Small Peptides with Physiological Activity

2. Glutathione, GSH (Glu-Cys-Gly)

• It functions as an antioxidant, protecting cellular contents from
oxidizing agents such as peroxides and superoxides.
• In GSH, Glu is bonded to Cys through the side-chain carboxyl
group rather than through the α-carbon carboxyl group
Small Peptides with Physiological Activity

3. Enkephalins
• Two pentapeptides found in the brain are known as enkephalins,
naturally occurring analgesics (pain relievers)
• The two enkephalins differ only in the amino acid at the carboxyl
end of the peptide chain.
Small Peptides with Physiological Activity

3. Enkephalins
• It is thought that the aromatic side chains of tyrosine and
phenylalanine in these peptides play a role in their activities.
• It is also thought that there are similarities between the three-
dimensional structures of opiates, such as morphine, and those of
the enkephalins.
• As a result of these structural similarities, opiates bind to the
receptors in the brain intended for the enkephalins and thus
produce their physiological activities.
 Small Peptides with Physiological Activity
4. Oxytocin and Vasopressin
• Each of these peptides contains nine amino acid residues.
• Each has an amide group (rather than a free carboxyl group) at the C-terminal
end, and each has a disulfide link between cysteine residues at positions 1
and 6
• The difference between these two peptides is that oxytocin has an isoleucine
residue at position 3 and a leucine residue at position 8.
• Vasopressin has a phenylalanine residue at position 3 and an arginine residue
at position 8.
• Both of these peptides have considerable physiological importance as
hormones.
 Polypeptides Have Characteristic
Amino Acid Compositions
• The order in which the amino acid residues of a peptide molecule
are linked is the amino acid sequence of the molecule.
• differences in the chemical and physiologic properties of peptides
result from differences in the amino acid sequence.

Bradykinin vs. Boguskinin

• Inhibits inflammation • completely inactive,
of tissues hence, the name
bogus or false

• Arg-Pro-Pro-Gly-Phe- • Arg-Pro-Pro-Gly-Phe-
Ser-Pro-Phe-Arg Ser-Pro-Phe
Proteins
Video presentation 2
Protein
 Each protein has a unique structure!

The important properties and functions of proteins can be

more easily understood if we know something about their
structures and the bonding accounting for their structures

The structure of proteins is subdivided into four

organizational levels
(according to the type of interactions of the amino acid):
 Primary 1o
 Secondary 2o
 Tertiary 3o
 Quaternary 4o
 Protein Structure

Primary Assembly
STRUCTURE

PROCESS
Secondary Folding

Tertiary Packing

Quaternary Interaction
 Protein Assembly
• occurs at the ribosome
• involves polymerization
of amino acids attached
to tRNA
• yields primary structure

The 1o structure of proteins are translations of

information contained in genes.
 PRIMARY STRUCTURE OF PROTEINS

 Primary structure describes the

number, type and sequence of amino
acids that make up the polypeptide
chain.
 The backbone of the protein molecule.
 Linear
 Ordered (The polypeptide backbone
does not assume a random structure,
but instead generally forms regular
arrangements of amino acids)
 PRIMARY STRUCTURE OF PROTEINS
 Understanding the primary structure
of proteins is important because
many genetic diseases result in
proteins with abnormal amino acid
sequences, which cause improper
folding and loss or impairment of
normal function
 If the primary structures of the
normal and the mutated proteins are
known, this information may be used
to diagnose or study the disease.
 Polypeptides Have Characteristic
Amino Acid Compositions

• Normal red blood cells:

…..Val-His-Leu-Thr-Pro-Glu-Glu-Lys-Ser-Ala-….

• Sickle-cell:

…..Val-His-Leu-Thr-Pro-Val -Glu-Lys-Ser-Ala-…..

• Georgetown anemia:

…..Val-His-Leu-Thr-Pro-Glu- Lys -Lys-Ser-Ala-….

 Primary Structure
 Peptide bonds are not broken
by conditions that denature
proteins, such as heating or
high concentrations of urea.
 Prolonged exposure to a
strong acid or base at elevated
temperatures is required to
hydrolyze these bonds non
enzymically.
 Protein Structure

Primary Assembly
STRUCTURE

PROCESS
Secondary Folding

Tertiary Packing

Quaternary Interaction
 Secondary Structure
 The secondary structure of protein is the
coiling and folding of its polypeptides.
• Coiling and folding occur in the cytosol and
involve localized spatial interaction among
primary structure elements, i.e. the amino
acids
• Polypeptide chains are either:
• Coiled into a spiral spring (helices)
• Linked together to form the -pleated
sheet
 Secondary structure

α-helix β-sheet

Secondary structures, α-helix and β-sheet,

have regular hydrogen-bonding patterns.
 Secondary Structure
• non-linear
• Three- dimensional
• localized to regions of an
amino acid chain
• formed and stabilized by
hydrogen bonding
 Secondary Structure
 The only bond responsible for the
2o structure of proteins is H-
bonding between peptide bonds,
the – C = O of one peptide group
and the – N – H of another
peptide form inter-segment H-
bonds.

 The H-bonds of the α-helix are parallel to the long

axis of the helix
 These H- bonds lock the α-helix into place
 The polypeptide chain in an α-helix is right-handed.
 The α-helix is the most stable helical arrangement
Helix Structure
 Each turn of an α-helix contains
3.6 amino acids. Thus, amino
acid residues spaced three or four
residues apart Proline disrupts an
α-helix because its secondary
amino group is not geometrically
compatible with the right-handed
spiral of the α-helix.
 The helix is so tightly wound that
the space in the center is too
small for solvent molecules to
enter
 Pleated-sheet structure or β-conformation
 Folding (zigzag, sheet-like arrangement) occurs, forming pleated
sheets, due to H-bonding:
• between different polypeptide chains lying side by side
• segments of polypeptide chains, which are almost fully
extended.

 The hydrogen bonds are perpendicular to the polypeptide

backbone
 R groups are located above and below the plane of the sheet.
 Proteins with this structure are crystalline and quite insoluble in
aqueous solvents
Parallel structure
 Chains are running in
the same direction, the
–COOH and -NH2 ends
of the proteins lying all
at the top or all at the
bottom of the sheet.
Antiparallel structure
 Protein chains alternate in such
a way that the -COOH end of
one chain is next to the –NH2
end of the other.
 Chains are running in opposite
directions
 More stable than parallel
because of fully co-linear H-
bonds form
 Protein Structure

Primary Assembly
STRUCTURE

PROCESS
Secondary Folding

Tertiary Packing

Quaternary Interaction
 Protein
Packing
•occurs in the
cytosol
•involves
interaction
between
secondary
structure
elements and
solvent
•yields tertiary
structure
 Tertiary Structure
o Supersecondary structures
are usually produced by
packing side chains from
adjacent secondary
structural elements close to
each other.

 The overall three-dimensional shape (globular) that

results from the interaction of groups in the side
chain (-R) of the amino acids widely separated from
each other within the chain
• The bending and folding is irregular and it is the result
of the formation of different types of bonds between
the amino acid residues.
• The nature of the R-groups (polar or non-polar) of the
constituent amino acids and their interactions plays
an important role in determining and maintaining the
specific shape of a protein molecule.

Folding of the polypeptide:

• Most of the hydrophilic groups on
the outside and the hydrophobic
groups on the inside.
• This arrangement is more stable
(globular proteins).
 Interactions Responsible for 3o Structure
Linkages that aid in holding the protein
in a rather rigid structure
Disulfide bonds
 A disulfide bond is a covalent
linkage formed from the
sulfhydryl group (–SH) of each of
two cysteine residues, to
produce a cystine residue.
 The two cysteines may be
separated from each other by
many amino acids in the primary
sequence of a polypeptide, or
may even be located on two
different polypeptide chains.
 Interactions Responsible for 3o Structure
Linkages that aid in holding the protein
in a rather rigid structure
Disulfide bonds
 The folding of the polypeptide
chain(s) brings the cysteine
residues into proximity, and
permits covalent bonding of
their side chains.
 A disulfide bond contributes to
the stability of the three-
dimensional shape of the
protein molecule, and prevents
it from becoming denatured in
the extracellular environment.
 Interactions Responsible for 3o Structure
Linkages that aid in holding the protein
in a rather rigid structure
Hydrophobic Interactions
(van der Waals Forces)
 Amino acids with
nonpolar side chains
tend to be located in
the interior of the
polypeptide molecule,
where they associate
with other
hydrophobic amino
acids.
 Interactions Responsible for 3o Structure
Linkages that aid in holding the protein
in a rather rigid structure
Hydrogen Bonds
 Amino acid side chains containing
oxygen- or nitrogen-bound
hydrogen, such as in the alcohol
groups of serine and threonine, can
form hydrogen bonds with such as
the oxygen of a carboxyl group or
carbonyl group of a peptide bond
 Formation of hydrogen bonds
between polar groups on the surface
of proteins and the aqueous solvent
enhances the solubility of the
protein.
 Interactions Responsible for 3o Structure
Linkages that aid in holding the protein
in a rather rigid structure

Ionic interactions / Salt linkages /

electrostatic attraction
 Negatively charged groups, such
as the carboxylate group (–
COO–) in the side chain of
aspartate or glutamate, can
interact with positively charged
groups, such as the amino group
(– NH3+) in the side chain of
lysine.
 Salt bridges
Ion-ion
Protein Structure
 Protein Structure

Primary Assembly
STRUCTURE

PROCESS
Secondary Folding

Tertiary Packing

Quaternary Interaction
 Protein Interaction

 occurs in the cytosol, in close proximity to

other folded and packed proteins
 involves interaction among tertiary structure
elements of separate polymer chains
 yields quaternary structure
• non-linear
• 3 dimensional
3D structure of proteins

Tertiary
structure
Quaternary structure
 Quaternary Structure

 Quaternary structure describes the arrangement

of sub-units in a protein consisting of more than
one polypeptide chain, where the sub-units may
be identical or different
QUATERNARY STRUCTURE
 The final level of protein structure
and pertains to those proteins
that consist of multiple
polypeptide chains.
 Many proteins consist of a single
polypeptide chain, and are
defined as monomeric proteins.
 Other proteins consist of two or
more polypeptide chains that
may be structurally identical or
totally unrelated.
 QUATERNARY STRUCTURE

• Subunits are held together by noncovalent

interactions (for example, hydrogen bonds, ion-ion,
and hydrophobic interactions).
• Subunits may either function
independently of each other,
or may work cooperatively, as
in hemoglobin, in which the
binding of oxygen to one
subunit of the tetramer
increases the affinity of the
other subunits for oxygen.
1) Deoxy-Hemoglobin with low affinity for oxygen (Also
called the Taut state or T-state)
2-3) Binding of an oxygen molecule to the first sub-unit
brings about conformational changes that influences the
affinity of adjacent sub-units (T-state changes to R-state
or Relaxed state)
4) Oxy-Hemoglobin saturated with oxygen in full R-state
 Reasons for
quaternary structure

 By combining more than one sub-unit into one

functioning protein, enhanced biological activity and
control can be achieved.
 Main points to consider for the reasons of having
associated sub-units
• Enhanced stability (Reducing surface area vs.
protein volume)
• Genetic economy & efficiency (limited genetic
information needed)
• Coordinated regulation of proteins
• Defects easily repaired by replacing flawed sub-units
 Types of Proteins Conformation

Fibrous protein Globular protein

Fibrous protein
 This protein does not have tertiary structure.
 Secondary structure is important.
 Consist of -helix and β-pleated sheets
 Insoluble in water
 Structural functions
a) α-Keratin
• Several α-helices held together
by bonds formed between
adjacent chains.
• The bonds (disulfide bridges)
form cross-links and the bundles
of molecules have strength and
the ability to stretch.
• Found in mammals, these
proteins constitute almost the
entire dry weight of hair, wool,
nails, claws, quills, horns, hooves,
and much of the outer layer of
skin.
• The α-keratin helix is a right-
handed helix
b) Collagen

 It is found in connective tissue

such as tendons, cartilage, the
organic matrix of bone, and the
cornea of the eye.
 It is left-handed and consists of
three polypeptide chains
wrapped around each other in a
rope-like twist, or triple helix.
c) Silk Fibroin
• Fibroin, the protein of silk, is
produced by insects and spiders.
• Its polypeptide chains are
predominantly in the β-
conformation.
• The overall structure is stabilized by
extensive hydrogen bonding
between all peptide linkages in the
polypeptides of each β-sheet and by
the optimization of van der Waals
interactions between sheets.
• Cannot be stretched butit is very
supple (bent or twisted)
Globular proteins
 Tertiary structure important (bent and folded into
spherical or globular shape)
 Soluble in water
 Most enzymes and regulatory proteins (hormones,
antibodies) are globular proteins.
a) Myoglobin
 a single-chain globular protein that
consists of 153 amino acids and a
heme group (an iron-containing
porphyrin)
 consists mainly of - helices linked
together by various turns
• A relatively small oxygen-binding
protein of muscle cells.
 Binds and stores oxygen in skeletal
muscles from blood and supplies the
oxygen to active muscle groups during
harsh respiration.
Myoglobin
• Storage and distribution of
oxygen by muscle
myoglobin permit these
animals to remain
submerged for long periods
of time.
• Particularly abundant in the
muscles of diving mammals
such as the whale, seal, and
porpoise
b) Hemoglobin
• Consists of four polypeptide
chains ( two identical α-chains
consisting of 141 amino acid
residues and two identical
β-chains consisting of 146
amino acid residues)
• Binds oxygen in lungs and
releases it to metabolically
active cells undergoing
respiration throughout the
body.
β-peptides consist of β amino acids, which have
their amino group bonded to the β carbon rather than
the α carbon
 Because the backbones of β-peptides are longer than those
of peptides that consist of α-amino acids, β-peptides form
different secondary structures.
 Generally, β-peptides form a more stable helix than α-
peptides
 hemoglobin

Myoglobin
 PROTEIN DENATURATION
• Protein denaturation results in the unfolding and
disorganization of the protein's secondary, tertiary and
quaternary structures, which are not accompanied by
hydrolysis of peptide bonds.
• The breaking of any bond in protein EXCEPT the primary
bond (peptide bond)
PROTEIN DENATURATION
• When protein is in the cell, it is in its natural
conformation, in its native state.
• If this native state is changed in any way, the protein is
said to be denatured.
 Protein Denaturation

• Denaturation often radically changes both

the physical and chemical properties of
the protein

• Proteins lose their activity, although under

certain conditions this loss may be
reversible (renaturation)
 Some selected physical and
chemical denaturing agents

1. Heat – disrupts H-bonds and hydrophobic

attractions by making molecules vibrate too violently;
produces coagulation, as in the frying of an egg
2. Microwave radiation – causes violent vibrations of
molecules that disrupt H-bonds
3. Ultraviolet radiation – operates very similarly to the
action of heat (e.g., sunburn)
4. Acids and bases – disrupts salt linkages
5. Violent whipping or shaking – causes molecules in
globular shapes to extend to longer lengths, which
then entangle
 Some selected physical and
chemical denaturing agents

6. Detergent – affects H-bonds and salt linkages

7. Organic solvents (e.g., ethanol, 2-propanol, acetone) –
interfere with H-bonds, because these solvents also can
form H-bonds; quickly denatures protein in bacteria,
killing them (the disinfectant action of 70% ethanol)
8. Strong acids and bases – disrupt H-bonds and salt
bridges; prolonged action leads to actual hydrolysis of
peptide bonds
9. Salts of heavy metals (e.g., salts of Hg2+, Ag+, Pb2+) –
metal ions combine with – SH groups and form
poisonous salts; precipitates proteins
10. Reducing agents – oxidize disulfide linkages to produce –
SH groups
Some practical aspects of protein denaturation

Heat and UV

 Egg white proteins have to be denatured by

cooking for them to become utilizable by our
system
 Sterilization uses UV and heat in the form of
steam to coagulate the proteins of bacteria
Some practical aspects of protein denaturation

Salts of heavy metal ions esp. Hg2+, Pb2+, Ag+

 Used as antiseptics in low concentrations, in higher

concentrations they act as poisons.
 When ingested they precipitate the proteins in cells
of body tissues.
 Effective treatment consists of feeding with egg
white, followed by an emetic-vomiting (the egg
white forms complex with the poison and taken out
of circulation by emetic)
Some practical aspects of protein denaturation

Organic compounds such as soap, detergents, phenol,

and aliphatic alcohol

 -The hydrophobic portions of these compounds

interact with the hydrophobic core of the protein,
while the
 hydrophilic portion is H-bonded with the aqueous
environment.
 This causes swelling and concomitant unfolding of
the protein molecules.
Some practical aspects of protein denaturation

Permanent hair waving

- Keratin has a high proportion of S-containing amino

acids: the –S – S – linkages give shape to the hair

- Process involves the breaking of these linkages by

reducing agent
→brings disorderliness of linkages
→placed on curlers and set in the desired pattern
→finally neutralized with an oxidizing agent to reform
– S –S – linkages this time between different
amino acids
 Some practical aspects of protein denaturation

Permanent hair waving

 Some Proteins Contain Chemical Groups Other Than Amino Acids
• Some proteins
contain permanently
associated chemical
components in
addition to amino
acids, these are
called conjugated
proteins.
• The non–amino acid
part of a conjugated
protein is usually
called its prosthetic
group.
• Conjugated proteins
are classified on the
basis of the chemical
nature of their
prosthetic groups