Proteins:

Proteins are naturally occurring, extremely

complex substance that consists of amino acid
residues joined by peptide bonds. Proteins are
present in all living organisms and include many
essential biological compounds such as
enzymes, hormones, and antibodies.
Classification of Proteins:

Proteins have been classified in different ways;

1.Functions they perform

2. On the basis of composition of proteins

3. On the basis of difference in overall 3D structure.

1. On the basis of the biological functions the proteins
are differentiated into following:

1. Defense proteins. eg. Antibodies in blood (γ

globulin)
2. Digestive proteins. These are enzymes present in
gastrointestinal secretions for degradation of
foodstuff. eg. Trypsins.
3. Transport proteins: Which carry molecules to diff
tissues. eg. Hemoglobin which transports oxygen in
blood.
4. Contractile proteins: Help in movement and
locomotion. Eg. Myosin and actin proteins.

5. Visual proteins: Help in vision and found in retinal

cells. eg Rhodopsins.

6. Storage proteins: Act as reserve food eg. Casein

protein found in milk and Ovalbumin present in egg
white.
7. Receptor proteins: Proteins that bind with signaling
molecules and initiate chemical respose.
2. On the basis of composition of proteins

On this basis proteins are divided into 2 groups

1. Conjugated proteins
2. Non-conjugated proteins

Conjugated proteins
These proteins consist of an organic or inorganic non-
protein group called prosthetic group. g. Glycoprotein,
metalloprotein and hemoprotein, lipoproten etc.
Non conjugated proteins are those that do not
contain any additional group.

3. Based on the overall differences in 3D structure.

On this basis the proteins are divided into 2 groups.
1. Fibrous proteins
2. Globular proteins

Fibrous proteins are elongated in shape and appear

like threads. They are large molecules and composed
of two or more polypeptide chains. They are insoluble
in water. Eg. Collagen protein
Globular proteins: Globular proteins have a compact
structure due to folding, bending and twisting of
polypeptide chains. It is a sphere like shape. They are
water soluble. Majority of the proteins belong to this
class. All enzymes are globular proteins.
 Structure of proteins:

Proteins structure has been categorized in to 4 levels.

1. Primary structure

2. Secondary structure

3. Tertiary structure

4. Quaternary structure
1. Primary structure: The linear sequence of amino
acids forming the backbone of proteins (polypeptides).

2. Secondary structure: The spatial arrangement of

protein by twisting of the polypeptide chain.

3. Tertiary structure: The three dimensional structure

of a functional protein.

4. Quaternary structure: Some of the proteins are

composed of two or more polypeptide chains referred
to as subunits. The spatial arrangement of these
subunits is known as quaternary structure.
aA
Primary structure:

The identity of amino acids that are present

The relative amount of each amino acid.
The exact sequence of amino acids in the protein.

Each protein has a unique sequence of amino acids

which is determined by the genes contained in DNA.

The primary structure of a protein is responsible for

its function.
The amino acid composition of a protein determines
its physical and chemical properties.

A number of diseases are due to abnormalities in the

amino acid sequences of proteins i.e. changes
associated with primary structure of protein.
Dimensions of a peptide chain:
The dimensions of a fully extended polypeptide
chains.
The two adjacent α-carbon atoms are placed at a
distance of 0.36nm.
The phi and psi angles in a peptide:

Each amino acid contains two bonds that can readily

rotate - this includes the phi angle and the psi angle.
The phi angle is the angle between the alpha carbon
atom and the nitrogen while the psi angle is the angle
between the alpha carbon and the carbon of the
carbonyl group.
SECONDARY STRUCTURE OF PROTEIN

The conformation of polypeptide chain by twisting or

folding is called as secondary structure. The amino
acids are located close to each other in their
sequence.

Due to folding two types of secondary structures are

identified.
The α-helix and β- pleated sheet.
 α-Helix
α-Helix is the most common spiral structure of protein. It
has a rigid arrangement of polypeptide chain. α-Helical
structure was proposed by Pauling and Corey (1951).

1. The α-helix is a tightly packed coiled structure with

amino acid side chains extending outward from the
central axis.

2. The α-helix is stabilized by extensive hydrogen bonding.

It is formed between H atom attached to peptide N, and O
atom attached to peptide C. The hydrogen bonds are
individually weak but collectively they are strong enough
to stabilize the helix.
3. All the peptide bonds, except the first and last in a
polypeptide chain, participate in
hydrogen bonding.

4. Each turn of α-helix contains 3.6 amino acids and

travels a distance of 0.54 nm. The spacing of each
amino acid is 0.15 nm.

5. α-Helix is a stable conformation formed

spontaneously with the lowest energy.
 Proteins
contain
right
handed
helix which
is a more
stable
structure.
β-Pleated sheet

This is the second type of structure (hence β after α)

proposed by Pauling and Corey. β-Pleated sheets (or
simply β-sheets) are composed of two or more
segments of fully extended peptide chains.

In the β-sheets, the hydrogen bonds are formed

between the neighboring segments of polypeptide
chain(s).
Parallel and anti-parallel β-sheets
The polypeptide chains in the β-sheets may be
arranged either in parallel (the same direction) or
anti-parallel (opposite direction).
β-Pleated sheet may be formed either by separate
polypeptide chains (H-bonds are interchain) or a
single polypeptide chain folding back on to itself (H-
bonds are intrachain).
Occurrence of β-sheets: Many proteins contain β-
pleated sheets. As such, the α-helix and β-sheet are
commonly found in the same protein structure. In the
globular proteins, β-sheets form the core structure.
 TERTIARY STRUCTURE OF PROTEIN

The three-dimensional arrangement of protein

structure is referred to as tertiary structure.

It is a compact structure with hydrophobic side chains

held interior while the hydrophilic groups are on the
surface of the protein molecule.

This type of arrangement ensures stability of the

molecule.
Bonds of tertiary structure:
Besides the hydrogen bonds, disulfide bonds ( S S),
ionic interactions (electrostatic bonds), hydrophobic
interactions and van der Waals forces also contribute
to the tertiary structure of proteins.
 QUATERNARY STRUCTURE OF PROTEIN
A great majority of the proteins are composed of single
polypeptide chains.

Some of the proteins, however, consist of two or more

polypeptides which may be identical or unrelated.

Such proteins are termed as oligomers and possess

quaternary structure. The individual polypeptide chains
are known as monomers, protomers or subunits.

A dimer consists of two polypeptides while a tetramer

has four.
Bonds in quaternary structure:
The monomeric subunits are held together by
nonconvalent bonds namely hydrogen bonds,
hydrophobic interactions and ionic bonds.

Importance of oligomeric proteins:

These proteins play a significant role in the regulation
of metabolism and cellular function.

Examples of oligomeric proteins:

Hemoglobin, aspartate transcarbomylase, lactate
dehydrogenase.
HEMOGLOBIN:
Hemoglobin (Hb) is the red blood pigment found in
erythrocytes
The normal concentration of Hb in blood in males
is 14–16 g/dl, and in females 13–15 g/dl.

Hemoglobin performs two important biological

functions concerned with respiration

1. Delivery of O2 from the lungs to the

tissues.
2. Transport of CO2 from tissues to lungs for
Structure of globin:
Globin consists of four polypeptide chains of two
different primary structures (monomeric units). It is
made up of two α-chains and two β-chains.
Each α-chain contains 141 amino acids while β-chain
contains 146 amino acids.
Bonds responsible for protein structure:

Protein structure is stabilized by two types of

bonds Covalent and non-covalent.
1. Covalent bonds: The peptide and disulfide bonds are
the strong bonds in protein structure.

Disulfide bonds: A disulfide bond ( S S ) is formed by the

sulfhydryl groups ( SH) of two cysteine residues to
produce cystine.

The disulfide bonds may be formed in a single

polypeptide chain or between different polypeptides.
These bonds contribute to the structural conformation
Non-covalent bonds:
1. Hydrogen bonds
2. Hydrophobic bonds
3. Electrostatic bonds
4. Van der Waals forces
AAAA
Myoglobin
Myoglobin (Mb) is monomeric oxygen binding
hemoprotein found in heart and skeletal muscle.
It has a single polypeptide (153 amino acids) chain
with heme moiety.

Myoglobin (mol. wt. 17,000) structurally resembles

the individual subunits of hemoglobin molecule.
Myoglobin functions as a reservoir for oxygen. It
further serves as oxygen carrier that promotes the
transport of oxygen to the rapidly respiring muscle
cells.
Binding of O2 to hemoglobin and Myoglobin:

Hb has four chains so it binds with 4 oxygen

molecules while Mb binds to one oxygen.
Myoglobin has much higher affinity for O2 than
hemoglobin. Hence O2 is bound more tightly
with myoglobin than with hemoglobin.
Cooperative binding of O2 to hemoglobin:

The oxygen dissociation curve for hemoglobin is

sigmoidal in shape. This indicates that the binding of
oxygen to one heme increases the binding of oxygen
to other hemes.

Thus the affinity of Hb for the last O2 is about 100

times greater than the binding of the first O2 to Hb.
This phenomenon is referred to as cooperative
binding of O2. On the other hand, release of O2 from
one