PROTEIN

•Protein:
Protein may be defined as any of group of complex organic macromolecules that contain carbon, hydrogen,
oxygen, nitrogen & usually sulfur and are composed of one or more chains of amino acids. Proteins are
fundamental components of all living cells and include many substances, such as enzymes, hormones, and
antibodies that are necessary for the proper functioning of an organism.

•Peptide bond:
The covalent bond which is formed between the α- carbonyl group of amino acid to the α- amino group of
another amino acid is known as peptide bond. The formation of a dipeptide bond from two amino acids is
accompanied by the loss of water molecule.

Figure: Formation of peptide bond

•Bonds in protein structure:
1. Ionic bond:-
Ionic bond is a bond between two charged ions. The electrostatic force between an
anion and cation is called ionic bond. Ionic bond is an important bond in biological
system.

2. Hydrogen bond:-
Hydrogen bonding is an attractive force in which hydrogen is attached with a higher
electronegative atom (O, F, and N). Usually hydrogen bond is represented by dotted
line. Hydrogen bond is the most important bond in biological system as the two
strands of DNA molecule are attached together through the hydrogen bond.

3. Van der Waals forces:-

It is an attractive force between two atoms when they come closer to each other.
This bond occurs due to unequal distribution of electrons.
Functions of proteins:
Proteins are the most versatile macromolecules in living systems and serve crucial functions in
essentially all biological processes. The most important functions are-
1. Enzymatic catalysis:-
About 99% reactions are influenced by enzymes. Enzymes make a reaction extensively fast (10 6
times faster). At the same time it increases the amount of products. For example: Pepsin is a
digestive enzyme that works in the stomach to break down proteins in food.
2. Transport and storage:-
Many small molecules and ions are transported by specific proteins. For example- hemoglobin
transports oxygen in erythrocytes, whereas myoglobin, a related protein, transports oxygen in
muscle.
3. Co-ordinated motion:-
Proteins are the major component of muscle. Muscle contraction is accomplished by the sliding
motion of two kinds of protein filaments.
4. Mechanical support:-
The high tensile strength of skin and bone is due to the presence of collagen and fibrous protein.
5. Immune protection:-
Antibodies are highly specific proteins that recognize and combine with such foreign substrates
as viruses, bacteria and cells from other organism. Proteins thus play a vital role in
distinguishing between self and non-self.
6. Generation and transmission of nerve impulses:-
The response of nerve cells to specific stimuli is mediated by receptor proteins. Receptor
proteins that can be triggered by specific small molecules, such as acetylcholine, which are
responsible for transmitting nerve impulses at synapsis that is at junctions between nerve cells.
7. Control of growth and differentiation:-
Controlled sequential expression of genetic information is essential for the orderly growth and
differentiation of cells. Protein helps to maintain this.
• Levels of Protein Structure
Primary Structure of Protein
The Primary structure of proteins is the exact ordering of amino acids forming
their chains.
Secondary Structure of Protein
Secondary structure of protein refers to local folded structures that form
within a polypeptide due to interactions between atoms of the backbone.
Tertiary Structure of Protein
This structure arises from further folding of the secondary structure of the
protein.
Quaternary Structure of Protein
The spatial arrangement of various tertiary structures gives rise to the
quaternary structure.
Different types of regular elements in secondary structure of protein:
α-helix:
In the amino acid sequence the >CO group of each amino acid forms a hydrogen bond with the >NH group
of the amino acid that is situated four residues ahead in the sequence. This type of secondary structure of
protein is called α-helix structure and the bonding is called (n+4) bonding. This type of structure was
proposed by Linus Pauling and Roberty Corey in 1951.
Structure:
i. The α-helix is a rod-like structure formed by tightly coiled polypeptide backbone.
ii. The R- side chain branch out from the main chain.
iii. The fundamental interactions that hold the polypeptide unit in that arrangement are hydrogen bonds
between the N-H group of one amino acid residue and the C=O group of the amino acid four residues
ahead in the chain.
iv. An α-helix coil can wind in the right-handed or left-handed direction.
v. The length of a single helix in a chain can vary from one coil (3.6 residues) to as long as 1000Ǻ (about
600 residues).
vi. The distance between adjacent amino acids along an α-helix is approximately 1.5 Ǻ.
 Figure: α-helix structure of protein

# α-helix coiled coil structure-

If two α-helix cross each other then the
structure is called α-helix coiled coil structure. It is
a very stable structure which can have a length of
1000 Ǻ or more. α-helix coiled coils are found in
myosin and tropomyosin, in muscle, in fibrin in
blood clots and in keratin in hair.
β-sheet or β-plated sheet:
β-sheet is formed by linking two or more β-strands (a
polypeptide chain) by hydrogen bonds. The structural
element of β-sheet differs in several ways from α-helix.
Structure:
i. In the β- configuration, the polypeptide chain is nearly
fully extended (approximately 3.5 Ǻ).
ii. β-sheet is constructed by combining two or more regions
of the polypeptide.
iii. β-plated sheet is stabilized by hydrogen bonds between
NH and CO in different polypeptide strands.
Figure: β-sheet structure of protein
iv. If polypeptide chains run in the same direction (both are
N-C or C-N), the β-sheet is parallel. If the chains alternate
in direction, it is described as antiparallel.
v. The antiparallel arrangement is more common in proteins.
Peptide bond is planar and rigid – why/explain?
In a pair of amino acids linked by a peptide bond, six atoms lie in the same plane. For this reason polypeptide chains are
planner.
 Peptide bond is rigid because-
 The bond between carbonyl carbon and nitrogen atom is not pure single bond. It is a partial double bond. So it is not
free to rotate.
 The distance between the C & N of the peptide bond is typically 1.32 Ǻ which is between the values expected for a
C-N single bond (1.49 Ǻ) and C=N double bond (1.27 Ǻ).
Importance of non-rigid structure:
Protein has two types of conformations.
1. Active conformation
2. Inactive conformation

The role of non-rigid structure is to convert the inactive conformation to active conformation and the active to inactive
one.