Proteins

Proteins

Proteins are most abundant biomolecules in all living organisms. The term protein is derived from Greek word ‘Proteious’ meaning primary or holding first place. They are main functional units for the living things. They are involved in every function of the cell including respiration. Proteins are polymers of α-amino acids.

Amino acids

Amino acids are compounds which contain an amino group and a carboxylic acid group. The protein molecules are made up α-amino acids which can be represented by the following general formula.

There are 20 α-amino acids commonly found in the protein molecules. Each amino acid is given a trivial name, a three letter code and a one letter code. In writing the amino acid sequence of a protein, generally either one letter or three letter codes are used.

Classification of proteins

Proteins are classified based on their structure (overall shape) into two major types. They are fibrous proteins and globular proteins.

Fibrous proteins

Fibrous proteins are linear molecules similar to fibres. These are generally insoluble in water and are held together by disulphide bridges and weak intermolecular hydrogen bonds. The proteins are often used as structural proteins. Example: Keratin, Collagen etc…

Globular proteins

Globular proteins have an overall spherical shape. The polypeptide chain is folded into a spherical shape. These proteins are usually soluble in water and have many functions including catalysis (enzyme). Example: myoglobin, insuline

Structure of proteins

Proteins are polymers of amino acids. Their three dimensional structure depends mainly on the sequence of amino acids (residues). The protein structure can be described at four hierarchal levels called primary, secondary, tertiary and quaternary structures as shown in the figure 14.16

1. Primary structure of proteins:

Proteins are polypeptide chains, made up of amino acids are connected through peptide bonds. The relative arrangement of the amino acids in the polypeptide chain is called the primary structure of the protein. Knowledge of this is essential as even small changes have potential to alter the overall structure and function of a protein.

2. Secondary structure of proteins:

The amino acids in the polypeptide chain forms highly regular shapes (sub-structures) through the hydrogen bond between the carbonyl oxygen () and the neighbouring amine hydrogen (-NH)of the main chain.α-Helix and β-strands or sheets are two most common sub-structures formed by proteins.

α-Helix

In the α-helix sub-structure, the amino acids are arranged in a right handed helical (spiral) structure and are stabilised by the hydrogen bond between the carbonyl oxygen of one amino acid (n^th residue) with amino hydrogen of the fifth residue (n+4^th residue). The side chains of the residues protrude outside of the helix. Each turn of an α-helix contains about 3.6 residues and is about 5.4 Aº long. The amino acid proline produces a kink in the helical structure and often called as a helix breaker due to its rigid cyclic structure.

β-Strand

β-Strands are extended peptide chain rather than coiled. The hydrogen bonds occur between main chain carbonyl group one such strand and the amino group of the adjacent strand resulting in the formation of a sheet like structure. This arrangement is called β-sheets.

3. Tertiary structure:

The secondary structure elements (α-helix & β-sheets) further folds to form the three dimensional arrangement. This structure is called tertiary structure of the polypeptide (protein). Tertiary structure of proteins are stabilised by the interactions between the side chains of the amino acids. These interactions include the disulphide bridges between cysteine residues, electrostatic, hydrophobic, hydrogen bonds and van der Waals interactions.

4. Quaternary Structure

Some proteins are made up of more than one polypeptide chains. For example, the oxygen transporting protein, haemoglobin contains four polypeptide chains while DNA polymerase enzyme that make copies of DNA, has ten polypeptide chains. In these proteins the individual polypeptide chains (subunits) interacts with each other to form the multimeric structure which are known as quaternary structure. The interactions that stabilises the tertiary structures also stabilises the quaternary structures.

Denaturation of proteins

Each protein has a unique three-dimensional structure formed by interactions such as disulphide bond, hydrogen bond, hydrophobic and electrostatic interactions. These interactions can be disturbed when the protein is exposed to a higher temperature, by adding certain chemicals such as urea, alteration of pH and ionic strength etc., It leads to the loss of the three-dimensional structure partially or completely. The process of a losing its higher order structure without losing the primary structure, is called denaturation. When a protein denatures, its biological function is also lost.

Since the primary structure is intact, this process can be reversed in certain proteins. This can happen spontaneously upon restoring the original conditions or with the help of special enzymes called cheperons (proteins that help proteins to fold correctly).

Example: coagulation of egg white by action of heat.

Importance of proteins

Proteins are the functional units of living things and play vital role in all biological processes

• All biochemical reactions occur in the living systems are catalysed by the catalytic proteins called enzymes.

• Proteins such as keratin, collagen act as structural back bones.

• Proteins are used for transporting molecules (Haemoglobin), organelles (Kinesins) in the cell and control the movement of molecules in and out of the cells (Transporters).

• Antibodies help the body to fight various diseases.

• Proteins are used as messengers to coordinate many functions. Insulin and glucagon control the glucose level in the blood.

• Proteins act as receptors that detect presence of certain signal molecules and activate the proper response.

• Proteins are also used to store metals such as iron (Ferritin) etc.