Class Chemistry English Volume · Part

Cys . 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 ( C=O) 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+ th residue).

The side chains of the residues protrude outside of the helix. Each turn of an α -helix contains about . residues and is about . A o 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.

Figure . Secondary structure of proteins α -Helix β -sheet . 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. . 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. Figure .

Four levels of protein structure . . 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. Figure . Denaturation of proteins . .

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. .

. Enzymes: There are many biochemical reactions that occur in our living cells. Digestion of food and harvesting the energy from them, and synthesis of necessary molecules required for various cellular functions are examples for such reactions. All these reactions are catalysed by special proteins called enzymes.

These biocatalysts accelerate the reaction rate in the orders of and also make them highly specific. The high specificity is followed allowing many reactions to occur within the cell. For example, the Carbonic anhydrase enzyme catalyses the interconversion of carbonic acid to water and carbon dioxide. Sucrase enzyme catalyses the hydrolysis of sucrose to fructose and glucose.

Lactase enzyme hydrolyses the lactose into its constituent monosaccharides, glucose and galactose. . . Mechanism of enzyme action: Enzymes are biocatalysts that catalyse a specific biochemical reaction.

They generally activate the reaction by reducing the activation energy by stabilising the transition state. In a typical reaction enzyme (E) binds with the substrate (S) molecule reversibly to produce an enzyme-substrate complex (ES). During this stage the substrate is converted into product and the enzyme becomes free, and ready to bind to another substrate molecule. More detailed mechanism is discussed in the unit XI surface chemistry.

E + S [ES] Substate Enzyme - substrate complex Enzyme [ES] E+P Figure . Mechanism of enzyme action (lock and key model)