Biomolecules

ENZYMES

An enzyme is a catalyst which is utilised in metabolic reactions. Almost all enzymes are proteins.

"Lock and Key" Model: The lock and key model was suggested by Emil Fischer in 1894. Emil Fischer postulated that both the enzyme and the substrate possess specific complementary geometric shapes that fit exactly into one another. This model explains the specificity of enzyme. But this model fails to explain the stabilization of the transition state which an enzyme achieves.

Induced Fit Model: This is the most accepted model and is a modification over the lock and key model. The induced fit model was proposed by Daniel Koshland in 1958. According to this model, since enzymes are rather flexible structures; the active site is continually reshaped by interactions with the substrate when the substrate interacts with the enzyme. In some cases, the substrate molecule also changes shape slightly when it enters the active site. The active site continues to change until the substrate is completely bound. The final shape and charge is determined at this point of enzyme-substrate reaction.

There are many differences between enzyme catalysts and inorganic catalysts. Inorganic catalysts work efficiently at high temperatures and high pressures, enzymes get damaged at high temperatures (above 40°C). But enzymes which are isolated from thermophilic organisms show thermal stability.

Mechanisms of Enzymatic Actions

Enzyme lowers the activation energy by creating an environment in which the transition state is stabilized.
Enzyme lowers the energy of the transition state by creating an environment with the opposite charge distribution to that of the transition state. But an enzyme does this without distorting the substrate.
Enzyme provides an alternative pathway.
Enzyme reduces the reaction entropy charge by bringing substrates together in the correct orientation to react.
Increase in temperatures speeds up reactions. But if the enzyme is heated too much, its shape deteriorates and it regains it shape only when the temperature comes back to normal. Some enzymes work best at low temperatures, e.g. thermolabile.
The catalytic cycle of an enzyme action can be described in the following steps:
The substrate binds to the active site of the enzyme, fitting into the active site.
The binding of the substrate induces the enzyme to alter its shape, fitting more tightly around the substrate.
The active site of the enzyme breaks the chemical bonds of the substrate and the new enzyme- product complex is formed.
The enzyme releases the products of the reaction and the free enzyme is ready to bind to another molecule of the substrate.

Factors Affecting Enzyme Activity

Temperature and pH: Enzymes usually function in a narrow range of temperature and pH. Each enzyme shows its highest activity at optimum temperature and optimum pH. Beyond that range, the activity declines. Low temperature preserves the enzyme temporarily in inactive state, while high temperature destroys the enzyme.

Fig Ref: Class 11 Biology NCERT Textbook

Concentration of Substrate: The velocity of enzymatic action at first rises with an increase in substrate concentration. But the velocity of reaction does not rise once it reaches a maximum velocity (V_max). This happens because there are fewer molecules of enzyme and no free enzyme molecule is left to bind with the additional substrate molecules.

Effect of Inhibitor: When the inhibitor closely resembles the substrate and inhibits the activity of an enzyme, it is known as competitive inhibitor. Because of its close structural similarity with the substrate, the inhibitor competes with the substrate for the binding site on the enzyme. Such competitive inhibitors are often used in the control of bacterial pathogens.

Classification and Nomenclature of Enzymes

Enzymes are divided into 6 classes each with 4-13 subclasses and named accordingly by a four-digit number.

Oxidoreductases/dehydrogenases: Enzymes which catalyse oxidoreduction between two substrates S and S’.

Transferases: Enzymes catalysing a transfer of a group, G (other than hydrogen) between a pair of substrate S and S’.

Hydrolases: Enzymes catalysing hydrolysis of ester, ether, peptide, glycosidic, C-C, C-halide or P-N bonds.

Lyases: Enzymes that catalyse removal of groups from substrates by mechanisms other than hydrolysis leaving double bonds.

Isomerases: Includes all enzymes catalysing inter-conversion of optical, geometric or positional isomers.

Ligases: Enzymes catalysing the linking together of 2 compounds, e.g., enzymes which catalyse joining of C-O, C-S, C-N, P-O etc. bonds.

Co-factors

In many cases, non-protein constituents are bound to the enzyme which makes the enzyme catalytically inactive. Such non-protein constituents are called cofactors. In such cases, the protein portion of the enzyme is called the apoenzyme. There are three kinds of cofactors, viz. prosthetic groups, co-enzymes and metal ions.

Prosthetic Groups:

Prosthetic groups are organic compounds. They are distinguished from other cofactors in that they are tightly bound to the apoenzyme. For example, in peroxidase and catalase, which catalyze the breakdown of hydrogen peroxide to water and oxygen, haem is the prosthetic group and it is a part of the active site of the enzyme.

Co-enzymes:

Co-enzymes are also organic compounds but their association with the apoenzyme is only transient. A co-enzyme’s association; with apoenzyme; usually occurs during the course of catalysis. Moreover, co-enzymes serve as co-factors in a number of different enzyme catalyzed reactions. The essential chemical components of many coenzymes are vitamins, e.g., coenzyme nicotinamide adenine dinucleotide (NAD) and NADP contain the vitamin niacin.

Metal Ions: A number of enzymes require metal ions for their activity. Such metal ions form coordination bonds with side chains at the active site and at the same time form one or more cordination bonds with the substrate, e.g., zinc is a cofactor for the proteolytic enzyme carboxypeptidase. Catalytic activity is lost when the co-factor is removed from the enzyme which proves that they play a crucial role in the catalytic activity of the enzyme.