Enzymes- classification, nomenclature, mechanism, properties and Michaelis-Menton kinetics

 

                                                                         ENZYMES

Definition:

Enzymes are globular proteins that catalyse the many thousands of metabolic reactions taking place within cells and organism. The molecules involved in such reactions are metabolites. Metabolism consists of chains and cycles of enzyme-catalysed reactions, such as respiration, photosynthesis, protein synthesis and other pathways. These reactions are classified as

anabolic (building up of organic molecules). Synthesis of proteins from amino acids and synthesis of polysaccharides from simple sugars are examples of anabolic reactions.

catabolic (breaking down of larger molecules). Digestion of complex foods and the breaking down of sugar in respiration are examples of catabolic reactions.

Enzymes can be extracellular enzyme as secreted and work externally exported from cells. Eg. digestive enzymes; or intracellular enzymes that remain within cells and work there. These are found inside organelles or within cells. Eg. Insulin

Nomenclature of Enzymes:

Most of the enzymes have a name based on their substrate with the ending –ase. For example lactase hydrolyses lactose and amylase hydrolyses amylose. Other enzymes like renin, trypsin do not depict any relation with their function.

Classification of Enzymes:

Enzymes are classified into six groups based on their mode of action.

s.no	Enzyme	Mode of action	Example
1	Oxidoreductase	Oxidation and reduction (redox) reactions	Dehydrogenase
2	Transferase	Transfer a group of atoms from one molecule to another	Transaminase, phosphotransferase
3	Hydrolases	Hydrolysis of substrate by addition of water molecule	Digestive enzymes
4	Isomerase	Control the conversion of one isomer to another by transferring a group of atoms from one molecule to another	Isomerase
5	Lyase	Break chemical bond without addition of water	Decarboxylase
6	Ligase	Formation of new chemical bonds using ATP as a source of energy	DNA ligase

 Properties of Enzyme:

1. All are globular proteins.
2. They act as catalysts and effective even in small quantity.
3. They remain unchanged at the end of the reaction.
4. They are highly specific.
5. They have an active site where the reaction takes place.
6. Enzymes lower activation energy of the reaction they catalyse.

Mechanism of Enzyme:

In a enzyme catalysed reaction, the starting substance is the substrate. It is converted to the product. The substrate binds to the specially formed pocket in the enzyme – the active site, this is called lock and key mechanism of enzyme action. As the enzyme and substrate form a ES complex, the substrate is raised in energy to a transition state and then breaks down into products plus unchanged enzyme.

Enzyme Cofactors:

Many enzymes require non-protein components called cofactors for their efficient activity. Cofactors may vary from simple inorganic ions to complex organic molecules. They are of three types: inorganic ions, prosthetic groups and coenzymes.

Holoenzyme – active enzyme with its non protein component.

Apoenzyme – the inactive enzyme without its non protein component.

Inorganic ions -- help to increase the rate of reaction catalysed by enzymes. Example: Salivary amylase activity is increased in the presence of chloride ions.

Prosthetic groups are organic molecules that assist in catalytic function of an enzyme. Flavin adenine dinucleotide (FAD) contains riboflavin (vit B2), the function of which is to accept hydrogen. ‘Haem’ is an iron containing prosthetic group with an iron atom at its centre.

Coenzymes are organic compounds which act as cofactors but do not remain attached to the enzyme. The essential chemical components of many coenzymes are vitamins. Eg. NAD, NADP, Coenzyme A, ATP

Inhibitors of Enzyme:

Certain substances present in the cells may react with the enzyme and lower the rate of reaction. These substances are called inhibitors. It is of two types competitive and non-competitive.

Competitive Inhibitor:

Molecules that resemble the shape of the substrate and may compete to occupy the active site of enzyme are known as competitive inhibitors. For Example: the enzyme that catalyses' the reaction between carbon di oxide and the CO2 acceptor molecule in photosynthesis, known as ribulose bisphosphate carboxylase oxygenase (RUBISCO) is competitively inhibited by oxygen/carbon-di-oxide in the chloroplast. The competitive inhibitor is malonate for succinic dehydrogenase.

Non-competitive Inhibitors:

There are certain inhibitors which may be unlike the substrate molecule but still combines with the enzyme. This either blocks the attachment of the substrate to active site or change the shape so that it is unable to accept the substrate. For example the effect of the amino acids alanine on the enzyme pyruvate kinase in the final step of glycolysis. Certain non-reversible/irreversible inhibitors bind tightly and permanently to an enzyme and destroy its catalytic properties entirely. These could also be termed as poisons. Example – cyanide ions which blocks cytochrome oxidase in terminal oxidation in cell aerobic respiration, the nerve gas sarin blocks a neurotransmitter in synapse transmission.

Allosteric Enzymes:

They modify enzyme activity by causing a reversible change in the structure of the enzyme active site. This in turn affects the ability of the substrate to bind to the enzyme. Such compounds are called allosteric inhibitors. Eg. The enzyme hexokinase which catalysis glucose to glucose-6 phosphate in glycolysis is inhibited by glucose 6 phosphate. This is an example for feedback allosteric inhibitor.

End Product Inhibition (Negative Feedback Inhibition):

When the end product of a metabolic pathway begins to accumulate, it may act as an allosteric inhibitor of the enzyme controlling the first step of the pathway. Thus the product starts to switch off its own production as it builds up. The  process is self – regulatory. As the product is used up, its production is switched on once again. This is called end-product inhibition.

Michaelis-Menton Constant (Km) and Its Significance:

When the initial rate of reaction of an enzyme is measured over a range of substrate concentrations (with a fixed amount of enzyme) and the results plotted on a graph. With increasing substrate concentration, the velocity increases rapidly at lower substrate concentration. However the rate increases progressively, above a certain concentration of the substrate the curve flattened out. No further increase in rate occurs. This shows that the enzyme is working at maximum velocity at this point. On the graph, this point of maximum velocity is shown as Vmax.