Enzymes

Introduction

An enzyme is a biological catalyst that accelerates chemical reactions in living organisms. Most enzymes are proteins, although some, known as ribozymes, are made of RNA. Enzymes function by lowering the activation energy required for reactions, thereby increasing their rate without being consumed in the process. Each enzyme is specific to a particular substrate, the molecule it acts upon, and converts it into products.

Enzymes play crucial roles in various biological processes, including digestion, metabolism, and cellular regulation. They are essential for breaking down nutrients, synthesizing macromolecules, and facilitating metabolic pathways. Enzyme activity can be influenced by factors such as temperature, pH, and the presence of inhibitors or activators, which can enhance or reduce their function. Enzymes are also utilized in industrial and medical applications, highlighting their importance beyond biological systems.

Q. How do enzymes differ from other catalysts?

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Q. What are the main applications of enzymes in industry?

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Holoenzyme

A holoenzyme is a catalytically active enzyme that consists of an apoenzyme combined with its cofactor. It represents the complete form of the enzyme that is capable of catalyzing biochemical reactions. Holoenzymes are essential for various cellular processes and are typically composed of protein subunits that may require additional non-protein components to function effectively. For example, DNA polymerase is a holoenzyme that plays a critical role in DNA synthesis.

Apoenzyme

An apoenzyme is the inactive protein component of an enzyme that requires a cofactor to become active. It does not possess catalytic activity on its own and must bind to a cofactor to form a holoenzyme. The apoenzyme is responsible for the specific recognition of substrates, while the cofactor facilitates the catalytic process. For instance, the apoenzyme of carbonic anhydrase becomes active only when it binds to a zinc ion, which is essential for its function.

Co-factors

Cofactors are non-protein chemical compounds that are necessary for the activity of certain enzymes. They can be either inorganic ions (such as metal ions like magnesium, zinc, or iron) or organic molecules (known as coenzymes). Cofactors assist in the enzyme’s catalytic activity by stabilizing enzyme-substrate complexes or participating directly in the chemical reaction. For example, magnesium ions serve as cofactors for many enzymes involved in DNA and RNA synthesis.

Co-enzyme

Coenzymes are a specific type of organic cofactor that are often derived from vitamins. They are small, non-protein molecules that bind to the apoenzyme and assist in the transfer of chemical groups during enzymatic reactions. Coenzymes can be modified during the reaction and may require regeneration to return to their original state. Common examples of coenzymes include NAD+ (nicotinamide adenine dinucleotide) and FAD (flavin adenine dinucleotide), which play crucial roles in metabolic pathways such as cellular respiration.

Prosthetic Groups

Prosthetic groups are tightly bound non-polypeptide units that are permanently attached to the enzyme and are essential for its activity. Unlike coenzymes, which may dissociate from the enzyme after the reaction, prosthetic groups remain attached throughout the enzyme’s function. They often play a critical role in the enzyme’s structure and function. An example of a prosthetic group is the heme group in hemoglobin, which is vital for oxygen transport in the blood.

Q. What is prosthetic group? Write a note on different prosthetic group found in an enzyme?

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Enzymes are biological catalysts that facilitate biochemical reactions in living organisms. They are classified based on the type of reaction they catalyze. The International Union of Biochemistry and Molecular Biology (IUBMB) has established a systematic classification system that divides enzymes into six main classes. Below is an outline of enzyme classification along with examples for each category.

Oxidoreductases

Function: Catalyze oxidation-reduction reactions, where electrons are transferred between molecules.

Example: Pyruvate dehydrogenase: Catalyzes the conversion of pyruvate to acetyl-CoA, facilitating the oxidation of pyruvate.

Transferases

Function: Transfer functional groups (e.g., methyl, phosphate) from one molecule to another.

Example: Transaminase: Transfers an amino group from one amino acid to a keto acid, playing a crucial role in amino acid metabolism.

Hydrolases

Function: Catalyze hydrolysis reactions, breaking bonds by adding water.

Example: Pepsin: An enzyme in the stomach that hydrolyzes peptide bonds in proteins, aiding in digestion.

Lyases

Function: Catalyze the addition or removal of groups to form double bonds or break bonds without hydrolysis.

Example: Aldolase: Catalyzes the cleavage of fructose-1,6-bisphosphate into glyceraldehyde-3-phosphate and dihydroxyacetone phosphate during glycolysis.

Isomerases

Function: Catalyze the rearrangement of atoms within a molecule, converting one isomer into another.

Example: Phosphoglucomutase: Converts glucose-1-phosphate to glucose-6-phosphate, facilitating the mobilization of glucose from glycogen.

Ligases

Function: Catalyze the joining of two large molecules by forming new chemical bonds, often coupled with the hydrolysis of ATP.

Example: DNA ligase: Joins DNA fragments by forming phosphodiester bonds, essential for DNA replication and repair.

Enzymes are big in size compared to substrates which are relatively smaller. Evidently, a small portion of the huge enzyme molecule is directly involved in the substrate binding and catalysis.

The active site (or active centre) of an enzyme represents as the small region at which – the substrate(s) binds and participates in the – catalysis.

– Salient features of active site

1. The existence of active site is due to the tertiary structure of protein resulting in three- dimensional native conformation.

2. The active site is made up of amino acids (known as catalytic residues) which are far from each other in the linear sequence of amino acids (primary structure of protein). For instance, the enzyme lysozyme has 129 amino acids. The active site is formed by the contribution of amino acid residues numbered 35, 52, 62, 63 and 101.

3. Active sites are regarded as clefts or crevices or pockets occupying a small region in a big enzyme molecule.

4. The active site is not rigid in structure and shape. It is rather flexible to promote the specific substrate binding.

5. Generally, the active site possesses a substrate binding site and a catalytic site. The latter is for the catalysis of the specific reaction.

6. The coenzymes or cofactors on which some enzymes depend are present as a part of the catalytic site.

7. The substrate(s) binds at the active site by weak non-covalent bonds.

8. Enzymes are specific in their function due to the existence of active sites.

9. The commonly found amino acids at the active sites are serine, aspartate, histidine, cysteine, lysine, arginine, glutamate, tyrosine etc. Among these amino acids, serine is the most frequently found. 10. The substrate [S] binds the enzyme (E) at the active site to form enzyme-substrate complex (ES). The product (P) is released after the catalysis and the enzyme is available for reuse.

E+S=ES   E + P