Enzymes and Regulation | Enzymology

Enzymes are proteins that act as catalysts in biochemical reactions, speeding up the rate at which the reaction occurs. Enzymes are regulated by several factors, including substrate concentrations, pH, temperature, and the presence of inhibitors or activators. Inhibitors bind to the active site of the enzyme, blocking the substrate from binding and preventing the reaction from occurring. Activators bind to allosteric sites on the enzyme, causing a conformational change that increases the enzyme’s affinity for the substrate and facilitates the reaction.

Types of enzyme

Simple enzyme

They are made up of protein only like Pepsin, Trypsin, …

Holoenzyme or conjugated enzyme

The entire activated complex of the apoenzyme plus the co-factor is called the holoenzyme.

Apoenzyme + Co-factor = Holoenzyme

Apoenzyme (Protein part)

Many enzymes require a co-factor in order to function. The protein portion of the enzyme is called apoenzyme.

Co-factor

Enzymes are composed of one or several polypeptide chains. However, there are a number of cases in which non-protein constituents called cofactors are bound to the enzyme to make the enzyme catalytically active. In these instances, the protein portion of the enzymes is called the apoenzyme and the non-protein portion is called the cofactor.

Three kinds of cofactors may be identified: Co-enzymes, Prosthetic groups, and Metal ions.

Coenzyme: It is an organic compound that binds to the active sites of certain enzymes to assist in the catalysis of a reaction. When a cofactor is loosely attached to the protein and can be easily separated from it, it is called a coenzyme.

They are loosely bound to the apoenzyme. Coenzymes can function as an intermediate carrier of electrons during these reactions or be transferred between enzymes as functional groups. Their association with apoenzyme is only transient (usually occurring during the course of catalysis). Most of them are vitamin derivatives.

Prosthetic group: Co-factors are usually either nonprotein organic compounds or metal ions. A cofactor that is firmly attached to the apoenzymes (protein portion) is called a prosthetic group.

Metal activators: They form coordinate bonds with side chains at the active site and at the same time form one or more coordinate bond bonds with the substrate.

Substrates

Substrates are the molecules on which enzymes act. Enzymes are largely proteins that are highly specific for their substrates, meaning that each enzyme is tailored to interact with a specific molecule or molecule. Examples of substrates for enzymes include carbohydrates, proteins, lipids, nucleic acids, small molecules such as hormones, and other molecules.

Enzymes are also known to interact with multiple substrates in order to catalyze a reaction. For example, a protease enzyme may interact with a protein substrate to break down the protein into its constituent amino acids. Similarly, a glycoside hydrolase enzyme may interact with a carbohydrate substrate to break down the carbohydrate into its constituent monosaccharides.

In addition to these examples, enzymes can interact with other substrates such as lipids, nucleic acids, and small molecules. In conclusion, substrates for enzymes are the molecules on which the enzymes act, and they can be carbohydrates, proteins, lipids, nucleic acids, small molecules, and other molecules.

Classification of enzymes based on the occurrence

Enzymes can be classified into four main categories based on their occurrence: extracellular, intracellular, cell membrane-associated, and intercellular.

1. Intracellular enzymes: These enzymes are found inside the cells, performing a variety of metabolic functions. Examples include proteases, glycosidases, and kinases.
2. Extracellular enzymes: These enzymes are found outside of the cell, typically being secreted by the cell to perform a specific task. Examples include amylases, lipases, and cellulase.
3. Endogenous enzymes: These enzymes are produced by the organism itself and are found in the body. Examples include pepsin, trypsin, and chymotrypsin.
4. Exogenous enzymes: These enzymes are not produced by the organism, but are instead obtained from external sources. Examples include enzymes used in food processing and the production of biofuels.
5. Endoenzymes or intracellular enzymes: These are the enzymes that act within the cell in which they are produced and are called endoenzymes.
6. Exoenzymes or extracellular enzymes: These are the enzymes that act outside the cell from which they are produced and are called exoenzymes.
7. Isoenzymes or isozymes: An enzyme may exist in two or more different molecular forms. Different species of the same enzyme are called isoenzymes.
8. Cell membrane-associated enzymes: These enzymes are found on the surface of the cell membrane and help to break down lipids and proteins. Examples include lipases and phospholipases.
9. Interphospholipasecellular enzymes: These enzymes are found between cells and help to mediate intercellular communication. Examples include adenosine triphosphate (ATP), guanosine triphosphate (GTP), and cyclic adenosine monophosphate (cAMP).

Chemical nature of enzyme

All enzymes isolated or purified so far are proteins in characters. Proteins are synthesized in the cell from 20 different kinds of amino acids. Each amino acid molecule has a carboxyl group (-COOH) and an amino group (-NH₂). During protein synthesis, the carboxyl group of one amino acid links with the amino group of other amino acids thus forming peptide linkage.

In proteins 200 to 300 such linked peptide linkages are present. The arrangement of amino acids in protein molecules can be co-related with the arrangement of nucleotides (units of nucleic acid) in DNA molecules.

In certain cases, enzymes require other substances like calcium and magnesium ions whose presence in small amounts is responsible for the action of a given enzyme. In such a case, the term coenzymes are applied.

A complete enzyme, commonly known as a holoenzyme, consists of coenzymes, plus protein apoenzymes. When cells secrete enzymes, these are often first produced in an inactive form of enzymes that are said to be proenzymes.

Mode of action of the enzyme

During biochemical reactions in the body, the enzymes first combine with the substrate to form an intermediate complex before yielding the products of the reactions.

In the process, the substrate molecules are thought to fit in substrate molecules ate thought to fit into the active sites located on the surface of the enzyme molecule just as one particular kind of key fits into one particular kind of lock. This results in the rapid formation named by adding the suffix “ase” to the name of the substrate on which they act. Some of them are:

1. Proteinases: Proteases are enzymes that catalyze the breakdown of proteins into smaller polypeptides or amino acids process is called proteolysis. They are widely used in industrial, chemical, and biological processes. They are also used in food processing, detergents, pharmaceuticals, and biotechnology.
2. Amylases: Amylases are enzymes that catalyze the breakdown of starches into smaller components simple sugars.
3. Lipases: Lipases are enzymes that catalyze the breakdown of fats and other lipids into smaller components fatty acids.
4. Nucleases: This type of enzyme help in the breakdown of nucleic acids (DNA and RNA) into their constituents nucleosides and nucleotides.

Classification of enzyme

1. Oxidoreductases: These enzymes catalyze oxidation-reduction reactions, transferring electrons from one molecule to another.
2. Transferases: These enzymes catalyze the transfer of functional groups between molecules.
3. Hydrolases: These enzymes catalyze the hydrolysis of a substrate by adding water molecules.
4. Ligases: These enzymes catalyze the formation of a bond between two molecules with the simultaneous hydrolysis of ATP or other energy-rich molecules.
5. Lyases: These enzymes catalyze the cleavage of C-C, C-O, C-N, and other bonds by means other than hydrolysis and oxidation.
6. Isomerases: These enzymes catalyze the interconversion of isomers of a molecule.

Factors affecting enzymatic activities

1. Temperature: Temperature affects enzyme-catalyzed reactions in the same way that it affects ordinary chemical reactions. As the temperature rises, the rate of chemical reaction increases owing to an increase in the number of activated molecules. But when the temperature rises above a certain limit, the enzyme loses its activity as protein; enzymes may be completely denatured at high temperatures. Therefore, for every enzyme under a given set of conditions, there is a temperature at which the activity of the enzyme is at a maximum. This is known as optimum temperature.
2. Effect of pH: Each enzyme has its optimum pH at which the most rapid activity occurs. Extreme acidity or alkalinity usually causes irreversible destruction of the enzyme. Pepsin acts in the acidic medium of gastric juice and has an optimum pH of 2-0.
3. Enzyme concentration: The concentration of enzyme is directly proportional to the chemical reaction up to a certain extent. An increase in the enzyme concentration would increase the rate of reaction.
4. Substrate concentration: The concentration of substrate also shows the progressive activities up to a certain extent. An increase in the substrate concentration will increase the chance of a substrate molecule coming in contact with an active site.
5. Product concentration: The increased concentration of product falls the rate of chemical reactions as there is a gradual decrease in the concentration of substrate.
6. Other factors:
   1. Strong light inactivates the enzymes.
   2. Ultraviolet (UV) light is effective in destroying enzyme activity.
   3. The presence of salts may influence enzymatic activity by participating with the enzyme due to its proteinaceous nature.

FAQs

Q: What is an enzyme?
A: Enzymes are protein molecule that facilitates a specific reaction towards equilibrium and acts as biocatalyst or biological catalyst (catalysts accelerates chemical reaction) that participate in almost all the metabolic processes occurring in the body.

In the body, several biochemical changes occur in many steps, each step is catalyzed by a specific enzyme. In living beings, all biochemical activities require specific enzymes. The activity of enzymes may vary from one cell to another.

Q: How do enzymes work?
A: Enzymes work by binding to a substrate molecule and inducing a change in its shape. This change in shape makes the substrate molecules more reactive, allowing them to interact with other molecules in the reaction.

Q: What are the three main types of enzymes?
A: The three main types of enzymes are oxidoreductase, transferases, and hydrolases. Oxidoreductases catalyze oxidation-reduction reactions, transferases catalyze the transfer of functional groups between molecules, and hydrolases catalyze the hydrolysis of bonds.

Q: What is the active site of an enzyme?
A: The active site of an enzyme is the region of the enzyme molecule that binds to the substrate and catalyzes the reaction. It contains amino acid residues that interact with the substrate molecule to induce a conformational change.

Q: How do substrate molecules bind to enzymes?
A: Substrate molecules bind to enzymes via weak interactions such as hydrogen bonds and van der Waals forces. These weak interactions allow the substrates to fit into the active site of the enzyme and induce a conformational change that facilitates the reaction.

Q: What are enzymes regulated by?
A: Enzymes are regulated by the concentration of their substrates, the pH of the environment, and the presence of metal ions or other molecules. These factors can either enhance or inhibit the activity of the enzyme.

Q: What is the difference between an enzyme and a coenzyme?
A: An enzyme is a protein that catalyzes a chemical reaction, whereas a coenzyme is a non-protein molecule that is required for the activity of an enzyme. Coenzymes can be either organic molecules or metal ions.

Q: How can enzymes be denatured?
A: Enzymes can be denatured by extreme temperatures, pH levels, or the presence of certain chemicals. Denaturation changes the shape of the enzyme and prevents it from binding to its substrate.

Q: What is the role of enzymes in metabolic pathways?
A: Enzymes play a key role in metabolic pathways by catalyzing the reactions that form the metabolic pathways. They speed up the reactions, making them more efficient and allowing the organism to gain energy from the reactions.

Q: How can enzymes be used in biotechnology?
A: Enzymes can be used in biotechnology to catalyze desired reactions, such as the production of certain chemicals or the breakdown of certain molecules. They can also be used to modify existing molecules, such as proteins, to create new molecules with novel properties.