Enzyme Structure

Enzymes are a linear chain of amino acids that generate the three-dimensional structure. The sequence of amino acids enumerates the structure, which in turn identifies the catalytic activity of the enzyme. The structure of the enzyme denatures when heated, leading to loss of enzyme activity, which is typically connected to the temperature.

Enzymes are larger than their substrates, and their size varies, which range from sixty-two amino acid residues to an average of two thousand five hundred residues present within fatty acid synthase. Only a small section of the structure is involved in catalysis and are situated next to binding sites. The catalytic site and binding site together constitute the enzyme’s active site. A small number of ribozymes exists which serves as an RNA-based biological catalyst. It reacts in complex with proteins.

Enzymes Classification

Earlier, enzymes were assigned names based on the one who discovered it. With further researches, classification became more comprehensive.

According to the International Union of Biochemists (I U B), enzymes are divided into six functional classes and are classified based on the type of reaction in which they are used to catalyze. The six types of enzymes are oxidoreductases, hydrolases, transferases, lyases, isomerases, ligases.

Following are the enzymes classifications in detail:

Types	Biochemical Property
Oxidoreductases	The enzyme Oxidoreductase catalyzes the oxidation reaction where the electrons tend to travel from one form of a molecule to the other.
Transferases	The Transferases enzymes help in the transportation of the functional group among acceptors and donors molecules.
Hydrolases	Hydrolases are hydrolytic enzymes, which catalyze the hydrolysis reaction by adding water to cleave the bond and hydrolyze it.
Lyases	Adds water, carbon dioxide or ammonia across double bonds or eliminate these to create double bonds.
Isomerases	The Isomerases enzymes catalyze the structural shifts present in a molecule, thus causing the change in the shape of the molecule.
Ligases	The Ligases enzymes are known to charge the catalysis of a ligation process.

Oxidoreductases

These catalyze oxidation and reduction reactions,e.g. pyruvate dehydrogenase, which catalyzes the oxidation of pyruvate to acetyl coenzyme A.

Transferases

These catalyze the transfer of a chemical group from one compound to another. An example is a transaminase, which transfers an amino group from one molecule to another.

Hydrolases

Hydrolases

They catalyze the hydrolysis of a bond. For example, the enzyme pepsin hydrolyzes peptide bonds in proteins.

Lyases

These catalyze the breakage of bonds without catalysis, e.g. aldolase (an enzyme in glycolysis) catalyzes the splitting of fructose-1, 6-bisphosphate to glyceraldehyde-3-phosphate and dihydroxyacetone phosphate.

Isomerases

They catalyze the formation of an isomer of a compound. Example: phosphoglucomutase catalyzes the conversion of glucose-1-phosphate to glucose-6-phosphate (transfer of a phosphate group from one position to another in the same compound) in glycogenolysis (conversion of glycogen to glucose for quick release of energy.

Ligases

Ligases catalyze the joining of two molecules. For example, DNA ligase catalyzes the joining of two fragments of DNA by forming a phosphodiester bond.

In a more elaborate note types of enzymes:

• Oxidoreductases: These enzymes bring about oxidation and reduction reactions and hence are called oxidoreductases. In these reactions, electrons in the form of hydride ions or hydrogen atoms are transferred. When a substrate is being oxidized, these enzymes act as the hydrogen donor. These enzymes are called dehydrogenases or reductases. When the oxygen atom is the acceptor, these enzymes are called oxidases.
• Transferases: These enzymes are responsible for transferring functional groups from one molecule to another. Example: alanine aminotransferase which shuffles the alpha‐amino group between alanine and aspartate etc. Some transferases also transfer phosphate groups between ATP and other compounds, sugar residues to form disaccharides such as hexokinase in glycolysis.
• Hydrolases: These enzymes catalyze reactions that involve the process of hydrolysis.They break single bonds by adding water. Some hydrolases function as digestive enzymes because they break the peptide bonds in proteins. Hydrolases can also be a type of transferases as they transfer the water molecules from one compound to another. Example: Glucose-6-phosphatase that removes the phosphate group from glucose-6-phosphate, leaving glucose and H₃PO₄.
• Lyases:  These enzymes catalyze reactions where functional groups are added to break double bonds in molecules or where double bonds are formed by the removal of functional groups. Example: Pyruvate decarboxylase is a lyase that removes CO₂ from pyruvate. Other examples include deaminases and dehydratases.
• Isomerases: These enzymes catalyze the reactions where a functional group is moved to another position within the same molecule such that the resulting molecule is actually an isomer of the earlier molecule. Example: triosephosphate isomerase and phosphoglucose isomerase for converting glucose 6-phosphate to fructose 6-phosphate.
• Ligases: These enzymes perform a function that is opposite to that of the hydrolases. Where hydrolases break bonds by adding water, ligases form bonds by removal of the water component. There are different subclasses of ligases which involve the synthesis of ATP.

EC MAJOR CLASSES of Enzymes

1. Oxidoreductases… [ dehydrogenases]                   catalyzes oxidation reduction reactions, often using coenzyme as NAD+/FAD

Alcohol dehydrogenase  ethanol + NAD+ —> acetaldehyde + NADH

2. Transferases…  catalyze the transfer of functional group

Hexokinase D-glu + ATP —> D-glu-6-P + ADP

3. Hydrolyases… catalyzes hydrolytic reactions adds water across C-C bonds

Carboxypeptidase A   [aa-aa] n + H2O —> [aa-aa] n-1 + aa

4. Lyases…  cleave C-C, C-O, C-N & other bonds often genrating a C=C bond or ring

Pyruvate decarboxylase   pyruvate —> acetaldehyde + CO2

5. Isomerases… [mutases]  catalyze isomerizations

Maleate isomerase  maleate —> fumarate

6. Ligases…   condensation of 2 substrates with splitting of ATP

Pyruvate Carboxylase    PYR + CO 2 + ATP —> OAA + ADP + P

Cofactors

Cofactors are non-proteinous substances that associate with enzymes. A cofactor is essential for the functioning of an enzyme. An enzyme without a cofactor is called an apoenzyme. An apoenzyme and its cofactor together constitute the holoenzyme.

There are three kinds of cofactors present in enzymes:

• Prosthetic groups: These are cofactors tightly bound to an enzyme at all times. A fad is a prosthetic group present in many enzymes.
• Coenzyme: A coenzyme is bound to an enzyme only during catalysis. At all other times, it is detached from the enzyme. NAD⁺ is a common coenzyme.
• Metal ions: For the catalysis of certain enzymes, a metal ion is required at the active site to form coordinate bonds. Zn²⁺ is a metal ion cofactor used by a number of enzymes.

Examples of Enzymes

Following are some of the examples of enzymes:

Beverages

Alcoholic beverages generated by fermentation vary a lot based on many factors. Based on the type of the plant’s product, which is to be used and the type of the enzyme applied, the fermented product varies.

For example, grapes, honey, hops, wheat, cassava roots, and potatoes depending upon the materials available. Beers, wines and other drinks are produced from plant fermentation.

Food Products

Bread can be considered as the finest example of fermentation in our everyday life.

A small proportion of yeast and sugar is mixed with the batter for making bread. Then one can observe that the bread gets puffed up as a result of fermentation of the sugar by the enzyme action in yeast, which leads to the formation of carbon dioxide gas. This process gives the texture to the bread, which would be missing in the absence of the fermentation process.

Drug Action

Enzyme action can be inhibited or promoted by the use of drugs which tend to work around the active sites of enzymes.

Mechanism of Enzyme Reaction

Any two molecules have to collide for the reaction to occur along with the right orientation and a sufficient amount of energy. The energy between these molecules needs to overcome the barrier in the reaction. This energy is called activation energy.

Enzymes are said to possess an active site. The active site is a part of the molecule that has a definite shape and the functional group for the binding of reactant molecules. The molecule binding with the enzyme is called the substrate group. The substrate and the enzyme form an intermediate reaction with low activation energy without any catalysts.

reactant(1)+reactant(2)→productreactant(1)+enzyme→intermediateintermediate+reactant(2)→product+enzyme

The basic mechanism of enzyme action is to catalyze the chemical reactions, which begins with the binding of the substrate with the active site of the enzyme. This active site is a specific area that combines with the substrate.

Enzyme-Substrate Interactions

ENZYME  REACTION  PATH        E + S <—> [ES] <—> E + P       enzymes catalyze reactions by        lowering the energy of activation… Ea                    mcb3.20*            Karp figure

There is no difference in free energy between an enzyme catalyzed reaction and an uncatalyzed react-ion, but an uncatalyzed reaction requires a higher energy input than a catalyzed reaction.