What Are Enzymes?

“Enzymes can be defined as biological polymers that catalyze biochemical reactions.”

The vast majority of enzymes are proteins with catalytic capabilities that are essential for maintaining
various life processes. Metabolic processes and other chemical reactions in the cell are carried out by a set of
enzymes that are necessary to sustain life.

The initial stage of metabolic process depends upon the enzymes, which react with a molecule and is called
substrate. Enzymes convert the substrates into other distinct molecules and are called the products.

The regulation of enzymes has been a key element in clinical diagnosis because of their role in maintaining
life processes. The macromolecular component of all enzymes consists of protein, except in the class of
RNA catalysts called ribozymes. The word ribozyme is derived from the ribonucleic acid enzyme. Many
ribozymes are molecules of ribonucleic acid which catalyze reactions in one of their own bonds or among
other RNAs.

Enzymes exist in all fluids and tissues of the body. Intracellular enzymes catalyze all the reactions that occur
in metabolic pathways. The enzymes in plasma membrane regulate catalysis in the cells in response to
cellular signals and enzymes in the circulatory system regulate clotting of blood. Almost all the significant
life processes are based on the enzyme functions.

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 vary, 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.

Also read: Amino acids

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 6 types of enzymes
are oxidoreductases, hydrolases, transferases, lyases, isomerases, ligases.

Following are the enzymes classifications in detail:

Types Biochemical Property

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

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.

Cofactors
Co-factors 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.

Also Read: Digestive 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 the definite shape
and the functional group for the binding of reactant molecules. The molecule binding to 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+r
eactant(2)→product+enzyme

The basic mechanism of enzyme action is to catalyze chemical reactions, which begin at 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
Enzymes are the biocatalysts with high molecular weight proteinous compound. It enhances the reactions
which occur in the body during various life processes. It helps the substrate by providing the surface for the
reaction to occur. The enzyme comprises of hollow spaces occupying groups such as -SH, -COOH, etc., on
the outer surface. The substrate which has the opposite charge of the enzyme fits into these spaces just like a
key fits into a lock. This substrate binding site is called the active site of an enzyme (E).

The favourable model of enzyme-substrate interaction is called the induced-fit model. This model states that
the interaction between substrate and enzyme is weak and these weak interactions induce conformational
changes rapidly and strengthen binding and bring catalytic sites close enough to substrate bonds.

There are four major possible mechanisms of catalysis:

Catalysis by Bond Strain

The induced structural rearrangements in this type of catalysis produce strained substrate bonds that attain
transition state more easily. The new conformation forces substrate atoms and catalytic groups like aspartate
into conformations that strain substrate bonds.

Covalent Catalysis

The substrate is oriented to active place on the enzymes in such a manner that a covalent intermediate
develops between the enzyme and the substrate, in catalysis that occurs by covalent mechanisms. The best
example of this is involving proteolysis by serine proteases that have both digestive enzymes and various
enzymes of the blood clotting cascade. These proteases have an active site serine whose R group hydroxyl
produces a covalent bond with a carbonyl carbon of a peptide bond and causes hydrolysis of the peptide
bond.

Catalysis Involving Acids and Bases

Other mechanisms also contribute to the completion of catalytic events that are initiated by strain
mechanism like the use of glutamate as a general acid catalyst.

Catalysis by Orientation and Proximity

Enzyme-substrate interactions bring reactive groups into proximity with one another. Also, groups like
aspartate are chemically reactive and their proximity and towards the substrate favours their involvement in
catalysis.

Action and Nature of Enzymes

Once substrate (S) binds to this active site, they form a complex (intermediate-ES) which then produces the
product (P) and the enzyme (E) The substrate which gets attached to the enzyme has a specific structure and
that can only fit in a particular enzyme. Hence by providing a surface for the substrate, an enzyme slows
down the activation energy of the reaction. The intermediate state where the substrate binds to the enzyme is
called the transition state. By breaking and making the bonds, the substrate binds to the enzyme (remains
unchanged), which converts into the product and later splits into product and enzyme. The free enzymes
then bind to other substrates and the catalytic cycle continues until the reaction completes.

The enzyme action basically happens in two steps:

Step1: Combining of enzyme and the reactant/substrate.

E+S → [ES]

Step 2: Disintegration of the complex molecule to give the product.

[ES]→E+P

Thus, the whole catalyst action of enzymes is summarized as:

E + S → [ES] → [EP] → E + P

Biological Catalysts

Catalysts are the substances which play a significant role in the chemical reaction. Catalysis is the
phenomenon by which the rate of a chemical reaction is altered/ enhanced without changing themselves.
During a chemical reaction, a catalyst remains unchanged, both in terms of quantity and chemical properties.
An enzyme is one such catalyst which is commonly known as the biological catalyst. Enzymes present in
the living organisms enhance the rate of reactions which take place within the body.

Enzymes, the biological catalysts are highly specific, catalyzing a single chemical reaction or a very few
closely related reactions. The exact structure of an enzyme and its active site determines the specificity of
the enzyme. Substrate molecules bind themselves at the enzyme’s active site. Substrates initially bind to the
enzymes by noncovalent interactions, including hydrogen bonds, ionic bonds, and hydrophobic interactions.
Enzymes lower the activation energy and the reactions proceed toward equilibrium more rapidly than the
uncatalyzed reactions. Both prokaryotic and eukaryotic cells commonly use allosteric regulation in
responding to changes in conditions within the cells.

The nature of enzyme action and factors affecting the enzyme activity are discussed below.

Factors Affecting Enzyme Activity

The conditions of the reaction have a great impact on the activity of the enzymes. Enzymes are particular
about the optimum conditions provided for the reactions such as temperature, pH, alteration in substrate
concentration, etc.

Generally, an increase in temperature increases the activity of enzymes. Because enzymes function in cells,
the optimum conditions for most enzymes are moderate temperatures. At elevated temperatures, at a certain
point activity decreases dramatically when enzymes are denatured. Purified enzymes in diluted solutions are
denatured more rapidly than enzymes in crude extracts. Incubation of enzymes for long periods may also
denature enzymes. It is more suitable to use a short incubation time in order to measure the initial velocities
of the enzyme reactions.

The International Union of Biochemistry recommends 30 °C as the standard assay temperature. Most
enzymes are very sensitive to changes in pH. Only a few enzymes function optimally below pH 5 and above
pH 9. The majority of enzymes have their pH-optimum close to neutrality. The change in pH will change the
ionic state of amino acid residues in the active site and in the whole protein. The change in the ionic state
may change substrate binding and catalysis. The choice of substrate concentration is also crucial because at
low concentrations the rate is dependent on the concentration, but at high concentrations, the rate is
independent of any further increase in substrate concentration.

Active site
Enzymatic catalysis relies on the action of amino acid side chains arrayed in the active centre. Enzymes bind
the substrate into a region of the active site in an intermediate conformation.

The active site is often a pocket or a cleft formed by the amino acids that participate in substrate binding and
catalysis. The amino acids that make up the active site of an enzyme are not contiguous to one another along
the primary amino acid sequence. The active site amino acids are brought to the cluster in the right
conformation by the 3-dimensional folding of the primary amino acid sequence. Of the 20 different amino
acids that make up protein, the polar amino acids, aspartate, glutamate, cysteine, Serine, histidine, and lysine
have been shown most frequently to be active site amino acid residues. Usually, only two to three essential
amino acid residues are directly involved in the bond leading to product formation. Aspartate, glutamate,
and histidine are the amino acid residues that also serve as proton donors or acceptors.

Temperature and pH

Enzymes require an optimum temperature and pH for their action. The temperature or pH at which a
compound shows its maximum activity is called optimum temperature or optimum pH respectively. As
mentioned earlier, enzymes are protein compounds. A temperature or pH more than optimum may alter the
molecular structure of the enzymes. Generally, an optimum pH for enzymes is considered to be ranging
between 5 and 7.

• Optimum T°
• The greatest number of molecular collisions
• human enzymes = 35°- 40°C
• body temp = 37°C
• Heat: increase beyond optimum T°
• The increased energy level of molecules disrupts bonds in enzyme & between enzyme & substrate H,
ionic = weak bonds
• Denaturation = lose 3D shape (3° structure)
• Cold: decrease T°
• molecules move slower decrease collisions between enzyme & substrate

Concentration and Type of Substrate

Enzymes have a saturation point i.e., once all the enzymes added are occupied by the substrate molecules, its
activity will be ceased. When the reaction begins, the velocity of enzyme action keeps on increasing on
further addition of substrate. However, at a saturation point where substrate molecules are more in number
than the free enzyme, the velocity remains the same.

The type of substrate is another factor that affects the enzyme action. The chemicals that bind to the active
site of the enzyme can inhibit the activity of the enzyme and such substrate is called an inhibitor.
Competitive inhibitors are chemicals that compete with the specific substrate of the enzyme for the active
site. They structurally resemble the specific substrate of the enzyme and bind to the enzyme and inhibit the
enzymatic activity. This concept is used for treating bacterial infectious diseases.