Enzymes, their structure, classification and function

Enzymes
The human body is composed of different types of cells, tissues, and other complex organs. For
efficient functioning, our body releases some chemicals to accelerate biological processes such
as respiration, digestion, excretion, and a few other metabolic activities to sustain a healthy life.
Hence, enzymes are pivotal in all living entities which govern all the biological processes.
What are enzymes?
“Enzymes can be defined as biological polymers that catalyze biochemical reactions.”
Most of the enzymes are proteins with catalytic capabilities crucial to perform different
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 the substrate. Enzymes convert the substrates into other distinct molecules, which
are known as products.
The regulation of enzymes has been a key element in clinical diagnosis because of their role in
maintaining life processes. The macromolecular components of all enzymes consist 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 are found in all tissues and fluids of the body. Catalysis of all reactions taking place in
metabolic pathways is carried out by intracellular enzymes. The enzymes in the plasma
membrane govern the catalysis in the cells as a response to cellular signals and enzymes in the
circulatory system regulate the clotting of blood. Most of the critical life processes are
established on the functions of enzymes.
Enzyme Structure
Enzymes are a linear chain of amino acids, which give rise to a three-dimensional structure. The
sequence of amino acids specifies the structure, which in turn identifies the catalytic activity of
the enzyme. Upon heating, the enzyme’s structure denatures, resulting in a loss of enzyme
activity, which typically is associated with temperature.
Compared to its substrates, enzymes are typically large with varying sizes, ranging from 62
amino acid residues to an average of 2500 residues found in fatty acid synthase. Only a small
section of the structure is involved in catalysis and is situated next to the binding sites. The
catalytic site and binding site together constitute the enzyme’s active site. A small number of
ribozymes exist which serve 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 them. With further
research, classification became more comprehensive.
According to the International Union of Biochemists (IUB), 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 kinds of enzymes are hydrolases, oxidoreductases, lyases, transferases, ligases,
and isomerases.
Classification of enzymes discussed 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 donor 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, catalyzing the
oxidation of pyruvate to acetyl coenzyme A.
Transferases
These catalyze transferring of the chemical group from one to another compound. 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 (phosphate group is
transferred from one to another position in the same compound) in glycogenolysis (glycogen is
converted to glucose for energy to be released quickly).
Ligases
Ligases catalyze the association of two molecules. For example, DNA ligase catalyzes the
joining of two fragments of DNA by forming a phosphodiester bond.
Cofactors
Cofactors are non-proteinous substances that associate with enzymes. A cofactor is essential for
the functioning of an enzyme. The protein part of enzymes in cofactors is apoenzyme. An
enzyme 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. FAD (flavin adenine
dinucleotide) is a prosthetic group present in many enzymes.
Coenzyme: A coenzyme binds to an enzyme only during catalysis. At all other times, it is
detached from the enzyme. NAD (Nicotinamide adenine dinucleotide) 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. Zinc 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 enzyme applied, the fermented
product varies.
For example, grapes, honey, hops, wheat, cassava roots, and potatoes depending upon the
materials available. Beer, 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 because 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 using 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 that
binds to the enzyme is referred to as the substrate group. The substrate and the enzyme form an
intermediate reaction with low activation energy without any catalysts.
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.
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.
Biological catalysts, enzymes, are extremely specific that catalyze a single chemical reaction, or
some closely associated reactions. An enzyme’s exact structure and its active site decide an
enzyme’s specificity. Substrate molecules attach themselves at the active site of an enzyme.
Initially, substrates associate themselves by noncovalent interactions to the enzymes which
include ionic, hydrogen bonds and hydrophobic interactions. Enzymes reduce the reactions and
activation energy to progress towards equilibrium quicker than the reactions that are not
catalyzed. Both eukaryotic and prokaryotic cells usually make use of allosteric regulation to
respond to fluctuations in the state inside 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.
Typically, enzyme activities are accelerated with increasing temperatures. As enzymes are
functional in cells, the feasible conditions for nearly all enzymes are temperatures that are
moderate. At higher temperatures, given a specific point, there is a drastic decrease in the activity
with the denaturation of enzymes. In diluted solutions, purified enzymes denature quickly
compared to enzymes in crude extracts. Denaturation of enzymes can also take place when
enzymes are incubated for long durations. More appropriate is to utilize a shorter time duration
when it comes to incubation time to gauge the starting velocities of such enzyme reactions.
The International Union of Biochemistry (IUB) suggests the standard assay temperature to be 30
°C. Almost all enzymes are extremely sensitive to pH change. Just some enzymes feasibly
operate with pH above 9 and below 5. Most enzymes have their pH – optimum near to neutrality.
Any alteration of pH causes the ionic state of amino acid residues to change in the whole protein
and in the active site. The modifications in the ionic state can modify catalysis and substrate
binding. The preference of substrate concentration is critical as at lower concentrations, the rate
is driven by concentration, however, at high concentrations, the rate does not depend on any
increase in the concentration of the substrate.
Active site
Enzymatic catalysis depends upon the activity of amino acid side chains assembled in the active
centre. Enzymes bind the substrate into a region of the active site in an intermediate
conformation.
Often, the active site is a cleft, or a pocket produced by the amino acids which take part in
catalysis and substrate binding. Amino acids forming an enzyme’s active site is not contiguous to
the other along the sequence of primary amino acid. The active site amino acids are assembled to
the cluster in the right conformation by the 3-dimensional folding of the primary amino acid
sequence. The most frequent active site amino acid residues out of the 20 amino acids forming
the protein are polar amino acids, aspartate, cysteine, glutamate, histidine, Serine, and lysine.
Typically, only 2-3 essential amino acid residues are involved directly in the bond causing the
formation of the product. Glutamate, Aspartate, and Histidine are the amino acid residues which
also serve as a proton acceptor or donor.
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 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 molecule 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.
Salt concentration
 Changes in salinity: Adds or removes cations (+) & anions (–)
 Disrupts bonds, disrupts the 3D shape.
 Disrupts attractions between charged amino acids.
 Affect 2° & 3° structure.
 Denatures protein.
 Enzymes intolerant of extreme salinity
Functions of Enzymes
The enzymes perform several functions in our bodies. These include:
 Enzymes help in signal transduction. The most common enzyme used in the process
includes protein kinase that catalyzes the phosphorylation of proteins.
 They break down large molecules into smaller substances that can be easily absorbed by
the body.
 They help in generating energy in the body. ATP synthase is the enzyme involved in the
synthesis of energy.
 Enzymes are responsible for the movement of ions across the plasma membrane.
 Enzymes perform several biochemical reactions, including oxidation, reduction,
hydrolysis, etc. to eliminate the non-nutritive substances from the body.
 They function to reorganize the internal structure of the cell to regulate cellular activities.
Quiz Questions.
Almost all enzymes are proteins, so which enzyme is not a protein?
Except for ribozymes, all enzymes are protein-based.
Define enzymes?
Enzymes can be defined as biological polymers that catalyze biochemical reactions.
What is the induced fit theory?
The concept of induced fit states that when a substrate binds to an enzyme, it brings about a
change in the shape of the enzyme which either enhances or suppresses the activity of the
enzyme.
What are the examples of enzymes in plants?
Examples of plant-derived enzymes include amylase, protease, and peroxidase.
Can an enzyme be called a polymer?
Yes, most enzymes are made up of proteins which are polymers of amino acids.
What are the types of enzymes present?
The types of enzymes are:
Oxidoreductases
Transferases
Hydrolases
Lyases
Ligases
Isomerases
What is an active site of an enzyme?
The enzyme’s active site is a cleft or a pocket within the enzyme where the substrate molecule
binds and undergoes chemical reactions to be converted into the product.