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Enzymes: Biological Polymers that Catalyze Biochemical Reactions, Lecture notes of Biochemistry

Rajiv Gandhi UniversityBiochemistry

Enzymes are pivotal in all living entities which govern all the biological processes. the structure, classification, and mechanism of enzyme reactions. It also provides examples of enzymes in beverages, food products, and drug action. the interaction between enzymes and substrates, and the four possible major mechanisms of catalysis. It explains the action and nature of enzymes and how they bind to substrates in the active site.

Typology: Lecture notes

2022/2023

Available from 10/16/2023

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E
Enzymes E
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.
Enzymes
“Enzymes can be defined as biological polymers that catalyze biochemical
reactions.”
The majority of 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.
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E

Enzymes E

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.

Enzymes

“Enzymes can be defined as biological polymers that catalyze biochemical

reactions.”

The majority of 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 (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 kinds of enzymes are hydrolases, oxidoreductases,

lyases, transferases, ligases and isomerases.

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 at all

times. 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 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 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.

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 involves proteolysis by serine proteases that have both digestive enzymes and various enzymes of the blood clotting cascade. These proteases possess an active site serine whose R group hydroxyl generates a covalent bond with a carbonyl carbon of a peptide bond and results in the hydrolysis of the peptide bond. Catalysis Involving Acids and Bases Other mechanisms add to the completion of catalytic events which are launched by strain mechanisms such as the usage of glutamate as a general acid catalyst. Catalysis by Orientation and Proximity Enzyme-substrate interactions induce reactive groups into proximity with one another. Also, groups like aspartate are chemically reactive, and their proximity 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. 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.

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 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 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  The Dead Sea is called dead for a reason Functions of Enzymes The enzymes perform a number of functions in our bodies. These include

  1. Enzymes help in signal transduction. The most common enzyme used in the process includes protein kinase that catalyzes the phosphorylation of proteins.
  2. They break down large molecules into smaller substances that can be easily absorbed by the body.
  3. They help in generating energy in the body. ATP synthase is the enzyme involved in the synthesis of energy.
  4. Enzymes are responsible for the movement of ions across the plasma membrane.
  5. Enzymes perform a number of biochemical reactions, including oxidation, reduction, hydrolysis, etc. to eliminate the non-nutritive substances from the body.
  6. They function to reorganize the internal structure of the cell to regulate cellular activities.