The human body is composed of different types of cells, tissues, and other complex organs. In order to function efficiently, there are certain chemicals released by our body to speed up certain biological processes like digestion, respiration, excretion, and other metabolic activities in order to maintain a healthy life. Thus, enzymes play an important role in all higher multicellular organisms including plants by regulating all the biological processes.
Let us have a detailed look at what are enzymes, their structure, types, mechanism and different factors affecting its activity.
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.
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
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:
|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.|
These catalyze oxidation and reduction reactions,e.g. pyruvate dehydrogenase, which catalyzes the oxidation of pyruvate to acetyl coenzyme A.
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.
They catalyze the hydrolysis of a bond. For example, the enzyme pepsin hydrolyzes peptide bonds in proteins.
These catalyze 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.
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 catalyze the joining of two molecules. For example, DNA ligase catalyzes the joining of two fragments of DNA by forming a phosphodiester bond.
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:
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.
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.
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.
\(reactant(1) + reactant(2) \rightarrow product\\ reactant(1) + enzyme \rightarrow intermediate\\ intermediate + reactant(2) \rightarrow product + enzyme\)
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.
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.
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.
Thus, the whole catalyst action of enzymes is summarized as:
E + S → [ES] → [EP] → E + P
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.
Enzymatic catalysis relies on the action of amino acid side chains arrayed in the active center. 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.
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
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