ENZYMES

Enzymes are protein substances produced by living organisms and which catalyze or speed up the rate of chemical reactions in them. The reaction between an enzyme and a substrate molecule is akin to the “lock and key mechanism” of a padlock in which the key fits tightly into the lock in order to be fastened or zipped up. Enzymes are specific in their action; and because of this specificity, both the enzymes and the reacting molecules (i.e., substrates) fits together in a complementary fashion. Though this lock and key mechanism of enzyme-substrate reaction explained the specificity of enzyme action; it cannot elucidate on the stabilization of the transition state of enzyme-substrate reaction, an important process for the formation of the product in a faster fashion. In enzymatic reactions, the substances or molecules that enzymes act upon are generally known as substrates while the new molecules formed at the end of the reaction are known as products.

One characteristic of enzymes is that all enzymes are proteins but not all proteins are enzymes. This implies that for a substance to qualify as an enzyme, it must be proteinous in nature. However, there are some few exceptions that exist in catalytic ribonucleic acid molecules (RNAs) – which are not necessarily proteinous in nature. RNA molecules that are capable of catalytic activities in the absence of proteins exist; and such molecules are known as ribozymes. Since they are proteinous in nature, enzymes can easily lose their biological function when denatured. And denatured enzymes can no longer carry out their normal catalytic activities because they have been separated into their different components which are individually devoid of any catalytic activity. Enzymes act in several ways.

They lower the activation energy of a biochemical reaction; and in doing so they generally create an environment in which the transition state of the reaction can be stabilized. Enzymes also bring substrates of reacting molecules together in the correct orientation so that they can react among each other; and in doing so they reduce the entropy of the reaction. Entropy is defined as a measure of the disorderliness or randomness of a system. Enzymes provide an alternative pathway for a biochemical reaction to proceed. Enzymes also require cofactors or coenzymes for their catalytic activities in vivo. Cofactors are the non-protein components of enzymes that take part in the catalytic functions of enzymes. Generally, most enzymes are usually made up of two main parts: the apoenzymes and the cofactors; and such enzymes are different from enzymes that are largely pure proteins in nature.

Apoenzymes are the protein components of enzymes while the cofactors as aforementioned are the non-protein components. Apoenzymes can also be called apoproteins. For enzymes that are not pure enzymes and that contains both the apoenzyme and cofactor in one molecule; the cofactors usually assume two different orientations. Cofactors can either be tightly attached to their apoenzymes or loosely attached to the apoenzymes. If the cofactor is loosely attached to its apoenzyme it is called a coenzyme. But cofactors that are tightly attached to their enzymes are generally called prosthetic groups. Holoenzymes are the complete catalytic enzyme molecules that comprise the apoenzymes and cofactors. Enzymes perform almost the same function that catalysts perform in vitro; but the only difference is that enzymes perform their work in vivo (i.e. inside living systems) while the later (i.e., catalysts) perform their function outside living systems (i.e., in vitro).

They accelerate cellular and metabolic reactions inside living systems. Enzymes are biological catalysts; and they are found in every part of living organisms where they facilitate the biosynthesis of key molecules of life. There is rarely no biochemical reaction that is catalyzed without the activities of enzymes; and this explains the significant roles of these biological catalysts in living systems. Enzymes help in activating both catalytic and metabolic reactions in living organisms. When reacting molecules or substrates (e.g., A and B) go into biochemical reaction in the presence of enzymes, the enzymes bring the reacting molecules closer to their active sites to form an enzyme-substrate complex (AB) that is further catalyzed to form products (e.g., C and D) as shown in Figure 1.

Figure 1: Schematic illustration of enzyme-substrate reaction. AB= enzyme-substrate complex.

Since uncatalyzed biochemical reactions (i.e., reactions devoid of enzymatic activities) tend to be generally slow, it is crucial that biochemical reactions in living systems undergo enzymatic catalysis. Active sites are the compartments found on the surfaces of enzymes on which substrates are bound specifically. This site can also be called the enzyme’s catalytic site. Active sites or catalytic sites are critical for enzymatic catalysis because substrates must be bound specifically on the enzyme’s active site and positioned for further enzymatic activity. The active sites of enzymes illustrate the specificity of enzyme-substrate reaction; and this site shows that enzymes are specific in their action. By bringing reacting molecules together at their catalytic sites, enzymes lower the activation energy required for the reaction to proceed. Activation energy is defined as the energy required bringing substrates together at the catalytic sites of an enzyme so that they can reach their transition state. Once the transition state (i.e. the state at which the enzyme substrate complex is formed) of the reacting molecules in a biochemical reaction is reached, the reaction can then proceed in a much more faster rate and products are formed at the end of the reaction. At their active sites, the enzymes concentrate the reacting molecules or substrates; and because these substrates are well concentrated in such a manner that the enzyme-substrate complex is formed, the reaction can proceed unperturbed in a much faster rate than uncatalyzed reactions.

In the course of catalyzing a biochemical reaction in vivo, enzymes do not affect the equilibrium state of the reaction. They only increase the rate at which the reaction occurs by lowering the activation energy of the process so that the entire reaction can proceed in a much faster rate and at a lower temperature with optimum product formation. Enzymes are usually classified based on the type of biochemical reaction that they catalyze. In naming an enzyme, the biochemical reaction catalyzed by the enzyme in question and the substrates that the enzyme is expected to act upon are both taken into consideration before arriving at a final name for the enzyme molecule. And the names of enzymes end with the suffix ase”. However, enzyme classification is coordinated by the International Union of Biochemistry and Molecular Biology (IUBMB). IUBMB is the global nomenclature committee that establishes and appraises a systematic scheme for the classification of enzymes. Based on the guidelines of the IUBMB, enzymes are classified into six (6) general classes designated numbers 1 – 6; and each of these classes can be further divided into subclasses and sub-subclasses depending on the reactions that the enzymes catalyze. The six major classes of enzymes include: oxidoreductases, transferases, hydrolases, lyases, isomerases, and ligases. These six (6) classes of enzymes are briefly highlighted in this section.

  • Oxidoreductases: Oxidoreductases are classes of enzymes that catalyze redox (oxidation-reduction) reactions. Typical example is lactate dehydrogenase (LDH) which catalyzes the reduction of pyruvate in the glycolytic pathway. Oxidoreductases generally catalyze biochemical reactions in which electrons are transferred from one molecule to another.
  • Transferases: Transferases are classes of enzymes that catalyze biochemical reactions in which groups (e.g. hydroxyl groups, OH) are transferred from one molecule to another. Aspartate transferase is a typical example of a transferase. Transferases generally catalyze group transfer reactions in living systems.
  • Hydrolases: Hydrolases are classes of enzymes that catalyze biochemical reactions in which functional groups are transferred to water. They mainly take part in hydrolysis reaction. Gluco-6-phosphatase is a typical example of a hydrolase.
  • Lyases: Lyases are classes of enzymes that add groups to double bonds in biochemical reactions. They also form double bonds in biochemical reactions by removing groups. Typical example of a lyase is fumarase formerly known as fumarate hydratase; and fumarase play critical role in the tricarboxylic acid (TCA) cycle.
  • Isomerases: Isomerases are classes of enzymes that take part in isomerization reactions (i.e. reactions in which isomers are formed) in living systems. Alanine racemase which play significant biological roles in the metabolism of bacterial cells is a typical example of an isomerase. Isomerases generally take part in biochemical reactions in which groups are transferred within reacting molecules to form isomers.
  • Ligases: Ligases are classes of enzymes that catalyze biochemical reactions in which bonds are formed between molecules. Typical example of a ligase is glutamine synthetase which plays several metabolic roles in living organisms. Isomerases take part in condensation reactions; and they mainly catalyze the formation of bonds such as carbon-nitrogen (C-N) bonds, carbon-carbon (C-C) bonds and carbon-oxygen (C-O) bonds among others.  

Each classified enzyme molecule comprises four digits known as the enzyme classification or enzyme commission (EC) number. The first number shows the class name of the enzyme; the second number shows the subclass name of the enzyme; and the third number and fourth number shows the additional side groups such as hydroxyl groups and phosphate groups attached to the enzyme molecule. For example, the EC number of pyruvate kinase (a glycolytic enzyme that regulates glycolysis) is 2.7.3.40. The first number (which is the main enzyme class) “2” denotes the class name of the enzyme (i.e. transferase); the second number (which is the subclass of the enzyme) “7” denotes the subclass of the enzyme and it shows the transfer of a phosphate group; the third number (which is the sub-subclass of the enzyme molecule) “3” indicates that an alcohol group accepts the phosphate; and the fourth number (which is the serial number of the enzyme) “40” shows the arbitrary number assigned to pyruvate kinase.

Microorganisms express several enzymes that enhance their cellular and metabolic activities. While some of these microbial enzymes are of immense industrial and economic importance because of the reactions they catalyze; others are beneficial to the microbes producing them especially in the aspect of their pathogenesis in which they increase the virulence of the organism in the phase of an infection. Knowing how enzymes work, their classification and their biological roles in living systems is crucial for the effective manipulation of microbial processes for beneficial purposes; and this is the main objective of this section.

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