Enzyme: Definition, Mechanisms, Nomenclature, Structure, Classification, and Function

What are Enzymes?

Enzymes are the reaction catalysts of biological systems and hence are also known as biocatalysts. Enzymes are central to every biochemical process. With the exception of a few classes, all enzymes are proteins.

Definition and Importance

Enzymes are the most remarkable and highly specialized proteins. They have a high degree of specificity for their substrates, accelerate chemical reactions and function in aqueous solutions under very mild conditions.

The study of enzymes has immense practical importance. In some diseases, especially inheritable genetic disorders, there may be a deficiency or total absence of one or more enzymes. Measurements of enzyme activity in blood samples are important in diagnosing certain illnesses. Enzymes are also important practical tools in chemical engineering, food technology, and agriculture.

Discovery and History (Eduard Buchner, 1897)

Biological catalysis was first recognized and described in the late 1700s, in studies on the digestion of meat by secretions of the stomach. In the 1850s, Louis Pasteur concluded that fermentation of sugar into alcohol by yeast is catalyzed by “ferments.” He postulated that these ferments were inseparable from the structure of living yeast cells.

In 1897, Eduard Buchner discovered that cell-free yeast extracts could ferment sugar to alcohol, proving that fermentation was promoted by molecules that continued to function when removed from cells. Buchner’s experiment marked the dawn of the science of biochemistry. Frederick W. Kuhne later gave the name enzymes, derived from the Greek enzymos, “leavened”.

Chemical Nature and Structure of Enzymes

The structure and function of enzymes are listed below:

Proteins and RNA as Enzymes (Ribozymes)

Enzymes are mostly composed of proteins. However, some ribonucleic acids (RNA) called ribozymes can catalyze reactions as well. There are proteins obtained from amino acids which are polymerized in a certain manner that defines the size and shape, and the ability to act as a catalyst.

Composition and Structural Levels (Primary → Quaternary)

All enzymes usually have quaternary structures which are very important in the catalytic roles. There is a small groove in the protein structure of the enzyme where the substrate binds and the chemical transformation takes place. This groove enables enzymes to selectively bind to the substrates and perform the catalysis of the chemical reactions.

Primary structure is the sequence of the amino acids followed by the secondary structure which is the folding of the polypeptide chain into specific coiled structure, such as alpha helix and beta sheets. While tertiary structure means the overall three dimensional arrangement of all atoms in a protein. Some proteins contain two or more separate polypeptide chains, or subunits, which may be identical or different. The arrangement of these protein subunits in three-dimensional complexes constitutes quaternary structure.

Active Site and Substrate Specificity

The active site of an enzyme is the place on the enzyme where substrate molecules are attached and a chemical reaction takes place. Enzymes are stereospecific which implies that they only attach to a certain substrate in compliance with the shapes and chemical properties of the substrate.

Classification of Enzymes

The classification of enzymes is discussed below

Oxidoreductases

• Oxidoreductases are involved in oxidation/reduction reactions where one molecule is oxidized by having its electrons removed while the other molecule is reduced by gaining the electrons.

• These include enzymes for powerhouse processes like the electron transport chain during cellular respiration.

• Examples include dehydrogenases that pass hydrogen atoms (and their electrons) to the substrates.

Transferases

• Transferases include enzymes that either add an amino, acyl or phosphate group to a molecule or remove it to another molecule.

• They are needed in metabolic processes, particularly in the biosynthesis of amino acids, nucleotides and lipids.

• An example is kinases, enzymes that donate phosphate groups from ATP to substrates in signal transduction or cellular regulation.

Hydrolases

• Hydrolases involve chemical reactions where a substrate undergoes hydrolysis which is the breaking of chemical bonds by the use of water molecules.

• Examples include participation in the digestion, and degradation of food molecules, participation in the recycling of proteins and signal transduction which involves the removal of phosphate groups from the proteins.

• It may be proteases that break down proteins, lipases that break down lipids, phosphatases that remove phosphate groups.

Lyases

• Lyases break the chemical bonds in molecules and make new double bonds, or add groups to double bonds without the processes of hydrolyzing or oxidation.

• They carry out processes that are in the metabolic maps such as the citric acid cycle which involves cleavage of citrate into oxaloacetate and acetyl-CoA.

• For instance, there are decarboxylases which remove carboxyl groups and dehydratases which remove water molecules.

Isomerases

• Enzymes that change the position of atoms in the molecule transforming one isomer into another are called isomerases.

• That is, they are essential for supporting the metabolism and homeostasis of cells by converting substances into their active forms.

• Examples include glucose-6-phosphate isomerase that catalyses the interconversion of glucose-6-phosphate with fructose-6-phosphate during glycolysis.

Ligases

• Ligases catalyse the formation of a molecule from two smaller molecules, usually using up ATP or other nucleotide triphosphate.

• They are involved in DNA synthesis and repair, as well as in the biosynthesis of complex molecules in which a new covalent bond is created.

• Examples include DNA ligase, involved in suturing together two DNA strands during DNA replication or DNA repair mechanism.

Mechanism of Enzyme Action

The mechanism of enzyme action involves several models that describe how enzymes interact with substrates to catalyze chemical reactions:

Lock and Key Model

• The lock and key structure states that an enzyme has a rigid active site that is complementary to the substrate molecule in form, shape and size, similar to a key fits into a lock.

• This model indicates that the enzyme and substrate have to groove complementary to each other from the onset, so are selective and fast in catalyzing reactions.

• When a substrate molecule is attached to the active site the enzyme helps to transform the substrate into the product by stabilizing the transition state and reducing the activation energy.

Induced Fit Model

• In the induced fit model, it is believed that the active site of the enzyme is flexible and changes shape upon the binding of the substrate.

• Also, at the beginning of the interaction, the enzyme and substrate may not fit each other perfectly.

• As the substrate is bound to the enzyme, it undergoes a conformational change to gain a better match of the enzyme and the substrate.

• This induced fit mechanism helps to improve the solid and appropriate catalytic site, brings stability to the transition state, and brings about the change of the substrate into the product.

Enzyme-Substrate Complex Formation

• In catalysis, enzyme-substrate complex is the bonding between the enzyme and substrate molecules for a limited amount of time.

• When the substrate molecule comes across the enzyme, it fits into the active site of the enzyme, and the two join to form the enzyme-substrate complex.

• Based on the structures and properties mentioned, this complex maintains different noncovalent bonding sources. For example, hydrogen bonds, electrostatic interactions, and van der Waals interactions.

• At the active site of the enzyme-substrate complex, the enzyme enables the change of the substrate into the product since the energy that is needed to complete this process is reduced.

Enzyme Kinetics

The enzyme kinetics is discussed below

Michaelis-Menten Concept

The ES complex is the key to understanding this kinetic behavior. Leonor Michaelis and Maud Menten in 1913 postulated that the enzyme first combines reversibly with its substrate to form an enzyme-substrate complex in a relatively fast reversible step. The ES complex then breaks down in a slower second step to yield the free enzyme and the reaction product.

Factors Affecting Enzyme Activity

Temperature

• The temperature factor has an optimal range within which the enzyme is most active, and this is usually 37°C for human enzymes.

• Very high or very low temperatures can inactivate enzymes permanently we call this process denaturation.

pH

• Different enzymes have specific pH values due to the constitution of amino acids within the active site of the enzymes.

• pH variations usually cause instability to a protein by affecting hydrogen bonding and electrostatic forces which are essential in enzyme functioning.

Substrate Concentration

• Enzyme activity rises directly with the substrate concentrations up to the point of the maximum velocity (Vmax) where all the active sites are occupied.

• Beyond Vmax, there is no effect of increasing the relative concentration of the substrate in the reaction rate.

Enzyme Concentration

• Higher enzyme concentrations imply a greater number of active sites for the attachment of the substrate thus enhancing the rate of reaction.

• Activity may level off if the substrate concentration reaches its low amount even when the enzyme is plentiful in the solution.

Inhibitors and Activators

• Inhibition can be reversible, competitive or noncompetitive in type, in which inhibitors directly interact with enzymes thereby decreasing their activity.

• Activators are known to attach to enzymes and confirm their classical code, functionality, high efficiency, and speeds of reactions.

Enzyme Inhibition

The enzyme inhibition is discussed below

Competitive Inhibition

• Competitive inhibitors can bind to the active site of the enzyme preventing binding of another substrate.

• These substances bind themselves to the enzyme and directly fight the substrate for the chance to bind onto the active site.

• High concentrations of substrate can dispel competitive inhibition in that they reduce the opportunity of the inhibitor to compete for the active site.

Noncompetitive Inhibition

• Noncompetitive inhibitors bind to distinct sites on the enzyme not at the active site of the enzyme.

• In this case, it can be seen that this binding alters the conformation of the enzyme and hence a reduction in the activity of the enzyme is observed.

• Noncompetitive inhibition can be irreversible and does not involve direct competition with the substrate. It cannot be removed by raising the concentration of the substrate because it does not affect the Ki value.

Uncompetitive Inhibition

• Some are uncompetitive inhibitors because they only attach themselves to the enzyme-substrate complex rather than the free enzyme.

• This binding normally takes place at the allosteric site and it causes a change in the enzyme’s active site’s binding capacity to the substrate.

• Uncompetitive inhibitors decrease the Vmax as well as the Km of the enzyme and thus decrease the velocity of the reaction.

Allosteric Inhibition

• These bind at other sites of the enzyme and the altering of the shape of the enzyme in the process reduces effectiveness.

• In this binding, the activity of the enzyme in question can either be reduced or enhanced depending on the nature of the compound referred to as the allosteric modulator.

• Allosteric regulation is reversible and depends on the signal in the cell or something that the cell requires.

Applications of Enzymes

The applications of enzymes are discussed below:

Industrial Applications

In food processing, enzymes are used to improve food taste, texture or even nutrient content in food products. Detergents, especially enzymes, enhance the cleaning requirement and limit the usage of raw materials that are so damaging to articles.

The enzymes in textiles are for wearing and creasing fabrics or for making stonewashed denim and in paper industries, they help in bleaching pulp and modifying the fibres.

Medical Applications

Diagnostic test equipment involves enzymes since it is easy to diagnose diseases through tests involving enzymes. Lysosomal storage disorders are some of the diseases treated by enzyme replacement therapies. Supplements for the enzymes also aid people suffering from pancreatic or other digestive diseases, to digest food and assimilate nutrients.

Environmental Applications

A few examples of bioremediation include enzymes which are used in the degradation of substances such as oil and industrial chemicals in the environment. They also find application in wastewater treatment because they enhance the rate of decomposition of organic matter. Enzymes transform biomass into biofuels including ethanol hence providing a better option in comparison to the fossil products.

Enzymes NEET MCQs (With Answers & Explanations)

Important topics for NEET exam are:

• Classification of Enzymes

• Enzyme Kinetics

• Enzyme Inhibition

Practice Questions for NEET

Q1. To isolate protoplast, one needs:

1. Pectinase

2. Cellulase

3. Both pectinase and cellulase

4. Chitinase

Correct answer: 3) Both pectinase and cellulase

Explanation:

Enzymes such as cellulases and pectinases are needed to dissolve the cell wall, which is primarily composed of cellulose, hemicellulose, and pectin. These enzymes break down the complex polysaccharides in the cell wall, facilitating processes like plant cell wall softening or cell wall degradation during fruit ripening. In industrial applications, such as the extraction of juice from fruits or the production of biofuels, these enzymes help release valuable compounds. Additionally, in laboratory research, enzymes are used to isolate protoplasts by removing the cell wall without harming the cell membrane.

Hence, the correct answer is option 3) both pectinase and cellulase.

Q2. Choose the option that does not accurately describe the characteristics of enzyme catalase.

1. The cofactor exhibits an inorganic and proteinaceous nature.

2. Haem serves as the necessary prosthetic group for the enzyme.

3. The cofactor necessary for optimal activity must be firmly bound to the apoenzyme.

4. It facilitates the decomposition of hydrogen peroxide into water and oxygen.

Correct answer: 1) The cofactor exhibits an inorganic and proteinaceous nature.

Explanation:

Option 1 does not accurately describe the characteristics of enzyme catalase. While catalase does require a cofactor for its activity, the cofactor is not both inorganic and proteinaceous. The cofactor for catalase is a heme group, which is an iron-containing prosthetic group. The heme group is essential for catalase's function in facilitating the decomposition of hydrogen peroxide into water and oxygen.

Hence, the correct answer is option 1) The cofactor exhibits an inorganic and proteinaceous nature.

Q3. In the context of its catalytic function in the conversion of glucose-1-phosphate to glucose-6-phosphate, which enzyme classification is most appropriate for phosphoglucomutase?

1. Oxidoreductase

2. Isomerase

3. Kinase

4. Lyase

Correct answer: 2) Isomerase

Explanation:

Phosphoglucomutase is classified as an isomerase enzyme. Isomerases are a class of enzymes that catalyze the interconversion of isomers, which are molecules with the same molecular formula but different structural arrangements. In the case of phosphoglucomutase, it facilitates the conversion of glucose-1-phosphate into glucose-6-phosphate by rearranging the positions of phosphate groups within the molecule. This rearrangement is a structural isomerization reaction, and thus, phosphoglucomutase is classified as an isomerase enzyme.

Hence, the correct answer is option 2)Isomerase.

Also Read-

• MCQs on Enzymes

• Biomolecules

• Metabolites

Recommended Video for Enzymes