Enzymes | Agriculture Optional Notes for UPSC PDF Download

Introduction

Enzymes play a crucial role in all living organisms by facilitating various biological processes like respiration, digestion, and excretion, which are essential for maintaining a healthy life. The human body consists of a variety of cells, tissues, and complex organs, and it releases chemicals to enhance these metabolic activities, ensuring efficient functioning.

Enzymes

“Enzymes can be defined as biological polymers that catalyze biochemical reactions.”

The majority of enzymes are proteins with essential catalytic abilities that play a vital role in various processes. Enzymes are essential for sustaining life by facilitating metabolic processes and other chemical reactions within cells.

The initial phase of metabolic processes relies on enzymes, which interact with specific molecules known as substrates. Enzymes transform these substrates into different molecules called products.

Enzyme regulation is a crucial aspect of clinical diagnosis due to their involvement in maintaining life processes. Enzymes are typically composed of protein, with the exception of a class of RNA catalysts known as ribozymes, derived from ribonucleic acid enzymes. Many ribozymes are RNA molecules that catalyze reactions within their own bonds or with other RNAs.

Enzymes are present in all tissues and body fluids. Intracellular enzymes are responsible for catalyzing reactions in metabolic pathways, while enzymes in the plasma membrane govern cellular responses to signals, and enzymes in the circulatory system regulate blood clotting. Most essential life processes rely on the functions of enzymes.

Structure of Enzymes

Enzymes act as biological catalysts, accelerating chemical processes by offering an alternative route without undergoing any changes to their own structure or composition.

Enzymes consist of numerous amino acids connected in a specific manner, resulting in various enzyme types. These amino acid chains fold into distinctive shapes, and it is these shapes that give each enzyme its unique chemical potential. Additionally, many enzymes include a non-protein component called a co-factor.

Types of Enzymes

Biochemical reactions within the body fall into six primary categories, each corresponding to enzymes with specific functions:

• Oxidoreductases: These enzymes facilitate oxidation and reduction reactions, transferring electrons in the form of hydride ions or hydrogen atoms. When a substrate undergoes oxidation, these enzymes act as hydrogen donors and are called dehydrogenases or reductases. When oxygen is the acceptor, they are referred to as oxidases.
• Transferases: These enzymes are responsible for transferring functional groups from one molecule to another. For instance, alanine aminotransferase shifts the alpha‐amino group between alanine and aspartate. Some transferases also move phosphate groups between ATP and other compounds or sugar residues to create disaccharides, like hexokinase in glycolysis.
• Hydrolases: These enzymes catalyze reactions that involve hydrolysis, breaking single bonds by adding water. Some hydrolases act as digestive enzymes by cleaving peptide bonds in proteins. They can also function as transferases since they transfer water molecules between compounds, e.g., glucose-6-phosphatase, which removes the phosphate group from glucose-6-phosphate, yielding glucose and H₃PO₄.
• Lyases: These enzymes catalyze reactions in which functional groups are added to break double bonds in molecules or where double bonds are formed through the removal of functional groups. For instance, pyruvate decarboxylase is a lyase that removes CO2 from pyruvate. Other examples include deaminases and dehydratases.
• Isomerases: These enzymes catalyze reactions in which a functional group is relocated to a different position within the same molecule, resulting in the creation of an isomer of the original molecule. For example, triosephosphate isomerase and phosphoglucose isomerase convert glucose 6-phosphate into fructose 6-phosphate.
• Ligases: These enzymes have a function opposite to hydrolases. While hydrolases break bonds by adding water, ligases form bonds by removing the water component. Ligases encompass various subclasses involved in the synthesis of ATP and other similar processes.

Enzymes Work

Every chemical reaction in the universe requires a certain amount of energy to take place. When there isn't enough activation energy provided, catalysts play a crucial role in reducing the activation energy and facilitating the reaction. This principle applies to both animals and plants, where enzymes help lower the activation energy required for complex molecule reactions.
The following steps simplify how enzymes accelerate reactions:

• Step 1: Enzymes possess an "active site" where one of the substrate molecules can bind, forming an enzyme-substrate complex.
• Step 2: This enzyme-substrate complex then interacts with the second substrate to produce the product, and the enzyme is released as the second product.

There are several theories explaining how enzymes function, but two important ones are discussed here.

Theory 1: Lock and Key Hypothesis 

This theory is widely accepted and posits that the substrate precisely fits into the enzyme's active site to create an enzyme-substrate complex. It also explains the specificity of enzymes in their actions, as they are tailored to specific substrate molecules.

Theory 2: Induced Fit Hypothesis 

Similar to the lock and key hypothesis, this theory suggests that the shape of the enzyme molecule changes as it approaches the substrate molecule, ensuring an exact fit into the enzyme's active site.

Various factors influence enzyme activity within cells:

• Concentration of Enzymes and Substrates: The reaction rate increases with rising substrate concentration up to a point, after which further increases in substrate concentration do not significantly impact the reaction rate. This is because, beyond a certain substrate concentration, all enzyme active sites are occupied, and no further reactions occur.
• Temperature: Enzyme activity increases with higher temperatures due to increased molecular kinetic energy. There is an optimal temperature at which enzymes work most effectively, often corresponding to the body's normal temperature. Exceeding this temperature limit can lead to enzyme denaturation and a decrease in reaction rate.
• pH: Enzymes are sensitive to changes in pH and operate within a specific pH range. Deviating from the optimal pH level can lead to enzyme denaturation and a slowdown in the reaction.
• Inhibitors: Certain substances can inhibit the action of specific enzymes by binding to their active sites, preventing substrate binding and slowing down the reaction.

Enzymes Classification

In the early days of enzyme discovery, enzymes were typically named after their discoverers. However, as research progressed, a more systematic classification system was developed.

According to the International Union of Biochemists (IUB), enzymes are classified into six functional classes based on the types of reactions they catalyze. These six classes of enzymes are hydrolases, oxidoreductases, lyases, transferases, ligases, and isomerases.

Below is a detailed breakdown of enzyme classification:

• Oxidoreductases: These enzymes catalyze oxidation and reduction reactions. For example, pyruvate dehydrogenase catalyzes the oxidation of pyruvate to acetyl coenzyme A.
• Transferases: Transferases facilitate the transfer of chemical groups from one compound to another. An example is transaminase, which transfers an amino group from one molecule to another.
• Hydrolases: Hydrolases catalyze the hydrolysis of chemical bonds. For instance, the enzyme pepsin hydrolyzes peptide bonds in proteins.
• Lyases: Lyases catalyze bond cleavage without the addition of water. An example is aldolase, an enzyme in glycolysis that catalyzes the splitting of fructose-1,6-bisphosphate into glyceraldehyde-3-phosphate and dihydroxyacetone phosphate.
• Isomerases: Isomerases catalyze the conversion of a compound into its isomer. For instance, phosphoglucomutase catalyzes the conversion of glucose-1-phosphate to glucose-6-phosphate, involving the transfer of a phosphate group within the same compound. This process is essential in glycogenolysis, where glycogen is converted into glucose for rapid energy release.
• Ligases: Ligases catalyze the joining of two molecules. DNA ligase, for example, facilitates the connection of two DNA fragments by forming a phosphodiester bond.
• Cofactors: Cofactors are non-protein substances that associate with enzymes and are crucial for their functioning. The protein part of enzymes without cofactors is called apoenzyme. When an enzyme and its cofactor come together, they form a holoenzyme.
  There are three main types of cofactors in enzymes:
  • Prosthetic groups: These tightly bound cofactors are always attached to the enzyme. An example is FAD (flavin adenine dinucleotide), which serves as a prosthetic group in many enzymes.
  • Coenzymes: Coenzymes temporarily bind to an enzyme only during catalysis and detach at other times. NAD is a common coenzyme.
  • Metal ions: Some enzymes require metal ions at the active site to form coordinate bonds for catalysis. Zinc is a frequently used metal ion cofactor in several enzymes.

 Examples of Enzymes

• Beverages: Alcoholic beverages, produced through fermentation, can vary significantly depending on the plant materials and enzymes used. For instance, beer, wine, and other drinks are created by fermenting materials like grapes, honey, hops, wheat, cassava roots, and potatoes.
• Food Products: A common example of fermentation in our daily lives is seen in breadmaking. In this process, a small amount of yeast and sugar is mixed into the dough. As a result of fermentation triggered by the enzyme action in yeast, carbon dioxide gas is generated, causing the bread to rise. This fermentation process gives bread its characteristic texture.
• Drug Action: Enzyme activity can be either inhibited or enhanced by the use of drugs that target the active sites of enzymes. These drugs can modulate or regulate enzyme function.

Mechanism of Enzyme Reaction

For a reaction to take place, two molecules must come into contact with the correct orientation and with enough energy to surpass the energy barrier known as activation energy. Activation energy is the energy required to initiate the reaction.

Enzymes have a specialized region called the active site, which is a portion of the molecule with a specific shape and functional group for binding to reactant molecules. The molecule that attaches to the enzyme is known as the substrate. When the substrate and enzyme bind, they create an intermediate reaction with reduced activation energy, eliminating the need for external 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.

Enzyme-Substrate Interactions

Enzymes serve as biocatalysts, large protein-based compounds that play a crucial role in accelerating various biochemical reactions within the body during essential life processes. They assist by providing a surface for reactions to occur. Enzymes feature cavities on their outer surface, which contain groups like -SH and -COOH. Substrate molecules, possessing opposite charges to the enzyme, fit into these cavities, akin to a key fitting into a lock. This specific region where substrate binding occurs is known as the enzyme's active site (E).

The preferred model for enzyme-substrate interaction is the induced-fit model. It proposes that the interaction between the substrate and enzyme is initially weak, with these weak interactions causing rapid conformational changes that strengthen binding and bring the catalytic sites closer to the substrate bonds.

There are four primary mechanisms of catalysis:

• Catalysis by Bond Strain: Structural rearrangements induce strain in substrate bonds, making it easier for them to reach the transition state. These conformational changes force substrate atoms and catalytic groups, such as aspartate, into conformations that strain the substrate bonds.
• Covalent Catalysis: In this mechanism, the substrate is oriented in a way that leads to the development of a covalent intermediate between the enzyme and substrate. A prime example is proteolysis by serine proteases, which include digestive and blood clotting enzymes. These proteases feature an active site serine whose hydroxyl group forms a covalent bond with a carbonyl carbon in a peptide bond, leading to peptide bond hydrolysis.
• Catalysis Involving Acids and Bases: Certain mechanisms complement catalysis initiated by strain, such as the use of glutamate as a general acid catalyst.
• Catalysis by Orientation and Proximity: Enzyme-substrate interactions bring reactive groups into proximity, favoring their participation in catalysis. Chemically reactive groups like aspartate benefit from being close to the substrate.
• Enzyme Action and Nature: When a substrate (S) binds to the enzyme's active site, they form an intermediate complex (ES), which subsequently yields the product (P) and restores the enzyme (E). The specific structure of the substrate must match the enzyme's active site, allowing the enzyme to lower the activation energy for the reaction by providing a suitable surface. The intermediate state in which the substrate binds to the enzyme is referred to as the transition state. As the substrate binds to the enzyme, breaking and forming bonds, the enzyme remains unchanged and assists in the conversion of substrate into product, eventually releasing the product and the enzyme. Free enzymes can then bind to other substrates, continuing the catalytic cycle until the reaction is complete.

The enzyme's action unfolds in two steps:
Step 1: Binding of the enzyme and substrate/reactant.
E + S → [ES]
Step 2: Disintegration of the complex molecule to yield the product.
[ES] → E + P
In summary, the entire catalytic process of enzymes can be depicted as:
E + S → [ES] → [EP] → E + P

Biological Catalysts

Catalysts are substances that play a significant role in chemical reactions. Catalysis is the process by which a chemical reaction's rate is altered or enhanced without undergoing any change itself. In the course of a chemical reaction, a catalyst remains unchanged in terms of both quantity and chemical properties. Enzymes, often referred to as biological catalysts, are a prime example of this. Enzymes found in living organisms accelerate the rates of reactions occurring within the body.

Biological catalysts, or enzymes, exhibit an extremely high degree of specificity, catalyzing a single chemical reaction or closely related reactions. An enzyme's specificity is determined by its precise structure and the configuration of its active site. Substrate molecules bind to the active site of an enzyme. Initially, substrates attach themselves through noncovalent interactions with enzymes, including ionic, hydrogen bonds, and hydrophobic interactions. Enzymes facilitate reactions and lower activation energy, allowing reactions to reach equilibrium more rapidly than non-catalyzed reactions. Both eukaryotic and prokaryotic cells typically employ allosteric regulation to respond to internal cellular changes.

The subsequent discussion covers the nature of enzyme action and the factors that influence enzyme activity:

Factors Affecting Enzyme Activity

Several factors have a significant impact on enzyme activity, including the conditions under which the reaction occurs, such as temperature, pH, and changes in substrate concentration.

• Temperature:
  • Enzyme activities tend to increase with rising temperatures, up to a certain point. Most enzymes function optimally at moderate temperatures typically found in cells.
  • At higher temperatures, enzyme activity decreases sharply due to enzyme denaturation.
  • Diluted solutions of purified enzymes denature more quickly compared to enzymes in crude extracts.
  • Prolonged incubation times can also lead to enzyme denaturation, so shorter incubation periods are preferred to measure initial reaction velocities.
• pH:
  • Enzymes are highly sensitive to changes in pH. The optimal pH for most enzymes is typically close to neutrality.
  • Deviations from the optimal pH can alter the ionic state of amino acid residues throughout the protein, affecting catalysis and substrate binding.
  • Some enzymes can operate at pH values outside the neutral range, but most have a narrow pH range for optimal activity.
• Substrate Concentration:
  • Enzyme activity is influenced by the concentration of the substrate. At lower substrate concentrations, the rate of the reaction is directly proportional to the concentration.
  • However, at high substrate concentrations, the rate reaches a plateau, as all available enzyme active sites are already occupied.
• Active Site:
  • Enzymatic catalysis depends on the activity of amino acid side chains within the enzyme's active center.
  • The active site is often a pocket or cleft created by specific amino acids involved in catalysis and substrate binding.
  • Amino acid residues comprising the active site are not contiguous along the primary amino acid sequence; their 3D folding brings them together in the proper conformation.
  • Common active site amino acid residues include polar amino acids like aspartate, cysteine, glutamate, histidine, serine, and lysine.
  • Typically, only 2-3 essential amino acid residues directly participate in bond formation during substrate-to-product conversion. Glutamate, aspartate, and histidine may also serve as proton acceptors or donors.
• Salt Concentration:
  • Changes in salt concentration can disrupt the ionic bonds between charged amino acids in enzymes and alter their 2nd and 3rd-degree structures.
  • Enzymes can be denatured by extreme changes in salinity.
  • Enzymes may be sensitive to salt concentration, and some may not function well under high or low salt conditions.
• Type of Substrate:
  • The type of substrate can influence enzyme activity.
  • Competitive inhibitors are chemicals that structurally resemble the specific substrate and compete with it for the enzyme's active site, inhibiting enzymatic activity.
  • Some substrate chemicals can bind to the enzyme's active site and inhibit its function.
• Optimum Temperature and pH:
  • Enzymes have an optimum temperature and pH at which they exhibit maximum activity.
  • Temperatures or pH levels above or below the optimum can disrupt the enzyme's molecular structure.
• Saturation and Substrate Concentration:
  • Enzymes reach a saturation point when all available enzyme active sites are occupied by substrate molecules, and further substrate addition does not increase the reaction rate.
  • The velocity of enzyme action increases with increasing substrate concentration until saturation is reached.
• Salt Concentration:
  • Changes in salinity can disrupt bonds and attractions between charged amino acids in the enzyme, affecting its 2nd and 3rd-degree structure.
  • Extreme changes in salt concentration can lead to enzyme denaturation.
  • Some enzymes are sensitive to salt concentration variations.

Functions of Enzymes

Enzymes play various vital roles in our bodies, including:

• Facilitating Signal Transduction: Enzymes, such as protein kinases, are commonly involved in the process of phosphorylating proteins, which is a fundamental step in signal transduction within cells.
• Breaking Down Large Molecules: Enzymes help break down large molecules into smaller compounds that can be easily absorbed and utilized by the body.
• Energy Generation: The enzyme ATP synthase is responsible for synthesizing adenosine triphosphate (ATP), which is the primary energy currency of the body.
• Ion Transport: Enzymes play a role in facilitating the movement of ions across the cell's plasma membrane, which is crucial for maintaining proper cellular function.
• Catalyzing Biochemical Reactions: Enzymes are involved in a wide range of biochemical reactions, including oxidation, reduction, hydrolysis, and more, which are essential for eliminating non-nutritive substances from the body.
• Regulating Cellular Activities: Enzymes contribute to the reorganization of the internal structure of cells, helping to regulate various cellular processes and activities.