Enzymes: All Explained | Zoology Optional Notes for UPSC PDF Download

Introduction

Life depends on a series of chemical reactions, but the majority of these reactions do not occur spontaneously. Catalysts play a crucial role in accelerating these reactions to sustain life. This phenomenon, known as catalysis, is essential for the biochemical reactions necessary for all life processes.

Catalysis Definition

Catalysis is defined as the "acceleration of a chemical reaction by some substance which itself undergoes no permanent chemical change." In the context of life processes, enzymes act as catalysts for biochemical reactions, playing a pivotal role in living organisms.

Discovery of Enzymes

The existence of enzymes has been known for over a century. In 1833, French chemist Anselme Payen discovered the first enzyme, diastase. Louis Pasteur recognized in 1860 that enzymes were essential to fermentation. The term "enzyme" was coined by German physiologist Wilhelm Kuhne in 1877, emphasizing their role in leavening.

Independence of Enzymes
In 1897, German chemist Edward Buchner demonstrated that cell-free extracts of yeast could ferment sugars independently of the cell, marking a crucial discovery of enzymes' functional independence.

Isolation of Enzymes
In 1926, American biochemist J. B. Sumner isolated the first enzyme, urease, in pure crystalline form from the jack bean. This contradicted prevailing opinions and firmly established the protein nature of enzymes.

Enzyme Properties and Functions

Definition of Enzymes
Enzymes are macromolecular biological organic catalysts responsible for supporting almost all chemical reactions that maintain animal homeostasis without undergoing alteration.

Basic Concepts/General Properties

1. Differences from Chemical Catalysts
   • Higher reaction rates (10⁶ - 10¹²)
   • Milder reaction conditions (temperature, pH)
   • Greater reaction specificity (no side products)
   • Capacity for regulation
2. Reversibility of Enzyme Reactions
   • Enzyme reactions are always reversible, accelerating or catalyzing chemical reactions.
3. Equilibrium Position Acceleration
   • Enzymes speed up the rates at which the equilibrium positions of reversible reactions are attained.
4. Thermodynamic Impact
   • In terms of thermodynamics, enzymes reduce the activation energies of reactions, enabling them to occur more readily.
5. Substrate Conversion
   • Enzymes convert substrates (reactants at the beginning of a process) into different molecules, called products.
6. Metabolic Process Dependency
   • Almost all metabolic processes in the cell require enzymes to occur at rates fast enough to sustain life.
7. Enzyme-Mediated Pathways
   • The set of enzymes made in a cell determines which metabolic pathways occur in that cell.
8. Enzymology
   • The study of enzymes is called enzymology.
9. Biochemical Reaction Types
   • Enzymes are known to catalyze more than 5,000 biochemical reaction types.
10. Composition
    • Most enzymes are proteins, although a few are catalytic RNA molecules.

11. Specificity
    • Enzymes' specificity arises from their unique three-dimensional structures, with each enzyme catalyzing the reaction of a single type of molecule or a group of closely related molecules.

Enzyme Chemical Nature and Structure

Enzymes were traditionally believed to be exclusively proteins; however, since the 1980s, the catalytic capabilities of certain nucleic acids, known as ribozymes or catalytic RNAs, have challenged this notion.

• Protein Structure Composition: A large protein enzyme molecule comprises one or more amino acid chains connected by peptide bonds. The amino acid sequence dictates the characteristic folding patterns crucial to enzyme specificity. Changes such as variations in temperature or pH can lead to denaturation, potentially affecting enzymatic ability. Denaturation may or may not be reversible.Active Site Structure: The key to enzyme activity lies in the active site, a structure where substrate molecules bind and undergo chemical reactions. The active site consists of residues forming temporary bonds with the substrate (binding site) and residues catalyzing the substrate reaction (catalytic site). Typically, the active site is a groove or pocket located within the enzyme, either in a deep tunnel or between multimeric enzyme interfaces.
• Allosteric Regulation: Apart from the active site, enzymes have an allosteric site that binds an effector molecule, providing an additional mechanism for enzyme regulation. Allosteric modifications, often present in proteins with multiple subunits, allow one step of a reaction to regulate another. This flexibility in molecular interactions is beyond the highly specific active site.
• Cofactors and Holoenzymes: Enzymes may be associated with a non-protein cofactor, a direct participant in catalysis. Cofactors can be coenzymes (organic, dialyzable, thermostable, loosely attached) like vitamins or inorganic metal ions. The cofactor may be tightly or loosely bound to the enzyme, referred to as a prosthetic group when tightly connected. The entire active complex, including the protein and cofactor, is termed the holoenzyme.

Equation: 
Apoenzyme + Cofactor = Holoenzyme

Zymogen
A zymogen is an enzymatically inactive precursor of an enzyme, often a proteolytic enzyme (or proteinase). Some zymogens adopt the -ogen suffix in their names, like trypsinogen or pepsinogen, while others use the prefix pro-, as seen in pro-collagenase or pro-carboxypeptidase.

Naming and Classification of Enzymes

Enzymes play vital roles in biochemical processes, and their names often reflect their activities. However, due to naming ambiguities and the increasing number of discovered enzymes, a systematic classification system was established. Biochemists, through international agreement, adopted the Enzyme Commission (EC) system for naming and classifying enzymes.

Enzyme Commission (EC) System

The EC system classifies enzymes into six main divisions, each with subclasses, based on the type of reaction catalyzed. Each enzyme is assigned a four-part classification number, and a systematic name identifies the reaction it catalyzes. The numbering system proceeds with EC (enzyme commission):

1. Oxidoreductases (EC 1)

   • Catalyze oxidoreduction reactions.
   • Transfer electrons from one molecule (oxidant) to another (reductant).
   • Examples include oxidases, dehydrogenases, peroxidases, hydroxylases, and oxygenases.
     Example Reaction: A⁻ + B → A + B⁻

2. Transferases (EC 2)

   • Catalyze the transfer of specific functional groups (e.g., methyl or glycosyl groups) from one molecule (donor) to another (acceptor).
   • Examples include acetyltransferases, methylases, protein kinases, and polymerases.
     Example Reaction:  group + Yt ransferase X + Y group WhereX is the donor, Y is the acceptor, and "group" is the transferred functional group.

3. Hydrolases (EC 3)

   • Catalyze the hydrolysis of chemical bonds, typically dividing large molecules into smaller ones.
   • Examples include esterases, proteases, glycosidases, nucleosidases, and lipases.
     Example Reaction: A−B + H₂O→ A − OH + B − H

4. Lyases (EC 4)

   • Catalyze the breaking of various chemical bonds (C-C, C-O, C-N) by means other than hydrolysis.
   • Result in the formation of a double bond or a new ring.
     Example Reaction: ATP → cAMP + PPiATP → cAMP + PPi

5. Isomerases (EC 5)

   • Convert a molecule from one isomer to another, maintaining the same molecular formula but with a different physical structure.
   • Examples include triose phosphate isomerase and bisphosphoglycerate mutase.
     Example Reaction: A−B→B−A

6. Ligases (EC 6)

   • Catalyze reactions that join smaller molecules, making larger ones.
   • Involve energy-raising processes, often coupled with ATP hydrolysis.
   • Examples include tyrosine- tRNA ligase.

7. Example Reaction: Ab + C → A - C + b
   Example Enzyme:
   Tyrosine-tRNA Ligase: ATP + L-tyrosine + t-RNA →→ L-tyrosyl-tRNA + AMP + PPi

Specificity of Enzyme Action

Enzymes exhibit remarkable specificity in catalyzing reactions, making them invaluable in diagnostics and research. This specificity is crucial for understanding their role in biochemical processes. There are four main types of specificity:

1. Absolute Specificity

• Also known as high or substrate specificity.
• Enzymes catalyze only one particular reaction.
• Examples: a) Uricase - acts only on uric acid. b) Arginase - acts only on arginine. c) Carbonic anhydrase - acts only on carbonic acid. d) Lactase - acts on lactose.

2. Structural or Group Specificity

• Enzymes act on molecules with specific functional groups.
• Examples: a) Trypsin - hydrolyzes central peptide bonds with basic amino acids (arginine, lysine, histidine). b) Chymotrypsin - hydrolyzes central peptide bonds with aromatic amino acids. c) Aminopeptidase - hydrolyzes peripheral peptide bonds at the amino terminal of polypeptide chains.

3. Linkage Specificity

• Enzymes act on a specific type of chemical bond irrespective of the molecular structure.
• Examples: a) Amylase - acts on α 1-4 glycosidic bonds in starch, dextrin, and glycogen. b) Lipase - hydrolyzes ester bonds in various triglycerides.

4. Stereochemical Specificity

• Enzymes act on a particular steric or optical isomer.
• Examples: a) L-amino acid oxidase - acts only on L amino acids. b) D-amino acid oxidase - acts only on D amino acids. c) α-glycosidase - acts only on α-glycosidic bonds present in starch, dextrin, and glycogen.

Understanding the diverse specificities of enzymes provides insights into their applications in various biochemical pathways and contributes to their use as diagnostic and research tools.

Factors Affecting Enzyme Activity

The activity of enzymes is influenced by various environmental conditions, and changes in these conditions can significantly impact the rate of enzymatic reactions. Several factors play a role in regulating enzyme activity:

1. Temperature:

• Effect: Increasing temperature generally increases the rate of enzyme-catalyzed reactions due to elevated kinetic energy and more frequent collisions between molecules.
• Optimum Temperature: Each enzyme has an optimum temperature at which it functions most efficiently. Above the optimum temperature, the enzyme can denature, leading to a loss of activity.
• Example: Most human enzymes have an optimum temperature around 37.0 °C.

2. pH - Acidity and Basicity:

• Effect: pH measures the acidity or basicity of a solution, affecting enzyme activity. Enzymes have specific pH ranges (optimal pH) in which they function best.
• Optimum pH: Different enzymes have different optimum pH values. Extreme pH values can lead to denaturation of enzymes.
• Example: Pepsin functions optimally at a low pH (around 2) found in the stomach.

3. Concentration:

• Effect: Changes in enzyme and substrate concentrations impact the rate of reaction.
• A. Substrate Concentration: Increasing substrate concentration initially increases the rate, but saturation occurs when the enzyme is fully utilized.
• B. Enzyme Concentration: Increasing enzyme concentration generally increases the reaction rate until saturation is reached.

4. Cofactors:

• Definition: Cofactors are substances required by some enzymes for proper function.
• Types:
  1. Coenzymes: Organic molecules often containing vitamins.
  2. Inorganic Metal Ions: Act as enzyme activators.
  3. Prosthetic Groups: Coenzymes permanently bound to the enzyme.

5. Inhibitors:

• Effect: Inhibitors can either slow down or block enzymatic activity, providing a form of cellular control.
• A. Reversible Inhibitors:
  • Competitive: Structurally similar to the substrate, competing for the active site.
  • Non-competitive: Bind elsewhere on the enzyme, altering its shape and inhibiting the reaction.
• B. Irreversible Inhibitors: Bind covalently and permanently to the enzyme, preventing normal function.
• Example: Aspirin is an irreversible inhibitor of cyclooxygenase, an enzyme involved in prostaglandin synthesis.

Understanding these factors is crucial for manipulating enzyme activity for various applications, including diagnostics, research, and industrial processes.

Sources of Enzymes

Enzymes, crucial in various industrial processes, can be sourced from a variety of living organisms. The selection of sources is influenced by factors such as production cost, predictability of enzyme content, and the ease of obtaining raw materials. The major sources include microbes, animals, plants, and, more recently, transgenic organisms.

1. Enzymes from Microbial Sources:

• Advantages:
  • Abundant enzyme production.
  • Predictable and controllable enzyme content.
  • Low production cost.
  • Reliable supplies of raw materials.
• Microorganisms Used:
  • Aspergillus species
  • Bacillus species
  • Kluyveromyces (Saccharomyces) species
• Characteristics:
  • Genetic engineering allows easy manipulation for increased enzyme production.
  • Recovery, isolation, and purification processes are simpler compared to animal or plant sources.
• Examples of Commercially Produced Enzymes:
  • α-Amylase
  • Cellulase
  • Protease
  • Lipase
  • Pectinase
  • Phytase
  • Catalase
  • Insulinase

2. Enzymes from Animal and Plant Sources:

• Animal Sources:
  • Good sources for enzymes such as lipases, esterases, and proteases.
  • Examples include lysozyme obtained from hen eggs and rennet obtained from animal tissue.
• Plant Sources:
  • Certain plants serve as excellent sources for specific enzymes.
  • Examples include papain from papaya and bromelain from pineapple.
• Examples of Enzymes Obtained:
  • Papain
  • Bromelain
  • Lysozyme
  • Rennet
  • Trypsin
  • Chymotrypsin
  • Urokinase
  • Lactate dehydrogenase

3. Enzymes from Mammalian Cell Cultures:

• Potential for Commercial Production:
  • Possibility of direct production by mammalian cell cultures.
  • Mainly utilized for therapeutic enzymes due to cost constraints.
• Examples:
  • Tissue plasminogen activator (produced by cell cultures)
• Challenges:
  • High production costs are a significant constraint.

4. Transgenic Organisms:

• Transgenic Animals:
  • Used for producing therapeutic proteins.
  • Foreign genes are expressed in the mammary gland, facilitating secretion into milk.
• Transgenic Plants:
  • Ideal bioreactors for bulk enzyme production.
  • Combines low production costs of plant biomass with minimal purification requirements.
• Examples of Commercially Produced Enzymes:
  • α-Amylase
  • Xylanase
  • Phytase

Note: The selection of sources depends on factors such as cost-effectiveness, safety, and the specific application of the enzyme. Advances in genetic engineering have facilitated the optimization of enzyme production strains, contributing to the efficiency and economy of industrial enzyme production.

Enzyme Deficiency and Associated Health Issues

Enzymes play a crucial role in various bodily functions, and their depletion can lead to health disorders. Here are the causes of enzyme depletion and associated health issues:

Causes of Enzyme Depletion:

1. Pesticides and Chemicals: Exposure to pesticides and chemicals can deplete enzymes.
2. Hybridization and Genetic Engineering: Genetic modifications and hybridization processes may affect enzyme levels.
3. Bovine Growth Hormone: The use of growth hormones in animals may impact the enzymes present in animal products.
4. Pasteurization: The heat treatment of food during pasteurization can destroy enzymes.
5. Irradiated Food: Irradiation of food can lead to enzyme degradation.
6. Excess Intake of Fats: High consumption of unsaturated and hydrogenated fats may contribute to enzyme deficiencies.
7. Cooking at High Temperatures: Cooking food at high temperatures can degrade enzymes.
8. Microwaving: Microwaving may impact the enzymatic content of food.
9. Radiation and Electromagnetic Fields: Exposure to radiation and electromagnetic fields might affect enzyme function.
10. Geopathic Stress Zones: Living in geopathically stressed areas may contribute to enzyme depletion.
11. Fluoridated Water: Water containing fluoride may affect enzyme activity.
12. Heavy Metals: Exposure to heavy metals can lead to enzyme depletion.
13. Mercury Amalgam Dental Fillings: Dental fillings containing mercury may contribute to enzyme deficiencies.

Health Disorders Associated with Enzyme Deficiencies:

1. Protease Deficiency:

• Anxiety
• Low blood sugar
• Kidney problems
• Water retention
• Depressed immunity
• Bacterial and viral infections
• Cancer
• Appendicitis
• Bone problems (osteoporosis, arthritis, bone spurs)

2. Amylase Deficiency:

• Skin problems (rashes, hives, fungal infections, herpes, canker sores)
• Lung problems (asthma, bronchitis, emphysema)
• Liver or gall bladder disease

3. Lipase Deficiency:

• High cholesterol
• Obesity
• Diabetes
• Cardiovascular problems (hardening of the arteries)
• Chronic fatigue
• Spastic colon
• Dizziness

4. Cellulase Deficiency:

• Gas and bloating
• Acute food allergies
• Facial pain or paralysis
• Candidiasis (bowel and vaginal yeast infections)

Additional Enzyme Deficiencies:

• Sucrase, Lactase & Maltase Deficiency:
  • Symptoms include mental and emotional problems, abdominal cramps, diarrhea, and allergic reactions.
• Combination Deficiency:
  • Individuals with more than one deficiency may experience severe digestive issues, Crohn's disease, Colitis, and Irritable Bowel Syndrome.
• Gluten Intolerance:
  • Associated with Celiac Disease, Malabsorption Syndrome, and Crohn's Disease. Can lead to sugar intolerance due to injury to brush border cells.

Enzyme deficiencies and associated health issues highlight the importance of maintaining optimal enzyme levels for overall well-being. Research in the field of food enzymes continues to uncover new insights into their roles in health and disease.

Significance of Enzymes

Catalysts for Chemical Reactions:​

• Enzymes are essential for every chemical reaction in the body, serving as catalysts.
• Connected to every organ, enzymes regulate detoxification and energy production within cells.

Digestion and Nutrient Delivery:

• Required for food digestion and the delivery of vitamins and minerals.

Prevention of Putrefaction and Fermentation:

• Prevent partially digested proteins, carbohydrates, and fats from putrefying or fermenting in the body.

Live Energy of Organisms:

• Described as the 'live energy' of all organisms.

Importance of Enzyme Supplementation:

• Cooking, chemicals, and food processing destroy natural enzymes, making enzyme supplements crucial.

Plant-Based vs. Animal-Based Enzymes:

• Plant-based enzymes become active upon entering the body, while animal sources are active only in the small intestine in an alkaline setting.

Assimilation of Nutrients:

• Ensure the assimilation of vitamins, minerals, proteins, fats, and carbohydrates.

Support for Gall Bladder Function:

• Enzymes aid gall bladder function, reduce inflammation, alleviate lactose intolerance, and aid general digestion.

Therapeutic Uses of Enzymes:

Assay of Plasma Enzymes:

• Used routinely in clinical biochemistry for diagnostic purposes.
• Enzymes like Lactate Dehydrogenase (LDH), Alanine Transaminase (ALT), Alkaline Phosphatase (ALP), Aspartate Transaminase (AST), and Creatine Kinase (CK) help identify damaged cells.

Inborn Errors of Metabolism:

• Genetic diseases due to defects in genes coding for enzymes.
• Diagnosis involves observing a build-up of metabolic intermediates in plasma or urine.

Enzymes as Reagents in Clinical Biochemistry:

• Employed in solution medium, immobilized on a surface, or as labels in immunoassay techniques.
• Used in assays for various substances such as glucose, lactate, pyruvate, urea, and cholesterol.

Application in Forensic Science:

• Seminal acid phosphatase activity for semen identification.
• Detection of saliva through amylase activity.
• Monitoring ethanol levels using alcohol dehydrogenase.
• Enzyme assays for the presence of agrochemicals, pharmaceuticals, and HIV infections.
• Polymorphic enzymes used for establishing individual identity.

Enzymes in Digestion:

• Aid digestion (e.g., amylases, proteases, lipase).

Industrial Applications:

Textile Industry:​

• Amylase used as a softening agent.
• Proteolytic enzymes for leather processing.

Paper Manufacturing:

• Endoxylanases used for bleaching wood pulp.

Organic Compound Manufacturing:

• Bacterial enzymes for producing acetone, butanol, lactic acid, etc.

Food Industry:

• Papain for meat tenderizing.
• Rennin for cheese manufacturing.
• Yeast enzymes in beverage production.

Baking:

• Use of amylases, proteases, glucose oxidase, and lipase in improving dough handling and bread quality.

Alcohol Industry:

• Enzymes used in fermentation for beer brewing.

Fruit Juices:

• Pectin-degrading enzymes used to maximize juice production.

Washing Powders:

• Proteases, amylases, cellulase in detergents for stain removal.

Textile Industry:

• Proteases for de-hairing in leather processing.
• Cellulase for bio-polishing in fabric treatment.

Contact Lens Solution and Pet Toothpaste:

• Enzymes used in contact lens solution and pet toothpaste.

Immobilized Enzymes:

Advantages of Immobilization:​

• Allows enzyme reuse and continuous use.
• Stabilizes enzymes.

Methods of Immobilization:

• Adsorption, covalent linkage, cross-linking, matrix entrapment, and encapsulation.

Applications:

• Glucose syrup production from starch using immobilized enzymes is a vital food industry process.