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Enzymes

Unit Overview

UNIT 1 MODULE 1: CELL AND MOLECULAR BIOLOGY

This module focuses on enzymes, which are crucial biological catalysts facilitating metabolic reactions.

Objectives

  • To explain that enzymes are globular proteins that catalyze metabolic reactions.
  • To define metabolism, anabolism, and catabolism.
  • To explain the mode of action of enzymes through concepts such as the active site, enzyme-substrate complex, lowering of activation energy, and specificity.
  • To explain the properties of enzymes.
  • To elaborate on the induced-fit hypothesis.
  • To discuss the effects of pH, temperature, enzyme concentration, and substrate concentration on enzyme action.
  • To construct and interpret graphs showing the effects mentioned above on enzyme actions.
  • To explain competitive and non-competitive inhibition's effects on enzyme activity.
  • To use examples, including succinic dehydrogenase, nicotine, and insecticides (pyrethroids) as enzyme inhibitors.
  • To investigate and explain temperature and substrate concentration effects on enzyme-catalyzed reactions.

Introduction to Enzymes

  • Biological Catalysts: Enzymes are biological catalysts mainly composed of globular proteins, characterized by their specific tertiary structure. They lower the activation energy of reactions, increase the rate of metabolic reactions, and exhibit specificity, typically acting on one reaction only.
  • Non-Protein Catalysts: Include ribozymes (RNA molecules) and abzymes (antibodies), which also facilitate chemical reactions.

What Are Globular Proteins?

  • Globular proteins possess 3D structures that typically form ball-like shapes with hydrophobic (water-repelling) regions sequestered inward and hydrophilic (water-attracting) regions on the surface, making them soluble in water. They play various metabolic roles, including acting as enzymes, plasma proteins, and antibodies in mammals.

Nomenclature of Enzymes

  • The International Union for Biochemical Societies has established a systematic classification for enzymes:
      - Enzymes are named based on the substrate they act upon and the type of reaction they catalyze, usually ending with the suffix -ase (e.g., maltase, sucrase, amylase).

Naming Conventions

  • Enzymes are often named for the reactions they catalyze:
      - Sucrase breaks down sucrose,
      - Protease breaks down proteins,
      - Lipase breaks down lipids,
      - DNA polymerase adds nucleotides to a DNA strand.

Classification of Enzymes by Function

  1. Oxidoreductases: Transfer hydrogen atoms, electrons, or oxygen from substrates to acceptor molecules (e.g., oxidases, dehydrogenases).
  2. Transferases: Transfer small groups of atoms from one substrate to another (e.g., transaminases).
  3. Hydrolases: Split chemical bonds via hydrolysis, involving water (e.g., lipases act on ester linkages in lipids).
  4. Isomerases: Catalyze internal rearrangements within substrates (e.g., phosphoglucomutase).

Metabolism

  • Metabolism: Refers to the sum of all chemical reactions occurring within a living cell, providing energy for vital processes and synthesizing new organic material. Enzymes regulate metabolic pathways by altering substrates to yield end products, ensuring metabolic efficiency.
  • Metabolic Pathways: Can be classified as anabolic or catabolic.
      - Anabolic Pathways: Require energy to synthesize smaller molecules into larger ones (e.g., synthesizing glycogen from glucose).
      - Catabolic Pathways: Release energy by breaking down larger molecules into smaller components (e.g., food digestion).

Enzyme Functionality

How Enzymes Work
  • Most cellular reactions require high activation energy, which could be detrimental to cells. Enzymes lower this energy threshold, facilitating reactions at lower temperatures.
Activation Energy
  • Activation Energy (E$_{a}$): The initial energy required to initiate a chemical reaction. It represents the energy barrier that reactants must overcome to transform into products.
Energy Profile of Reactions
  • Catalyzed reactions exhibit lower activation energies compared to uncatalyzed reactions. Enzymes provide a favorable microenvironment for reactions without altering the overall free energy change of the substrates and products.
Mechanism of Action
  1. Substrate Binding: Substrates bind to the active site of the enzyme, forming the enzyme-substrate complex.
  2. Induced Fit Model: Upon substrate interaction, the enzyme undergoes conformational changes to optimize fit and promote the reaction is known as the "induced-fit hypothesis." This suggests that both the enzyme and substrate contribute to the precise fitting required for catalysis, enhancing reaction specificity and efficiency.
  3. Product Formation: After the reaction, products are released, and the enzyme is free to catalyze subsequent reactions.

Active Site

  • Active Site: A specific region on the enzyme where substrate molecules bind. The active site is characterized by a unique arrangement of amino acid residues that enhances interaction with the substrate.
  • The specificity of the active site is determined by:
      - Different side chains,
      - Amino acid modifications,
      - The resulting final structure of the enzyme.

Substrate Characteristics

  • The substrate fits the active site in a complementary way regarding shape, size, solubility, and charge. It is typically smaller than the enzyme but designed for specificity toward that active site.

Mechanisms of Enzyme Action

Models of Enzyme Action
  1. Lock-and-Key Hypothesis: Suggests that the active site has a rigid structure perfectly complementary to the substrate, resembling a lock and key. Only specifically shaped substrates can bind effectively to the enzyme.
  2. Induced-Fit Hypothesis: Proposes a more flexible interaction, where binding of the substrate induces a conformational change in the enzyme that enhances fit and catalytic efficiency.
Catalytic Cycle Example (Sucrase)
  1. Enzyme available with an empty active site.
  2. Substrate (sucrose) enters the active site and binds through weak bonds.
  3. Enzyme-substrate complex forms via an induced fit.
  4. Substrate is converted to products (glucose and fructose) within the active site.
  5. Products are released, making the active site available for new substrate molecules.

Features of Enzymes

Recyclability
  • Enzymes remain unchanged following catalysis, enabling them to undergo multiple reaction cycles.
Cofactors
  • Many enzymes require additional non-protein components (cofactors) for optimal activity:
      - Inorganic Ions: Such as Zn$^{2+}$, Fe$^{2+}$, Mg$^{2+}$ essential for enzyme structure and activity.
      - Prosthetic Groups: Organic molecules tightly bound to the enzyme (e.g., FAD).
      - Coenzymes: Organic molecules that loosely associate with enzymes (e.g., NAD, derived from vitamins).
Reversible Reactions
  • Enzyme-catalyzed reactions can proceed in both directions depending on the concentrations of substrates and products, achieving a state of equilibrium.
Inhibition
  • Inhibitors: Molecules that decrease enzyme activity, categorized into:
      - Competitive Inhibitors: Compete with substrates for the active site, preventing enzyme-substrate complex formation.
      - Non-competitive Inhibitors: Bind to an alternative site on the enzyme, altering its ability to catalyze reactions regardless of substrate concentration.
      - Allosteric Regulation: Involves allosteric sites affecting the enzyme's active site and activity inversely depending on whether activators or inhibitors are bound.
Specificity
  • Enzymes exhibit a range of specificity, typically catalyzing one specific reaction. For example, catalase exclusively disassembles hydrogen peroxide, while pancreatic lipase targets a variety of lipids.

Factors Affecting Enzyme Activity

  1. Substrate & Enzyme Concentration: Reaction rates increase with substrate concentration until saturation occurs.
  2. Temperature: Enzymes function optimally within a specific temperature range, usually around 37$^{ ext{°C}}$ for human enzymes, with activity declining at extremes.
  3. pH Levels: Enzymes are sensitive to pH changes, with extreme pH potentially leading to denaturation and loss of functionality.

Summary

  • Enzymes are indispensable for biological processes, acting as catalysts to accelerate reactions by significantly lowering activation energy requirements. Their specificity, structural features such as active sites, and interaction dynamics with substrates and inhibitors are fundamental to their functional role in metabolism and biochemical pathways.