Enzymes Study Notes

Enzymes

UNIT 1 MODULE 1: CELL AND MOLECULAR BIOLOGY

Objectives

• To explain that enzymes are globular proteins that catalyse metabolic reactions.
• To define metabolism, anabolism and catabolism.
• To explain the mode of action of enzymes in terms of:
    - active site
    - enzyme and/or substrate complex
    - lowering of activation energy
    - enzyme specificity
• To explain the properties of enzymes.
• To explain the induced-fit hypothesis.
• To explain the effects of:
    - pH
    - temperature
    - enzyme concentration
    - substrate concentration
    on enzyme action.
• To construct and interpret graphs showing the effects of pH, temperature, enzyme concentration, and substrate concentration on enzyme action.
• To explain the effects of competitive and non-competitive inhibitors on enzyme activity.
• To use succinic dehydrogenase, nicotine, and insecticides (pyrethroids) as examples of enzyme inhibitors.
• To investigate the effects of temperature and substrate concentration on enzyme-catalyzed reactions, and explain these effects.

Introduction

• Enzymes as Biological Catalysts:
    - Enzymes are primarily globular proteins characterized by a specific tertiary shape.
    - There are also non-protein catalysts, including ribozymes (RNA molecules) and abzymes (antibodies).
    - Enzymes facilitate chemical reactions by increasing the rate of metabolic reactions and lowering activation energy.
    - Almost all biological reactions are mediated by enzymes, which are generally specific to a particular reaction.

What are Globular Proteins?

• Structure of Globular Proteins:
    - Globular proteins possess three-dimensional structures that generally form ball-like shapes, with hydrophobic regions oriented towards the center and hydrophilic regions facing outward, making them soluble in water.
    - They typically fulfill metabolic roles, functioning as enzymes in various organisms, plasma proteins, and antibodies in mammals.

Nomenclature of Enzymes

• International Classification:
    - Enzymes are named based on the substrate they act upon and the reaction they catalyze, culminating in the suffix -ase.
    - Examples include maltase, sucrase, and amylase.

Naming Conventions

• Examples of Enzyme Functions:
    - Sucrase: Breaks down sucrose.
    - Protease: Breaks down proteins.
    - Lipase: Breaks down lipids.
    - DNA Polymerase: Synthesizes DNA by adding nucleotides to DNA strands.

Classification of Enzymes by Function

• Types of Enzymes:
    - Oxidoreductases: Transfer hydrogen atoms, electrons, or oxygen atoms from substrates to acceptor molecules (e.g., oxidases, dehydrogenases).
    - Transferases: Transfer small groups of atoms from one substrate to another (e.g., transaminases).
    - Hydrolases: Split chemical bonds by hydrolysis (e.g., lipases that work on ester linkages in lipids).
    - Isomerases: Catalyze internal atom rearrangement in substrates (e.g., phosphoglucomutase).

Metabolism

• Definition of Metabolism:
    - Metabolism refers to the sum of chemical reactions within each living organism's cells, providing energy for essential processes and synthesizing new organic material.
• Role of Enzymes in Metabolism:
    - Enzymes regulate metabolic pathways, altering substrates at each step to yield the final products.

Anabolic and Catabolic Pathways

• Types of Metabolic Pathways:
    - Anabolic Pathways: Require energy to synthesize larger molecules from smaller ones (biosynthesis).
      - Example: Synthesis of glycogen from glucose.
    - Catabolic Pathways: Release energy through the breakdown of large molecules into smaller ones (degradation).
      - Example: Digestion of food, facilitated by various enzymes for nutrient absorption in the small intestine.
• Reversibility of Pathways:
    - Metabolic pathways can be either reversible or irreversible, with most being reversible.

Enzymes – How They Function

• Activation Energy:
    - High temperatures are generally required for most cellular reactions, which can be damaging.
    - Activation energy is the energy required to initiate a chemical reaction, serving as the necessary push for the reaction to occur.

Energy Profile of Reactions

• Activation Energy Visualization:
    - A typical energy profile shows that an uncatalyzed reaction requires a higher activation energy compared to a catalyzed reaction.
    - Enzymes lower activation energy and thus increase reaction rates by providing a more favorable microenvironment for reactions, without altering the free energy of the reactants and products.

Active Site

• Overview of Active Sites:
    - The active site consists of a sequence of 3 to 12 specific amino acids located primarily on the enzyme's surface for accessibility.
    - Characterized by various chemical groups and bonds, the active site ensures that only complementary substrates interact with the enzyme, attributable to the specific three-dimensional protein structure formed from primary, secondary, and tertiary configurations.

Lock-and-Key and Induced-Fit Hypotheses

• Lock-and-Key Hypothesis:
    - Proposes a rigid active site shape that perfectly matches the substrate, analogous to a key fitting a lock.
    - Only substrates with compatible shapes can form an enzyme-substrate complex, but the model is limited and not universal to all enzyme functions.

• Induced-Fit Hypothesis:
    - Represents a more dynamic scenario where the active site is flexible and adjusts to accommodate the substrate, enhancing catalytic efficiency and broadening substrate specificity.
    - Proposed that the interaction can, therefore, lead to a more optimized fit and subsequent formation of the enzyme-substrate complex before product release.

Principle of Enzyme Action

• Mechanics of Enzyme Function:
    - Enzymes enhance reaction rates by:
      - Bringing molecules into optimal proximity and orientation.
      - Weakening critical bonds within the substrate to facilitate reaction.
      - Reducing the energetic requirement for reactions to occur.
      - Remaining chemically unaltered and available for repeated use.

Features of Enzymes

• Recyclable and Specific:
    - Enzymes are recyclable, remaining unchanged post-reaction, and can re-engage with new substrates.
    - They exhibit specificity, often catalyzing only one reaction type or closely related reactions.
• Cofactors:
    - Some enzymes necessitate non-protein components (cofactors) for optimal functionality, categorized as:
      - Inorganic Ions (e.g., $ext{Zn}^{2+}, ext{Fe}^{2+}, ext{Mg}^{2+}$) that provide structural orientation.
      - Prosthetic Groups (e.g., FAD), organic substances tightly bound to enzymes.
      - Coenzymes (e.g., NAD, NADP) which transiently associate with enzymes to aid in the reaction process.

Enzyme Inhibition

• Opposition of Enzyme Activity:
    - Inhibition occurs when molecules reduce enzymatic reaction rates, encompassing:
      - Competitive Inhibition: Compounds with similar structures vie for the active site, preventing substrate access and formation of products.
      - Non-competitive Inhibition: Inhibitors bind to regions other than the active site, altering the enzyme's conformation and blocking substrate fit, with no effect from substrate concentration changes.
      - Allosteric Regulation: Molecules binding to allosteric sites alter catalytic efficiency by modifying the active site structure.

Factors Affecting Enzyme Activity

• Concentration Effects:
    - Increases in substrate or enzyme concentration can enhance reaction rates until saturation is reached (Vmax).
    - Enzymes function optimally within specific temperature and pH ranges—temperatures exceeding 60°C can denature enzymes, and extreme pH levels can disrupt enzyme function.

Summary of Enzyme Dynamics

• Enzymes serve as critical biological catalysts, expediting the majority of chemical reactions in cells by lowering activation energy, essential for meeting cellular metabolic demands. Their structure, particularly the active site, determines their specificity and facilitated reactions during substrate binding. By understanding enzyme function, including mechanisms of inhibition and regulating conditions, comprehensive insights into metabolic processes can be achieved.