B

Week 6 Lecture 4 - Enzymes

Enzymes

Key Concepts

  • Active Site:
    • The specific region of an enzyme where the substrate binds and catalysis occurs.
  • Induced Fit:
    • The change in shape of the enzyme's active site to better accommodate the substrate after binding.
  • Activation Energy (EA):
    • The energy barrier that must be overcome for a reaction to occur.
    • Enzymes lower E_A to speed up reactions.
  • Optimal pH and Temperature:
    • Enzymes function best within a specific range of pH and temperature.
  • Enzyme Inhibitors:
    • Substances that reduce or prevent enzyme activity.
    • Types: Irreversible, Reversible (Competitive, Non-competitive).
  • Regulation:
    • Mechanisms to control enzyme activity.
    • Types: Genetic, Allosteric, Covalent.
  • Feedback Inhibition:
    • A process where the end product of a metabolic pathway inhibits an earlier enzyme in the pathway.

Introduction to Enzymes

  • Biological catalysts that accelerate reactions.
  • Substrate-specific, catalyzing only particular reactions.
  • Highly regulated for metabolic control.

Enzymes and Activation Energy

  • Even exergonic (spontaneous) reactions require overcoming an energy barrier (E_A).
  • Enzymes lower E_A for both exergonic and endergonic reactions, speeding up the reaction.

Active Site and Catalytic Cycle

  • The active site is where the substrate binds.
  • Chemical and physical interactions at the active site lower E_A.
  • Shape match between active site and substrate ensures specificity (initially described as "lock and key").
  • The active site can change shape upon substrate binding, known as "induced fit".

Enzyme Catalysis Strategies

  • Enzymes may form temporary covalent bonds with the substrate during catalysis.

Lysozyme: A Specific Example

  • Lysozyme is an enzyme present in tears.
  • Breaks down oligosaccharides in bacterial cell walls.
  • Important for preventing eye infections.

Factors Affecting Reaction Rates

  • Temperature:
    • Below optimum: fewer collisions between enzyme and substrate.
    • Above optimum: enzyme denatures (loses its structure and function).
  • pH:
    • Deviations from optimum pH can protonate/deprotonate amino acid residues in the active site, affecting activity.

Cofactors

  • Some enzymes require cofactors for catalysis.
    • Inorganic ions (e.g., Fe, Zn, Cu).
    • Complex organic molecules (coenzymes) such as vitamins, NAD+, and FAD.

Enzyme Inhibition

  • Inhibitors can be drugs, toxins, or normal metabolites that regulate enzyme activity.
  • Irreversible Inhibitors:
    • Bind covalently to the enzyme, often to a serine residue.
  • Reversible Inhibitors:
    • Competitive: Bind to the active site, blocking substrate binding.
    • Non-competitive: Bind away from the active site, altering enzyme shape and activity.

Examples of Enzyme Inhibitors

  • Penicillin:
    • An irreversible inhibitor of transpeptidase, an enzyme essential for bacterial cell wall synthesis.
    • Discovered by Fleming in 1928 from the Penicillium notatum mold.
  • Viagra (Sildenafil):
    • A reversible inhibitor of cGMP specific phosphodiesterase type 5.
    • Affects pollen tube growth in plants as well as humans

Enzyme Control Mechanisms

  • Allosteric Control:
    • Molecule (metabolite) binds away from the active site.
    • Can stabilize the active form (allosteric activator) to switch a metabolic pathway on.
    • Can stabilize the inactive form (allosteric inhibitor) to switch a metabolic pathway off.
    • Inhibitor is often the end product of a metabolic pathway (feedback inhibition).
    • Co-operativity: Substrate binding at one active site affects other active sites in quaternary enzymes.
  • Covalent Control:
    • Enzymes can be regulated by phosphorylation and dephosphorylation.
    • Kinases: Transfer phosphate groups (P) from ATP to proteins.
    • Phosphatases: Remove phosphate groups (P) from proteins.
    • Phosphorylation can activate or deactivate enzymes.
  • Genetic Control:
    • Controls whether enzymes are present or not.
    • Slower than allosteric and covalent control (seconds to minutes).

Feedback Inhibition

  • The end product of a metabolic pathway inhibits an enzyme that catalyzes an earlier reaction in the pathway.
  • The end product can also inhibit the expression of the enzyme itself, involving repressor proteins.

Enzyme Control Example: Wood Frogs

  • Glycogen phosphorylase:
    • Releases glucose from glycogen.
    • Found in liver and muscle (isozymes).
    • Regulation: both allosteric and covalent.
    • Covalent control involves phosphorylation via a protein kinase.
  • Wood frogs release glucose (by increasing glycogen phosphorylase activity) as they begin to freeze in winter, acting as an antifreeze along with urea.
  • Alaskan wood frogs survive colder temperatures better than Ohio wood frogs due to higher kinase (PKA) and glycogen phosphorylase activity.
  • More glycogen phosphorylase activity leads to more glucose released from the liver, helping them survive colder temperatures.

Enzyme Compartmentalization

  • Enzymes are located in specific areas within cells where the reactions they catalyze need to occur.
  • In eukaryotes, enzymes involved in the citric acid cycle are found in the mitochondrial matrix, where the citric acid cycle takes place.