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.