Enzyme Function, Regulation & Catalysis

Enzyme Catalysis & Thermodynamics

• Enzymes are biological catalysts that:
  • Lower the activation energy (E_a) required for a reaction to proceed.
  • Accelerate the reaction rate, allowing cellular processes to occur on biologically useful time-scales.
• Crucially, enzymes do NOT change the overall free-energy change of a reaction.
  • \Delta G ("change in free energy") is identical with or without the enzyme present.
  • Exam cue: “Same \Delta G, smaller E_a” is a classic test question.
• The lowered activation barrier stabilizes the transition state, making it easier for reactants to proceed to products.

Active-Site Structure & Formation

• Proteins (enzymes) fold so that specific amino-acid residues converge in 3-D space.
  • This cluster of residues forms the active site.
  • Folding is essential; an unfolded enzyme cannot form a functional active site.
• Substrate binds to the active site through complementary shape, charge, or hydrogen-bond interactions.
  • Binding often induces a slight conformational change ("induced fit") that further stabilizes the transition state.

Factors Affecting Enzyme Activity

Substrate Concentration

• Reaction rate increases with substrate concentration until the enzyme becomes saturated (reaches V_{\max}).
• At low [S], rate ≈ proportional to [S]; at high [S], rate plateaus (all active sites occupied).
• Practical implication: cells can regulate metabolism by adjusting substrate availability.

pH

• Each enzyme has an optimal pH where its charged residues and structure are most stable.
  • Example: Pepsin (stomach protease) functions best in highly acidic conditions (pH ≈ 1–2).
• Deviations from the optimum can:
  • Alter ionization of active-site residues.
  • Change protein folding → decreased activity or denaturation.

Temperature

• Enzymes possess an optimal temperature, balancing kinetic energy and structural stability.
  • Too low → insufficient molecular collisions.
  • Too high → thermal agitation unfolds (denatures) the protein.
• Denaturation = loss of tertiary structure → active site destroyed → enzyme inactive.
  • Example context: some human cellular regions (e.g., slightly warmer mitochondria) may favor enzymes with a slightly higher optimum.

Cofactors & Coenzymes ("Helpers")

• Cofactors: inorganic ions (e.g., Ca^{2+}, Mg^{2+}, Zn^{2+}) that bind the enzyme and assist catalysis.
  • Often induce conformational changes that fashion or stabilize the active site.
  • Supplements marketed as “zinc” or “magnesium” exploit this biochemical role.
• Coenzymes: small organic molecules, frequently vitamin-derived (e.g., NAD⁺, FAD, CoQ10).
  • May transiently carry electrons, atoms, or functional groups between enzymes.
• Without the required cofactor/coenzyme, many enzymes are apoenzymes (inactive); binding converts them into the active holoenzyme form.

Enzyme Regulation by Inhibitors & Activators

• Competitive inhibitor
  • Resembles the substrate; binds active site.
  • Competes directly, lowering the effective number of available active sites.
  • Can be overcome by increasing [S].
• Non-competitive inhibitor
  • Binds at an allosteric site (not the active site).
  • Alters enzyme conformation so the active site functions poorly or not at all.
  • Increasing [S] does not fully restore activity.
• Inhibitors may be:
  • Reversible (dissociate) or irreversible (covalently attach, permanently inactivating the enzyme).
• Activators bind allosteric sites to increase enzyme activity, often by stabilizing an active conformation.

Feedback Inhibition Example: Threonine → Isoleucine Pathway

• Substrate: \text{Threonine (Thr)} – specifically the 309-threonine mentioned in the lecture.
• Enzyme 1: Threonine dehydratase converts Thr → Product 1 (P1), an intermediate.
• Sequence: P1 → P2 → P3 → P4 → Isoleucine (end product) across five enzymatic steps.
• Negative feedback (allosteric inhibition):
  • Excess isoleucine binds threonine dehydratase at an allosteric site.
  • Conformational change shuts down the first step, slowing further isoleucine production.
  • Protects cell from over-accumulation and conserves energy/resources.

Activation-Energy Diagram (Visual Recap)

• Two curves share identical start & end free energies.
  • No-enzyme curve peaks at high E_a.
  • Enzyme-catalyzed curve peaks lower.
• Arrow highlights that E_a is the only difference; \Delta G remains unchanged.
• Interpretation: Enzymes accelerate reactions; they do not alter thermodynamic favorability.

Key Exam & Real-World Connections

• Memorize: “Enzymes lower E_a, not \Delta G.”
• Recognize examples in nutrition:
  • Vitamin/cofactor supplements (e.g., CoQ10 labels in grocery store aisles) aim to enhance enzymatic efficiency.
• Understand physiological relevance:
  • pH-dependent enzymes across organs (pepsin in stomach vs. alkaline phosphatases in intestine).
  • Temperature stress (fever) can denature proteins, explaining clinical symptoms.
• Ethical angle: Over-supplementation of cofactors can disrupt homeostasis; regulation is vital.
• Conceptual link: Negative-feedback loops mirror broader homeostatic principles discussed in earlier lectures (e.g., hormone regulation).