Enzyme Structure and Catalytic Mechanisms (1A) - Bio & Biochem

1. What does a low $K_m$ indicate about an enzyme for its substrate?

   High apparent affinity (less substrate needed to reach $\frac{V_{max}}{2}$). Lower $K_m$ means stronger binding, requiring less substrate for significant activity.

2. What is a cofactor in enzyme function?

   A nonprotein helper required for activity (metal ion or organic molecule). Cofactors provide essential chemical functionalities that the protein component lacks for catalysis.

3. What is the transition state in an enzyme-catalyzed reaction?

   The highest-energy, unstable intermediate along the reaction pathway. It represents the peak energy barrier that must be overcome for reactants to form products.

4. What are the effects of noncompetitive (pure) inhibition on $K_m$ and $V_{max}$?

   $V_{max}$ decreases; $K_m$ unchanged. Inhibitor reduces functional enzyme concentration without impacting substrate binding affinity.

5. What is the definition of $V_{max}$ for an enzyme?

   Maximum rate when enzyme active sites are saturated with substrate. $V_{max}$ quantifies the enzyme's full catalytic capacity when all sites are occupied.

6. What are the effects of uncompetitive inhibition on $K_m$ and $V_{max}$?

   Both $K_m$ and $V_{max}$ decrease. Apparent affinity increases, but overall catalytic capacity is reduced due to trapped complexes.

7. What is an apoenzyme and what is a holoenzyme?

   Apoenzyme: protein alone; holoenzyme: apoenzyme plus required cofactor(s). Apoenzyme lacks cofactors and is inactive; holoenzyme is the complete, functional form.

8. What is the active site of an enzyme?

   The region that binds substrate and performs catalysis. This specific pocket on the enzyme facilitates substrate interaction and chemical transformation.

9. What are the effects of competitive inhibition on $K_m$ and $V_{max}$?

   $K_m$ increases; $V_{max}$ unchanged. Inhibitor decreases apparent affinity but maximum velocity is achievable with excess substrate.

10. What is the induced-fit model of enzyme-substrate binding?

    Substrate binding triggers a conformational change that improves fit. Enzyme flexibility allows adjustment to substrate shape, enhancing binding specificity and catalytic efficiency.

11. What parameter best represents catalytic efficiency for comparing enzymes?

    $\frac{k_{cat}}{K_m}$. This ratio integrates turnover and affinity, enabling comparison of enzymes under non-saturating conditions.

12. Which statement is correct: enzymes change $K_{eq}$ or enzymes change $E_a$?

    Enzymes change $E_a$ (decrease it); they do not change $K_{eq}$. Enzymes accelerate both forward and reverse reactions equally, preserving equilibrium but reducing energy barrier.

13. What is the definition of turnover number $k_{cat}$?

    Catalytic cycles per enzyme per second at saturation: $k_{cat}=\frac{V_{max}}{[E]_T}$. $k_{cat}$ measures enzyme efficiency by quantifying substrate conversions per unit time at saturation.

14. What is the lock-and-key model of enzyme-substrate binding?

    Active site is preformed and complementary to the substrate shape. Rigid enzyme structure ensures precise substrate recognition without conformational changes during binding.

15. Identify the type of inhibition: inhibitor binds only free enzyme at active site.

    Competitive inhibition. Inhibitor competes with substrate for the active site, reducing available enzyme for catalysis.

16. What catalytic mechanism uses proton donation/abstraction by active-site residues?

    General acid-base catalysis. Active-site amino acids act as acids or bases to stabilize intermediates via proton transfer.

17. What is the difference between a coenzyme and a prosthetic group?

    Coenzyme binds transiently; prosthetic group is tightly or covalently bound. Binding duration distinguishes transient helpers from permanently integrated ones in enzyme structure.

18. Identify the type of inhibition: inhibitor binds only the $ES$ complex.

    Uncompetitive inhibition. Inhibitor stabilizes the enzyme-substrate complex, preventing product release.

19. Identify the type of inhibition: inhibitor binds equally well to $E$ and $ES$ at an allosteric site.

    Noncompetitive (pure) inhibition. Binding at a separate site affects enzyme function without altering substrate affinity.

20. What is the definition of an enzyme in biochemical terms?

    A biological catalyst that increases reaction rate without being consumed. Enzymes accelerate biochemical reactions by lowering activation energy while remaining unaltered post-reaction.

21. What is the Michaelis constant $K_m$ in Michaelis-Menten kinetics?

    Substrate concentration where $v_0 = \frac{V_{max}}{2}$. $K_m$ reflects enzyme-substrate affinity, indicating half-maximal velocity substrate level.

22. State the Michaelis-Menten equation for initial velocity $v_0$.

    $v_0 = \frac{V_{max}[S]}{K_m + [S]}$. This hyperbolic equation models enzyme kinetics under steady-state assumptions for single-substrate reactions.

23. What is the primary way enzymes increase reaction rate?

    They lower the activation energy $E_a$ by stabilizing the transition state. By reducing $E_a$, enzymes increase the fraction of molecules with sufficient energy to react.

24. Which thermodynamic quantity is unchanged by enzyme catalysis: $\Delta G$ or $E_a$?

    $\Delta G$ is unchanged; $E_a$ is decreased. Enzymes affect reaction kinetics but not the overall free energy change or equilibrium position.

25. What catalytic mechanism uses a transient covalent enzyme-substrate intermediate?

    Covalent catalysis. Temporary bond formation facilitates reaction by altering substrate reactivity.

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