Enzyme structure and function Knowledge-Based Study

Study notes

1. What Are Enzymes?

   Enzymes are biological catalysts that accelerate chemical reactions in living organisms without being consumed or permanently altered in the process. Nearly all enzymes are globular proteins consisting of one or more polypeptide chains folded into unique, highly specific three-dimensional conformations.

   Lowering Activation Energy

   Every chemical reaction requires an initial input of energy to break chemical bonds in the reactant molecules, termed the activation energy ($E_a$). By stabilizing the transition state of the reaction, enzymes substantially reduce this energy barrier.

   • Thermodynamic Constants: Enzymes accelerate both forward and reverse rates equally to reach equilibrium faster, but they do not alter the free energy change ($\Delta G$) of the reaction.
   • Reusability: Because enzymes are not consumed during catalysis, a single enzyme molecule can process thousands of substrate molecules per second.

   The Active Site

   Enzymes interact with specific reactant molecules called substrates at a specialized pocket or groove known as the active site. The active site is formed by a small number of amino acid residues that are brought together by the folding of the tertiary or quaternary structure.

   Models of Substrate Binding

   Two primary historical and modern models describe enzyme-substrate binding:

   1. Lock-and-Key Model: Proposed by Emil Fischer, this model suggests that the shape of the substrate and the active site are preformed and fit together with rigid, exact complementarity.
   2. Induced-Fit Model: Proposed by Daniel Koshland, this refined model indicates that the active site is flexible. Binding of the substrate induces conformational changes in the enzyme, aligning catalytic groups into precise orientation and straining substrate bonds.

   How Enzymes Facilitate Catalysis

   Once an enzyme-substrate complex (ES) is formed, the active site uses specific chemical strategies to convert substrates into products:

   • Orientation: Holding two substrates in the optimal spatial arrangement for a reaction to occur.
   • Bond Stress: Distorting substrate chemical bonds toward their transition-state configuration.
   • Microenvironment: Providing localized acidic, basic, or nonpolar conditions distinct from the aqueous cytosol.
   • Direct Participation: Transiently forming covalent bonds between active-site side chains and the substrate.

   Cofactors and Coenzymes

   Many enzymes require non-protein chemical partners to function effectively:

   • Inorganic Cofactors: Metal ions such as $Fe^{2+}$, $Mg^{2+}$, or $Zn^{2+}$.
   • Coenzymes: Organic molecules, often derived from dietary vitamins, such as NAD$^+$, FAD, and Coenzyme A.

   Environmental Influences on Rate

   The rate of an enzyme-catalyzed reaction depends directly on physical and chemical environmental factors:

   1. Temperature

   Increasing temperature raises kinetic energy, leading to more frequent collisions between enzymes and substrates. However, exceeding the optimum temperature disrupts non-covalent bonds (hydrogen and ionic bonds) stabilizing the tertiary structure, causing denaturation and loss of catalytic function.

   2. pH

   Each enzyme functions maximally at an optimal pH. Deviations from this range alter the ionization states of acidic and basic amino acid side chains within the active site, disrupting substrate binding and potentially denaturing the protein.

   3. Substrate and Enzyme Concentration

   At constant enzyme concentration, adding substrate increases reaction velocity until all active sites are occupied. At this point, the enzyme is saturated, and the reaction proceeds at its maximum velocity ($V_{max}$).

   Enzyme Inhibition

   Inhibitors are specific chemical agents that decrease or abolish enzyme activity, serving critical roles in metabolic regulation and pharmacology.

   Reversible Inhibitors

   • Competitive Inhibitors: Resemble the substrate structurally and directly compete for binding at the active site. Increasing substrate concentration can overcome this inhibition, maintaining the original $V_{max}$ while increasing the apparent $K_m$.
   • Non-competitive (Allosteric) Inhibitors: Bind to a distinct regulatory site, termed an allosteric site, causing a conformational change that reduces catalytic efficiency regardless of substrate concentration. This decreases $V_{max}$ without changing substrate affinity ($K_m$).

   Feedback Inhibition

   In metabolic pathways, the end product frequently functions as an allosteric inhibitor of the pathway's initial regulatory enzyme, preventing cellular overproduction of unnecessary metabolites.