Molecular Basis of Enzyme Function

Enzyme Basics & Structure - Protein Powerhouses

• Enzymes: Biological catalysts (mostly proteins) that ↑ reaction rates; not consumed.
• Properties: High catalytic power, specificity (substrate-specific), regulated activity.
• IUBMB Classification (6 Classes): 📌 Mnemonic: Oh These Huge Lads Are Little (OTHLIL).

  Class	Reaction Type
  1. Oxidoreductases	Redox reactions
  2. Transferases	Group transfer
  3. Hydrolases	Hydrolysis
  4. Lyases	Group removal/addition (non-hydrolytic)
  5. Isomerases	Isomerization
  6. Ligases	Joining molecules (ATP-dependent)

• Components:
  • Apoenzyme: Inactive protein part.
  • Cofactor: Non-protein part for activity (inorganic ions like $Mg^{2+}$, $Zn^{2+}$).
  • Coenzyme: Organic cofactor (often vitamin-derived).
  • Prosthetic Group: Tightly bound coenzyme/cofactor.
  • Holoenzyme: Active enzyme; $Apoenzyme + Cofactor \rightleftharpoons Holoenzyme$.
• Active Site: Specific substrate-binding region; contains binding & catalytic sites.

⭐ Ribozymes: RNA with enzymatic activity, not all enzymes are proteins.

Enzyme Action & Kinetics - Reaction Accelerators

• Mechanism: Enzymes accelerate reactions by lowering activation energy ($E_a$) via transition state stabilization.
  • 
• Models:
  • Lock-and-Key: Rigid active site precisely fits substrate.
  • Induced-Fit: Substrate binding induces enzyme conformational change for optimal fit.

• Kinetics:
  • Michaelis-Menten Equation: $V_0 = \frac{V_{max}[S]}{K_m + [S]}$
    • 
  • $K_m$ (Michaelis Constant): [S] at $\frac{1}{2}V_{max}$. Inverse measure of affinity (↓$K_m$ = ↑affinity).
    • 📌 $K_m$: Koncentration for half Max.

    ⭐ $K_m$ is numerically equal to the substrate concentration at which reaction velocity is $\frac{1}{2}V_{max}$.

  • $V_{max}$ (Maximum Velocity): Rate at enzyme saturation; proportional to [Enzyme].
  • Lineweaver-Burk Plot: $\frac{1}{V_0} = (\frac{K_m}{V_{max}})\frac{1}{[S]} + \frac{1}{V_{max}}$
    • X-intercept: $-\frac{1}{K_m}$; Y-intercept: $\frac{1}{V_{max}}$; Slope: $\frac{K_m}{V_{max}}$.
    • 
• Factors Affecting Activity:
  • [Substrate]: ↑[S] → ↑$V_0$ until $V_{max}$.
  • [Enzyme]: ↑[Enzyme] → ↑$V_{max}$.
  • Temperature: Optimal ~37°C (human); extremes denature.
  • pH: Optimal pH specific; extremes denature.

Enzyme Inhibition & Regulation - Catalyst Controllers

• Reversible Inhibition: Comparison of types:

  Type	Binding Site	$K_m$	$V_{max}$	Lineweaver-Burk Plot	Mnemonic 📌
  Competitive	Active site	↑	↔	Intersect on Y-axis	Competitive: $K_m$↑, $V_{max}$↔ (Kome Up, $V_{max}$ stays)
  Non-competitive	Allosteric site	↔	↓	Intersect on X-axis	Non-competitive: $K_m$↔, $V_{max}$↓ ($K_m$ stays, $V_{max}$ decays)
  Uncompetitive	ES complex only	↓	↓	Parallel lines	Uncompetitive: $K_m$↓, $V_{max}$↓ (UNique: both UNder)

• Irreversible Inhibition: Covalent modification of enzyme, often "suicide" inhibitors (e.g., penicillin, aspirin, organophosphates).
• Allosteric Regulation: Modulators bind to allosteric site (not active site), altering enzyme activity (positive/negative). Shows cooperativity, sigmoidal kinetics.
• Covalent Modification: Activity regulated by adding/removing chemical groups.
  • Phosphorylation/dephosphorylation (kinases/phosphatases).
  • Zymogen activation: inactive precursor (e.g., pepsinogen) cleaved to active enzyme (e.g., pepsin).
• Feedback Inhibition: End product of a metabolic pathway inhibits an early enzyme in that pathway, regulating its own synthesis.
• Clinical Inhibitors (Examples):
  • Statins (e.g., atorvastatin): Competitive inhibitors of HMG-CoA reductase (cholesterol synthesis).
  • ACE inhibitors (e.g., captopril): Treat hypertension.
  • Allopurinol: Inhibits xanthine oxidase (gout treatment).

⭐ Methanol poisoning is treated with ethanol, which acts as a competitive inhibitor for alcohol dehydrogenase, preventing methanol's conversion to toxic formaldehyde.

High‑Yield Points - ⚡ Biggest Takeaways

• Enzymes: Biological catalysts that lower activation energy, not consumed in reactions.
• Active site: Binds substrate; specificity by Lock & Key or Induced Fit models.
• Michaelis-Menten kinetics: Km indicates substrate affinity (↑Km = ↓affinity); Vmax is maximum velocity.
• Competitive inhibitors: Bind active site, ↑Km, Vmax unchanged.
• Non-competitive inhibitors: Bind allosteric site, ↓Vmax, Km unchanged.
• Allosteric regulation: Modulators bind non-active sites, altering activity.
• Coenzymes (vitamins) & cofactors (metal ions) are often vital.