Biochemistry
Enzymes
Biological catalysts — proteins (mostly) that speed up reactions a million-fold
Enzymes are biological catalysts — almost all are proteins (some RNAs called ribozymes). Speed up reactions by 10⁶-10¹⁷ × through specific binding of substrate at active site. Lower activation energy without being consumed. Highly specific (lock and key or induced fit). Optimal conditions: physiological T (~37°C for humans), pH (varies — pepsin pH 2; trypsin pH 8). Regulated by: substrate concentration (Michaelis-Menten), inhibitors (competitive, non-competitive), allostery, post-translational modification. Without enzymes, life impossible (most reactions too slow). Examples: catalase (H₂O₂ → H₂O + O₂), lactase, DNA polymerase, ATP synthase.
- Speed-up factor10⁶ to 10¹⁷ × uncatalyzed
- SpecificityHigh; specific substrate, specific reaction
- Active siteWhere substrate binds; determines specificity
- Optimal T~37°C for humans; varies by organism
- Optimal pHVaries (pepsin 2; trypsin 8; most ~7)
- NamingOften ends in -ase (catalase, lactase, etc.)
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Why enzymes matter
- Metabolism. All metabolic reactions enzyme-catalyzed.
- Drug development. Many drugs are enzyme inhibitors.
- Biotech. Enzymes in detergents, food, manufacturing.
- Diagnostics. Enzyme levels indicate disease.
- Industrial. Cheese, beer, paper.
- Forensics. DNA testing.
- Origin of life. Catalysis foundational.
Common misconceptions
- Enzymes are consumed. Catalysts; not consumed.
- Enzymes change equilibrium. Only rate.
- All enzymes proteins. Most; some are RNA (ribozymes).
- One enzyme one reaction. Usually; some have multiple activities.
- Higher T always faster. Until denaturation; optimum exists.
- Enzyme function temperature-independent. Highly T-dependent.
Frequently asked questions
How do enzymes work?
Substrate binds active site (specific shape). Active site stabilizes transition state — lowers activation energy. Specific amino acids in active site participate (acid-base catalysis, covalent catalysis, metal ion catalysis, electrostatic, induced strain). Reaction proceeds. Product released; enzyme returns to original state. Cycle repeats. Reduces Ea by ~10-30 kJ/mol — gives factor 10⁶-10¹⁷ rate increase.
What's specificity?
Each enzyme catalyzes specific reaction with specific substrate. Determined by active site shape and chemistry. Lock and key (Fischer 1894): rigid fit. Induced fit (Koshland 1958): enzyme molds to substrate. Modern view: combination + dynamic. Examples: hexokinase (glucose only), lactase (lactose only), trypsin (cleaves at Lys/Arg only).
What's Michaelis-Menten kinetics?
Most enzymes follow this kinetic pattern. Rate = Vmax × [S] / (Km + [S]). Vmax: maximum rate (when enzyme saturated). Km: substrate concentration at half Vmax. Lower Km = higher affinity. At low [S]: rate ∝ [S]. At high [S]: rate constant. Used for: characterizing enzymes, comparing them, predicting drug effects. Lineweaver-Burk plot: linear form for analysis.
How are enzymes regulated?
Many ways. (1) Substrate concentration: rate depends on [S]. (2) Competitive inhibitors: bind active site (e.g., methotrexate inhibits dihydrofolate reductase). (3) Non-competitive: bind elsewhere. (4) Allosteric: substrate binding at one site affects activity (e.g., hemoglobin). (5) Post-translational: phosphorylation, glycosylation. (6) Gene expression: how much enzyme made.
What's a coenzyme?
Small organic molecule needed for enzyme function. Often vitamins or derivatives. Examples: NAD/NADH (redox; from niacin B3), FAD/FADH₂ (redox; from riboflavin B2), CoA (acyl group transfer), ATP (energy currency), TPP (vitamin B1). Cofactors: also include metals (Fe, Mg, Zn). Often: enzyme contains metal binding site or coenzyme binding pocket.
What about ribozymes?
RNA-based enzymes. Older than protein enzymes. Examples: ribosome (peptide bond formation by rRNA), self-splicing introns, hammerhead ribozyme. Suggests "RNA world" hypothesis: RNA was both genetic material and catalyst before proteins evolved. Cech, Altman Nobel Prize 1989. Rare but important.
What's enzyme inhibition?
Reduce enzyme activity. Many drugs are enzyme inhibitors. (1) Competitive: bind active site, compete with substrate. Can be overcome by more substrate. (2) Non-competitive: bind elsewhere; can't be overcome. (3) Allosteric: bind allosteric site. (4) Suicide: form covalent bond with enzyme. Examples: aspirin (cyclooxygenase), penicillin (transpeptidase), statins (HMG-CoA reductase).