Biochemistry · Short notes

Enzymes: Short Notes & Cheat Sheet

Enzyme classes, Michaelis–Menten and Lineweaver–Burk kinetics, types of inhibition, cofactors, regulation, isoenzymes and diagnostic enzymes.

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Short notes

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The enzyme classes

1 OxidoreductasesDehydrogenases, oxidases2 TransferasesKinases, transaminases3 HydrolasesEsterases, proteases, lipases4 LyasesDecarboxylases, aldolase5 IsomerasesMutases, epimerases6 LigasesSynthetases; use ATPEnzyme classes
The EC number's first digit gives the class. Hydrolases (class 3) include most digestive enzymes.

Basics and kinetics

  • Enzymes speed reactions by lowering the activation energy; they do not change the equilibrium.
  • EC classes: 1 oxidoreductases, 2 transferases, 3 hydrolases, 4 lyases, 5 isomerases, 6 ligases (7 translocases added in 2018).
  • Michaelis–Menten: v = Vmax[S] / (Km + [S]). Km is the substrate concentration at half Vmax; a low Km means high affinity.
  • Lineweaver–Burk (double reciprocal) plot: the y-intercept is 1/Vmax and the x-intercept is −1/Km.
  • Activity depends on temperature (optimum near 37 °C in humans), pH (pepsin about pH 2, trypsin about pH 8) and substrate concentration.

Inhibition

  • Competitive inhibitors bind the active site: Km rises, Vmax is unchanged, and extra substrate overcomes them (methotrexate on DHFR, statins on HMG-CoA reductase).
  • Ethanol or fomepizole compete with methanol and ethylene glycol for alcohol dehydrogenase, which is why they are antidotes.
  • Non-competitive inhibitors bind elsewhere: Vmax falls and Km is unchanged.
  • Uncompetitive inhibitors bind only the enzyme–substrate complex: both Vmax and Km fall.
  • Irreversible inhibitors bind covalently: aspirin (COX), organophosphates (acetylcholinesterase), disulfiram (aldehyde dehydrogenase).

Cofactors, regulation and clinical enzymes

  • An apoenzyme plus its cofactor forms the active holoenzyme. Cofactors are metal ions or organic coenzymes, many derived from vitamins.
  • Regulation: allosteric control (sigmoidal kinetics), feedback inhibition, covalent modification such as phosphorylation, and zymogen activation (trypsinogen → trypsin).
  • Isoenzymes catalyse the same reaction but differ in structure: CK-MB (heart), CK-MM (muscle), CK-BB (brain); LDH-1 (heart), LDH-5 (liver and muscle).
  • Diagnostic enzymes: ALT (liver-specific), AST (liver, heart, muscle), ALP (bone, cholestasis), GGT (alcohol, cholestasis), lipase and amylase (pancreatitis; lipase is more specific), CK (muscle damage).

Cheat sheet

High-yield facts in one place. Cover the right-hand column and test yourself.

Inhibition types

TypeKm · Vmax
Competitive↑ · unchanged
Non-competitiveUnchanged · ↓
Uncompetitive↓ · ↓
IrreversibleEnzyme permanently lost

Vitamin → coenzyme

VitaminCoenzyme
B1 thiamineThiamine pyrophosphate (TPP)
B2 riboflavinFAD, FMN
B3 niacinNAD⁺, NADP⁺
B5 pantothenic acidCoenzyme A
B6 pyridoxinePyridoxal phosphate (PLP)
B7 biotinCarboxylation cofactor
B9 folic acidTetrahydrofolate
B12 cobalaminMethylcobalamin, adenosylcobalamin

Memory aids

Over The HILL
Oxidoreductases, Transferases, Hydrolases, Isomerases, Lyases, Ligases (the EC classes, not in number order).

Exam traps

  • Enzymes change the rate, not the position of equilibrium.
  • In competitive inhibition Vmax is unchanged, because enough substrate can outcompete the inhibitor.
  • A low Km means high affinity, not low activity.
  • ALT is more liver-specific than AST.

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