Molecular Biology: Enzymes - MCAT Review

Enzyme Structure and Function

Function of Enzymes

• Enzymes act as catalysts to increase reaction rates without being consumed.
• Structure is crucial for enzyme function; changes in structure affect function.
• Key reactions catalyzed by enzymes include:
  • Metabolism
  • DNA/RNA synthesis
  • Protein synthesis
  • Digestion

Enzyme Classification by Reaction Type

• Enzymes are named based on the reaction type + "ase":
  • Oxidase/Reductase: Oxidation and reduction reactions
  • Dehydrogenase: Removes/adds hydrogen
  • Kinase/Phosphatase: Adds/removes phosphate groups
  • Protease/Amylase/Lipase: Hydrolyze proteins, carbohydrates, fats
  • DNAse/RNAse/Nuclease: Hydrolyze phosphodiester bonds
  • Polymerase: Synthesizes DNA/RNA/proteins
  • Transcriptase: Transcribes RNA from DNA; reverse transcriptase does the reverse
  • Ligase: Forms bonds between DNA/RNA strands

Reduction of Activation Energy

• Enzymes lower the activation energy required for reactions.

Substrates and Enzyme Specificity

• Enzymes interact with substrates at their active site.
• Specificity is due to structural interactions:
  • Lock and Key Model: Rigid active site
  • Induced Fit Model: Flexible active site adapts to substrate
• Enzymes can distinguish between stereoisomers.

Mechanisms of Catalysis

• Enzymes can be proteins or RNA (e.g., ribosome).
• Structure determines function with four levels:
  • Primary: Sequence of protein/RNA chain
  • Secondary: Hydrogen bonding (alpha helices, beta sheets)
  • Tertiary: 3-D structure involving R-group interactions
  • Quaternary: Multiple chains (dimers, trimers, etc.)
• Cofactors (metal ions) and coenzymes (small molecules) assist enzyme function.
• Fat-Soluble Vitamins: A, D, E, K (can be toxic at high levels)
  • A: Vision
  • D: Bone health
  • E: Cell membranes
  • K: Clotting
• Water-Soluble Vitamins: B1, B12, Folate, C
  • B1: Deficiency causes Wernicke-Korsakoff syndrome/Beriberi
  • B12: Deficiency leads to macrocytic anemia
  • Folate: Important for DNA synthesis
  • C: Important for collagen synthesis
• Enzyme activity is optimal under specific conditions (temperature, pH, salt concentration).

Control of Enzyme Activity

Kinetics

• Enzyme catalysis changes reaction kinetics without being consumed.
• Michaelis-Menten Model: Describes reaction rate vs. substrate concentration
  • Vmax: Maximum reaction rate
  • Km: Substrate concentration at half Vmax
• Cooperativity affects substrate binding:
  • Positive: Increases binding likelihood
  • Negative: Decreases binding likelihood

Feedback Regulation

• Pathway products inhibit their own pathway (e.g., hexokinase in glycolysis).

Types of Inhibition

• Competitive: Competes with substrate
• Non-Competitive: Binds elsewhere, altering function
• Mixed: Affects both Vmax and Km
• Uncompetitive: Binds only the enzyme-substrate complex

Regulatory Enzymes

• Allosteric: Binding to a site changes active site conformation.
• Covalently-modified: Phosphorylation/deactivation
• Zymogens: Inactive until activated by another enzyme (e.g., pepsinogen to pepsin)