Enzymes

• Enzymes are proteins that act as biological catalysts for intra & extracellular reactions to determine structure & function
• Enzymes affect the metabolism of cells & whole organisms
• The specific tertiary structure of enzymes determines the shape of the active site, which is complementary to a specific substrate
• Formation of enzyme-substrate (ES) complexes lowers the activation energy of metabolic reactions
• Example of an enzyme that catalyses intracellular reactions: Catalase catalyses the decomposition of hydrogen peroxide into water + oxygen
• Examples of enzymes that catalyse extracellular reactions:

  • Amylase: carbohydrase catalyses digestion of starch to maltose in saliva/small intestine lumen
  • Trypsin: pancreatic endopeptidase catalyses hydrolysis of peptide bonds in small intestine lumen
• Induced fit model of enzyme action:

  • Shape of active site is not directly complementary to substrate & is flexible
  • Conformational change enables ES complexes to form when substrate adsorbs
  • This puts strain on substrate bonds, lowering activation energy
  • Bonds in enzyme-product complex are weak, so product desorbs
• Lock and key model of enzyme action:

  • Active site has a rigid shape determined by tertiary structure, complementary to 1 substrate
  • Formation of ES complex lowers activation energy
  • Bonds in enzyme-product complex are weak, so product desorbs
• Factors affecting the rate of enzyme-controlled reactions:

  • Enzyme concentration
  • Substrate concentration
  • Concentration of inhibitors
  • pH
  • Temperature
• How substrate concentration affects rate of reaction:

  • Rate increases proportionally to substrate concentration until the maximum number of ES complexes form
• How enzyme concentration affects rate of reaction:

  • Rate increases proportionally to enzyme concentration until the maximum number of ES complexes form
• How temperature affects the rate of enzyme-controlled reactions:

  • Rate increases as kinetic energy increases & peaks at optimum temperature
  • Above optimum, denaturation occurs as ionic & H-bonds in 3° structure break
• Temperature coefficient (Q10):

  • Measures the change in rate of reaction per 10°C temperature increase
  • Q10 = R2 / R1 (where R represents rate)
• How pH affects rate of reaction:

  • Enzymes have a narrow optimum pH range
  • Outside the range, denaturation occurs as H+ / OH- ions interact with H-bonds & ionic bonds in 3° structure
• Competitive inhibitors:

  • Bind to the active site, temporarily preventing ES complexes from forming
  • Increasing substrate concentration decreases their effect
• Non-competitive inhibitors:

  • Bind at allosteric binding site, triggering a conformational change of the active site
  • Increasing substrate concentration has no impact on their effect
• End-product inhibition:

  • One of the products of a reaction acts as a competitive or non-competitive inhibitor for an enzyme involved in the pathway, preventing further formation of products
• Irreversible inhibitors:

  • Permanently prevent formation of ES complexes
  • Heavy metal ions e.g. mercury, silver cause disulphide bonds in tertiary structure to break
• Reversible inhibitors:

  • May be competitive or non-competitive
  • Bind to enzyme temporarily, allowing ES complexes to form after the inhibitor is released
• Metabolic poison:

  • Substance that damages cells by interfering with metabolic reactions, usually an inhibitor
• Examples of metabolic poisons:

  • Cyanide: non-competitive, irreversible, inhibits cytochrome c oxidase
  • Malonate: competitive, inhibits succinate dehydrogenase
  • Arsenic: competitive, inhibits pyruvate dehydrogenase
• How some medicinal drugs act as inhibitors:

  • Penicillin: non-competitive inhibitor of transpeptidase
  • Ritonavir: inhibits HIV protease
• Inactive precursors in metabolic pathways:

  • Some enzymes in metabolic pathways are synthesised as inactive precursors to prevent damage to cells
  • One part of the precursor acts as an inhibitor, and ES complexes form when it is removed
• Cofactors:

  • Non-protein compounds required for enzyme activity
  • Include coenzymes, inorganic cofactors, and prosthetic groups
• Coenzymes:

  • Organic cofactors that do not bind permanently
  • Often transport molecules or electrons between enzymes
• Inorganic cofactors:

  • Facilitate temporary binding between substrate and enzyme
  • Often metal ions e.g. Cl- is the cofactor for amylase
• Prosthetic groups:

  • Tightly-bound cofactors that act as a permanent part of the enzyme’s binding site
  • Example: Zn2+ for carbonic anhydrase
• Producing a desired concentration of solution from a stock solution:

  • Volume of stock solution = required concentration x final volume needed concentration of stock solution
  • Volume of distilled water = final volume needed - volume of stock solution
• what is the temperature coefficient?

  The temperature coefficient for a biological reaction is the ratio between the rates of that reaction at two different temperatures