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Enzymes, con\'t. Substrate Activation (catalytic mechanisms). Strain on substrate Weakens bonds Makes more accessible for reaction Acid/base catalysis Covalent (nucleophilic/electrophilic) catalysis. Enzyme kinetics. Study of reaction rates—can tell lots about reaction mechanisms.

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substrate activation catalytic mechanisms
Substrate Activation(catalytic mechanisms)
  • Strain on substrate
    • Weakens bonds
    • Makes more accessible for reaction
  • Acid/base catalysis
  • Covalent (nucleophilic/electrophilic) catalysis
enzyme kinetics

Enzyme kinetics

Study of reaction rates—can tell lots about reaction mechanisms

simplifying assumptions
Simplifying assumptions
  • No back reaction
  • k3 is rate limiting
  • [ES] is constant (steady state assumption)
slide10
Km
    • Measure of binding affinity (roughly)
    • The lower the Km, the tighter the binding
  • Vmax
    • Maximum rate of enzyme
    • Determined by turnover number (kcat)

How best to calculate them?

regulation1
Regulation
  • Irreversible inhibitors—generally not natural part of cell
    • Drugs and toxins
    • Covalent modification
    • Aspirin
  • Reversible
    • Substrate level regulation
    • Competitive inhibitors
    • Noncompetitive inhibitors
    • Allosteric regulation (activators and inhibitors)
    • Covalent modification (reversible)
    • Proteolytic cleavage
regulation2
Regulation

Reversible

  • Substrate level regulation
  • Competitive inhibitors
  • Noncompetitive inhibitors
  • Allosteric regulation (activators and inhibitors)
  • Covalent modification (reversible)
  • Proteolytic cleavage
reversible covalent modification

Reversible covalent modification

Phosphorylation

Dephosphorylation

proteolytic cleavage

Proteolytic cleavage

Only extracellular

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