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Biochemistry

Biochemistry. Lecture 8. Why Enzymes?. Higher reaction rates Greater reaction specificity Milder reaction conditions Capacity for regulation. Metabolites have many potential pathways of decomposition Enzymes make the desired one most favorable. Enzymatic Substrate Selectivity. No binding.

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Biochemistry

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  1. Biochemistry Lecture 8

  2. Why Enzymes? • Higher reaction rates • Greater reaction specificity • Milder reaction conditions • Capacity for regulation • Metabolites have many potential pathways of decomposition • Enzymes make the desired one most favorable

  3. Enzymatic Substrate Selectivity No binding Binding but no reaction Example: Phenylalanine hydroxylase

  4. How to Lower G? Enzymes organizes reactive groups into proximity

  5. How to Lower G? Enzymes bind transition states best

  6. How is TS Stabilization Achieved? • acid-base catalysis: give and take protons • covalent catalysis: change reaction paths • metal ion catalysis: use redox cofactors, pKa shifters • electrostatic catalysis: preferential interactions with TS End result? Rate enhancements of 105 to 1017!

  7. How is TS Stabilization Achieved? • covalent catalysis: change reaction paths

  8. Enzyme Kinetics • Kinetics is the study of the rate at which compounds react • Rate of enzymatic reaction is affected by • Enzyme • Substrate • Effectors • Temperature

  9. How to Do Kinetic Measurements

  10. What equation models this behavior? Michaelis-Menten Equation

  11. Meaning of Vmax and Km

  12. Simple Enzyme Kinetics • The final form in case of a single substrate is • kcat (turnover number): how many substrate molecules can one enzyme molecule convert per second • Km (Michaelis constant): an approximate measure of substrate’s affinity for enzyme • Microscopic meaning of Km and kcat depends on the details of the mechanism

  13. Two-substrate Reactions • Kinetic mechanism: the order of binding of substrates and release of products • When two or more reactants are involved, enzyme kinetics allows to distinguish between different kinetic mechanisms • Sequential mechanism • Ping-Pong (Double Displacement) mechanism

  14. Distinguishing Mechanism Ping-Pong Ternary Complex

  15. Enzyme Inhibition • Inhibitors are compounds that decrease enzyme’s activity • Irreversible inhibitors (inactivators) react with the enzyme • one inhibitor molecule can permanently shut off one enzyme molecule • they are often powerful toxins but also may be used as drugs • Reversible inhibitors bind to, and can dissociate from the enzyme • - they are often structural analogs of substrates or products • - they are often used as drugs to slow down a specific enzyme • Reversible inhibitor can bind: • To the free enzyme and prevent the binding of the substrate • To the enzyme-substrate complex and prevent the reaction

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