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Enzymes (Ch. 6)

Enzymes (Ch. 6). Intro Basics of catalysis General types of catalysis Quantification of catalysis enzyme kinetics and inhibition Specific examples Allostery and enzyme regulation. Biological reaction: sugar + oxygen ↔ CO 2 + water. High energy “Transition state”

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Enzymes (Ch. 6)

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  1. Enzymes (Ch. 6) • Intro • Basics of catalysis • General types of catalysis • Quantification of catalysis • enzyme kinetics and inhibition • Specific examples • Allostery and enzyme regulation

  2. Biological reaction: sugar + oxygen ↔ CO2 + water High energy “Transition state” Intermediate between R & P Activation energy EA Kinetic barrier to reaction ENERGY (G°) DG < 0 Reactants (R) Products (P) Reaction should be spontaneous Equil should favor products REACTION PROGRESS

  3. The energy barrier is critical for life • Potentially deleterious reactions are blocked by EA • Complex molecule degrading to simpler constituents nucleotide DNA http://asm.wku.edu http://encyclopedia.quickseek.com/

  4. How do enzymes speed up reactions? • New reaction pathway • Lower activation energy • Decreased energy barrier 2H2O2→ 2H2O + O2 Hydrogen peroxide Isolated: EA ~ 86 kJ/mol In the presence of catalase: EA ~ 1kJ/mol

  5. Binding of substrate to enzyme creates a new reaction pathway Without enzyme With enzyme EA = DG‡ An enzyme changes EANOTDG Affects RATE, not EQUILIBRIUM http://w3.dwm.ks.edu.tw/

  6. How is EA lowered? EA = DG‡ = DH - TDS entropy enthalpy • Enzyme’s ‘goal’ is to reduce DG‡ • Two ways enzymes can affect DG • Improve DH • Improve DS DG‡ = Gtrans.state – Greactants Enzymes alter the free energy of the transition state

  7. BH+ BH+ A A - Example: More favorable DH Charge unfavorable Unstable transition st. OH- + OH- B H2O + A Ionic interaction stabilizes the positive charge BH + AOH

  8. Example: More favorable DS One molecule Lower disorder (low S) Unfavorable entropically Two molecules More ‘freedom’ Higher disorder (high S)

  9. Example: More favorable DS ENZYME ENZYME Enzyme/Transition state complex Still a single molecule Not much difference entropically Enzyme/Reactant COMPLEX Essentially a single molecule

  10. Remember • Enzymes lower the energy barrier • Decrease EA (DG‡) • Provide an environment where: • Transition state is stabilized (lower enthalpy) • Change of disorder (entropy) is minimized

  11. Enzymes create a new reaction pathway DGo vs. DG‡ transition state vs. reaction intermediates rate limiting step

  12. Factors contributing to enzyme catalysis • Weak interactions between enzyme and transition state • Transient covalent bonds between S and E • Entropy optimization in ES complex formation • Solvation shell surrounding S & E (entropy/hydrophobic interactions) • Substrate distortion upon binding to noncomplementary E • Proper alignment of catalytic functional groups

  13. Common catalytic mechanisms • General acid/base catalysis • Proton transfer • Reactions with charged intermediates/AAs • Fumarase • Precise positioning of acid/base: reaction occurs faster than specific acid/base reactions • Free H+/OH-

  14. Common catalytic mechanisms • Covalent catalysis • Covalent bond formation between E and S • Reaction path is altered and new path has lower Ea • Chymotrypsin (combination)

  15. Common catalytic mechanisms • Metal catalysis (metalloenzymes) • Ionic interactions • Stabilize charged TS or orient charged substrate for reaction • Carboxypeptidase • Oxidation/reduction • Reversible changes in oxidation state of the metal • Electron transfer reactions • Transition metals • Catalase ezample

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