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Lecture 12

Lecture 12. Enzyme mechanisms. +. HB. +. NADH. Common enzyme reactions. Oxidation and reductions (cofactors are involved!). (Oxidation of an alcohol to a ketone). +. +. B :. NAD +. H. O. + BH +. C. H. C. O. H. R. BH +. H. C. O. H. H. B :. C. O. R.

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Lecture 12

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  1. Lecture 12 Enzyme mechanisms

  2. + HB + NADH Common enzyme reactions Oxidation and reductions (cofactors are involved!) (Oxidation of an alcohol to a ketone) + + B: NAD+

  3. H O + BH+ C H C O H R BH+ H C O H H B: C O R Common enzyme mechanisms Isomerizations B:

  4. R 4 R R R O 1 1 1 O C O C C R C C 5 R R R 3 3 3 R R R 2 2 2 H More common enzyme mechanisms Making and breaking C-C bonds Aldol condensation O B: H C C

  5. Example of reactions Phosphorylation/ dephosphorylation

  6. Lysozyme • Discovered by Fleming, 1922 • Lyses the cell wall of bacteria by cleaving the polysaccharides in bacterial cell walls

  7. Lysozyme specificity • Hexamer (or longer) of sugars binds • 4th sugar residue must be distorted • Cleaves between the 4th and 5th • sugar

  8. O O O H O Glu C 35 O O O H O H H C A s p Glu C O 5 2 35 - O O - O O C A s p + 5 2 - O O Lysozyme mechanism General acid base catalysis Stabilization of carbocation

  9. Lysozyme mechanism

  10. Covalent Catalysis by Enzymes • Formation of acylserine intermediate by chymotrypsin

  11. Covalent Catalysis by Enzymes

  12. Identifying Covalent Catalysis Identical rates reflect rate-limiting breakdown of a common intermediate

  13. H C 3 Mechanism and rate ENZYME fast O ENZYME C O Acyl-enzyme intermediate H2O slow H+ - + ENZYME

  14. Identification of catalytic residues ENZYME + ENZYME Only serine 195 reacts with DIPF (no other serine in the protein reacts) Irreversible reaction: inactivates enzyme

  15. Catalytic Triad } General acid and base catalysis Serine proteases (esterases) all have similar mechanisms. Ser195 - Nucleophile His57 Asp102

  16. H N R 2 3 Catalytic Triad

  17. Chymotrypsin • pH-rate profile

  18. Chymotrypsin Mechanism:

  19. Hexokinase • Mr 100,000 • Glucose >> H2O ~106 ATP + Glucose ADP + Glucose-6-Phosphate

  20. Hexokinase Mechanism • Induced fit • Glucose unbound

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