Principles of Biochemistry Chapter 6 Mechanisms of Enzymes PDF

Horton Moran Scrimgeour Perry Rawn Principles of Biochemistry Chapter 6 Mechanisms of Enzymes Copyright © 2006 Pearson Prentice Hall, Inc.  Homework problems you might see again Ch 6 – 1, 3, 4, 5, 10  Review of simple chemical...

Horton Moran Scrimgeour Perry Rawn Principles of Biochemistry Chapter 6 Mechanisms of Enzymes Copyright © 2006 Pearson Prentice Hall, Inc.  Homework problems you might see again Ch 6 – 1, 3, 4, 5, 10  Review of simple chemical mechanisms Nucleophilic substitutions Cleavage reactions Oxidation-reduction reactions  Nucleophilic Substitution Double bonds and detectable intermediate  Nucleophilic Substitution Direct displacement and undetectable intermediate Energy Diagram Single step Energy Diagram With intermediate Enzymatic Catalysis A + B  A–B EAB  A–B EAB  [EAB]  A–B pKa values of aa: free vs in protein Acid-Base Catalysis  Acid-Base Catalysis Cleavage of C-N with water and :B  Acid-Base Catalysis Cleavage by donation of H by HB+ pH affects enzymatic rates Example: papain Activity Example: papain pH rate profile Example: papain Rate-limiting step: binding of E and S Triose Phosphate Isomerase Triose Phosphate Isomerase Triose Phosphate Isomerase  Energy Diagram Reaction catalyzed by triose phosphate isomerase  Superoxide dismutase Subsequent reaction catalyzed by catalase Superoxide dimutase Copper reduced E-Cu2+ +.O2-  E-Cu+ + O2 Copper oxidized E-Cu+ +.O2- + 2H+  E-Cu2+ + H2O2  Binding modes of enzymatic catalysis Proximity effect Weak binding of substrates to enzymes Induced fit Transition-state stabilization Proximity effect Weak binding of E to S  Induced fit Hexokinase + glucose vs + water  Transition state analog Example: triose phosphate isomerase transition state Substrate of Lysozyme: bacterial cell wall polysaccharide Conformations of N-acetylmuramic acid Sites A, B, C, E, F Site D Activation of pancreatic zymogens Chymotrypsin, trypsin, and elastase are homologous Binding sites Catalytic site of chymotrypsin Catalytic triad of chymotrypsin