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Lecturenoteschap6-10 - BCMB/BIOL/CHEM 3100 Chapter 6 Mechanisms of Enzymes Energy diagrams Chemical modes of enzyme catalysis modes of enzyme

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1 BCMB/BIOL/CHEM 3100 Chapter 6 Mechanisms of Enzymes Energy diagrams Chemical modes of enzyme catalysi Chemical modes of enzyme catalysis Acid-Base catalysis Covalent catalysis Binding modes of enzyme catalysis Proximity effect Transition state stabilization 1 Transition state analogs Induced fit Serine Proteases Energy diagrams show the progress of a reaction _______________ : high energy, unstable state in energy, unstable state in which a molecule is best suited to undergo a chemical reaction; state in which chemical bonds are being broken and formed. Lifetime ~ 10 -14 to 10 -13 sec 2 Fig 6.1 Energy diagram for a single-step reaction Lifetime 10
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2 Fig 6.2 Energy diagram for reaction with intermediate occurs in the __________ trough between the two transition states • Lifetime > ~10 -14 to 10 -13 sec • In this case, the rate 3 determining step in the forward direction is formation of the first transition state Fig 6.3 Enzymatic catalysis of the reaction A+B A-B Proximity effect: “proper” positioning of substrates Transition state stabilization : lowers activation energy 4
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3 What is the enzyme active site? A few polar residues and H 2 O molecules are found at the otherwise hydrophobic active site of an enzyme ______________ : polar amino acids that undergo changes during enzymatic catalysis 5 Ionic side chains are involved in two types of chemical catalysis: 1. _______________ 2. _______________ Table 6.1 6 Note: pKa of ionizable groups of amino acids in proteins vary from pKa of free amino acids (compare Table 3.2 to Table 6.2)
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4 Table 6.2 pKa Values of amino acid ionizable groups in proteins Group pK a Terminal -carboxy l3 - 4 Side-chain carboxyl 4-5 Imidazole 6-7 Terminal -amino 7.5-9 Thiol 8-9.5 Phenol 9.5-10 7 -Amino ~10 Guanidine ~12 Hydroxymethyl ~16 Chapter 6 Mechanisms of Enzymes Energy diagrams Chemical modes of enzyme catalysi Chemical modes of enzyme catalysis Acid-Base catalysis Covalent catalysis Binding modes of enzyme catalysis Proximity effect Transition state stabilization 8 Transition state analogs Induced fit Serine Proteases
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5 Chemical modes of enzyme catalysis Acid-Base catalysis Covalent catalysis 9 _________________: acceleration of a reaction by transfer of a protein B: = base (proton acceptor) •A general base ( B: ) can act as a proton acceptor to remove protons from OH, NH, CH or other XH BH+ = conjugate acid (proton donor) 10 • This produces a stronger nucleophilic reactant (X: - )
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6 General base catalysis reactions (continued) • A ( B: ) can remove a proton ____________ from water and thereby generate the equivalent of OH - in neutral solution 11 Proton donors can also catalyze reactions • A ( BH + ) can donate protons A ____________ • A covalent bond may break more easily if one of its atoms is protonated (below) 12
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7 All or part of a substrate is bound to ________________: part or entirety of S forms covalent bond with E and then with second S • All or part of a substrate is bound _________ to the enzyme to form a ________________ • Group X can be transferred from A- X to B in two steps via the covalent ES complex X -E 13 A- X + E X -E + A X -E + B B- X + E 6.10 6.11 Sucrose phosphorylase exhibits covalent
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This note was uploaded on 12/03/2011 for the course CHEM 3100 taught by Professor Dervartanian during the Fall '09 term at University of Georgia Athens.

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Lecturenoteschap6-10 - BCMB/BIOL/CHEM 3100 Chapter 6 Mechanisms of Enzymes Energy diagrams Chemical modes of enzyme catalysis modes of enzyme

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