lecturenoteschap6-10-4slides

lecturenoteschap6-10-4slides - BCMB/BIOL/CHEM 3100 Chapter...

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1 BCMB/BIOL/CHEM 3100 Chapter 6 Mechanisms of Enzymes Energy diagrams Chemical modes of enzyme catalysis Acid-Base catalysis Covalent catalysis 1 Binding modes of enzyme catalysis Proximity effect Transition state stabilization Transition state analogs Induced fit Serine Proteases Energy diagrams show the progress of a reaction _______________ : high energy, unstable state in which a molecule is best suited to undergo a chemical reaction; state in 2 Fig 6.1 Energy diagram for a single-step reaction chemical reaction; state in which chemical bonds are being broken and formed. Lifetime ~ 10 -14 to 10 -13 sec Fig 6.2 Energy diagram for reaction with intermediate • __________ occurs in the trough between the two transition states 3 • Lifetime > ~10 -14 to 10 -13 sec • In this case, the rate 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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2 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 5 ______________ : polar amino acids that undergo changes during enzymatic catalysis 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) Table 6.2 pKa Values of amino acid ionizable groups in proteins Group pK a Terminal -carboxyl 3-4 Side-chain carboxyl 4-5 Imidazole 6-7 Ti l i 75 9 7 Terminal -amino 7.5-9 Thiol 8-9.5 Phenol 9.5-10 -Amino ~10 Guanidine ~12 Hydroxymethyl ~16 Chapter 6 Mechanisms of Enzymes Energy diagrams Chemical modes of enzyme catalysis Acid-Base catalysis Covalent catalysis 8 Binding modes of enzyme catalysis Proximity effect Transition state stabilization Transition state analogs Induced fit Serine Proteases
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3 Chemical modes of enzyme catalysis Acid-Base catalysis Cl t t l i 9 Covalent catalysis _________________: acceleration of a reaction by transfer of a protein B: = base (proton acceptor) BH+ = conjugate acid (proton donor) 10 •A general base ( B: ) can act as a proton acceptor to remove protons from OH, NH, CH or other XH • This produces a stronger nucleophilic reactant (X: - ) General base catalysis reactions (continued) _____________ ( B: ) can remove a proton from water and thereby generate the equivalent of OH - in neutral solution 11 Proton donors can also catalyze reactions ____________ ( BH + ) can donate protons • A covalent bond may break more easily if one of its atoms is protonated (below) 12
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4 • 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 ________________: part or entirety of S forms covalent bond with E and then with second S 13 • Group X can be transferred from A- to B in two steps via the covalent ES complex X -E A- X + E X -E + A X -E + B B- X + E 6.10 6.11 Sucrose phosphorylase exhibits covalent catalysis (6.11-6.13) Step one : a glucosyl residue
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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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lecturenoteschap6-10-4slides - BCMB/BIOL/CHEM 3100 Chapter...

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