lecturenoteschap6-09-2slides

lecturenoteschap6-09-2slides - BCMB/BIOL/CHEM 3100 Chapter...

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1 1 BCMB/BIOL/CHEM 3100 Chapter 6 Mechanisms of Enzymes Energy diagrams Chemical modes of enzyme catalysis Acid-Base catalysis Covalent catalysis Binding modes of enzyme catalysis Proximity effect Transition state stabilization Transition state analogs Induced fit Serine Proteases 2 Energy diagrams show the progress of a reaction Fig 6.1 Energy diagram for a single-step reaction _______________ : high 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
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2 3 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 determining step in the forward direction is formation of the first transition state 4 Fig 6.3 Enzymatic catalysis of the reaction A+B A-B Proximity effect: “proper” positioning of substrates Transition state stabilization : lowers activation energy
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3 5 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 Ionic side chains are involved in two types of chemical catalysis: 1. _______________ 2. _______________ 6 Table 6.1 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 7 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 Terminal -amino 7.5-9 Thiol 8-9.5 Phenol 9.5-10 -Amino ~10 Guanidine ~12 Hydroxymethyl ~16 8 Chapter 6 Mechanisms of Enzymes Energy diagrams Chemical modes of enzyme catalysis Acid-Base catalysis Covalent catalysis Binding modes of enzyme catalysis Proximity effect Transition state stabilization Transition state analogs Induced fit Serine Proteases
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5 9 Chemical modes of enzyme catalysis Acid-Base catalysis Covalent catalysis 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: - ) _________________: acceleration of a reaction by transfer of a protein B: = base (proton acceptor) BH+ = conjugate acid (proton donor)
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6 11 General base catalysis reactions (continued) •A _____________ ( B: ) can remove a proton from water and thereby generate the equivalent of OH - in neutral solution 12 Proton donors can also catalyze reactions •A ____________ ( BH + ) can donate protons • A covalent bond may break more easily if one of its atoms is protonated (below)
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7 13 • 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 A- X + E X -E + A X -E + B B- X + E ________________: part or entirety of S forms
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lecturenoteschap6-09-2slides - BCMB/BIOL/CHEM 3100 Chapter...

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