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19 - Monday October 19th 2008 Biochemistry 405 Lecture#9...

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1 Monday, October 19 th, 2008 Biochemistry 405 – Lecture #9 Kane Hall 130 10:30- 11:20 am Lecturer: Wim Hol Slide Set #1
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2 Refresher on: The pK of amino acid side chains (and of the N-term –NH 2 and the C-term -COOH) In different molecules, pK values of the same group are often not the same. They depend on two factors: a. “Through-bond effects”: These make e.g. the –NH 2 of Lysine have a pK of ~10.6 whereas the N-terminal –NH 2 of a peptide has a pK of ~7. b. “Environment effects”: The “canonical” pK of a side chain can be altered by one or more units (up or down) by bringing that group in a special environment. This is quite often the case in enzyme active sites. And also in the case of the N-terminal – NH 2 of the β chain of hemoglobin.
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3 Enzyme Catalysis 1. Enzyme Catalysis - Cofactors: co-enzymes and prosthetic groups - Specificity - Activation energy & Catalysis - Five categories of catalysis (not mutually exclusive) - Mechanism of Ribonuclease A 2. Proteases - Serine protease mechanism - Convergent evolution
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4 Catalysis by Enzymes and Enzyme Names Enzyme catalysis can : - be extremely substrate specific, or quite substrate-unspecific - be very fast, or quite slow - involve only protein side chains, or involve also very complex “co-factors” - involve one substrate, or more substrates - be quite pH-dependent - occur with almost no, or with large conformational changes Enzymes are usually named by appending “-ase” to the name of the substrate, or one of the substrates.
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5 Cofactors Enzymes have functional groups, provided mainly by amino acid side chains, which are for instance are quite good in: - acid-base reactions - forming certain types of covalent bonds But enzymes are not so good in oxidation–reduction reactions and group–transfer processes. The latter types of reactions are often catalyzed by enzymes associated with “cofactors”. Cofactors can be: - Metal ions like Cu 2+ , Fe 2+ , Zn 2+ ; - Organic cofactors are also called “coenzymes”. If permanently associated with enzymes, cofactors are also called “Prosthetic groups”. Cofactors must be regenerated (of course).
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6 NAD and NADP: Important Coenzymes
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7 Reaction Coordinate A + B P + Q The “reaction coordinate” is the path of minimum free energy G during the reaction. The highest point along this path is the “free energy of activation”. The configuration of substrate(s) at this point is the “transition state”X. The G of X # is the free energy of the ”transition state” of the reaction
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Reaction Rate Acceleration By “Transition State Stabilization” Enzymes speed up reactions by providing a reaction pathway with a transition state whose free energy of activation is lower, by ΔΔ G # cat , than that of the uncatalyzed reaction. The larger the absolute value of ΔΔ G # cat , the better the enzyme.
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9 Reaction Intermediates & Rate-Determining Step Enzymatic reactions usually proceed in multiple steps via “intermediates” (I).
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