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BioChem Week 12

by: Lauran Notetaker

BioChem Week 12 CHEM 3653 - 001

Lauran Notetaker

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Week 12
Dr. Paul A. Sims
Class Notes
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This 6 page Class Notes was uploaded by Lauran Notetaker on Thursday April 21, 2016. The Class Notes belongs to CHEM 3653 - 001 at University of Oklahoma taught by Dr. Paul A. Sims in Winter 2016. Since its upload, it has received 9 views. For similar materials see Biochemistry in Chemistry at University of Oklahoma.


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Date Created: 04/21/16
April 5, 2016 Chapter 11: Chemical Logic of Metabolism Autotroph - self feeding Heterotroph - feeding on others Common Nucleophiles in Biochemical Reactions: Alkoxide Hydroxide ion Carbanion Carboxylate Thiolate Amine Imidazole Types of Nucleophilic Substitution Reactions SN1 - Carbocation intermediate SN2 - pentavalent transition state Common substrates in acyl substitutions Ester Thioester Carboxylic acid Amide Acyl phosphate Nucleophilic Addition Reactions: Carbonyl carbons are well suited for addition reactions Aldol condensation - carbonyl to which the enolate ion adds is an aldehyde or ketone Claisen condensation - carbonyl to which the enolate ion adds is an ester Beta-hydroxycarbonyls are readily dehydrated NAD+ is a widely used redox cofactor oxidase - If the electron acceptor is oxygen reductase - if the reaction proceeds in the reverse direction Oxidation is a biological energy source Glycolysis is a fermentation Fats generate far more metabolic energy from oxidation than carbohydrate because it generates more reducing equivalents NAD+ is a major oxidant NADPH is a major reductant ATP is most abundant NTP is most often used as phosphate donor ATP is favorable under virtually any physiological conditions The solvent-capacity of a cell is the finite capacity for the total amount of dissolved substances in a cell Reactions in Substrate cycles are favorable Major Sources of Energy for ATP Synthesis Substrate level phosphorylation energy comes from breakdown of a higher-energy substrate Oxidative phosphorylation energy comes from the exergonic redox reactions in mitochondria Photophosphorylation energy comes from light Metabolic control analysis assigns each enzyme in a pathway a flux control coefficient (FCC) If FCC = 1 the relevant enzyme is truly rate limiting If FCC = 0 the activity of the enzyme is irrelevant to regulation Metabolism is studied at various levels Chapter 12: Carbohydrate Metabolism: Glycolysis, Gluconeogenesis, Glycogen Metabolism, and the Pentose Phosphate Pathway Glycolysis Phase 1: Energy Investment Hexokinase - the First ATP investment (Priming the Pump) Glucose-6-Phosphate Isomerase Phosphofructokinase - Second ATP Investment Fructose-1,6-Biphosphate Aldolase - Cleavage to Two triose phosphates Triose Phosphate Isomerase (TIM) Glyceraldehyde-3-phosphate dehydrogenase Phosphoglycerate Kinase - first substrate level phosphorylation Phosphoglycerate Mutase - preparing to synthesize the next “high-energy” compound GAPDH conserves the energy of oxidation by coupling an exergonic reaction to an endergonic reaction To avoid the Deep Free Energy Well we use a thioester intermediate Phase 2: Energy Generation April 7, 2016 Near equilibrium reaction Glucose-6-phosphate to Fructose-6-phosplate Setting the stage chemically for more symmetrical for aldol cleavage ~B: abstract C2 hydrogen clicker question: Must know Aldolase Mechanism (slide 13/72) Lysine attacts P. Carbon Difference between TIM and previous example Both have Enediol intermediate Example: Aldose to TIM: Ketose to Equivalencies of Carbons: 1 to 6 2 to 5 3 to 4 GAPDH 4 - protinate with Energy of oxidation of an aldehyde to a carboxylic acid is conserved in the form of ATP through Reaction 7 Reaction 8: 2 to 3 Phosphoglycerate, the name making sense Mutase Prepares to synthesize the next “high energy” compound Reaction 9: Enolase synthesis of second Microscopic Ionization States pKa are ~ 2 apart Need HE for glycolysis Need EH for gluconeogenesis Don’t know what protonation state to be in Kcat = 10^6 M^-1s^-1 Km Know difference between macroscopic pKa and Microscopic pKa dont have to know equations, will be given (slide 24) Slide 25 arrow should be going straight to products clicker question: clicker question: Explanation: small steps are used commonly in glycolysis and glycogenesis and are freely reversible three steps considered irreversible HK PFK PK


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