lecture_20a - Metabolism II and Glycolysis 5/7/03 Organic...

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Metabolism II and Glycolysis 5/7/03
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Organic reaction mechanisms Much can be learned by studying organic model reactions when compared to enzyme catalyzed reactions. 1. Group transfer reactions 2. Oxidations and reductions 3. Eliminations, isomerizations and rearrangements 4. Reactions that make or break carbon-carbon bonds
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ATP ATP is the energy carrier for most biological reactions ATP + H 2 O -> ADP + P i ATP + H 2 O -> AMP + PP i
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Coupled Reactions
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Recycling ATP & ADP
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Heterolytic cleavage or bond formation is catalyzed using either nucleophiles or electrophiles.
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Nucleophiles R NH 2 + H + R N + H H H R NH 2 O R' R'' R N C OH R'' R' H Basic reaction of amine Nucleophilic reaction of an amine
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Biologically important nucleophiles
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R NH 2 O R' R'' R N C OH R'' R' H R N H R' R'' + Amine Ketone or aldehyde Carbinolamine intermediate Imine Movement of an electron pair from a position and pointing to the electron deficient center attracting the pair.
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Common biological electrophiles
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Group transfer reactions Acetyl group transfer Nucleophile attack on an acyl carbonyl to form a tetrahedral intermediate Peptide bond hydrolysis Phosphoryl group transfer nucleophile attack on a phosphate to yield a trigonal bipyramid intermediate Kinase reactions involving transfer of phosphate from ATP to organic alcohols Glycosyl group transfers substitution of one group at the C1 carbon of a sugar for another Y + A X Y A + X
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Thioesters (Acetyl-coenzyme A) High energy compound Carrier of acetyl and acyl groups Can be used to drive exogenic processes e.g. GTP from GDP
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Oxidations and reductions Oxidation : Loss of Electrons Reduction: Gain of Electrons Many redox reactions involve the breaking of a C-H bond and the loss of two bonding electrons Y + H O C R R H N R NH 2 O H + Y H R NH 2 O R R O H H + +
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Electron transfer reactions to oxygen undergo transfer of one electron at a time (Pauli exclusion principle) Oxidations to oxygen from NADH require two electron steps to be changed to one electron steps. Stable radical structures like FMN or FAD and cytochromes are involved.
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Reduction of NAD+ to NADH
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Electron transfer reactions B A B A red red n + + + = + n ox ox + = + + red n ox n ox red 0 B B A A ln RT G G
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Half-cell reactions either donate or accept electrons Electron donor (reducing agent) Electron acceptor (oxidizing agent)
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Work is non -pressure volume work or G = -w’ = -w elec W elec = nF E or G = -nF E [ ] [ ] [ ] [ ] = + + red n ox n ox red o B B A A ln nF RT - E E F = Faraday constant = 96,485 Coulombs per mole of electrons E 0 = standard reduction potential or midpoint potential Nernst Equation- electromotive force -EMF- reduction potential
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lecture_20a - Metabolism II and Glycolysis 5/7/03 Organic...

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