BCHM-3050 Lecture Notes - Lecture 11: Dihydrolipoamide Dehydrogenase, Pyruvate Dehydrogenase, Oxidative Decarboxylation
19 Jun 2018
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Oxidative process of energy generation
TCA cycle: central aerobic pathway for oxidized metabolic fuels
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Energy mode from oxidation of substrates = stored in reduced e- carriers
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Three stages
Stage 1.5: carbon incorporated into acetyl-CoA via PDH
Stage 1: glycolysis
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Purpose: generation of chemically activated two carbon fragment
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Stage 2: citric acid cycle
Oxidize acetyl-CoA
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Make:
CO2
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Reduced e- carriers
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Small amount of ATP
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Purpose: strip the two carbon fragment of electrons and form CO2
molecules
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Stage 3: reduced e- carriers are reoxidized
Electron transport and oxidative phosphorylation
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Mitochondria- THE POWERHOUSE OF THE CELL!!!!
Matrix (stage 1.5 and 2): pyruvate is oxidized and the TCA cycle occurs
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Intermembrane space (stage 3): ATP generation
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Has its own ssDNA
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mtDNA = encode many of the proteins needed for TCA
From mother
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Has own ribosome for mRNA translation
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Stage 1.5: pyruvate dehydrogenase converts pyruvate to acetyl-CoA
PDH complex: multienzyme complex
Oxidative decarboxylation of an alpha keto acid
Carboxyl group of pyruvate is released as CO2
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Pyruvate dehydrogenase (E1)
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Dihydrolipoamide transacetylase (E2)
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Dihydrolipoamide dehydrogenase (E3)
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Require 5 coenzymes
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Thiamine pyrophosphate (TPP)
TPP bound to E1 subunit
tightly
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Catalyze cleavage of C-C bond on pyruvate during decarboxylation
Pyruvate = alpha keto acid
Unstable carbanion intermediate during decarboxylation
Cant stabilize the transition state
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How? Stabilize carbanion intermediate via covalent catalysis
Enzymatic decarboxylation of the substrate
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Decarboxylation allows the carbanion intermediate to be
stabilized by resonance
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Lipoamide: e- carrier and acyl group carrier
Lipoamide: coenzyme on E2 subunit
Accepts hydroxyethyl (two carbon aldehyde fragment) from TPP as
acetyl group
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Use lysine swinging arm
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Has reduced (SH) and oxidized (S) forms
Lipoamide is both a electron carrier and acyl group carrier
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Coenzyme A activate acyl group
Accept acetyl group from lipoamide
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Has free thiol AND ADP group
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Thiol react to form thioesters
Energy rich compound
Related to resonance stabilization
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High potential energy for acyl group transfer than ester
Help activate acyl group for transfer to CoA
ATP hydrolysis
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Not bound to PDH
Transient
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Dissociable substrate for E2
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Riboflavin, FMN, and FAD = coenzyme structure
Accept pair of e- from reduced lipoamide
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FAD = tightly bound to E3 subunit
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Flavin coenzymes: 2 e- oxidoreduction rxns
Proceed one or two e- at a time
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Reduction through stable semiquinone free radical specie
Gives flavins catalytic versatility allowing them to interact w either
two electron or one electron donor acceptor pairs
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Allow them to interact directly w oxygen
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Nicotinamide adenine dinucleotide (NAD)
Accept pair of e- from reduced FADH
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Nicotinamide: accepts 2 e- in form of hydride
Form reduced NADH
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Can only transfer 2e- at a time
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Mechanism for PDH (5 steps)
Rxn 1: TPP + pyruvate = hydroxyethyl TPP
Decarboxylation
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3 Carbons
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Rxn 2: hydroxyethyl TPP = hydroxyethyl
Hydroxyethyl passed to E2 and added to lipoamide
On swing arm of lipoamide
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2 carbons
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Rxn 3: acetyl group added to CoA-SH
Make acetyl CoA and dihydrolipoamide
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2 carbons
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Rxn 4: E3 reoxidizes lipoamide
Transfer e- to an E3 cys-cys disulfide bond
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Rxn 5: E3 transfers e- from lipoamide to NAD+
Produce NADH
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Regulation of PDH
Major control point
Exergonic
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E1 component: inactivated by phosphorylation
PDH kinase
At serine residue
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PDH kinase: activated by high lvls of
ATP
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NADH
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Acetyl-CoA
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PDH phosphatase: reactivate PDH
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E2 component: inhibited by acetyl-CoA
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E3: inhibited by NADH
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Chapter 13: Pyruvate dehydrogenase
Monday, June 18, 2018
8:48 PM
Document Summary
Tca cycle: central aerobic pathway for oxidized metabolic fuels. Energy mode from oxidation of substrates = stored in reduced e- carriers. Stage 1. 5: carbon incorporated into acetyl-coa via pdh. Purpose: generation of chemically activated two carbon fragment. Purpose: strip the two carbon fragment of electrons and form co2 molecules. Matrix (stage 1. 5 and 2): pyruvate is oxidized and the tca cycle occurs. Has its own ssdna mtdna = encode many of the proteins needed for tca. Stage 1. 5: pyruvate dehydrogenase converts pyruvate to acetyl-coa. Carboxyl group of pyruvate is released as co2. Catalyze cleavage of c-c bond on pyruvate during decarboxylation. Decarboxylation allows the carbanion intermediate to be stabilized by resonance. Accepts hydroxyethyl (two carbon aldehyde fragment) from tpp as acetyl group. Lipoamide is both a electron carrier and acyl group carrier. High potential energy for acyl group transfer than ester. Help activate acyl group for transfer to coa. Proceed one or two e- at a time.
