CH 11' The citric acid cycle

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CH 11. The citric acid cycle

• The citric acid cycle a metabolic pathway to
  convert carbon atom in biopolymer to CO2 and to
  conserve metabolic energy (as ATP)
• fig 11.1
• Occur in cytosol of prokaryotes and in
  mitochondria of eukaryotes
• Like a web or network the pathways
  intermediates can participate in many reactions
  -gt a central pathway
• Eight reactions, cycle
• Entered as acetyl groups

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1. The pyruvate dehydrogenase complex covers
pyruvate to acetyl-CoA

• Pyruvate should be transported to
  mitochondria
• The pyruvate dehydrogenase complex contains
  multiple copies of three different enzymes
• Pyruvate CoA NAD ? acetyl-CoA CO2 NADH
• fig 11.2
• Enormous size 60-140 subunits, gt 4600kD
• A core of 60 subunit (dodecahedron) subunits
  arranged to its surface

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Figure 11.01 The citric acid cycle in context.
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Figure 11.02 Structor of the E2 core of the
pyruvate dehydrogenase complex from B.
stearothermophilus.
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• The pyruvate dehydrogenase complex contains
  multiple copies of three different enzymes
• Decarboxlation of pyruvate by E1 with cofactor
  TPP
• Transfer of the hydroxyethyl group to E2 (with
  lipoamide)

Figure 11.04 Lipoamide.
Figure 11.03 Thiamine pyrophosphate (TPP).
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The pyruvate dehydrogenase complex contains
multiple copies of three different enzymes 3.
Transfer of the acetyl group to CoA by E2 4.
Restoration of pyruvate dehydrogenase complex by
reduction of FAD 5. Reoxidation of FADH2 by NAD
Figure 11.05 Flavin adenine dinucleotide (FAD).
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Figure 11.06 Reactions of the pyruvate
dehydrogenase complex.
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• The pyruvate dehydrogenase complex contains
  multiple copies of three different enzymes
• the long lipoamide group of E2 acts a swinging
  arm.
• Gatekeeper regulated by i) NADH and acetyl CoA
  (inhibitors)
• ii)
  hormone-controlled phosphorylation and
• 
  dephosphorylation
• Multienzyme complex carry out multistep
  reaction sequence efficiently
• cf enzymes of glycolysis and TCA cycle
  associate loosely?

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2. The eight reactions of the citric acid cycle
Acetyl-CoA GDP Pi 3 NAD Q ? 2 CO2 CoA
GTP 3 NADH QH2

• - Acetyl-CoA enter the cycle
• Highly exergonic (as GTP and reduced cofactros)

Figure 11.07 Reactions of the citric acid cycle.
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• Citrate synthase synthesize carbon-carbon bond
  without metal ion
• oxaloacetate (4C) Acetyl-CoA (2C) ?
  citrate (6C)

Conformational changes in citrate synthase from
chicken.
Figure 11.09 The citrate synthase reaction.
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2. Aconitase can react only one carboxymethyl
arms although two of them are symmetric
citrate (6C) ? aconitate ? isocitrate (6C)
3. Isocitrate dehydrogenase oxidative
decarboxylation of isocitrate to a-ketoglutarate
with reduction of NAD to NADH
isocitrate (6C) ? a-ketoglutarate (5C)
CO2 4. a-ketoglutarate dehydrogenase
? multienzyme complex (similar to pyruvate
dehydrogenase), ? oxidative decarboxylation
with reduction of NAD to NADH
a-ketoglutarate (5C) ? Succinyl-CoA (4C)
CO2 two C of released CO2 molecules are not
directly derived from acetyl-CoA
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Figure 11.10 Fates of carbon atoms in the citric
acid cycle.
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5. Succinyl-CoA synthetase highly exergonic,
combined with generation of GTP
(ATP) Succinyl-CoA (4C) ? Succinate(4C) 6.
Succinate dehydrogenase ? located in
inner-mitochondrial membrane ? with reduction of
FAD to FADH2, ?FADH2 is roxidized by
lipid-soluble electrton carrier
ubiquinone isocitrate (6C) ? fumarate (4C)
The succinyl-CoA synthetase reaction.
Substrate binding in succinyl-CoA synthetase.
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7. fumarase can react only one carboxymethyl
arms although two of them are symmetric
fumarate (4C) ? malate (4C) 8. Malate
dehydrogenase ? regeneration of oxaloacetate
with reduction of NAD to NADH ? standard free
energy 29.7 kJ/mol, how is it occur?
malate (4C) ? oxaloacetate (4C) The citric
acid cycle is an energy-generating catalyzing
cycle. ? The entire pathway acts in a catalytic
fashion to dispose of carbon atoms ? Small
addition of fumarate, succinate stimulate large
uptake of O2 (oxidative phosphorylation) ? More
ATP is generated through reoxidation of the
reduced cofactors by O2. (NADH X ATPs, QH2 X
ATPs) ? Pasteur effect decrease of glucose
consumption when the yeast was shifted from
anaerobic to aerobic growth conditions.
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The citric acid cycle is regulated at three
steps. three metabolically irrrevewrsible
steps ? citrate synthase depends on substrate
concentration, inhibited by citrate (also inhibit
phosphofructokinase) ? isocitrate dehydrogenase
inhibited by NADH (also inhibits citrate synthase
and a-ketoglutartae dehydrogenase) ?
a-ketoglutartae dehydrogenase inhibited by
succinyl-CoA (also competitive inhibitor of
citrate synthase) ? Ca2 ions activate both
dehydrogenase ? ADP activate isocitrate
dehydrogenase
Figure 11.13 Regulation of the citric acid cycle.
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Evolution of the citric acid cycle (CAC) cyclic
pathway minimizes waste ? genome project study
of genes for CAC enzymes in bacteria (fig
11-14) ? reverse of CAC primitive CO2 fixation
before phortosynthesis? (fig 11-15)
Pathways that might have given rise to the citric
acid cycle.
A proposed reductive biosynthetic pathway based
on the citric acid cycle.
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3. The citric acid cycle is both catabolic and
anabolic In mammals, 6 intermediates are
precursors or products of other
substances Citric acid cycle intermediates are
precursors of other molecules Intermediates of
CAC can be siphoned off to form other
compounds ? amino acids nucelotides
alpha-ketoglutarate NH4 ? glutamate H2O ?
monosaccharides OAA ? fatty acids by
cytosol AYP-citrate lyase (location!!) citrate
ATP CoA ? ADP Pi
OAA acetyl-CoA OAA ? malate
? pyruvate (cytosol) ? pyruvate
(mitochondria)
Citric acid cycle intermediates as biosynthetic
precursors.
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3. The citric acid cycle is both catabolic and
anabolic Citric acid cycle intermediates are
precursors of other molecules Intermediates of
CAC can be siphoned off to form other compounds
? amino acids nucelotides
alpha-ketoglutarate NH4 ? glutamate
H2O ? monosaccharides OAA ? fatty acids
citrate transport system.
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Glyoxylate cycle in plant (Box 11-B)
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Anaplerotic reactions replenish citric acid cycle
intermediates ? anaplerotic reactions reactions
to replenish intermediates diverted from the
CAC ? Synthesis of OAA by pyruvate carboxylase,
activated by acetyl-CoA pyruvate CO2
ATP H2O ? OAA ADP Pi ? production of
Succinyl-CoA by degradation of fatty acids
? production of a-ketoglutarate, succinyl-CoA,
fumarate, OAA by degradation (transamination) of
amino acids (direction of the reaction depends on
the concentration of each product)
Aspartate pyruvate ? OAA alanine ?
vigorously exercising muscles high concentration
of pyruvate is shuntted to CAC intermediates by
pyruvate carboxylase and alanine
aminotransferase ? No intermediate is oxidized
during the CAC.
Figure 11.18 Anaplerotic reactions of the citric
acid cycle.
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