the citric acid cycle and the pentose phosphate pathway
TRANSCRIPT
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The Citric Acid Cycle and the Pentose Phosphate Pathway
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The Citric acid cycle
3NAD+ + FAD + GDP + Pi + acetyl-CoA
3NADH + FADH + GTP + CoA + 2CO2
Overall reaction
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SS
E2
HSS
E2
SSH
E2
SS
E2
SS
E2
SSH
E2
HSS
E2
SS
E2
CH3OCH3O
CH3OCH3O
Acetyl reaction center transferes though the E2 dihydrolipoyl coenzyme repeats
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Citrate Synthase
HO
CH2
O
C
HO O
OH3C C SCoA
O+
HO
CH2
O
C
OH
O
HO
CH2
HO O
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Induced fit needs binding of oxaloacetate before Acetyl CoA can bind.
CoAS COH
CH2
CH3CCoAS
O
CoAS CoAS
CH3
C
O OH
CH2
OCH2
Proposed intermediateAcetyl-CoA
Acetonly CoA Carboxymethyl-CoA
(ground-state analog) (transition state analog)
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AconitaseHO
CH2
O
C
OH
O
HO
CH2
HO O
HO
CH2
O
CH
OH
O
CH
HO O
Citrate Cis-Aconitate
HO
CH2
O
HC
OH
O
C
HO O
HHO
Isocitrate
The double bond is placed on the Pro-R arm
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NAD+- Dependent Isocitrate dehydrogenase
NAD+ NADH
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-Ketoglutarate dehydrogenase
HO
CH2
O
H2C
C
HO O
O
CoAS O
HO
CH2
O
CH2
CO2
This enzyme is just like pyruvate dehydrogenase, a multi enzyme complex that is specific for longer CoA derivatives
NAD+
NADH
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Succinyl-CoA Synthetase or succinate thiokinase
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Succinate dehydrogenase
HO O
HO
CH2
O
CH2
HO O
HO
CH
O
CH
+ 2e- + 2H+
The FAD on the enzyme itself is reduced
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Succinate dehydrogenase is the only membrane bound enzyme in the citrate cycle
O
O
H3CO
H3CO
CH3
CH2
CH3
n n = 6-10
Succ dh--FADH2 +
OH
OH
H3CO
H3CO CH3
CH2
CH3
n
Ubiquinone or Coenzyme Q
Oxidized form
Reduced form
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Fumarase
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Malate dehydrogenase
HO O
HO
H2C
O
C OHH O
HO O
HO
H2C
O
C
NAD+
NADH
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Regulation of the citric acid cycle
Standard free energy changes in the citric acid cycle
Reaction Enzyme G' G'
1 Citrate synthase -31.5 Negative
2 Aconitase ~5 ~0
3 Isocitrate dh -21 Negative
4 -KG dh -33 Negative
5 Succinyl-CoA synthase -20.1 ~0
6 Succinate dh +6 ~0
7 Fumarase -3.4 ~0
8 Malate dh +29.7 ~0
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A single molecule of glucose can potentially yield ~38 molecules of ATP
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Phosphopentose pathway
Produces NADPH and ribose-5-phosphate
NADH and NADPH although chemically similar they are not metabolically exchangeable.
Many anabolic pathways require the reducing power of NADPH for synthesis including Fatty acid synthesis and the synthesis of cholesterol.
3G-6-P + 6NADP+ + 3H2O 6NADPH + 6H+ 3CO2 + 2F6P + GAP
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The pathway consists of three parts
1. Oxidative reactions:
3G-6-P + 6NADP+ + 3H2O 6NADPH + 3CO2 + 3Ribulose-5-PO4
2. Isomerization and epimerization reactions:
3Ribulose-5-PO4 Ribose -5-PO4 + 2Xylulose-5-PO4
3. A series of C-C bond cleavage and formations:
Ribose-5-PO4 + 2Xyluose-5-PO4 2F-6-P + GAP
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Glucose-6 phosphate dehydrogenase
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Phosphogluconate dehydrogenase
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Ribulose-5-PO4 isomerase
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Two enzymes control the rearrangement of carbon skeletons which result in the production of Glyceraldehyde-3-phosphate and Fructose-6-phosphate.
Transketolase transfers C2 units: TPP requiring enzyme like pyruvate dehydrogenase
Transaldolase transfers C3 units: uses a shiffs base with an active lysine group
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Transketolase requires TPP
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The transition of carbon skeletons in the Phosphopentose pathway
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The pentose pathway control
The need for NADPH is controlled by glucose dehydrogenase, however, when ribose -5-phosphate is needed (DNA and RNA synthesis) it can be made from the reverse of the transaldolase and transketolase reactions from Fructose-6-PO4 and GAP
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NADPH is needed for glutathione reductase
Reduced glutathione is needed for glutathione peroxidase, which destroy hydrogen peroxide and organic peroxides. This enzyme requires selenium as a cofactor.
H3+N CH
COO-
CH2 CH2 C NH
O
CH
CH2
C
O
NH CH2 COO-
H3+N CH
COO-
CH2 CH2 C NH
O
CH
CH2
C
O
NH CH2 COO-
S
SH3+N CH
COO-
CH2 CH2 C NH
O
CH
CH2
C
O
NH CH2 COO-
SH
2
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Glutathione keeps proteins with reduced sulfhydryls
SH from oxidizing to R S S R’
P-SH + P’-SH + O2 P-S-S-P’ + H2O
P-S-S-P’
G-SH
P-SH + G-S-S-P
G-SH
G-S-S-G + HS-P
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Glutathione reductase contains FAD
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Reaction of glutathione with peroxides
2GSH + RA-O-O-H G-S-S-H + ROH + H2O
A steady supply of glutathione is required for erythrocyte integrity
~ 400,000,000 individuals are deficient in glucose dehydrogenase!
Without a fully functioning glucose dehydrogenase, glutathione concentrations Hemolytic Anemia can
occur if certain drugs are used.
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Primaquine, an antimalarial drug is problematic with individuals with glucose
dehydrogenase deficiencies
N
H3CO
NH CH
CH3
CH2 CH2 CH2 NH2
Primaquine
Similar effects are seen when people eat Fava beans. Fava beans stimulate peroxide formation and the demand for NADPH can not be met.
Mature red blood cells lack a nucleus and the ability to make new proteins and membranes. Damage cannot be repaired so cells lyse.
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A defective G-6-P dh confers a selective advantage on individuals living where malaria is endemic. However, only heterozygotic females are resistant to malaria, not males. Plasmodium falciparum can adopt to a cell with decreased levels of phosphopentose products. This enzyme is in the X chromosome and females with two x chromosomes produce half good and half bad blood cells. Plasmodium cannot adapt to the G-6-P dh deficiency if it is sporadic or random.