citric acid cycle. figure 17-2 citric acid cycle
TRANSCRIPT
Citric Acid Cycle
Figure 17-2
Citric Acid Cycle
Summary of Citric Acid Cycle
Acetyl-CoA + 3 NAD+ + FAD + GDP + Pi
2 CO2 + 3 NADH + 3H+ + FADH2 + GTP + CoA-SH
Reactions of the Citric Acid Cycle
Citrate Synthase(citrate condensing enzyme)
Acetyl- SCoA Oxaloacetate
H3C C
O
S CoA
C
H2C
COOH
COOH
O+
H2C
C
H2C
HO
COOH
COOH
COOH
Citrate
CoA–SH
∆Go’ = –31.5 kJ/mol
Figure 17-10 part 1
Mechanism of Citrate Synthase
(Formation of Acetyl-SCoA Enolate)
Figure 17-10 part 2
Mechanism of Citrate Synthase
(Acetyl-CoA Attack on Oxaloacetate)
Figure 17-10 part 2
Mechanism of Citrate Synthase
(Hydrolysis of Citryl-SCoA)
Regulation of Citrate Synthase
• Pacemaker Enzyme (rate-limiting step)
• Rate depends on availability of substrates
– Acetyl-SCoA
– Oxaloacetate
Aconitase
Stereospecific
Addition
Cis- aconitate(~3%)
I socitrate(~6%)
H2C
C
H2C
HO
COOH
COOH
COOH
Citrate(~91%)
H2C
C
HC
COOH
COOH
COOH
H2C
HC
CH
COOH
COOH
COOH
HO
H2OH2O
∆Go’ = ~0
Iron-Sulfur Complex(4Fe-4S]
Thought to coordinate citrate –OH to facilitate elimination
Page 325
Stereospecificity of Aconitase Reaction
Prochiral Substrate Chiral Product
Figure 11-2
Stereospecificity in Substrate Binding
NAD+–DependentIsocitrate Dehydrogenase
I socitrate
H2C
HC
CH
COOH
COOH
COOH
HO
NAD+ NADH + H+
- ketoglutarate
H2C
CH2
C
COOH
COOHO
+ CO2
Mn2+ or Mg2+
Oxidative Decarboxylation
NOTE: CO2 from oxaloacetate
∆Go’ = -20.9 kJ/mol
Figure 17-11 part 1
Mechanism of Isocitrate Dehydrogenase
(Oxidation of Isocitrate)
Figure 17-11 part 2
Mechanism of Isocitrate Dehydrogenase
(Decarboxylation of Oxalosuccinate)
Mn2+ polarizes C=O
Figure 17-11 part 2
Mechanism of Isocitrate Dehydrogenase(Formation of -Ketoglutarate)
Regulation of Isocitrate Dehydrogenase
• Pulls aconitase reaction
• Regulation (allosteric enzyme)
– Positive Effector: ADP (energy charge)
– Negative Effector: ATP (energy charge)
• Accumulation of Citrate: inhibits Phosphofructokinase
Accumulation of Citrate
CO2
Isocitrate dehydrogenase
CO2
Isocitrate dehydrogenase
-Ketoglutarate Dehydrogenase
NAD+ NADH + H+
- ketoglutarate
H2C
CH2
C
COOH
COOHO
+ CO2+ CoASH
Succinyl- CoA
H2C
CH2
C
COOH
SCoAO
Oxidative Decarboxylation
Mechanism similar to PDH
CO2 from oxaloacetate
High energy thioester
∆Go’ = -33.5 kJ/mol
-Ketoglutarate Dehydrogenase
(Multienzyme Complex)
• E1: -Ketoglutarate Dehydrogenase or -Ketoglutarate Decarboxylase
• E2: Dihydrolipoyl Transsuccinylase
• E3: Dihydrolipoyl Dehydrogenase (same as E3 in PDH)
Regulation of -Ketoglutarate Dehydrogenase
• Inhibitors
– NADH
– Succinyl-SCoA
• Activator: Ca2+
Origin of C-atoms in CO2
H2C
C
H2C
HO
COOH
COOH
COOH
Citrate I socitrate
H2C
HC
CH
COOH
COOH
COOH
HO
- ketoglutarate
H2C
CH2
C
COOH
COOHO
Succinyl- CoA
H2C
CH2
C
COOH
SCoAO
Both CO2 carbon atoms derived from oxaloacetate
Succinyl-CoA Synthetase(Succinyl Thiokinase)
GDP + Pi GTP
+ CoASH
Succinyl- CoA
H2C
CH2
C
COOH
SCoAO
H2C
H2C
COOH
COOH
Succinate
High Energy Thioester —> Phosphoanhydride Bond
Plants and Bacteria: ADP + Pi —> ATP
Randomizationn of labeled C atoms
∆Go’ = ~0
Thermodynamics(Succinyl-SCoA Synthetase)
Succinyl-SCoA+ H2O Succinate + CoA
GDP + Pi GTP + H2O
Succinyl-SCoA + GDP + Pi
² Go' = –32.6 kJ / mol
² Go' = +30.5 kJ / mol
² Go' = –2.1 kJ /molSuccinate + GTP + CoA
Page 581
Evidence for Phosphoryl-enzyme Intermediate
(Isotope Exchange)
Absence of Succinyl-SCoA
Figure 17-12 part 1
Mechanism of Succinyl-CoA Synthetase
(Formation of High Energy Succinyl-P)
Figure 17-12 part 2
Mechanism of Succinyl-CoA Synthetase
(Formation of Phosphoryl-Histidine)
Figure 17-12 part 3
Mechanism of Succinyl-CoA Synthetase(Phosphoryl Group Transfer)
Substrate-level phosphorylation
Nucleoside Diphosphate Kinase
(Phosphoryl Group Transfer)
GTP + ADP ——> GDP + ATP
∆Go’ = ~0
Succinate Dehydrogenase
Randomization of C-atom Labeling
Membrane-Bound Enzyme
H2C
H2C
COOH
COOH
Succinate
CH
HC COOH
HOOC
Fumarate
FAD FADH2
∆Go’ = ~0
Figure 17-13
Covalent Attachment of FAD
FAD used for Alkane Alkene
• Reduction Potential– Affinity for electrons; Higher E, Higher Affinity
– Electrons transferred from lower to higher EEh
o’ = Go’/nF = -(RT/nF)ln (Keq)
FAD/FADH2
Succinate/Fumarate
NAD+/NADH
Isocitrate/α-Ketoglutarate
Reduction Potential
Fumarase
H2O
CH
HC COOH
HOOC
Fumarate
HC
H2C COOH
HO COOH
Malate
∆Go’ = ~0
Page 583
Mechanism of Fumarase
Malate Dehydrogenase
NAD+ NADH + H+
HC
H2C COOH
HO COOH
Malate
C
H2C COOH
O COOH
Oxaloacetate
∆Go’ = +29.7 kJ/mol
Low [Oxaloacetate]
Thermodynamics
Malate + NAD+ Oxaloacetate + NADH + H+
Acetyl-SCoA + Oxaloacetate Citrate + CoA
Malate + NAD+
+ Acetyl-SCoA
² Go' = +29.7 kJ / mol
² Go' = –31.5 kJ / mol
² Go' = –1.8 kJ /molNADH + H+ +
Citrate + CoA
Figure 17-14
Products of the Citric Acid Cycle
Page 584
ATP Production from Products
of the Central metabolic Pathway
= 32 ATP
NADH 2.5 ATPFADH2 1.5 ATP
Amphibolic Nature of Citric
Acid Cycle
Carbons of Glucose:1st cycle
1 2 36 5 4
3, 4
2,51,6
2,51,61,62,5
2,51,61,62,5
Carbons of Glucose:2nd cycle:
Carbons 2,5:After 1½ turns:all radioactivity is CO2
Carbons of Glucose:2nd cycle:
Carbons 1,6:After 2 turns:¼ radioactivity in each carbon of OAA
Carbons of Glucose:3rd cycle:
Carbons 1,6:After 3 turns:½ radioactivity is CO2
Each turn after willlose ½ remainingradioactivity
Carbon Tracing from Glucose
• Glucose radiolabeled at specific Carbons– Can determine fate of individual carbons
• Carbons 1,6– 1st cycle: 1, 4 of oxaloacetate– Starting at 3rd cycle ½ radioactivity CO2/cycle
• Carbons 2,5– 1st cycle: 2, 3 of oxaloacetate
– 2nd cycle: all eliminated as CO2
• Carbons 3,4– All eliminated at CO2 during Pyruvate Acetyl-CoA
You are following the metabolism of pyruvate in which the methyl-carbon is radioactive: *CH3COCOOH.
-assuming all the pyruvate enters the TCA cycle as Acetyl-CoA, indicate the labeling pattern and its distribution in oxaloacetate first formed by operation of the TCA cycle.
Generation of Citric Acid Cycle Intermediates
Pyruvate Carboxylase
Mitochondrial Matrix
Pyruvate Carboxylase
Animals and Some Bacteria
ATP
HCO3–
(CO2)H3C C COOH
O
COOH
CH2
CO COOH
Oxaloacetate
ADP + Pi
+
PyruvatePyruvate
Carboxylase
Biotin Cofactor(CO2 Carrier)
NHC
HN
H2CS
CH
O
(CH2)4 C NH
O
(CH2)4 CH
C
NH
O
Biotin
Lysine
Reaction Mechanism I(Dehydration/Activation of HCO3
–)
NHC
HN
H2CS
CH
O
(CH2)4 C NH
O
(CH2)4 Enzyme
O P O
O
O–
P
O
O–
O–AMP –O COH
O
HCO3–
ATP
CO
–ONH
CN
H2CS
CH
O
(CH2)4 C NH
O
(CH2)4 Enzmye
Biotinyl-Enzyme
ADP + Pi
Carboxybiotinyl- Enzyme
Reaction Mechanism II(Transfer of CO2 to Pyruvate)
C C CH2–
OO
–O CO
–ONH
CN
H2CS
CH
O
(CH2)4 C NH
O
(CH2)4 EnzymeC C CH2
O–
O
–O
CO
O–C C CH2
OO
–O
Pyruvate EnolateCarboxybiotinyl-Enzyme
Oxaloacetate
Biotinyl- Enzyme
Fates of Oxaloacetate
Regulation!
COO–
C
CH3
O
ATP COO–
C
CH2
O
COO–
ADP + Pi
Pyruvate
+ HCO3–
Oxaloacetate
PyruvateCarboxylase
Gluconeogenesis
Citric AcidCycle
Regulation of Pyruvate Carboxylase
Allosteric ActivatorAcetyl-SCoA
Glyoxylate Cycle
Glyoxysome
Plants and Some Microorganisms
Citrate Synthase(citrate condensing enzyme)
Acetyl- SCoA Oxaloacetate
H3C C
O
S CoA
C
H2C
COOH
COOH
O+
H2C
C
H2C
HO
COOH
COOH
COOH
Citrate
CoA–SH
Aconitase
Cis- aconitate(~3%)
I socitrate(~6%)
H2C
C
H2C
HO
COOH
COOH
COOH
Citrate(~91%)
H2C
C
HC
COOH
COOH
COOH
H2C
HC
CH
COOH
COOH
COOH
HO
H2OH2O
Glyoxylate Cycle Enzymes
CHO
COOH
Glyoxylate
H2C
HC
CH
COOH
COOH
COOHHO
H3C C S–CoA
O
H2C
H2C
COOH
COOH
CoA-SH
CH
H2C
COOH
COOH
HO
CHO
COOH
Glyoxylate
+
SuccinateI socitrate
I socitrateLyase
Acetyl–SCoA Malate
+
MalateSynthase
Plants and Some Microorganisms
Malate Dehydrogenase
NAD+ NADH + H+
HC
H2C COOH
HO COOH
Malate
C
H2C COOH
O COOH
Oxaloacetate
Net Reaction of Glyoxylate Cycle
Net increase of one 4-carbon unit!
2 Acetyl-CoA 1 Oxaloacetate
Figure 17-18
Glyoxylate Cycle and the Glyoxysome
Regulation of the Citric Acid Cycle
Regulatory Mechanisms
• Availability of substrates– Acetyl-CoA– Oxaloacetate
– Oxygen (O2)
• Need for citric acid cycle intermediates as biosynthetic precursors
• Demand for ATP
Table 17-2
Free Energy Changes of Citric Acid Cycle Enzymes
Regulation of Pyruvate Dehydrogenase
• Product Inhibition (competitive)
– NADH
– Acetyl-SCoA
• Phosphorylation/Dephosphorylation
– PDH Kinase: inactivation
– PDH Phosphatase: reactivation
Figure 17-15
Covalent Modification and Regulation of PDH
Regulation of PDH Kinase(Inactivation)
• Activators– NADH– Acetyl-SCoA
• Inhibitors– Pyruvate– ADP– Ca2+ (high Mg2+)
– K+
Regulation of PDH Phosphatase(Reactivation)
• Activators– Mg2+
– Ca2+
Regulation of Citrate Synthase
• Pacemaker Enzyme (rate-limiting step)
• Rate depends on availability of substrates
– Acetyl-SCoA
– Oxaloacetate
Regulation of Isocitrate Dehydrogenase
• Pulls aconitase reaction
• Regulation (allosteric enzyme)
– Positive Effector: ADP (energy charge)
– Negative Effector: ATP (energy charge)
• Accumulation of Citrate: inhibits Phosphofructokinase
Regulation of -Ketoglutarate Dehydrogenase
• Inhibitors
– NADH
– Succinyl-SCoA
• Activator: Ca2+
Figure 17-16
Regulation of the Citric Acid Cycle