Download Biochemical Energetics – The Citric Acid Cycle Objectives

Biochemical Energetics – The Citric Acid Cycle Objectives & Handout
The First of the Final Common Pathways
Objectives
I.
II.
The Pyruvate Dehydrogenase Complex.
A. Reaction
1. Pyruvate is oxidatively decarboxylated to acetate (ethanoate) then covalently linked to the
sulfhydral group of Coenzyme-A forming Acetyl-CoA.
B. Subunit structure.
1. Pyruvate dehydrogenase (enzyme activity 1 or E1).
2. Dihydrolipoyl transacetylase (enzyme activity 2 or E2).
3. Dihydrolipoyl dehydrogenase (enzyme activity 3 or E3).
4. Pyruvate dehydrogenase kinase.
5. Pyruvate dehydrogenase phosphatase.
C. Necessary coenzymes and cosubstrates.
1. Which are the soluble cosubstrates?
2. What are the prosthetic groups (coenzymes) covalently linked to:
a) Pyruvate dehydrogenase (E1 subunit)?
b) Dihydrolipoyl transacetylase (E2 subunit)?
c) Dihydrolipoyl dehydrogenase (E3 subunit)?
D. Reaction Mechanism.
1. Reaction broken into many parts.
The Tricarboxylic Acid Cycle {The TCA Cycle; The CitricAcid Cycle; The Krebs Cycle}
A. What is the “fuel” of the TCA Cycle?
1. What molecule / ion is oxidized as it travels around the TCA Cycle?
B. What are the products of one turn of the TCA Cycle?
C. Summarize the reactions of the citric acid cycle.
1. Oxidation steps
a) How is the step catalyzed by the α-ketoglutarate dehydrogenase complex similar to the
reaction catalyzed by the pyruvate dehydrogenase complex?
2. Re-arrangement steps.
3. Substrate level phosphorylation step.
D. State the reactants and products of the “first step” of the Citric Acid Cycle and the product(s) of the
“last step” of the Citric Acid Cycle.
E. Describe how the Tricarboxylic Acid Cycle (TCA) provides precursors (NADH / FADH2) for
energy generation under aerobic conditions.
F. Discuss the control points of the Tricarboxylic Acid Cycle
1. Describe how TCA Cycle intermediate concentrations control the rate of the TCA Cycle.
a) Reaction(s) that increase the concentration of intermediates.
(1) Anapleurotic reactions.
b) Places where the intermediate concentration can be / is decreased.
c) Use of TCA Cycle intermediates as precursors for anabolic reactions.
(1) Amphibolic pathway.
2. Describe how acetate (acetyl-CoA) availability controls the rate of the TCA Cycle.
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a) Describe how the rate of the pyruvate dehydrogenase complex is controlled.
b) Allosteric effectors and their actions.
c) Control by reversible covalent modification.
(1) The reactions catalyzed by Pyruvate Dehydrogenase Kinase and Pyruvate
Dehydrogenase Phosphatase.
(2) Allosteric control of Pyruvate Dehydrogenase Kinase and Pyruvate Dehydrogenase
Phosphatase activity.
3. Describe the allosteric enzymes within the Citric Acid Cycle.
a) Describe the allosteric modulators and their effects on the allosteric enzymes that control
The Citric Acid Cycle.
G. Ask yourself “What If Questions”
1. Would the cell survive if the TCA Cycle was completely inhibited?
2. What necessary cellular molecules could not be synthesized if the TCA Cycle was completely
inhibited?
Pyruvate Dehydrogenase Complex
Function & Chemical Reaction:
Subunit Composition:
1.
2.
3.
4.
5.
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©Kevin R. Siebenlist, 2017
Necessary Coenzymes & Cosubstrates:
1.
2.
3.
4.
5.
O
H 3C
HS-CoA
H3C
C
S
CoA
O
C
S
SH
Dihydrolipoyl
transacetylase
SH
SH
O
C
Pyruvate
C
NH
NH
O
O
H 3C
E2
C
C
O
O
Thiamine
Pyrophosphate
(TPP)
FAD
HN
C
Pyruvate
dehydrogenase
E1
OH
H 3C
C
Dihydrolipoyl
dehydrogenase
E3
H 3C
NADH
TPP
O
C
O
C
H
OH
S
FADH2
S
TPP
O
NAD
CO2
3
©Kevin R. Siebenlist, 2017
The Tricarboxylic Acid Cycle - Proper
Overall Reaction
Acetyl-S-CoA + 3 NAD+ + FAD + ADP + PO4-3 + H2O
CoA-SH + 2 CO2 + 3 NADH + FADH2 + ATP + 2 H+
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O
O
NADH
O
C
C
NAD+
H3C
O
O
O
O
CH2
O
HO
Oxaloacetate
OH
HC
O
C
1
C
8
C
CoA-SH
S
Acetyl-CoA
CH2
O
CoA
C
C
C
CH2
CH2
C
C
O
O
O
O
O
O
Citrate
Malate
H2O
7
O
H
CH2
4 - -Ketoglutarate Dehydrogenase
C
HC
5 - Succinyl-CoA Synthetase
HO
C
O
O
C
3 - Isocitrate Dehydrogenase
C
H
O
2 - Aconitase
O
C
2
1 - Citrate Synthase
O
Fumarate
7 - Fumarase
O
FADH2
O
C
O
FAD
NAD+
3
O
C
CH2
CH2
CH2
CH2
C
NADH
CO2
O
C
C
O
O
Isocitrate
8 - Malate Dehydrogenase
6
O
CH
C
6 - Succinate Dehydrogenase
O
O
C
O
5
O
O
C
Succinate
CO2
O
4
CoA-SH
CH2
O
-Ketoglutarate
ÿ
CH2
CoA-SH
ATP
NAD+
O
ADP+PO4-3 C
CoA
S
NADH
Succinyl-S-CoA
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Control of the TCA Cycle
By Controlling the Concentration of Pathway Intermediates:
Pyruvate Carboxylase Reaction CO2 (HCO3–)
+
ADP
+
PO4–3
ATP
+
H2 O
O
H3C
C
O
Biotin
C
Pyruvate
O
O
C
O
Pyruvate
Carboxylase
O
C
H2
C
O
C
Oxaloacetate
O
Other uses for TCA Cycle Intermediates:
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ATP, NADH,
Acetyl-CoA
—
Pyruvate
Dehydrogenase
Phosphatase
Catalyzes the
Removal of PO4–3
Acetyl-CoA
—
+
PEP, AMP,
Ca+2 ,Mg+2
E1
(—) O3PO
Pyruvate, ADP
Ca2+, Mg2+
—
Pyruvate
Dehydrogenase
Kinase
+
E2
NADH
—
E3
+
+
NAD
Coenzyme A
Catalyzes the
Addition of PO4–3
ATP, NADH
Acetyl-CoA
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+ ADP
Citrate Synthase
– ATP & NADH (Allosteric Inhibitors)
Citrate & Succinyl-CoA (Competitive Feedback Inhibitors)
+ Ca+2, NAD, & ADP
Isocitrate Dehydrogenase
– NADH & ATP
+ Ca+2
-Ketoglutarate Dehydrogenase
– NADH & Succinyl-CoA
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