Citric acid cycle Flashcards
How does pyruvate get into the CAC?
Pyruvate gets converted to acetyl-CoA by PDC and then enters the Kreb’s Cycle.
How many reactions are there in the CAC?
8
All the reactions of glycolysis occur in the ________.
cytosol
Describe, very generally, the amphibolic nature of the CAC.
The CAC is involved in both catabolism of carbohydrates and anabolism of carbs, fats, nucleic acids, etc.
Only one _____ is made per cycle of the CAC.
GTP
NADH is cashed in at the mitochondria for how many ATP, practically?
FADH2?
- 5
1. 5
Glycolysis will not be affected if not taking in oxygen as long as what occurs?
Lactic acid fermentation continues to supply NAD+
When not undergoing an emergency, during low oxygen conditions, what will occur to glycolysis?
It will slow
What is paradoxical about the CAC and oxygen?
It cannot run without oxygen but, not a single molecule of oxygen is needed for any of the 8 reactions of this cycle or PDC.
What happens to the CAC when malonate is added?
Glycolysis goes on but oxygen consumption is stopped.
Malonate is similar to succinate but is 3C. It works with succinate DH and blocks the consumption of oxygen, stopping the cycle.
When succinate, fumerate, malate or oxaloacetate are added to the simple reaction (yeast extract with metabolites), the reaction is accelerated a lot. Why?
These aren’t just substrates, they are catalysts.
What are catalysts?
Bring two substrates together and increase the rate of reaction.
They are not used up in the reaction.
Facilitate reaction and then are regenerated.
What are the 8 enzymes of the CAC, starting from after PDC, in order?
1 - Citrate synthase 2 - Aconitase 3 - Iso-citrate DH 4 - a-ketogluterate DH 5 - Succinyl-Coenzyme A synthetase 6 - Succinate DH 7 - Fumerase 8 - Malate DH
What are the five co-factors of PDC?
NAD+, TPP, Lipoate, FAD, CoA
2 of the co-factors of the PDC reaction can be considered substrates. These are?
Why is it more correct to refer to them as co-factors?
CoA
NAD+
Still call them co-factors and not substrates because they are eventually regenerated.
Which enzyme leads to generation of GTP in the CAC?
Succinyl-coenzyme A synthetase
_________ enzymes do not require ATP; _________ enzymes require ATP for synthesis.
Synthases
Synthetases
Aconitase is similar to what enzyme type?
Isomerase
Fumerase is similar to what type of enzyme?
DH
Describe PDC. Do not describe its co-factor or enzyme components.
Multi-enzyme complex containing three enzymes associated together non-covalently.
Describe E1 of PDC.
Pyruvate dehydrogenase
- TPP cofactor bound to E1
Describe E2 of PDC
Dihydrolipoyl transcacetylase
- lipoic acid co-factor
- CoA substrate
Describe E3 of PDC
Dihydrolipoyl DH
- FAD bound
NAD+ substrate
What are the advantages of the multienzyme complex?
1 - Higher rate of reaction
2 - Minimize side reactions
3 - Coordinate control
How does the multienzyme complex accomplish a higher rate of reaction?
Because the product of one enzyme acts as the substrate of the other and is available for the active site of the next enzyme without much diffusion.
What is the possible side reaction of PDC?
After E1, 2C intermediate can come out as acetaldehyde which can be toxic.
How is the side reaction of PDC minimized by having a multi-enzyme complex?
Product of E1 is immediately taken by E2 to reduce to possibility of the side reaction.
Describe how the multi-enzyme complex affords coordinated control.
One enzyme can control the rest. Together, can be controlled very well.
What is the active part of CoA?
SH (reduced)
What is the reduced active part of CoA, oxidized?
SH - reduced
S - oxidized
In the PDC mechanism, which co-factors are immobilized, which are mobile?
FAD, TPP, lipoamide are covalently bound (immobile)
CoA and NAD+ are non-covalently bound (mobile)
What is the co-factor for E1?
TPP (ylid form)
What is the co-factor bound to E2?
Lipoamide (transiently bound to CoA)
What is the co-factor bound to E3?
FAD (Transiently bound to NAD+)
PDC is similar to what enzyme in terms of regulation?
Glycogen synthase.
inactive when phosphorylated, active when not phosphorylated
What enzyme phosphorylates PDC?
PDC kinase
How is PDC kinase activated, or more specifically, what activates it?
NADH, Acetyl CoA
What inhibits PDC kinase?
Pyruvate, ADP, Ca2+, K+, high Mg2+
What activates the PD phosphatase?
Mg2+, Ca2+
Explain the role of PP1 in PDC.
PP1 is a universal phosphatase. Chops off phosphate to make PDC active.
Insulin stimulates insulin-stimulated protein kinase, which phosphorylates the top part ofthe Gm unit of PP1, superactivating it.
What is the paradox of PDC activation by insulin?
Insulin is not an emergency hormone, stimulates glucose uptake and synthesizes glycogen = anabolic hormone.
However, activates PDC, a catabolic enzyme.
This is not a paradox however since it only acts catabolically for glucose, and acts anabolically in other cases.
When there is excess glucose and the glycogen stores are full, PDC will stimulate fat synthesis.
What deficiency causes Beriberi?
Thiamin - vitamin B1
major co-factor for PDC
Describe beriberi.
Thiamin deficiency, major co-factor for PDC, needed for CAC.
Most harmful to the brain, cannot run glycolysis anearobically. Muscles also affected.
Irreversible neurologic damage.
Describe arsenic poisoning.
Arsenic acts violently with dihydrolipoamide, becoming covalently bound to arsenic.
This completely kills off PDC activity.
Which enzyme is affected in the PDC complex by arsenic poisoning?
E2
What is the first reaction of the CAC?
Citrate synthase.
Describe the mechanism for citrate synthase.
Acetyl-CoA binds to citrate synthase.
Brings acetyl-CoA and oxoloacetate together to form citrate.
One oxygen from water added, CoA-SH (reduced) removed.
Exergonic.
What does binding of oxoloacetate do to citrate synthase?
Results in a conformation change which facilitates binding of Acetyl-CoA.
Induced-fit model.
What enzyme performs the second reaction of the CAC?
Aconitase
Aconitase is similar to what enzyme in function?
Isomerase
What does Aconitase do?
Changes the OH and H around in citric acid to form isocitrate.
Removes water to form cis-Aconitase and adds water to that to form isocitrate.
Describe the biological wonder of aconitase.
If done chemically, equal chance to get two products (both forms of isocitrate).
However, biologically, can only get the normal product.
Why is only one product formed biologically by aconitase?
Due to enzyme conformation, chemically confined with limited choice.
Free reaction gives both products.
What is the enzyme of reaction 3 of the CAC?
Isocitrate DH
What are the two isoforms of Isocitrate DH?
One isoform uses NAD+, the other NADP+
What is released during reaction 3? What does the substrate carbon count become?
CO2
6C –> 5C
What is the enzyme of reaction 4?
Alpha-ketoglutarate DH
Describe reaction 4’s enzyme.
Complex of three different enzymes, similar to PDC.
NAD+ is the electron acceptor too.
What is the differences between PDC and a-ketoglutarate DH?
Substrates and end products are different.
A-ketoglutarate instead of pyruvate.
Succinyl-CoA is a product.
What is the enzyme for reaction 5?
Succinyl-CoA synthetase.
What is formed by reaction 5?
GTP (and succinate)
In reaction 5, we go from a _C substrate to a _C product.
5
4
Describe the mechanism for reaction 5.
Histidine in enzyme (succinyl-CoA synthetase)
Enzymes binds to succinyl-CoA and incorporates Pi.
CoA leaves and is replaced by phosphate.
This intermediate is unstable and gives away the phosphate to the His group of the enzyme.
The His group then gives away the phosphate to GDP, to make GTP.
Is succinyl-CoA synthetase a phosphoenzyme?
No, gets phosphorylated very transiently, quickly gives away phosphate to GDP to form GTP.
What is the enzyme of reaction 6?
Succinate DH
Describe reaction 6. i.e. what occurs to the substrate?
Oxidation of succinate to fumarate.
Where is succinate DH located?
Tightly bound to the inner mitochondrial membrane. Link between CAC and ETC.
What inhibits SDH (succinate DH)?
Malonate, has similar structure to succinate but competitively inhibits SDH.
Succinate DH is also what?
Complex 2
Reaction 6 is ________.
reversible
What is the enzyme of reaction 7?
Fumerase
Describe reaction 7.
Hydration of fumerate to malate
What form of fumerate is not recognized by fumerase?
Cis-fumerate
Fumerase is a highly _________ enzyme.
Stereospecific
What is produced by reaction 7?
Malate
Reaction 7 is slightly ________.
exergonic
What is the enzyme of reaction 8 of the CAC?
L-malate DH
Describe reaction 8.
Oxidation of malate to oxaloacetate
L-malate DH is an _____-dependent enzyme
NAD+
How does reaction 8 go forward?
Very endergonic, around +30Kj.
Pulled forward by next three reactions that are highly exergonic.
Oxaloacetate gets used up immediately after it gets formed.
The actual delta G of reaction 8 is _________.
negative
The energy released in the oxidation reactions of the CAC are conserved. How?
Reduction of 3 NAD+ to NADH (Reactions 3, 4 and 8);
Reduction of FAD+ to FADH2 (Reaction 6);
Production of GTP (Reaction 5)
1 glucose runs how many cycles of the CAC?
How much NADH is produced?
FADH2?
GTP?
2
6 NADH
2 FADH2
2 GTP
How many ATP are made practically in the tissues?
30 - 32
What enzyme of the CAC is not used in anaerobic bacteria?
a-ketoglutarate DH
Describe the amphibolic nature of the CAC.
TCS is catabolic but, CAC is also a metabolic hub which acts as an important part of anabolism or synthesis of molecules.
Citric acid can also be used for the synthesis of what?
Fatty acids and sterols
a-ketoglutarate is a precursor for what?
Glutamate, purines, arginine, prolite, glutamine
Succinyl-CoA can be used to synthesize what?
Porphorin ring of Hb.
Oxaloacetate can be used to synthesize what?
Aspartic acid, aspargine, pyrimidines
What product of the CAC is used for gluconeogenesis?
Oxaloacetate
How is oxaloacetate used in neoglucogenesis?
Converted back to PEP, then neoglucogenic pathway to produce glucose
What is produced from the catabolism of all the macromolecules?
Acetyl-CoA
What is the regulation for PDC?
Activators: AMP, CoA, NAD+, calcium
Inhibitors: ATP, acetyl-CoA, NADH, fatty acids
What is the regulation for Citrate synthase?
Activator: ADP
Inhibitor: NADH, Succinyl-CoA, citrate, ATP
What is the regulation for isocitrate DH?
Inhibited by ATP
Activated by calcium and ADP
Describe the regulation of a-ketoglutarate DH.
Inhibit: Succinyl-CoA, NADH
Activate: Calcium
What three enzymes of that play a role in the CAC, either directly or indirectly, are inhibited by NADH?
PDC, a-ketoglutarate DH, citrate synthase
