BIOCHEM EXAM 4: TCA Cycle

TCA is a central pathway that connects…

anabolic and catabolic processes

What catabolic processes other than glycolysis can produce Acetyl-CoA that feeds into glycolysis?

oxidative deanimation of amino acids and beta-oxidation of fatty acids

What molecule is combined w/ oxaloacetate to restart the TCA Cycle?

Acetyl-CoA

Is the main function of the TCA Cycle anabolic or catabolic?

catabolic

What are the main products of the TCA Cycle?

ATP, NADH, FADH2

Where do NADH and FADH2 feed into for ATP Production?

OXPHOS

Acetyl-CoA + 3NAD+ + FAD + ADP + P_i - 2H2O →

2CO₂ + 3NADH + 3H + FADH2 + ATP + CoA

What is the overall delta G of TCA Cycle?

-40 kJ/mol

Pyruvate Dehydrogenase Complex (Substrate to Product)

Pyruvate + CoA + NAD+ → acetyl-CoA + CO₂ + NADH

What is the Pyruvate Dehydrogenase Complex?

a multi-enzyme complex that requires 5 coenzymes

What are the 3 enzymes involved in the PDC?

1. Pyruvate dehydrogenase

2. Dihydrolipoyl transacetylase

3. Dihydrolipoyl dehydrogenase

What are the 5 coenzymes involved in the PDC?

• CoA

• NAD+

• Thiamine (B1)

• Lipoic Acid

• FAD

Thiamine Structure

Lipoic Acid Structure

FAD does what in the PDC?

participates but is not reduced

Where is Thiamine (B1) Deficiency or “beriberi common?

Asia after industrial processing of rice (thiamine leeches out of the husk)

What disease do the following symptoms align with?

• Weight loss

• Emotional disturbances and impaired sensory perception

• Weakness and pain in the limbs

• Heart rate issues

• Edema

Thiamine (B1) deficiency

Arsenite and mercury have very similar…

poisoning symptoms

In eukaryotes, what transports Pyruvate into the mitochondrial matrix?

the Mitochondrial Pyruvate Carrier (MPC)

What is Step 1of the TCA Cycle?

Oxaloacetate + Acetyl-CoA → Citrate

Describe Step 1 of the TCA Cycle.

Oxaloacetate (Citrate Synthase→) Citrate

What is the commitment step for the entire TCA Cycle?

Step 1

What kind of rxn is Step 1 of the TCA Cycle?

Group Transfer (condensation)

What is the name of this structure?

Citrate

What is unique about citrate?

it is pro-chiral (it can be converted to chiral molecule in one step)

Which Carboxylic Acid Groups on Citrate are pro-S arm and the pro-R arm?

C1 (pro-S arm)

C3 (pro-R arm)

What is significant about the pro-S and pro-R arms of Citrate?

allow for the molecule to be “passed “ in specific orientation despite symmetry

What is Step 1 of the TCA Cycle inhibited by?

ATP

What is Citryl-CoA?

the intermediate of Step 1

What is different about the compartmentalization of TCA in prokaryotes?

everything happens in the same cytosolic compartment

What is Step 2 of the TCA Cycle?

Citrate → Isocitrate

Describe Step 2 of the TCA Cycle.

Citrate (Aconitase → ) Isocitrate

What is cis-Aconitate?

the intermediate of Step 2

What kind of rxn is Step 2 of the TCA Cycle?

Isomerization

Which arm loses water in Step 2?

pro-R arm

What is the consequence of pro-chirality?

Because aconitase acts specifically on the pro-R arm of citrate, the 2 Cs from acetyl-CoA are not released as CO2 during the first turn of the TCA

Why is Fluroacetate referred to as a trojan horse inhibitor?

it is not a direct inhibitor of any of the enzymes in isolation BUT once inside of the mitochon. → metabolizes into irreversible inhibitor of aconitase, fluorocitrate

What is an alternative to the PDC for making Acetyl-CoA?

Acetyl-CoA synthetase

If you replace the H in red with a F, what did you make?

Fluoroacetate

Fluorocitrate is highly…

poisonous

What is Step 3 of the TCA Cycle?

Iso-Citrate → Alpha-Ketoglutarate

Describe Step 3 of the TCA Cycle.

Isocitrate (Isocitrate dehydrogenase →) Alpha-Ketoglutarate

Which Step of the TCA Cycle loses 1 C?

Step 3

What kind of rxn is Step 3 of the TCA Cycle?

redox

What is Oxalosuccinate?

the intermediate of Step 3

What steps are key regulatory points in eukaryotes along w/ PDH Complex?

• Step 3 (Isocitrate Dehydrogenase)

• Step 4 (Alpha-Ketoglutarate Dehygrogenase)

What is Step 3 of the TCA Cycle inhibited by?

ATP and NADH

What is Step 3 of the TCA Cycle stimulated by?

ADP

What 2 Steps lose just 1 C?

Steps 3 + 4

What is Step 4 of the TCA Cycle?

Alpha-Ketoglutarate → Succinyl CoA

Describe Step 4 of the TCA Cycle.

Alpha-Ketoglutarate (Alpha-Ketoglutarate dehydrogenase →) Succinyl CoA + NADH

Alpha-Ketoglutarate dehydrogenase is a complex of 3 enzymes that also

employs same 5 coenzymes as PDH Complex

What type of rxn is Step 4 of the TCA Cycle?

redox

What is Step 4 of the TCA Cycle inhibited by?

ATP, NADH, and succinyl-CoA

Which step of the TCA Cycle produces ATP?

Step 5

Which steps of the TCA Cycle produces NADH?

Steps 3, 4, & 8 (redox)

Which step of the TCA Cycle produces FADH2?

Step 6 (redox)

All steps of the TCA Cycle are extremely thermodynamically favorable except?

Step 2

What is Step 5 of the TCA Cycle?

Succinyl-CoA → Succinate

Describe Step 5 of the TCA Cycle.

Succinyl CoA (Succinyl CoA Synthetase →) Succinate + ATP

What type of rxn is Step 5 of the TCA Cycle?

ligation

Which Step of the TCA Cycle loses chirality?

Step 5

What is confusing about succinyl CoA synthetase ?

its named backward; breaks down succinyl CoA instead of making it

Which Step’s mechanism of action depends on Histidine?

Step 5

In the liver, the ATP made in Step 5 is

GTP

What is Step 6 of the TCA Cycle?

Succinate → Fumurate

Describe Step 6 of the TCA Cycle.

Succinate (Succinate dehydrogenase →) Fumarate

What type of rxn is the Step 6 of the TCA Cycle?

redox

Why is FAD used in Step 6 of the TCA Cycle?

bc the rxn does not have enough redox potential to reduce NAD+

All enzymes of the TCA Cycle are soluble proteins in the matrix of the mitochondria EXCEPT.. from Step…

Succinate dehydrogenase; Step 6

Which enzyme is an integral membrane protein on the inner mitochondrial matrix?

Succinate dehydrogenase

What Complex is Succinate dehydrogenase a part of?

Complex 2

What is Step 7 of the TCA Cycle?

Fumurate → Malate

Describe Step 7 of the TCA Cycle.

Fumurate (Fumarase →) L-Malate

What is the specific stereoisomer that Step 7 of the TCA Cycle produces?

L-Malate

What is Step 8 of the TCA Cycle?

Malate → Oxaloacetate

Describe Step 8 of the TCA Cycle.

Malate (Malate dehydrogenase →) Oxaloacetate

Step 8 can go in either…

direction

Malate can be shuttled out of the mitochondria for…

gluconeogenesis

Steps 1-4 have Cs from…

Acetyl-CoA

After 1 turn of the TCA Cycle, what happens to the carboxyl carbon of acetate?

None lost on 1st turn, but position changes

After 2 turns of the TCA Cycle, what happens to the carboxyl carbon of acetate?

Completely lost as CO2

What is the fate of the methyl carbon of the acetate?

it will become more and more diluted with each turn but can never be “fully lost” as CO2

Why can the methyl carbon of the acetate never be “fully lost” as CO2?

because of the specific chemistry of the pro-S and pro-R arms of

Entry into the TCA Cycle is …

highly controlled

What are the downregulators that allosterically control the PDH Complex at high E charge?

NADH, Acetyl-CoA, ATP

What are the upregulators that allosterically control the PDH Complex at low E charge?

NAD+, FAD, ADP, Pyruvate

Once Active PDH is phosphorylated by Kinase it becomes?

Inactive PDH

Once Inactive PDH is dephosphorylated by Phosphatase it becomes?

Active PDH

What positively regulates PDH in the liver?

epinephrine

Regulation can be…

tissue dependent

What structure is this?

Epinephrine/adrenaline

Intermediate TCA Enzymes are also…

highly controlled

Negative Regulators of Isocitrate Dehydrogenase

ATP and NADH

Positive Regulators of Isocitrate Dehydrogenase

ADP

Negative Regulators of Alpha-Ketoglutarate Dehydrogenase

ATP, succinyl CoA, and NADH

Intermediate TCA Products can be used as…

precursors

What is citrate used to synthesize, and which TCA step produces it?

Fatty acids and sterols; Step 1

What is alpha-ketoglutarate used to synthesize, and which TCA step produces it?

Glutamate → Other amino acids and purines; Step 3

What is succinyl-CoA used to synthesize, and which TCA step produces it?

Porphyrins, heme, and chlorophyl; Step 4