M2: Pyruvate Dehydrogenase Complex L9 Flashcards
What is the pyruvate dehydrogenase complex (PDC)?
Pyruvate dehydrogenase is the enzyme that catalyzes the reaction:
pyruvate + CoA + NAD+ –> acetyl-CoA + CO2 + NADH
Where does glycolysis occur? PDC? CAC? Aerobic metabolism?
Glycolysis: cytoplasm
PDC, CAC & Aerobic metabolism: mitochondrion
When does PDC act on pyruvate?
Once pyruvate is in the mitochondria.
How does pyruvate get into the mitochondria?
Pyruvate gets into mitochondrion through the pyruvate translocase (H+ symport).
What is the entrance point for carbons into the CAC?
Acetyl-CoA
What is the goal of the CAC?
To generate reducing agents.
What proteins make up the PDC?
(E1) Pyruvate dehydrogenase (E2) Dihydrolipoyl transacetylase (E3) Dihydrolipoyl dehydrogenase E3-binding protein Pyruvate dehydrogenase kinase Pyruvate dehydrogenase phosphatase
What 5 coenzymes/cofactors are required for the PDC? What proteins do they bind to?
- Thiamine pyrophosphate (TPP): bound to E1
Substrate=Pyruvatve - Lipoic acid: covalently linked to a Lys on E2 (lipoamide)
- Coenzyme A (CoA): substrate for E2
- Flavin adenine dinucleotide (FAD): bound to E3
- Nicotinamide adenine dinucleotide (NAD+): substrate for E3.
Why are the active sites of the 3 PDC enzymes in close proximity?
So that the product of E1 is passed on to the second, and so on. Substrate channeling.
What is the role of PDC?
To generate Acetyl-CoA from pyruvate.
Memorize Pyruvate dehydrogenase reaction.
L9 S6.
What happens in step 1 of PDC? What enzyme is used? Is this step reversible or irreversible? Why?
E1 = pyruvate dehydrogenase
- Nucleophilic attack by Thiamine Pyrophosphate (TPP) leading to a decarboxylation of pyruvate
- C1 of pyruvate released as CO2
- C2 and C3 attached to TPP as hydroxyethyl group = hydroxyethyl-TPP
Irreversible reaction because CO2 diffuses out of mitochondria.
What is step 2 of the PDC? What enzyme is used? Is this step reversible/irreversible?
E2 = Dihydrolipoyl Transacetylase
Reversible
Step 2 regenerates activity of step 1:
The reactive center of lipoamide is a disulfide bond which can be readily and reversibly reduced to make acetyl-dihydrolipoamide. The 2 electrons removed in the oxidation reduce the S-S of the lipoyl group on E2 to SH. TPP is regenerated here!
Acetyl-dihydrolipoamide is a high energy intermediate bc it has a thio-ester bond.
How does lipoamide affect substrate channeling?
Lipoamide is E2’s “swinging arm” to perform substrate channeling between E1 and E3
What is step 3 of the PDC? What enzyme is used? Is this step reversible/irreversible?
E2 = Dihydrolipoyl Transacetylase
Reversible
Step 3: Trans-esterification to CoA =
Acetyl group from Acetyl-dihydrolipoamide gets put onto CoA to make acetyl-CoA. Dihydrolipoamide is produced (fully reduced lipoamide).
What is the summary of the E2 products?
E2 generates acetyl-CoA and regenerates TPP for E1.
Why is Acetyl-CoA a good entry point of the CAC?
Because it has an acetyl thio-ester bond which makes it a high energy compound (its hydrolysis = -31.5 kJ/mole).
What is step 4 and 5 of the PDC? What enzyme is used? Is this step reversible/irreversible?
E3= Dihydrolipoyl Dehydrogenase
Reversible
Step 4: E3 re-oxidizes dihydrolipoamide to lipoamide (removes H’s and regenerates thio-ester bond). Since E3 contains a bound FAD prosthetic group, the oxidation of dihydrolipoamide is coupled to the reduction of FAD to FADH2.
Step 5: enzyme-bound FADH2 reoxidized to FAD by NAD+, thus generating NADH.
What is the aim of E3 (steps 4 and 5)?
E3 restores E2 and its own FAD for another round of generation of acetyl-CoA (for CAC).
E3 generates NADH (for Ox-phos).
Why is the PDC reaction irreversible?
Because the first step is irreversible.
What are the mechanistic advantages of multienzyme complexes?
- Minimized distances for substrates in between active sites: increased reaction rate without having to maintain large pools of intermediates
- Metabolic intermediates are channeled between successive enzyme sites: 2 important effects:
- side reactions are minimized
- protection for chemically labile intermediates - Coordinated control of reactions: shutting off one enzyme effectively shuts the system down.
Why is the regulation of PDC so important?
- No other pathway in mammals for synthesis of acetyl-CoA from pyruvate
- Animals cannot synthesize glucose from acetyl CoA. Thus, conversion of pyruvate to acetyl CoA commits glucose carbons to oxidation in CAC or fatty acids synthesis.
What are the two levels of control of the PDC?
- Product inhibition by acetyl-CoA and NADH
- Covalent modification (phophorylation of E1 Pyruvate dehydrogenase).
How is the PDC regulated by product inhibition?
- At E3, NADH competes for the binding of NAD and at E2, Acetyl-CoA competes for the binding of CoA. Since step 3 and 5 are reversible and there’s more NADH or Acetyl-CoA the reaction goes backwards.
- Since the reaction is going backwards, the substrate for E2 is Acetyl-CoA (instead of CoA), it can no longer accept the Hydroxyethyl-TPP intermediate from E1 to regenerate TPP. This causes a buildup of the Hydroxyethyl-TPP intermediate which causes less TPP.
- Since TPP is required for pyruvate to be decarboxylated (E1). This backs up the whole system and you end up with an accumulation of pyruvate.