Pyruvate Dehydrogenase Flashcards
What does PDH stand for?
(In the context of enzymes)
Pyruvate dehydrogenase
What role does the PDH complex serve?
(In an overall sense)
It act as a link between glycolysis and the TCA cycle by converting pyruvate into acetyl-CoA so that it may pass into the mitochondrial matrix and feed into the cycle.
Identify:
The specific overall reaction carried out by PDH.
Oxidative decarboxylation of pyruvate to form acetyl-CoA.
This generates an NADH as well. (2 NADH overall, as left with 2 pyruvate at the end of glycolysis).
List:
The THREE enzymes that make up the pyruvate dehydrogenase (PDH) complex.
- E1: Pyruvate dehydrogenase.
- E2: dihydrolipoyl transacetylase.
- E3: dihydrolipoyl dehydrogenase.
Which binding domains (BD) comprise the pivot point for the lipoyl domain (LpD) ‘swinging arms’?
E1BD & E3BD
How many reactions and coenzymes contribute to the oxidative decarboxylation of pyruvate by the PDH complex?
Five reactions and coenzymes.
Note: CoA-SH and NAD+ act as substrates too.
Describe:
The ΔG°’ of the PDH catalysed reaction, and what this indicates.
It is large and negative, indicating that it is spontaneous and irresversible.
Specifically, it is -33.4 kJ mol-1.
List:
The FIVE coenzymes of the PDH complex.
- TPP (thiamine pyrophosphate; from vitamin B1)
- Lipoic acid
- CoA (coenzyme A; from vitamin B5)
- FAD (flavin adenine dinucleotide; from vitamin B2)
- NAD+ (nicotinamide adenine dinucleotide; from vitamin B3)
What is the role of the LpD (lipoyl domain) ‘swinging arms’ in the PDH complex?
To deliver electrons and intermediates from one active site to another.
What part of the PDH complex is the coenzyme TPP bound to, and by what kind of interaction?
Non-covalently bound to E1.
What part of the PDH complex is the coenzyme lipoic acid bound to, and by what kind of interaction?
Covalently bound to a Lys on E2.
This forms a lipoamide.
What part of the PDH complex is the coenzyme CoA bound to, and by what kind of interaction?
Non-covalently bound to E2.
It is a substrate of E2 and forms part of the product (acetyl-CoA) of the PDH complex.
What part of the PDH complex is the coenzyme FAD bound to, and by what kind of interaction?
Covalently bound to E3.
What part of the PDH complex is the coenzyme **NAD+** bound to, and by what kind of interaction?
Non-covalently bound to E3.
It is a substrate of E3, and is converted to NADH.
Why can thiamine deficiency lead to severe neurological symptoms?
The brain exclusively utilises aerobic respiration to generate energy.
Thiamine is not stored nor synthesised well in most vertebrates, and so must be obtained via diet.
What disease is caused by chronic thiamine deficiency?
Beri Beri disease
Main symptoms include neurological dysfunction, paralysis, limb atrophy, and cardiac failure.
What happens when lipoic acid binds with Lys on E2 and E3BP?
It forms a long lipoamide arm that can swing between the active sites of E1, E2, and E3.
What is unique or important about the disulfide bond of the lipoamide arm?
It may be reduced to a dithiol group, which can then act as an electron carrier or acyl carrier.
It undergoes redox reactions for these roles.
How does arsenic alloesterically inhibit the PDH complex?
It readily and irreversibly binds to the dithiol group of the lipoamide arms.
What is important about the thiol group of CoA?
(Thiol = a carbon-bonded sulfhydryl ; C-SH)
It can covalently bind with an acyl group to form a thioester bond.
This has a high hydrolysis potential (i.e. large negative ΔG), and essentially ‘activates’ the molecule with the acyl group.
An example is acetyl-CoA.
What acts as the electron acceptor in the E3 reaction of the PDH complex?
NAD+
Define:
Prosthetic group
(in the context of enzymes)
A non-amino acid component that covalently binds to enzymes and assists in their function.
For example, FAD covalently binds to E3 of the PDH complex.
Identify:
The enzyme(s), substrate, end product, and any other important byproducts/reactants of the PDH complex reaction I.
- E1: Pyruvate dehydrogenase
- Decarboxylation of pyruvate to a 2C acetyl group.
- Binding of this acetyl group to TPP to form a reactive hydroxyethyl-TPP.
Note: TPP first binds to E1 before reacting with the pyruvate.
CO2 is the byproduct of this step.
Identify:
The enzyme, substrate, end product, and any other important byproducts/reactants of the PDH complex reaction II.
- E1: pyruvate dehydrogenase to E2: dihydrolipoyl transacetylase
- A redox reaction whereby the hydroxyethyl-TPP of E1 is oxidised as the hydroxethyl is transferred to the lipoamide disulphide arm of E2 (reduction) to form a thioester intermediate (acetyl-dihydrolipoamide).
Identify:
The enzyme, substrate, end product, and any other important byproducts/reactants of the PDH complex reaction III.
- E2: dihydrolipoyl transacetylase
- Acetyl group transferred to CoA by E2.
- Simultaneously, the lipoamide is reduced (dihydrolipoamide).
Identify:
The enzyme, substrate, end product, and any other important byproducts/reactants of the PDH complex reaction IV.
- E2: dihydrolipoyl transacetylase to E3: dihydrolipoyl dehydrogenase
- Redox reaction where the dihydrolipoamide arm is oxidised by reducing the FAD prosthetic group of E3.
Note: in this step, the hydrides attached to FAD are then transferred to the disulfide of the E3 dihydrolipoyl (thus reducing it). This is the disulfide interchange.
Identify:
The enzyme, substrate, end product, and any other important byproducts/reactants of the PDH complex reaction V.
- E3: dihydrolipoyl dehydrogenase
- NAD+ is reduced by FADH2 after it has reoxidised the disulfide of E3.
In this FAD is an important intermediate.
What is the disulfide interchange during step IV of the PDH reaction complex?
When the FADH2 passes its two hydrides to the disulfide of the E3 dihydrolipoyl temporarily.
What are the starting substrates and end products of the PDH complex reaction?
Also known as the transition or prepatory stage for the TCA cycle.
- SS: 2 pyruvate + 2 CoA-SH + 2 NAD+
- EP: 2 acetyl-CoA + 2 NADH
Note: TPP, FAD, and lipoate are also vital for the process.
List:
FOUR key advantages of multi-complex enzymes.
(Like the PDH complex)
- Higher reaction rate.
- Reduction of diffusion dependency.
- Reduced side reactions.
- Multiple regulation sites + coordinated regulation.
