Study Guide notes

Question 1

Describe the general reaction mediated by the pyruvate dehydrogenase complex? What cofactors are associated? is it a thermodynamically favorable or unfavorable reaction?

Answer 1

General: converts a 3C intermediate (pyruvate) to a 2C intermediate (acetyl-CoA) and CO2
2 cofactors enter/exit:
1. CoA-SH added (activates acetate for citrate synthesis in TCA because OAA and acetate are not reactive enough on their own)
2. NAD+ –> NADH (reoxidizes FAD)

3 cofactors are permanently bound:

1. E1 = TPP
2. E2 = lipoic acid
3. E3 = FAD+

The reaction is a highly EXERGONIC (thermo favorable) reaction

Question 2

What is E1? How does E1 in the pyruvate DH complex function? What is the role of its cofactor?

Answer 2

Name = pyruvate dehydrogenase
Function = decarboxylation
-Covalently bound to TPP which facilitates pyruvate cleavage by stabilizing the carbanion state that forms when you break the bond between the carbonyl and the carboxylate to RELEASE CO2

-E1 covalently links to TPP to form hydroxythyl-TPP and stabilizes via resonance

Question 3

What is E2? How does E2 in the pyruvate DH complex function? What is the role of its cofactor?

Answer 3

Name = dihydrolipoyl transacetylase
Function = activates acetate for condensation with CoA
-Covalently bound to lipoamide (lipoic acid) which has a disulfide bond that can be reduced creating a thiol group that can accept and acetate, forming a high energy thioester. This molecule is isoenergetic with CoA and the acetyl group can therefore be transferred to the CoA sufhydryl group without input of energy, forming Acetyl-CoA

Question 4

What is E3? How does E3 in the pyruvate DH complex function? What is the role of its cofactor?

Answer 4

Name = dihydrolipoyl dehydrogenase
Function = reoxidize lipoamide (lipoic acid)
-Covalently bound FAD cofactor reoxides the lipoamide (becomes FADH2) and then it is reoxidized (to FAD) by NAD+, which binds reversibly and forms NADH

Question 5

What are the steps of TCA?

Answer 5

(go through steps, enzymes, and intermediates, and what type of reaction occurs at each step)

Question 6

Describe the total energetics of TCA and PDH

Answer 6

PDH: 1 NADH, 1 Acetyl CoA, 1 CO2
CA: 3 NADH, 1 FADH2, 1 GTP, 2 CO2

Question 7

Where do the CO2’s from the TCA cycle come from?

Answer 7

from OAA, NOT acetate

Question 8

What is the significance in the energetics of the Malate dehydrogenase reaction?

Answer 8

Thermodynamically unfavorable (delta G = +7.1)
But, because OAA --> citrate is VERY exergonic, the reaction is pulled forward and OAA almost immediately converted into citrate once it is made, keeping the [products]:[reactants] low enough to make it favorable. 

It is important the the reaction is unfavorable for gluconeogenesis because then TCA stops and OAA –> malate to leave the mitochondria