Prep For TCA

Question 1

After pyruvate is made from glycolysis where does its go

Answer 1

From the cytoplasm to the matrix of the mitochondria

Question 2

After pyruvate (3 carbons) is sent to the mitochondrial matrix, what happens

Answer 2

Pyruvate is oxidized (loses 2 electrons) and decarboxylated (loses co2)

“Oxidatively decarboxylated”

To turn into acetyl coa (2 carbons)

Question 3

What is the structure of acetyl coa

Answer 3

The acetyl group (c=o) is linked to the sh group of co enzyme A

This bind it’s called the thioester bond

Question 4

If the thioester bond of the acetyl coa is hydrolyzed is it endergonic or excergonic

What does this mean

Answer 4

Highly exergonic meaning it has high acetyl group transfer potential

(can transfer its acetyl group very well to other molecules)

Question 5

What is the conversion of pyruvate to acetyl coa called

What enzyme catalyzes this reaction

Answer 5

The bridge reaction or pyruvate oxidation

Pyruvate dehydrogenase

Question 6

What are the three enzymes in the pyruvate dehydrogenase complex that turn pyruvate to acetyl coa

Answer 6

Pyruvate dehydrogenase (E1)

Dihydrolipoyl transacetylase (E2)

Dihydrolipoyl dehydrogenase (e3)

Question 7

Why are e1 e2 and e3 needed for the bridge reaction

Answer 7

It allows the substrates from each reaction to move from one active site of the enzyme to that next

This short distance between all the Enzymes minimized side reactions and speeds up the reaction rate because it take less time to go from one place to the other

Question 8

What is the prosthetic group of E1 and what reaction does it catalyze

Answer 8

TPP (thymine pyrophosphate)

Oxidative decarboxylation of pyruvate

Question 9

What is the prosthetic group of E2 and what reaction does it catalyze

Answer 9

Lipoamide

Transfer of the acetyl group to coA

Question 10

What is the prosthetic group of E3 and what reaction does it catalyze

Answer 10

FAD

Regeneration of the oxidized form of lipoamide

Question 11

How are the enzymes situated in the pyruvate dehydrogenase complex

Answer 11

The e2 is at the core

E1 and e3 surrounding the core

Question 12

What is the linker region

Answer 12

The region on E2that flips back and forth from e1 and e3

Question 13

What five coenzymes does the pyruvate dehydrogenase complex need

Answer 13

TPP, LIPOAMIDE, FAD (catalytic coenzymes)

CoA, NAD+ (stoichiometric coenzymes, act as actual substrates)

Question 14

How does first step the reaction catalyzed by e1 work

Answer 14

The TPP cofactor of E1 is in the ylid form (+ and - charges next to each other)

Pyruvate react with the carbanion of TPP

It’s becomes decarboxylated (lose co2) and becomes hydroxyethyl TPP

Question 15

How does second step the reaction catalyzed by e1 work

Answer 15

The previously made hydroxy ethyl TPP is oxidized to an acetyl group (c=o)

Then the acetyl group gets transferred to Lipoamide (e2) where the Lipoamide disulphide bond is reduced

The e2 swings to the active site of e1 for this to happen

Question 16

What is the structure of E2 transacetylase

Answer 16

The enzyme has a lysine residue that’s covelently linked to Lipoamide

The Lipoamide acts as an arm that swings from e1 or e3

Question 17

How does the reaction catalyzed by e2 work

Answer 17

The previous acetyl group that was attached to the E2 Lipoamide (acetyl Lipoamide) is transferred to CoA

The thioester bond is still intact

The Lipoamide is fully reduced (dihydrolipoamide)

Question 18

After dihydrolipoamide is made from being fully reduced, how does the next reaction with E3 happen

Answer 18

The fully reduced dihydrolipoamide need to transfer its electrons to another molecule (become oxidized)

To turn back into Lipoamide

Question 19

How does the reaction catalyzed by e3 work

Answer 19

The Dihydrolipoyl amide transfers electrons to FAD (cofactors of E3)

This make FADH2 (reduced) and regenerated Lipoamide (oxidized)

The electrons from fadh2 get transferred to NAD+ to make FAD and NADH

Question 20

What does the NADH do after being form after the E3 step of the bridge reaction

Answer 20

It can move down the electron transport chain

Question 21

Once acetyl CoA is made what happens

Answer 21

It’s either oxidzed to become co2 through the citric acid cycle

Or it’s used to build fatty acids

Question 22

In animals is the conversion of pyruvate to acetyl CoA reversible

Answer 22

No irreversible

Question 23

How is the pyruvate dehydrogenase complex regulated

Answer 23

Allosterically regulated

Or

Covalently modified

Question 24

How is the pyruvate dehydrogenase complex allosterically regulated

Answer 24

The acetyl CoA binds to E2 in inhibits it from making more acetyl CoA

Or the NADH bind to E3 and inhibits it

Question 25

How is the pyruvate dehydrogenase complex regulated through covalent modification

Answer 25

The E1 serine residue gets phosphorylated by kinase and inactivate the pyruvate dehydrogenase (entires reaction)

Or the e1 PDH gets dephosphorylated by phosphatase and is active

Question 26

When the muscle is at rest ( energy change is high) how is the pyruvate dehydrogenase complex regulated

Answer 26

This means there is high NADH ATP AND ACETYL COA

We don’t need more atp

these three things stimulate pyruvate dehydrogenase kinase which inactivates the PDH to stop the citric acid cycle from starting

This makes it so that less atp is made from TCA

Question 27

When the muscle is active ( energy change is low) how is the pyruvate dehydrogenase complex regulated

Answer 27

There’s more pyruvate since glycolysis is happening more to get more atp

There’s also more adp since there’s less atp

The adp and pyruvate inhibit pyruvate dehydrogenase kinase which activate PDH