Week 2 - TCA Cycle

Question 1

What reaction is catalyzed by the pyruvate dehydrogenase complex (PDC)? Where does it occur?

Answer 1

The conversion of pyruvate to Acetyl-CoA. The loss of CO2 is involved here. It occurs in the mitochondrial matrix of eukaryotes. The efficiency of the PDC is maintained via substrate channeling.

Question 2

What are the essential features of the TCA cycle?

Answer 2

Reduction of NAD+, reduction of FAD, loss of CO2.

Question 3

What is special about the structure of the Coenzyme A molecule?

Answer 3

It has a sulphydryl group, as indicated here by the ‘S’, and a number of chemical entities can be attached to that sulphur. They are not a permanent part of the enzyme’s structure. They associate, fulfill a function, and dissociate. The function is to accept and carry acetyl groups. The reactive thiol group (the sulfur) is where coenzyme A will attach the acetyl group and carry it.

Question 4

What is another name for Vitamin B5?

Answer 4

Pantothenic acid.

Question 5

What are the 5 coenzymes required for the conversion of pyruvate to Acetyl-CoA?

Answer 5

Thiamine pyrophosphate (TPP), lipoyllysine, and FAD are
prosthetic groups.
NAD+ and CoA-SH are co-substrates.
Catalysed by the pyruvate dehydrogenate complex.

Question 6

How does the structure of pyruvate dehydrogenate complex differ in prokaryotes and eukaryotes?

Answer 6

The pyruvate dehydrogenase complex is organized in cubic symmetry in Gramnegative bacteria, having 60 subunits in three functional proteins.
In eukaryotes and Gram-positive bacteria it is organized in dodecahedral symmetry, and consists of a total of 96 subunits, organized into three functional proteins in the human enzyme (it contains three subenzyme complexes).

Question 7

What is lipoyllysine?

Answer 7

Lipoic acid covalently linked to a lysine residue. This is another example of an electron carrier, so we can have a reduced disulphide (forming a ring structure) or an oxidised one (the two sulfurs not joined, and each carrying a H atom). The oxidised form can carry an acetyl group.

Question 8

What are the individual functions of the 3 enzymes in the pyruvate dehydrogenase complex (PDC)?

Answer 8

Enzyme 1 (Pyruvate dehydrogenase) - Decarboxylation of pyruvate to an aldehyde, and oxidation of aldehyde to a carboxylic acid. 
Enzyme 2 (Dihydrolipoyl transacetylase) - Formation of acetyl-CoA (product 1). 
Enzyme 3 - (Dihydrolipoyl dehydrogenase) - Reoxidation of the lipoamide cofactor, and regeneration of the oxidized FAD cofactor, generation of NADH.

Question 9

What is thiamine pyrophosphate (TPP)?

Answer 9

A form of Vitamin B1.

Question 10

What are the overall key steps of the pyruvate dehydrogenation complex (PDC)?

Answer 10

We have pyruvate coming in, we have loss of CO2, we reduce NAD to form NADH, and we produce Acetyl CoA.

Question 11

What does a deficiency in thamin / vitamin B1 cause?

Answer 11

A disease known as Beri Beri, characterised by the loss of neural function.

Question 12

Why is Acetyl-CoA seen as a central molecule in metabolism?

Answer 12

It’s a starting block for several anabolic processes, and the end product for many other catabolic processes.

Question 13

What does the TCA cycle generate?

Answer 13

3 NADH
1 FADH2
1 GTP - can be transferred over to ATP later via transphospholylase / transferase, but ATP not directly generated through the TCA cycle.

Question 14

What is Vitamin B2 also known as? What is its importance in metabolism?

Answer 14

Riboflavin. It is the precursor of FMN (Flavin Mononucleotide) and FAD (Flavin Adenine Dinucleotide). The word ‘flavis’ is latin for ‘yellow’, so this is the B vitamin that will turn your urine yellow if you take a supplement.

Question 15

Vitamin B2 deficiency symptoms?

Answer 15

Riboflavin deficiency symptoms: sore throat, lesions of the lips and mucosa of the mouth, glossitis, conjunctivitis, seborrheic dermatitis.

Question 16

In which complexes of the respiratory chain do you find flavin prosthetic groups?

Answer 16

Complexes I and II.

Question 17

What makes the mitochondria special?

Answer 17

They are an organism within their own right, they have their own DNA and their own ribosomes for synthesising their own proteins. It is also where the TCA cycle occurs in eukaryotes.

Question 18

Which enzyme in the TCA cycle does not occur in the mitochondrial matrix?

Answer 18

Succinate dehydrogenase, which is actually buried in the inner mitochondrial membrane. It produces our only equivalent of FADH2, i.e. we’re extracting electrons, and we’re producing a reduced electron carrier.

Question 19

At which steps in the TCA cycle to we produce our three equivalents of NADH?

Answer 19

Step 3 - Isocitrate dehydrogenase.
Step 4 - a-Ketoglutarate dehydrogenase.
Step 8 - Malate dehydrogenase.

Question 20

At which step do we produce our only equivalent of GTP?

Answer 20

Step 5 - Succinyl-CoA synthetase. This step involves substrate-level phosphorylation.

Question 21

At which steps do we produce CO2?

Answer 21

Steps 3 and 4, which coincide with the first two NADH generation steps.

Question 22

What is the structure of citric acid / citrate? How does it end up by the end of the TCA cycle?

Answer 22

It’s a tricarboxylic acid - a 3-carbon backbone with 3 carboxylic acid groups attached. Two of these carbon atoms have just come from the Acetyl-CoA, which came from pyruvate. In the TCA cycle, we lose two carbons via the loss of two carboxylic acids (CO2), so by the end of the cycle we have a 4-carbon molecule (malate). Oxaloacetate is just malate that has been oxidised. This then combines with the next acetyl-CoA to once again become a 6-carbon molecule, and back around the cycle it goes.

Question 23

At which step do we get reduction of FAD to FADH2?

Answer 23

Step 6 - Succinate dehydrogenase.

Question 24

Where are the two carbon atoms that are lost as CO2 derived from?

Answer 24

Oxaloacetate.

Question 25

In step 2 of the TCA cycle - Aconitase, why are the Fe-S (Iron-Sulfur complexes) important?

Answer 25

They act in both the binding of the substrate and in the catalytic addition or removal of H2O.

Question 26

What does step 2 of the TCA cycle involve? What is the name of the intermediate here?

Answer 26

The conversion of citrate to isocitrate via aconitase. The intermediate molecule is called aconitate. It is basically just a reaction to reshuffle some atoms so we get movement of the hydroxyl group across.

Question 27

What does step 4 of the TCA cycle involve?

Answer 27

We start with a-Ketoglutarate, we have formation of CO2 and production of NADH, and we form a Coenzyme A-linked compound (succinyl-CoA), all via the enzyme a-Ketoglutarate dehydrogenase. Very similar reaction to the one at pyruvate dehydrogenase complex.

Question 28

Why is the oxidation of Acetyl-CoA so complex?

Answer 28

The citric acid cycle not only acts as a method of producing energy carriers for the electron transport chain (ETC), but is also a pathway for the provision of precursors for the synthesis of many important biochemicals.

Question 29

What are anaplerotic reactions?

Answer 29

They are chemical reactions that form intermediates of a metabolic pathway.

Question 30

What is the net reaction of the TCA cycle?

Answer 30

Acetyl-CoA + 3NAD+ + FAD + GDP + Pi + 2H2O —>

CoA-SH + 3NADH + 3H+ + FADH2 + GTP + 2CO2