Metabolism 4

Question 1

What happens in the Link reaction?

Answer 1

-pyruvate oxidised to acetyl CoA + CO2
-in anaerobic conditions
-1 molecule of NADH formed

Question 2

What enzymes are in the pyruvate dehydrogenase complex?

Answer 2

-pyruvate decarboxylase
-dihydrolipoyl transacetylase - transfers acetyl fragment
-dihydrolipoyl dehydrogenase - transfers electrons to NADH

Question 3

What cofactors do pyruvate dehydrogenase bind to?

Answer 3

-thiamine pyrophosphate (TPP)
-lipoamide
-FAD/FADH2
-coenzyme A
-NAD+/NADH

Question 4

Describe coenzyme A

Answer 4

-an activated carrier molecule - carries acetyl group via thioester linkage
-hydrolysis of linkage in energetically favourable
-can be coupled with a +ΔG reaction

Question 5

What is FAD and how is it different from FADH2?

Answer 5

-FAD = activated carrier molecule that can carry 2 e- (like NADH)
-binds 2 proteins rather than 1 when reduced, becoming FADH2

Question 6

Describe step 1 of the Link reaction

Answer 6

-pyruvate is decarboxylated to CO2 + hydroxy-ethyl fragment
-carried out by pyruvate dehydrogenase
-the fragment is bound to a TPP cofactor on pyruvate decarboxylase
-loss of carboxyl group (+3) as CO2 (+4) provides an electron for C2 carbon to become C-

Question 7

Describe step 2 of the Link reaction

Answer 7

-hydroxy-ethyl-TPP oxidised to ethyl fragment by lipoamide cofactor on dihydrolipoyl transacetylase
-forms acetyl-dihydrolipoamide

Question 8

Describe step 3 of the Link reaction

Answer 8

-acetyl-dihydrolipoamide reacts with coenzyme A to form acetyl CoA + dihydrolipoamide
-these are oxidised by FAD cofactor to form FADH2
-FADH2 reduces NAD+ to NADH

Question 9

What is made in the Krebs cycle?

Answer 9

-lots of electron carriers
-makes ATP by substrate level phosphorylation

Question 10

What are the steps of the Krebs cycle?

Answer 10

1. citrate formation
2. citrate isomerisation
3. the first decarboxylation
4. the second decarboxylation
5. ATP formation
6. succinate oxidation
7. fumarate hydration
8. malate oxidation

Question 11

Describe the first step of the Krebs cycle

Answer 11

-citrate synthase removes proton from methyl group on acetyl CoA to form CH2^-
-CH2^- acts as a nucleophile towards carbonyl group of oxaloacetate
-energetically favourable CoA-intermediate hydrolysis drives the forward reaction

Question 12

Describe the second step of the Krebs cycle

Answer 12

-aconitase isomerises citrate (tertiary alcohol) to isocitrate (secondary alcohol)
-does this by removing water then adding it back - hydroxyl group moves from C3 to C4
-makes next reaction easier as now breaking C-H rather than C-C

Question 13

Describe the third step of the Krebs cycle

Answer 13

-isocitrate dehydrogenase catalyses oxidation of C4
-hydroxyl group converted to carbonyl
-NAD+ molecule reduced in this process
-unstable intermediate is formed that is rapidly decarboxylated
-produces 𝛼-ketoglutarate + CO2

Question 14

What is the importance of CO2?

Answer 14

-very stable - more so than the reactants
-easily escapes from site of reaction
-more products than reactants = +ive entropy

Question 15

Describe the fourth step of the Krebs cycle

Answer 15

-𝛼-ketoglutarate dehydrogenase catalyses oxidation of C5 from +3 to +4 and C4 from +2 to +3
-releases CO2
-oxidation (-ΔG) coupled to NADH + succinyl CoA formation (+ΔG)

Question 16

Describe the fifth step of the Krebs cycle

Answer 16

-succinyl-CoA synthetase catalyses hydrolysis of thioester bond
-replaced with a phosphoester bond to form succinyl phosphate
-thioester bond hydrolysis is energetically favourable
-phosphate transferred to ADP to form ATP by substrate level phosphorylation

Question 17

Describe the mechanism of succinyl-CoA synthetase

Answer 17

-coenzyme A displaced by bound phosphate group to form succinyl phosphate
-histidine side-chain removes Pi to form succinate + phosphohistidine
-Pi group transferred to ADP forming ATP by substrate level phosphorylation

Question 18

Describe the sixth step of the Krebs cycle

Answer 18

-succinate dehydrogenase uses FAD cofactor to oxidise succinate to fumarate
-FAD is the cofactor reduced rather than NAD+
-free energy change of the reaction is insufficient to reduce NAD+ as C=C is weaker than C=O

Question 19

What is succinate dehydrogenase?

Answer 19

A transmembrane protein bound to inner mitochondrial membrane

Question 20

Describe the seventh step of the Krebs cycle

Answer 20

-fumarase converts fumarate to malate by adding water across the C=C bond to form a hydroxyl group
-facilitates oxidation in step 8 by avoiding necessity for C=C formation

Question 21

Describe the eighth step of the Krebs cycle

Answer 21

-malate dehydrogenase uses NAD+ to convert malate to oxaloacetate
-malate hydroxyl group converted to carbonyl using 2H from water to form NADH

Question 22

In the Krebs cycle, what provides the oxygen for CO2?

Answer 22

H2O, not O2

Question 23

What does it mean to say the Krebs cycle is an amphibolic cycle?

Answer 23

It acts catabolically and anabolically

Question 24

How many NADH and FADH2 molecules are generated per acetyl CoA and per glucose?

Answer 24

-NADH = 3 per acetyl CoA, 6 per glucose
-FADH2 = 1 per acetyl CoA, 2 per glucose