Citric acid Cycle - RM

Question 1

Where does over 90% of ATP production in aerobic conditions occur? What two processes contribute to it?

Answer 1

mitochondria, CAC and oxidative phosphorylation

Question 2

What cells have the most mitochondria? Why?

Answer 2

cells with high energy needs
heart for contraction
kidney for transport
liver for biosynthesis

Question 3

Why are mitochondria located near structures requiring ATP?

Answer 3

decreases the diffusion path from where ATP is made to where it’s needed, speeds process

Question 4

Which mitochondrial membrane is the permeability barrier?

Answer 4

inner mitochondrial membrane

Question 5

What enzymes are embedded in the inner mitochondrial membrane? Which way do they face?

Answer 5

oxidative phosphorylation enzymes, facing matrix

Question 6

What occurs in the matrix of the mitochondria?

Answer 6

citric acid cycle, oxidative phosphorylation

Question 7

What two molecules can diffuse freely without a transport system between the matrix of the mitochondria and the cytoplasm?

Answer 7

oxygen and carbon dioxide

Question 8

What is there no transport system for across the mitochondrial matrix? What is the result of this?

Answer 8

NADH, it is compartmentalized into matrix NADH and cystolic NADH–reducing equvialents are shuttled between the two to reduce matrix NADH as fuel for oxidative phosphorylation

Question 9

What are the three functions of the citric acid cycle?

Answer 9

converts many fuels into common mobile fuel (NADH)
serves as final meeting place of all oxidizable substrates
provides intermediates for biosynthesis

Question 10

What enzyme oxidizes pyruvate? What does it form? Where does the reaction occur?

Answer 10

pyruvate dehydrogenase complex, acetyl coA, mitochondrial matrix

Question 11

What is referred to as the link between glycolysis and citric acid cycle?

Answer 11

pyruvate dehydrogenase complex (converts end product of glycolysis pyruvate into starting substrate of CAC acetyl coA)

Question 12

What is E1 of the pyruvate dehydrogenase complex? What type of reaction does it catalyze? What is its prosthetic group?

Answer 12

pyruvate dehydrogenase, condensation/decarboxylation, TPP

Question 13

What is E2 of the pyruvate dehydrogenase complex? What type of reaction does it catalyze? What is its prosthetic group?

Answer 13

dihydrolipoyl transacetylase, 2 reactions: oxidative transfer, transacetylation, lipoamide

Question 14

What is E3 of the pyruvate dehydrogenase complex? What type of reaction does it catalyze? What is its prosthetic group?

Answer 14

dihydrolipoyl dehydrogenase, dehydrogenation, FAD

Question 15

What is TPP? Can we make this?

Answer 15

thiamine pyrophosphate, no- must obtain thiamine from diet

Question 16

What molecule would accumulate in your blood if you have beriberi?

Answer 16

pyruvate (can’t metabolize it without TPP)

Question 17

Why does lipoamide have a reactive disulfide bond?

Answer 17

the 5 membered ring puts strain on S-S

Question 18

What does dihydrolipoyl dehydrogenase do in the reaction if acetyl coA has already been formed?

Answer 18

reoxidizes dihydrolipoamide to lipoamide using FAD so the reaction can proceed again

Question 19

Why does the swinging arm model for the pyruvate dehydrogenase complex confer an advantage?

Answer 19

makes it kinetically efficient since the substrates and enzymes don’t have to float around till they find each other (multiple lipoamides are used per E2 to make spacing work), not limited by diffusion

Question 20

How does arsenite kill?

Answer 20

forms chelation complex with reduced lipoamide (dihydrolipoamide) to poison the cofactor–won’t be able to survive since you can’t do oxidative phosphorylation without the citric acid cycle

Question 21

What does citrate synthetase do?

Answer 21

condenses acetyl coA and OAA and cleaves a thioester bond to form citrate and coA

Question 22

Is the hydrolysis of the thioester by citrate synthetase wasteful since it releases -7.5 kcal/mol?

Answer 22

no, it is used later to pull along malate dehydrogenase reactions

Question 23

What does aconitase do? Why?

Answer 23

dehydrates citrate and rehydrates it to isocitrate, moves hydroxyl to a secondary carbon from a tertiary one so it can be oxidized in the next step

Question 24

Why does the aconitase reaction produce isocitrate if it favors citrate 10:1?

Answer 24

isocitrate is removed in the next step (lechatliers principle)

Question 25

What kind of center does aconitase have?

Answer 25

iron-sulfur center

Question 26

What does isocitrate dehydrogenase do? What are the products?

Answer 26

oxidative decarboxylation of isocitrate, produces alpha-ketoglutarate (with OAA intermediate) and NADH

Question 27

Why does alpha-ketoglutarate undergo the same 4 step reactions as pyruvate via the alpha-ketoglutarate complex?

Answer 27

it has the same structure, just with an added CH2-COOH

Question 28

What does alpha-ketoglutarate get converted to by the alpha-ketoglutarate dehydrogenase complex?

Answer 28

succinyl coA, NADH, CO2

Question 29

What does succinyl coA synthetase do? What cofactor does it use?

Answer 29

cleaves the thioester bond of succinyl coA to produce GTP, uses coA cofactor
-substrate level phosphorylation

Question 30

Which reaction in the citric acid cycle demonstrates the common intermediate principle? How?

Answer 30

succinyl coA synthetase, it displaces coA to bind succinyl-phosphate (E-succinyl phosphate), transfer phosphate to histidyl residue on E and release succinate (E-P), to regenerate enzyme transfers P to GDP to form GTP and E

Question 31

What does succinate dehydrogenase do? What is unique about this reaction?

Answer 31

oxidizes succinate to fumarate, complex is bound to IMM and transfers electrons to FAD (directly into electron transport chain) rather than NADH (mobile electron carrier)

Question 32

What does fumarase do?

Answer 32

hydrates fumarate to form malate

Question 33

What does malate dehydrogenase do? Is this reaction favorable? How does it occur?

Answer 33

oxidizes malate to oxaloacetate (OAA), not favorable (+7.1 kcal/mol), gets pulled along by citrate synthetase reaction releasing energy it can use

Question 34

Why is it favorable to have a large malate pool and a small OAA pool in resting state?

Answer 34

malate can exit to the cytoplasm and serve as a substrate for gluconeogenesis while OAA cannot