PDH and TCA cycle

Question 1

PDH 3 multi-enzyme complex

Answer 1

E1- pyruvate decarboxylase
E2- dihydrplipoyl transacetylase
E3- dihydrolipoyl dehydrogenase

Question 2

PDH the 5 coenzymes

Answer 2

1) CoA [E2 substrate]- derived from pantothenic acid
2) FAD+ [E3]- derived from riboflavin
3) NAD+ [E3 substrate]- derived from niacin
4) TPP -enzyme E1- derived from thymine
5) lipoamine [E2]- 10-carbon fatty acid that acts as arm to move substrate/product between enzyme complexes

Question 3

Beri-beri

Answer 3

• thiamine deficiency
• damage to PNS and weakened muscles, cardiovascular disorders
• common in far east

Question 4

general vitamin deficiencies

Answer 4

riboflavin and niacin precursors of FAD+ and NAD+.
riboflavin deficiency tends to occur with other B vitamin deficiencies.
naicin deficiency cause pellagra [fatal if untreated]

Question 5

mercury and arsenite poisoning

Answer 5

bind to lipoyl groups in E2; causes CNS pathologies

Question 6

pyruvate dehydrogenase deficiency

Answer 6

• genetic mutations in components of PDH complex will lead to problems [incidence unknown; rare]
• causes lactic acid build up and CNS pathologies

Question 7

citrate synthase reaction [1]

Answer 7

• citrate synthase catalyses the first step in the TCA cycle

- acetyl CoA from glycolysis combines with oxaloacetate to form citrate [releasing CoA]

Question 8

aconitase reaction [2]

Answer 8

• second step in TCA cycle, aconitase converts citrate to isocitrate
• an isomerase reaction

Question 9

fumarase reaction [7]

Answer 9

• catalyses the hydration of fumarate to malate

- the enzyme requires no cofactors

Question 10

alpha-ketogluterate DH reaction [4]

Answer 10

alpha-ketoglutarate DH catalyses the oxidative addition of CoA

Question 11

succinyl CoA synthase reaction [5]

Answer 11

• removal of the CoA moiety to produce succinate provides the energy to phosphorylate GDP
• this is the only triphosphate nucleotide to be produced directly by the TCA cycle

Question 12

succinate DH reaction[6]

Answer 12

• succinate is oxidised to fumarate

- FAD+ is used as the electron acceptor, forming NADH2

Question 13

isocitrate DH [3]

Answer 13

• mediated by isocitrate DH, oxidises isocitrate to alpha-ketoglutarate
• NAD+ is reduced to NADH, and carbon dioxide is released

Question 14

malate DH reaction [8]

Answer 14

• malate DH catalyses the oxidation of malate to form oxaloacetate

Question 15

control of TCA cycle

Answer 15

• strongest regulation applies to the 2 steps where carbon dioxide is released
• both ATP and NADH inhibit these reactions, while ADP and calcium ions [signals for muscle contraction] are activators

Question 16

overview of cellular respiration

Answer 16

• electrons from NADH and FADH2 are transferred to oxygen along the ETC [respiratory chain]
• components located in the inner mitochondrial membrane [IMM]
• energy released is used to pump protons into the intermembrane space to create a proton gradient
• protons flow back through ATP-synthase complex to generate ATP
• whole pathway tightly coupled

Question 17

overview of the ETC

Answer 17

4 protein complexes [I-IV]

• 3 proton pumps [ complex I, III, IV]
• 1 link to TCA cycle [complex II]

2 smaller components:
Coenzyme Q [CoQ]; also called ubiquinone [UbQ]
- cytochrome C

Question 18

complex I: NADH dehydrogenase

Answer 18

Complex I: NADH dehydrogenase

• At least 34 polypeptides
• Complex I accepts electrons from NADH [oxidizing it to NAD+]
• Transfers electrons to CoQ [via RMN and Fr-S cofactors]
• 4 H+ pumped from matrix into intermembrane space

Question 19

complex II: succinate dehydrogenase

Answer 19

Complex II: succinate dehydrogenase

• Part of TCA cycle [succinate to fumarate]
• Succinate to fumarate reaction generates FADH2
• FADH2 oxidised to regenerate FAD+
• Released electrons transferred to CoQ via Fe-S proteins
• As a prosthetic group FAD+/FADH2 doesn’t dissociate from the enzyme.
• The enzyme participates directly in both the TCA cycle and the ETC.

Question 20

complex III: cytochrome c reductase

Answer 20

• Heme prosthetic group
• Accepts electrons from CoQ
• Electrons transferred to small protein cytochrome c
• 2 protons pumped across IMM

Question 21

complex IV: cytochrome c oxidase

Answer 21

• 13 protein subunits containing 2 heme groups and 3 copper ions
• Reducing oxygen to 2x water requires:
• • 4 reduced cytochrome c molecules
• • 8 proteins from matrix
• And produces:
• 4 pumped protons [others from the water]

Question 22

agents affecting oxidative phosphorylation

Answer 22

• Site-specific inhibitors of the ETC
• ATPase inhibitors e.g. oligomycin
• Uncouplers; neutralize the proton gradient and prevent ATP synthesis

Question 23

ETC uncouplers

Answer 23

Chemicals:
- E.g. dinitrophenol; forms proton ionophore that dissipated H+ gradinent
Natural:
- Uncoupling proteins
- Mitochondria from brown adipose tissue
- ETC energy used to generate heat; non-shivering thermogenesis
- Newborns and hibernating animals

Question 24

Coenzyme Q

Answer 24

• Also called CoQ10
• Small lipid soluble compound [a hydrophobic quinone]
• Diffuses rapidly within IMM- mobile carrier
• Accept electrons from Fe-S proteins from Complex I and II
• Transfers electrons to complex III/ cytochrome c [‘Q cycle’]

Question 25

cytochrome c

Answer 25

• Peripheral membrane protein loosely bound to IMM
• Binds to complex III and transfers electrons to complex IV
• Highly conserved

Question 26

complex V: ATP synthase

Answer 26

• Embedded in inner mitochondrial membrane
• Composed of 2 subunits:
• • F1 ATPase (generates ATP)
• • F0 coupling factor; a proton channel
• H+ pumps to cytosolic side of mitochondrial membrane r-enter matrix through F0 proton channel
• the passage of protons through the channel drives the rotation of the C-ring of F0
• this alters the conformation of beta-subunit of F1 domain
• this in turn drives formation of ATP from /ADP and PI