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BIOC384 > Module 10 - Redox, PDH, and Citrate Cycle > Flashcards

Module 10 - Redox, PDH, and Citrate Cycle Flashcards

1
Q

What does the E mean about a molecule? What is dE?

A

oxidants with higher affinity for electrons have positive dE, oxidants with lower affinity for electrons have negative dE

dE:
E of the reductant (the donor) - E of the oxidant (the acceptor)

or

oxidized - reduced

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2
Q

Why is the citrate cycle the hub of metabolism?

A

produces NADH and FADH2, links the oxidation of various metabolic fuels to ATP synthesis, and provides metabolites for biosynthetic pathways

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3
Q

Many reactions such as amino acid metabolism and the citrate cycle take place in the…

A

mitochondrial matrix

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4
Q

What are the main reactants and products of the citrate cycle?

A

acetyl CoA (from pyruvate) is the main reactant

products are 1 GTP, 1 FADH2, and 3 NADH (with 2 CO2 as exhaust/waste)

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5
Q

What is the overall net reaction of the citrate cycle?

A

Acetyl-CoA + 3 NAD + + FAD + GDP + Pi + 2 H2O →
CoA + 2 CO2 + 3 NADH + 3 H+ + FADH2 + GTP

dG = -57.3 kJ/mol

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6
Q

Where does the citrate cycle occur?

A

mitochondria

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7
Q

What are the key regulated enzyme in the citrate cycle?

A

pyruvate dehydrogenase (pyruvate to acetyl CoA)
citrate synthase (oxaloacetate to citrate)
isocitrate dehydrogenase (isocitrate to a-ketoglutarate)
a-ketoglutarate dehydrogenase (a-ketoglutarate to succinyl-CoA)

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8
Q

What is an example of the citrate cycle in everyday biochemistry?

A

citrate production by Aspergillus fermentation under optimal culture conditions

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9
Q

The Fe-Cu redox reaction occurs in…

A

cytochrome c oxidase in the electron transport system

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10
Q

How is the dG for a redox reaction calculated from the dE? How do they change in relation to each other?

A

dG = -nF(dE)
(where n is the number of electrons transferred)

dE>0, dG<0, favorable
dE<0, dG>0, unfavorable

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11
Q

What is the Nernst equation and when is it used?

A

if you know the actual concentrations of the oxidant and reductant, you can calculate the actual reduction potential using:
E’o + RT ln(e- acceptor / e- donor)

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12
Q

What are the five coenzymes used in the PDH complex?

A

NAD+, FAD, CoA, TPP, and a lipoid acid (lipoamide)

all derived from vitamins

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13
Q

What type of reactions are NAD vs. NADP used for?

A

NAD+: catabolic reactions
NADP: anabolic reactions

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14
Q

What is acetyl coA?

A

a cofactor in biosynthetic pathways to produce fatty acids, acetylcholine, heme, and cholesterol

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15
Q

What produces pantothenic acid and what is it used to produce?

A

dietary coA is degraded by gut enzymes to yield pantothenic acid, which then is used in a series of reactions to produce the CoA enzyme

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16
Q

What characterizes beriberi disease?

A

anorexia, cardiovascular and neurological symptoms

17
Q

How do certain food affect TPP production?

A

uncooked fish and worms produce thiaminase to break down thiamine

18
Q

What is the role of lipoamide?

A

provide a reactive disulfide that can participate in redox reactions within the enzyme active site of pyruvate dehydrogenase

19
Q

What are E1, E2, and E3 of the PDH complex?

A

E1: pyruvate dehydrogenase
E2: dihydrolipoyl acetyltransferase
E3: dehydrolipoyl dehydrogenase

20
Q

What is the PDH reaction?

A

pyruvate + CoA + NAD+ —> Acetyl CoA + CO2 + NADH

21
Q

How big is the PDH complex? How many active sites are in the complex?

A

400 A diameter, 7800 kDA, and 60 active sites

22
Q

What is the general role of the PDH cycle?

A

transition from glycolysis to the citrate cycle by converting pyruvate to acetyl coA

23
Q

Describe the structure of the E2 amino terminal bridge?

A

ball: lipoamide in the E2 lipoyl domain
chain: 62 amino acid flexible segment
pivot: 35 amino acid E1/E3 binding domain
linker: 40 amino acid segment between E1 and E3

24
Q

What is the function and purpose of the E2 ball and chain?

A

the lipoamide ball and chain swings across a 50-A gap between E1 and E2 sites to mediate an acetyl group transfer from TPP on E1 to the CoA on E2
the pivot moves from E1 to E3 to facilitate this translocation

25
Q

What is arsenite?

A

a naturally occurring inhibitor of lipoamide coenzymes, creates didentate adducts on the dihydrolipoamide (covalently modifies the enzyme and inactivates the E2 subunit)

26
Q

What are the 5 steps of the PDH reaction?

A
  1. E1 binds pyruvate and catalyzes a decarboxylation
  2. hydroxyethyl TPP reacts with the disulfide to form TPP and an acetyl-dihydrolipoamide
  3. lipoamide group carries the acetyl to the E2 active site where CoA picks it up
  4. dihydrolipoamide is reoxidizes by E3, transferring 2e- and 2H+ to the FAD (reduced to FADH2)
  5. FADH2 is reoxidizes by transferring 2 e- to NAD+ (reduced to NADH and H+)
27
Q

What is the reductant in the last step of the PDH reaction?

A

FADH2 (reduces NAD+ to become FAD again for use in the next cycle)

28
Q

What are the two metabolic fates of acetyl-CoA?

A

citrate cycle converts to ATP via OxPhos

store metabolic energy in form of fatty acids (in adipose tissue as triglycerides)

29
Q

How does PDK work?

A

pyruvate dehydrogenase kinase phosphorylates the serine on E1, which inhibits the PDH complex

30
Q

How does PDP work?

A

pyruvate dehydrogenase phosphatase dephosphorylates the serine on the E1 to activate the PDH complex

31
Q

What are allosteric regulators of PDK?

A

NADH, acetyl CoA, and ATP activate PDK to inhibit PDH

NAD+, CoA, ADP, and Ca2+ inhibit PDK and activate PDH

32
Q

What are allosteric regulators of PDP?

A

Ca2+ activate PDP to activate PDH

33
Q

What effect does fluoroacetate have on the citrate cycle?

A

it is converted to fluorocitrate, which blocks citrate export from the mitochondria

34
Q

What is the most exergonic reaction of the citrate cycle?

A

the a-ketoglutarate dehydrogenase reaction

35
Q

When glucose is oxidized there are 6 CO2 produced. 4 come from the citrate cycle, but what about the other 2?

A

2 CO2 are produced during the PDH reaction that convert pyruvate to acetyl CoA

36
Q

What is the function of the 4Fe-4S cluster?

A

removal of an OH group from citrate by aconitase

37
Q

What are the dual functions of aconitase?

A

convert citrate to isocitrate, or RNA binding protein

38
Q

Why is the dG of the last step of the citrate cycle about 0 even though the standard change in free energy is +28?

A

Oxaloacetate is the substrate for the first reaction and is quickly converted to citrate. Therefore, it never builds up and the product concentration stays low, driving the reaction to the right.

39
Q

How was the citrate cycle determined to be a cycle instead of linear?

A

carbon-14 labeling experiments showed that carbons entering the citrate cycle are not the same carbons lost as CO2 in the same round of the citrate cycle

rather, multiple rounds of the citrate cycle were needed to eliminate the labeled carbons

BIOC384 (13 decks)

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