Lesson 13 - Pyruvate Dehydrogenase Complex (PDC) and the Citric Cycle (TCA)

Question 1

is a central area of metabolism

Answer 1

a process where anabolic and catabolic pathways intersect

Question 2

TCA:

Answer 2

intersection of amino acid, fatty acid and carbohydrate metabolism

Question 3

considering the structure of pyruvate (C3H3COO3-), how does pyruvate get into the mitochondrion

Answer 3

a mitochondrial pyruvate carrier

Question 4

how does the structure of the mitochondrion facilitate the exchange of metabolites betwween the TCA and ETC

Answer 4

IM is embedded with components of the ETC
– reduced coenzymes are “fed” directly in

Question 5

predict what the most importnat produts are that are directly produced from glycolysis and the citric acid cycle

Answer 5

e-‘s in the form of reduced coenzymes

Question 6

how does the cell harness (conserve) potential energy through these processes to synthesis ATP during oxidative phosphorilation

Answer 6

• the free energy of electron transfer from NADH –> H2O is conserved in a H+ gradient across the IM

Question 7

pyruvate dehydrogenase complex, PDC, an example of a multienzyme complex:

Answer 7

1 - two or more noncovalently associated enxymes
2 - catalyze sequential reactions
3 - increase the frequency of collisions and overall reaction rate (free enzymes very close together)
4 - place a series of reactions rate coordinate control (allosteric molecule)

Question 8

requires 5 cofactors (mostly from diet)

Answer 8

1 - coenzyme A (CoA or CoA-SH)
2 - Lipoamide
3 - TPP
4 - NAD+
5 - FAD

Question 9

where does NAD come from

Answer 9

dietary Niacin (vitamin B3)
- sever niacin deficiency causes the disease pellagra
symptopms include skin rahs, diarrhea, and neurological problems
vitamin b missing in a corn rich diet
^^^ present in corn, but in the form of a protein bound form (NAD+/NADH) that drastically reduces its absorption in the intestine
- soaking corn in lime solution (calcium oxide) releases niacin from it’s protein-bound form

Question 10

where does FAD come from

Answer 10

• dietary riboflavin

Question 11

where does CoA come from

Answer 11

• derived from dietary pantothenic acid

Question 12

where does TPP come from

Answer 12

dietary thiamine
- polished rice is deficient in thiamine
- whole rice is rich in thiamine

Question 13

dietary lipoic acid is covalently attached to

Answer 13

• a Lys residue on E2 –> involved in a group transfer reaction

Question 14

Reaction 1: to get the acetyl-CoA

Answer 14

pyruvate + NAD+ + CoA –> acetyl-CoA + NADH + CO2

by pyruvate dehydrogenase complex (E1 + E2 + E3)

Question 15

what kind of molecule is Acetyl-CoA

Answer 15

thioester; “high energy” –> FAR from equilibrium

Question 16

what type of reaction is reaction 1

Answer 16

group transfer
- pyruvate reacts with the TPP carbination of E1 to form an addition product that undergoes decarboxylation giving hydroxyethyl-TPP

Question 17

what type of reaction is rxn 2

Answer 17

group transfer
- the hydroxyethyl group is transferred by E1 to a lipoamide swinging arm on E2 resulting in oxidation of the 2-carbon fragment to an acetyl group and reduction of the lipoamide disulfide to dihydrolipoamide (with actyl group bound)

Question 18

for reaction 3 does the lipoamide emerge from this reaction fully oxidixed or reduced

Answer 18

fully reduced

Question 19

does NAD+ emerge from rxn 4&5 in the oxidized or reduced state

Answer 19

reduced?

Question 20

rxn 1

Answer 20

acetyl-CoA + oxaloacetate + H2O –> CoA + Citrate

by citrate synthase
- irreversible under cellular conditions, delta G negative

Question 21

rxn 2

Answer 21

citrate <–> isocitrate

by aconitase

Question 22

rxn 3

Answer 22

isocitrate + NAD+ –> alpha ketoglutarate + NADH + CO2 + H+

by isocitrate dehydrogenase

– oxidative decarboxylation, NADH + H+ generated

Question 23

rxn 4

Answer 23

alpha ketoglutarate + CoA + NAD+ –> Succinyl - CoA + NADH + CO2 + H+

by alpha ketoglutarate dehydrogenase

– mechanistically identical to PDC

Question 24

rxn 5

Answer 24

succinyl - CoA + GDP + Pi <–> succinate + GTP + CoA

by succinyl-CoA synthetase

– energy of thioester bond hydrolysis
- conserved in substrate level phosphrylation

Question 25

rxn 6

Answer 25

succinate + FAD <–> Furmarate + FADH2

by succinate dehydrogenase

– AKA complex II of the ETC
– located in IM NOT MATRIC; FADH2 produced

Question 26

rxn 7

Answer 26

fumarate + H2O <–> malate

fumarase

– stepwise addition of H2O across double bond

Question 27

rxn 8

Answer 27

malate + NAD+ <–> Oxaloacetate + NADH + H+

Question 28

what reactions are the far equilibrium rxns

Answer 28

1,3,4

Question 29

TCA net equation

Answer 29

acetyle-CoA + 3 NAD + FAD + GDP + P + 2H2O –> CoA-SH + 3NADH + FADH2 + 3H+ + GTP + 2CO2

Question 30

reduced coenzymes funneled into ETC …

Answer 30

ultimately produce significant ATP

Question 31

+ NAD+, CoA, ADP, Ca 2+ indicates

Answer 31

that the cell needs to make ATP, low energy charge (EC); catabolize glucose to synthesize ATP

Question 32

what are the targets of regulation in PDC and TCA

Answer 32

far from equilibrium rxns

Question 33

• NADH, ATP indicate

Answer 33

cellls have an ample ATP, high energy charge (EC); store glucose, don’t catabolize