TCA Cycle + Pentose Phosphate Pathway

1:citrate synthesis

picture

what drives citrate synthesis

hydroylsis of thioester bond + irreverisble

what is the one achiral molecule in TCA cycle

citrate

citrate synthesis is an excellent example of what upon binding oxaloacetate

induced fit, citrate synthase undergoes conformational change upon binding oxaloacetate

2: aconitase

picture.

what happens in the aconitase step

there is a hydroxyl transfer from C3 to C4 (dehyrdation + rehydration), making the alchol secondaty bc a primary can not be oxidized in next step

isocitrate dehyrdogenase

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what are the two forms of isocitrate dehyrdogenase

mintocondrial generates NADH only, where as in the cytoplasm and mitocndrial NADP+ can be created

what are the products of the isocitrate step

NADH + alpha-ketoglutarate

isocitrate mechanism steps

1. hydride transfer to NAD+, Hs from C4 leave + carbonyl forms

2. decarboxylation, CO2 leaves, pi bond between C3+C4

3. enol rearrangemtn, C4=carbonyl

4 alpha-ketoglutarate dehydrogenase complex

..

pentose phosphate pathway first stage

oxidative stage, where sugar is oxidized and decarboxylated created NADPH

pentose phospahate pathway purpose

produces NADPH for reductive biosynthesis and antioxidant defense, as well as ribose-5-phosphate for nucleotide synthesis

NADPH

source of biosynthetic reducing power, + protects the cell from oxidative stress reduces reactive oxygen

kept HIGH

NADH

-particpates in catabolic rxns for energy production, NAD+ is oxidating agent, KEPT LOW

glutathione

antioxdiant that can reduce reactive oxygen species, preventing oxidavtice damage

pentose phospahte pathway second stage

non-oxidative stage, start: three rubulose-5-phosphate (3x 5C)

end: two molecules of fructose-6-phosphate (2x 6C) and one glyceraldehyde-3-phosphate (1x 3C)

how many times does the oxidative stage of the pentose-phospahte pathway occur

3x, starting with 3 Glc 6-phosphates, creates 6 NADPH

goal of the non-oxidative stage

to take phosphorylated pentoses and get them back to sugars that are glycolytic intermediates

what is the cost of the pentose-phosphate pathway

18C → 15 C of glycolytic potential

what is the single greates enzyme deficet in humans

Glc-6-phosphate dehyrdogenase which is the 1st step of pentose-phospahte pathway

what happens if you have a deficet in Glc-6-phosphate dehydrogenase

-symptom: abnomral red blood cell breakdown

-confers: malaria resistance, parasite can not handle reactive oxygen species

net reaction of pentose-phosphate pathway

3 Glc 6-phosphate + 6 NADP+ + 3H2O → 2Fru 6-phosphate + glyceraldehyde 3-phosphate + 6 NADPH + 3CO2 + 6H+

what is the entry point of the non oxidative stage

ribulose 5-phosphate that is generated in the oxidative stage

transketolase equation

draw the transketolase mech

-TPP attacks at carbonyl center

-histidine deprotonates

-carbanion attacks at carbonyl

-acid/base chem

transaldolase mechanism

same as aldolase in glycolysis

transaldolase equation

pyruvate dehyrdogenase equation

pyruvate dehydrogenase cofactors

lipoamide, FAD, TPP,

NAD+ can only do single e- transfers, what molecule can do two?

FAD

FAD info

part of flavens, permanetly assoicated with the enzyme and will never be final e- acceptor

lipoaminde

does thioester transfers and has a very long hydrocarbon tail

FAD→( FADH)→FADH2 why is FADH an intermediate?

free radical but extremely delocalized thru ring strucutre, making it semi-stable

when the energy charge is high then

pyruvate dehyrdogenase is deactivated

energy charge range

0(All AMP)-1 (all ATP) typically held around 0.8-0.95

how is pyruvate dehydrogenase regulated

-energy charge

-phosphorylation of E1 protein, when phosphorylated then inactive

what enzyme regulated pyruvate dehydrogenase activty

pyruvate dehydrogenase kinase, activated by high energy charge (ATP NADH)

what molceules can be freely transported into the matrix of the mitocondria

pyruvate

what molecules can not be exported out of the matrix of the mtiocondria

NADH

what molecule can not enter the mitocondria

NADH

overall was is produced in the TCA cycle

3 NADH, 1QH2, 1GTP

what are the products of the alpha-ketoglutarate dehydrogenase step

succinyl-CoA + CO2 + NADH

what is unique about the succinyal synthase step

it is the only substrate level phosphorylation of the TCA cycle

5:Succinyl Co-A Synthase

what is produced as a result of the succinyl-CoA Synthase step

GTP, CoA-SH, Succinate

draw the succinyl-CoA mechanism

drew succinyal

how are the negative chrages sheilded in the succinyl-CoA Synthase Step

two helices are near the binding site + point their dipoles near where the reaction takes place, balancing negative charges

6: Succinate Dehydrogenase

…

what is produced from the succinate dehydrogenase step

fumarate, QH2

in the succinate dehydrogenase step where are the electrons transfered

from succinate to FAD → FADH2 then to ubiquinol Q→ QH2

ubiquinone

conjugated system that delocalizes radicals

-can do single or double e- transfers

-lipid soluble NOT WATER (50+ hydrocarbon tail)

7:fumerase

fumerase products

malate (sterospecfic)

which steps of TCA cycle are irreversible

1:citrate synthase

3:isocitrate dehydrogenase

4: alpha ketoglutarate dehydrogenase

8: malate dehydrogenase

for malate to have the correct sterochem hwo should it be drawn

-OH on left

-OH dashed, H=wedged

what steps of the TCA cycle produced NADH

-3:isocitrate dehydrogenase

-4:alpha ketoglutarate dehydrogenase

-8:malate dehydrogenase

which step produced FADH2

-6: succinate dehydrogenase, but it does not stay there, gets transfered to ubiquitol

where is the 1 GTP produced

5: succinyal CoA Synthase

what is NADH used for

ATP production (glycolysis), also for e- transport chain

numenoic to remember TCA cycle INTERMEDIATES

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numeonic to remember TCA cycle enzymes

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