Citric Acid Cycle

purpose of the citric acid cycle

oxidize the acetyl group of acetyl CoA from pyruvate to CO2 and generate high energy carriers

how many nadh is produced per turn

3 nadh

how many fadh2 is produced per turn

1 fadh2

how many gtp is produced per turn

1 

where does glycolysis take place

cytoplasm

where does the citric acid cycle take place

mitochondrial matrix

where does the ETC take place

inner mitochondrial membrane

how is CO2 released

when pryuvate is turned into acetyl CoA

The formation of isocitrate

The formation of alpha-ketoglutarate

pyruvate dehydrogenation rxn

pyruvate + CoA + NAD+ —> acetyl CoA + CO2 + NADH + H+

irreversible

components of pyruvate dehydrogenase

E1, E2, E3

TPP, FAD, NADH, and lipoic acid are all used as cofactors to load an an acetyl unit from pyruvate onto CoA for initiation of the citric acid cycle

role of TPP

decarboxylation of alpha keto acids

role of lipoic acid

redox and acyl transfer co factor

role of CoA-SH

acetyl carrier

role of FAD

reoxidies to make lipoamide

role of NAD+

final electron acceptor

mechanism in pyruvate dehydrogenation rxn decarboxylation

pyruvate loses CO2, when bound to TPP, forming a hydroxyethyl TPP intermediate

mechanism in pyruvate dehydrogenation rxn acyl transfer

the hydroxyethyl group is oxidized and transferred to lipoamide, forming acetyl lipoamide

mechanism in pyruvate dehydrogenation rxn reduction

lipoamide is reduced by FAD

citrate synthease rxn

Acetyl CoA + oxaloacetate + H2O —> citrate + CoA-SH

is the formation of citrate favorable

yes; it is pushed in the forward direction

mechanism of citrate synthase part 1

oxalacetate binds first, inducing a confirmational change

mechanism of citrate synthase part 2

forms a pocket for acetyl CoA, and generates an enolate anion

acontinase

isomerizes citrate to isocitrate

why is citrate isomerized into isocitrate

citrate is a tert alcohol a poor substrate for oxidation but isocitrate is a good substrate for this. 

step1 of citrate to isocitrate

elimination to cis aconitate

step2 of citrate to isocitrate

rehydration to isocitrate (adding water)

what catalyzes the conversion of citrate to isocitrate

4Fe-4S cluster to orient substrate and mediate water release and addition. 

isocitrate dehydrogenase

converts isocitrate to alpha ketoglutarate releasing CO2 and generating NADH

alpha ketoglutarate dehydrogenase

converts alpha keto glutarate into succinyl CoA producing another NADH and releasing CO2

succinyl CoA synthase rxn

succinyl CoA + GDP + Pi —> Succinate + GTP + CoASH

near equillibrium

succinyl CoA synthase rxn mechanism

High energy thioester drives phosphorylation of a histidine residue forming a phosphohistidine intermediate. phosphate is then transferred onto GDP via an SN2 mechanism

succinate dehydrogenase (SDH)

oxidizes succinate to fumarate forming FADH2

fumarase

hydrates fumarate to maltate

malate dehydrogenase

oxidizes malate producing oxalacetate generating NADH

pulled forward by rapid consumption of oxaloacetate in citrate synthase step.

forward determining steps

formation of citrate - citrate dehydrogenase

formation of alpha ketoglutarate- isocitrate dehydrogenase

formation of succinyl CoA- alpha ketoglutarate dehydrogenase

structure of pyruvate dehydrogenase

structure of acetyl CoA

structure of TPP+ E1

structure of of lipoamide

structure of TPP

structure of acetyldihydrolipoamide E2 complex

structure of dihydrolipoamide E2

structure of oxaolactetate

structure of citrate

structure of cis aconitase

structure of isocitrate

oxalsuccinate

intermediate before forming alpha ketoglutarate in citric acid

structure of oxalsuccinate

structure of alpha ketoglutarate

structure of succinyl CoA

structure of succinate

structure of fumarate

structure of maltate

what protein allows for the thioesterfication of PDC

cysteine

lipoamide

area where thioesterification happens to facillitate acetyl co a formation and this has to be regenerated

fumarate to maltate has what type of intermediate

carb anion