L17 - TCA cycle

what is the TCA cycle

the citric acid cycle - a set of 8 reactions in which an acetyl group is condensed with oxaloacetate, 2 CO₂ are lost, and oxaloacetate is regenerated

what does each round of the citric acid cycle generate

3 NADH, 1 FADH₂/QH₂, and 1 GTP

where do the reduced coenzymes go from the TCA cycle

go onto the electron transport system, initiating oxidative phosphorylation and ATP synthesis

how is flux through the citric acid cycle regulated

primarily by feedback inhibition at three steps - the intermediates of the TCA cycles are precursors for other pathways or replenished by outside pathways

what is the major oxidative pathways

TCA which oxidizes acetyl CoA in a series of oxidation-reduction reactions that move electrons to carriers

what can also generate acetyl CoA

glucose metabolism, fatty acids and amino acids - acetyl CoA is at the center of the entry into the TCA cycle

what is are the simplified 8 steps in the citric acid cycle

acetyl CoA (2 C molecule) enters the cycle and electrons are transferred to NAD⁺ or FAD - regeneration of a 4 C molecule allows the cycle to restart

where are the 2 carbons lost as CO₂

between isocitrate and alpha-ketoglutarate and between alpha-ketoglutarate and succinyl-CoA

what is the starting step of the citric acid cycle and what is the enzyme

acetyl-CoA converts to Citrate

what enzyme converts acetyl-CoA to Citrate

citrate synthase

what does citrate get converted into and what enzyme does the conversion

isocitrate via aconitase (there’s a CON posing as citrate in the CIA)

what does isocitrate get converted into and what enzyme does the conversion

alpha-Ketoglutarate via isocitrate dehydrogenase and NADH produced here, as well as the first release of CO₂ (named after the molecule is acts on - sometimes you can get dehydrated on keto)

mnemonic for TCA cycle intermediate

CIKSSFMO? - can I keep selling s*x for money, officer? - citrate, isocitrate, alpha-ketoglutarate, succinyl-CoA, succinate, fumarate, malate, and OAA

what does alpha-ketoglutarate get converted into and what enzyme does the conversion

succinyl-CoA via alpha-ketoglutarate dehydrogenase (named after what it acts upon) - NADH produced here

what does succinyl-CoA get converted into and what enzyme does the conversion

succinate via succinyl-CoA synthetase - GTP made here (remember the S’s)

what does succinate get converted into and what enzyme does the conversion

fumarate via succinate dehydrogenase - QH₂ and FADH₂ produced here (succulents are fragile when dry)

mnemonic for citric acid enzymes

S,AD,DSDFD - So, at dawn, Devil sipped down five drinks - citrate Synthase, Aconitase, isocitrate Dehydrogenase, alpha-ketoglutarate Dehydrogenase, succinyl-CoA Synthetase, succinate Dehydrogenase, Fumarase, malate Dehydrogenase

what does fumarate get converted into and what enzyme does the conversion

malate via fumarase - water is invested here

what does malate get converted into and what enzyme does the conversion

OAA via malate dehydrogenase which is an equilibrium-controlled step in the mitochondria - NADH is produced here

what happens to acetyl CoA in the TCA cycle

becomes fully oxidized - 4 electron pairs of acetyl-CoA that are ultimately used to reduce NAD⁺ (3) and FAD (1) in the citric acid cycle

why is the TCA cycle needed

it is difficult to cleave between the 2 C of acetyl CoA because it is a high-energy thioester bond, so it gets condensed with OAA to make 6 carbon citrate which is easy to rearrange in order to perform a beta-cleavage reaction

what does the beta-cleavage look like in glycolysis - why does the cell need to turn glucose into fructose

in the phosphgluco isomerase reaction between G6P and F6P, the isomerization moves the carbonyl group from C1 to C2 which is necessary to get DHAP and G3P from beta-cleavage instead of a 2C and 4C product, which would require 2 separate metabolic pathways to work with instead of one (glycolysis)

what does citrate synthase do to acetyl-CoA and OAA

adds an acetyl group to OAA - one of the few enzymes that can synthesize a C-C bond without a metal ion cofactor because the thioester bond provides the energy needed

what does aconitase do to citrate

isomerizes it to isocitrate - citrate is a symmetrical molecule, yet only one of its two carboxymethyl arms undergoes dehydration and rehydration during the aconitase reaction

what does isocitrate dehydrogenase do to isocitrate

oxidizes it and reduces NAD⁺, releasing the first CO₂ - uses an intermediate (oxalosuccinate) which has a carboxyl group on the beta-C which is eliminated as CO₂ - this is an oxidation decarboxylation reaction

what does alpha-ketoglutarate dehydrogenase complex do to alpha-ketoglutarate

oxidative decarboxylation to yield succinyl CoA and releases the second CO₂ - substrate is oxidized and NAD⁺ is reduced, resulting in a carboxylate group being lost as CO₂ - the 4 C molecule that remains is transferred to Coenzyme A which creates the high energy thioester bond

what mediates the reaction of alpha-ketoglutarate conversion to succinyl-CoA

alpha-ketoglutarate dehydrogenase complex - multi-enzyme complex that resemble pyruvate dehydrogenase complex - uses CoA and releases CO₂ and NADH

what does succinyl-CoA synthetase do

cleaves succinyl CoA’s high energy thioester bond, making it an exergonic, substrate-level phosphorylation reaction - this is the ONLY substrate-level reaction in the TCA cycle - the overall change in free energy for the net reaction is zero

what is substrate-level phosphorylation

an exergonic reaction coupled to the transfer of a phosphoryl group to a nucleoside diphosphate - distinguished from oxidative phosphorylation

difference between substrate level and oxidative phosphorylation

Substrate-level phosphorylation is the direct transfer of a phosphate group from a high-energy molecule to ADP to form ATP, while oxidative phosphorylation is the indirect production of ATP using energy from electron transport and a proton gradient across the mitochondrial membrane

what does succinyl CoA synthetase require

a reversible reaction that requires energy from GTP or ATP to form a bond - this is in contrast to synthases that don’t require an input of energy like citrate synthase

where does QH₂ come from

succinate to fumarate requires Q, and the conversion releases QH₂

what does succinate dehydrogenase require

FAD as a prosthetic group in order to catalyze the reversible dehydrogenation of succinate to fumarate - FAD it tightly bound to the enzyme and is reduced to FADH₂

what must happen to FADH₂ to convert succinate to fumarate

it must be oxidized to permit regeneration of the enzyme

what does succinate dehydrogenase produced besides FADH₂

ubiquinol (QH₂) - ubiquinone (Q), a lipid-soluble electron carrier in the ETC, can accept the electrons, and is reduced to form ubiquinol

what does fumarase do to fumarate

catalyzes the reversible hydration of a double bond to form malate

what does malate dehydrogenase do

regenerates OAA via an oxidation reduction reaction where the standard free energy is positive (unfavorable) but the product enters the highly exergonic reaction of citrate synthase into citric acid, which pulls it forward - releases NADH⁺ and H⁺

what does citrate synthase do

a highly exergonic reaction that keeps the substrate OAA low by continually converting it

where does the TCA cycle occur

in the mitochondria, allowing direct access of reduced electron carriers to the ETC - despite their mitochondrial location, all TCA enzymes are encoded by nuclear (not mitochondrial) genes

how many molecules of cully oxidized CO₂ are produced per acetyl group

for each acetyl group that enter the cycle, 2 molecules of fully oxidized CO₂ are produced

what is the total overall electron loss in TCA

4 pairs of electrons (8 total), which are used to reduce 3 NAD⁺ to NADH and 1 FAD to FADH₂

how much ATP is produced by the citric acid cycle

1 GTP is generated directly by substrate-level phosphorylation, and about 12 ATP equivalents are generated for each turn of the cycle

what are the fates of carbons in the citric acid cycle

the 2 Cs released in the first round of the citric acid cycle did not come from acetyl-CoA (comes from OAA combining with acetyl-CoA) - the net result of each round of the citric acid cycle is the loss of two C as CO₂ for each acetyl-CoA that enters the cycle

what are net numbers per turn of the citric acid cycle

3 NADH out, 1 GTP out, FADH₂ out, 1 CoA-SH, and 2 CO₂

how are the 6 carbons of glucose lost as CO₂

pyruvates processing (2 CO₂ are released from the 2 pyruvate) and 4 CO₂ are released throughout - In the context of the Citric Acid Cycle, Succinate Dehydrogenase (Complex II) reduces Coenzyme Q to QH₂ using electrons from FADH₂ which is why QH₂ = FAHD₂

where does regulation occur in the citric acid cycle

at citrate synthase, isocitrate dehydrogenase, and alpha-ketoglutarate dehydrogenase which are all allosterically regulated vis negative feedback inhibition by NADH and activated by ADP and/or Ca⁺

what citric acid cycle intermediates are precursors of other molecules

fatty acids, cholesterol, amino acids, nucleotides, heme, pyruvate, and glucose

what are anaplerotic reactions

metabolic "filling-up" reactions that replenish intermediates of the citric acid (TCA) cycle that have been removed for biosynthesis - pyruvate + CO₂ + ATP + H₂O → OAA + ADP + P_i

what can pyruvate be converted into to boost the activity of the citric acid cycle

alpha-ketoglutarate and it is likely to happen during exercise - being converted into TCA intermediates provides both fuel to run (acetyl-CoA), and by replenishing (anaplerosis) the necessary components to keep it turning when intermediates are removed for other metabolic pathways

what does amino acid formation look like in the citric acid cycle

intermediates like alpha-ketoglutarate can be used in processes to form amino acids - when paired with amino and the enzyme glutamate dehydrogenase, glutamate, a precursor of the amino acids glutamine, arginine, and proline, and water are formed

what pathways take place in the cytosol

glycolysis and lactate fermentation

what pathways happen in the mitochondrial inner membrane (MIM)

pyruvate transport via the mitochondrial pyruvate carrier - how pyruvate enters the mitochondria

what pathways happen in the mitochondrial matrix

pyruvate processing (pyruvate dehydrogenase and pyruvate carboxylase), TCA, and oxidative phosphorylation

what is the citrate transport system

citrate and pyruvate can cross the mitochondrial membrane via specific transport proteins - citrate-malate or citrate-pyruvate shuttle - since acetyl-CoA can’t travel freely across the inner mitochondrial membrane - lipid biosynthesis

where is NAD⁺ used as a cofactor

isocitrate dehydrogenase, alpha-ketoglutarate dehydrogenase, and malate dehydrogenase (MIA is such a NAD)

where is FAD used as a cofactor

covalently bound to succinate dehydrogenase and is reduced to FADH₂

where is Coenzyme A used as a cofactor

essential for the formation of the high--energy intermediate, succinyl-CoA which is catalyzed by alpha-ketoglutarate dehydrogenase complex

where is TPP and lipoic acid used as cofactors

required by alpha-ketoglutarate dehydrogenase complex to facilitate oxidative decarboxylation of alpha-ketoglutarate

where is Fe-S clusters used as a cofactor

acting as a metal cofactor for aconitase

where does GDP/AFP get used as a cofactor

succinyl-CoA synthetase

what is alpha-ketoglutarate

a 5 c dicarboxylic acid

how is succinate converted in three steps of OAA

the succinate is oxidized to yield fumarate, a 4 C dicarboxylic acid and FADH₂, and then water is added to fumarate to make malate which is then oxidized to yield OAA and NADH

what is the TCA cycle the final oxidation of glucose

the glucose is oxidized in the mitochondria as far as it can go to CO₂ and water which results in a very high energy yield - here, NADH can be regenerated to NAD⁺ by transferring electrons (in cytoplasm in orokaryotes)

what are the simplified 4 steps of TCA

1. oxidation of pyruvate

2. the production of isocitrate (step 1 and 2)

3. two decarboxylation reactions (step3 and 4)the

4. the regeneration of OAA (step 5,6,7,8)