Biochemistry Chapter 17

what does the citric acid cycle harvest

high energy electrons

citric acid cycle

series of oxidation– reduction reactions that result in the oxidation of an acetyl group to two molecules of CO2 – the final pathway for the oxidation of fuel molecules – oxidation generates high-energy electrons used to power ATP synthesis – important sources of precursors for biosynthesis – also called the tricarboxylic acid (TCA) cycle or Krebs cycle

CAC

citric acid cycle

what is the final pathway for the oxidation of fuel molecules

CAC

what reactions make up the CAC

oxidation-reduction

acetyl CoA

acetyl coenzyme A. most fuel molecules enter the CAC as this

what do most fuel molecules enter the CAC as

acetyl CoA

acetyl CoA

pyruvate dehydrogenase complex

a large enzyme complex that oxidatively decarboxylates pyruvate to acetyl CoA under aerobic conditions

where do reactions of the pyruvate dehydrogenase complex and CAC take place

in the mitochondrial matrix

what happens to acetyl CoA in the CAC (carbon)

two remaining carbons are completely oxidized to CO2

what are the two mitochondrial membranes

inner and outer

where is the matrix of the mitochondria

inside the inner mitochondrial membrane (all the way in center)

what does the CAC do

removes electrons from acetyl CoA and uses them to reduce NAD+ and FAD to NADH and FADH2

ETC

electron transport chain

electron transport chain

a series of membrane proteins that electrons released in the reoxidation of NADH and FADH2 flow through to generate a proton gradient across the inner mitochondrial membrane

why do protons flow through ATP synthase

to generate ATP from ADP and inorganic phosphate

what links glycolysis to the citric acid cycle

the pyruvate dehydrogenase complex

pyruvate dehydrogenase complex

a highly integrated unit of three distinct enzymes in the mitochondrial matrix. – oxidatively decarboxylates pyruvate to acetyl CoA

why does pyruvate dehydrogenase complex connect glycolysis to CAC

because the reaction catalyzed by it is an irreversible link

why must conversion of pyruvate to acetyl CoA steps be coupled

because free energy from decarboxylation step drives formation of NADH and acetyl CoA

what are the catalytic cofactors of conversion of pyruvate to acetyl CoA

thiamine pyrophosphate, lipoic acid, FAD

TPP

thiamine pyrophosphate

what are the stochiometric cofactors of conversion of pyruvate to acetyl CoA

CoA and NAD+

stochiometric cofactor

cofactor that functions as substrate

what does the citric acid cycle oxidize

two-carbon units

what does citrate synthase catalyze

the addition of acetyl CoA and oxaloacetate, yielding citrate and CoA

what is the reaction of citrate synthesis

aldol addition and a hydrolysis

what does citrate synthase proceed through

energy rich citryl CoA

how does the mechanism of citrate synthesis prevent undesirable reactions

minimizes hydrolysis of acetyl CoA to acetate and CoA side reaction, and exhibits sequential, ordered kinetics

what are the sequential, ordered kinetics of citrate synthase

Oxaloacetate binds first, followed by acetyl CoA. – Oxaloacetate induces a structural rearrangement that creates an acetyl CoA-binding site

what is citrate isomerized to

isocitrate

iron-sulfur protein (nonheme iron protein)

protein that contains iron that is not bonded to heme (ex: aconitase)

what does aconitase catalyze

the isomerization of citrate into isocitrate through dehydration step and hydration step

what is isocitrate oxidized and decarboxylated to

alpha ketoglutarate

what does isocitrate dehydrogenase catalyze

the oxidative decarboxylation of isocitrate, forming alpha ketoglutarate and NADH

NADH

high transfer-potential electron carrier

what does isocitrate dehydrogenase proceed through

the unstable oxalosuccinate

what is released from oxalosuccinate to yield alpha ketoglutarate

CO2

what is succinyl coenzyme A formed by

the oxidative decarboxylation of alpha ketoglutarate

what does the alpha ketoglutarate dehydrogenase complex catalyze

the oxidative decarboxylation of alpha ketoglutarate to succinyl CoA, yielding NADH

what regenerates NADH (CAC)

alpha ketoglutarate’s oxidative decarboxylation (alpha ketoglutarate + NAD+ + CoA)

what does succinyl CoA synthetase catalyze

the cleavage of a thioester linkage of succinyl Coa, yielding succinate

what is succinyl CoA synthetase coupled to and why

the phosphorylation of ADP or GDP because the delta G for the hydrolysis is comparable to that of ATP

is succinyl CoA synthetase catalyzation reaction reversible or irreversible

readily reversible

what may be coupled to the formation of succinate

ATP or GTP formation

what are the two isozymic forms of the enzyme succinyl CoA synthetase

GDP and ADP requiring

GDP requiring enzyme (succinyl CoA synthetase)

predominates in tissues performing anabolic reactions (ex: liver) and the GTP is used to power succinyl CoA synthesis

ADP requiring enzyme (succinyl CoA synthetase)

predominates in tissues performing large amounts of cellular respiration (ex: skeletal and heart mucle)

how is oxaloacetate regenerated

by the oxidation of succinate

what do succinate dehydrogenase, fumarase, and malate dehydrogenase catalyze

successive reactions of four-carbon compounds to regenerate oxaloacetate

what is generated in oxidation of succinate

FADH2 and NADH

why is it important for oxaloacetate to be regenerated

can initiate another cycle afterwards

where is FADH2 generated in CAC

succinate to fumarate

where is NADH generated in CAC

malate to oxaloacetate

succinate dehydrogenase

iron-sulfur protein. has isoalloxazine ring of FAD covalently attached to His side chain. is embedded in inner mitochondrial membrane. is directly associated with ETC

how is succinate oxidized to fumarate (by what)

by succinate dehydrogenase

what is the hydrogen acceptor in succinate to fumarate oxidation

FAD, because the free energy change is insufficient to reduce NAD+

how is fumarate hydrated to L-malate

by fumarase

fumarase

catalyzes the stereospecific trans addition of H+ and OH-, yielding only the L-isomer of malate

what is malate oxidized to

oxaloacetate

malate dehydrogenase

catalyzes the oxidation of malate, yielding oxaloacetate and NADH

what is the delta G of malate oxidation to oxaloacetate

significantly positive

what is the reaction of malate oxidation to oxaloacetate driven by

the use of the products - oxaloacetate by citrate synthase and NADH by the ETC

what is the net reaction of the citric acid cycle

Acetyl Coa + 3 NAD+ + FAD + ADP + Pi + 2H2O —> 2 CO2 + 3 NADH + FADH2 + ATP + 2H+ + CoA

what is important to know about the carbons in CAC

the two carbon atoms that enter each cycle as acetyl CoA are not the ones that leave as Co2 during the initial two decarboxylation reactions

what is the stoichiometry of the CAC (carbon, hydrogen, phosphoryl compound, water)

two carbon atoms enter in form of acetyl CoA, and two leave in the form of CO2. four pairs of hydrogen atoms leave in four oxidation reactions (yielding three NADH and one FADH2). one compound with high phosphoryl-transfer potential (usually ATP) is generated. two water molecules are consumed

how many reactions make up the full citric acid cycle

8 enzyme catalyzed reactions

what allows for substrate channeling in the CAC

a physical association of the CAC enzymes into a supramolecular compelx

where is NADH generated in the CAC (3)

isocitrate to alpha ketoglutarate by isocitrate dehydrogenase, alpha ketoglutarate to succinyl CoA by alpha ketoglutarate dehydrogenase complex, malate to oxaloacetate by malate dehydrogenase

where is FADH2 generated in the CAC

succinate to fumarase by succinate dehydrogenase

what is the formation of acetyl CoA from pyruvate in animal cells

irreversible

what are the two principal fates of acetyl CoA

metabolism by the CAC or incorporation into lipids

how is the activity of the pyruvate dehydrogenase complex controlled

tightly controlled allosterically and by reversible phosphorylation

how is the pyruvate dehydrogenase complex regulated allosterically

high concentrations of reaction products inhibit the reaction by informing the enzyme there is no need to metabolize pyruvate to acetyl CoA - acetyl CoA inhibits the transacetylase component (E2) and NADH inhibits the dihydrolipoyl dehydrogenase (E3)

what does acetyl CoA inhibit (pyruvate dehydrogenase complex)

transacetylase component (E2)

what does NADH inhibit (pyruvate dehydrogenase complex)

dihydrolipoyl dehydrogenase (E3)

how is the activity of the pyruvate dehydrogenase complex regulated (generally)

by reversible phosphorylation

how is the activity of the pyruvate dehydrogenase complex regulated (full)

active PDH uses kinase and ATP to turn inactive, release ADP. Inactive PDH uses H2O and phosphatase to turn active, release Pi.

at rest, what are the ratios of NADH/NAD+, acetyl CoA/CoA, and ATP/ADP

high

why are the ratios of NADH/NAD+, acetyl CoA/CoA, and ATP/ADP high at rest

promotes phosphorylation and inactivation of the complex by activating PDK

what happens during activity in CAC (biological conditions)

high ADP and pyruvate activate the complex by inhibiting the kinase. Ca2+ stimulates the phosphatase, enhancing pyruvate dehydrogenase activity

isocitrate dehydrogenase and alpha ketoglutarate dehydrogenase

allosteric enzymes that primarily regulate the rate of cycling in CAC. the first two enzymes that harvest high energy electrons in the cycle

what must the CAC intermediates be

rapidly replenished if any are used for biosynthesis

what do mammals lack

the enzymes for net conversion of acetyl CoA into oxaloacetate or other cycle intermediates

anaplerotic reaction

reaction that leads to the net synthesis, or replenishment, of pathway components

pyruvate carboxylase

catalyzes formation carboxylation of pyruvate to oxaloacetate. used in gluconeogenesis and is dependent on presence of acetyl CoA