Chapter 17 Flashcards by Gail I

the eight enzymes of the citric acid cycle function in a multistep catalytic cycle to oxidize an … to two … with the concomitant generation of three …, one …, and one …

acetyl group; CO2; NADH; FADH2; GTP

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the free energy released when the reduced coenzymes of the citric acid cycle ultimately reduce O2 is used to generate

ATP

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acetyl groups enter the citric acid cycle as … the … complex, which contains three types of enzymes and five types of coenzymes, generates … rom the glycolytic product …

acetyl-CoA; pyruvate dehydrogenase multienzyme complex; acetyl-CoA; pyruvate

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the … of E2 of pyruvate dehydrogenase multienzyme complex acts as a tether that swings reactive groups between enzymes in the complex

lipoyllysyl arm

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… catalyzes the condensation of acetyl CoA and oxaloacetate in a highly exergonic reaction

citrate synthase

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… catalyzes the isomerization of citrate to …, and … catalyzes the oxidative decarboxylation of … to … to produce the citric acid cycle’s first CO2 and NADH

aconitase; isocitrate; isocitrate dehydrogenase; isocitrate; alpha-ketoglutarate

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… catalyzes the oxidative decarboxylation of alpha-ketoglutarate to produce … and the citric acid cycle’s second CO2 and NADH

alpha-ketoglutarate dehydrogenase; succinyl-CoA

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… couples the cleavage of succinyl-CoA to the synthesis of … (or in some organisms, …) via a … intermediate

succinyl-CoA synthetase; GTP; ATP; phosphoryl-enzyme

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the citric acid cycle’s remaining three reactions, catalyzed by .., .., and …, regenerate … to continue the citric acid cycle

succinate dehydrogenase; fumarase; malate dehydrogenase; oxaloacetate

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neither of the CO2 molecules released in a given turn of the citric acid cycle are derived from the …that entered the same turn of the cycle. instead, they are derived from the … that was synthesized from the acetyl groups that entered previous turns of the cycle

acetyl group; oxaloacetate

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entry of glucose-derived acetyl-CoA into the citric acid cycle is regulated at the … step by … (by NADH and acetyl-CoA) and by …

pyruvate dehydrogenase; product inhibition; covalent modification

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the citric acid cycle itself is regulated at the steps catalyzed by .., …, and …

citrate synthase; NAD+ dependent isocitrate dehydrogenase; alpha-ketoglutarate dehydrogenase

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regulation is accomplished mainly by …, …, and …

substrate availability; product inhibition; feedback inhibition

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… reactions deplete citric acid cycle intermediates. some citric acid cycle intermediates are substrates for …, …,a nd …

cataplerotic; gluconeogenesis; fatty acid biosynthesis; amino acid biosynthesis

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… reactions, such as the pyruvate carboxylase reaction, replenish citric acid cycle intermediates

anaplerotic

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the … cycle, which operates only in plants, bacteria, and fungi, requires the glyoxysomal enzymes … and … this variation of the citric acid cycle permits net synthesis of … from acetyl-CoA

glyoxylate; isocitrate lyase; malate synthase; glucose

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the citric acid cycle is a central pathway for recovering energy from several metabolic fuels, including …, …, and …, that are broken down to acetyl-CoA for …

carbohydrates; fatty acids; amino acids; oxidation

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citric acid cycle consists of … reactions

eight

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the citric acid cycle is named after the product of its first reaction, …

citrate

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the circular pathway, which is also called the … cycle or the … cycle, oxidizes acetyl groups from many sources, not just pyruvate. bc it accounts for the major portion of carbohydrate, fatty acid, and amino acid oxidation, the citric acid cycle is often considered the “hub” of cellular metabolism

Krebs; tricarboxylic acid (TCA)

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the net rxn of the citric acid cycle is
3NAD+ + FAD + GDP + Pi + acetyl-CoA –> 3 NADH + FADH2 + GTP + CoA + 2CO2
the oxaloacetate that is consumed in the first step of the citric acid cycle is … in the last step of the cycle. thus, the citric acid cycle acts as a … that can oxidize an … number of … groups

regenerated; multistep catalyst; unlimited; acetyl

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in eukaryotes, all the enzymes of the citric acid cycle are located in the …, so all substrates, including NAD+ and GDP, must be generated in the … or be transported into it from the cytosol. similarly, all the products of the citric acid cycle must be consumed in the … or transported into the …

mitochondria; mitochondria; mitochondria; cytosol

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the carbon atoms of the two molecules of CO2 produced in one round of the cycle are not the two carbons of the acetyl group that began the round. these acetyl C atoms are lost in subsequent rounds of the cycle. however, the net effect of each round of the cycle is the … of one … group to …

oxidation; acetyl; 2 CO2

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citric acid cycle intermediates are precursors for the biosynthesis of

other compounds

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the oxidation of an acetyl group to 2 CO2 requires the transfer of … pairs of electrons. The reduction of … to … accounts for three pairs of electrons; the reduction of … to … accounts for the fourth pair. much of the free energy of oxidation of the acetyl group is conserved in these reduced coenzymes. energy is also recovered as GTP (or ATP). approximately … ATP are formed when the four pairs of electrons are eventually transferred to O2

four; 3 NAD +; 3 NADH; FAD; FADH2; 10

pyruvate dehydrogenase is a multienzyme complex that catalyzes a five-part rxn in which pyruvate releases …, and the remaining acetyl group becomes linked to …

CO2; coenzyme A

the pyruvate dehydrogenase rxn sequence requires the cofactors …, …, …, …, and ...

TPP; lipoamide; coenzyme A; FAD; NAD+

… are groups of noncovalently associated enzymes that catalyze two or more sequential steps in a metabolic pathway

multienzyme complexes

(advantages of multienzyme complexes) enzymatic rxn rates are limited by the frequency with which enzymes … with their substrates. when a series of rxns occurs within a multienzyme complex, the distance that substrates must diffuse between … is minimized, thereby enhancing the reaction rate

active sites

(advantages of multienzyme complexes) the channeling (passing) of metabolic intermediates between successive enzymes in a metabolic pathway reduces the opportunity for these intermediates to …, thereby minimizing …

react with other molecules; side rxns

(advantages of multienzyme complexes) the rxns catalyzed by a multienzyme complex can be …

coordinately controlled

pyruvate dehydrogenase is a multienzyme complex that contains multiple copies of three enzymes: … (E1) … (E2) … (E3)

pyruvate dehydrogenase dihydrolipoyl transacetylase dihydrolipoyl dehydrogenase

mammalian complexes contain about 12 copies of …, which facilitates the binding of E3 of pyruvate dehydrogenase to the E2 core, and several copies of a … and a … that function to regulate the activity of the complex

E3 binding protein; kinase; phosphatase

the pyruvate dehydrogenase complex catalyzes five sequential rxn with the overall stoichiometry: pyruvate + CoA + NAD+ --> ...

acetyl-CoA + CO2 + NADH

one of the enzymes required for the pyruvate dehydrogenase rxns is

lipoamide

(sequence of rxns catalyzed by pyruvate dehydrogenase complex) 1. pyruvate dehydrogenase (E1), a …-requiring enzyme, decarboxylates pyruvate witht he formation of a … intermediate the ability of TPP's thiazolium ring to add to carbonyl groups and act as an … makes it the coenzyme most utilized in alpha-keto acid decarboxylation rxns

TPP; hydroxyethyl-TPP; electron sink

(sequence of rxns catalyzed by pyruvate dehydrogenase complex) 2. unlike pyruvate decarboxylase, pyruvate dehydrogenase does not convert the hydroxyethyl-TPP intermediate into acetyldehyde and TPP. instead, it's transferred tot he next enzyme, … (#2), which contains a … group

dihydrolipoyl transacetylase; lipoamide

lipoamide consist of … linked via an amide bond to the e-amino group of a Lys residue. the reactive center of lipoamide is a cyclic disulfide that can be reversibly reduced ot yield …

lipoic acid; dihydrolipoamide

(sequence of rxns catalyzed by pyruvate dehydrogenase complex) 2. the hydroxyethyl group derived from pyruvate attacks the lipoamide disulfide, and TPP is eliminated, thus regenerating … the hydroxyethyl carbanion is oxidized to an … as the lipoamide disulfide is reduced

active E1; acetyl group

(sequence of rxns catalyzed by pyruvate dehydrogenase complex) 3. E2 catalyzes a … rxn in which the acetyl group is transferred to CoA, yielding acetyl-CoA and dihydrolipoamide-E2

transesterification

(sequence of rxns catalyzed by pyruvate dehydrogenase complex) 4. acetyl-CoA has now been formed, but the lipoamide group of E2 must be regenerated. … (E3) reoxidizes dihydrolipoamide to complete the catalytic cycle of E2. oxidized E3 contains a reactive … group and a tightly bound .. the oxidation of dihydrolipoamide is a disulfide interchange rxn

dihydrolipoyl dehydrogenase; Cys-Cys disulfide; FAD

(sequence of rxns catalyzed by pyruvate dehydrogenase complex) 5. finally, reduced E3 is … the sulfhydryl groups are reoxidized by a mechanism in which FAD funnels electrons to .., yielding …

reoxidized; NAD+; NADH

(sequence of rxns catalyzed by pyruvate dehydrogenase complex) Due to the precise positioning of the ﬂavin and nicotinamide ring, electrons are rapidly transferred from the enzyme disulﬁde through FAD to NAD+, so a reduced … (FADH−) has but a transient existence. Thus, FAD appears to function more as an electron ... than as a source or sink of electrons.

ﬂavin anion ; conduit;

the entire pyruvate dehydrogenase complex can be inactivated by the reaction of the … group with certain …-containing compounds

lipoamide; arsenic

the eight enzymes of the citric acid cycle catalyze …, …, …, …, and … rxns

condensation; isomerization; oxidation-reduction; phosphorylation; hydration

… catalyzes the condensation of acetyl-CoA and oxaloacetate

citrate synthase

the citrate synthase rxn proceeds with an … kinetic mechanism in which oxaloacetate binds before acetyl-CoA

ordered sequential

the enzyme for citrate synthase has an open and closed form. the conformation change generates the … and seals the … site so that the solvent cannot reach the bound substrate

acetyl-CoA binding site; oxaloacetate binding

(rxn mechanism for citrate synthase) enol of acetyl-CoA is generated in the rate-limiting step of the rxn when Asp 375 … fro the methyl group. His 274 forms an H-bond with the enolate O

removes a proton

(rxn mechanism for citrate synthase) … is formed in a concerted acid-base catalyzed step, in which the acetyl-CoA enolate attacks oxaloacetate. His 320 donates a proton to oxaloacetate's … group citrate synthase is one of the few enzymes that directly forms a … without the assistance of a metal ion cofactor

citryl-CoA; carbonyl; carbon-carbon bond

(rxn mechanism for citrate synthase) citryl-CoA is hydrolyzed to … and … --> provides rxn's thermodynamic driving force

citrate; CoA

… catalyzes the reversible isomerization of citrate and isocitrate, with … as an intermediate

aconitase; cis-aconitate

aconitase contains a … that presumably coordinates the OH group of citrate to facilitate its elimination

[4FE, 4S]

iron-sulfur clusters normally participate in … processes; aconitase is an intriguing exception

redox

Although addition of water across the double bond of cis-aconitate could potentially yield ...stereoisomers, aconitase catalyzes the stereospeciﬁ c addition of OH− and H+ to produce only one isocitrate stereoisomer.

four

dietary iron is transported through bloodstream by the protein …, enters cells through receptor-mediated endocytosis, in which the receptor is .., and any excess iron is stored by the protein …

transferrin; transferrin receptor; ferritin

aconitase undergoes extensive conformation changes to become known as …, which binds to specific sequences on the mRNAs encoding the transferrin receptor and ferritin

iron regulatory protein-1 (IRP1)

… catalyzes the oxidative decarboxylation of isocitrate to alpha ketoglutarate (also known as …)

isocitrate dehydrogenase; 2-oxoglutarate

The … reaction produces the first CO2 and NADH of the citric acid cycle. Note that this CO2 began the citric acid cycle as a component of oxaloacetate, not of acetyl-CoA

isocitrate dehydrogenase

NAD+ dependent isocitrate dehydrogenase, which also requires a Mn2+ or Mg2+ cofactor, catalyzes the oxidation of a secondary alcohol (isocitrate) to a ketone (…) followed by the decarboxylation of the carboxyl group beta to the ketone

oxalosuccinate

the … intermediate of the isocitrate dehydrogenase rxn exists only transiently

oxalosuccinate

… catalyzes the oxidative decarboxylation of an alpha-keto acid. this rxn produces the second CO2 and NADH of the citric acid cycle

alpha-ketoglutarate dehydrogenase

each round of the citric acid cycle oxidizes two C atoms to …, the C atoms of the entering acetyl groups are not oxidized to CO2 until subsequent rounds of the cycle

CO2

alpha-ketoglutarate dehydrogenase is a multienzyme complex containing: … (E1) … (E2) … (E3)

alpha-ketoglutarate dehydrogenase dihydrolipoyl transsuccinylase dihydrolipoyll dehydrogenase

the rxns catalyzed by the alpha-ketoglutarate dehydrogenase complex occur by mechanisms identical to those of the pyruvate dehydrogenase complex. again, the product is a "high-energy" thioester, in this case, ...

succinyl-CoA

… (also called …) couples the cleavage of the "high-energy" succinyl CoA to the synthesis of a "high-energy" … Mammalian enzymes usually synthesize GTP and plants and bacterial enzymes usually s synthesize ATP

succinyl-CoA synthetase; succinate thiokinase

(mechanism for succinyl-CoA synthetase) succinyl-CoA reacts with Pi to form … and …

succinyl-phosphate; CoA

(mechanism for succinyl-CoA synthetase) the phosphoryl group is then transferred from succinyl-phosphate to a … on the enzyme, releasing succinate

His residue

(mechanism for succinyl-CoA synthetase) the phosphoryl group on the enzyme is transferred to …, forming ...

GDP; GTP

the energy of succinyl-CoA is conserved through the formation of …; first, …, then a …, and finally ...

"high-energy" compounds; succinyl-phosphate; 3-phospho-His-residue; GTP

The rxn catalyzed by succinyl-CoA synthetase is another example of … By this point in the citric acid cycle, one acetyl equivalent has been completely oxidized to … CO2. … NADH and one … have also been generated. to complete the cycle, succinate must be converted back to …

substrate-level phosphorylation; 2; 2; 1; oxaloacetate

… catalyzes the stereospecific dehydrogenation of succinate to fumarate

succinate dehydrogenase

In general, FAD function biochemically to … (such as succinate) to … (such as fumarate), whereas NAD+ participates in the more exergonic oxidation of … to … or …

oxidize alkanes; alkenes; alcohols; aldehydes; ketones

succinate dehydrogenase is the only …. of the citric acid cycle (the others occupy the inner compartment of the mitochondrion, its so called …), so it is positioned to funnel electrons directly into the electron transport machinery of the mitochondrial membrane

membrane-bound enzyme; matrix

… (…) catalyzes the hydration of the double bond of fumarate to form malate. the hydration rxn proceeds via a carbanion transition state

fumarase; fumarate hydratase

… catalyzes the final reaction of the rxn of the citric acid cycle, the regeneration of oxaloacetate

malate dehydrogenase

the rxn catalyzed by citrate synthase, the first rxn of the citric acid cycle, is highly exergonic because of the cleavage of the thioester bond of citryl-CoA. We can now understand the necessity for such a seemingly wasteful process. it allows citrate formation be … even at the low … concentrations present in cells and thus helps keep the citric acid cycle rolling

exergonic; oxaloacetate

the need for … regulates the citric acid cycle capacity at the pyruvate dehydrogenase step and at the three rate-controlling steps of the cycle

energy

regulatory mechanisms depend on …, …, …, and …

substrate availability; product inhibition; covalent modification; allosteric effects

for every acetyl-CoA that enters the cycle, … molecules of NAD+ are reduced to NADH, which accounts for three of the electron pairs, and one molecule of FAD is reduced to FADH2, which accounts for the fourth electron pair. In addition, one GTP (or ATP) is produced

three

the electrons carried by NADH and FADH2 are funneled into the electron-transport chain, which culminates with the reduction of … to … The energy of electron transport is conserved in the synthesis of ATP by …

O2; H2O; oxidative phosphorylation

For every NADH that passes its electrons on, approximately … ATP are produced from ADP + Pi. For every FADH2, approximately … ATP are produced. Thus, one turn of the citric acid cycle ultimately generates approximately … ATP

2.5; 1.5; 10

when glucose is converted to two molecules of pyruvate by glycolysis, … of ATP are generated and … of NAD+ are reduced. The NADH molecules yield approximately … molecules of ATP on passing their electrons to the electron-transport chain

two molecules; two molecules; 5

two turns of the citric acid cycle (one for each acetyl group) generate … ATP

one molecule of glucose can potentially yield … molecules of ATP under aerobic conditions, when the citric acid cycle is operating. In contrast, only … molecules of ATP are produced per glucose molecule under anaerobic conditions

about 32; 2

(regulatory systems for citric acid cycle) product inhibition by … and …--> these compounds compete with NAD+ and COA for binding sites on their respective enzymes

NADH; acetyl-COA

(regulatory systems for covalent modification by …/… of …: in eukaryotes, the products of the pyruvate dehydrogenase rxn, NADH and acetyl-CoA, also activate the … associated with the enzyme complex the resulting phosphorylation of a specific dehydrogenase Ser residue inactivates the pyruvate dehydrogenase complex.

phosphorylation; dephosphorylation; E1; pyruvate dehydrogenase kinase

insulin, the hormone that signals fuel abundance, reverses the inactivation by activating …, which removes the phosphate groups from pyruvate dehydrogenation. In response to increases in blood glucose conc., insulin promotes the synthesis of … as well as glycogen

pyruvate dehydrogenase phosphate; acetyl-CoA

a proposed mechanism of flux control must operate within the … ranges of the effectors

physiological concentration

three of the enzymes are likely to function far from equilibrium under physiological conditions (negative delta G): …, …, and ...

citrate synthase; NAD+-dependent isocitrate dehydrogenase; alpha-ketoglutarate dehydrogenase

bc oxygen consumption, NADH reoxidation, and ATP production are tightly coupled, the citric acid cycle must be regulated by … that coordinate … with ...

feedback mechanisms; NADH production; energy expenditure

unlike the rate-limiting enzymes of glycolysis and glycogen metabolism, which regulate flux by elaborate systems of allosteric control, substrate cycles, and covalent modification, the regulatory enzymes of the citric acid cycle seem to control flux primarily by three simple mechanisms: … … and … by intermediates further along the cycle

substrate availability product inhibition competitive feedback inhibition

perhaps the most crucial regulators of the citric acid cycle are its substrates, … and …., and its product, …

acetyl-CoA; oxaloacetate; NADH

… is an allosteric activatory of isocitrate dehydrogenase, whereas … inhibits the enzme

ADP; ATP

… regulates the citric acid cycle at several pts. it activates …, which in turn activates the pyruvate dehydrogenase complex to produce acetyl-CoA

Ca2+; pyruvate dehydrogenase phosphatase

Ca2+ also activates both … and … Thus, Ca2+ the signal that stimulates muscle contraction, also stimulates the production of the ATP to fuel it

isocitrate dehydrogenase; alpha-ketoglutarate dehydrogenase

…: a loose complex of the enzymes that catalyze the steps of a metabolic pathway such that the intermediates can be efficiently transferred between enzymes

metabolon

the citric acid cycle is …

amphibolic

(cataplerotic rxn for citric acid) … uses oxaloacetate

glucose biosynthesis (gluconeogenesis)

(cataplerotic rxn for citric acid) … is a cytosolic process that requires acetyl Co-A. Cytosolic acetyl-CoA is generated by the breakdown of …, which can cross the membrane, in a rxn catalyzed by ...

fatty acid biosynthesis; ATP-citrate lyase

(cataplerotic rxn for citric acid) … uses alpha-ketoglutarate and oxaloacetate as starting materials. for example, alpha-ketoglutarate is converted to glutamate by reductive amination catalyzed by a … that utilizes either NADH or NADPH

amino acid biosynthesis; glutamate dehydrogenase

any decrease in the rate of the cycle caused by insufficient oxaloacetate or other intermediates allows the concentration of … to rise

acetyl-CoA

plants, bacteria, and fungi, but not animals, possess enzymes that mediate the net conversion of … to …, which can be used for gluconeogenesis

acetyl-CoA; oxaloacetate

…: membrane-bounded plant organelle that is a specialized peroxisome

glyoxysome

Reactions 1 and 2. Glyoxysomal oxaloacetate is condensed with acetylCoA to form ..., which is isomerized to ...as in the citric acid cycle. Since the glyoxysome contains no aconitase, Reaction 2 presumably takes place in the ....

citrate; isocitrate; cytosol

Reaction 3. G lyoxysomal isocitrate lyase cleaves the isocitrate to ...and ...(hence the cycle’s name).

succinate ; glyoxylate

Reaction 4. Malate synthase, a glyoxysomal enzyme, condenses glyoxylate with a second molecule of acetyl-CoA to form .... Reaction 5. G lyoxysomal malate dehydrogenase catalyzes the oxidation of malate to ...by NAD+.:

malate; oxaloacetate

The glyoxylate cycle therefore results in the net conversion of two acetyl-CoA to ....instead of to four molecules of ...as would occur in the citric acid cycle.

succinate; CO2

succinate product of glyoxylate cycle (1) It can be converted to oxaloacetate in the mitochondrion, continuing the citric acid cycle and thereby making the glyoxylate cycle an ...process (Section 17-5B); or (2) it can be transported to the cytosol, where it is converted to oxaloacetate for entry into ...

anaplerotic; gluconeogenesis

Organisms that lack the glyoxylate pathway cannot undertake the net synthesis of ...from acetyl-CoA. This is the reason humans cannot convert fats (that is, fatty acids, which are catabolized to acetyl-CoA) to ...(that is, glucose).

glucose; carbohydrates