Biochemistry Citric Acid Cycle, Chapter 16

Front 1

1. Yeast can grow both aerobically and anaerobically on glucose. Explain why the rate of glucose consumption decreases when yeast that has been obtained under anaerobic conditions is exposed to Oxygen?

Back 1

the amount of glucose consumption required to maintain the proper ATP levels in the cell is greatly reduced in aerobically growing cells. In short, glucose is oxidized completely under aerobic conditions and fewer molecules of glucose must be consumed to produce an amount of ATP equivalent to the amount produced under anaerobic conditions.Yeast can grow both aerobically and anaerobically on glucose.

Hint 1

1. The decrease in glucose consumption when oxygen is present is known as the Pasteur Effect. Under anaerobic conditions , there is a net production of only two molecules of ATP for each molecule of glucose converted to ethanol and CO2 by the anaerobic glycolytic pathway. When Oxygen is introduced, the cell can utilize glucose much more efficiently, producing 30-32 molecules of ATP for each glucose molecule oxidized completely to CO2 and water by glycolysis, the citric acid cycle and the respiratory electron transport chain. Thus

Front 2

2. Trace the fate of 14CH3 –labeled acetyl CoA through two rounds of the citric acid cycle. Assume that the labeled acetyl CoA enters only in the first round.

Back 2

2. First round. The carbon atoms are retained and end up as the carbon atoms of oxaloacetate. The CH3 carbon ends up as carbons 2 (C=O) and 3 (CH2) of OAA. In the second round those original acetyl carbons are not lost but get distributed to all carbons of OAA at the succinyl CoA synthetase step. You should determine this answer by going through the reactions of the TCA cycle.

Front 3

3. Trace the fate of the isotopic label of [2-18 O]-pyruvate through the pyruvate dehydrogenase reaction complex and one round of the TCA cycle.

Back 3

3. In the pyruvate dehydrogenase reaction the C=O carbon becomes the carboxyl carbon of Acetyl CoA. As in question two, this carbonyl group is not lost and becomes the carboxyl groups of OAA. It remains as only one of the carboxyl groups of citrate, isocitrate, aconitate, ketoglutarate and succinyl CoA. However it gets randomized to the two carboxyl groups of succinate, fumarate, malate and OAA after the succinylCoA synthetase reaction.

Front 4

4. The following labeled glucose molecules are metabolized to 14CO2 via glycolysis and the TCA cycle. Which labeled molecule yields 14CO2 fastest and which takes longest to yield 14CO2 ? Assume pyruvate only enters the TCA cycle only as acetyl-CoA. A) 1-14C-glucose B) 2-14C-glucose C) 3-14C-glucose.

Back 4

4. Glc-3 becomes pyruvate carboxyl and is the first released as CO2 in the pyruvate dehydrogenase reaction. Glc-2 becomes the carboxyl group of Acetyl CoA and is retained and becomes the two carboxyl groups of succinate and OAA. In the second round of the TCA cycle they are released as CO2. Glc-1 becomes the CH3 group of acetyl-CoA. As answer 2 shows, the CH3 carbon ends up as carbon 2 (C=O) and 3 (CH2) of OAA in the first round. In the second round those original acetyl carbons are not lost but get distributed to all carbons of OAA at the succinyl CoA synthetase step. Therefore, 3-14C-glucose releases labeled CO2 faster than 2-14C-glucose and 1-14C-glucose releases CO2 the slowest.

Front 5

5. Which statements are true or false.

a. Dihydrolipoamide dehydrogenase catalyzes the only redox reaction in the pyruvate dehydrogenase complex.
b. Hydrolysis of the thioester bond of acetyl CoA yields insufficient energy to drive phosphorylation of ADP.
c. Even if aconitase were unable to discriminate between the two ends of the citrate molecule, the CO2 released would still come from oxaloacetate rather than the acetyl CoA substrate of the citrate synthase reaction.
d. Malate cannot be converted to fumarate because the TCA cycle is unidirectional.

Back 5

a. Dihydrolipoamide dehydrogenase catalyzes the only redox reaction in the pyruvate dehydrogenase complex. False. There is a reduction in the dihydrolipoyl transacetylase step.

b. Hydrolysis of the thioester bond of acetyl CoA yields insufficient energy to drive phosphorylation of ADP. False.Acetyl-CoA has a ∆G˚´ of -31.4 kJ/mol.

c. Even if aconitase were unable to discriminate between the two ends of the citrate molecule, the CO2 released would still come from oxaloacetate rather than the acetyl CoA substrate of the citrate synthase reaction. False.

d. Malate cannot be converted to fumarate because the TCA cycle is unidirectional. False.

Front 6

6. Lipoic acid is bound to enzymes that catalyze oxidative decarboxylation of a-keto acids.

a. What is the chemical mode of attachment of lipoic acid to enzymes?

b. Using chemical structures, show how the lipoic acid participates in the oxidative decarboxylation of a-keto acids.

Back 6

6. a) Lipoic acid is bound to enzymes through an amide bond with epsilon amino group of a lysine residue. b)See Figs. 16-4 and 16-6 and pages 603 and 605 in 474 in Lehninger or pages 66 and 69 in your coursepack.

Front 7

7. How is the pyruvate dehydrogenase complex regulated? What are the allosteric effects and the covalent modification effects?

Back 7

Allosteric effects. Inhibition of enzyme 1 by product inhibition by NADH + acetyl CoA. Thus, high ratios of NADH/NAD and AcetylCoA/ CoA inhibit Enzyme1. Enzyme 3, lipoamide dehydrogenase will also be inhibited. Covalent modification. Pyruvate dehydrogenase kinase phosphorylates a seryl residue of Enzyme 1 and causes Enzyme 1 to be inactive. NADH and Acetyl CoA allosterically activate the kinase. An inhibitor of the kinase is Ca++ which increases in concentration in muscle tissue during muscular activity. A protein phosphatase dephosphorylates the inactive enzyme 1 and the PDH complex becomes active. Ca++ is an activator of the phosphatase. So the products of of PDH activity regulate their own production both by allosteric control and by regulating covalent modification.

Front 8

8. What is meant by the statement that the TCA cycle is amphibolic? Give examples of processes affected by the TCA cycle intermediates.

Back 8

The TCA cycle is amphibolic because it paticipates both in synthesis and in catabolism of amino acids, glucose and fatty acids. Succinyl CoA is an intermediate of porphyrin biosynthesis. Alpha ketoglutarate is a precursor for synthesis of the amino acid glutamate and glutamine. Citrate is a precursor for fatty acid synthesis. Oxaloacetate can be utilized for gluconeogenesis or aspartate synthesis.

Front 9

9. How are ATP, ADP and Ca+2 involved in the regulation of the citrate cycle?

Back 9

9. ATP is an inhibitor of and ADP is an activator of the isocitrate dehydrogenase. Ca+2 is involved in the regulation of the covalent modification of PDH

Front 10

10. What are the anaplerotic reactions? Give two examples. What is the rationale for activation of pyruvate carboxylase by acetyl CoA?

Back 10

The term, “Anaplerotic”, is based on a greek word which means replenishment. Under certain conditions the concentration of OAA is low and in order for the citric acid cycle to be efficient the OAA concentration has to be increased. It is done by the pyruvate carboxylase reaction, Pyruvate + CO2 + H20 + ATP <===> OAA +ADP + Pi. Acetyl CoA is a potent activator of the pyruvate carboxylase. If there is a sudden increase in the acetyl CoA concentration and for it to be metabolized by the TCA cycle the concentration of OAA should be increased. Thus acetyl CoA allosterically activates the pyruvate carboxylase. Another anaplerotic enzyme is found in bacteria. They have the phospho-enol pyruvate carboxylase reaction, PEP + CO2 -> OAA + Pi. Acetyl CoA is also an activator of this enzyme. PEP carboxykinase and malate enzyme are also anaplerotic reactions. The malate enzyme reaction is seen in Table16-2 on page 79 in your course pack. Reaction is pyruvate + HCO3-1+ NADPH -> malate + NADP. Some malate enzymes use NADH instead of NADPH.

Front 11

1. Cellular respiration is the process by which cells
A. oxidize organic fuels to CO2 and H2O.
B. consume O2 and produce CO2.
C. convert O2 to H2O.
D. breakdown sugars to CO2 and H2O.

Back 11

B. consume O2 and produce CO2

Front 12

2. Amino acids, fatty acids, and glucose are oxidized and enter the citric acid cycle as
A. pyruvate.
B. acetate.
C. oxaloacetate.
D. acetyl-CoA.

Back 12

D. acetyl-CoA.

Front 13

3. The first reaction of the citric acid cycle, which generates citrate, is
A. a condensation reaction.
B. an oxidative decarboxylation reaction.
C. dehydrogenation reaction.
D. a dehydration reaction.

Back 13

A. a condensation reaction.

Front 14

4. For every molecule of glucose, how many molecules of CO2 are released in the citric acid cycle?
A. one
B. two
C. four
D. six

Back 14

C. four

Front 15

5. Which of the following is true about the pyruvate dehydrogenase complex?
A. It converts pyruvate to oxaloacetate.
B. It catalyzes oxidative decarboxylation.
C. It is located in the cytosol of eukaryotic cells.
D. It requires NADH.

Back 15

B. It catalyzes oxidative decarboxylation.

Front 16

6. What role does coenzyme A play in the citric acid cycle?
A. It is an electron carrier.
B. It carries hydride ions.
C. It is an acyl group carrier.
D. It is an oxidizing agent.

Back 16

C. It is an acyl group carrier.

Front 17

7. Which of following is true about all of the dehydrogenase enzymes that participate in the citric acid cycle?
A. They catalyze condensation reactions.
B. They generate CO2.
C. They convert a single bond to a double bond.
D. They generate reduced electron carriers.

Back 17

D. They generate reduced electron carriers.

Front 18

8. What types of reactions do phosphorylases catalyze?
A. Displacement reactions in which an attacking phosphate becomes covalently attached at the point of bond breakage.
B. The removal of a phosphoryl group from a phosphate ester.
C. The transfer of a phosphoryl group from a nucleoside triphosphate to an acceptor molecule.
D. Ligation reactions in which phosphate esters join molecules.

Back 18

A. Displacement reactions in which an attacking phosphate becomes covalently attached at the point of bond breakage.

Front 19

9. Which of the following enzymes catalyzes a condensation reaction in which no nucleoside triphosphate is required as an energy source?
A. kinases
B. synthases
C. ligases
D. synthetases

Back 19

B. synthases

Front 20

10. Which of the following conditions has a negative effect on the pyruvate dehydrogenase complex?
A. a high ratio of [ADP]/[ATP]
B. a high level of Ca2+
C. a high ratio of [NAD+]/[NADH]
D. a high ratio of [acetyl-CoA]/[CoA]

Back 20

D. a high ratio of [acetyl-CoA]/[CoA]

Front 21

11. In non-vertebrate organisms, the glyoxylate cycle is needed to convert
A. triacylglycerols to fatty acids.
B. acetate to carbohydrates.
C. glyoxylate to ATP.
D. oxaloacetate to malate.

Back 21

B. acetate to carbohydrates

Front 22

12. In what way are the glyoxylate cycle and citric acid cycles linked?
A. NADH produced in the glycoxylate cycle enters the citric acid cycle.
B. Acetyl-CoA produced in the glycoxylate cycle enters the citric acid cycle.
C. Succinate produced in the glycoxylate cycle enters the citric acid cycle.
D. Oxaloacetate produced in the glycoxylate cycle enters the citric acid cycle.

Back 22

C. Succinate produced in the glycoxylate cycle enters the citric acid cycle.

Front 23

13. The citric acid cycle is amphibolic pathway, which means that
A. it serves in both anabolic and catabolic processes.
B. it is linked to other cycles.
C. it can catalyze reactions that are both exergonic and endergonic.
D. it can move in both a forward and reverse direction.

Back 23

A. it serves in both anabolic and catabolic processes.

Front 24

14. Biotin
A. serves as a cofactor in dehydrogenation reactions.
B. transfers one-carbon groups.
C. is a cofactor that transfers acetyl groups.
D. carries CO2 groups.

Back 24

D. carries CO2 groups.

Front 25

15. Which of the following citric acid cycle reaction steps is not inhibited by a high [NADH]/[NAD+]?
A. conversion of alpha-ketoglutarate to succinyl-CoA
B. conversion of succinyl-CoA to succinate
C. conversion of isocitrate to alpha-ketoglutarate
D. condensation of oxaloacetate and acetyl-CoA to form citrate

Back 25

B. conversion of succinyl-CoA to succinate

Front 26

16. Some plants that have been genetically engineered to express elevated levels of citrate synthase have increased crop productivity because
A. citric acid increases soil pH.
B. citric acid production is a rate-limiting step.
C. citric acid chelates metal ions.
D. citric acid is toxic to some plant pathogens.

Back 26

C. citric acid chelates metal ions.

Front 27

17. Anaplerotic reactions, such as the conversion of pyruvate to oxaloacetate, are useful to the citric acid cycle because they
A. generate a steady supply of intermediates for the citric acid cycle.
B. produce molecules needed to regulate the citric acid cycle.
C. link the citric acid cycle to the glyoxylate cycle.
D. siphon away excess intermediates from the citric acid cycle.

Back 27

A. generate a steady supply of intermediates for the citric acid cycle.

Front 28

What is respiration?

Back 28

Most eukaryotic cells and many bacteria are capable in aerobic conditions of
oxidizing metabolites in the
presence of O2 to CO2 and H2O.

Front 29

What is cellular respiration?

Back 29

The molecular processes that cells consume O2 and oxidize carbon atoms of
metabolites to produce CO2

Front 30

Catabolism of proteins, fats and carbohydrates in three stages of cellular respiration. Stage 1:

Back 30

oxidation of fatty acids, glucose (pyruvate) and some amino acids yield acetyl-CoA.

Front 31

Catabolism of proteins, fats and carbohydrates in three stages of cellular respiration. Stage 2:

Back 31

oxidation of acetyl groups in the TCA cycle. There are 4
steps in which electrons are abstracted and NADH and FADH2 are produced.

Front 32

Catabolism of proteins, fats and carbohydrates in three stages of cellular respiration. Stage 3:

Back 32

Electrons of NADH and FADH2 are then funneled into a chain of mitochondrial electron carriers in eukaryotes or, in bacteria, the plasma membrane bound electron carriers.

Front 33

The citric acid cycle (TCA cycle) is the _______ phase of cellular respiration where …………..

Back 33

central
acetyl-CoA carbon is metabolized and converted to CO2.

Front 34

Overall reaction in step 1 of cellular respiration is catalyzed by?

Back 34

the Pyruvate Dehydrogenase complex.

Front 35

What enzymes and coenzymes participate in the Pyruvate Dehydrogenase complex?

Back 35

5 coenzymes and three enzymes participate in this enzyme complex.
CoA,
NAD,
TPP,
Lipoate,
and FAD.

Front 36

What is the structure of Coenzyme A (CoA)?

Back 36

A hydroxyl group of pantothenic acid is linked to ADP that also has a phosphate group esterified to the three hydroxy group of its ribose.

Front 37

In the structure of Coenzyme A, The pantothenic acid carboxyl group is in amide linkage with?

Back 37

ß mercaptoethylamine.

Front 38

In the structure of Coenzyme A, The --SH group of the mercaptoethylamine forms?

Back 38

A thioester with the acetate in acetyl-coenzyme A (acetyl CoA).

Front 39

In the structure of Coenzyme A, pantothenic acid is what type of vitamin?

Back 39

Type of Vitamin B

Front 40

Lipoic acid (lipoate) in amide linkage with?

Back 40

a Lys residue.

Front 41

The lipoyllysyl moiety( dihydro-lipoyl transacetylase) is?

Back 41

the prosthetic group of E2 of the PDH complex

Front 42

The lipoyl group can exist as?

Back 42

an oxidized, disulfide form or reduced, dithiol form or in an acetylated form.

Front 43

Lipoic acid (lipoate) does what?

Back 43

It acts as a carrier of hydrogen as well as a carrier for acyl groups.

Front 44

The attachment of lipoate to the end of a Lys side chain in E2 produces?

Back 44

a long, flexible arm that can move from the active site of E1 to the active sites of E2 and E3

Front 45

The Pyruvate Dehydrogenase complex consists of _______ enzymes?

Back 45

three distinct enzymes.

Front 46

The Pyruvate Dehydrogenase complex consists of three distinct enzymes. What are they?

Back 46

They are are:
pyruvate dehydrogenase (E1),
dihydrolipoyl transacetylase (E2) and dihyrolipoyl dehyrogenase.

Front 47

There are how many enzymes in the Pyruvate Dehydrogenase complex depending on the species.

Back 47

Many copies
The PDH complex in mammals is about 50 nm in diameter

Front 48

The 3-dimensional structure of PDH shows the core structure in green which is ………………………….. to form a pentagonal dodecahedron.

Back 48

60 molecules of E2 arranged in 20 trimers

Front 49

The 3-dimensional structure of PDH shows the lipoyl domain of E2 reaching out to
be in contact with?

Back 49

the catalytic sites of E1 arranged around the E2 core.

Front 50

The 3-dimensional structure of PDH shows the E3 subunits are also bound to & do what?

Back 50

the core where the swinging arm on E2 can reach their active sites.

Front 51

The 3-dimensional structure of PDH, a lipoyl group is attached to?

Back 51

the lipoyl domain of E2.

Front 52

E2 has 3 functionally distinct domains. What are they?

Back 52

The amino terminal lipoyl domain has the lipoyl
residue(s)

the central E1 binding domain

E3 binding domain

the inner core acyltransferase domain having the acyltransferase active site.

Front 53

The number of lipoyl domains in diffent species are?

Back 53

variable

Front 54

The domains of E2 are separated by ……………… and
interspersed with ……………………… allowing ………………………….. to effectively separate the domains.

Back 54

by 20-30 amino acid residues rich in Ala and Pro

charged amino acid residues

an extended structure

Front 55

In PDH, The active site of E1 has bound?

Back 55

TPP

Front 56

In PDH, The active site of E3 has bound?

Back 56

FAD.

Front 57

This basic E1-E2-E3 structure of the PDH has been conserved in evolution and is seen in a number of complexes used for similar metabolic reactions. One important reaction would be?

Back 57

the α- ketoglutarate dehydrogenase reaction that also occurs in the TCA cycle.

Front 58

How does the PDH complex work?

Back 58

By substrate channeling and the intermediates never leaving the enzyme
surface.

Front 59

Oxidative decarboxylation of pyruvate to acetyl CoA by
the PDH complex. What are the five steps?

Back 59

(1) Pyruvate reacts with bound TPP of E1 and undergoes decarboxylation to form the hydroxyethyl TPP

(2) We have transfer of 2 electrons and an acetyl group from E1 to form reduced lipoyllysine of E2 as well
as acetylating one of the lipoyl -SH groups to give an acetyl thio-ester.

(3) we have a transesterification whereby the -SH group of CoA replaces the -SH group of E2 to produce acetyl-CoA and fully reduced lipoyllysine.

(4) E3 oxidizes the reduced lipoyllysine to form FADH2 and

(5) E3 catalyzes the reduction of NAD by reduced FADH2.

Front 60

Having the enzymes in a complex facilitates
channeling of substrates in Oxidative decarboxylation of pyruvate to acetyl CoA by the PDH complex allows?

Back 60

A greater efficiency of the reaction and preservation of unstable intermediates.

Front 61

Oxidative decarboxylation of pyruvate to acetyl CoA by
the PDH complex. What is the first step?

Back 61

(1) Pyruvate reacts with bound TPP of E1 and undergoes decarboxylation to form the hydroxyethyl TPP

Front 62

Oxidative decarboxylation of pyruvate to acetyl CoA by
the PDH complex. What is the second step?

Back 62

(2) We have transfer of 2 electrons and an acetyl group from E1 to form reduced lipoyllysine of E2 as well
as acetylating one of the lipoyl -SH groups to give an acetyl thio-ester.

Front 63

Oxidative decarboxylation of pyruvate to acetyl CoA by
the PDH complex. What is the third step?

Back 63

(3) we have a transesterification whereby the -SH group of CoA replaces the -SH group of E2 to produce acetyl-CoA and fully reduced lipoyllysine.

Front 64

Oxidative decarboxylation of pyruvate to acetyl CoA by
the PDH complex. What is the fourth step?

Back 64

(4) E3 oxidizes the reduced lipoyllysine to form FADH2

Front 65

Oxidative decarboxylation of pyruvate to acetyl CoA by
the PDH complex. What is the fifth and last step?

Back 65

(5) E3 catalyzes the the reduction of NAD by reduced FADH2.

Front 66

Reactions of the Citric Acid Cycle. The carbon atoms that are at the top of the chemical formulas in steps 1 - 4 came from?

Back 66

acetate of acetyl CoA.

Front 67

Note in the first turn of the Citric Acid Cycle, the two carbons released as CO2 __ __ ____ from acetate.

Back 67

do not come

Front 68

In the Citric Acid Cycle, ________ & _______ are symmetric molecules.

Back 68

Succinate and fumarate

Front 69

In reactions of the Citric Acid Cycle, in what steps is energy conserved in the form of NADH or FADH2 via electron transfer to NAD+ or FAD. ?

Back 69

NADH – Steps 3, 4 and 8
FADH2 – Step 6

Front 70

What reactions of the Citric Acid Cycle are irreversible?

Back 70

Reactions 1,3 and 4.

Front 71

What is the formation of citrate?

Back 71

Acetyl CoA + Oxaloacetate are condensed to form citrate.

Front 72

Is the Citrate synthase reaction is endogonic or exergonic?

Back 72

The reaction is highly exergonic

Front 73

What is the transient intermediate of the Citrate synthase reaction and is equivalent to …….?

Back 73

Citroyl-CoA

a Claisen condensation involving a thioester, acetyl CoA and a ketone, oxaloacetate.

Front 74

The Citrate synthase reaction mechanism has oxaloacetate binding ___________, which allows?

Back 74

a conformational change in the enzyme allowing the binding of acetyl CoA

Front 75

What is Step 2 of TCA?

Back 75

Formation of isocitrate via the aconitase reaction.

Front 76

In the formation of isocitrate (step 2 of TCA), Aconitase catalyzes the interconversion between citrate and isocitrate by?

Back 76

the reversible addition of water to an enzyme bound intermediate, cisaconitate.

Front 77

What is the enzyme bound intermediate of the formation of isocitrate via the aconitase reaction?

Back 77

cisaconitate.

Front 78

The enzyme of the formation of isocitrate via the aconitase reaction has an ____ _____ center (from aconitase) which acts in?

Back 78

iron-sulfur

binding of the substrate and in catalysis.

Front 79

An iron from aconitase is bound to ……… of citrate
and interacts with the ______ group of citrate.

Back 79

one of the carboxyl groups

hydroxyl

Front 80

Step 3 reaction of TCA?

Back 80

Oxidation of Isocitrate to α-Ketoglutarate + CO2 is catalyzed by isocitrate dehydrogenase.

Front 81

Oxidation of Isocitrate to α-Ketoglutarate + CO2 is catalyzed by?

Back 81

isocitrate dehydrogenase.

Front 82

What are the two forms of isocitrate dehydrogenase?

Back 82

one specific for NAD+ and one specific for NADP+.

Front 83

In eukaryotic cells, the NAD+-specific form of isocitrate dehydrogenase is in the ________ and is the enzyme involved in?

Back 83

mitochondria
the TCA cycle.

Front 84

The NADP+ specific enzyme of isocitrate dehydrogenase resides?

Back 84

both in the mitochondrial matrix and the cytosol.

Front 85

The two forms of isocitrate dehydrogenase enzymes’ function are believed to be involved in?

Back 85

NADPH production which are required for anabolic
reactions.

Front 86

The Oxidation of Isocitrate to α-Ketoglutarate + CO2 reaction requires ____ and _____________ is a reaction intermediate.

Back 86

Mn2+
Oxalosuccinate

Front 87

In the Oxidation of Isocitrate to α-Ketoglutarate + CO2 reaction (step 3 TCA), Mn2+ is involved in the ……….. formed during the reaction.

Back 87

decarboxylation and stabilization of the enol-form

Front 88

Step 4 of the TCA?

Back 88

Oxidation of Ketoglutarate to Succinyl-CoA is catalyzed by the α-ketoglutarate dehydrogenase (KDH) complex.

Front 89

Oxidation of Ketoglutarate to Succinyl-CoA is
catalyzed by?

Back 89

the α-ketoglutarate dehydrogenase (KDH) complex.

Front 90

What reaction is virtually identical to the pyruvate
dehydrogenase reaction?

Back 90

Oxidation of Ketoglutarate to Succinyl-CoA

Front 91

The α-KDH complex in step 4 of TCA is similar and different to the PDH complex in both structure and function. How are they the same?

Back 91

It includes three enzymes, homologous to E1, E2, and E3 of the PDH complex, the enzyme bound TPP, the enzyme bound lipoate, FAD, NAD+ and coenzyme A.

The E2 of KDH has a covalently bound lipoyl group similar to E2 of PDH.

The E3 enzyme of both complexes are identical.

Front 92

The α-KDH complex in step 4 of TCA is similar and different to the PDH complex in both structure and function. How are they different?

Back 92

While E1 of the PDH complex binds pyruvate, E1 of the KDH complex binds
α-ketoglutarate.

Front 93

What is step 5 of TCA?

Back 93

Succinyl-CoA is converted to Succinate by Succinyl-CoA synthetase

Front 94

In step 5 of TCA, Succinyl-CoA is converted to Succinate by?

Back 94

Succinyl-CoA synthetase

Front 95

What are the three steps of the The succinyl CoA synthetase reaction mechanism (step 5 of TCA).

Back 95

(1) A phosphoryl group replaces the CoA of succinyl-CoA bound to the enzyme forming a high energy acyl-P.

(2) The succinyl-P donates its Phosphoryl group to
a His residue forming a high-energy phosphohistidyl enzyme.

(3) The phosphoryl group is transferred from the
His group to the terminal Phosphate of GDP or ADP forming GTP or ATP

Front 96

The transfer of Pi to GTP or to ATP in the succinyl CoA synthetase reaction mechanism is known as?

Back 96

substratelevel Phosphorylation.

Front 97

The succinyl CoA synthetase (step 5 TCA) has two subunits.

Back 97

the α-subunit (Mr, 32 kD) has the P-His residue and binding site for CoA

the β-subunit (Mr 42 kD) confers specificity for either ADP or GDP

Front 98

It is important to note that GTP and ATP of the succinyl CoA synthetase reaction are?

Back 98

interconvertible.

Front 99

It is important to note that GTP and ATP of the succinyl CoA synthetase reaction are interconvertible. The GTP formed by succinyl CoA synthetase can?

Back 99

transfer its terminal phosphate to ADP to form ATP in a reaction catalyzed by nucleoside diphosphate kinase.

Front 100

The GTP formed by succinyl CoA synthetase can transfer its terminal phosphate to ADP to form ATP in a reaction. What is the formula rxn?

Back 100

GTP + ADP ←→ GDP + ATP

Delta G’O = 0 kJ/mol

Front 101

What is step 6 of TCA?

Back 101

Succinate Dehydrogenase oxidizes succinate to fumarate.

Front 102

What oxidizes succinate to fumarate (step 6)?

Back 102

Succinate Dehydrogenase

Front 103

In eukaryotes, succinate dehyrogenase (of TCA: step 6) is tightly bound to?

Back 103

the inner mitochondrial membrane.

Front 104

In prokaryotes, succinate dehyrogenase (of TCA: step 6) is tightly bound to?

Back 104

The inner membrane.

Front 105

succinate dehyrogenase (of TCA: step 6) has 3 different
____________ and one molecule of ……...

Back 105

iron-sulfur clusters

covalently-bound FAD

Front 106

In succinate dehyrogenase (of TCA: step 6), What passes from succinate through FAD and iron-sulfur clusters in the molecule. And then they are transferred to the ?

Back 106

Electrons

The electrons are then transferred to the electron chain.

Front 107

What is a is a strong competitive inhibitor of
Succinate (step 6 TCA)?

Back 107

Malonate

Front 108

What is step 7 of TCA?

Back 108

Fumarate is hydrated to L-malate by the enzyme fumarase or fumarate dehydratase.

Front 109

In step 7 of TCA, Fumarate is hydrated to L-malate by?

Back 109

the enzyme fumarase or fumarate dehydratase.

Front 110

In step 7 of TCA, Fumarase reaction of Fumarate is specific for ________ and not _____ .

Back 110

L-malate and not for D-malate

Front 111

What is step 8 of TCA?

Back 111

L-malate is oxidized to oxaloacetate via the L-malate dehydrogenase that is NADspecific.

Front 112

What is step 8 of TCA, L-malate is oxidized to oxaloacetate via the?

Back 112

L-malate dehydrogenase that is NAD specific.

Front 113

Is the L-malate is oxidized to oxaloacetate via the L-malate dehydrogenase (step 8 of TCA) endergonic or exergonic?

Back 113

quite endergonic.

Front 114

The L-malate is oxidized to oxaloacetate via the L-malate dehydrogenase (step 8 of TCA) endergonic. However the reaction moves freely in the direction of _________ since …….

Back 114

oxaloacetate (OAA) formation

OAA is quickly consumed in the citrate synthase reaction.

Thus the OAA concentration in the cell is low (< 10-6 M).

Front 115

The L-malate is oxidized to oxaloacetate via the L-malate dehydrogenase (step 8 of TCA) is one of the few examples in nature where a ?

Back 115

symmetrical molecule citrate reacts in an enzyme reaction asymetrically.

Front 116

When acetate, labeled in the carboxyl group ( [1-C14] acetate), is incubated in animal tissues it is converted to.________ and the label in the TCA cycle intermediates can be?

Back 116

acetyl CoA


traced.

Front 117

What is the reason for this non-labeling of the 8th step of TCA?

Back 117

It was wrongly concluded that citrate could not be in the pathway from acetate to α-ketoglutarate.

even if citrate has no chiral center it has the potential to react asymmetrically if the enzyme that it is reacting with, has an asymmetric active site.

Thus it was suggested that aconitase may have three points to which citrate must be bound and citrate must undergo a specific three-point attachment to these binding points.

the binding of citrate to three such points can happen in only one way.


citrate is called a prochiral molecule and that is, a molecule that has no chiral center but is potentially capable of reacting asymmetrically with an asymmetric active site.

Front 118

What is a prochiral molecule?

Back 118

a molecule that has no chiral center but is potentially capable of reacting asymmetrically with an asymmetric active site. (like citrate)

Front 119

How is the energy of TCA cycle oxidations are
efficiently conserved?

Back 119

two CO2 molecules are released and the energies released in these oxidations are conserved in the reduction of three
NAD+, and one FAD and synthesis of 1 ATP or GTP.

Front 120

oxidation of the 3 NADH and FADH2 by the mitochondrial
electron transfer chain (like in Chapter 19) will yield how many molecules of ATP for each molecule of glucose which will be completely oxidized to form 6 molecules of CO2.

Back 120

30-32

Front 121

What Products are obtained in one turn of the TCA Cycle.

Back 121

In one turn, 3NADH, 1 FADH2, 1 GTP (or ATP)and 2 CO2 are formed.

Front 122

TCA cycle _______ are important
biosynthetic intermediates.

Back 122

Metabolites

Front 123

the TCA cycle is an ________ pathway.

Back 123

amphibolic

Front 124

Besides TCA role in the oxidative catabolism of
carbohydrates, fatty acids and amino acids, the cycle provides?

Back 124

precursors for many biosynthetic pathways.

Front 125

Besides TCA role in the oxidative catabolism of
carbohydrates, fatty acids and amino acids, the cycle provides precursors for many biosynthetic pathways.
What are 4 of them?

Back 125

α- ketoglutarate and oxaloacetate (OAA) can serve as precursors of amino acids, glutamate and aspartate,
respectively.

OAA can also be used for glucose synthesis in gluconeogenesis.

Succinyl CoA is a precursor for synthesis of the porphyrin ring of heme groups seen in hemoglobin and in cytochromes.

Citrate is a precursor for fatty acid synthesis.

Front 126

What is the role of TCA cycle in anabolism?

Back 126

Intermediates of the TCA cycle are drawn off as precursors in many biosynthetic pathways.

Front 127

How many anaplerotic reactions replenish the depleted TCA cycle intermediates?

Back 127

4

Front 128

Anaplerotic reactions are needed to replenish?

Back 128

TCA Cycle intermediates.

Front 129

Since TCA cycle intermediates are removed to serve as biosynthetic precursors there must be ………………….. in order for the cycle to continue.

Back 129

reactions to replenish them

Front 130

Anaplerotic comes from the greek word anaplerosis which means?

Back 130

“to replenish”.

Front 131

What is the role of biotin in the reaction catalyzed by pyruvate carboxylase?

Back 131

Biotin is attached to the enzyme through an amide bond with the ε-amino group of a lys residue forming biotinyl enzyme.

Front 132

What is the steps of biotin in the reaction catalyzed by pyruvate carboxylase

Back 132

First carboxy-P is formed from ATP and HCO3.

The carboxy group is transferred to biotin to form carboxybiotinyl-enzyme.

The carboxy group is transferred to another biotin
at another catalytic site.

Pyruvate is bound to the enzyme and is converted to its enol form.

The carboxy group which is an activated form of CO2, is then transferred to the enolpyruvate to form oxaloacetate.

Front 133

The biotinyl-lysine chain acts like a long flexible arm in transferring?

Back 133

the activated CO2 from one catalytic site to another.

Front 134

biotinyl-lysine chain behaves in a similar way as the lipoyllysine in E2 of PDH acting as?

Back 134

a flexible tether transferring bound reaction intermediates to different active sites in enzyme complexes.

Front 135

What are the biological tethers of the biotinyl-lysine chain?

Back 135

The cofactors lipoate, biotin and ß-mercatoethylamine
and pantothenate form long, flexible arms in the enzymes to which they are covalently bound, acting as tethers that
move intermediates from one active site to the next

Front 136

The TCA cycle is under tight regulation at two
Levels. What are they?

Back 136

Conversion of pyruvate to Acetyl CoA at the pyruvate dehydrogenase complex level

Conversion of pyruvate to Acetyl at the entry of acetyl CoA into the cycle that is at the citrate synthase level.

Front 137

What is the regulation of metabolite flow from the PDH complex through the TCA cycle?

Back 137

The PDH complex is allosterically inhibited when [ATP/ADP], [NADH/NAD+], and [acetyl-CoA/CoA] ratios are highly indicative of an energy-sufficient metabolic state.

availability of acetyl- CoA and oxaloacetate would limit citrate synthase activity.

In muscle tissue, Ca+2 signals contraction and thus stimulates energy-yielding metabolism to replace the
ATP consumed.

Front 138

The TCA is also regulated at the _______ & _______ reactions.

Back 138

isocitrate dehydrogenase and at the α-ketoglutarate dehydrogenase

Front 139

there is a PDH kinase and a PDH phosphatase in the PDH complex. How does The E1 and PDH activities get activated?

Back 139

The kinase phosphorylates a Ser residue in E1 and inactivates E1 activity.

The kinase is allosterically activated by ATP.

High [ATP] reflects a sufficient supply of energy
and PDH activity is not needed.

When [ATP] declines the kinase activity decreases and the protein phosphatase action increases to dephosphorylate E1.

The E1 and PDH activities are now active.

Front 140

Both plant and and mammalian PDH complexes are regulated by _______/_________ action but the Escherichia coli PDH complex is not.

Back 140

kinase/phosphatase