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Flashcards in S1B4 - TCA Cycle Deck (52):
1

What metabolite from the citric acid cycle is used in...

  • gluconeogenesis?
  • fatty acid synthesis?

  • oxaloacetate is used in gluconeogenesis
  • citrate is involved in the pathway of fatty acid synthesis

2

How is the succinate dehydrogenase complex of the citric acid cycle related to the electron transport chain?

The succinate dehydrogenase complex catalyzes oxidation of succinate to fumarate.

Note that succinate dehydrogenase is embedded in the inner mitochondrial membrane as complex II of the electron transport chain.

3

What metabolic poison inhibits the enzyme aconitase?

Fluorocitrate, a metabolite of the pesticide fluoroacetate, inhibits the enzyme aconitase.

4

What reaction in the citric acid cycle (TCA cycle) produces GTP?

Succinyl-CoA synthetase converts succinyl-CoA to succinate and CoA. In the process, substrate-level phosphorylation produces GTP. The entire reaction is:

  • Succinyl CoA + Pi + GDP ↔ Succinate + CoA + GTP

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5

For each acetyl-CoA molecule that goes through the citric acid cycle and the electron transport chain, how many molecules of ATP are produced?        
 

The net result of the oxidation (using both substrate level and oxidative phosphorylation) of one molecule of acetyl CoA is:

  • 3 NADH x 3 ATP/NADH → 9 ATP
  • 1 FADH2 x 2 ATP/FADH2 → 2 ATP
  • 1 GTP → 1 ATP equivalent

For a total of 10-12 ATP molecules per acetyl CoA (12 is the ideal yield but the actual yield may be given as 10 is some texts because of imperfect efficiency.)

6

Which citric acid cycle reaction results in generation of FADH2?

FADH2 is produced in the conversion of succinate to fumarate. This reaction is catalyzed by succinate dehydrogenase.

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7

What are some vitamins necessary for the α-ketoglutarate dehydrogenase complex to function?

The α-ketoglutarate dehydrogenase complex is one of the three regulated steps of the citric acid cycle. It requires many coenzymes, including:

  • Vitamin B1
  • Vitamin B2
  • Vitamin B3
  • CoA
  • Lipoic acid

Note: these are the same cofactors as in the pyruvate dehydrogenase complex.

8

In the Krebs cycle, which enzyme catalyzes the conversion of citrate into isocitrate?

Aconitase catalyzes the isomerization of citrate into isocitrate.

Fluorocitrate, a metabolite of the pesticide fluoroacetate, inhibits the enzyme aconitase.

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9

Which low energy molecule stimulates isocitrate dehydrogenase?
Which two high energy molecules inhibit isocitrate dehydrogenase?

Isocitrate dehydrogenase is stimulated by ADP (low energy state).

Isocitrate dehydrogenase is inhibited by ATP and NADH (high energy state).

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10

What enzyme converts malate into oxaloacetate in the citric acid cycle?        
 

Malate dehydrogenase oxidizes malate to oxaloacetate, and the cycle can begin anew.

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11

In addition to the formation of alpha-ketoglutarate, what are the products of the reaction catalyzed by isocitrate dehydrogenase?

In the isocitrate dehydrogenase reaction, NAD+NADH, 1st molecule of CO2 is released.

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12

What are the substrates and product of the enzyme citrate synthase?

Citrate synthase catalyzes the transfer of a 2-carbon acetyl group from acetyl-CoA to oxaloacetate, forming the 6-carbon molecule citrate.

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13

What are some molecules that inhibit the enzyme α-ketoglutarate dehydrogenase?        
 

α-ketoglutarate dehydrogenase is inhibited by:

  • NADH
  • Succinyl CoA
  • ATP
  • GTP

14

Which Krebs cycle reaction is catalyzed by the α-ketoglutarate dehydrogenase complex?        
 

The α-ketoglutarate dehydrogenase complex converts α-ketoglutarate to succinyl-CoA.

The α-ketoglutarate dehydrogenase reaction catalyzes:

NAD+ → NADH, 2nd molecule of CO2 is released

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15

In the second-to-last step of the Krebs cycle, fumarate is converted into ______________.        
 

Mitochondrial fumarase converts fumarate to malate.

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16

In which step of the citric acid cycle is the second molecule of CO2 released?

The α-ketoglutarate dehydrogenase reaction catalyzes:

NAD+ → NADH, 2nd molecule of CO2 is released

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17

How many GTP, NADH, FADH2, and CO2 are produced per turn of the citric acid cycle?
 

For each turn, the citric acid cycle produces:

  • 1 GTP
  • 3 NADH
  • 1 FADH2
  • 2 CO2

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18

Beginning with citrate, what are the substrates of the citric acid cycle?        
 

The order of the citric acid cycle can be remembered with the following mnemonic:

"Citrate Is Krebs’ Starting Substrate For Making Oxaloacetate."

  • Citrate
  • Isocitrate
  • α-Ketoglutarate
  • Succinyl CoA
  • Succinate
  • Fumarate
  • Malate
  • Oxaloacetate

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19

In which cellular compartment does the citric acid cycle take place?        
 

The citric acid cycle (tricarboxylic acid cycle or Krebs cycle) takes place in the mitochondrial matrix.

20

How is pyruvate transported into the mitochondria? What is the consequence of this transport on the energy yield from glucose metabolism?        
 

Because the PDC is located in the mitochondrial matrix and the inner mitochondrial membrane is impermeable to pyruvate, pyruvate must be transported across the inner membrane by pyruvate translocase. The transport of pyruvate into mitochondria consumes energy, lowering the total ATP production of aerobic glucose metabolism.

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21

Describe the key brain histology characteristics of pyruvate dehydrogenase complex deficiency.        
 

Key histological features of the brain seen with pyruvate dehydrogenase deficiency include gray matter degeneration with brainstem necrosis and capillary proliferation.

22

Which two cofactors does pyruvate dehydrogenase complex E3 require?        
 

E3 requires, as cofactors, FAD (vitamin B2) and NAD+ (vitamin B3).

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23

What is the treatment for pyruvate dehydrogenase deficiency?        
 

The treatment for pyruvate dehydrogenase complex deficiency is to increase the intake of nutrients that can be shunted toward ketogenesis (fats and ketogenic amino acids such as leucine and lysine).

24

How does phosphorylation regulate pyruvate dehydrogenase complex E1 activity?

The regulation of the pyruvate dehydrogenase complex can be allosteric or via phosphorylation/dephosphorylation. 

Pyruvate dehydrogenase kinase (PDH kinase) and pyruvate dehydrogenase phosphatase are part of the PDC and act on E1. Phosphorylation by PDH kinase inhibits E1 (this can be remembered because there is abundant ATP in the high-energy state and ATP can be used to inhibit E1), while dephosphorylation through PDH phosphatase activates E1. Recall that the E1 subunit of the pyruvate dehydrogenase complex catalyzes the rate-limiting step of the PDC reaction. 

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25

What cofactor(s) does pyruvate dehydrogenase complex E2 require?

E2 requires, as cofactors, CoA ( CoA made from vitamin B5 aka pantothenate) and lipoic acid.

It is this step that produces acetyl-CoA (hence the need for CoA in this step)

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26

Which pyruvate dehydrogenase complex enzyme is the rate limiting step?        
 

E1 catalyzes the rate limiting step of the PDC reaction.

E1 requires, as a cofactor, thiamine pyrophosphate (TPP), a derivative of vitamin B1. 

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27

What metabolites activate the pyruvate dehydrogenase complex? What metabolites inhibit the pyruvate dehydrogenase complex?
 

The PDC is activated by pyruvate, NAD+, ADP, and Ca2+.

  • This makes sense because pyruvate is a substrate for the PDC, NAD+ and ADP signal a low energy state in the cell, and Ca2+ influx during muscle contraction drives further energy production. 

The PDC is inhibited by ATP, acetyl-CoA, and NADH. 

  • This makes sense because ATP and NADH signal a high energy state and acetyl-CoA is a product of the PDC reaction. 

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28

What is the pathogenesis of arsenic poisoning?        
 

Arsenic poisoning interferes with lipoic acid cofactor containing enzymes, including the pyruvate dehydrogenase complex (PDC), α-ketoglutarate dehydrogenase, and branched-chain α-keto acid dehydrogenase. 

29

What are the symptoms of arsenic poisoning?        
 

Signs of arsenic poisoning are similar to PDC deficiency and include:

  • Lactic acidosis
  • Neurological disturbances
  • Garlic scented breath
  • "Rice-water" stools which are often bloody

30

What is the main clinical manifestation of pyruvate dehydrogenase deficiency?        
 

PDC deficiency is associated with neurological deficits (hypotonia, poor feeding, lethargy, seizures, mental retardation).

31

Pyruvate dehydrogenase deficiency leads to an increase in the serum concentration of what two substances?        
 

PDC deficiency causes an increase in serum alanine via alanine aminotransferase, and an increase in lactic acid via lactate dehydrogenase.

32

Which pyruvate dehydrogenase complex enzyme requires thiamine pyrophosphate as a cofactor?        
 

E1 requires, as a cofactor, thiamine pyrophosphate (TPP), a derivative of vitamin B1. 

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33

What is the most common mutation in pyruvate dehydrogenase deficiency? What is the inheritance pattern?

The most common form is caused by mutations in the X-linked E1 gene.

The E1 mutation affects females as well so it is considered X-linked dominant.

34

Which enzyme in the pyruvate dehydrogenase complex leads to the production of NADH?

In reactions catalyzed by the E3 subunit of the pyruvate dehydrogenase complex, FAD oxidizes a lipoic acid intermediate back to lipoic acid so that it can participate in more reactions.  In the process, FAD is reduced to FADH2.  FADH2 is then used to reduce NAD+ to NADH, regenerating FAD. The NADH can then be used in oxidative phosphorylation by the electron transport chain. 

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35

Where is the pyruvate dehydrogenase complex located?
 

The PDC is located in the mitochondrial matrix.

36

What are the enzymes that make up the pyruvate dehydrogenase complex?        
 

The PDC consists of multiple copies of three catalytic enzymes: E1 (pyruvate dehydrogenase), E2 (dihydrolipoyl transacetylase), and E3 (dihydrolipoyl dehydrogenase).

Two regulatory enzymes, pyruvate dehydrogenase kinase and pyruvate dehydrogenase phosphatase, are also part of the pyruvate dehydrogenase complex.
 

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37

In pyruvate dehydrogenase complex deficiency, which of the following is found?        

A) Inability to perform glycolysis

B) Absence of oxidative phosphorylation

C) Elevated serum lactate

D) Devreased serum pyruvate

E) Hyperglycemia
 

C) Elevated serum lactate

In PDC deficiency, pyruvate accumulates and is converted to lactate by lactate dehydrogenase. Because pyruvate is still made, glycolysis occurs and hyperglycemia is not a clinical feature. The mitochondria still function and are able to use NADH produced from sources other than the TCA cycle to generate ATP, so oxidative phosphorylation remains intact.

38

What reaction is catalyzed by the pyruvate dehydrogenase complex?        
 

The following reaction is catalyzed by the pyruvate dehydrogenase complex:

Pyruvate + NAD+ + CoA → acetyl-CoA + CO2 + NADH

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39

In the reactions catalyzed by the pyruvate dehydrogenase complex, which is not a cofactor?        

A) Vitamin B12

B) Vitamin B2

C) Lipoic acid

D) Vitamin B3

E) VItamin B1
 

A) Vitamin B12

The PDC has 3 primary enzymes, each of which requires cofactor(s):

E1 uses vitamin B1 (thiamine pyrophosphate) as a cofactor

E2 uses CoA and lipoic acid as cofactors

E3 uses vitamin B2 (FAD) and vitamin B3 (NAD) as cofactors

Vitamin B12 (cobalamin) is a cofactor for the enzymes methylmalonyl Coenzyme A mutase and methionine synthase.

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40

Which multi-subunit enzyme links glycolysis to the citric acid cycle?        
 

The Pyruvate Dehydrogenase Complex (PDC) converts pyruvate into acetyl-CoA through several reactions, linking glycolysis (cytoplasm) and the citric acid cycle (mitochondria).

41

What is the entry point in the TCA cycle for metabolites from...

  • fatty acid and glycerol metabolism?
  • Polysaccharide metabolism?
  • Protein metabolism?

They enter the TCA cycle as Acetyl-CoA. See picture.

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42

What are some of the important roles of citrate?

Roles of citrate:

  • metabolite in the TCA cycle
  • Source of other synthetic pathways (e.g., fatty acids)
  • Regulation of other reactions (e.g., phosphofructokinase I, inhibits it)
  • Source of reducing equivalents

43

What is the rate limiting step of the TCA cycle?

Oxitadive decarboxylation of isocitrate to form alpha-ketoglutarate is the rate limiting step of the TCA cycle.

This reaaction is catalyzed by isocitrate dehydrogenase.

This reaction produces the first NADH and first CO2
 

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44

What other metabolic enzyme is alpha-ketoglutarate dehydrogenase similar to? What is an important difference?

α-ketoglutarate dehydrogenase is similar to the PDH complex.

  • 3 catalytic subunits E1, E2, E3
  • Requires TPP, lipoic acid, CoASH, FAD, NAD+
  • Not regulated by phosphorylation

45

TCA cycle metabolites α-ketoglutarate and succinyl-CoA are intermediates of what other metabolic pathways?

α-ketoglutarate and Succinyl-CoA are also intermediates in the amino acid metabolism pathway.

 

 

46

At what point in the TCA cycle does the only substrate leve phosphorylation occur?

The reaction from succinyl-CoA to succinate, catalyzed by Succinyl CoA synthetase/Succinyl thiokinase, is the only substrate level phosphorylation of the TCA cycle.
 

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47

In the malate-aspartate shuttle, which molecule moves into the inter-membrane space in exchange for glutamate?
 

A glutamate-aspartate antiporter moves aspartate into the inter-membrane space in exchange for glutamate. Aspartate is first converted to oxaloacetate, which is then converted to malate.

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48

What pump moves malate into the mitochondrial matrix?
 

A malate-α-ketoglutarate antiporter moves malate into the mitochondrial matrix.

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49

What is the purpose of the malate-aspartate shuttle?

NADH produced during catabolism of glucose to pyruvate in the cytosol cannot cross the inner mitochondrial membrane → shuttle mechanisms like malate-aspartate shuttle allow NADH reducing equivalents to cross into the mitochondria to produce ATP.

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50

What generally determines the rate of TCA cycle activity?

Control of the TCA cycle:

  • Rate of ATP utilization generally determines the rate of TCA cycle activity
  • Other control mechanisms are important
    • Citrate synthase inhibited by succinylCoA
    • Isocitrate DH stimulated by ADP, inhibited by ATP
    • α-KGDH inhibited by succinylCoA, NADH and GTP

51

What other control mechanisms besides the rate of ATP utilization are important in determining the rate of TCA cycle activity?

Control of the TCA cycle:

  • Rate of ATP utilization generally determines the rate of TCA cycle activity
  • Other control mechanisms are important
    • Citrate synthase inhibited by succinylCoA
    • Isocitrate DH stimulated by ADP, inhibited by ATP
    • α-KGDH inhibited by succinylCoA, NADH and GTP

52

What is the net ATP production from aerobic oxidation of one glucose?

The grand total of aerobic oxidation of one glucose is 38 ATP.

  • 8 from glycolysis
  • 6 from pyruvate dehydrogenase
  • 24 from the TCA cycle

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