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Biochemistry > Chp 20: TCA Cycle > Flashcards

Chp 20: TCA Cycle Flashcards

1
Q
  1. What are the names for the TCA cycle?
A
  • Tricarboxylic Acid Cycle
  • Krebs Cycle
  • Citric Acid Cycle
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2
Q
  1. What is the function of the TCA cycle?
A
  • To produce energy in the form of NADH, FAD(2H), and GTP from acetyl CoA and other metabolites.
  • The NADH and FAD(2H) reduce the electron transport chain
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3
Q
  1. What are the substrates of the TCA cycle?
A
  • Acetyl CoA
  • NAD+
  • GDP
  • Pi
  • FAD
  • H2O
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4
Q
  1. What are the products of the TCA cycle?
A
  • CoASH
  • NADH
  • H+
  • GTP
  • FAD(2H)
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5
Q
  1. What are the control enzymes of the TCA cycle?
A

2 primary control enzymes

  • isocitrate dehydrogenase
  • alpha-ketoglutarate dehydrogenase
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6
Q
  1. What is the regulation of the TCA cycle?
A
  • NADH allosterically inhibits both isocitrate dehydrogenase and alpha-ketoglutarate dehydrogenase
  • Ca2+ activates both isocitrate dehydrogenase and alpha-ketoglutarate dehydrogenase
  • ADP allosterically activates isocitrate dehydrogenase. That is, when the ratio of ATP to ADP+AMP is low, the enzyme is activated. Don’t try to remember which nucleotide binds to the enzyme
  • Ignore the effect of citrate upon citrate synthase and NADH upon malate dehydrogenase
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7
Q
  1. What are the compartments of the TCA cycle? (where do the reactions take place)
A

Mitochondrial matrix

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8
Q
  1. What are the tissues of interest for the TCA cycle?
A

All cells except red blood cells (they do not have mitochondria)

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9
Q
  1. Name the four dehydrogenase enzymes of the TCA cycle.
A
  • Isocitrate dehydrogenase
  • Alpha-ketoglutarate dehydrogenase
  • Succinate dehydrogenase
  • Malate dehydrogenase
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10
Q
  1. What are the substrates and products of the isocitrate dehydrogenase reaction?
A

Isocitrate + NAD+ → a-ketoglutarate, NADH + H+ + CO2

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11
Q
  1. What are the substrates and products of the alpha-ketoglutarate dehydrogenase reaction?
A

a-ketoglutarate + NAD+ + CoASH → Succinyl CoA +NADH + H+ + CO2

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12
Q
  1. What are the substrates and products of the succinate dehydrogenase reaction?
A

Succinate + FAD ⇔ Fumarate + FADH2

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13
Q
  1. What are the substrates and products of the malate dehydrogenase reaction?
A

Malate + NAD+ ⇔ Oxaloacetate + NADH + H+

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14
Q
  1. What is the approximate energy yield from the oxidation of one acetyl CoA molecule?
A 
3 NADH (each NADH = 2.5 ATP) 7.5 ATP
  1 FAD(2H) = 1.5 ATP
  1 GTP = 1.0 ATP

TOTAL: 10 ATP (high energy bonds)

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15
Q
  1. Name the enzyme of the TCA cycle that catalyzes a substrate level phosphorylation. (Fig 20.3)
A

Succinyl CoA synthetase or succinate thiokinase:

Succinyl CoA + GDP + Pi → Succinate + CoASH + GTP

  • A synthetase catalyzes the formation of a new bond by coupling it with the breaking of a high-energy bond (as opposed to a synthase, which does not require the breaking of a bond). The energy from breaking the succinyl CoA thioester bond is used to synthesize the high-energy phosphate bond of GTP
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16
Q
  1. What is the difference between a substrate level phosphorylation and oxidative phosphorylation?
A
  • Substrate-level phosphorylation is the formation of high-energy phosphate bonds by phosphorylation of ADP to ATP (or GDP to GTP) coupled to cleavage of a high-energy metabolic intermediate. No oxygen is required.
  • Oxidative phosphorylation is the formation of high-energy phosphate bonds by phosphorylation of ADP to ATP coupled to the transfer of electrons from reduced coenzymes to molecular oxygen via the electron transport chain; this occurs in the mitochondria
  • The difference: substrate-level phosphorylation does not require the reduced coenzymes, the electron transport system, or molecular oxygen
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17
Q
  1. Compare NADH and FADH with respect to their mechanism of accepting or donating electrons
A
  • NADH accepts or donates a hydride ion (H-, one proton and two electrons)
  • FAD(2H) accepts or donates one or two hydrogen atoms (H , one proton and one electron)
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18
Q
  1. Compare NADH and FADH with respect to their affinity for the apoenzyme
A
  • NADH has low affinity and is often written as a substrate
  • FAD(2H) has high affinity and is a prosthetic group
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19
Q
  1. Compare NADH and FADH with respect to their reactivity in solution
A
  • NADH is fairly stable in solution and only reacts with enzymes
  • FAD(2H) is unstable in solution, forms free radicals, and will react with many other molecules or structures
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20
Q
  1. Compare NADH and FADH with respect to their ability to act as a feedback inhibitor or activator.
A
  • NADH is a good feedback inhibitor because it is stable and can travel
  • FAD(2H) is not a feedback inhibitor because it is unstable and cannot travel
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21
Q
  1. What is the purpose of the thioester bond in acetyl CoA and succinyl CoA?
A
  • In acetyl CoA, the high-energy thioester bond energy (-12 or -13 kcal/mol) is used in the citrate synthase reaction to drive the TCA cycle forward
  • In succinyl CoA, the high-energy thioester bond energy is used for the synthesis of GTP and to drive the TCA cycle forward.
    • The ΔG for GTP formation from GDP is +7kcal/mol. Breaking the thioester of the succinyl CoA provides about a -12 kcal/mol. The extra change in free energy drives the reaction and the TCA cycle forward
22
Q
  1. Name the five cofactors of the a-ketoglutarate dehydrogenase reaction and from which vitamin each are derived.
A
  • NAD+ (niacin)
  • CoASH (pantothenate)
  • FAD (riboflavin)
  • Lipoate (none, synthesized in body so does not require vitamin precursor)
  • TPP – Thiamine Pyrophosphate (thiamine)
23
Q
  1. What is the advantage of a multienzyme complex? (Fig 20.8)
A

It greatly decreases the time it takes to form the end product. In a normal pathway, where the enzymes are free-floating in solution, most of the time is taken up by the product of each reaction diffusing to the next active site. In a multienzyme complex, the product of each intermediate reaction is handed directly to the next enzyme and only the ultimate product is released.

24
Q
  1. Given the ΔG0! for each enzymatic step in a sequence of enzymatic reactions, be able to state the delta-G0! for the overall reaction.
A

The ΔG0! for a pathway is the sum of the ΔG0!s for the reactions in the pathway:

The ΔG0! for the TCA cycle:
-7.7 + 1.5 – 5.3 – 8 – 0.7 + 0 + 0 + 7.1 = -13 kcal/mol

  • The -13 kcal/mol is the free energy that is lost and not preserved in the products. This loss of free energy drives the cycle in the forward direction. Most of this 13 kcal/mol is lost as heat
  • Under biological conditions, there is never enough product buildup to reverse the direction of the cycle between succinyl CoA and isocitrate so the cycle is irreversible
  • We do not know the efficiency of the TCA cycle but it is very high:
    • Total energy available from acetyl CoA = 228 kcal/mol
    • The products of the TCA cycle (3 NADH, 1 FAD(2H), GTP) contain about 207 kcal/mol
    • Efficiency [207/228] x 100 = 91%
25
Q
  1. Several enzyme reactions in the TCA cycle are considered irreversible. Why?
A

The reactions have substantial negative ΔG0! and the physiological concentrations of the products never raise high enough to reverse the reaction.

The two irreversible reactions are

  • Isocitrate dehydrogenase:

Isocitrate + NAD+ → a-ketoglutarate, NADH + H+ + CO2→

  • Alpha-ketoglutarate dehydrogenase:

a-ketoglutarate + NAD+ + CoASH → Succinyl CoA + NADH + H+ + CO2

26
Q
  1. How is the rate of the TCA cycle linked to muscle contraction and the utilization of ATP?
A
  • Muscle contraction dramatically changes the concentration of ATP, ADP, and AMP in the cell. ATP decreases and ADP & AMP increase. This change in concentration causes the ATP synthase in the mitochondrial membrane to become active, and the enzyme will stay active until the normal ATP and ADP levels are restored
  • The hydrogen ion concentration gradient across the mitochondrial membrane is the driving force for the synthesis of ATP from ADP by ATP synthase. As ATP is synthesized, protons flow from the outside of the membrane to the inside of the membrane, and as a result, the hydrogen ion concentration gradient decreases
  • A drop in the hydrogen ion concentration gradient increases the flow of electrons through the electron transport chain and the oxidation of NADH to NAD+. Thus, the concentration of NADH decreases.
  • As [NADH] decreases, isocitrate dehydrogenase and alpha-keoglutarate dehydrogenase are less inhibited and there is an increase in their rate of reactions. These two enzymes control the rate of the TCA cycle so the entire cycle speeds up
  • As the TCA cycle increases, the use of acetyl CoA increases so its concentration also drops
  • When the ATP concentration is restored, everything acts in reverse. That is, the hydrogen ion gradient will increase, the electron transport chain will slow down, the NADH concentration will increase, the control enzymes will be more inhibited, the rate of the entire TCA cycle will decrease and the concentration of acetyl CoA will increase
  • Calcium release during muscle contraction is also a major control factor for the TCA cycle. The calcium activates the same two control enzymes
27
Q
  1. Name two control enzymes of the TCA cycle.
A
  • Isocitrate dehydrogenase
  • alpha-ketoglutarate dehydrogenase
28
Q
  1. Name four dietary sources of acetyl CoA
A
  • Fat: for every 2 carbons of fatty acid, 1 unit of acetyl CoA is made (so an 8-carbon fatty acid makes 4 CoAs)
  • Carbohydrate: a 6-carbon sugar makes 2 pyruvates, but only 2 of the 3 carbons of each pyruvate makes it into an acetyl CoA. The other carbon atoms gets released as CO2
  • Protein: catabolized into amino acids. Some amino acids are converted to pyruvate and then to acetyl CoA. Other amino are converted directly to acetyl CoA without becoming pyruvate. Still other amino acids are not converted to acetyl CoA
  • Alcohol: ethanol is oxidized straight to acetyl CoA
  • Ketone bodies are NOT dietary. These are produced in the liver from acetyl CoA that is produced from fatty acids
29
Q
  1. Which enzyme reaction in the TCA cycle is similar to the pyruvate dehydrogenase reaction? How could this relationship come about?
A
  • Alpha-ketoglutarate dehydrogenase and pyruvate dehydrogenase are similar multienzyme complexes. The only different is the specificity of the complexes, one for pyruvate and one for alpha-ketoglutarate, and a few control proteins that bind to activators and inhibitors.
  • These two reactions are similar in the following ways:
    • Both complexes use an alpha-keto carboxylic acid as a substrate
    • Both produce an acyl CoA and CO2 as products
    • Both use the same cofactors: thiamine pyrophosphate, lipoic acid, CoA, NAD+, and FAD
    • Both are inhibited by ATP & NADH
  • This relationship came about by: gene duplication and mutation being responsible for the similarity in these enzyme complexes. First, the genes for some common ancestral complex duplicated themselves. Then through a process of mutation and selection, two separate complexes evolved.
30
Q
  1. Why are the symptoms for pyruvate dehydrogenase complex deficiency so apparent in the central nervous system and not in most other tissues?
A
  • Because fatty acids cannot readily pass the blood-brain barrier, the brain is almost totally dependent upon glucose for energy.
  • To get an adequate amount of energy from glucose, the brain cells must run aerobic glycolysis, the pyruvate dehydrogenase complex, and the TCA cycle
  • If the pyruvate dehydrogenase complex is deficient, the energy from the complex and from the TCA cycle would be missing. The brain would be totally dependent upon the energy from anaerobic glycolysis, and this is insufficient
  • Most other cells also oxidize fatty acids as an energy source so if the pyruvate dehydrogenase complex is deficient, there is an alternate source of energy
31
Q
  1. Explain how the rate of the pyruvate dehydrogenase complex is related to the rate of utilization of ATP. (Fig 20.12 & 20.16)
A
  • Most of this mechanism is the same as in Obj 11 above
  • Consider that the cell is using ATP at a constant rate and then the rate of ATP utilization increases. The [ATP] will decrease and the [ADP] and [AMP] will increase
  • As a result, the rate of ADP conversion to ATP by ATP synthase and hydrogen ions entering the mitochondria through ATP synthase will increase
  • As a result, the concentration of protons (hydrogen ions) on the ouside of the mitochondria membrane will decrease so the rate of the electron transport chain will increase
  • As a result, more NADH will be oxidized to NAD+ so the concentration of NADH will drop
  • As a result, the flux (amount of) metabolites through the TCA cycle will increase because NADH is no longer inhibiting the isocitrate dehydrogenase and alpha-ketoglutarate. Also, the ratio of [ATP]/[ADP]+[AMP] has dropped so ADP will be activating isocitrate dehydrogenase.
  • As a result, more acetyl CoA will be used by the TCA cycle so the concentration of acetyl CoA will drop
  • As a result, the PDC will be activated by the decrease in NADH, ATP, and acetyl CoA
  • As a result, more energy will be produced from aerobic glycolysis, the PDC, the TCA cycle, and oxidative phosphorylation until the ratio of [ATP]/[ADP]+[AMP] returns to the normal level
  • Other info: the pyruvate dehydrogenase complex is inhibited by a high [ATP]/[ADP]+[AMP] ratio, high [NADH], high acetyl CoA while it is activated by low [ATP]/[ADP]+[AMP], low [NADH], low acetyl CoA, and high [Ca2+]
    o Unless this is happening in a muscle cell, the change in Ca2+ is not very important
  • May help to remember that the total amount of ATP + ADP + AMP and NAD+ + NADH in a cell is constant
32
Q
  1. Explain how muscle contraction is related to the rate of the pyruvate dehydrogenase reaction.
A

Same as Obj 16, except Ca2+ becomes very important and the change in the [ATP]/[ADP]+[AMP] ratio is much greater than in a non-muscle cell

33
Q
  1. Name five pathways that use TCA cycle intermediates as substrates.
A
  • Fatty acid synthesis uses citrate
  • Amino acid synthesis uses a-ketoglutrarate to synthesize some amino acids like glutamate, glutamine, GABA, and several others
  • Heme synthesis uses succinyl CoA
  • Gluconeogenesis uses malate
  • Amino acid synthesis uses oxaloacetate to synthesize aspartate and asparagine
34
Q
  1. What is the effect of biosynthetic pathways (that use up TCA cycle intermediates) on the TCA cycle?
A

These biosynthetic pathways remove TCA cycle intermediates (metabolites) and thus lower the concentration of the intermediates. If the metabolites were not replaced by anaplerotic reactions, the TCA cycle would stop

35
Q
  1. If TCA cycle intermediates are constantly being removed for biosynthesis, why doesn’t the cycle stop?
A

The cycle doesn’t stop because the intermediates are replenished by anaplerotic (filling up) pathways

4 major anaplerotic pathways:

  • Pyruvate → Oxaloacetate
  • Aspartate → Oxaloacetate
  • Glutamate → alpha-ketoglutarate
  • Odd-chain fatty acids, valine, and isoleucine → Succinyl CoA
36
Q
  1. What is the enzyme of the anaplerotic reaction that links glycolysis and the TCA cycle?
A

Pyruvate carboxylase

37
Q
  1. What are the substrates and products of the anaplerotic reaction that links glycolysis and the TCA cycle?
A

ATP + CO2 (or HCO3-) + pyruvate → Oxaloacetate + ADP + Pi

38
Q
  1. What is the biological compartment of the anaplerotic reaction that links glycolysis and the TCA cycle?
A

Mitochondrial matrix

39
Q
  1. What is the regulatory factor (activator) of the anaplerotic reaction that links glycolysis and the TCA cycle?
A

High concentrations of acetyl CoA

40
Q
  1. What coenzyme is used in the anaplerotic reaction that links glycolysis and the TCA cycle?
A

Biotin (whenever you add CO2 or HCO3-, think biotin)

41
Q
  1. How does the system regulate the production of the TCA cycle intermediate oxaloacetate?
A

As the concentration of oxaloacetate is depleted through efflux of TCA cycle intermediates, the rate of citrate synthase reaction decreases and the concentration of acetyl-CoA increases. Excess acetyl CoA activates pyruvate carboxylase to synthesize more OAA from pyruvate

42
Q
  1. Why are the symptoms for pyruvate carboxylase deficiency so apparent in the central nervous system and not in most other tissues?
A
  • Unlike most other tissues that can oxidize fatty acids, the brain depends upon glucose to produce energy (ATP). Furthermore, the glucose must be oxidized using aerobic glycolysis (lots of ATP). Anaerobic glycolysis will not produce enough energy. To run aerobic glycolysis, glycolysis, the PDC, and the TCA cycle must all function
  • Without the pyruvate carboxylase reaction, there would be no way to adequately replace the TCA cycle intermediates that were used for anabolic reactions. The TCA cycle would continue to run and there would be no oxaloacetate to react with acetyl CoA. Acetyl CoA would build up and decrease the rate of the PDC. The ATP concentration would drop to dangerous and perhaps lethal levels
  • In addition, the low [ATP]/[ADP]+[AMP] would activate anaerobic glycolysis, which would causes lactic acidosis of the brain in extreme cases
  • Most non-brain tissues can use fatty acids for energy so a deficiency of pyruvate carboxylase is not so apparent
43
Q
  1. In addition to pyruvate, name two other classes of compounds that can be used to as substrates for anaplerotic reactions.
A
  • Amino acids and odd-chain fatty acids
  • Note: the TCA cycle cannot be resupplied with intermediates by even-chain-length fatty acid oxidation or by ketone body oxidation
44
Q
  1. Concerning Otto Shape, can succinate be oxidized without oxygen being consumed?
A
  • No, succinate dehydrogenase requires oxygen to function, in order to oxidize/strip electrons from FADH2 in the ETC
  • ETC needs oxygen to take electrons
45
Q
  1. Concerning Otto Shape, explain the effect of increased muscle contraction upon the concentrations of ATP, ADP, AMP, NADH, FAD(2H), and Acetyl CoA.
A

Muscle contraction will:

  • Increase the concentrations of ADP and AMP while decreasing the concentration of ATP since it will be used to contract the muscle
  • Increase the concentration of NAD+ and decrease the concentration of NADH because the electron transport chain will be accepting electrons at an increased rate
  • Increase the concentration of FAD and decrease the concentration of FAD(2H) because the electron transport chain will be accepting electrons at an increased rate
  • Decrease the concentration of acetyl CoA because the TCA cycle will be using it at an increased rate
46
Q
  1. What effect does increased muscle contraction have upon the rate of the TCA cycle and the pyruvate dehydrogenase reaction?
A
  • The rate of the TCA cycle will increase because NADH has decreased, the ratio of [ATP]/[ADP]+[AMP] has dropped, and the [Ca2+] has increased. Thus. isocitrate dehydrogenase was no longer inhibited by NADH and became activated by ADP and Ca2+. Alpha-ketoglutarate dehydrogenase was no longer inhibited by NADH and became activated by Ca2+
  • The rate of the PDC will increase. The PDC was activated because it was no longer inhibited by NADH and acetyl CoA while being activate by ADP and Ca2+
  • Note: Dr. Y told us not to try to remember whether the allosteric site was bound to ATP, ADP, or AMP but to focus instead on [ATP]/[ADP]+[AMP]. This is a measure of whether the cell needs energy or not. If the pathway makes energy, the control enzyme will be turned on by a drop in the [ATP]/[ADP]+[AMP]
47
Q
  1. Concerning Otto Shape, what effect does the increased calcium ion concentration in a contracting muscle have upon the rate of the TCA cycle and the pyruvate dehydrogenase reaction? (Fig 20.16)
A
  • The rate of the TCA cycle will increase because the [Ca2+] has increased. Thus, isocitrate dehydrogenase and a-ketoglutarate dehydrogenase, the major control enzymes of the TCA cycle, became activated by increasing [Ca2+]
  • The rate of the PDC will increase because increasing [Ca2+] activates the PDC. Increased [Ca2+] activates a phosphatase that removes phosphate and turns the inactive PDC into active PDC
48
Q
  1. Concerning Otto Shape, most of the pyruvate produced during exercise was either oxidized to acetyl CoA or reduced to lactate. Why did training increase the amount of pyruvate being oxidized?
A
  • Training will increase the relative amount of pyruvate being oxidized by the PDC compared to the amount of pyruvate being reduced to lactate because trained muscles have a better oxygen supply and more mitochondria with more mitochondrial enzymes
  • The change in the ratio of ATP/(AMP+ADP) and the increase in [Ca2+] activates glycolysis, the PDC, and the ETC. However, the rate of the ETC depends upon O2, which is often limiting, especially in strenuous exercise. So even though the rate of oxidation of NADH is fast, it is not fast enough to prevent a cellular building of NADH
  • An increase in NADH inhibits the TCA cycle and so acetyl CoA increases in concentration. Eventually, both NADH and acetyl CoA inhibit the PDC. This slows the amount of pyruvate being oxidized by the PDC
  • At the same time, glycolysis is making pyruvate at a much faster rate than can be used. The cell ends up with very high concentrations of pyruvate and NADH, the substrates for lactate dehydrogenase and the production of lactate. The more strenuous the exercise, the more lactate the cell will make
  • A trained muscle will have more oxygen available and more mitochondria
  • Therefore, the trained muscle will be able to oxidize more NADH, FAD(2H), and acetyl CoA. Therefore, a trained muscle will be able to oxidize more of the pyruvate made by glycolysis and reduce less pyruvate to lactate
49
Q
  1. Concerning a patient who suffers from anorexia nervosa and may have developed subclinical deficiencies of many vitamins, which vitamins would you prescribe to be positive that the pyruvate dehydrogenase and the pyruvate carboxylase reactions would have an adequate amount of cofactors?
A
  • Pyruvate dehydrogenase: riboflavin, thiamine, pantothenate, and niacin (lipoate is synthesized in the body, no vitamin required)
  • Pyruvate carboxylase: biotin
50
Q
  1. Concerning Al Martini: Given that a-ketoacids build up in the heart in wet beriberi, develop a scenario that would explain why peripheral vessels dilate and cardiac muscles lose their contractility
A
  • A deficiency in thiamine is common in alcoholic patients. Thiamine is a vitamin used to make thiamine pyrophosphate. Thiamine pyrophosphate is a cofactor (coenzyme) in several alpha-keto acid dehydrogenase reactions
  • The pyruvate dehydrogenase complex and the alpha-ketoglutarate dehydrogenase reactions both catalyze important reactions in pathways that lead to the generation of ATP. If thiamine is deficient, ATP will not be generated at an adequate rate and alpha-keto acids (pyruvate and alpha-ketoglutarate) would accumulate. Without adequate ATP, muscles cannot contract adequately. Smooth muscles will dilate and the contractility of the heart will diminish
51
Q
  1. Concerning Al Martini who is an alcoholic, why does he have a thiamine deficiency?
A
  • Alcohol inhibits thiamine uptake
  • Poor diet
  • Thiamine (vitamin B1) is stored in very small quantities in the body which makes the body dependent on constant dietary intake of the vitamin. This causes a person with a poor diet to be more susceptible to thiamine deficiency

Biochemistry (10 decks)

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