Preparation for the Cycle - Chapter 18

Question 1

What role does pyruvate dehydrogenase play? What steps is it between?

Answer 1

It is the one-way link between glycolysis and cellular respiration (Tricarboxylic Acid cycle).

It directs pyruvate into the formation of acetyl CoA.

Question 2

What is gained during glycolysis per glucose molecule?

Answer 2

2 ATP
2 NADH

Question 3

What is the pyruvate dehydrogenase complex?

Answer 3

a multi-enzyme assembly located in the mitochondrial matrix that facilitates the oxidative decarboxylation of pyruvate, converting it into Acetyl CoA, allowing entrance into the tricarboxylic acid cycle

Question 4

Describe the structure of acetyl CoA.

Answer 4

2-carbon unit attached to a thiol group of CoA
includes a high-energy thioester linkage between the sulfur atom and the carbonyl atom

Question 5

Where does the pyruvate dehydrogenase complex operate?

Answer 5

Pyruvate is translocated into the mitochondrion under aerobic conditions. It works inside the mitochondrion.

Question 6

What role does acetyl CoA play in the citric acid cycle?

Answer 6

The two-carbon acetyl unit condenses with the 4-carbon oxaloacetate to produce the 6-carbon citrate. Over the cycle, the acetyl unit is fully oxidized to 2 molecules of CO2.

During this oxidation process, high-energy electrons are captured by electron carriers (ex. NADH), which later power the synthesis of ATP via oxidative phosphorylation.

Question 7

What does Acetyl CoA do when condensed with oxaloacetate? How many carbons do they both have? What happens after?

Answer 7

They (2 carbon acetyl CoA and four carbon oxaloacetate) form citrate (6 carbons).

After, the acetyl unit is oxidized to 2 molecules of CO2, and high-energy electrons are captured by carriers and funneled into the inner mitochondrial membrane.

Question 8

Describe the process of pyruvate dehydrogenase forming acetyl CoA from pyruvate.

Answer 8

Pyruvate (3-carbon molecule) loses a carbon as CO2.
The remaining 2 carbons form acetyl CoA.
NAD+ is reduced to NADH and receives 2 electrons (later helps generate ATP in ETC).

Question 9

Is pyruvate dehydrogenase’s reaction reversible or irreversible?

Answer 9

Irreversible; one way flow between glycolysis and the citric acid cycle

Question 10

What are the three steps involved in synthesizing Acetyl CoA from pyruvate?

Answer 10

1. Decarboxylation
2. Oxidation
3. Transfer to CoA

Question 11

Which enzyme is responsible for the decarboxylation of pyruvate? Which step is this in the synthesis of Acetyl CoA?

Answer 11

Pyruvate dehydrogenase removes a carboxyl group from pyruvate, releasing CO₂ and forming a two-carbon compound
Step 1

Question 12

Which enzyme is responsible for the transfer of the acetyl unit to CoA? Which step is this in the synthesis of Acetyl CoA?

Answer 12

Dihydrolipoyl transacetylase
Step 3

Question 13

Which coenzyme is necessary during the oxidation step of acetyl CoA synthesis?

Answer 13

NAD+; 2 electrons are transferred to NAD+, producing NADH

Question 14

What are the three components of the pyruvate dehydrogenase complex?

Answer 14

Pyruvate dehydrogenase - E1
Dihydrolipoyl transacetylase - E2
Dihydrolipoyl dehydrogenase - E3

Question 15

What is the prosthetic group of E1 (pyruvate dehydrogenase) in the pyruvate dehydrogenase complex?

Answer 15

Thiamine pyrophosphate (TPP)

Question 16

What does E1 (pyruvate dehydrogenase) do in the pyruvate dehydrogenase complex?

Answer 16

Catalyzes the first step, where pyruvate loses CO₂ (oxidative decarboxylation) and attaches to TPP, forming a hydroxyethyl-TPP intermediate

Question 17

What does E2 (Dihydrolipoyl Transacetylase) of the pyruvate dehydrogenase complex do?

Answer 17

Transfers the two-carbon acetyl group from the acetyl-lipoamide to coenzyme A (CoA), forming acetyl CoA. The lipoamide arm moves between E₁ and E₃ during the reaction.

Question 18

What is the prosthetic group of E2 (dihydrolipoyl transacetylase) in the pyruvate dehydrogenase complex?

Answer 18

Lipoamide

Question 19

What is the prosthetic group of E3 (dihydrolipoyl dehydrogenase) in the pyruvate dehydrogenase complex?

Answer 19

FAD

Question 20

What does E3 (Dihydrolipoyl dehydrogenase) of the pyruvate dehydrogenase complex do?

Answer 20

Reoxidizes the reduced lipoamide (dihydrolipoamide) back to lipoamide, allowing it to participate in the next cycle of Acetyl CoA synthesis

FAD is reduced to FADH₂ and then
transfers electrons to NAD⁺, producing NADH

Question 21

How is pyruvate dehydrogenase complex regulated?

Answer 21

Tightly, by high energy signals (ATP, NADH, acetyl CoA) that inhibit the complex to conserve energy when it’s already abundant.

Question 22

What molecule is this?

Answer 22

Thiamine pyrophosphate (TPP)

Question 23

Which vitamin is TPP derived from?

Answer 23

Thiamine (Vitamin B1)

Question 24

List the 3 roles of thiamine pyrophosphate (TPP).

Answer 24

1. Decarboxylation: TPP helps remove CO₂ from α-keto acids, crucial in
   metabolism (and the first step of acetyl CoA synthesis from pyruvate).
2. Transketolase Activity: It participates in the pentose phosphate pathway
   for nucleotide synthesis and generating reducing agents.
3. Branched-chain Amino Acid Metabolism: TPP is also involved in breaking
   down these amino acids

Question 25

Describe TPP’s neurological importance. List 2 disorders that can be caused by deficiency.

Answer 25

Thiamine deficiency can lead to conditions like beriberi and Wernicke-Korsakoff syndrome, as TPP is crucial for glucose metabolism in the brain.

Question 26

Why is TPP so reactive?

Answer 26

The C2 carbon of the thiazole ring can lose a proton, creating a highly reactive carbanion that is often involved in nucleophilic attacks on carbonyl groups (like alpha-keto acids).

Question 27

What is the mechanism that causes decarboxylation of pyruvate during acetyl CoA synthesis?

Answer 27

TPP’s carbanion does a nucleophilic attack on the carbonyl of pyruvate, releasing CO2 and forming a hydroxyethyl-TPP intermediate.

Question 28

What molecule is this?

Answer 28

Hydroxyethyl-TPP (intermediate during decarboxylation step of acetyl CoA synthesis)

Question 29

Why can lipoamide accept the acetyl group from hydroxyethyl-TPP during acetyl CoA formation?

Answer 29

Due to a special disulfide group

Question 30

What is this molecule?

Answer 30

Lipoamide (acetyl group from hydroxyethl-TPP intermediate)

Question 31

What is this molecule?

Answer 31

Acetyl lipoamide

Question 32

How is lipoamide formed?

Answer 32

Lipoic acid is covalently attached via an amide bond to a lysine residue presenting in E2.

Question 33

Which parts of the lipoic acid and E2 are involved in the amide bond that creates lipoamide?

Answer 33

Carboxyl group of lipoic acid and amino group of lysine side chain

Question 34

Why does the flexibility of the lysine residue on lipoamide matter?

Answer 34

It allows it to behave as a swinging arm, aiding the transfer of the acetyl group from different enzymes in the pyruvate dehydrogenase complex. This increases the efficiency of metabolic processes.

Question 35

What two things are formed after the acetyl transfer to lipoamide?

Answer 35

Acetyl-Lipoamide and the reduced, carbanion form of TPP

Question 36

What happens to acetyl-lipoamide?

Answer 36

It is oxidized, forming Acetyl CoA.

Question 37

What mechanism causes the transfer of the acetyl group from acetyl-lipoamide to Coenzyme A?

Answer 37

Nucleophilic attack by the thil of CoA on the acetyl group of Acetyl-Lipoamide.

Question 38

What two things are formed after the acetyl group is transfered from Acetyl-lipoamide to CoA?

Answer 38

Acetyl CoA and Dihydrolipoamide

Question 39

Why is dihydrolipoamide essential?

Answer 39

It is the reduced form of lipoamide that must be reoxidized to partake in subsequent cycles of Acetyl CoA synthesis.

Question 40

List all the reactions and steps of the pyruvate dehydrogenase complex (including movement of carbons and electrons).

Answer 40

1.Decarboxylation of Pyruvate (E1):
Pyruvate loses a CO₂ molecule, forming a two-carbon hydroxyethyl group
attached to the cofactor thiamine pyrophosphate (TPP).
2. Transfer to Lipoamide (E1):
The hydroxyethyl group is oxidized and transferred to the lipoamide arm,
forming an acetyl-lipoamide complex. The TPP cofactor is regenerated.
3.Transfer to Coenzyme A (E2):
The acetyl group is transferred from the lipoamide to coenzyme A (CoA),
forming acetyl-CoA, which enters the citric acid cycle.
4.Oxidation of Lipoamide (E3):
The reduced lipoamide is reoxidized by transferring electrons to FAD, converting it to FADH₂.
5. Transfer of Electrons to NAD⁺ (E3):
FADH₂ then transfers its electrons to NAD⁺, producing NADH and regenerating FAD.
6.Regeneration of Lipoamide:
The lipoamide arm returns to its oxidized state, ready for the next cycle of reactions.

Question 41

What are the two potential fates of Acetyl CoA? How are they selected?

Answer 41

1. Citric acid cycle - when energy is low, enables the production of ATP, CO2, NADH, and FADH2, which feed into the electron transport chain
2. Fatty acid synthesis - when energy is plentiful; fatty acids are stored as triglycerides in adipose tissue

Question 42

Describe the two allosteric regulation methods for the synthesis of acetyl CoA.

Answer 42

1. High levels of the products (NADH and acetyl CoA) inhibit the pyruvate dehydrogenase complex.
2. High levels of substrates (pyruvate and NAD+) activate the PDC.

Feedback loop that ensures the PDC functions when energy is needed and slows when energy is plentiful

Question 43

Describe the 3 covalent modification regulatory methods for the pyruvate dehydrogenase complex.

Answer 43

1. Phosphorylation of the PDC by the pyruvate dehydrogenase kinase (PDK), which inactivates the PDC
2. Dephosphorylation of the PDC by the pyruvate dehydrogenase phosphatase (PDP), which activates the PDC
3. High NADH and acetyl CoA levels activate the PDK and lead to phosphorylation of the PDC, turning off the PDC when energy is abundant.

Question 44

What does the pyruvate dehydrogenase kinase do?

Answer 44

phosphorylates and inactivates the PDC

Question 45

What does pyruvate dehydrogenase phosphatase do?

Answer 45

dephosphorylates and activates the PDC

Question 46

What indicates high energy charge? What does it lead to?

Answer 46

High levels of ATP and NADH lead to the inhibition of the PDC, slowing down ATP production.

Question 47

What indicates low energy charge? What does it lead to?

Answer 47

High ADP and low NADH levels lead to the lifting of inhibition on PDC and increased conversion of pyruvate to acetyl CoA, which drives the citric acid cycle and boosts ATP production

Question 48

What role does calcium play in regulation of the PDC?

Answer 48

Increased calcium levels stimulate the phosphatase that dephosphorylates E1, activating the PDC and boosting acetyl CoA (and ATP) production.

Question 49

List 4 of the advantages of
organizing into a single large complex
the enzymes that catalyze the formation
of acetyl CoA from pyruvate.

Answer 49

1. The reaction has active sites in proximity, boosting efficiency.
2. The reactants don’t leave the enzyme until the final product is formed, minimizing reactant loss due to diffusion and side reactions.
3. All enzymes are present in correct amounts.
4. Regulation is more efficient because regulatory enzymes (kinase and phosphatase) are part of the complex.

Question 50

What happens when someone has a phosphatase deficiency?

Answer 50

Pyruvate dehydrogenase is always phosphorylated and, therefore, always inactive.

Rather than processing to acetyl CoA and entering the citric acid cycle, pyruvate is processed by lactate dehydrogenase to lactate, which can lead to lactic acidosis.

Question 51

What is a treatment for lactic acidosis?

Answer 51

The ketogenic diet reduces the need for glucose metabolism via glycolysis.

Question 52

What is HIF-1 alpha? What does it do? Under what conditions?

Answer 52

a transcription factor that stabilizes and is activated during hypoxia (low oxygen) conditions (often in cancerous tumors)

promotes the Warburg Effect

Question 53

What is the Warburg Effect? Why does it happen? What produces it? How does it happen?

Answer 53

Warburg effect is when cancer cells preferentially use glycolysis for ATP generation instead of oxidative phosphorylation in the presence of oxygen.

This happens to support the needs of rapidly dividing cancer cells because glycolysis is faster (even though it produces significantly less ATP).

This is produced by the activation of the HIF-1alpha transcription factor under low oxygen conditions.

HIF-1alpha stimulates PDK’s expression, which phosphorylates and inactivates the PDC and reduces conversion of pyruvate into acetyl CoA.

Question 54

Why do cancer cells have acidic environments?

Answer 54

HIF-1alpha stimulates PDK’s expression, leading to the phosphorylation and inactivation of PDC, which reduces conversion of pyruvate to acetyl CoA.

Pyruvate then converts into lactate instead, which is secreted by the cancerous cells.

Question 55

How does lactate production benefit cancer cells?

Answer 55

1.Biosynthesis: The intermediates generated from glycolysis can be channeled into
various biosynthetic pathways, supporting the synthesis of nucleotides, lipids, and amino acids necessary for cell proliferation.
2. Acidic Microenvironment: The production and secretion of lactate can create an acidic tumor microenvironment, which can facilitate invasion, metastasis, and
immune evasion.

Question 56

How do mercury and arsenite inhibit the PDC? What is an antidote?

Answer 56

They bind to the two sulfur atoms of dihydrolipoamide.

2,3-dimercaptopropanol (BAL) is an antidote, binding to arsenite and creating a more soluble complex that is excreted from the body.

Question 57

What happens to the PDC in diabetic neuropathy?

Answer 57

Elevated glucose levels lead to an overproduction of lactic acid.
Additionally, hyperactivation of PDK 2/4 results in inhibition of the pyruvate
dehydrogenase complex.
The conversion of pyruvate to lactate in abundance makes the environment more acidic. This acidosis stimulates acid-sensing nociceptors, G-protein-coupled receptors in the DRG, exacerbating the perception of pain.