EXAM 2

What does the Pyruvate Dehydrogenase (PDH) complex do?

Irreversibly converts 3-carbon pyruvate into 2-carbon acetyl-CoA in the mitochondrial matrix.

What is the Pyruvate Dehydrogenase (PDH) reaction?

Pyruvate + CoA-SH + NAD⁺ → acetyl-CoA + CO₂ + NADH + H⁺.

Where does Pyruvate Dehydrogenase (PDH) work?

In the mitochondrial matrix.

Is the PDH reaction reversible?

No. It is irreversible under physiological conditions.

What are the five PDH cofactors?

• TPP — vitamin B1

• Lipoate — made in the body; not a vitamin

• CoA — vitamin B5

• FAD — vitamin B2

• NAD⁺ — vitamin B3

Which other enzyme uses the same five cofactors as PDH?

α-Ketoglutarate dehydrogenase.

What happens to PDH when thiamine is deficient?

Less TPP is available, so PDH activity decreases.

How does thiamine deficiency affect α-ketoglutarate dehydrogenase?

Its activity decreases because it also requires TPP.

Why can thiamine deficiency cause lactic acidosis?

Pyruvate oxidation decreases, causing more pyruvate to be converted into lactate.

Who is at increased risk of thiamine deficiency?

People with alcohol use disorder, poor oral intake, persistent vomiting, or parenteral nutrition without vitamins.

When should thiamine be given in relation to IV dextrose if deficiency is a concern?

Before or with dextrose when feasible, because glucose increases demand on thiamine-dependent enzymes. Never delay treatment of severe hypoglycemia.

What should be checked if a parenteral nutrition patient develops unexplained lactic acidosis?

Check whether the nutrition includes adequate vitamins, especially thiamine.

Are B vitamins used directly as fuel to make ATP?

No. They help form coenzymes needed for energy metabolism.

Which coenzymes come from B vitamins?

• B1 → TPP

• B2 → FAD

• B3 → NAD⁺

• B5 → CoA

Does taking extra B vitamins increase ATP production in someone without a deficiency?

Generally, no. Supplementation corrects deficiency but does not automatically increase TCA cycle activity or ATP production.

What are three major causes of increased lactate?

1. Inadequate oxygen delivery, such as hypoxemia or shock.

2. Blocked mitochondrial oxygen use, such as cyanide poisoning.

3. Impaired pyruvate oxidation, such as thiamine deficiency.

Does normal pulse oximetry rule out cyanide poisoning or a PDH defect?

No. Oxygen may be present in the blood, but cells may be unable to use it properly or oxidize pyruvate normally.

What can an inherited PDH deficiency cause?

Recurrent lactic acidosis because pyruvate cannot be efficiently converted to acetyl-CoA.

Why can a ketogenic diet help with PDH deficiency?

It reduces carbohydrate-derived pyruvate and provides ketone bodies that can form acetyl-CoA without the PDH reaction.

Where do most TCA cycle reactions occur?

in the mitochondrial matrix.

What does citrate synthase do?

It joins 2-carbon acetyl-CoA with 4-carbon oxaloacetate to form 6-carbon citrate.

What happens to oxaloacetate during the TCA cycle?

It is regenerated at the end of each turn and can be reused.

Why is only a small pool of oxaloacetate needed?

Oxaloacetate is regenerated each turn, allowing the same molecules to support many turns of the cycle.

Which two TCA cycle enzymes release CO₂ and produce NADH?

Isocitrate dehydrogenase and α-ketoglutarate dehydrogenase.

Does PDH also release CO₂?

Yes. PDH releases CO₂ when it converts pyruvate into acetyl-CoA.

Where does the oxygen atom in the final water of the ETC come from?

Molecular oxygen (O₂), which is reduced to water at Complex IV.

Are the two CO₂ molecules released during one TCA turn the two carbons just added by acetyl-CoA?

No. The newly added acetyl-CoA carbons are not the two carbons immediately released in that turn.

What is the yield from one acetyl-CoA oxidized in the TCA cycle?

• 3 NADH

• 1 FADH₂ equivalent

• 1 GTP

• 2 CO₂

Do NADH and FADH₂ directly phosphorylate ADP to make ATP?

No. They carry electrons to the ETC, which supports oxidative phosphorylation.

Where do the three NADH from one TCA turn send their electrons?

All three send electrons to Complex I of the ETC.

Which TCA cycle enzyme produces GTP directly?

Succinyl-CoA synthetase.

Why is GTP production by succinyl-CoA synthetase called substrate-level phosphorylation?

A phosphate is transferred directly to GDP without ATP synthase or the proton gradient.

How can GTP be used to make ATP?

Nucleoside-diphosphate kinase transfers the phosphate from GTP to ADP, producing ATP.

How many ATP equivalents does one GTP count as?

One ATP equivalent.

What does succinate dehydrogenase do?

It converts succinate to fumarate and produces enzyme-bound FADH₂. It is also ETC Complex II.

What does malate dehydrogenase do?

It converts malate to oxaloacetate and produces NADH, completing the cycle.

Which TCA enzyme is also part of the ETC?

Succinate dehydrogenase, which is Complex II.

ow many NADH are produced by complete oxidation of one glucose?

ten NADH total.

Where do the 10 NADH from one glucose come from?

• Glycolysis: 2 NADH in the cytosol

• PDH: 2 NADH in the mitochondrial matrix

• Two TCA turns: 6 NADH in the mitochondrial matrix

Which pathway produces the most NADH from one glucose?

The TCA cycle, producing 6 NADH over two turns.

How many ATP equivalents does one acetyl-CoA yield from the TCA cycle?

Approximately 10 ATP equivalents: 7.5 from 3 NADH, 1.5 from 1 FADH₂, and 1 from GTP.

How many ATP equivalents come from complete oxidation of one pyruvate to CO₂?

Approximately 12.5 ATP equivalents, including 2.5 ATP equivalents from PDH-derived NADH.

How much ATP does one glucose yield overall?

Approximately 30–32 ATP, depending on the shuttle used for glycolytic NADH.

What does TCA cycle flux mean?

The rate at which materials move through the TCA cycle.

What factors affect TCA cycle flux?

• ATP demand

• the mitochondrial NADH/NAD⁺ ratio

• the availability of acetyl-CoA and TCA intermediates.

What are the main control points of the TCA cycle?

Isocitrate dehydrogenase and α-ketoglutarate dehydrogenase.

How do high ATP/ADP and NADH/NAD⁺ ratios affect PDH and TCA enzymes?

They inhibit PDH and several TCA cycle enzymes, slowing energy metabolism.

Why does the TCA cycle slow when the ETC is blocked?

NADH cannot be efficiently oxidized back to NAD⁺, so NADH rises and NAD⁺-dependent reactions slow.

Does the TCA cycle directly use oxygen in any of its reactions?

No. However, it depends indirectly on oxygen because the ETC needs oxygen to regenerate NAD⁺ efficiently.

What is sodium nitroprusside used for?

It is an IV vasodilator used to lower blood pressure in certain clinical situations.

How can sodium nitroprusside cause lactic acidosis?

Its metabolism can release cyanide, which inhibits ETC Complex IV and prevents cells from using oxygen normally.

What is the treatment approach for suspected sodium nitroprusside-related cyanide toxicity?

Stop the infusion, provide supportive care, and administer an appropriate antidote, such as hydroxocobalamin or sodium thiosulfate, as clinically indicated.

How can oxaloacetate be used to make glucose?

Oxaloacetate is converted to phosphoenolpyruvate (PEP) by PEP carboxykinase and can enter gluconeogenesis.

How is citrate used to make fatty acids and cholesterol?

Citrate can leave the mitochondria and provide cytosolic acetyl-CoA for fatty acid and cholesterol synthesis.

How can α-ketoglutarate and oxaloacetate be used?

They can serve as precursors for amino acid synthesis.

What is succinyl-CoA used to synthesize?

Heme

Why must TCA intermediates be replenished?

Intermediates are removed for other pathways, so replenishment is needed to maintain TCA cycle activity.

What reaction does pyruvate carboxylase catalyze?

It converts pyruvate into oxaloacetate in the mitochondria.

What does pyruvate carboxylase require?

ATP and biotin (vitamin B7).

What activates pyruvate carboxylase?

Acetyl-CoA activates it allosterically.

What are the two major functions of pyruvate carboxylase?

It replenishes TCA cycle intermediates and supplies oxaloacetate for gluconeogenesis.

Why can't acetyl-CoA itself replenish the TCA cycle?

Acetyl-CoA adds two carbons to oxaloacetate, but two carbons are released as CO₂ before oxaloacetate is regenerated. It does not produce a net gain of TCA intermediates.

Why does the liver produce ketone bodies during fasting?

Fatty acid β-oxidation can produce acetyl-CoA faster than the TCA cycle can oxidize it, so excess acetyl-CoA is converted into ketone bodies.

Does the TCA cycle completely stop during fasting?

No. It continues, but its capacity to oxidize acetyl-CoA may be limited.

How can excessive dextrose delivery increase CO₂ production?

Excess carbohydrate metabolism increases CO₂ production through PDH and TCA cycle decarboxylation reactions.

Why can overfeeding make ventilator weaning more difficult?

Excess CO₂ production increases the amount of CO₂ the patient must eliminate through breathing.

What is an important nutrition consideration for patients receiving ventilatory support?

Avoid overfeeding. Preventing excess calorie delivery is important for limiting excess CO₂ production.

What do mutant IDH1 and IDH2 produce in certain acute myeloid leukemias?

They convert α-ketoglutarate into 2-hydroxyglutarate.

How does 2-hydroxyglutarate affect cancer cells?

It interferes with gene regulation and normal cell maturation.

Which drug inhibits mutant IDH1?

Ivosidenib.

Which drug inhibits mutant IDH2?

Enasidenib.

B vitamins are not fuels, they are precursors of the coenzymes TPP, FAD, NAD⁺, and CoA. Replacing them corrects a deficiency; extra vitamins in a person with adequate status do not raise _____

TCA flux or ATP production

What is the oxidized form of NAD?

NAD⁺. It accepts electrons during oxidation reactions.

What is the reduced form of NAD?

NADH. It carries and donates high-energy electrons.

What vitamin is NAD⁺ made from?

Niacin (vitamin B3).

What does NAD⁺ accept when a substrate is oxidized?

A hydride ion (H⁻), which contains one proton and two electrons.

Why must NAD⁺ be regenerated?

Without NAD⁺, NAD⁺-dependent reactions slow down or stop, limiting glycolysis and energy production.

How does lactate dehydrogenase regenerate NAD⁺?

It converts pyruvate to lactate while converting NADH back to NAD⁺.

What is the main mitochondrial pathway for regenerating NAD⁺?

The electron transport chain (ETC) reoxidizes NADH to NAD⁺.

What are the four main mitochondrial compartments?

Outer membrane, intermembrane space, inner membrane, and matrix.

Where are the ETC complexes and ATP synthase located?

In the inner mitochondrial membrane.

Where are most TCA cycle enzymes located?

In the mitochondrial matrix.

Which TCA cycle enzyme is located in the inner mitochondrial membrane?

Succinate dehydrogenase, also called ETC Complex II.

Where do electrons from NADH enter the ETC?

Complex I.

Where do electrons from succinate enter the ETC?

Complex II, through succinate dehydrogenase and its enzyme-bound FAD/FADH₂.

Which electron sources bypass Complex I?

Electrons from fatty acid oxidation and the glycerol-3-phosphate shuttle can enter through coenzyme Q.

What is the usual electron pathway after coenzyme Q?

Complex III → cytochrome c → Complex IV → oxygen.

Which ETC complexes pump protons (H⁺)?

Complexes I, III, and IV pump H⁺ into the intermembrane space

Does Complex II pump protons?

No. Complex II transfers electrons but does not pump H⁺.

What is the proton-motive force?

stored energy created by the difference in H⁺ concentration and electrical charge across the inner mitochondrial membrane.

Why can't H⁺ freely cross the inner mitochondrial membrane?

The lipid bilayer blocks charged ions, so H⁺ needs a protein pathway to cross.

What is the final electron acceptor in the ETC?

Oxygen (O₂), which is reduced to water at Complex IV.

What reaction occurs at Complex IV?

O₂ + 4 e⁻ + 4 H⁺ → 2 H₂O.

What happens to ATP production when oxygen is unavailable?

Electron transport and proton pumping decline, causing oxidative ATP production to decrease

What are reactive oxygen species (ROS)?

Reactive molecules formed when some electrons partially reduce oxygen. They can damage proteins, lipids, and DNA.

Which direction do protons flow through ATP synthase?

from the intermembrane space back into the mitochondrial matrix.

. How does ATP synthase make ATP?

The downhill flow of H⁺ powers ATP synthase to convert ADP + Pi into ATP.

What does coupling mean in oxidative phosphorylation?

Electron transport builds the H⁺ gradient, and ATP synthase uses that gradient to make ATP.

How does increased ATP demand affect respiration?

ADP levels rise, stimulating ATP synthesis and respiration if oxygen and fuel are available.

What happens when ADP levels are low?

ATP synthesis and respiration slow down.