21. Biochemistry | Metabolism - Bioenergetics and Oxidative Phosphorylation

What is the overall definition of cellular respiration?

The process by which cells consume O2 and oxidize fuel molecules (glucose, fatty acids, amino acids), producing CO2 and ATP as bioenergy.

What process occurs in Phase I of cellular respiration?

Oxidation of cellular fuels to Acetyl-CoA and entry into the TCA cycle.

What are the key events that happen in Phase I of cellular respiration?

Carbs → Glycolysis → Pyruvate → Acetyl-CoA → TCA Cycle; FAs → β-oxidation → Acetyl-CoA; AAs → deamination → TCA intermediates.

What occurs in Phase II of cellular respiration?

Oxidative phosphorylation via the electron transport chain (ETC) to produce ATP.

What are the reducing equivalents in cellular respiration?

NADH and FADH2.

What is the function of mitochondria in cellular respiration?

To act as the powerhouse of the cell by producing ATP via oxidative phosphorylation.

What are the key features and function of the outer mitochondrial membrane?

It is semi-permeable to ions and small molecules.

What are the key features and function of the intermembrane space?

It is the site where protons are pumped to generate the proton gradient.

What are the key features and function of the inner mitochondrial membrane?

It houses ETC complexes I-V and ATP Synthase (Complex V).

What are the key features and function of the mitochondrial matrix?

It contains enzymes for the TCA cycle, β-oxidation, and mitochondrial NADH/FADH2 pool.

What happens if NADH and FADH2 are made outside the mitochondria?

They cannot cross the mitochondrial membrane alone and require shuttle systems.

What does the glycerol phosphate shuttle convert and what is its ATP yield and tissue distribution?

It converts 1 NADH → 1 FADH2, yields 1.5 ATP, and is used in the brain and skeletal muscle.

What does the malate-aspartate shuttle convert and what is its ATP yield and tissue distribution?

It converts 1 NADH (cytosol) → 1 NADH (mitochondria), yields 2.5 ATP, and is active in the liver, kidney, and heart.

How many protons are pumped per NADH and FADH2, and what is the ATP yield?

NADH (enters at Complex I): 10 H+ → ~2.5 ATP; FADH2 (enters at Complex II): 6 H+ → ~1.5 ATP.

What is the effect of ETC inhibitors on ATP synthesis?

They decrease the proton gradient, ATP synthesis, and respiration rate except in the case of Complex V and ATP Translocase

What is the function of Complex I in the ETC, how many protons are pumped, and is it transmembrane?

NADH dehydrogenase (ubiquinone) oxidizes NADH, pumps 4 H+

What is the function of Complex II in the ETC, how many protons are pumped, and is it transmembrane?

Succinate dehydrogenase (TCA intermediate) / CoQ transfers electrons from FADH2 without pumping protons. It is not transmembrane.

What is the function of Complex III in the ETC, how many protons are pumped, and is it transmembrane?

Cytochrome bc1 complex pumps 4 H+ using its key source QH2

What is the function of Complex IV in the ETC and what are its inhibitors?

Cytochrome oxidase pumps 2 H+ and transfers electrons to O2 using key source cytochrome c

What is the function of Complex V and what is its inhibitor?

ATP Synthase (F1F0 ATPase) uses proton flow to make ATP

What does the ATP/ADP Translocase do?

Exchanges ATP (matrix) for ADP (cytosol)

For Complex I, what is the mechanism, effect, and clinical relevance of its inhibitor(s)?

Rotenone+ Amytal block NADH → Q transfer; ↓ proton gradient, ↓ ATP synthesis, ETC slows; CNS depressant and insecticide for home gardens and ticks/lice respectively

For Complex III, what is the mechanism, effect, and clinical relevance of its inhibitor(s)?

"Antimycin A blocks electron flow through cytochrome b/c₁; ↓ H⁺ pumping, ↓ ATP; Streptomyces antibiotic, used as fungicide + mice killer

"

For Complex IV, what is the mechanism, effect, and clinical relevance of its inhibitor(s)?

"Cyanide (CN⁻) / Azide inhibit electron transfer to O₂, halts ETC → cell death; ETC halts → life-threatening toxicity; lethal poisoning

"

For Complex V, what is the mechanism, effect, and clinical relevance of its inhibitor(s)?

"Oligomycin; Inhibits ATP synthase proton flow → halts ATP production; ↑ proton gradient, ↓ ATP synthesis, ↓ respiration rate; Failure to export ATP results in ↑ [ATP] leading to ↑ proton gradient, ↓ respiration rate s/p negative feedback

"

For ATP/ADP Exchanger, what is the mechanism, effect, and clinical relevance of its inhibitor(s)?

"Atractyloside, Bongkrekic Acid; Blocks ADP/ATP exchange → feedback inhibition of ETC; Traps ATP in mitochondria, no ADP import → ↓ respiration; Leads to ATP accumulation in mitochondria

"

What is the mechanism of action and clinical relevance of 2,4-dinitrophenol (DNP)?

It is a proton carrier that collapses the proton gradient, resulting in weight loss agent (banned); causes hyperthermia

What is the mechanism of action and clinical relevance of valinomycin?

It is a K+ ionophore that collapses the mitochondrial membrane potential. Comes from Streptomyces

What is the mechanism of action and clinical relevance of thermogenin (UCP1)?

An endogenous uncoupler in brown adipose tissue dissipates the proton gradient to generate heat. CR = Non-shivering thermogenesis in neonates, hibernating animals

What are three uncouplers?

2,4-dinitrophenol (DNP); Valinomycin; Thermogenin (UCP1)

What happens to proton gradient, respiration, and ATP s/p uncoupler?

Proton gradient ↓, Respiration ↑ (to compensate for decreased proton gradient), ATP ↓

What does an uncoupler do?

Collapses complexes’ proton gradient, but allow ETC complex to flow, just can’t produce any actual ATP from it

What happens in cyanide poisoning and how is it treated?

Cyanide inhibits Complex IV; treated with thiosulfate (converts CN- to thiocyanate) and nitrite (creates methemoglobin to bind CN-).

What is the function of Pyruvate Dehydrogenase (PDH)?

It converts pyruvate to acetyl-CoA in the mitochondria, reducing 1 NAD+ to 1 NADH.

What happens if Pyruvate Dehydrogenase (PDH) is dysfunctional or inhibited?

Pyruvate accumulates → ↑ lactic acid → lactic acidosis; ↓ entry into TCA cycle

What is the function of NADH Dehydrogenase (Complex I)?

It oxidizes NADH and pumps 4 H+ into the intermembrane space.

What happens if NADH Dehydrogenase (Complex I) is dysfunctional or inhibited?

↓ ATP, ↑ NADH; blocked by Rotenone, Amytal

What is the function of Succinate Dehydrogenase (Complex II)?

It oxidizes FADH2 and transfers electrons to ubiquinone; part of the TCA cycle.

What happens if Succinate Dehydrogenase (Complex II) is dysfunctional or inhibited?

↓ electron flow from FADH₂; ↓ ATP from FAD-linked sources

What is the function of Cytochrome bc1 Complex (Complex III)?

It transfers electrons via cytochromes and pumps 4 H+.

What happens if Cytochrome bc1 Complex (Complex III) is dysfunctional or inhibited?

↓ ATP; blocked by Antimycin A

What is the function of Cytochrome Oxidase (Complex IV)?

It transfers the final electrons to O2 to form H2O and pumps 2 H+.

What happens if Cytochrome Oxidase (Complex IV) is dysfunctional or inhibited?

ETC halts; cyanide or azide inhibition causes rapid death if untreated.

What is the function of ATP Synthase (Complex V)?

It synthesizes ATP using the proton gradient generated by the ETC.

What happens if ATP Synthase (Complex V) is dysfunctional or inhibited?

ATP synthesis stops, and the proton gradient increases; it is inhibited by Oligomycin.

What is the function of Glycerol-3-Phosphate Dehydrogenase?

It is part of the shuttle in brain/muscle, converting NADH → FADH₂ + DHAP

What happens if Glycerol-3-Phosphate Dehydrogenase is dysfunctional or inhibited?

Less ATP produced b/c bypass of Complex I; only 1.5 ATP per NADH

What is the function of Malate-Aspartate Shuttle enzymes?

They transfer NADH equivalents from the cytosol into the mitochondria efficiently.

What happens if Malate-Aspartate Shuttle enzymes are dysfunctional or inhibited?

Blockage → ↓ mitochondrial NADH, ↓ ATP

What is the function of ATP/ADP Translocase?

It exchanges mitochondrial ATP for cytosolic ADP across the inner membrane.

What happens if ATP/ADP Translocase is dysfunctional or inhibited?

ATP accumulates in the mitochondria and respiration halts; it is inhibited by Atractyloside.

What is the function of Thermogenin (UCP1)?

It is an uncoupler protein in brown fat that dissipates the proton gradient to generate heat.

What happens if Thermogenin (UCP1) is dysfunctional?

Thermogenesis is impaired in neonates and hibernating animals.

What is the function of Rhodanese?

It detoxifies cyanide by converting it to thiocyanate using thiosulfate.

What happens if Rhodanese is dysfunctional?

Cyanide remains toxic and continues to inhibit Complex IV.

What is the function of Methemoglobin (via nitrite)?

It binds cyanide, protecting Complex IV by diverting cyanide away.

What happens if Methemoglobin (via nitrite) is dysfunctional?

Cyanide continues to bind Complex IV, blocking the ETC.

What are the inhibitors of Complex I?

Rotenone, Amytal

What are the inhibitors of Complex III?

Antimycin A

What are the inhibitors of Complex IV?

Cyanide (CN-), Azide

What are the inhibitors of Complex V?

Oligomycin

What are the inhibitors of ATP/ADP Translocase?

Atractyloside, Bongkrekic acid

What are symptoms of cyanide poisoning?

Symptoms can appear within seconds of exposure to cyanide gas. Central nervous system (CNS) symptoms leading to coma. (headache, confusion, anxiety, agitation, lethargy, seizures). Can be a CV emergency. Chest pain or tightness, Rapid or slow breathing, Rapid or slow heart rate, Hypotension, and Pulmonary edema

A 1-year-old child is found unresponsive at home. EMS notes a bitter almond odor on breath. Arterial blood gas reveals severe lactic acidosis and normal pO₂. Antidote treatment begins immediately. Which of the following explains how nitrite contributes to this treatment?

A. Blocks cyanide entry into the mitochondria
B. Reduces cyanide to thiocyanate for renal excretion
C. Oxidizes Fe²⁺ in hemoglobin to Fe³⁺, creating methemoglobin
D. Competes with oxygen at Complex IV
E. Enhances ATP synthesis by upregulating Complex V

C

• A. ❌ Cyanide can enter mitochondria passively; nitrite doesn't prevent entry.

• B. ❌ That’s thiosulfate’s job: converts CN⁻ to thiocyanate for excretion.

• ✅ C. Nitrite oxidizes Fe²⁺ → Fe³⁺ (methemoglobin), which binds cyanide and frees Complex IV.

• D. ❌ Cyanide, not nitrite, competes with oxygen at Complex IV.

• E. ❌ Nitrite has no effect on Complex V activity.

A 40-year-old gardener presents with nausea, dizziness, and confusion after using a pesticide. Labs show high NADH levels and reduced ATP. Which mitochondrial complex is most likely affected?

A. Complex I
B. Complex II
C. Complex III
D. Complex IV
E. Complex V

A

• ✅ A. Rotenone is a pesticide that inhibits Complex I → NADH accumulates, ATP drops.

• B. ❌ Complex II isn't the entry point for NADH.

• C. ❌ Antimycin A inhibits Complex III, but that’s a Streptomyces-derived antibiotic, not a garden pesticide.

• D. ❌ Cyanide inhibits Complex IV; different clinical picture.

• E. ❌ Complex V inhibition wouldn’t elevate NADH.

A patient is undergoing metabolic testing. Their mitochondrial membranes are found to be selectively permeable to potassium but not protons. Which substance is most likely responsible for this effect?

A. Oligomycin
B. 2,4-DNP
C. Rotenone
D. Valinomycin
E. Antimycin A

D

• A. ❌ Oligomycin inhibits ATP synthase (Complex V), not ion transport.

• B. ❌ DNP carries protons, not potassium.

• C. ❌ Rotenone inhibits Complex I — unrelated to potassium transport.

• ✅ D. Valinomycin is a K⁺ ionophore → disrupts membrane potential → acts as uncoupler.

• E. ❌ Antimycin A inhibits Complex III, not a K⁺ transporter.