Cellular respiration

Name the four stages of aerobic respiration and state where in the eukaryotic cell each one takes place.

In the diagram of aerobic respiration, state which stage corresponds to each numbered box (1, 2, and 3), name the molecules labelled A and B, and indicate where in the cell each stage takes place.

Where in the cell does glycolysis occur, and what net products are obtained from one molecule of glucose in this stage?

For each glucose molecule, glycolysis has a net balance of $2\ \text{ATP}$ and $2$ NADH. Explain why it is called a 'net' balance, detailing how many ATP are consumed in the first phase and how many are produced in the second.

What is pyruvate and what are its two main fates after glycolysis depending on whether oxygen is available or not? State what type of metabolic pathway it follows in each case.

Define fermentation and name the two main types with their final products, indicating an organism or tissue that carries out each one.

In lactic acid fermentation, pyruvate is converted into lactate. Explain why this process allows $\text{NAD}^+$ to be regenerated and in what situations human muscles use it.

Yeasts and our muscle cells can respire or ferment depending on the available oxygen. Explain how the cell 'decides' between one pathway and the other (the Pasteur effect) and what advantage it obtains when, oxygen being present, it reduces glucose consumption while maintaining the same ATP supply.

What is the Krebs cycle? State which two-carbon molecule enters it coming from the oxidation of pyruvate and which gas is released in its reactions.

Draw or describe a mitochondrion, pointing out its outer membrane, its inner membrane with the cristae and the matrix, and state in which zones the Krebs cycle and the respiratory chain occur.

You can do it on paper and send a photo with your answer.

In the Krebs cycle, acetyl-CoA joins oxaloacetate and, after a series of reactions, the oxaloacetate is regenerated. Explain why this pathway is called a 'cycle' and detail what energy products and what waste product are generated per turn.

Mitochondria possess their own DNA, their own ribosomes and divide by binary fission. Explain what evolutionary origin these data suggest (the endosymbiotic theory) and why these organelles are the right place to house cellular respiration.

In a class debate on cellular origins, a student claims: "The enzymes of glycolysis and those of the mitochondrial electron transport chain must have evolved at the same time in the first living cells to prevent cytosolic $\text{NAD}^+$ from being depleted."

1. a) Refute the student's statement by providing two geochemical arguments about the conditions of early Earth's atmosphere and one evolutionary argument based on the endosymbiotic theory.
2. b) If the first organisms had neither oxygen nor complex membrane-dependent electron transport systems, biochemically justify the unavoidable need to couple glycolysis to fermentation reactions for the continuity of cellular life.
3. c) Predict what would happen to an obligate anaerobic bacterium, whose only route for regenerating $\text{NAD}^+$ is lactic fermentation, if a mutation inactivated its lactate dehydrogenase in a medium where glucose is its only carbon and energy source.

Explain the role played by $\text{NAD}^+$ and FAD in cellular respiration and what happens to their reduced forms (NADH and $\text{FADH}_2$) in the electron transport chain.

ATP synthase works like a rotary molecular motor. Explain what makes it spin, what reaction it catalyses and in which membrane it is located in the mitochondrion.

Assays are performed with isolated mitochondria supplied with different respiratory substrates: when malate is provided (which generates intramitochondrial NADH), $\text{O}_2$ consumption is recorded along with a synthesis ratio of about $2.5\ \text{ATP}$ per electron pair; when rotenone (an inhibitor of Complex I) is added, $\text{O}_2$ consumption ceases, but it is restored upon supplying succinate (which reduces FAD to $\text{FADH}_2$), yielding only about $1.5\ \text{ATP}$ per electron pair. a) Justify at the molecular and chemiosmotic level the biophysical cause of this difference in energy yield between both substrates. b) Reasonably deduce what would happen to $\text{O}_2$ consumption and ATP synthesis from succinate if a specific inhibitor of Complex IV (cytochrome c oxidase) is added. c) In skeletal muscle, electrons from glycolytic NADH enter the respiratory chain via the glycerol-3-phosphate shuttle, whereas in the myocardium they do so through the malate-aspartate shuttle. Calculate the difference in the total net ATP yield per mole of fully oxidized glucose between both tissues and justify the metabolic cause of this discrepancy.

To experimentally test the chemiosmotic hypothesis, intact mitochondria are isolated and suspended in a medium at pH 8.0 without ADP or oxidizable substrates. After allowing the matrix to reach this pH, they are abruptly transferred to a medium at pH 4.0 containing ADP and $\text{P}_i$, in the total absence of oxygen and electron donors. a) Predict with justification whether ATP will be synthesized under these artificial conditions and describe the biophysical mechanism through which ATP synthase exploits this situation. b) What would happen to ATP synthesis if the inner mitochondrial membrane had previously been treated with an ionophore substance that allows the free passage of protons? Justify your answer. c) Reason why, under normal physiological conditions, oxygen depletion halts oxidative phosphorylation.

Cyanide blocks the last complex of the respiratory chain (cytochrome c oxidase). Predict what will happen to oxygen consumption, ATP synthesis, and the fate of pyruvate in a poisoned cell, and reason why cyanide is lethal even if glucose is available.

2.4-Dinitrophenol (DNP) is an uncoupler: it makes the inner mitochondrial membrane permeable to protons without ATP being produced. Predict, with reasoning, what will happen to oxygen consumption, to ATP synthesis and to the body temperature of someone who ingests it, and explain why it came to be used as a slimming drug with deadly consequences.

Carbon monoxide binds to haemoglobin with more affinity than oxygen. a) Explain what effect it has on the transport of $\text{O}_2$ to the tissues. b) Reason which stages of cellular respiration will be affected and why cells switch to fermentation even when they have glucose. c) Compare the toxicity mechanism of carbon monoxide with that of cyanide.