Lipid and protein catabolism

Explain what β-oxidation is, where in the cell it occurs, and what product it feeds into the Krebs cycle. State also which electron-carrier molecules are generated during the process.

In β-oxidation, fatty acids are shortened by two carbon atoms at a time. Explain why it receives that name (on which carbon of the chain the oxidation occurs) and what fragment is released in each round of the process.

Order the three types of energy biomolecules (carbohydrates, lipids, and proteins) according to the energy they provide per gram, and explain why the body preferentially uses carbohydrates and turns to proteins only in extreme situations.

A saturated fatty acid with $18$ carbon atoms is completely degraded by β-oxidation. Calculate how many rounds of β-oxidation are needed and how many acetyl-CoA molecules are obtained, reasoning the calculation.

Palmitic acid ($\text{C}_{16}\text{H}_{32}\text{O}_2$) yields about $106\ \text{ATP}$ upon complete oxidation with a consumption of $23\ \text{moles of }\text{O}_2$. In turn, glucose ($\text{C}_6\text{H}_{12}\text{O}_6$) generates about $36\ \text{ATP}$ consuming $6\ \text{moles of }\text{O}_2$.

1. a) Calculate the energy yield per carbon atom ($\text{ATP}/\text{C}$) of both substrates and biochemically justify the reason for this difference by analyzing the average oxidation state of carbon in carbohydrates and lipids.
2. b) Glycogen is stored in a hydrated form (retaining approximately $2\ \text{g}$ of water per gram of dry glycogen), whereas triglycerides accumulate in an anhydrous form. Knowing that $1\ \text{g}$ of pure fat provides about $9\ \text{kcal}$ and $1\ \text{g}$ of dry glycogen provides $4\ \text{kcal}$, calculate the total weight that a migratory bird would have to accumulate to have a reserve of $18,000\ \text{kcal}$ if stored as triglycerides versus hydrated glycogen, and deduce the adaptive advantage this represents.
3. c) During intense muscular exertion in which the $\text{O}_2$ supply becomes limiting, calculate which substrate yields more ATP molecules per mole of $\text{O}_2$ consumed ($\text{ATP}/\text{O}_2$) and predict which one the muscle will prioritize in that situation.

Where are reserve fats stored in the organism? Explain what happens in adipose tissue when the body needs energy (lipolysis) and which molecules are then released into the blood.

Before being oxidised, fatty acids must be activated by binding to coenzyme A. Explain what coenzyme A is and what general role it plays as a carrier of acyl groups in metabolism.

Reason why 1 g of fat yields more ATP than 1 g of glucose, referring to the degree of reduction of the carbons in the hydrocarbon chain of fatty acids and the quantity of electrons they can donate to the respiratory chain.

During prolonged fasting or a diet very high in fat, ketone bodies in the blood increase. Explain what ketone bodies are and reason why they appear when the Krebs cycle cannot assimilate all the acetyl-CoA coming from β-oxidation.

The glycerol coming from triglycerides can enter glycolysis converted into a three-carbon intermediate. Explain why that part of fats can indeed be transformed into glucose, while even-chain fatty acids, in animals, cannot (acetyl-CoA is not gluconeogenic).

In uncontrolled diabetes, the production of ketone bodies increases even though there is plenty of glucose in the blood. Explain this apparent paradox (without insulin, glucose barely enters muscle and fat cells) and reason why the accumulation of ketone bodies can cause ketoacidosis.

A classmate states in a debate: "Mammals cannot synthesize glucose from fats under any circumstances, because in the Krebs cycle 2 carbons enter as acetyl-CoA and 2 carbons are released as $\text{CO}_2$, which prevents a net gain of oxaloacetate for gluconeogenesis."

1. a) Explain why your classmate's reasoning is correct for even-chain fatty acids, demonstrating with the carbon balance of the Krebs cycle why the degradation of acetyl-CoA does not allow the net synthesis of glucose in mammals.
2. b) Refute their general conclusion: demonstrate what happens when odd-chain fatty acids are oxidized, detailing what molecule their last thiolysis yields, how it enters the Krebs cycle, and why this does allow a net gain of carbon skeletons for gluconeogenesis.
3. c) Predict with reasoning what would happen to the blood glucose level of an animal in prolonged fasting if propionate is administered intravenously versus if acetate is administered.

Dietary proteins are not stored in the body. Explain what happens to excess amino acids: which group is removed, how the excess nitrogen is eliminated, and what the fate of the rest of the molecule is.

Urea is formed in the liver from ammonium. Explain why the organism invests energy in converting ammonium, which is very toxic, into urea, and state how the latter is eliminated from the body.

The amino acids of ingested proteins can follow three fates: building new proteins, being transformed into other nitrogenous molecules or being degraded to obtain energy. Explain them briefly and state which one takes priority when the diet is balanced.

Describe the deamination of amino acids and explain the fate of the two resulting parts: the amino group (and its conversion to urea) and the carbon skeleton (which can enter catabolic pathways as pyruvate, acetyl-CoA, or Krebs cycle intermediates).

A very protein-rich diet subjects the liver and the kidney to extra work. Explain, in terms of nitrogen metabolism (deamination, the urea cycle and excretion), why this type of diet can be problematic in people with liver or kidney disease.

Amino acids are classified into glucogenic (their degradation produces pyruvate or Krebs cycle intermediates) and ketogenic (they produce acetyl-CoA or acetoacetyl-CoA). Explain what this classification means and why during fasting glucogenic amino acids can serve to make glucose.

At $48$ hours after birth, a breastfed newborn presents progressive lethargy, vomiting, and respiratory alkalosis. Blood analysis reveals severe hyperammonemia ($[\text{NH}_4^+] > 450\ \mu\text{mol/L}$), a marked elevation of glutamine and alanine, and undetectable concentrations of citrulline and urea.

1. a) Knowing that the first two enzymes of the cycle are mitochondrial (carbamoyl phosphate synthetase I and ornithine transcarbamylase, responsible for forming citrulline) and the remaining ones are cytosolic, deduce with justification in which organelle and in which section of the cycle the enzymatic defect is located.
2. b) Justify at the molecular level why ammonium accumulation is particularly toxic to neurons: relate the excess of $\text{NH}_4^+$ to the displacement of the glutamate dehydrogenase equilibrium, the depletion of $\alpha$-ketoglutarate, and the arrest of mitochondrial ATP production.
3. c) Design a therapeutic intervention combining macronutrient intake management with the administration of sodium phenylbutyrate (a drug that conjugates with glutamine to form a derivative excreted directly in the urine), justifying how each measure reduces nitrogen toxicity.

The following table compares the three main strategies of amino nitrogen excretion in vertebrates:

1. a) Reasonably identify which molecule (ammonium, urea, or uric acid) corresponds to each strategy and relate the invested ATP cost to the water availability in the habitat of the animals that use them.
2. b) The Perez's frog (Pelophylax perezi) uses strategy A during its aquatic larval stage (tadpole), but switches to strategy B after metamorphosis into a terrestrial adult. Justify the enzymatic changes that must be induced in its liver during this process, as well as the osmotic and energy balance that explains this transition.
3. c) Predict and justify the consequences on the viability and embryonic development of a bird of a mutation that inactivated uric acid synthesis, causing the embryo to excrete only urea inside the shelled egg.

The diagram summarizes how the catabolic pathways of carbohydrates, lipids, and proteins converge in aerobic cellular catabolism:

1. a) Identify the catabolic processes indicated by ?1 and ?2. If a drug selectively inhibits the mitochondrial carnitine shuttle, deduce which pathway (?1, ?2, or glycolysis) will be blocked and which substrates the cell will need to prioritize to maintain acetyl-CoA levels.
2. b) During prolonged fasting, a large portion of the Krebs cycle oxaloacetate is diverted to hepatic gluconeogenesis while pathway ?1 is hyperactivated. Justify what alternative fate the accumulated acetyl-CoA will follow, given that it cannot condense into the Krebs cycle.
3. c) If rotenone (an inhibitor that blocks electron transfer from NADH to complex I of the respiratory chain) is added, predict how the intramitochondrial ratio $[\text{NADH}]/[\text{NAD}^+]$ will change and what direct consequence this will have on the rate of the Krebs cycle.

The blood and urinary parameters of a volunteer are analyzed during a four-week hunger strike. In the first $24$ hours, hepatic glycogen is completely depleted; however, blood glucose remains stable at around $60\text{ mg/dL}$. Plasma levels of acetoacetate and $\beta$-hydroxybutyrate increase by more than $25$-fold starting on day four, whereas urinary urea excretion shows an initial peak on days 2–3 and then drops to stable minimum values.

1. a) Justify where plasma glucose comes from starting on the second day if glycogen is no longer available, and explain why the net breakdown of muscle proteins (reflected in urea) decreases so markedly after the first week.
2. b) Explain why the brain cannot directly oxidize fatty acids derived from adipose tissue and how the synthesis of ketone bodies acts as a protective mechanism for skeletal muscle mass.
3. c) If this individual were accidentally administered a high dose of insulin on day 15 of fasting, predict and justify what would happen to lipolysis in adipocytes, to ketone body production, and to the energy supply to the brain.

In an exercise stress test, the respiratory exchange ratio is recorded ($\text{RER} = \text{V}_{\text{CO}_2} / \text{V}_{\text{O}_2}$). At a moderate intensity ($50\,\%\ \text{VO}_{2\text{max}}$), the $\text{RER}$ is $0.71$; at high intensity ($85\,\%\ \text{VO}_{2\text{max}}$), it rises to $0.98$. At kilometer 32 of a marathon, a runner completely exhausts their muscle and liver glycogen stores (the phenomenon known as "hitting the wall") and their pace drops abruptly.

1. a) Interpret the $\text{RER}$ values by explaining which fuel predominates in each case, and biochemically justify why the complete oxidation of a fatty acid generates a ratio close to $0.70$ while that of glucose is equal to $1.00$.
2. b) If fatty acids provide more than twice as much energy per gram as carbohydrates, explain why the athlete is forced to noticeably reduce their running pace when relying exclusively on them (compare the $\text{O}_2$ consumption per ATP generated and the maximum enzymatic flux rate of $\beta$-oxidation versus glycolysis).
3. c) For acetyl-CoA derived from $\beta$-oxidation to enter the Krebs cycle, oxaloacetate is required, whose pool is largely replenished (anaplerosis) from glycolytic pyruvate via pyruvate carboxylase. Justify what happens to the Krebs cycle (and to fat oxidation) when pyruvate availability drops drastically (anaplerotic role).

During the months of hibernation, the black bear (Ursus americanus) does not eat, drink, or urinate, and despite this it maintains its body temperature and barely loses $5\,\%$ of its muscle mass. Physiological analyses yield the following data:

1. Its respiratory quotient ($\text{RQ} = \text{volume of CO}_2\text{ produced} / \text{volume of O}_2\text{ consumed}$) drops from $1.0$ before hibernation to $0.71$ during dormancy.

2. Its plasma osmolarity and blood volume remain constant without fluid intake.

3. Blood urea levels do not increase.

From these data:

1. a) Interpret the value of $\text{RQ} = 0.71$: identify which metabolic fuel it is using almost exclusively, and justify why this fuel yields a respiratory quotient clearly lower than $1.0$.
2. b) Explain the origin of the metabolic water that prevents the animal's dehydration, indicating in which organelle, enzyme complex, and specific reaction of cellular respiration it is generated.
3. c) Justify why the preferential use of this fuel prevents muscle atrophy due to gluconeogenesis, and explain which pathway the nitrogen from amino acid catabolism follows so that the animal does not suffer ammonium toxicity without producing urine.