Metabolism, anabolism and catabolism

Define metabolism and explain the difference between anabolism and catabolism, giving an example of each type of process.

Classify the following processes as anabolic or catabolic and briefly justify your choice: protein synthesis, cellular respiration, photosynthesis, and food digestion.

Metabolic transformations occur in pathways consisting of many linked reactions, each catalysed by an enzyme. Explain what a metabolic pathway is and the advantages of breaking down a transformation into numerous steps.

Distinguish between autotrophic and heterotrophic organisms from a metabolic point of view (carbon and energy source) and give an example of each type.

In an investigation on muscle metabolism, a cell line is analyzed with a mutation that renders the enzyme glycogen synthase constitutively active and insensitive to inhibition by phosphorylation, so that it remains at 100 % activity even during intense adrenaline surges.

1. a) During a vigorous muscle contraction triggered by adrenaline, glycogen phosphorylase is activated by a phosphorylation cascade. Reasonably predict the immediate metabolic consequence of both enzymes (synthase and phosphorylase) acting simultaneously at maximum speed and justify why this phenomenon (futile cycle) is energetically detrimental to the cell.
2. b) Explain how coordinated reciprocal regulation (through reversible covalent modification and allosteric modulators such as AMP and ATP) prevents this conflict from occurring in normal muscle fibers during rest and exercise.

What is ATP and why is it known as the cell's "energy currency"? State what happens when it is hydrolysed to ADP.

Describe the chemical composition of the ATP molecule (nitrogenous base, sugar and phosphate groups) and state which bond is broken when it is hydrolysed to ADP and why that bond is said to be energy-rich.

Give two examples of processes in daily life that depend on the energy released by hydrolysing ATP (muscle contraction, active transport, synthesis of molecules, transmission of the nerve impulse) and explain one of them briefly.

Photosynthetic organisms obtain their ATP from light and heterotrophs from nutrients, but all of them produce it by the same final mechanism: harnessing a proton gradient. Explain what chemiosmosis is and in which membranous structures it takes place in each type of organism.

Why is ATP, and not glucose, the immediate source of energy for the cell? Reason your answer by comparing how energy is released in each case (in small, usable doses versus the rapid, uncontrolled combustion that releasing all of glucose's energy at once would involve).

Anabolic reactions need, in addition to ATP, reducing power in the form of NADPH. Explain what NADPH contributes to syntheses and how its function differs from that of NADH in metabolism.

Classify the following activities of a muscle cell according to whether they consume or release ATP, justifying each case: contraction, glycogen synthesis, glucose breakdown in glycolysis and active transport of ions across the membrane.

During physical exercise, a person's oxygen consumption can be multiplied by ten or more. Explain what relationship this fact has with cellular metabolism and reason why oxygen is only needed for part of energy metabolism.

A poison blocks the hydrolysis of ATP without preventing its synthesis. Predict, with reasoning, what will happen to the cellular concentration of ATP, to anabolism, to catabolism and to cellular work, and explain why the cell will end up dying even though it is 'full' of ATP.

A 70 kg adult human has at any given moment a constant total mass of only about 50 g of ATP. However, their basal and daily activity requires hydrolyzing and resynthesizing approximately 50 kg of ATP every 24 hours.

1. a) Calculate how many times a day on average each ATP molecule is recycled in this individual and deduce the average time (in seconds or minutes) that elapses between the synthesis of an ATP molecule and its subsequent hydrolysis.
2. b) If our body could not recycle ADP and had to store the required 50 kg for the day in advance as free ATP, justify the insurmountable consequences this would cause on cell volume and cellular osmotic pressure. Reason why neutral fats (triacylglycerols) and polysaccharides are physiologically ideal macromolecules as long-term energy stores compared to ATP.

A student states: "Given that the direct combustion of one mole of glucose in the laboratory and its complete cellular oxidation release the same net amount of energy ($\Delta G^\circ = -2870\ \text{kJ/mol}$), it would be more advantageous for the living cell to burn glucose in a single, fast reaction to synthesize all the ATP at once and avoid intermediate losses." a) Refute this statement by justifying two cytological or thermodynamic reasons why the instantaneous release of that energy would be destructive or unfeasible for the cell. b) Explain the biological advantage of stepwise oxidation and justify the key role played by coenzymes such as $\text{NAD}^+$ and FAD as redox potential intermediates.

What is an enzyme and why are the reactions of metabolism said to be catalysed reactions? State what happens to the enzyme at the end of the reaction.

What is the activation energy of a reaction? Explain how enzymes manage to make metabolic reactions occur quickly at the temperature of the human body.

In a bacterium, the synthesis pathway of the essential amino acid L from precursor P consists of three consecutive steps catalyzed by enzymes $E_1, E_2$, and $E_3$. Enzyme $E_1$ is allosteric and undergoes feedback inhibition by product L itself. a) Predict with justification what would happen to the concentration of the pathway intermediates and to the cellular energy balance if a mutation alters the allosteric site of $E_1$, preventing the binding of L but keeping its catalytic activity intact, when the bacterium grows in a medium with abundant exogenous L. b) If another mutation completely inactivates enzyme $E_2$, reason which compound will accumulate and whether the activity of $E_1$ will be maintained or slowed down in the absence of L in the medium. c) Justify the selective advantage of placing allosteric control on the first committed enzyme of the pathway and not on the last one ($E_3$).

Explain why living beings are said to be open systems from the point of view of the exchange of matter and energy, and what difference there is in this respect with an isolated machine.

Look at the diagram of matter and energy exchange in metabolism. State which process (anabolism or catabolism) A and B represent, which molecule is indicated by ?, and explain, with an example, how the energy released by one process fuels the other.

Consider the following two independent metabolic reactions under physiological conditions:

1. $\text{Glucose} + \text{P}_\text{i} \rightarrow \text{Glucose-6-phosphate} + \text{H}_2\text{O} \quad (\Delta G^{\circ\prime} = +13.8\text{ kJ/mol})$

2. $\text{ATP} + \text{H}_2\text{O} \rightarrow \text{ADP} + \text{P}_\text{i} \quad (\Delta G^{\circ\prime} = -30.5\text{ kJ/mol})$

1. a) Justify at the molecular level why the hydrolysis of ATP has such a strongly exergonic $\Delta G^{\circ\prime}$ (refer to electrostatic charge repulsion and resonance stabilization of the products formed).
2. b) Write the equation for the net coupled reaction catalyzed by the enzyme hexokinase, calculate its overall $\Delta G^{\circ\prime}$, and explain how this energy coupling mechanism enables cellular processes that, in isolation, would be thermodynamically unfavorable.

A student poses an apparent paradox: "The second law of thermodynamics dictates that spontaneous processes proceed with a $\Delta G < 0$. Since anabolism builds complex molecules through strongly endergonic reactions ($\Delta G > 0$), does the biosynthesis of macromolecules not violate the laws of physics?"

1. a) Refute the student's objection by justifying, through the principle of energetic coupling and the intermediate role of the ATP/ADP system, how the cell manages to make an overall anabolic pathway thermodynamically favorable.
2. b) If an uncoupling agent of oxidative phosphorylation (such as DNP) that dissipates the mitochondrial electrochemical proton gradient is added to a suspension of hepatocytes, reasonably predict what will happen to the rate of glucose catabolism, to the synthesis of biomolecules (anabolism), and to the temperature of the medium.

A critic of evolutionary theory claims that the origin and maintenance of complex, ordered living beings from simple precursors is physically impossible because it contradicts the second law of thermodynamics, according to which disorder (entropy) must necessarily increase.

1. a) Using the formulation $\Delta S_\text{universe} = \Delta S_\text{system} + \Delta S_\text{surroundings} \ge 0$, refute this argument by distinguishing between an open system and an isolated one, and justify how cellular catabolism makes it possible to compensate for the local decrease in internal entropy generated during anabolism.
2. b) Design a thought experiment in which you enclose an animal and its food in a rigid, perfectly airtight, and adiabatic container (isolated from the outside with respect to matter and heat). Predict the vital and thermodynamic fate of the system over time and explain why Earth's biosphere does not suffer that same entropic collapse thanks to continuous solar flux.