Complex patterns. What is meant by intermediary metabolism?

Opposites. Differentiate between anabolism and catabolism.

Graffiti. While walking to biochemistry class with a friend, you see the following graffiti spray painted on the wall of the science building: “When a system is in equilibrium, the Gibbs free energy is maximum.” You are disgusted, not only at the vandalism, but at the ignorance of the vandal. Your friend asks you to explain.

Why bother to eat? What are the three primary uses for cellular energy?

Match ’em.

Charges. In vivo, ATP is usually bound to magnesium or manganese ions. Why is this the case?

Energy to burn. What factors account for the high phosphoryl-transfer potential of nucleoside triphosphates?

Back in time. Account for the fact that ATP, and not another nucleoside triphosphate, is the cellular energy currency.

Currency issues. Why does it make good sense to have a single nucleotide, ATP, function as the cellular energy currency?

Environmental conditions. The standard free energy of hydrolysis for ATP is −30.5 kJ mol⁻¹ (−7.3 kcal mol⁻¹).

What conditions might be changed to alter the free energy of hydrolysis?

Brute force? Metabolic pathways frequently contain reactions with positive standard free energy values, yet the reactions still take place. How is this possible?

Energy flow. What is the direction of each of the following reactions when the reactants are initially present in equimolar amounts? Use the data given in Table 15.1.

A proper inference. What information do the ΔG°′ data given in Table 15.1 provide about the relative rates of hydrolysis of pyrophosphate and acetyl phosphate?

A potent donor. Consider the following reaction:

Isomeric equilibrium. Using the information in Table 15.1, calculate ΔG°′ for the isomerization of glucose 6-phosphate to glucose 1-phosphate. What is the equilibrium ratio of glucose 6-phosphate to glucose 1-phosphate at 25°C?

Activated acetate. The formation of acetyl CoA from acetate is an ATP-driven reaction:

Acid strength. The pK of an acid is a measure of its proton-group-transfer potential.

Raison d’être. The muscles of some invertebrates are rich in arginine phosphate (phosphoarginine). Propose a function for this amino acid derivative.

Recurring motif. What is the structural feature common to ATP, FAD, NAD⁺, and CoA?

Ergogenic help or hindrance? Creatine is a popular, but untested, dietary supplement.

Standard conditions versus real life 1.The enzyme aldolase catalyzes the following reaction in the glycolytic pathway:

The ΔG°′ for the reaction is +23.8 kJ mol⁻¹ (+5.7 kcal mol⁻¹), whereas the ΔG in the cell is −1.3 kJ mol⁻¹ (−0.3 kcal mol⁻¹). Calculate the ratio of reactants to products under equilibrium and intracellular conditions. Using your results, explain how the reaction can be endergonic under standard conditions and exergonic under intracellular conditions.

Standard conditions versus real life 2. In Section 15.2, we showed that a reaction, , with a ΔG°′ = +16.7 kJ mol⁻¹ (+4.0 kcal mol⁻¹) has an of 1.15 × 10⁻³. The is increased to 2.67 × 10² if the reaction is coupled to ATP hydrolysis under standard conditions. The ATP-generating system of cells maintains the [ATP]/[ADP][P_i] ratio at a high level, typically of the order of 500 M⁻¹. Calculate the ratio of B/A under cellular conditions.

Not all alike. The concentrations of ATP, ADP, and P_i differ with cell type. Consequently, the release of free energy with the hydrolysis of ATP will vary with cell type. Using the following table, calculate the ΔG for the hydrolysis of ATP in liver, muscle, and brain cells. In which cell type is the free energy of ATP hydrolysis most negative?

Oxidation issues. Examine the pairs of molecules and identify the more-reduced molecule in each pair.

Running downhill. Glycolysis is a series of 10 linked reactions that convert one molecule of glucose into two molecules of pyruvate with the concomitant synthesis of two molecules of ATP (Chapter 16). The ΔG°′ for this set of reactions is −35.6 kJ mol⁻¹ (−8.5 kcal mol⁻¹), whereas the ΔG is −90 kJ mol⁻¹ (−22 kcal mol⁻¹). Explain why the free-energy release is so much greater under intracellular conditions than under standard conditions.

Outsourcing. Outsourcing, a common business practice, is contracting with another business to perform a particular function. Higher organisms were the original outsourcers, frequently depending on lower organisms to perform key biochemical functions. Give an example from this chapter of biochemical outsourcing.

Breakdown products. Digestion is the first stage in the extraction of energy from food, but no useful energy is acquired during this stage. Why is digestion considered a stage in energy extraction?

High-energy electrons. What are the activated electron carriers for catabolism? For anabolism?

Less reverberation. Thioesters, common in biochemistry, are more unstable (energy-rich) than oxygen esters. Explain why this is the case.

Classifying reactions. What are the six common types of reactions seen in biochemistry?

Staying in control. What are the three principal means of controlling metabolic reactions?

Kinetic versus thermodynamic. The reaction of NADH with oxygen to produce NAD⁺ and H₂O is very exergonic, yet the reaction of NADH and oxygen takes place very slowly. Why does a thermodynamically favorable reaction not occur rapidly?

Activated sulfate. Fibrinogen contains tyrosine-O-sulfate. Propose an activated form of sulfate that could react in vivo with the aromatic hydroxyl group of a tyrosine residue in a protein to form tyrosine-O-sulfate.

Opposites attract. The following graph shows how the ΔG for the hydrolysis of ATP varies as a function of the Mg²⁺ concentration (pMg = −log[Mg²⁺]).