Thermodynamics, Bioenergetics and Chemical Principles

Why can a clinical drug effect require a molecular-level explanation?

Because the patient-level outcome usually originates from a drug interacting with a protein, enzyme, transporter, receptor, or pathway inside cells.

What do ΔG < 0, ΔG = 0, and ΔG > 0 mean? and what does ΔG not tell you?

ΔG < 0: forward direction favorable; ΔG = 0: equilibrium; ΔG > 0: unfavorable unless coupled. ΔG gives direction only not the pathway or the speed.

Why can ATP hydrolysis be favorable but still slow without catalysis?

Thermodynamics and kinetics are different: a favorable reaction can still face a high activation barrier and proceed slowly.

What is the essential requirement for coupling an unfavorable process to a favorable one?

The favorable and unfavorable processes must be mechanistically (chemically) linked so one directlydrives the other; proximity alone is not enough

In the hexokinase reaction, where does the phosphate added to glucose come from?

Directly from the terminal phosphate of ATP; hexokinase transfers it to glucose, with no free Pi released.

Name the three kinds of work ATP drives, with one example of each.

Chemical work (biosynthesis), transport work (Na⁺/K⁺-ATPase), and mechanical work (muscle contraction / motor proteins).

Which four noncovalent interactions are emphasized, and what is distinctive about the hydrophobic effect?

Ionic interactions, hydrogen bonds, van der Waals interactions, and the hydrophobic effect. The hydrophobic effect is water-driven aggregation of nonpolar groups, not a special “hydrophobic bond.”

How do covalent and noncovalent interactions differ in their usual biological roles?

Covalent bonds form the molecular framework; weak, reversible noncovalent interactions usually govern folding, recognition, and binding.

If pH falls by 2 units, how does [H⁺] change?

[H⁺] increases 100-fold.

What does it mean when pH = pKa for an ionizable group?

Protonated and deprotonated forms are present about 1:1 (50:50).

At pH below pKa, which form generally predominates: protonated or deprotonated?

The protonated form.

Why is protonated aspirin neutral while protonated lidocaine is positively charged?

Charge depends on the chemical group: protonating a carboxylate gives neutral HA, whereas protonating an amine gives BH⁺