Protein Structure and Thermodynamics (Video Notes)

Vocabulary flashcards covering key terms from protein structure and thermodynamics discussed in the video notes.

Protein folding

The stepwise, ordered process by which a polypeptide attains its native, functional three‑dimensional structure (primary to quaternary).

Primary structure

The linear sequence of amino acids in a protein.

Secondary structure

Local conformations such as alpha helices and beta sheets formed by hydrogen bonding.

Tertiary structure

The overall three‑dimensional shape of a single polypeptide, including side‑chain interactions.

Quaternary structure

The assembly of multiple polypeptide chains into a functional protein complex.

Hydrophobic effect

Driving force for folding: burying nonpolar residues to reduce water order; water molecules are released from hydration shells, increasing solvent entropy.

Hydration shell

Layer of water molecules organized around a solute; disruption or release of these shells increases solvent entropy.

Enthalpy

Heat content of a system (H); ΔH indicates heat absorbed or released (negative ΔH = exothermic, positive ΔH = endothermic).

Entropy

Measure of energy dispersal or disorder (S); higher entropy means more disorder and is thermodynamically favorable.

Gibbs free energy

G; energy available to do work. ΔG indicates spontaneity: ΔG < 0 spontaneous, ΔG > 0 non‑spontaneous, ΔG = 0 at equilibrium.

Spontaneous

A process that proceeds in the direction of equilibrium without a continuous input of energy (ΔG < 0).

Exothermic

ΔH < 0; heat released to surroundings during a process.

Endothermic

ΔH > 0; heat absorbed from surroundings during a process.

Equilibrium constant (Keq)

The ratio of product to reactant concentrations at equilibrium.

ΔG°' (Delta G naught prime)

Standard Gibbs free energy change under biochemical standard conditions (1 M, 298 K, 1 atm, pH 7); serves as a reference point.

Reaction quotient (Q)

The molar ratio of products to reactants at any moment (not necessarily at equilibrium).

Nonstandard conditions

Conditions other than standard; ΔG = ΔG°' + RT ln Q applies.

Standard conditions

Set values: 1 M concentrations, 298 K (25°C), 1 atm, pH 7.

Degrees of freedom

Translational, rotational, and vibrational motions that contribute to a molecule's entropy.

Isolated system

A system with no exchange of matter or energy with its surroundings.

Closed system

A system that exchanges energy but not matter with its surroundings.

Open system

A system that exchanges both energy and matter with its surroundings.