Protein Folding, Stability, and Denaturation (1A) - MCAT Biological and Biochemical Foundations of Living Systems

Peptide bonds are broken by proteolysis, not typical denaturation. Denaturation typically disrupts noncovalent interactions, whereas proteolysis enzymatically hydrolyzes covalent peptide bonds.

It releases ordered water molecules from nonpolar surfaces. Exposing nonpolar areas to water orders solvent molecules, so burial reduces this order and boosts entropy.

The temperature where $50%$ is unfolded and $\Delta G = 0$. At Tm, the folded and unfolded states are equally populated, with equilibrium constant K=1 and zero free energy change.

Higher $T$ favors unfolding because $T\Delta S$ increases. Unfolding entropy becomes dominant at high temperatures, as the -TΔS term in ΔG shifts toward positive contributions.

β-mercaptoethanol (or DTT). These reducing agents cleave disulfide bridges, destabilizing structures reliant on cysteine cross-links during denaturation.

SDS (sodium dodecyl sulfate). As an anionic detergent, it binds hydrophobically and imparts charge repulsion, unfolding proteins for electrophoresis.

Urea (or guanidinium chloride). These chaotropes solvate nonpolar groups and weaken hydrogen bonds, promoting unfolding in biochemical experiments.

Primary structure is typically preserved. Denaturation affects higher-order structures by breaking noncovalent bonds, but the amino acid sequence remains intact.

Loss of native structure and function without peptide bond hydrolysis. Denaturation disrupts noncovalent interactions, leading to unfolding while preserving the covalent peptide backbone.

Molecular chaperones. They bind exposed hydrophobic regions on nascent or misfolded proteins, guiding proper folding and averting aggregates.

Molten globule. This state has compact secondary elements but lacks tight tertiary packing, serving as a folding intermediate.

The folding funnel (energy landscape) model. It visualizes folding as a downhill process on a multidimensional surface, avoiding kinetic traps to reach the native minimum.

The conformational ensemble. Proteins fluctuate among various states, with the native form being the most populated under equilibrium conditions.

Proline. Its cyclic side chain restricts backbone flexibility, preventing the regular hydrogen bonding needed for helix formation.

A disulfide bond ($\text{Cys-S-S-Cys}$). This covalent linkage provides structural rigidity by cross-linking distant parts of the protein chain or subunits.

Quaternary structure. It involves noncovalent interactions between separate chains, enabling complex protein assemblies like hemoglobin.

Tertiary structure. It integrates secondary structures and side-chain interactions to form a compact, functional 3D arrangement.

Secondary structure. It arises from hydrogen bonding and torsional angles in the polypeptide backbone, independent of side-chain interactions.

The lowest Gibbs free energy conformation under those conditions. Under physiological conditions, proteins adopt the conformation that minimizes Gibbs free energy, ensuring stability and functionality.

Gibbs free energy change, $\Delta G$. At constant temperature and pressure, a negative ΔG indicates a spontaneous process, governing protein folding thermodynamics.

Folding is spontaneous when $\Delta G < 0$. For the unfolded (U) to native (N) transition, spontaneity occurs when the free energy decreases, favoring the native state.

$\Delta G = \Delta H - T\Delta S$. This equation captures the balance between enthalpic contributions and entropic effects scaled by temperature in protein folding.

The hydrophobic effect (burial of nonpolar side chains). Nonpolar residues cluster inside to avoid water, driven by entropy gain from releasing structured solvent molecules.

Backbone hydrogen bonding between $\text{C=O}$ and $\text{N-H}$. These hydrogen bonds form regular patterns that stabilize the local folding in alpha-helices and beta-sheets.