1.7 Proteins

Every amino acid has a central carbon bonded to an amino group (–NH₂), a carboxyl group (–COOH), a hydrogen and a variable R group. There are 20 amino acids, and the R group decides each one's chemistry: nonpolar (hydrophobic), polar, or charged (acidic/basic).

Dehydration synthesis joins the carboxyl of one amino acid to the amino group of the next, forming a peptide bond. A chain has an N-terminus (free amino end) and a C-terminus (free carboxyl end) — another directional molecule.

Primary (1°) — the amino acid sequence, set by the gene. Held by peptide bonds.

Secondary (2°) — local α-helices and β-pleated sheets, held by hydrogen bonds between backbone atoms (not R groups).

Tertiary (3°) — the overall 3-D fold, from R-group interactions: hydrophobic R groups bury in the core, plus hydrogen bonds, ionic bonds and covalent disulfide bridges between cysteines.

Quaternary (4°) — two or more polypeptides assembled together (hemoglobin has four).

A protein works only if it folds correctly. High heat, extreme pH or high salt disrupt the weak interactions of 2°, 3° and 4° structure: the protein denatures and loses function. Peptide bonds (1°) stay intact.

Changing even one amino acid can change folding. In sickle-cell disease, one swap (glutamate → valine, polar → nonpolar) makes hemoglobin molecules stick together into fibers.

1° sequence → 2° backbone H-bonds → 3° R-group interactions → 4° multiple chains.

Worked example: A mutation replaces a nonpolar amino acid in a protein's core with a charged one. Predict the effect. → The charged R group won't be stable buried away from water, so tertiary folding changes and the protein likely loses function.