Macromolecules Lab

Formulas and masses are for the neutral, un-ionized molecules. Each link is shown as a simple condensation (one H₂O per link); in cells, nucleotides actually arrive as triphosphates and release pyrophosphate, but the finished strand has the same formula. Amino acids and fatty acids are a small teaching set. Motion is sped up.

A two-state teaching model: stability is a score in kcal/mol built from the hydrophobic core, salt bridges, a disulfide bridge, exposed nonpolar R groups, temperature and pH; fraction folded = 1 / (1 + e^{−stability/RT}). Real proteins have many more interactions, and acidic and basic R groups gain or lose charge gradually around their pK_a values. The 16-residue chain stands in for a real enzyme.

Problems are randomly generated. Masses use glucose 180 g/mol and water 18 g/mol unless the problem gives other values. The worked solution shows units cancelling (struck through in red) and builds line by line.