Structure and Function of Biological Macromolecules

A protein's amino acid sequence strongly influences how it folds, and its 3D shape determines what it can do. Environmental conditions (pH, temperature, ionic strength), molecular chaperones, chemical modifications, and interactions with other molecules can also affect its final structure and function.

The classic example of sequence-driven change is sickle-cell hemoglobin: a single glutamic acid → valine substitution at position 6 of the β-chain replaces a polar residue with a nonpolar one. The new hydrophobic patch makes hemoglobin molecules clump under low O₂, deforming red blood cells and illustrating how a change at the primary level can propagate up through every higher level of structure.

The linear sequence of amino acids in a polypeptide, held together by covalent peptide bonds. Read from N-terminus to C-terminus. The sequence is determined by the mRNA codon order, which in turn traces back to the DNA sequence of the gene.

Because every higher level of structure is built on top of this sequence, primary structure is considered the foundation: change one amino acid and you can change how the whole molecule folds and behaves.

Local folding patterns stabilized by hydrogen bonds between backbone atoms (the carbonyl oxygen and amide hydrogen of the peptide backbone), not R-groups. The two patterns to know are α-helices (a coiled, corkscrew-like structure) and β-pleated sheets, which consist of neighboring polypeptide segments held together by backbone hydrogen bonds.

The strands within a β-sheet may run parallel or antiparallel to one another; both arrangements are stabilized by the same type of backbone hydrogen bonding, just with slightly different geometries.

The overall 3D fold of a single polypeptide, driven by interactions between R-groups: the hydrophobic effect (nonpolar R-groups clustering in the protein core away from water), hydrogen bonds, ionic interactions between charged R-groups, van der Waals interactions, and disulfide bonds (covalent S-S bonds between two cysteines).

In many soluble proteins, the hydrophobic effect is a major driver of folding because nonpolar R-groups tend to become buried away from water. Hydrogen bonds, ionic interactions, van der Waals interactions, and disulfide bonds can also help stabilize tertiary structure - the dominant force depends on the specific protein and its environment.

When two or more polypeptide chains assemble into a single functional unit, the result is quaternary structure. Hemoglobin is the canonical example: four subunits (two α and two β), each carrying a heme group, that work together to bind four O₂ molecules cooperatively - binding of O₂ at one subunit increases the oxygen affinity of the others.

Not all proteins have quaternary structure; many function perfectly well as single polypeptides. When it exists, it adds an additional layer at which mutations, chemical modifications, or environmental changes can disrupt function.

Heat, extreme pH, or certain solvents disrupt the non-covalent interactions that hold tertiary and quaternary structures together. The polypeptide unfolds and loses function - the primary structure (its peptide bonds) is usually still intact even though the protein no longer works.

Frying an egg denatures its proteins irreversibly; this is also why high fevers are dangerous (enzymes start to lose shape) and why pepsin works at the highly acidic pH of the stomach but is inactivated at the more neutral pH of the small intestine.