Protein structure is subdivided into a distinct hierarchy of three classes. Each class is dictated by chemical bonding. Ultimately, these structure classes each contribute to the protein's function.

Primary structure is the distinct sequence of amino acid residues that make up a polypeptide or protein. If two peptides differ by only a single residue, they are different peptides, may have different charges, and different biochemical activities and effects.

Cys-Tyr-Phe-Gln-Asn-Cys-Pro-Arg-Gly-NH₂

Secondary structure is defined by the local conformations of the polypeptide chain resulting from intra-chain hydrogen bonding and short range interactions of the -R groups. Hydrogen bonding of amide groups play a major role.

Alpha Helix	Beta Sheets
A structure formed when the polypeptide chain coils along an imaginary central axis and is stabilized by hydrogen bonding between amide groups spaced four residues apart.	If two sections of chain run alongside one another, they can hydrogen bond to one another. The resulting 3-D effect is like a ruffled potato chip.

Tertiary structure focuses on the 3-D structure of the polypeptide chain in globular proteins. Secondary structures like alpha-helices and beta-sheets are held in place by connecting loops or bends. Much of the interior of globular proteins are helix and sheet because it is a hydrophobic environment and the amide bonds in the polypeptide backbone must be hydrogen bonded to satisfy their polarity.

The Biomolecules course addresses this topic in much greater detail.