The backbone of a protein is a polypeptide chain made up by linking amino acids together with the removal of water, as we saw in Chapter 20. In globular proteins these chains typically are 60 to 600 amino acids long, and several chains may be present in one molecule.

The exact sequence of 20 different amino acids at each position along a protein chain is coded originally in DNA (in the way that we will see at the end of this chapter), and a few of these amino acids then are modified chemically in some proteins after they are built into the polypeptide chain. But this sequence of amino acids is all that is coded by the DNA. The way that the protein chain folds in three dimensions, the molecular structure that results, and all of the chemical properties of the folded protein must be contained in the amino acid sequence alone. There are no magic templates for a new polypeptide chain, and nothing else to tell the new protein how to construct itself in three dimensions.

A polypeptide chain of a protein contains important internal constraints on its own geometry. The carbon atom from which an amino acid side chain branches off is called the alpha carbon (C_a), and the connection between alpha carbons along the chain is the peptide group or amide group: