Elements of Protein Structure

Primary Structure

Primary Structure is simply the sequence of amino acids as they appear in the polypeptide.

There are two ends to a polypeptide labled the N-term and the C-term. [term = terminus (end)]. The N and C come from the elements nitrogen and carbon, respetively. You will recall that the mainchain portion of each amino acid has an amine (nitrogen), an α carbon and then an organic acid (carbon). The organic acid of one amino acid forms an amide bond with the amine of another so that the new dipeptide still has an amine at one end and an organic acid at the other. This is true regardless of the length of the polypeptide.

Traditionally, listing the sequence starts at the N-term of of a polypeptide.

N-term		C-term
The picture above represents the primary sequence of a pentapeptide (5 amino acids) in 4 ways. structure (backbone atoms in red; sidechains in black) amino acids names three letter code for each amino acid one letter code for each amino acid In each case the tradition of starting the sequence from the N-terminal end (on the left) is used. Note: these structures only indicate how the amino acids are linked together. It indicates nothing about how they are folded into three dimensional space.

The last page of this module shows the amino acid sequence for Blood coagulation factor VII.... as well as how it relates to the overall 3 dimensional structure of the protein.