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THE PRIMARY STRUCTURE:

It is the linear arrangement of the amino acid sequences present in the protein. It is nothing but the formation of a peptide bond combining the carboxylic acid moiety of one amino acid with an amino moiety of another amino acid. Thus one end of the protein has a free (unlinked) amino group (the Nterminus) and the other end has a free
carboxyl group (the C-terminus). The sequence of a protein chain is conventionally written with its N-terminal
amino acid on the left and its C-terminal amino acid on the right. A short chain of amino acids (20-50 amino acid residues) linked by peptide bonds and having a definite sequence is called a peptide, while longer chains are referred to as polypeptides or proteins (up to 4000 amino acid residues). Fig.3 shows the primary structure of a set of amino acids and the formation of the peptide bonds between them.

Fig.3 Peptide bonds (yellow) link the amide nitrogen atom (blue) of one amino acid(aa) with the carbonyl carbon atom (gray) of an adjacent one in the linear polymers known as peptides or polypeptides depending on
their lengths.

THE SECONDARY STRUCTURE:

They are the core elements of protein architecture. The various spatial arrangements resulting from the folding of localized parts of a polypeptide chain are referred to as the secondary structures. When stabilizing hydrogen bonds are formed between residues, parts of the backbone fold into one or more well defined periodic structures such as the alpha helix, the beta sheet also called the beta pleated sheet, and a set of turns (See Fig.4).

Fig.4 Shows the Alpha Helix which is above with the red backbone, and the beta pleated sheet below with the blue backbone.