download free secondary structure of protein

In other words, if you replaced the 'R' groups in the last diagram by real groups you would have the primary structure of a particular protein.

At its simplest, the term is used to describe the order of the amino acids joined together to make the protein. Now there's a problem! The term 'primary structure' is used in two different ways. The peptide chain is known as the backbone, and the 'R' groups are known as side chains. The 'R' groups come from the 20 amino acids which occur in proteins. The end of the peptide chain with the -NH 2 group is known as the N-terminal, and the end with the -COOH group is the C-terminal.Ī protein chain (with the N-terminal on the left) will therefore look like this: The unchanged -COOH group is written at the right-hand end. The peptide chain is made up from what is left after the water is lost - in other words, is made up of amino acid residues.īy convention, when you are drawing peptide chains, the -NH 2 group which hasn't been converted into a peptide link is written at the left-hand end. When the amino acids combine together, a water molecule is lost.

You have to use this term because strictly speaking a peptide chain isn't made up of amino acids. If you joined lots and lots together (as in a protein chain), you get a polypeptide.Ī protein chain will have somewhere in the range of 50 to 2000 amino acid residues. If you joined three amino acids together, you would get a tripeptide. In chemistry, this would also be known as an amide link, but since we are now in the realms of biochemistry and biology, we'll use their terms. In each case, the linkage shown in blue in the structure of the dipeptide is known as a peptide link. It is possible for this to happen in one of two different ways - so you might get two different dipeptides. Glycine and alanine can combine together with the elimination of a molecule of water to produce a dipeptide. That means that the two simplest amino acids, glycine and alanine, would be shown as: It is much easier to see what is happening if you do that. However, for drawing the structures of proteins, we usually twist it so that the 'R' group sticks out at the side. In chemistry, if you were to draw the structure of a general 2-amino acid, you would probably draw it like this:

Download free secondary structure of protein