It is a convention when representing dipeptides, and also proteins, to show the unreacted amino group on the left side of the formula and the unreacted carboxylic acid group on the right side of the formula. The name of this dipeptide is glycylalanine. The -ine ending of the glycine is changed to -yl because it's -OH is lost in the dehydration reaction, making it a glycyl group. The glycyl group is attached to the alanine making glycylalanine. The use of the three letter abbreviations can also be used to represent the glycylalanine, again by showing the group with the free amino group first and then on to the next. Thus, Gly-Ala represents glycylalanine.
Amino Acid Residues
Note that the glycyl group is no longer an amino acid molecule. It lost its molecule status when it lost its -OH and bonded to alanine. Instead, we call it an amino acid residue. Similarly the alanine has lost a hydrogen and will also lose its hydroxyl group when it bonds to the next amino acid. It is now also an amino acid residue rather than an amino acid molecule.
So, in the reaction above, glycine and alanine molecules are joined together to make a dipeptide molecule of glycylalanine which contains a glycine residue and an alanine residue.
As drawn, we have a nitrogen atom with three single bonds and, of course, a pair of electrons. The single bond should allow for rotation, but this particular group does not seem to rotate about this bond. Also, if the nitrogen has these three bonds and a pair of electrons, four groups of electrons around it, it should be in a tetrahedral arrangement.
We'll continue to represent the amide bond as a single bond because for our purposes the exact alignment and location of all these atoms is not crucial. However, if we were to pursue that aspect of the structure of peptides and proteins it would be a very important issue. Rotation still occurs outside of the circled area, but the part inside the circle seems to flatten out and the electrons seem to rearrange.
E-mail instructor: Sue Eggling
Clackamas Community College