Peptides
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Peptides

Intermolecular Dehydration

Two amino acid molecules, such as glycine and alanine shown here, can bond together using the carboxylic acid group of one and the amino group of the other by means of a dehydration reaction to form what is called a dipeptide.

Equation showing the dehydration of glycine and alanine to make glycylalanine. [68025.jpg]

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.

Zwitter Ions

Although I prefer, and will use, the molecular representations of the amino acids, there is good reason to argue that the active form of amino acids is actually the zwitter ion (or dipolar ion) form.

Structure of zwitter ions. [68026.jpg]

Remember that the carboxylic acid group can donate a proton and the amino group is basic and can accept a proton. So, an amino acid can react with itself by the acid group donating a proton to the amino group, thus making one end of the molecule negative and the other end positive. One of the values of this change is that it increases the solubility of amino acids in water.
The amino acid zwitter ions can still join to one another by dehydration reactions. The oxygen in the departing water molecule still comes from the carboxylate group, but now both of the hydrogens come from the amino group.

Equation showing zwitter ion structures forming a dipeptide. [68028.jpg]

 

Dipeptide Structure

Once formed, whether it is from molecules or from zwitter ions, this amide bond doesn't really seem to behave quite like the way it's drawn.

Amide bond empasized in structure of dipolar peptide molecule. [68027.jpg]

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.

However, in a peptide this entire collection of atoms flattens out. It seems as though the nitrogen undergoes hybridization from the sp3 arrangement, which would be tetrahedral, to an sp2 hybridization, which is flat, and there seems to be a bit of double bonded nature to this carbon to nitrogen bond.

Structure of dipolar dipeptide ion with amide bond circled. [68029.jpg]

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.

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