As their name suggests, amino acids are compounds that contain both an amino group and a carboxylic acid unit. The amino acids of interest to most people are a-amino acids, which means that the amino group is attached to the carbon atom that is bonded to the carboxyl carbon. A generalized structure for a-amino acids is shown in Figure 1, where R represents any of the more than 20 substituents that are found in naturally occurring amino acids.
There are several structural features that are characteristic of amino acids. First, they exist as doubly charged ions called zwitterions. One piece of evidence that suggests the ionic nature of amino acids is their high melting points. Alanine (R=CH3), for example, melts at 315oC. Such a high melting point is unusual for small organic molecules, and it suggests that unusually strong intermolecular forces exist between alanine molecules. Consider the data shown in Figure 2. The simple amine, 2-aminobutane is a liquid that boils at 63oC. Clearly the forces of attraction between molecules of 2-aminobutane are much less than those between molecules of alanine. By the same token, the intermolecular interactions in 2-methylpropanoic acid, which boils at 153oC, must be considerably smaller than those in alanine. Even 2-amino-1-propanol, which contains two polar functional groups, is a liquid at room temperature. If the structure of alanine shown in Figure 2 were correct, i.e. if all the bonds were covalent, then you should expect this compound to be a liquid with a boiling point in the 200oC range. The fact that it's a solid with a melting point over 300oC indicates this is not the case. Clearly the intermolecular forces in alanine are much greater than the dipole-dipole interactions between the other molecules in Figure 2.
With the exception of glycine, where R = H, all of the amino acids are optically active. Using the same D-L convention that Fischer developed for sugars, all of the chiral amino acids are classified as L-amino acids. Figure 3 compares the Fischer projection of D-glyceraldehyde to that of a chiral amino acid.
Exercise 2 The four groups attached to the chiral center in cycteine are H, CH2SH, CO2H, and NH2. Enter each group into the appropriate text field according to its Cahn-Ingold-Prelog priority. 1 = 2 = 3 = 4 = Is the stereochemical designation for L-cysteine R or S? R S
Most amino acids are obtained by the hydrolysis of proteins. The process produces mixtures. One technique for separating the individual amino acids is called ion exchange chromatography. Another method that is frequently employed to monitor the composition of a mixture of amino acids is called electrophoresis. In order to undestand how these approaches work it is necessary to consider how the net charge on an amino acid varies as a function of pH, i.e. its pH profile. Figure 5 illustrates the change in charge as the pH of a solution of lysine is increased from 1 to 12.
Lysine contains a carboxylic acid group, the a-amino group, and a second amino group attached to the side chain. In a very acidic solution, pH=1, all of these groups are protonated. The net charge on the lysine is +2 (State A). As the pH of the solution is raised, by the addition of NaOH for example, the most acidic site in lysine will be deprotonated first. This is the carboxylic acid group. The pKa of the CO2H proton is 2.2. This means that when the pH of the solution reaches 2.2, 50% of the CO2H groups in lysine will be deprotonated. More NaOH will deprotonate the remaining CO2H groups until 100% of the lysine is present in State B. The net charge in State B is +1. As the pH increases, the NaOH will begin to deprotonate the a-aminium group which has a pKa of 9.0; at a pH of 9.0, 50% of the a-aminium ions will be deprotonated. The net charge on a lysine molecule in State C is 0. Once all of the a-aminium groups have been deprotonated, the NaOH will deprotonate the aminium group in the side chain. The pKa of this group is 10.5. When the pH equals 10.5, 50% of these groups will be deprotonated. Further addition of NaOH will deprotonate the remaining aminium groups in the sample. The net charge on a lysine molecule in State D is -1.
The pH at which the net charge of an amino acid is 0 is called the isoelectric point. It is represented by the symbol pI. At a given pH the net charges on amino acids with different pI values are different. Both ion exchange chromatography and electrophoresis depend on differences in the net charge on a molecule in order to separate the components of a mixture. In an electrohoresis experiment a sample is placed at the center of a bed of an electrically conductive solution of a polymer called a gel . If a volatge is applied across the gel, positively charged ions migrate toward the cathode (the negative electrode) while negatively charged ions move toward the anode. Molecules with no net charge do not move. Figure 5 animates the separation of a mixture of glycine, lysine, and aspartic acid at a pH of 6. At this pH the net charge on the aspartic acid is -1, while that on the lysine is +1. There is no net charge on the glycine.
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