Highlights Lecture #4 Spring 2017

Amino Acid Highlights

1. Amino acids are the building blocks of proteins. They all contain an alpha carboxyl group and an alpha amino group. The carbon attached to the alpha carboxyl and the alpha amino group is known as the alpha carbon.

2. All amino acids except glycine have four different groups attached to the alpha carbon. As a result, all amino acids except glycine have at least one asymmetric carbon – the alpha carbon. We call a compound with such an arrangement ‘chiral.’ The two chiral forms of amino acids are called ‘D’ and ‘L’. If one uses ordinary chemistry to make amino acids, mixtures of D and L are always produced. However, cells use enzymes to make amino acids and those enzymes always give the same configuration – L.

3. Glycine is the only amino acid with no asymmetric (chiral) carbon because it has two hydrogens attached to alpha carbon.

4. Only L amino acids are found in proteins formed biologically. We can think of D and L forms similar to left and right hands. Indeed, sometimes the two possible forms are referred to as ‘handedness’. Handed molecules like D and L alanine are mirror images of each other. Simple amino acids with only one asymmetric center will always have D and L forms as mirror images of each other.

5. Twenty amino acids are commonly found in proteins. The properties of the amino acids are determined by the composition of the R groups on each of them.

6. Amino acids with non-polar side chains can be amphipathic (amphiphilic) because part of them is hydrophobic (water hating) and part is hydrophilic (water liking).

7. Amino acids are grouped according to the properties of their R groups. You are responsible for knowing the names of the 20 amino acids, the groups they belong to as shown in class and the composition of any groups with ionizing side chains. (as a side note – please realize that there is nothing absolute about the groupings of amino acids. Many people have many different ways of chemically grouping amino acids. We use a simple scheme here, but there are other ways of grouping amino acids.)

8. So-called acidic amino acids have carboxyl groups (COOH/COO) in their side chains. These include glutamic acid and aspartic acid. Loss of a proton from the side chain causes the side chain to be charged negatively. Gain of the proton causes the side chain to have no charge.

9. Amino acids with amine-containing side chains (arginine, lysine, histidine) have groups that vary in charge from +1 (proton on) to 0 (proton off). Loss of a proton from the side chain causes the side chain to have no charge. Gain of the proton causes the side chain to have a positive charge.

10. Proline is an amino acid with a ring structure as part of its side chain AND its alpha amino group. It is the only amino acid with an alpha amino group that is not a primary amine (it is a secondary amine).

11. Cysteine is the only amino acid with a sulfhydryl group. Methionine also contains sulfure, but not in the form of a sulfhydryl group, since the sulfur is attached to two carbon atoms.

12. Some amino acids are modified after they are incorporated into proteins. The best examples are hydroxylysine and hydroxyproline. Both of these amino acids are found in the protein called collagen. Thyroxine is a modified form of tyrosine found in the thyroid gland.

13. Because amino groups and carboxyl groups can gain or lose protons, amino acids can have a variety of charges.

14.The pI of a molecule is the pH at which its charge is exactly equal. A molecule containing plus and minus charges but with a net charge of zero is known as a zwitterion.15. Peptide bonds are the covalent bonds that join together individual amino acids within a protein. Peptide bonds are formed in a reaction in the ribosome in which the carboxyl group of one amino acid is joined to the amino end of another amino acid. Proteins always have a free alpha amino end and a free alpha carboxyl end.

16. Calculating the charge on a polypeptide is simple. One simply tallies the charge of the alpha carboxyl group, the alpha amino group, and all of the R groups. This is why it is important to know which amino acids have R-groups that ionize and how they ionize. Note that the internal carboxyl/amino groups are destroyed in making the peptide bond and do not ionize.

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