Hydrophobic R-groups – Amino Acids

00:00 What I would like to do now is go through and describe each of the amino acids and point out some salient features of them as appropriate. The aromatic group of amino acids includes tyrosine, tryptophan and phenylalanine. Now, I've marked on the tyrosine, the locations of the alpha carboxyl, the alpha amine and the alpha carbon, and remind you again that the hydrogen is projecting above but not shown in this image. Tyrosine is noted has a hydroxyl group attached to the end of benzene ring. Tryptophan is notable for being an amino acid that has the largest R group, contains a benzene ring attached to another five-member ring as you can see here. Now this very large bulky group that's on tryptophan, tends to be a limitation in terms of space within a protein. The bulky R group can cause the protein to have to twist and turn, and accommodate that larger structure as a result. Phenylalanine has a simple benzene ring.

01:03 Now what I've also done on this slide is I've marked at physiological pH, the charges that appear on each molecule. You'll see that in each case the alpha carboxyl has a negative charge because it has lost a proton. In each case, the alpha amine has a positive charge because it is retaining a proton. The pKa of the alpha carboxyl group is about 2, physiological pH of course is about 7.4. The pKa of the alpha amine group is about 9, so for this reason the alpha amine retains the proton and the alpha carboxyl has lost its proton. Now one note about tyrosine and that is that the hydroxyl at the end of tyrosine can ionize at a high pH, this pH is above that of the physiological range however.

01:52 The second group of amino acids that I want to talk about are those that contain aliphatic R groups. In this case I've marked again in the green squares each of the R groups as they are contained in each amino acid. Focusing on glycine for example, we see glycine has an unusual R group, and that it only contains a hydrogen. Glycine therefore has the smallest R group of any of the naturally occurring amino acids in proteins, but because it contains an R group hydrogen and it also contains the hydrogen that's attached to the alpha carbon, it means that there're only three different things attached to the alpha carbon of glycine. For this reason glycine is the only amino acid of the 20 that's found in proteins that does not have a stereochemistry.

02:44 The next amino acid that is of interest is proline. You can see the proline has an R group that goes off of the alpha carbon, but it also comes back around and connects with the alpha amine as you can see forming a five-member ring. Now this connection at two points limits the ability of the R group of proline to rotate. If you look at all of the other R groups of all of the other proteins, you'll see they only have a single bond and can freely rotate.

03:14 Proline is constrained by the second bond that it's making with the alpha amino group and as a consequence, proline cannot rotate its R group, meaning that proline is a much more inflexible amino acid. Now this has some implications for bending that actually happens within proteins as we will describe later.

03:35 The next three amino acids isoleucine, valine and leucine are similar in containing R groups that have carbons and hydrogens and mainly rearrangements of those as you can see.

03:49 The last amino acid as shown here is methionine, and methionine is of interest because methionine contains sulfur. It's one of only two amino acids that contain sulfur and the sulfur is attached to two different carbons as you can see in the grouping here. That attachment to two different carbons means that the sulfur in methionine is very unreactive and doesn't do much, this is in contrast to the sulfur that we will see in cysteine.

04:16 Now, if we look at the charges at physiological pH, we can see that none of these amino acids have R groups that ionize and like we saw before the alpha amine has a plus charge in each case and the alpha carboxyl has a negative charge. Each of these amino acids at physiological pH would have a charge of zero.

04:39 The next two amino acids are those that are ionized, and they contain in their R groups, carboxyl groups. They include aspartic acid, shown on the left and glutamic acid, shown on the right. These two amino acids are virtually identical to each other with the exception that glutamic acid contains one extra carbon compared to aspartic acid. At physiological pH we see here that the R group ionizes, and this is because that the R group for these two amino acids has a pKa value of about 4, meaning that at a physiological pH of 7, the proton on the carboxyl group is lost, leaving the molecule with a net negative charge on the R group. The overall charge of each of these amino acids at physiological pH is -1.