Hydrophobic R-groups – Amino Acids

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.