Leah here from leah4sci.com/mcat and in this video, were going to look at the non-polar
hydrophobic amino acids. There are nine non-polar water faring amino acids and they include
glycine,alanine,valine,leucine,isoleucine,methionine,phenylalanine,tryptophan and proline. There are two more cystine and
tyrosine that are polar hydrophobic but we'll discuss that with the polar amino acids in
the next video.
Remember, for the mcat, you will have to know the name, the three letter and one letter
abbreviation as well as the structure for the r-group. Here's how I recommend memorizing
them. Cut up a piece of paper and write the amino acid name on the front, on the back
put the structure, the three and one letter codes and the fun fact about each one. Keep
these in your pocket and look at them every time you have a free second and every night,
write them, draw them again and again until you have it memorized.
The first amino acid we'll look at is glycine which is "GLY" or "G". Even though you have
to know the twenty common amino acids, recognize that there are only nineteen r-groups. Since
glycine has a hydrogen for its variable group, that's not actually a variable group, it's
just a hydrogen atom. We expect to have carbons and more on the regular r-groups because glycine
has a hydrogen side chain, the molecule is achiral. That means we don't have "R" and
"S" and therefore don't have D and L. This is the only achiral amino acid because remember
for chirality, You have to have a central carbon with four unique substituents but here
we have two hydrogen atoms and that means we have total of three unique, the amino,
the carboxyl and two hydrogen atoms. Notice for presenting amino acids in the dipolar
or zwitterion form because this is how it will exist at physiological pH. To learn more
about that, see the Zwitterion tutorial link below.
Because the glycine is so small, it's an ideal amino acid to put on the inside of twist and
bends and anywhere you can't squeeze a large side chain. Just imagine taking a three year
old kid and squeezing him between two adults on the couch or in the car, an adult can't
fit there but a tiny kid can easily squeeze in. Alanine which is "ALA" or "A" has a metal
group for each side chain. The metal group is considered linear, that makes it an aliphatic
side chain which refers to a non aromatic hydrophobic group or simply a linear side
chain. Alanine is also considered a small amino acid because CH3 is tiny compared to
a lot of the bulkier group we're gonna see later on. Alanine is a very interesting amino
acid and provides the bridge between amino acids and metabolism. Alanine can be converted
to pyruvate and pyruvate to alanine through transamination and that means if we need to
create amino acids from metabolic pathways or digest amino acids for energy, alanine
is the route to do this and alanine provides us that connection between glycolysis, gluconeogenesis
and even the citric acid cycle.
Valine which is "VAL" or "V" has a small brand side chain. I wrote it on line structure but
recognize that we have a Ch connected to the alpha carbon which is a backbone carbon and
the Ch is holding two methyl groups. The way I remember the structure is that the isopropyl,
this substituent is an upside down V. Even though it's a small side chain, the fact that
it has a branch on the carbon directly attached to the parent makes it bulky and valine doesn't
like to be inside alpha helices because the alpha helix is a tight turn and the branch
just doesn't play nice.
Lets look at the next to amino acids side by side. Leucine and isoleucine are both aliphatic
side chains because they have just carbons and hydrogens. If you look at the substituents
you'll notice that each one has four carbon atoms and that makes them constitutional isomers
of each other. Remember that constitutional isomers refers to molecules that have the
same molecular formula meaning the same number of the atoms but they differ in their connectivity.
Leucine which is "Leu" or "L" has and isobutyl side chain. Notice it has that isopropyl group
that we saw on valine but with an added Ch2 connected in between the isopropyl on the
parent this makes it not an isopropyl but an isobutyl side chain. Isoleucine which is
"Ile" or "I" is an isomer of leucine specifically a constitutional isomer. It has the same four
carbon substituent but this time, instead of having a branch at the end, all four are
connected in a row where the substituent itself is attached on the second carbon to the parent
chain and this secondary carbon attachment tells us that this is a sec butyl substituent
which is an isomer of isobutyl.
Another interesting fact for isoleucine is that in addition to having the chiral alpha
carbon, it has a second chiral carbon in the r-group itself. This chiral carbon has an
invisible hydrogen atom, a methyl group and ethyl group and the entire parent backbone.
Methionine which is "Met or "M" is very important amino acid. It's considered an aliphatic,
non-polar hydrophobic side chain even though it has that sulfur atom, this sulfur group
makes it a thioether because think about it and ether is "ROR" and thio tells us sulfur.
But with sulfur bound to carbon, the difference in polarity is not significant enough to make
is reactive with other groups and that keeps it non-polar. You'll see sulfur on cysteine
is a lot more reactive because it's "Sh" rather than S bound to two r-groups. If you look
at the way the substituent is written, it almost looks like the letter "M" . To help
you memorize the one letter code for this is the letter "M". Methionine is just one
of two amino acids that have sulfur in its r-group, the other being cysteine and this
allows us to differentiate between amino acids or proteins compared to nucleotides in DNA
and RNA which don't have any sulfur but they do have phosphorous. And even more important
to amino acids is that methionine is used as the start code on when you're translating
from MRNA into a polypeptide ultimately into a protein. Phenylalanine is "Phe" or "F".
It's not the letter "P" because that's proline and since the Phe has the F sound, phenylalanine
gives us "Fa" or "F". Notice that we have an arene or a benzene ring in the side chain.
This gives us the first aromatic side chain. Remember aromatic groups are hydrophobic because
you have mostly carbons and hydrogens interacting with each other with no polarity to interact
with something like water. Think back to naming aromatic compounds, you learned to have having
a benzene rings in two important substituents.
If you had an r-group with just benzene attached, that substituent was called a phenyl group.
If you had an r-group with the Ch2 and attached to that CH2, you had a benzene ring, this
was called a benzyl substituent. Phenyl has six carbons, benzyl has seven carbons because
we include the Ch2. The substituent for phenylalanine is technically a benzyl substituent but the
name phenylalanine lets you remember that it's a phenyl group sitting on alanine. Remember
alanine was just one carbon CH3, remove one of those hydrogens to allow for a new bond
and we get a CH2 bound to a phenyl group for phenylalanine.
Tryptophan, "Trp" or "W" has the largest and most complex r-group. I know that it's hard
to draw but remember the mcat is multiple choice so as long as you recognize that this
is the only amino acid with a bicyclo, aromatic compound, you'll know that it's tryptophan.
This is the amino acid that is blamed for making you sleepy after eating turkey and
the way I remember that it's Trp or W is I think of, if you're really tired, you can
trip and if you trip you might drop things so you say "Whoops". This entire thing is
an indole group but if you look at the smaller rink you'll notice that we have a nitrogen
bound to hydrogen which looks like it should be polar but it's not really, yes nitrogen
is partially negative which would make hydrogen partially positive except for the fact that
nitrogen's electron are too busy participating in resonance to be interested in interacting
with outside groups. If you refer to the aromaticity tutorial link below, you'll see that when
we have hetero cyclic compound, if the electrons are needed resonance, they're used. If they're
not needed, they're not used. In this case, the only way for nitrogen to participate on
resonance is to take these electrons and resonate them either right or left in the ring. This
is what makes it aromatic and this is what also makes it non-polar. Add that to the fact
that the NH is a tiny portion of the overall molecule and we can safely classify this as
a hydrophobic aromatic side chain.
Proline which is "Pro" or "P" is an interesting amino acid. In addition to having the substituent
attached to the alpha carbon, we actually have to remove one of the hydrogen atoms in
the backbone so that the substituent can swing around and attach back to that nitrogen. The
way I remember this is that the letter P swings around to attach back to the parent just like
the backbone swings around to attach to the nitrogen atom. Nitrogen still has a total
of four bonds, one to the r-group, one to the backbone carbon and 2 hydrogen atoms.
So nitrogen still has a positive charge even though it has two rather than three attached
to the hydrogen atoms. Proline is a very important structural amino acid in a polypeptide chain.
A regular chain can have amino acids attached to the carboxy and more attached to the nitrogen
group to form a linear chain that you can then twist and bend as needed. Proline, because
of that ring actually forces a kink into the chain. It forces the group to be pushed towards
each other and a way on that ring in the r-group and that means it can't be in a linear polypeptide
so you'll typically see it where you need a sharp bender twist in the grand scheme in
the tertiary or Quaternary structure of your protein.
This concludes the non-polar hydrophobic amino acids, be sure to watch the next video where
we look at polar including neutral acidic and basic. You can find this entire video
series, along with the amino acid practice quiz and cheat sheet by visiting my website,
leah4sci.com/aminoacids.