Proteins are part and parcel of what makes
life possible. The diversity of the building
blocks of proteins compared to other macromolecules
give proteins a rich and diverse array of
functions. In this lecture I will talk about
proteins starting with the building blocks,
the amino acids that make them up and divide them
into various groups, essential or nonessential
depending upon whether or not they can be
made by the organism. I'll discuss the basic
structure and stereochemistry of each amino
acid and how the side chains of each amino
acid give it the individual characteristics
that it have. Last I'll give the properties
and talk about the ionization of the amino
acids found in proteins.
Proteins, we can describe as the workhorses
of the cell. They perform all the essential
functions that cells need to stay alive. These
include catalysis, catalyzing of the reactions
that happen, signaling the process whereby
cells and part of an organism can communicate
with cells in another part of the organism.
The structure of proteins such as the fibrous
proteins found in our hair and our nails arises
from interesting features within individual
protein molecules. Last, proteins are very
important for the generation, creation and
storage of energy. All proteins on earth are
comprised of about 20 amino acids. The 20
amino acids are most commonly found in every
organism on earth. A 21st amino acid known
as Selenocysteine, in some cases found in
a few rare proteins.
Amino acids can be divided into various categories,
one of the categorization schemes is divide
amino acids into essential and nonessential groups,
depending upon whether or not the organism
can synthesize the amino acid within its cells.
Essential amino acids are those amino acids
that the cell needs to have in its diet because
it can't make those itself. Nonessential amino
acids are amino acids that cells can synthesize.
Now, the categorization of essential versus
nonessential varies from one organism to another
and it even varies a little bit with the age
of the organism, for example, humans have
different essential amino acids as adults
than they do as children.
Amino acids that are found in proteins we
call alpha amino acids, and they get this
name because every amino acid that's used
in proteins has a special carbon call the
alpha carbon seen here in green in the center
of the schematic diagram. All 20 of the amino
acids can be drawn in the same schematic scheme.
Now there is nomenclature that I want to go
through here that will help you to better
understand the amino acids in the proteins.
Every alpha carbon is attached to an alpha
carboxyl group, as shown here. And every alpha
carbon is also attached to an alpha amine,
these two giving the alpha amino acids their
name. The alpha carbon is in addition attached
on the top to a hydrogen as you can see here
and on the left to an R group. The R group is
what gives an amino acid its characteristic,
functions, shape, structure and properties.
Now, to show you an actual amino acid according
to the scheme that we're using here, I want
to show you cysteine. So if we look at the
organizational scheme on the right that was
on the last slide and compare to cysteine,
we can see for example the various things.
For example, cysteine has an alpha carbon
as seen here, an alpha carboxyl group, an
alpha amine and an R group that in this case
contains a sulfhydryl. Not shown on this figure,
but present on the alpha carbon is a hydrogen
above the alpha carbon.
Here is phenylalanine. Phenylalanine for example,
has an alpha carbon, an alpha carboxyl an
alpha amine and it has a side chain and in this
case contains a benzene ring. Again, the alpha
carbon contains a hydrogen above it.
Because the alpha carbon is attached to four
different groups it gives the alpha carbon
some properties that are important to understand.
You learned in organic chemistry for example
that if a carbon has four different molecules
attached to it, that there are two ways in
three-dimensional space that those atoms can
be organized around the alpha carbon.
This shows for example the sugar D-glyceraldehyde
and L-glyceraldehyde, two different forms
of a sugar that contain a carbon that have
four different groups attached them.
This is known as an asymmetric carbon and it’s
shown in the green circles seen here.
Now there are four different things attached to
this and because of this, there's two ways
that they can be organized. I've drawn the
blue and the yellow arrows to show how it
is that two groups, for example, are organized
here. We can see under the blue arrow on the left
that the gray ball is projecting towards the
viewer whereas the orangish ball in the back
is projecting away. In the L isomer, these
two positions are reversed, we see the orange
ball coming to the front and the gray ball
moving to the back.
Amino acids also are designated by the D and L designation
that are used for sugars. Interestingly, almost
all of the amino acids made by living cells
are in the same configuration, that
of the L configuration. Now, this is interesting
because if you take for example, a test tube
and you make amino acids chemically in a test
tube that are not being produced by the enzymes
of a cell, you get a mixture of 50% D and 50% L.
The reason that we get only L exclusively
in living cells is because living cells use
enzymes to make amino acids, and those enzymes
have a three-dimensional specific structure
that will only allow the synthesis of one
of the two different forms being present.
Now this turns out to be really interesting
and useful because we can then tell if we
analyze an amino acid whether it has a mixture
of D and L, or only L, or only D for that
matter, because a bias one way or the other
would suggest it was made by an enzyme and
therefore made by a living cell. This is used
for example when meteorites fall to earth
and they contain amino acids and scientists
are very interested in understanding, were
those amino acids produced biologically, or
produced by natural chemistry.