Structure of Proteins
have already read, amino acids (one is shown to the right) are the
monomers of proteins. Amino acids are composed of a central carbon atom (in
black) attached to four groups. One of the groups is simply a hydrogen atom (at the
bottom in green). Two other groups you have already learned about, the carboxyl
group is in navy blue (on the left side), and the amino group (for which this molecule is
named) is in purple on the right. Finally, there is a special group, called the
"R" group is at the top. I'll explain that in a moment.
When amino acids join together, they link up so that the carboxyl
group of one amino acid bonds to the amino group of another amino acid. This would
be like adding them on the right and left sides of the drawing above. The amino acid
is the first molecule you have learned about that contains the nitrogen atom... this makes
it rather special because we can only get nitrogen atoms through our diet. Believe
it or not, our air is mainly composed of nitrogen gas-- but our bodies don't know how to
use the nitrogen in the air, so we just breathe it in and then breathe it right back out
again. We have to eat our nitrogen.
The R group is very special because it isn't really any one group.
Instead, it can be one of 20 different groups. If it is one particular R
group, then it is a particular amino acid. And if it is a different R group, then it
is a different amino acid. That means that there are 20 different amino acids, each
with a different R group. Each amino acid even has its own name. But all
20 have a central carbon with a carboxyl group, hydrogen atom, and amino group off of it.
You do not need to know any of the individual amino acid names, just that there are
20 of them. Since there are 20 different amino acids, that would be
represented by 20 different colors of rectangles in my little boxcar
example. That's a lot!
Putting amino acids together to begin to build a protein...
We combine amino acids into chains, just like I showed you with the
boxcar example. The chains of amino acids are called polypeptides.
I want you to begin to think of the variety we can have in our polypeptides.
Let's start off by thinking about a polypeptide built from 10 amino acids. Keep in
mind that there are 20 possible amino acids that we can use to build this
polypeptide. If I refer to the 20 amino acids by a numbering system, I could call
them aa1, aa2, aa3, etc., ...up to aa20. Look at some of the polypeptides I could
||The amino acids that could be in a polypeptide
10 amino acids long
Do you see how many possibilities there are for making polypeptides? In fact, if
you understand math, you'll see that there are 2010 possibilities for a
polypeptide that is 10 amino acids long. Most polypeptides are hundreds or thousands
of amino acids long, so there can be even more variety in those.
We do not define a protein as a polypeptide (we were able to call a
polysaccharide a carbohydrate, though). The reason is because some proteins are
actually built from combinations of polypeptides. You see, proteins are defined by
their function. The protein called melanin, that is our skin pigment protein, is
defined by its color-giving properties for skin. If a protein requires two
polypeptides to function, just one of those polypeptides alone won't do anything and isn't
considered a protein. Therefore, to understand what a protein is, we really have to
see what happens with the polypeptides we build.
Proteins can have four structural levels
You have already learned about the first one. I'm going to
describe them to you a bit more. However, before I do that, I want to explain this a
little more to you. Since a protein is defined by its function, and protein function
depends on protein shape, each protein is going to have to have a particular shape.
Some functions of proteins are listed below. One of them, for example, is to allow
cells to attach to one another-- I hope that you can imagine that for one cell to stick to
another, the proteins on the cell surface have to be able to grab hold of one
another. That means that they have to have a particular shape for sticking to each
other. Keep in mind that we are going to have to take the chains of amino acids and
fold them into particular shapes.
|Primary structure-- you have already learned this one without knowing it. The
primary structure of a protein is the number of amino acids in each polypeptide, as well
as the order of the 20 amino acids within that polypeptide. Each of the three
polypeptides I drew above had the same number of amino acids, but a different order of the
20 amino acids within them, so each had a different primary structure.|
|Secondary structure-- I'm sure that you figured out that the polypeptide chain cannot
stay long and straight-- it has to bend or twist up a bit. Well, this bending and
twisting has a couple of parts to it. The part that the secondary structure does is
the initial bending or twisting. There are three such ways that your book describes
in Figure 4-10 for the secondary structure to occur:
|alpha-helix. This is a coiling up like a Slinky or spring.|
|beta-pleated sheet. This is a fan-shaped bending.|
|random coil. This is when you can't describe any real pattern to the folding.|
In this picture, you can see
all three types of secondary structures. This is a picture of the protein ovalbumin,
which is made up of one polypeptide chain. The pink areas are the regions along the
chain that are alpha-helixes. The yellow regions are the beta-pleated sheets.
And the whitish regions have no clear order to them, so they are considered the random
I made this image using a free program called RasMol. It is
distributed through UMass to the entire world, and allows scientists to look at just about
any protein that has been described to see its shape. This program even lets you
spin the molecules around in 3-D. Pretty cool, huh?
Ovalbumin, by the way, is a protein in egg whites. So you
probably eat this protein all the time!
Finally, you can see that this protein also
folds on top of itself... that is part of the next level of protein
structure, the tertiary structure. Keep reading to see about
|Tertiary structure-- This is the next step in the bending. Consider a polypeptide
that has a unique primary structure and is bent into an alpha-helix shape with its
secondary structure. Now you have something that looks like a
spring. You could bend that spring, fold that spring, even really tangle that
spring. If any of you ever experienced what happens when two people pull a Slinky
out as far as possible and then both let go-- you know that knotted mess you end up
with? That would be a tertiary structure. Based on an alpha-helix shape, I
drew the three different tertiary structures you see to your left.|
The blue one is where the coil-shape was bent onto itself.
It almost creates a tube in its middle. The green and the purple shapes are a bit
more irregular. But if you imagine that the polypeptide chain itself could be
really, really long, you can come up with many more possible shapes. And this is
when the secondary structure is just an alpha-helix. It could also be a beta-pleated
sheet and get folded or have random coils and get folded. You could even squash it
all up on itself for the tertiary structure. Can you see the tertiary structure in
the ovalbumin protein above?
|Quaternary structure-- This structure does not exist for all proteins. You see,
quaternary structure is when there is more than one polypeptide in a protein. Each
polypeptide has to somehow interact with the other polypeptides, and this gives a final
structure to the protein. If a protein is made up of only one polypeptide, then,
obviously, it only has three structures (no quaternary). Ovalbumin has no quaternary
Be sure to look at the figure in your
book where it
describes all the structures of a protein.
Function of Proteins
Here is a list of some of the functions of proteins.
For each one, the shape of the protein is critical for its function. Some of
these functions are included in your book text, and others I have added in so that you can
understand proteins better. Because there are so many possible shapes for proteins,
proteins can serve many, many functions. They do a lot more than the other
macromolecules... so if you are ever unsure about what kind of molecule does a particular
thing, and it doesn't have to do with energy production or your genetic code, the best
guess is always: protein!
|pigmentation-- like the melanin in your skin or the pigment in your iris|
|enzymes-- these are proteins that help to promote a chemical reaction. You know
how all living things are continually undergoing chemical reactions, right? Well,
somehow, our cells have to know which are the correct chemical reactions to have occuring
at any particular moment. Enzymes help us to only carry out the appropriate
|structure-- proteins have many roles in structure.
|cellular structure: proteins make up our cytoskeleton-- our cell skeleton-- that
gives our cells shape, as well as enabling movement (see next item in list)|
|other structure: the protein called keratin is the one that makes up the bulk of
your hair and nails, giving structure to these items.|
|movement-- it is only because our cells have protein cytoskeleton's that our cells can
move. As long as our cells can move, we can move, too.|
|carriers-- lots of things have to travel through our blood. Many of those things
are hydrophobic, like steroids and oxygen gas. So we have to wrap those hydrophobic
things up in something that can interact with water (like a little hydrophilic coat), and
that something is a carrier protein. Like hemoglobin.|
|channels-- protein pores that run like tunnels across the lipid bilayer will allow
specific materials that we need, like glucose, to slip through the membrane.|
|cell attachment proteins-- these face the outside of the cell membrane and allow the
cell to stick to other cells or to non-cellular material in the outside world.|
|receptors-- these face the outside of the cell and recognize chemicals like hormones
that pass by. They enable cells to notice chemical signals from the blood and from
The above list is not complete. It is also not intended as a memorization list--
just as a list to help you "get" the idea of what a protein can do. Can
you believe how diverse protein function is???