Proteins

Structure of Proteins

As you 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 make:

	The amino acids that could be in a polypeptide 10 amino acids long
Polypeptide 1	aa1	aa2	aa3	aa4	aa5	aa6	aa7	aa8	aa9	aa10
Polypeptide 2	aa3	aa17	aa11	aa5	aa3	aa19	aa1	aa14	aa10	aa17
Polypeptide 3	aa12	aa6	aa10	aa9	aa7	aa13	aa20	aa20	aa16	aa2

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.

appearance of the protein ovalbumin 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 coil regions.

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 that!

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. tertstruc.jpg (11818 bytes)

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 structure.

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 reactions.

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 other cells.

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???

� 2006 STCC Foundation Press, content by Dawn A. Tamarkin, Ph.D.

Structure of Proteins

Putting amino acids together to begin to build a protein...

Proteins can have four structural levels

Function of Proteins

Last changed: January 21, 2007