We’ll use this module to discuss the basics of protein structure. And again the theme is going to be shape. Let’s look first at the monomers that make up polypeptides, the amino acids. Here are the twenty that are used in all living things to make up our polypeptide chains, and therefore our proteins. Ten of them on the left have a charge, either because their acidic or basic. If they’re acidic, they can lose a proton by dissociation and become negatively charged. If they are basic, that’s arginine, lysine and histidine here, they have amino groups in their side chains that can gain protons and become positively charged. The other 5 in the list are uncharged but polar because they have components in the side chain that contain atoms linked by a polar covalent bonds and therefore have partial positive and negative charges, allowing them to interact in ways we’ll see in a moment. The 10 amino acids on the right are non-polar, largely hydrophobic. And you will see, they tend to aggregate with one another in order to remove themselves from the presence of water. Let’s look at amino acids and then how they form polypeptides. This is a bit of a reminder… If you look at any amino acid you can actually call it a ‘basic acid’ instead of an amino acid (we just don’t think that’s a very elegant term). But as you can see, every amino acid (all of the amino acids here and all the other 16 of them) have a positive and a negative charge at either end. The Germans refer to this as ‘zwitterions’… because that means two ions, because they have an amino group, which has acquired a proton and thus a positive charge, and they have a carboxyl group, which has lost a proton and therefore has a negative charge. These dissociations, or proton acquisitions occur at neutral pH, which is why all amino acids essentially are are ‘zwitterions’. They combine in the cell by the process of translation (which you have heard about and we’ll see again) by dehydration synthesis or water removal to form the polypeptide. The polypeptide backbone show is shown here in grey. What forms between the polypeptides are sometimes called peptide bonds, and I believe the illustration in your textbook says peptide bonds. But they’re really not peptide bonds! They are peptide linkages composed of several different bonds which I have circled here. In fact dehydration synthesis in general doesn’t result in the formation of bonds, but rather of linkages. And finally we talk often about polypeptides with reference to the C-terminal end or the N-terminal end. We say these things in order to say “Oh look there’s a functional component of the polypeptide near the C-terminus or near the N-terminus of the protein”. It helps us to talk about proteins in terms of their function. That is, what I just spoke about was the primary structure proteins. I don’t know if I mentioned it, but the primary structure is simply the amino acid sequence. Let’s talk about secondary structure. First we’ll look at the alpha helix. There are actually two or even three components of secondary structure. We’ll talk about the alpha helix first. So here on the left we have a ball and stick model of a polypeptide which has formed an alpha helical structure because of the ability of oxygens on carboxyl groups to form hydrogen bonds with nitrogen on amino acids nearby. The H-bonds actually form between every other amino acid in a polypeptide. And this is a natural consequence of the primary structure, the natural consequence of the actual amino acid sequence. So here is that alpha helix, illustrated with a ribbon structure to show you the backbone a polypeptide, to track the actual helix. Another major component of secondary
structure are the so-called beta sheets or beta pleaded sheets. Shown on the left is a pleated polypeptide. Here are the peptide linkages, or at least the region where they are. They’re not the linkages in their entirety, because this is only showing the backbone. It’s actually not showing the double-bonded oxygen to the carbon on each amino acid. So you don’t see the whole linkage here. But that’s where they would be. This is one amino acid to orient you so when you look at this on your own you can follow the individual amino acids in this portion of a polypeptide. The peptide linkages are planar. (I wish this illustration would have actually shown that), but the peptide linkages are planar… that is, because they don’t involve a single bond around which every atom can rotate, but rather, 3 bonds; a double bonded oxygen AND the bond between carbon and nitrogen, THAT linkage forms a plane. And so the entire structure of the polypeptide takes on a planar shape. And that’s what that ribbon is supposed to show you. And the result is that the side chains of the amino acids alternate from one side to the pleat (or plane) to the other. Well, when pleated strands like these (two or more of them) line up, H-bonds can again form between the Ns and the O’s in two or more pleated chains to form this pleated sheet. And so I’ve shown you the H-bonds with little red dots, showing you where they would form. So now you see the relative position of the oxygens on the carbons as well. So here’s a model of three-dimensional structure, showing a mix of helical and beta sheet, or red ribbon regions. Sometimes we refer to the regions of polypeptides that are neither helical nor pleated, as random coil. And this is a single polypeptide in which regions of pleated chains are linked together to form a pleated sheet, and interspersed in this polypeptide are the alpha helical region shown in green, and connecting each one of them (so that this is a single contiguous polypeptide), are these random coil regions. What causes proteins to fold into their 3-dimensional, or tertiary structure? Well largely, it’s interactions between the side chains of the amino acids which can be quite distant. Unlike secondary structure which is the result of nearby amino acid interactions, three-dimensional structure can be the result of interactions of side chains of amino acids that are quite distant from one another. So in this model from your textbook, the blue cones are the polar side chains. Again these can be the result of acidic and basic amino acids in the chain which have positive and negative charges because a gain or loss of an actual proton. Or, they can be the result of partial positive and negative charges on the other kinds of polar amino acid side chains. And the green buttons are the non-polar, or hydrophobic side chains. And what happens is that the hydrophobic side chains, because they don’t interact well in the acqueous environment with water, will tend to aggregate and tend to be on the inside, the interior core of a folded chain, leaving the surface to have most of the polar side chains, and therefore can interact well with water. The formation of three-dimensional structure involves a lot above weak interactions. And here are the kinds of interactions (you already know some of them). Ionic bonds (which by the way include H-bonds in essence) can form between opposite charges on either acidic and basic amino acids, or on these polar covalent, partially charged side chains. They can result from the many hydrophobic interactions which are actually the result of these things called Van der Walls interactions. You may remember from chemistry that Van der Waals interactions form when atoms get very close to one another. And that is basically what happens as hydrophobic components of side chains of amino acids get very close to one another in order to thoroughly exclude water molecules with which they cannot interact. So here they are… and this emphasizes strength in numbers. All these interactions individually are very weak, but when you have many of them, the three-dimensional structure proteins for example, is in fact very strong…, so strength in numbers. We can denature proteins, that is disrupt those weak bonds. Here’s urea denaturing a protein. And by denature we mean unfold, basically disrupt all of the Van der Waals forces, the ionic interactions, the H-bonds that are holding this three-dimensional structure together. If you remove urea, which you can do by the process have dialysis, you can sometimes get back the folded protein you started with. The protein would refold. What really happens when you remove the cause of denaturation, in this case urea, is that the protein will fold to its lowest energy conformation, or lowest free energy conformation, which is another way of saying it folds to its most stable state. Sometimes as I said, this could be the original structure of the polypeptide, the original three-dimensional structure. but in fact very often that isn’t the case. And we’ll see in a moment what I mean by that. Okay all this folding to get secondary structure and then to get three-dimensional structure leads to leads to many different polypeptides with many exquisitely different shapes… And again the theme here is shape, shape, shape! These are by the way, computer-generated space-filling models so they don’t look like the ones I showed you before that you could actually purchase plastic balls to demonstrate. But they are intended to show the same thing. The space occupied by the structures of the polypeptide or polypeptide chains, in space. And these are models of real proteins, so you see all the names here. You do not need to memorize these – it’s just to give you an idea of the many different shapes that polypeptides can acquire. The fourth level structure, or quaternary structure is shown here in a model of human hemoglobin, which consists of 4 chains: 2 alphas and 2 betas. So anytime you have 2 or more polypeptides you have quaternary structure. Hemoglobins have a ‘heme’ group, which is an organic molecule that’s not made of amino acids, with an iron in the center. And you may recall that this is the component of hemoglobins that actually binds oxygen. The iron actually binds the oxygen. When a polypeptide or a protein (made of several polypeptides) acquires inorganic or organic (or both) components that are not polypeptides and are not amino acids, we say they have acquired a prosthetic group. Of course the prosthetic group would be necessary for the function of the polypeptide. One of the last things I want to talk about is disulfide bonds which form between cysteines that happen to come close to one another in a polypeptide or even between two polypeptides. So as you can see from this illustration, on the right side actually, you can have interchain disulfide bonds between two different polypeptides. Or disulfide bonds (or disulfide bridges we’ve we sometimes call them) can form between cysteines within the same polypeptide. They form by oxidation and therefore can be disrupted by reduction using reductants. we will probably talk about the use of reductants to fully denature proteins, that is to break the covalent disulfide bridge, which does not break by using urea or other methods of denaturation. We will probably talk about using the reductants to complete the denaturation as a a method to study proteins later on. So here’s our ‘three-dimensional’ model of a polypeptide showing the tertiary structure, but here including some disulfide bridges. I pointed to one but they’re actually… I see 1, 2, 3, 4 of them here. The one I’m pointing to is actually linking two bits of random coil in this polypeptide. But as you can see, disulfide bridges will form whenever cysteines in 2 different regions of the polypeptide get close enough together. The important thing about disulfide bridges is that they stabilize three-dimensional structure. They don’t facilitate it. There’s no attraction between SH groups, the sulfhydryl groups of unoxidized cysteines, but if they come close together as a result of all those other weak interactions, you get this strong covalent bond that then stabilizes the three-dimensional structure. In addition to the structures you’ve seen here, strings of amino acids and even some 3-dimensional structure interactions create structures that we call domains. Originally they were defined as functional domains, that is regions of the polypeptide that perform an identifiable function. So for example the active site of enzymes would be a domain. It’s a region with a very specific structure, intended for very specific interaction. And active sites and enzymes are often formed by amino acids NOT contiguous necessarily, but that fold over and find themselves in the same vicinity, but are not necessarily close to one another if you were to just look at the amino acid sequence. So that would be a functional domain of a polypeptide. So domains often carry out specific functions. It turns out that many different proteins with very different overall functions share conserved domains which means that they share conserved common functions. So we can have a set of proteins, each of which accomplish something different overall, but in order to accomplish it, share a particular domain in common. I just want to show you an example of the domains have a protein. This is the CAP protein, or cyclic AMP binding protein a bacteria. It regulates bacterial operons (and I’d like you to look that up in the text if you don’t remember it). But this is the ribbon-and-helix drawing of such a molecule, and the important thing that I want to bring out here is that there’s a region which binds a cyclic AMP. That’s the cyclic AMP binding protein after all, so it better have a region that does that. That’s the domain on the top. There’s a domain below, which is structurally separate from the cyclic AMP binding domain, and that’s the domain that binds DNA. Because you may remember that the CAP protein is a gene regulatory protein, which in order to function, has to bind DNA in the vicinity of the genes that it regulates. So protein domains are structural units of proteins that often perform specific identifiable functions. And that brings us to the end of this presentation.