Transcription
Okay, so to start with, we're going to talk about how proteins uh fold up into their correct shape. And it's like a stepwise process. It's a bit like origami. In origami, you start with a flat sheet of paper, and you can't just fold it immediately into some beautiful crane or whatever shape you want to make. You have to go through stages and steps to get to the final product. And that's the same with protein folding. There are these stages, and they, they are termed um, the primary, primary, secondary, tertiary, and quaternary. That means first, second, third, fourth. So let me just write those out. Primary, secondary, tertiary. This means third. It always kind of throws people because it looks like it's spelt strained. Tertiary. And the fourth. This is right. So in this uh slide, these few slides, I'm going to go over one and two, primary, secondary, and then we'll do tertiary and quaternary on the next slide.
Um, all right. So primary protein structure. What the primary structure is talking about is very simple. It's just the order in which the amino acids appear in the chain for the protein. So on this slide here, the primary structure is just shown by the beads and the string. All right. Now, if we look at this diagram off to the right, it's a little bit clearer. This is, I think this is supposed to be hemoglobin. And here you can see the order in which the amino acids are placed in in the chain. Lysine, valine, phenylalanine, glycine, arginine, cysteine, glutamate, leucine. So, um, that's the primary structure, just the order of the amino acids in the chain.
Now, although it's very simple to think about primary, it's actually the most important level because if you just get one of these amino acids order wrong, like maybe there's this alanine here, there's something different, that maybe there's a phenylalanine there instead, that's a different order, that makes a different protein, basically. And so it will probably fold up in a different way. And if the folding up is different, and the shape, the final shape is different, then your tool won't work, and then you might have a problem. So although this seems simple, just the order of the amino acids, getting that order right is absolutely vital to the proteins being out at work correctly in your body. And we'll learn about how that order is maintained in unit four in 181, so in a couple, in about a month, month and a half's time. Uh, but for now, we're just going to say they're in the right order. So that's the primary, primary structure.
Now, the secondary level of structure, um, I'm going to describe it here, and then I'm going to clip over and I'm going to show you with my little model here. So I'm going to try something fancy with my video. We'll see if it works. So secondary structure. Secondary structure comes in two main types: an alpha helix, and that's this picture on the left, and a beta pleated sheet, and that's the structure on the right. So, um, two different forms. Um, and an individual chain can have bits of both of these forms in it. Now, um, I'm gonna flip over first of all to my video. So let's see if this is going to work. [Music] Hopefully I'm not going to shock you here. Here I am. Here I am. All right. So, uh, first of all, here's my chain. And so this is the primary sequence of my protein. It goes, um, if you can see this, um, yellow, dark pink, light pink, brown, yellow, blah, blah, blah. So if these all have names, they'd be the individual amino acids. All right. So primary. The next, I'm going to give this some secondary structure. So the first form of secondary structure is the alpha helix, and that would be me making this kind of coil up. So I'm making it like a little coil, like a spiral. All right. Now, when I make a coil in it, like I just did, um, you can see how the beads, which are the amino acids, are kind of stacked up one on top of the next, right? And if you remember on the, um, one of the other presentations, we talked about between each bead is a peptide bond, right? And the peptide bond is the, the C attached to the N and the double bond O and the H with the partial charges. All right. So, uh, think about that. And I'm gonna, um, slide back here a second. All right. So back to this slide. Okay. So here is a peptide bond, C double bond O, N H, all right, between amino acid one here and amino acid two here. Here's a bead, here's a bead, and here's the connection between the beads. Now, when you spiral them together, here's another bead and another bead, and the connection between them, and the connection between the next one. And when you stack them together like this, the peptide bonds between the beads line up so that the partial positive on this hydrogen is attracted to the partial negative on this oxygen sticking up from the layer underneath. So let me use some color there just so you can see it better. So this is a bead in the top layer. This is the bead in the next layer down of the spiral. But when you stack them like that, the peptide bonds align themselves up, and you get this between the partial positive from one layer and the partial negative from the layer underneath. So this should look familiar to you. Dotted line between partial charges. What is that? I'm gonna write it. Let's see if you can think about it before I write it. It's a hydrogen bond, right? So what holds this spiral in place? And I'm going to flip back to me again. So heads up, don't get shocked. Um, what holds this spiral in place is hydrogen bonds happening between these layers that are happening between the partial charges on the peptide bonds between the amino acids. So there's a partial charge between this dark green and this light green bead, and there's a partial charge between this black bead and this yellow bead, and they're attracting across this distance between the two layers. So that is what holds together the alpha helix. It's hydrogen bonding that occurs between the partial charges on the atoms of the peptide bond. I'm going to write that down because that's kind of complicated, huh? So hydrogen bonding that occurs between the partially charged atoms of the peptide bond. All right.
So the beta pleated sheet. The same thing is going on, right? It doesn't look very similar. But let me clean this up because this is scary looking. Um, on my beta sheet here, uh, what it's not really showing is that this, these strands are kind of going up here and then down here and then up here. It's snaking like a, like a line at Disneyland. Like if you're in line at Disneyland, they, you know, you up in a straight line, you snake. You up in a snake. So if I take my thing, it's hard to do vertically, but if I was to snake it up and down like this, they all kind of lie flat side by side, kind of like that. They're going up and down, and they're all sort of making a sheet. All right. And then the same thing happens that happened in the coil. Instead of being coiled on top of each other, they're lying side by side now. But you can still get the same hydrogen bonds between this, between this, between this, and between this. All right. So that's what is being shown. Uh, let me get my video off again. That's what's being shown here. So you can see there's hydrogen bond there between this positive, uh, slightly positive H and slightly negative O. Hydrogen bond here, hydrogen bond here, hydrogen bond here. In every situation, between the peptide bonds, you get this hydrogen bond attraction which holds the sheet in place. And what happens in reality is that once again, I'm going to bring myself back. Um, on a single protein like this, you might get a little bit of helix and then a little bit of sheet, and then a little bit more helix at the end or whatever. So you can get a mixture of these, um, shapes in a single folded protein. We'll see some examples of that in just a little bit. So that's primary and secondary protein folding.