Transcription
This slide is showing you the 20 amino acids that um living things use to build all their proteins from. Now there's only a couple things I wanted I want to get on to here.
Firstly, you do not have to memorize all these um so don't worry about that. Uh so but you can see here their names. So um glycine for example is name of amino acid, alanine, valine, cysteine. They tend to end in en. Not all of them, you know, but there's tryptophan down here um glutamic acid over here. But in is is a pretty common ending. Uh and then we also have is because you know we're scientists and we don't like to write a lot um so we have abbreviations for them. We have three letter abbreviations and we even have one letter abbreviations because we want to get real lazy. So for example glycine we use gly and g. Valene we use val and v. So some of them are pretty obvious but they're not all that obvious. So here's tryptophan, its three letter is trp which kind of makes sense. It's um one letter is w and that's because t is already taken by tyrosine. No, sorry, t is taken by threonine which is t. Tyrosine is a y. So you can see it gets complicated because there's 20 of them. So um we spread the letters around. All right, so again, you don't have to memorize those names, you don't have to memorize the abbreviations. I just want you to know that they're there and they exist.
Um now the other thing, if we relate back to our the previous video, you can see on here there is they all have this part in common on every single one of these diagrams. This is the same, doesn't matter which category they fall into, that's the same. Right, I can all the way through here um but what is different for each of these is the r group or the side chain and that's what's being like highlighted on this diagram like here, here, here. The r groups. All right.
Now one other thing that's slightly different here is that they have shown the amino group and the carboxyl group in its ionized form. Now this is something kind of more complex than we really need to get into for 181. So normally this would be nh2 on this, this would be an nh2 here and this would be a c double bond o o h right. Um but when these amino acids dissolve in water, which is kind of how they are in your body most the time because they're floating around in your bloodstream which is pretty watery um what happens kind of to this um oh is the h kind of disassociates or kind of falls off and it sticks over here instead. So you get a c-o-o minus a charge and a h3 plus here. It doesn't really matter for this class at all um but many diagrams show it like this so I just wanted to put that there and just explain it. I don't care how you draw it. If you write nh2 or if you write nh3 plus and co minus or coh, it doesn't matter. All right.
But what is important about this slide is to look at the side chains of all these amino acids. So again, the parts that are like highlighted in this in the colored squares. All right. And uh we categorize amino acids by the nature of their r groups and we can we call them hydrophilic or hydrophobic. And these are terms that you should um already remember from unit one. Hydrophobic things are things that do not like water. All right. And in general, things that are hydrophobic are non-polar. Remember they don't have a charge so they're not attracted to water. So these are amino acids with hydrophobic r groups. All right. That's why it's important that we know that they're um this is hydrophobic. Uh it's important that we note that their side chains are non-polar. Now if we look at these, there's no charges here. It's all cs and hs, cs and hs, cs and hs um lots of cs and hs around here. No um no charges. So if there's no charges or partial charges, then there's no attraction for water. All right. So these are our um hydrophobic r groups over on this side. That these green, the purple and the blue. These have all got hydrophilic. I spelt that wrong. Let me start that off again. High hydrophilic r groups. And what makes the ar the r groups hydrophilic is whether if they have a charge. So we can see here, look, a positive charge, a positive charge, a positive charge or a negative charge. Either kind, positive or negative, either kind of charge is going to attract water. Or even polar. Remember polar is when you have a partial charge, not a complete charge. But over here, oh, that's always going to be a polar group. Oh, nh2, uh nh2, these are all going to have partial charges because if you remember back to unit 1, oxygen is very electronegative, nitrogen is very electronegative. So those atoms are going to be not sharing the covalent the electrons in the covalent bond fairly. You're going to have a mismatch. Um you know, the electrons are going to be pulled to one end and you're going to get a negative cloud and a positive cloud, a positive spot. So all these amino acids, the blue, the purple and the green ones, because of their charges or partial charges on their r groups, those r groups are going to be hydrophilic.
Now sometimes we get sloppy and we say like this amino acid is hydrophobic because it's non-polar or this amino acid is hydrophilic because it's got a charge. That isn't strictly true. Right. So what we're talking about is just the r group part, just this part. Because all of these amino acids, all 20 of them, are hydrophilic because they all have the amino group and the carboxyl group and this is charged and this is charged. So the amino acid of the whole thing of the amino acid is always hydrophilic because of its amino group and its carboxyl group. But when we want to talk about amino acids, we specifically want to focus in on their r groups because that's what makes each one different. And we talk about the r groups whether they are polar hydrophilic or nonpolar therefore hydrophobic. All right. So these, this is talking about the r groups of the amino acids. Are they polar or not?
Now you might think that is very specific and nitpicky and why does it really even matter? It matters a great deal and we're going to get into that when we get to protein structure a couple of slides down the line.