Welcome to this episode of Real Chemistry. Today we're going to be talking about side chains on amino acids. Remember that amino acids are the building blocks of protein, and we're going to quickly learn how to identify amino acids as polar, nonpolar, or charged.
In most cases, this is relatively straightforward if you already know how to identify an organic molecule as polar or not. It can be a little more complicated in a few examples, and we'll highlight those. So first up, recall that the side chains are the part of an amino acid that varies, and they're highlighted in orange here. So this very first side chain we see contains nitrogen and oxygen, things that are going to generally make an organic molecule polar, and that in fact makes our side chain polar. Next up we have an amino acid with only carbon and hydrogen in its side chain, and that's going to make it 9-polar.
Not 9-polar. What's nine polar? It's going to make it non-polar. Maybe I was speaking German. In any case, that might be a little confusing because you might say, hey, isn't there some oxygen up here and some nitrogen up there?
And what that highlights is we're only looking at the side chains. Amino acids as a whole are polar, but we want to identify just what the properties of the side chains are. And that turns out to be important because when you combine amino acids into a protein, then those side chains will actually interact with each other.
And the types of interactions they can do depend on the side chain. Okay, charged is the easiest if you have an amino acid list that shows charges. Okay? And that's the amino acid list I always use because then it's really easy. You just see a charge hanging out.
And if you see a charge hanging out in the side chain, you know it's charged. Okay? If you don't have an amino acid list with those on it, then you may just want to Google one. If you have to memorize your amino acids, then you should definitely memorize which ones are charged. Okay.
So now we got polar, nonpolar, and charged. Let's just go through a few rules to identify those more generally and then do a practice problem. Okay?
Here's all the polar side chains. So the polar side chains, the way we can identify them is that they contain oxygen. So almost always our polar side chains contain oxygen. Notice there's an oxygen, an oxygen, an oxygen, an oxygen, an oxygen. The only exception to that is cysteine.
So cysteine has a sulfur and a hydrogen right on the end of its side chain. And that turns out to be polar as well. So cysteine is polar even though it doesn't have an oxygen. So that's one of those important ones that you might get wrong.
unless you were careful to remember that. So cysteine falls in the category of a polar side chain. Okay, so if it contains oxygen, or if it's cysteine, it's generally a polar side chain.
The only other exception to this is if there's a charge shown. If there's a charge shown explicitly, then that would be a charged amino acid, as we'll see here in a second. Okay, next up is our nonpolar side chains. Nonpolar side chains have a really good rule to identify them.
They just contain all carbon and hydrogen, with two small little itty bitty exceptions. Okay, so in almost all cases. So here we have nine amino acids.
Seven of them contain just carbon and hydrogen. So that's a really good rule of thumb. The two exceptions are methionine. And methionine has a sulfur in the middle of the carbon chain, which is different than our cysteine, which has it at the end of a carbon chain.
So it turns out that that sulfur, being in the middle of a bunch of carbons, gives you a nonpolar bond. And so methionine is nonpolar. The other important exception here is tryptophan.
It has a nitrogen hanging out on it. So you might initially think, oh, that's going to be either charged or are polar, but it turns out that tryptophan is nonpolar. So I would recommend just memorizing methionine and tryptophan.
Those are probably the two trickiest of our side chains to recognize as polar, nonpolar, or charged. Okay, last up are charged amino acids. And again, if you have the right amino acid list that shows the charges, then this is really trivial because all you got to do is look in your chain, and if you see a charge, then you know it's a charged side chain.
Now, this supersedes our rule about containing oxygen. So you will notice if you take close look, some of these have oxygen. And so you might want to be like, hey, they're polar. The truth is they are polar. They're also polar.
But the charged characteristic of the side chain is the dominant feature that's going to determine their side chain interactions. And so we categorize them as charged, though it would be not incorrect to say they're polar and charged. That's totally true. But we categorize these as charged. So here's the five charged amino acids.
Okay, let's quickly identify a few amino acids as charged, polar, or non-polar. First up, our amino acid on the top left. We take a look at it and you might be like, oh snap, there's oxygen. There is, but there's also explicitly a charged drum.
Very often when there's a charged drum, it'll be either like this or something like this. Okay, so keep an eye out. If you see NH2 or COO, definitely take a look for a charge there. So that guy turns out to be a charged amino acid.
All right, sweet. Now let's go to our next one. Here we got oxygen and there's no charge explicitly drawn. So since we have oxygen and there's no charge explicitly drawn, then this is going to be a polar side chain.
So remember that our polar side chains contain oxygen. Or our cysteine. So if you see cysteine in there, then you definitely want to remember to throw that in the polar camp. Okay, amino acid C here has a charge explicitly shown. So again, it's charged.
And lastly, I bet you can guess by the process of elimination what this one will be. Here we have only carbon and hydrogen. And so that's going to make this nonpolar.
So that's just a brief introduction to thinking through the properties of side chains, which we'll build on in a future video where we look at side chain interactions. Thanks for watching this episode of Real Chemistry.