Proteins and Amino Acids - Online Tutor, Practice Problems & Exam Prep

Peptides and Polypeptides

Life on Earth is composed of 4 major macromolecules. These macromolecules are called sugars, lipids, nucleic acids, and lastly, proteins. Now, of these 4 macromolecules, the ones that really do the heavy lifting and build practically every single part of your body are proteins. In fact, whether you're talking about a liquid or solid part of the human body, pretty much every single part of the human body is going to have some proteins in it. So in this video series, what we're going to do is we're going to take a deep dive into the world of proteins with the help of a little bit of organic chemistry. So let's go ahead and get started. And let's start with the most basic idea, what is the definition of a protein? Well, the definition of a protein is simply a polypeptide that has some kind of biological function. And the joining of these two ideas is really important. So if I just go to the lab and I created a polypeptide through some reactions but it doesn't do anything in the human body or in any kind of living system, that's not called a protein. In order to be a protein, it needs to not only be a polypeptide, but it needs to actually do something in the body that would result in some kind of biological change, okay?

Now, you might be asking what is a polypeptide. Well, in order to answer that question, we're going to need to start with what's a peptide first. So a peptide is the name that we give to a polymer that has monomeric units called alpha amino acids. So it's a big chain, that's what a polymer is, of similar units and each unit is called an alpha amino acid. So let's look at a picture of what an alpha amino acid is and that's right down here. So the name alpha amino acid comes completely from organic chemistry. And the idea is that every amino acid has the same types of groups around it. On one side, it has an amino group. Remember that amino group is the name that we give to a single bonded nitrogen with hydrogens on it, okay? The acid part comes from the idea of the carboxylic acid functional group which is over on this side. And in the name amino acid, we just shorten the name from carboxylic acid to just being acid. So now we have the idea of an amino acid. But where does that alpha name come in? Well, remember guys, this also comes from organic chemistry that in name and nomenclature of a carbonyl molecule, if you have a carbonyl which is a C double bond O on your molecule, the position right next to it is called the alpha position. So as you can see here, this is my carbonyl and that means the alpha position or the alpha carbon is going to be this one right here, okay? And what the name alpha amino acid means is that specifically at that alpha position, you're always going to have an amino group coming off of one side and a carboxylic acid coming off the other which is why we call it an alpha amino acid. You might have been saying that your whole life and not realize that that's actually what the name means, okay? So it turns out that the 20 most common alpha amino acids that we're going to focus on in this set of videos are going to differ only in one way. They're going to differ in the identity of the R group which we also call the side chain. So if you hear me say side chain, that's the same thing as R group. Now, what does R group mean again? Well, remember that in orgo, R group is any carbon structure. Any structure that has carbon in it that is unnamed, we're going to call an R group. So basically, there's going to be 20 different versions of this R that we're going to need to learn, identify, etc. And these are all going to be called side chains, okay? So now we have this idea of what a peptide is, right? It's all of these amino acids strung together. But what is a polypeptide then? Well, in order to understand that, we're going to need to understand the different types of peptides. And the way that these amino acids come together is through a peptide bond. Okay? So the way that you get these monomers to link into a peptide is to form a bond that we call a peptide bond which I'm going to show you in a second. That structure that we get that's called that peptide is also known as primary structure. So we're not going to use this term a lot for the next few videos, but later when we start talking more about the shape and function of proteins, we're going to need to remember that the straight chain of amino acids that are strung together are called the primary structure of a protein, okay? Now, let's just take a little visual at what these peptide bonds look like and then we'll talk about polypeptides. So here is an alpha amino acid, correct? Amino acid. You can also just not say the alpha part if you want. And what happens is that each amino acid loses one molecule of water and joins up to another amino acid. So what that winds up making is a chain that looks like this where you have amino acid 1 linking to amino acid 2 linking to amino acid 3. Now, notice what's the difference between what you see here and the first amino acid. It's missing some atoms, right? Notice that the oxygens are all gone that are in the middle. Notice that it used to have an OH here and notice that the N used to have 2 hydrogens on it here. But now when you look at these peptide bonds, that oxygen is gone and 2 hydrogens are gone because this hydrogen is gone, this hydrogen is gone, and this O is gone. And that's actually water. So for every unit that you link together into a peptide bond, you're going to lose one equivalent of water. That's going to be lost in the reaction. It's just going to go freely out into the system. That new bond that's created is called a peptide bond and that's the bond that we're looking at right here. Basically, it's the bond between this carbon and this nitrogen. It's the bond between this carbon and this nitrogen. That's the bond that makes the peptide possible because it's linking amino acid 1 to amino acid 2, amino acid 1 to amino acid 2. Does that make sense? Okay. Now, I guess before we go into the polypeptides part, I want to just make a note about some nomenclature, some naming that you need to know. Each dehydrated amino acid is also known as a residue. Okay? So you might be saying, well Johnny, what's the difference between a residue and an amino acid? An amino acid is the version of the molecule that still has the water on it. It still has the 2 Hs and the oxygen. A residue is the version of the molecule that has lost that mole of water so now, it's linked in a chain, okay? So if we were to look at this tripeptide, it's 3 peptides in a row, we would identify these as residue 1, residue 2, and residue 3 because they were 3 different amino acids that each lost water and linked up together. Does that make sense? Cool. Awesome. Also, we'll talk more about this later but just keep a mental note of the fact that residue 1 is always going to start on the side that has the nitrogen coming off of it. Notice that the other side has an oxygen, so the side of the nitrogen which we're going to learn more about later is the one where you start counting your one side, okay? So guys, now, we just have to define a polypeptide. So a dipeptide is simply the name that we give to a 2 amino acid polymer. So it would just be a peptide where there's only residue 1 and residue 2. A tripeptide which is what we're looking at right here would simply be a 3 amino acid polymer, really easy. But then the next one is oligopeptide. So that means it's a little bit more than 3 but it's not a huge amount and a peptide is defined as anything between 4-1...

Standard Amino Acids

So it turns out that scientists have isolated over 700 different molecules that count as amino acids in nature. They go and find living creatures and things, then they isolate them and realize, wow, this is an amino acid. There are 700 of those. But don't worry, we're not going to have to learn 700 in this section. We're really just going to be focusing on the 20 most common amino acids. It's really only going to be these 20. The other 680 that are possible show up in other types of macromolecules but not really in eukaryotic proteins, which would be like proteins of multicellular organisms like us, okay? So, what are the common traits of these 20 amino acids? Remember, I said earlier, they differ only in terms of that R side chain. But if you just had to eyeball it before knowing, before memorizing what your amino acids are, if you just had to look at one and say, is it standard or is it nonstandard, meaning rare, is it outside of this group of 20, how would you be able to tell the difference?

Well, in general, all of the 20 amino acids share these two characteristics. One is that they are alpha amino acids. We already discussed this, right? This is all about alpha amino acids, but just realize that it's possible to have beta, gamma, delta amino acids as well. They still count in the group of 700 but they don't count in the group of 20 common amino acids. Secondly, and this comes from the concept of chirality in organic chemistry, they're going to have an L configuration, which in the rules, the R and S rules of organic chemistry, means that they're going to have an S configuration in organic chemistry at the chiral center. So if there's a chiral center present in the amino acid, that chiral center has to be in an S configuration, okay? In biology, we call it L because it's just an old name given. And throughout this course, we're going to talk about them being L amino acids.

So let's go ahead and look at this example and identify which amino acids we believe to be rare. Now, you wouldn't be able to memorize all 20 amino acids by doing this but you might be able to pick out some amino acids that are not part of the 20.

So let's look at number 1. Let's just do this together. Is this an alpha amino acid that is part of the group of 20? No, it's not. Why? Because it does have an amine group and it does have an acid group. But what is it missing? Notice that the amine is not in the alpha position. This is the alpha carbon and that should have the nitrogen coming off it but it doesn't. Instead, we're coming off all the way off of the beta, gamma. This is on the gamma carbon. And it turns out that this is a very common amino acid in the human body but it's not found in proteins. This is actually a neurotransmitter in the brain called GABA. And the name GABA stands for gamma-Aminobutyric acid. So it's an amino acid but it's not found in proteins so we're not going to have to memorize that one. That is what's called a nonstandard or rare amino acid.