Proteins and Amino Acids

life on Earth is composed of four major macro molecules, thes macro molecules, air called sugars, lipids, nucleic acids and lastly proteins. Now, of these four macro molecules, 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, serious What we're gonna do is we're gonna 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 poly peptide 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 poly peptide 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 poly peptide, 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 poly peptide? Well, in order to answer that question, we're gonna need to start with what's a peptide first? So a peptide is the name that we give to a polymer that has monem Eric units called Alfa Amino Acids. So it's a big chain. That's what a polymer is off similar units, and each unit is called an Alfa amino acid. So let's look at a picture of what an Alfa amino acid is, and that's right down here. So the name ALF 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 hydrogen on it. Okay, The acid part comes from the idea of the carb oxalic acid functional group, which is over on this side and in the name amino acid. We just shortened the name from carb oxalic acid to just being acid. So now we have the idea of an amino acid. But where does that Alfa that Alfa name come in? We'll remember guys. This also comes from organic chemistry that in name in nomenclature of a carbonell molecule. If you have a carbon eel, which is a C double bond Oh, on your molecule, the position right next to it is called the Alfa position. So, as you can see here, this is my carbon Neil. And that means the Alfa position or the Alfa Carbon is going to be this one right here. Okay? And what the name Alfa Mito acid means is that at specifically at that alfa position, you're always gonna have an amino group coming off of one side and a carb oxalic acid coming off the other. Which is why we call it in Alfa 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 ALF amino acids that we're going to focus on in this set of videos are going to defer Onley in one way, they're gonna differ in the identity off the our group, which we also call the side chain. So if you hear me say side chain, that's the same thing as our group. Now, what does our group mean again? We'll remember that in or go. Our group is any carbon structure, any structure that has carbon in it. That is unnamed. We're gonna call in our group, so basically, there's going to be 20 different versions of this are that we're going to need toe, learn, identify, etcetera. And these were 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 poly peptide, then? Well, in order to understand that we're gonna need to understand the different types of pep tights and the way that these amino acids come together is through the through a peptide bond. Okay, so the way that you get these monomers toe 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 that structure that we get that's called that peptide is also known as primary structure. So we're not gonna 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 poly peptides. So here is an Alfa amino acid, correct amino acid. You can also just not say the Alfa 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, one linking toe amino acid to linking toe amino acid. Three. Now I notice what's the difference between what you see here and the first amino acid? It's missing? Some Adams, right? Notice that the oxygen's air all gone that are in the middle notice that it used tohave an O h here and notice that the end used to have two hydrogen on it here. But now, when you look at these peptide bonds, that oxygen is gone and two hydrogen zehr gone right because this hydrogen is gone, this hydrogen is gone, and this oh is gone, and that's actually water. So for every unit that you linked together into a peptide bond, you're going to you lose one equivalent of water that's going to be lost in the reaction is just gonna 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, Actually, I'll make that a little bit more clear. 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. Um, you know, I said one Tamino attitude. Amino acid, one toe amino acid to does that make sense? Okay, now, I guess before we go into the poly peptides part, I want to just make a note about some nomenclature. Some naming a me 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? In amino acid is the version of the molecule that still has the water on it. It still has the two h is 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, try peptide, it's three peptides in a row. We would identify these as residue one residue to and residue three, because they were three 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 one 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 gonna learn more about later, is the one where you start counting your one side. Okay, so, guys, now we just have to define poly peptide. So a di peptide is simply the name that we give to a two amino acid polymer. So it just be a peptide where there's only residue one and residue to a try. Peptide, which is what we're looking at right here, would simply be a three amino acid polymer, really easy. But then the next one is a legal pot peptides, so that means it's It's a little bit more than three, but it's not a huge amount, and illegal peptide is defined as anything between four and 10 amino acids. So it's just gonna be ah, little bit longer than this. It could just be one more residue or could go off the page and do 10 up to 10. And then finally, the idea of a poly peptide is that it's anywhere between 11 and 50. Okay, anywhere between 11 and 50 the chain is getting so long Now we call it a pet poly peptide. Now you might be saying, Johnny, but what about if I get to 51? Is that not a poly peptide anymore? Well, guys, it turns out that the line between these names is a little blurry because many textbooks or, you know, different sources will say that once it's over 50 you just call it protein because so big that it's gonna have some kind of biological function. But there's overlap between those definitions because sometimes when you're below 50 you could still be a protein. So we're just gonna go with this definition for now because that's what's in most textbooks. But just realize that it is a little bit more fluid. And just because you're 51 residues doesn't mean that you can't call it a poly peptide anymore. Just because you're 49 residues doesn't mean that you're not a protein. There's a little bit of, you know, mixing between those two definitions. Okay, so now that we understand the idea of what an Alfa amino acid is, what peptides are and how to define poly peptides, let's go ahead and focus on understanding our standard amino acids. In the next video

So it turns out that scientists have isolated over 700 different molecules that count as amino acids in nature. They go when they find living creatures and things, and then they isolate them. And they realized, Wow, this is an amino acid. There's 700 of those. But don't worry, we're not going to have to learn 700 in this section. We're really just gonna be focusing on the 20 most common amino acids. Why those? Well, because these air the the amino acids that are commonly found in proteins. Okay, so when you like deconstructive protein, it's really only gonna be these 20. The other 680 that are possible show up in other types of macro molecules, but not really in eukaryotic proteins, which would be like proteins of multi cellular organisms like us. Okay, so what are the common traits of these 20 amino acids? Remember I said earlier they differ on Lee in terms of that, our side chain. But if you just had to, like, eyeball before 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 Alfa amino acids. What? We already discussed this, right? This is all about Alfa 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 amino acids. Um, secondly, And this comes from the concept of Chire ality inorganic chemistry. They're going to have an L configuration which, in the rules of the RNs rules of organic chemistry, that means that they're gonna have an s configuration in organic chemistry at the Cairo Center. So if there is a Cairo center presence in the amino acid, that Karl center has to be an s configuration. Okay, in biology, we call it El because just a old name that's given and for throughout this course, we're going to talk about them being l amino acids. But just realize that the definition is actually that it's an s okay. Um cool. So let's go ahead and look at this example and identify which amino acids we believe to be standard and which ones 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, you know, acids that are not part of the 20. So let's look at number one. Let's just do this together. Um, is this an Alfa amino acid that is part of the group of 20? No, it's not. Why? Because it does have in the mean group, and it does have an acid group. But what is it missing? Notice that the amine is not in the Alfa position. This is the Alfa Carbon, and that should have the nitrogen coming off of 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 Gabba. Okay. And the name Gabba. You want to write it down. It stands for gamma amino butyric acid. So it's an amino acid, but it's not found in protein, so we're not gonna have to memorize that one. That is what's called a non standard or rare amino acid. Cool. Let's look at the next one. So the next one looks weird. I might be thinking. Okay, this just looks too weird. I'm going to say Oh, and by the way, we have to circle and square them. Right? So I don't think this is standard. I'm gonna put a box around this nonstandard. Okay, box quote. Let's go to the next one so immediately, I might wanna box this one out because it just looks really weird. It's probably not in amino, an Alfa amino acid, But let's just take a look at it really quick. Do we have in a mean group? And do we have a car? Oxalic acid? Yes. Is the amine coming off of the Alfa position? Well, this is the Alfa, and actually, yes, notice that I have nitrogen directly attached to it. So that would be in a amino acid alfa amino acid. Now is it in the right Cairo configuration Well, in order to answer that question, we're gonna have to actually figure out Arness using our Kyra ality rules. So let's go ahead and identify. This is the Carol center. Remember it, Carol center is just any atom with four different groups around it. We're gonna go ahead and prioritize them using molecular weight. And if you need a refresher on this, just go to R and s nomenclature or the RSS naming system in the clutch prep toolbar. And I have much more videos on this in the search bar, you can search for it. So anyway, let's go ahead and number our priorities. Our priorities in terms of atomic weight on the periodic table would be one because nitrogen comes first to because this carbon is bound to oxygen three cause this carbon is not bound to any hetero atoms. For hydrogen is the, you know, it is always the worst because it's the smallest atom, so it's always gonna get last place. So are we able to do RNs yet? No. Because remember that in order to RNs, your four always needs to be on the dash. It always needs in the back. So using our RNs naming system. We're gonna cross out four. We're gonna cross out three, because three, we're gonna switch these around. So this is now gonna be four. This is now gonna be three. And now I can trace. So this looks like 1 to 22 to 3321 You always ignore four, and it looks like a are, but since I had to switch it, this is gonna be an s. Okay, so is this a one of the 20 amino acids that we're gonna need to learn? Yes, it is. So we're gonna go ahead and circle that That is an Alfa Mito acid in the S configuration, which we're gonna call an l amino acid. Cool. So let's go to the next one. The next one. I see that this is an alfa amino acid because I have the amino. I have the car books like acid. I haven't our group. We're gonna have to do r and s configuration again. So let's go ahead and do this one more time. So this is my carl center. I have position one position to that. Carbon is bound to to oxygen, so it's gonna beat this one that's bound to only one oxygen. And then finally, this is four. So once again Well, actually, can I just go ahead and do RNs? Or do I need to switch notice that my four is now on the dash, Which means this is an easy situation. I can just trace, so I'm gonna go. 122223321 That's going clockwise. And remember that clockwise is in our and we don't switch. So this is actually in the our configuration. So is this, By the way, the our configuration is also known as a D amino acid. We'll talk more about that later. That's in biology. It's called D in organic chemistry. It's called our But for the purposes of this question, are we putting a box or circle around this? We are boxing this out because this is not in the right Kyle configuration. This would not be found in a biological protein. Finally, we're gonna look at this one if I could get out of the way. Cool. And what about this one? Is this an Alfa amino acid? Well, what I see is that once again, I haven't I mean, I have a car. Looks like acid. I do have a Kyrill center, so we just need to do our numbers again. So we've got one to three. This is just a ch three. So that gets the third priority. And finally, there's an implied hydrogen. Right, Because every carbon has the four bonds. So this is four. So do I have to switch these groups, or can I just trace around? I have to switch because remember that my four always must be on the dash, So I'm going to switch my four in my three. I'm gonna put my four here. I'm gonna put my three here now I can trace. Let's go ahead and trace. 122223321 It looks clockwise, So it looks like a are. But since we switched the groups, it has to be an s. So is this one of the 20 that you need to know? Yeah. Okay, So now we've identified what is kind of what what standard amino acids look like and what the non standard ones look like as well. In fact, there's a lot of different possibilities, but anything that has an R configuration nonstandard. Anything that's not Alfa in the off position Nonstandard. Okay, I just want to make one more point before we go, which is that I hope you noticed a pattern, which is that every single amino acid that I've drawn that is one of the 20 amino acids has the our group facing back. And I could have just used that as a shortcut. But I wanted you guys to learn how to do r and s again. So I did it. But just as a shortcut for the future. If you see the are going towards the back, if you see it going down and towards the back like we have here, notice that I'm just gonna highlight this down and towards the back, right? Do you see up there highlighting blue down and towards the back And then over here, down and towards the back. All of these are in the L or s configuration simply because whenever the our group is facing down and towards the back, that is going to be in the right configuration. So you could just memorize that for later to make it faster. Okay, so we're done with this video. Let's move onto the next one