Amino Acid Chart - Online Tutor, Practice Problems & Exam Prep

Amino acids are categorized into non-polar, polar, and charged groups, each with unique structures and functions. Essential amino acids, such as valine, leucine, isoleucine, methionine, tryptophan, phenylalanine, threonine, histidine, and arginine, must be obtained from diet as the body cannot synthesize them. Understanding their structures, such as the carboxylic acid groups in aspartic and glutamic acids, is crucial for grasping protein synthesis and function. Memory aids, like acronyms and stories, can enhance retention of these amino acids and their properties.

Nonpolar Amino Acids

So the first thing I wanted to mention is just how this worksheet, which I call the clutch prep amino acid breakdown, is arranged. Well, all of the amino acid backbones have already been drawn for you, so all we're going to be doing here is filling in the side chains. That means anything that's attached to the R group that's attached over here. Also, I've included more information than you need for this video because this is information that we're going to use later. So, for example, these pKa values that you see here, don't worry about those yet. We're not going to talk about pKas yet. These little pizza slices, don't worry about those yet. You're going to understand what that means in due time. And also, there are going to be little boxes. Don't worry about them either like over here. We're not going to fill that in yet. These are for following videos where we talk more in-depth about amino acids. But the idea is that you can put all of your notes about amino acids onto the sheet. Every amino acid has a note section, so you can write in little tips and tricks, and the idea is that you keep the sheet for a long time. Maybe even after you take this class, maybe even after you graduate undergraduate. Like, you could even use this in med school, pharmacy school, whatever you have. Keep everything in one place, and then you'll always have a great way to memorize your amino acids if you ever need to know them later. So let's go ahead and get started with the first set of amino acids which are going to be the nonpolar side chains. Remember, these are the ones that are hydrophobic. They don't like to be around water. They're going to want to curl up and bulk inside of the protein. So let's start with the simplest amino acid possible. Hint, it's also the only achiral amino acid. Notice that all these other nitrogens or amine groups are on wedges, correct? But the first one is on a stick. Why? It's because glycine is the only amino acid that has a hydrogen as its side chain to add to the original hydrogen that was already there, that every amino acid has. So this is the only amino acid that is achiral. And that's why we draw it just plainer. Okay? In terms of how you can remember this, this is actually the only one I'm not going to give you a big memory tip for because it's just so easy. All I'm going to ask you to do is remember that glycine is where it all starts. It's the simplest one, and its three-letter abbreviation is Gly. Its one-letter symbol is G. It's just, just memorize that one and for the other ones, we'll be building on top of that information. Okay? Cool. So let's go on to the next one. The next one is alanine. So alanine is the simplest hydrocarbon. Okay? So hydrogen isn't technically a hydrocarbon because it doesn't have the carbon part. Alanine is going to be a methyl group, CH₃ for the side chain. The way I like to memorize that is that the symbol for alanine is A, the abbreviation is Ala, and I just think of it as being the easiest hydrocarbon, so it's A. It's kind of like A is the beginning of the alphabet and alanine is the beginning of the hydrocarbons where it's just a methyl group and nothing more. Okay. So we've got glycine, we've got alanine. Now, let's go on to valine. So for valine, now we have to start thinking about these hydrocarbon side chains and figuring out ways to memorize what they look like. So for valine, this side chain thankfully is also very easy because valine, the symbol for it is V, and the side chain looks like a V. All you have to do is draw a V coming off of that position and you have your valine. Now we have glycine, alanine, and valine. Let's move on to leucine. So now we want to draw leucine. How do you draw leucine? Well, this is another hydrocarbon, and it's actually also going to have a V. So by the way, you're going to notice at the end is that I want you to memorize these amino acids in this specific order because if you memorize them in this order, we can build a story behind them and then they can make more sense. So part of the story is that leucine looks a lot like valine. It's still got that V. We're just going to add an extra CH₂. Okay? What that means is I'm going to add an extra CH₂ here and then I'm going to draw that V. Now, the V it's kind of upside down now, but there you go. That's your leucine. So if you draw leucine right after valine, what you can think of is that, oh, leucine is just it's a little bit more complicated valine. It's going to be valine with that extra CH₂ right here. Okay? Awesome. Remember that leucine, like all these abbreviations, I'm not going to spend a lot of time on because they're easy. Leucine is L. All of them are straightforward. Great. So let's go into isoleucine. So isoleucine is also going to be a variant of valine, so it's also going to have that V except that now we're going to go back to the way things were for valine. We're going to draw that first and theniselectable mike"> we're just going to add an extra carbon. Okay? So technically, if you remember from like organic chemistry 1, isoleucine is an isomer of leucine, but the way you can really think about it is that it looks a lot like valine. It's got that initial V. You just put the extra methyl group all the way at the end. So see how if you memorize them in this order valine, leucine, and isoleucine, you can start to build a story of like okay, the V starts off only a V. Then it's add a CH₂ plus a V. Then it's add the V plus a CH₃. Got it? Okay. Cool. So now let's go on to proline. Now proline starts to get a little bit weird because proline is the only amino acid that connects back to itself. Okay? It's the only one you can tell. I kind of gave you a hint because I'm just going to scroll down to right here. I gave you a hint because notice that it's the only nitrogen that's missing a hydrogen. All the other nitrogens have c NH₂ and this one I only put NH. Why is that? Well, because proline, it turns out, has a 5-member ring inside of it that connects back to the nitrogen. So what we would do is we would draw a 5-member ring. 1, 2, 3, 4, 5. Connect back to the nitrogen, and you're done. That's proline. The way I like to think about proline is "proline pentagon." Okay? And if you think about "proline pentagon," that's always going to be a good hint for you, that now you need to draw a 5-member ring in that amino acid. Okay? Also, just keep in mind that these abbreviations and symbols are still straightforward. Proline is P. There's nothing really to talk about there. Great. So let's move on. So we're doing great guys. I think we're, how many are we down? 5 already? 5 out of 20? So what's next? Methionine. So methionine is also nonpolar. It's in the nonpolar category. However, it's going to be the first one that has a heteroatom. What that means is it's going to have an atom in the side chain that's not carbon. In fact, this is going to have a sulfur in it. Okay? So how can we remember that? Well, first of all, let's start with the structure. How would you draw the structure? Well, the way I like to think about it is the structure is in the name. Methionine starts with an M. In fact, the symbol is an M. So what I always do is I draw an M to begin with. Let's draw our M. 1, 2, 3, 4. Like that. So see how I just drew an M? Awesome. Now, we need to add a sulfur somewhere. Now, you're going to have to kind of remember this, but there aren't that many with sulfur. So it's not that hard to remember. So the sulfur actually goes in the second to last carbon. We would add a sulfur right here, and then we would just draw the rest of the M. So see how it still looks like an M, it just has that sulfur there. Now, how could you remember that the sulfur goes there and not somewhere else? Well, you could memorize it, but I also have another trick. Methionine says "meth" at the beginning, so you just make sure that there's one methyl group at the end. Right? So when you think about Methionine, it's an M that has a sulfur that allows for there to be one methyl group all the way at the end. And if you remember that, you've got your Methionine down. Awesome. So now we're going to get to some weirder ones. Tryptophan is

Polar Amino Acids

Great job so far. We're almost halfway done with our amino acids. Now in this next video, we're going to learn the following 6 amino acids that are in the polar side chain category. Heads up, these side chains are about to get a lot more complicated, so we're going to need a more elaborate story to remember all of them including, like, the order that we're memorizing them and what the structures look like. Okay? So, to begin with, we're going to start with the tale of 2 sisters. We have 2 sisters named Cystine and Serine. Okay? And you know, I think they're identical twins or they're very they're very similar. I think they're fraternal twins. But they've kind of taken different paths in life, which is fine. Like, I'm not judging at all. But just saying that they don't really like to hang out very much. They do very different things. Let me get to the point. So Cystine spends a lot of time at the Sistine Chapel, which is a church. Right? So when she's praying in church, she's telling everyone to calm down. She's saying, "Shh. Like, we're trying to pray here." So she has an SH coming right off of that first carbon group. So that's Cystine. So that's the way she's, you know, decides to spend her Friday night and good for her. Right? Serine, on the other hand, likes to party. So Serine is the sister of Cystine, but instead of having instead of saying "Shh, we're in church, we're trying to pray," she's actually just drinking alcohol. So she's going to look exactly the same, but she's going to be partying it up, drinking the bubbly. As you can tell, you can see why they don't hang out a lot. These are the two sisters. I'm happy for them. They've they found their own happiness, but, you know, they just they're very different types of people even though they look the same.

Okay? Now it turns out that Serine has kind of a rowdy group of girls that she hangs out with. And, you know, you tend to find friends that like to do what you do. And she has these 2 other friends that also like to party just as hard as she does. These girls are like a wolf pack, and they go out militantly every night. So these girls are Threonine and Tyrosine. The way you can think of them is that alcohol is a serious threat and it makes you thirsty. So what am I talking about here? Well, alcohol, these are the 3 function groups with alcohol in them. "Serious" stands for Serine. "Threat" would be Threonine. And, "thirsty" would be Tyrosine because it has a Y as the letter. So, we're going to talk more about what these look like in a second and what we mean by that. But let's go ahead and start with the structure of threats. So Threonine. So alcohol is a serious threat. So Threonine actually looks a lot like Valine. So the way I could think about this is that remember Valine was the third Val was the third girl in the hydrophobics. Right? Non-polars? Well, Threonine threat is the third girl in the polar side chains. She looks a lot like Val except one big difference, she likes alcohol. Duh. She's hanging out with Serine. We're going to draw the same exact V as we would for Val, but we're just going to add an OH. Okay. And you could have added it to the top or to the bottom. I'm just going to add it to the bottom so that she looks more like Serine. So it's like a combination of Serine and Valine. Cool? Awesome. Best of both worlds. And what about their other homie? Their other homie is, Tyrosine. Now, Tyrosine is a little complicated because Threonine already took the T. So we had to think of another letter for Tyrosine, and that letter is going to be Y because it's the second letter in Tyrosine. And that's what I like to think of as being thirsty. Right? So I'm really old, so when I drink alcohol, I actually legitimately get thirsty. Like, I have to drink a lot of water before I go to bed or then I'm going to wake up with a headache. But you could also think of thirsty in another way if you wanted to. So, these girls, they're having fun. I'm not judging. So Tyrosine is getting thirsty with all this alcohol and also she kind of looks like a tire. Okay? You can just imagine this is quite the party. So Tyrosine actually looks just like Phenylalanine because Phenylalanine looks like a tire. Right? So let's draw out what Phenylalanine looks like. It would just be that tire shape coming right off of the carbon. Right? So it looks like the tire, but what's the only difference between Tyrosine and Phenylalanine? She likes to party, so she wants that alcohol, so we're going to add in that alcohol. Alright? And there you have it. We have the tale of two sisters and her wolf pack. Alright? So let's say they party all night long. We're not done. We have two more to go, but they all This is all the same story. So they go out, they party hard, they took an Uber back at 4 in the morning. What do they do in the morning? Like, what are their plans, you know, like, this is this is this is the squad. So what are the squad goals in the morning? Well, in the morning, they're trying to look cute so they're gonna work on their glutes. So they're all gonna go to the gym, and they're gonna work it out. And Tryin' is the n stands for asparagine. And cute, working on her glutes, is glutamine. So these are the two other friends that actually weren't partying with them last night. So they don't have alcohol. But they joined in the morning. Right? Maybe they got, like, brunch or something and then they they decided to work on their glutes. So how are we gonna remember the structure? So now, we kind of know the order that asparagine comes first and glutamine comes next. By the way, "cute" stands for cute. That's the idea of cute, glute. So how are we gonna remember the structure of asparagine and glutamine? Well, the other way to remember this, and I hope you're writing some of this down, by the way. You should be pressing pause and writing some of these things down, because it's gonna help you later. Well, the way you could think about this is that you only have one s but you've got 2 glutes. Right? So when you're trying to look cute and you're working on your glutes, well, you're working on one s, but you also you have 2 glutes. That's just kind of human anatomy. Right? At least for these girls. So Asparagine is going to have one carbon in between the amide group at the end, whereas Glutamine is going to have 2 carbons because she has 2 glutes. Okay? What that means is that this is my one carbon. I'm going to draw an amide here. Okay? So that's basically my ass, which sounds crazy, but that's that's that's the one s. Okay? For Glutamine, since you have 2 glutes, we're going to double that. We're going to say it's not just one carbon, it's a second carbon, and then you draw your amide group. And there you have it. You have basically the whole gang. This is what the gang looks like in the morning. They're all, you know, working out and you've got well, I mean, Cystine was never really part of the gang. She stayed home and slept. But you've got the wolf pack, and then you've got asparagine and glutamine that join in the morning, that are working with, you know, one ass, two glutes. And by the way, the way you can remember that it's like amides at the end because that's kind of the hard part to make that link. How do you remember that it's amides? Well, it ends in ane and the ends kind of look like amines. Right? So you could think like, oh, that's another amine then they end with -ine. So you could think, well, asparagine is the thing that looks like an amine, but with only one carbon, and glutamine is the thing that looks like an amine, but with two carbons. And then, the way you could think, asparagine being N, you can think tryin'. She's just trying to look cute. And then, glutamine is looking cute, so she's working on her glutes, and that's your Q and your Glutamine. Alright. So that was pretty fun. You're doing great. We only have 5 amino acids left to go. Let's go ahead and move on to the next video.

Charged Amino Acids

Hey everyone. So in this video, we're going to take a look at our acidic and basic amino acids. Let's first start out with our acidic amino acids. They take the form of aspartic acid and glutamic acid. Now we know that with amino acids, we have three-letter codes, as well as one-letter codes. Three-letter codes are pretty easy because for the majority of the amino acids, they're just the first three letters of the amino acid's particular name. In this case, for acidic and basic amino acids, that's going to fit the description for the three-letter code. Here, aspartic acid, ASP, ASP. Glutamic acid, GLU, GLU. Now, here when it comes to their one-letter code, it can be a little bit tricky. Here we're going to determine their one-letter code by sounding them out phonetically. So if we say aspartic acid, aspardic, it sounds like there's a D within the description. So aspardic. So that's why we're going to say that its one-letter code is D. For glutamic acid, so glutamicmic at the end. So depending on how you say it phonetically it sounds like an E. Glutamic. So that's why we're gonna go with E here. So we have the one-letter code for aspartic acid being D and the one-letter code for glutamic acid being E. I put them in this order because I remembered as drinking acid you're going to the emergency room. Right? So here we're talking about drink D for aspartic and emergency E for glutamic. So that's why we list them as aspartic first then glutamic. Now for aspartic acid, what does it resemble? Well, here when it comes to aspartic acid, we're going to say that this carbon here is just connected to a carboxylic acid group. Remember, these are acids. Biological acids are carboxylic acids. It's just one example of a type of biological acid. So here, this carbon would just be connected to a carboxylic acid. This would be what aspartic acid resembles. Now for glutamic acid, it's a little bit trickier. We're going to say we don't have just one carbon, we're going to say this carbon here is connected to another carbon, and that carbon is connected to a carboxylic acid. Now, we can say here that these two carbons are connected together or glued together, because if you look you have glu and then E, they're glued together to help make glutamic acid. So that's the way I remember what glutamic acid looks like. I have my initial carbon in red. It's going to be glued to another carbon, and it's that carbon that's connected to a carboxylic acid. Right? So right now, we've learned two ways of finding out what our acidic amino acids would be. Next, we have our basic amino acids. Basic because they have basic side chains. Now, here they are lysine, they are histidine, and there are arginine. So here again, the three-letter code is based on the first three letters in their name. So if we look here we have lysine, LYS, histidine, HIS, and then Arginine is ARG. Here when it comes to their one-letter code, it's a little bit trickier. So what do I say to myself to help me remember this? Well, I kind of think of an old cartoon I used to look at when I was smaller. It was based on this basic idea. So basic basic side chain. This basic idea of a cat and a mouse, and the cat would always try to catch the mouse, but could never do it. That's Tom and Jerry. So I'm kind of giving my age a little bit, but I kind of go with this idea of Tom and Jerry to help me remember the basic side chains of amino acids because it's a basic concept. We're gonna say here that KHR stands for kittens hunt rats. So this idea again is a play on Tom and Jerry, the cartoon show. Now here, if we take a look, we can say that for lysine LS or K, the way I remember that lysine is connected to K is that we can say that lysine is a liar, but that's okay. Alright. So what do we have here? We have Lysine is connected to K. So that's the way I remember the one-letter code for lysine. And if we were to take a look at lysine, we'd say that lysine resembles methionine. We're gonna say here, Lysine resembles Methionine. If we look at the alphabet we can say that L is next to M on the alphabet chart. So lysine resembles Methionine, so here we draw it as. Here go our carbons, and at the end because we're dealing with a basic side chain we'd have an amine group, so NH₂. So here this would represent lysine. For the next one, histidine, and arginine are a little bit trickier. Okay. So these, we're going to come up with other ways of recognizing them. Their one-letters are easier to see because with histidine, hist starts with an H. So for this one, we're going to say that this carbon is connected to a 5 membered ring. So what we're gonna do here is we're just gonna draw the 5 membered ring initially and then we're gonna we're gonna alter it. Because it's a basic side chain, we're gonna have the presence of nitrogen groups. We're gonna say that this carbon is connected to the 5 membered ring, and we're gonna pay attention to this carbon here in black. Now to draw this correctly, we're going to say that there's 2 nitrogens within this 5 membered ring. 1 of the nitrogens will be directly connected to that carbon in black and one of them will be one carbon away, so over here. The one carbon away is going to be double bonded because nitrogen ideally wants to make 3 bonds. So here we're going to put a double bond there, actually we're going to put these in blue keep up with the theme. And then the other nitrogen that's connected to that carbon in black, it needs to make 3 bonds as well, it's not double-bonded so in order to make its third bond it'll have a hydrogen branching off of it. So here, this represents histidine. It's basically our carbon in red connected to a 5-membered ring. The carbon in black is the one connected to that red carbon here. And it has 1 nitrogen directly connected to it and it has 1 nitrogen away from it. The one that's away from it is double bonded, the one that's next to it, connected to it, has a hydrogen and it's single bonded. Alright, so then those are those 2. And then finally here we have our arginine arginine. Depending on how you want to pronounce it. So here, this one's trickier. How do I remember_assigned_to_73_29_Start">what this structure looks like? Well, here we have ARG as its three-letter code, and we could think about where do I hear ARG? Argh. Well, you might hear argh if you bump your knee, hurt yourself, or step on a tack. So let's say you step on something sharp. Okay. And let's say you step on a tack. And you'll give out an expression of Argh! This hurts. Going along this theme is going to help us to remember what the structure of this amino acid resembles. We're going to say here that this amino acid, this carbon here will be connected to these carbons here and then that one will be connected to a nitrogen. In order to make its 3 bonds, it has a hydrogen on it. It's connected to a carbon which is double-bonded to another nitrogen. In order to make 3 bonds, it's single-bonded to a hydrogen. And then that double-bonded carbon is finally connected to its last nitrogen which is NH₂. Now, here we're thinking about stepping on something sharp pointing like a tack, something triangular at the top, and if we were to think of this triangular thing, this end here kind of resembles a triangle. So stepping on this amino acid is very painful. We're going to say here that this represents a triangle of amines. Triangle is for 3, and what do we have here? We have 1, 2, 3 carbons involved that are coming off of this red carbon, and then how many nitrogens do we have? We have 1, 2, 3 nitrogens. Okay, so that's a way of us remembering what the structure of this amino acid resembles. So let me erase all these circles. Okay. So that would be our final structure. So remember, when it comes to our acidic and basic amino acids based on their side chains, to remember the 2, just remember drink acid, you're going to the emergency room. So here D is for aspartic acid and E for the emergency room is_ss">is for glutamic acid. Then based on my childhood cartoon, Tom and Jerry, we're going to say that kittens hunt rats and we're going to say here that K is for Lysine, H here is for histidine, and then we have an R here for arginine arginine. So that's how we can remember the different types of letter coding for the amino acids. And then just remember some of the tricks that I talked about when it comes to their structures. We have our aspartic acid, which is just that carbon in red branching off to a carboxylic acid. Glutamic acid, where that red carbon glues itself to another carbon which that carbon is connected to a carboxylic acid. And then we have our lysine has a structure similar to methionine. We have our histidine is just a red carbon connected to a 5-membered ring. And then we have finally arginine arginine, that's a painful arc. Think of a triangular tack where you step on it. It's made up of 3 amines, so we have 3 carbons and 3 nitrogens. So keep that in mind when examining these different types of amino acids.

Essential Amino Acids

Lastly, I want to talk about all of these interesting pizza emojis all over the amino acid sheet. As you see, there are, I think, 9 of these that have pizza on them. So what does that mean? Well, it turns out that many of these amino acids, your body can make itself. So your body could take proteins and turn them and turn one amino acid into another amino acid. But there is a certain group of amino acids that are called essential amino acids. Now, what does essential mean? They are actually essential for survival. If you do not eat this protein, this amino acid, you will not have it in your body and you will probably die. So that's why it's important for us to be intaking protein all the time through the foods that we eat so that we can get some of our essential amino acids. Once again, these are amino acids that your body cannot synthesize on its own. We need to get it from an external food source, some other animal that made that amino acid that we then take in and use it ourselves. Basically, our bodies got lazy and said, hey, if I'm always getting food that has this amino acid, why do I need to keep making it? I'll just keep getting it from other animals. And that's actually what happened scientifically. So, these are a set of amino acids that you may need to memorize. Okay?

Now, the thing that's tricky is that there are a bunch of different special cases where in certain types of diseases, you might need this amino acid or you might need this amino acid. And some professors actually include that in their list of essential amino acids. So if you need to memorize your list of amino acids, of essential amino acids, what I'm going to show you the ones with the pizza slices are the ones that are universally accepted like on Wikipedia. These are the ones that everyone agrees are essential. Now, your professor or your textbook may add a few to this list, but they're more for special cases. It's like, oh, if you have this type of disease, then you need this amino acid, etcetera. Okay? So we're going to go over is the how many is this? It looks like 9 essential amino acids, but I'm just letting you know that your list might be 10 or 11 or 12 depending on the special cases that your book or your text or your professor wants you to learn. Okay? So we're just going to scroll really quick and just look at them just so we can get a big picture. What we see is that the essential ones are on some of them in the hydrophobic, in the side chains, the nonpolars. That would be valine, leucine, isoleucine, methionine, tryptophan, and phenylalanine. So 6 of them are in the non-polars. Okay? Then over here in the polar, we just have threonine. So threonine is essential. And then over here in our basics, 2 of them are essential. Histidine and arginine are essential. Okay? So these are the 9 that are the most agreed upon that you need to take in from other animals or plants or whatever in order to live. Okay?

Now, how are you going to remember these? The way I like to think about it is that, thankfully, a lot of these letters come together, are next to each other in the alphabet. So, what I would do is I would remember "favorites". So "favorite" stands for phenylalanine, valine, and threonine. So all these letters by the way are the actual letters that they use in their symbols. Okay? And then you've got histidine, isoleucine, skip J, lysine, leucine, methionine, and then W is just a random letter at the end that's tryptophan, but W, you would just flip the M, and then it's the same letters M just flipped. Okay? So now, I know that sounds kind of it's not that maybe it doesn't sound that helpful, but the way I like to think about it is like maybe the way you could think about it is like it's your favorite part of the alphabet but you're skipping J. So you're going from H all the way to M but you're skipping J and then you're adding W at the end. I bet there are some missed opportunities here with how easy this would be to memorize. Like, I'm already thinking it possibly use, like, H and M or, like, your favorite J. Like, I don't know. Like, there are a lot of different directions you could go. I'll leave this one up to you. You may not even need to know this. You may not need to memorize it. But in case you do, it's pretty easy. You can already like I'm already like memorizing it and I didn't even know this like a minute ago. Okay? So favorite and then all letters except for J and then you flip the M at the end. Okay? So those are your essential amino acids, at least the most commonly agreed upon. Let's go ahead and move on to the next video.

Blank Amino Acid Worksheet

Alright. So in this video, we're literally just going to learn through repetition and we're going to draw all the amino acids all over again from scratch. And hopefully, by doing it together, we're going to be able to go over a lot of these memory tools that we learned the first time and really solidify them. What this is also going to help us do is iron out any rough edges of things that we might have forgotten to memorize the first time, okay? So, and I'm going to try to go a little bit quickly because you can always pause the video if you need to, okay? So let's go ahead and start with our letters because we need to remember the orders first, okay? So let's remember our orders. Our order was GAVLIP, right? So GAVLI P. We're learning our nonpolars throughout the week, Monday, Wednesday, Friday. And now, we're done with our 1st nonpolars. Now, we're going to move on to our polars. Our polars, well, we have cysteine. I'm just going to write them here from now on. So cysteine and her

Non-Polar Sidechains - Fill in the missing sidechains on the following target tripeptide.

So here in this question, it says we have nonpolar side chains, and we have to fill in the missing side chains on the following target tripeptide. This is a tripeptide because it's 3 amino acids connected by 2 peptide bonds. So, if we take a look here, this would represent one amino acid, and we know that this amino acid is connected to the next one by this amide bond here or a peptide bond. This would be our 2nd amino acid, and then this would be finally our 3rd amino acid. When we're looking at our amino acid, we're looking at the N-terminus towards the C-terminus end, so we're moving in this direction. Now, here we have to give the side chain, the missing side chains or R groups based on this basic code given to us for the amino acids. We have LAM; these are our 3 amino acids. Here, it spells out the word "Lam". Now, we're going to say that our R groups or side chains are in positions 1, 2, 3. Based on the letter that we're given here we have to identify the amino acid and then identify its side chain or its R group. If we take a look here, L equals Leucine, A equals Alanine, and M here represents Methionine. We've identified our 3 amino acids, now we have to define identify their R groups. When it comes to Leucine here, we're going to say Leucine has a side chain represented as an isobutyl group, which is a CH2 group connected to another CHCHCH3CH3. This would be the side chain or R group for our Leucine amino acid. Now, for Alanine, it's one of the simplest amino acids. Its R group or side chain is just a methyl group, represented as CHCH3. Finally, we have Methionine here, which has a sulfide side chain represented by CH2CH2SCHCH3. This would be the side chain or R group for our Methionine. So when we're saying LAM here, we're talking about Leucine, Alanine, and Methionine connected together. This would be our final answer.

Non-Polar Sidechains - Fill in the missing sidechains on the following target tripeptide.

In this video, we're going to be drawing the tripeptide WIG. And WIG, remember, let's just go ahead and write out what this is. This would be tryptophan or tryptophan. It would be isoleucine and it would be glycine. Great. So we're actually going to start off with the hardest one and then it's going to get easier as we go. So tryptophan would mean that I have to draw, remember that you don't just draw the double ring structure right off of that carbon. You have to draw one more carbon. So, let's draw like, let's see what direction. I guess let's draw it like this. And now, I need to draw my W. So I'm gonna draw 1, 2, 3. 1, 2, 3. Cool? And now, we can finish off. We know that this needs to be a 5-member ring. This needs to be a 6-member ring and we need a nitrogen at the bottom of the W. And now, I can fill in my double bonds. What you can also do is you can draw circles which would mean that it's aromatic but I'm just going to draw my H here. And I'll just draw my double bonds anyway. There we go. So now we have tryptophan. Isoleucine. Remember that? Iso, it's given lip so it comes after leucine means that it's gonna look like val, but it just gonna have an extra CH2. So looks just like val but with an extra CH3 at the end. Awesome. Glycine, nothing to draw. Just going to be an H. By the way, that means that the stereochemistry of this is technically wrong. It should be in a straight line but it's fine. It's not a big deal. Let's just pretend that that H is rotated back and that we have another H rotated front and that is a totally fine way to draw it. But in the future, if you have glycine, you just wouldn't even draw that hydrogen at all. You would just skip it. Okay? Great. So we're done with this video. Let's move on to the next.

Non-Polar Sidechains - Provide the complete structure of the tripeptide P-F-W

I told you it was going to happen. I took the training wheels off. Now, you actually have to draw the entire tripeptide from scratch. So let's go ahead and draw the backbone first. The backbone would look like this: NH2. Now, this one's down. So it should be dashed. Then here's my N. Double bond O. Let's just draw the N's and double bond O's first. It's all one O, OH. So that's what a peptide looks like. You could just keep going on forever. Carbonyl N R. Carbonyl N R. So now, we just have to add our chirality. This one's going up so it should be wedged. This one's going down so it should be dashed. Great. Okay. So now we're going to do PF. This stands for proline, phenylalanine. And it looks like we're going to do tryptophan again. Not a bad idea because it's so tricky. Might as well try it twice. Proline is the only intramolecular one. It forms a ring. So that means that I actually want to form a 5-membered ring coming back to this nitrogen. What that means is that this

Polar Sidechains - Provide the Fischer Projection of Glutamine (Q)

In these questions, we're going to be practicing our polar side chains, and we're going to start off with drawing the Fischer Projection of glutamine, which we remember is Q. We should probably draw the structure first and then turn that into a Fischer Projection. Let's draw the structure. The way I'm going to draw it here, I'm going to draw it with the R group going out. So this is not the way you would draw it if it was a polypeptide. You would then have to draw the N going up. But I'm going to draw this like the way that we drew it when we were memorizing our amino acids, which is the N wedge and the R group going out. Okay? So, glutamine, remember how we're going to remember that? Well, glutamine was trying to look cute so she's working on her glutes. So that means that it is, first of all, the last of the polars. It also means that it's an amine that has 2 carbons in between because you have 2 GLUTs but one S. So I'm going to draw carbon-carbon and then in an amine structure. Great. And we're done. So now we have our structure drawn, and now we just have to turn this into a Fischer projection. Let's draw our Fischer Projection template. And remember that we had some rules for this. Remember, first of all, you always put the carboxylic acid at the top. You always put the R group at the bottom. So we can actually draw that in now. We could draw that it is this chiral carbon. Here is this one. So that means that we have CH2CH2C double bond, NH2. Yep. Cool. And now we just have to figure out where to put our amine. And remember that if it is an L-amino acid, which all of these are, you put it on the left. So we're going to put our amine here and our H here. And now, we just drew the Fischer projection of glutamine from memorizing it. Great job. Let's move on to the next practice problem.

Polar Sidechains - Provide the complete structure of the dipeptide Asn-Cys

Provide the complete structure of the dipeptide ASNCYS which we know as asparagine-cysteine. So let's go ahead and draw our backbone of our polypeptide, and that's going to look like this: NH2 carbonyl N carbonyl OH. Since it's a dipeptide, that's what it would look like. Remember that I have to draw the chirality of my R groups. The chirality would be down as dashed. When it's a side chain, down is dashed. When it's in an amine, down is wedged. But when it's a side chain, down is dashed. And then, when it's up, it's wedged. Great. Now, we just have to draw asparagine and cysteine. Great. So, how are we going to remember these? Well, remember that asparagine is on a Friday morning trying to look cute and work on our glutes with glutamine. So asparagine has just one S, so it's going to be one carbon, and then an amine. So that means that I have my carbon here, and I can immediately go into drawing my amine, which is actually not technically an amine - it's an amide

Polar Sidechains - Fill in the missing sidechains on the following target oligopeptide.

This practice question we're looking at both nonpolar and polar side chains. Here it says fill in the missing side chains of the following target oligopeptide. So, here oligopeptides means we have, basically 3 to 10 usually amino acids connected together by peptide bonds. Remember when we're looking at this amino acid chain we're looking at the N-terminus N to the C-terminus N. Now, here if we take a look we basically have to provide the side chains for positions 1, 2, 3, 4, 5. And, we're given here our target peptide which is f a s t n. We have to remember what amino acids are represented by these one letter codes. So, if we take a look we'd say f here represents Phenylalanine. Next, we'd say, a represents alanine. S here represents serine, t, threonine, and then n here, n's a little bit weird. N it is asparagine. Okay. So here that one's a little bit more difficult because asparagine starts with A, but here this is an N, so that one's a little bit different. Now, here we have to recall what other side chains for each one of these amino acids. So, Phenylalanine, phenyl, we know that phenyl means implies that we're dealing with a benzene ring. Here, it would just basically be a CH2 group connected to a Benzene ring. So, this would be our side chain for Phenylalanine. Then we're going to alanine which is one of the simplest amino acids, its side chain is just a methyl group. Next, we have S for Serine. Serine is a little bit different; Serine, we can think of here as just a CH2 group connected to an OH group. Next, what do we have? We have threonine. Threonine is similar in a way because it is an alkyl group connected to OH, but here, it's a carbon connected to a methyl connected to an OH group. And then finally, we're dealing here with asparagine. For this one, it's a little bit different. It is a CH2 group connected to a carbonyl group, so C double bond O, connected to an NH2 group. So here we have an amide group as our side chain for asparagine. This will represent our 5 side chains for this particular oligopeptide.

Acidic/Basic Sidechains - Provide the Fischer Projection of Amino Acid (H)

Now, we're going to practice our acidic and our basic side chains. Here, we have to draw the Fischer Projection of histidine (H), and let's go ahead and draw the structure. I'm going to put the amine at the bottom because I want to save room at the side for the R group. The R group is going to be a 5-membered ring with 2 nitrogens in it. So, I'm going to have a nitrogen, and then it's going to have the one that is closest has the H. That means that I would put double bond-double bond like that so that the double bond isn't touching the same nitrogen that has the H on it. Great. So now, we just have to draw out our Fischer projections. Let us go ahead and draw our template, and remember that your COOH always goes at the top. Remember that your R group always goes at the bottom, so it's going to be CH2 attached to this whole ring. Let's just draw that in. And that is going to have a double bond-double bond-H. And then since this is an L-amino acid, my nitrogen goes on the left, and my hydrogen goes on the right. And we're done. We have our histidine Fischer Projection done. Let's move on to the next question.

Acidic/Basic Sidechains - Provide the complete structure of the oligopeptide V-I-D-Y. Based on your knowledge of hydrophobicity, which side of the peptide is more likely bury itself within the protein?

Provide the complete structure of the oligopeptide called vidi. Based on your knowledge of hydrophobicity, which side of the peptide is most likely to bury itself within the protein? So, this is like kind of we've got our same thing redraw in an oligopeptide, but then we have to answer a conceptual question as well. I don't think it's going to be that hard. Let's go ahead and check. So let's draw our backbone first. Our backbone should look like this. NH2N. Wait. Is that the right number? We'll figure it out. Maybe you have to erase 1 if anything, but I think that's the right number. Now, just so I don't forget my hydrogens, let's go ahead and add them now because I know that every N on the side chain, on the side chain... Then, let's draw our R groups and see if we have enough slots for them. So, down is dashed, that's R group 1. Up is wedged, that's R group 2. Down is dashed, that's R group 3. Up is wedged, that's R group 4. And we drew it correctly. Great. So now we're ready for vidi. What does VIDI stand for? It stands for Valine, Isoleucine, Aspartic acid, and finally, Y is getting thirsty at the club, Tyrosine. Great, okay. Let's draw Valine. So, Valine is simply going to be a V. Done. Isoleucine, remember it goes Valine, it's gal LIP. So Valine, Leucine, Isoleucine. It looks just like Valine but with an extra CH3. Aspartic acid remember that Aspartic acid only has one S and it's a carboxylic acid, so it should just have one carbon and a carboxylic acid group. Finally, Tyrosine looks just like Phenylalanine but with an alcohol in the para position of the benzene ring, indicated by OH. Alright, we are not done yet, we drew our oligopeptide. But now there's this extra conceptual question that says, based on your knowledge of hydrophobicity, which side of the peptide is more likely to bury itself within the protein? So this is going to require us to classify these as either polar or nonpolar. Valine is nonpolar. Isoleucine is nonpolar. Aspartic acid is charged, so it's very polar. Tyrosine is polar. So does one side of this peptide like water more than the other? Absolutely. What we find is that there's actually kind of a spectrum here. Look, the ones over on this side are much more hydrophilic, right? Because this one's charged, which is the best, and this one's polar because it can hydrogen bond. It likes water. The ones over on this side are hydrophobic, meaning that they don't want to interact with water. They want to bury themselves in the protein to get away from water. So, the answer to this question is that the N-terminus is most likely to be buried within the protein. And what that means is that, conversely, the C-terminus is most likely to be found on the outside of the protein. Alright, that wasn't so bad. I hope that helped. Let's move on to the next video.

Here’s what students ask on this topic:

What are the essential amino acids and why are they important?

Essential amino acids are those that the human body cannot synthesize on its own and must be obtained through diet. These include valine, leucine, isoleucine, methionine, tryptophan, phenylalanine, threonine, histidine, and arginine. They are crucial for various bodily functions, including protein synthesis, tissue repair, and nutrient absorption. Without adequate intake of these amino acids, the body cannot perform these essential functions effectively, which can lead to various health issues. Therefore, consuming a balanced diet that includes sources of these amino acids is vital for maintaining overall health.

How can I memorize the structures of amino acids effectively?

Memorizing amino acid structures can be challenging, but using mnemonic devices and stories can help. For example, you can use acronyms like GAVLIP for non-polar amino acids (Glycine, Alanine, Valine, Leucine, Isoleucine, Proline) and the phrase 'Monday, Wednesday, Friday' for Methionine, Tryptophan, and Phenylalanine. Additionally, associating each amino acid with a visual or a story, such as 'Sistine and Serine' for cysteine and serine, can make the information more memorable. Writing down these structures repeatedly and using flashcards can also reinforce your memory.

What are the differences between acidic and basic amino acids?

Acidic amino acids, such as aspartic acid and glutamic acid, have side chains that contain carboxylic acid groups, making them negatively charged at physiological pH. Basic amino acids, including lysine, histidine, and arginine, have side chains with amine groups, which are positively charged at physiological pH. These charges affect the amino acids' roles in protein structure and function, influencing interactions like hydrogen bonding and ionic interactions within proteins and with other molecules.

How do pKa values relate to amino acids?

pKa values indicate the pH at which an amino acid's side chain can donate or accept a proton. This is crucial for understanding the amino acid's behavior in different pH environments. For example, the pKa of the carboxyl group is around 2, and the pKa of the amino group is around 9-10. Side chains with ionizable groups, like those in acidic and basic amino acids, have their own pKa values, which determine their charge state at a given pH. This affects protein folding, stability, and interactions.

What are the non-polar amino acids and their characteristics?

Non-polar amino acids include glycine, alanine, valine, leucine, isoleucine, proline, methionine, tryptophan, and phenylalanine. These amino acids have hydrophobic side chains that do not interact favorably with water. They tend to be found in the interior of proteins, stabilizing the protein structure by avoiding water. Their non-polar nature also influences protein folding and interactions with other non-polar molecules.