Charged Amino Acids - Video Tutorials & Practice Problems
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Charged Amino Acids
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In this video, we're gonna begin our discussion on our 4th and final amino acid group, the charged amino acids. So the charged amino acids all have r groups that are electrically charged, But they're not always charged, and it turns out that their charges depend on the pH of the solution that they're sitting in. But we'll talk about the pHs and the charges of R groups later on in our course in another video. But for now, in this video, all I want you guys to know is that the charged amino acids are specifically charged at physiological pH, which recall is a pH of about 7. And so this group of charged amino acids can actually be broken up into 2 smaller sub groups, and so there are 2 groups of charged amino acids. We have the negatively charged acidic amino acids, as well as the positively charged basic amino acids. And so over here on the far right, we have a mnemonic to help you guys memorize not only the 5 charged amino acids, but also how these 5 charged amino acids can be further categorized into their smaller subgroups. The negatively charged acidic amino acids, as well as the positively charged basic amino acids. And so this mnemonic is just dragons eat knights riding horses. And so we kind of already knew that. Right? Back in the medieval times, there were dragons, they were eating knights, riding horses, whatever. And so, what you'll see here is that our image is broken up into 2 parts. And so it's really breaking it up into our smaller, categories of the negatively charged acetic amino acids on the left, and the positively charged basic amino acids on the right. And so each of these letters here, the capital letters of these words, so the d, the e, and the k, r, and h, are representing the one letter amino acid codes for those 5 charged amino acids. And we have all 5 of those one letter codes on the left over here. And so, essentially, what you'll see is that the d represents aspartic acid, the e is for glutamic acid, k is for lysine, r is for arginine, and h is for histidine. And so, this means that aspartic acid and glutamic acid are the 2 negatively charged acidic amino acids. And so looking at this image right over here, notice that we have a dragon that is shooting fire and acid out of its mouth, and there's nothing positive about a dragon shooting fire and acid out of its mouth. It's clearly negative. And so up above, we have a negative sign, and so you can see that the dragons eating things and shooting fire and acid out of their mouth is a negative thing. And so that means that aspartic acid and glutamic acid are negatively charged acetic amino acids. And the dragon is Now, looking at our image over here on the right with the knights riding horses, you can see that we have a knight riding a horse, and that is something that is very noble and positive. And so these amino acids here, lysine, arginine, histidine, are the positively charged amino acids. And so, because horses do not shoot fire and acid out of their mouths, that means that they're not acidic, and that must mean that they are basic. And so if you want, you can even imagine our knight carrying a pumpkin spice latte and our horse marching into battle with some UGG boots. So super basic. And so hopefully, this will help you guys remember the 5 charged amino acids and how they can be broken up into the negatively charged amino acids and the positively charged amino acids. And so in our next lesson video, we're gonna focus specifically on the
2
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Charged Amino Acids
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So now that we understand this mnemonic up here a little bit better to memorize the 5 charged amino acids, we're gonna focus on the negatively charged acetic amino acids or this particular group that's boxed in up here. And so with these acidic amino acids, it turns out that all the r groups actually donate a hydrogen ion or h plus. And so when the r groups donate an h plus, that results in a negative charge. And again, there are only 2 amino acids that fall into this group, negatively charged and acetic amino acids, and they are aspartic acid and glutamic acid. And really, it's the presence of carboxylic acids acids that render these amino acids acidic in the first place. And so you really wanna be making this association between negatively charged and acetic amino acids. And so, let's jump into our example where we can look at the actual structure, the r group structure of the, these two amino acids. And so our first amino acid is aspartic acid, and so aspartic acid's three letter code is just a s p, and its one letter code is gonna be d because it fits in phonetically at this position here for aspartic acid. Now it turns out that alanine alanine, once again, is gonna be a leader for this amino acid, and so aspartic acid is really just alanine with, you guessed it, a carboxyl group. It's literally just alanine with a carboxyl group. And so all we need to do to get aspartic acid structure is to start off drawing alanine, so a c h, and we know the hydrogen numbers are gonna change, it's gonna end up being 2, and then we just draw a carboxyl group, so a c double bond o and an o h group. And it turns out that this h on this, o h group is gonna be acidic, so I'll put it in a different color. And so that's it. Now we've got our, carboxyl group and it's alanine with a carboxyl group. That's it. That's aspartic acid structure. Now, again, aspartic acid is an acid, so it can donate its hydrogen and that's what we're seeing in this process here. It's donating its acidic hydrogen. And so when that process happens, when the aspartic acid donates its hydrogen ion, it actually becomes as, aspartate. It becomes aspartate, and so we can see that right here. And so all we need to do to draw aspartate structure is to redraw aspartic acid without this acidic hydrogen. And so what we can do is just draw it in, c h 2, it's gonna be c double bond o, and then it's just gonna have an oxygen there without that acidic hydrogen, so the oxygen is gonna have a negative charge on it. And so that's why aspartic acid is a negatively charged acidic amino acid. And really it's, aspartate that that holds that negative charge. So over here our neck our next our second, amino acid in this group is glutamic acid, and glutamic acid's three letter code is glu, and its one letter code is e because it fits in phonetically at gluten MEK, acid. And so we've seen this glute here before. Right? We've seen glute. And glute, we saw with glutamine. So you can really associate these GLUTs with one another. So we've got glutamine and glutamic acid. And so really, what you'll see is that glutamic acid is really just glutamine with, you guessed it, a carboxyl group, instead of an amide group. So if you remember glutamine, then you can also get glutamic acid structure. So it's gonna be the same thing, so it'll have 2 CH twos and it'll also have a carboxyl group. So it'll have a c double bond o and an o, and then I'll put the h, the acidic h in a different color, h. So what we've got is a carboxyl group here instead of an amide group for, glutamate for glutamic acid's r group. Now, there's a second way to also memorize glutamic acid and that's just going back to that glute idea. So remember that the glutes are like your butt area and so imagine if you're again missing your entire butt area, you're just gonna be really really short. If you don't have any glutes, you're gonna be short, but if you have the glutes, which glutamic acid obviously has the gluten here, it's going to be a little bit longer. And so the second way that you can think of this is glutamic acid structure is just building off of aspartic acid structure and so it's just a little bit taller. Notice that it just has a little bit more, has a c h 2, an extra c h 2 that the aspart, aspartic acid doesn't have. And so that's how you memorize glutamic acid structure. And again, glutamic acid is an acid, so it can donate a hydrogen, okay, and it will donate this acidic hydrogen here. And so when it does that, glutamic acid actually becomes, glutamate, so it becomes glutamate and we can see glutamate right here. And so for glutamate all we need to do is redraw glutamic acid, so we'll have the c h 2, the c h 2 again, the c double bond o, and then all we need to do is just put in the o without the hydrogen, and now it's got a negative charge, so it's glutamate that holds that negative charge. And so this concludes our lesson on the negatively charged acetic amino acids. We've got some memory tools here and we'll be able to apply those memory tools once we finish with the positively charged amino acids which is in our next video. So I'll see you guys in that video.
3
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Charged Amino Acids
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So now that we've talked about the negatively charged acidic amino acids, we're gonna focus on the positively charged basic amino acids. And with these basic amino acids, they all contain r groups that are capable of accepting a positively charged hydrogen ion. And so, of course, arginine, and histidine. And so our and those are lysine, arginine, and histidine. And so our mnemonic for remembering those three amino acids is knights riding horses. And so lysine's one letter code is k for knights, arginines is r for riding, and histidines is h for horses. And so, really, it's the presence of these ionizable nitrogen atoms or these ionizable nitrogens in the r groups that render these amino acids basic. And so, really, you wanna make this association between positively charged and basic amino acids. And so in our example, we're gonna talk about the structures of these r groups themselves. And our first amino acid is lysine, and recall lysine's three letter code is just l y s, and again, its one letter code is k. And in our mnemonic, lysine is represented by a knight, and so up here in the top left corner, we have our knight. And really, lysine's R group looks like a knight's sword. It really looks like a knight's sword. So here we have a sword to represent that. And just like with a sword, you try to, poke somebody with the pointy end, you can think about our one letter code for lysine and ask yourself, how many pointy ends could I try to poke somebody with with this k here? And so when you count them up, there are 1, 2, 3, 4 pointy ends that you could really try to poke somebody with. You can't really use this point right here because it's kind of blocked off. So there's 4 pointy ends, and just like, the letter k has 4 pointy ends, there's going to be a 4 carbon start to the chain of lysine's r group. And so let's go ahead and draw that in. So we can go draw in our first carbon, so CH 2, our second CH 2, 3rd, and 4th. Perfect. So now we have a 4 carbon start to our chain. Now, the last part to remember is that at the very end of the sword, at the very tip of the sword, there's going to be an amino group. So there's an amino group at the very end of the sword. So we can draw in our amino group, NH, And it's actually gonna be an NH 3 because it's gonna be positively charged. And really again, it's the presence of these nitrogens in the r groups that make them basic and positively charged. Alright. So our next one is arginine. And actually, what we're gonna do is we're gonna skip arginine. We're gonna do histidine first, and then once we're done with histidine, we'll go back and we'll finish arginine. So let's jump on over to histidine. So recall, histidine's, three letter code is just h I s and its one letter code is h. And in our mnemonic, the h stands for a horse. And so up here in the top right, we have our horse. And really all histidine is, it's alanine, so it's our leader alanine, with a 5 membered ring branching off of it. So let's go ahead and draw that in right here. So we've got alanine, so it's gonna be c h, and we know the hydrogens are gonna change, it's gonna end up being 2. And then there's a 5 membered ring branching off, So let's draw that in. So we've got one side, 2 side, 3 side, 4 side, 5 side. Perfect. There's alanine with our 5 membered ring. So the next part is to remember, histidine's one letter code. So histidine's one letter code is an h. And just like the letter h has 2 parallel lines, so here's 1 and here's the other parallel line, just like, the h has 2 parallel lines, the ring in, histidine's R group is gonna have 2 double bonds and 2 nitrogen atoms. And so the next thing to remember is that just like the H in histidine, in our mnemonic stands for a horse, really, histidine's r chain or r group looks like a sideways horse. It really does. And so here's the way that it works. First, you draw in this double bond, these are the back legs, these are the front legs of a horse, and then you can put in our nitrogen right here, which would be like the neck of the horse. And so if you can imagine drawing a sideways horse over here, so let's draw our body of a horse. Here are our back legs, here are our front legs, and then here's our head or our neck of the horse. And then you can even draw a little tail here with a hydrogen. So we can do the same over here, draw in our little tail in the back if we wanted to with the hydrogen. And really, it's the neck of the horse that's going to be positively charged. So you can imagine the h appears like the head and it's this neck, the nitrogen here, positively charged. And so the last step is just to remember that the horse here is actually not stepping on the second 2nd nitrogen atom. So at this point, we have 2 double bonds, which is great, and we only have 1 nitrogen, so we know we're gonna need a second nitrogen. And so to figure out where it goes, we just remember that the second nitrogen is not stepping on, the other nitrogen atom. And so that means that if we had the nitrogen at this position, the horse would be stepping on it, so it can't go there. If we have it here, then then the horse would also be stepping on it, so can't go there, and the nitrogen is not gonna be in the tail. So that means that the only place the nitrogen can go is in this position here, and then we just fill in our extra hydrogen and that's it. That's the structure of histidine. So if you can remember these memory tools, hopefully, that'll help you remember the structure of histidine's R group. So now that we're done with, histidine, we're gonna go back and we're going to complete arginine. And so arginine's 3 letter code is gonna be a r g, and it's one letter code is just gonna be r for arginine. And remember that the r in our mnemonic stands for riding. And the riding is, or the arginine's r group, is kind of a mixture of the sword or lysine's r group and the horse or histidine's r group. It's like a mixture of the 2. It's got a little bit of features of both. And so that's what what we can put in here that the R group or arginine's R group has a mixture of features of a sword and a horse. And so because it has the features of the sword, we can think about those pointy ends that you could try to poke somebody with with its one letter code. So if we were to draw an r here, you would see that there's really only 3 pointy ends that you could try to poke somebody with. You could try to poke somebody somebody with this pointy end, this pointy end, or this pointy end. And you can't really use this one because it's kind of blocked off. So there's only 3 pointy ends, and just like there's 3 pointy ends in the r, there's going to be a 3 carbon start to the chain. So let's go ahead and draw in our 3 carbon start. So we got our c h 2, c h 2, and c h 2. Perfect. So now we've got our 3 carbon start. The next part is to remember that just like there are 3 pointy ends on the r, there's also going to be a triangular. So a triangle has 3 sides to it. There's gonna be a triangular nitrogen structure at the bottom of our sward here, and that triangular nitrogen structure kinda has similarities to, like, a horse in a in a way. And so here's the way that the triangular nitrogen structure works. First, you draw in the nitrogen, then there's a carbon, and then there's another nitrogen, and then there's a double bond up here to another nitrogen. And so you can see here how we have a triangular nitrogen structure, so it kind of goes like that. So there's our triangular nitrogen structure. And so, what you'll see is that all you need to do is fill in the hydrogens at this point. So, this one's going to have 2 or 1 hydrogen. This one's going to have 2 hydrogens. And then this one up here, the one that's with the double bond, is actually going to have 2 hydrogens as well. It's gonna have a NH 2. And this is the one that is going to be positively charged, the one that has the double bond. And so you can kind of imagine that if you were to have a horse, so this is how the horse comes into play. If you were to have a horse and then you were to have a guy, let's say, a guy is riding this sideways horse, he's gonna be up here, his two legs would kinda straddle down and be on top of the horse. And so that's what I think about when I see these double bonds here. These two double bonds are like the the guy's legs straddling the horse, riding the horse. And so that can help you remember. So r for riding has that features of the sword, but it's also got this triangular nitrogen structure at the bottom that somewhat resembles a person riding a horse. And so this is it for arginine structure. And again, we'll be able to utilize all of these memory tools in our practice problems, so I'll see you guys in those videos.
4
concept
Charged Amino Acids
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5m
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So in our previous videos, we've said that the 5 charged amino acids can be further split into 2 smaller sub categories, the negatively charged acidic amino acids and the positively charged basic amino acids. So in this video, we're gonna try to clear up any confusion that you might have about how to group the charged amino acids as either acids or bases. And so recall from our previous lesson videos that acids are substances that are capable of donating hydrogen ions to the environment. And bases, on the other hand, are substances that accept hydrogen ions from the environment. And so down below, you'll see we have our mnemonic for memorizing the charged amino acids, and that is dragons eat knights riding horses, where aspartic acid and glutamic acid are the negatively charged acidic amino acids, and lysine, arginine, and histidine are the positively charged basic amino acids. And they are positively charged because they have these extra hydrogen ions that are positive. And so, here we have a question, and it's asking, why aren't the positively charged amino acids, lysine, arginine, and histidine, grouped as being acidic if they have these hex extra hydrogens? If they have extra hydrogens, shouldn't they be able to donate those hydrogens and be categorized as acids and not as bases? Well, it turns out that this confusion has to do with the fact that we're not realizing that acid base groupings of amino acids are defined by the behaviors of the r groups under physiological conditions. And so recall that physiological pH is right around a pH of 7. And really, it's the pH of the solution that is going to determine whether the amino acids are gonna have a positive or a negative charge. But again, we'll focus more on pHs later in our course. For now, let's take a look at our example down below. What I want you guys to realize is on the left image over here, what we have is aspartic acid and aspartate, which we know is a negatively charged acidic amino acid from our mnemonic. And so the one letter codes are just d for both aspartic acid and for aspartate. And we know that, aspartate has this extra hydrogen here that is capable of being acidic, and aspartate, notice, is missing that hydrogen, and it has a negative charge on it. And so what you'll see here is that at lower pHs, this amino acid exists as aspartic acid with this extra hydrogen on its car boxyl group. But as the pH changes from low pHs up to physiological pH, right around a pH of 7, what happens is this reaction right here occurs, where the hydrogen is released. So this hydrogen is released to the environment, making it an acidic hydrogen. And notice over here what we have is a carboxylate group. And so essentially, this structure here for aspartate is the structure that exists at physiological pH. And so under physiological conditions, notice that aspartic acid is acting as an acid, and that's why we group it as an acid, because of its behavior, specifically at physiological pH. Now over here on the right hand image, what we have is lysine. And lysine, we know, is a positively charged amino acid that is basic. And lysine's one letter code is just a K. And notice that even when its R group does not have a charge, its name doesn't change, it's still lysine, and its one letter code is still a k. And so essentially, the reaction that you see over here is the one that takes place under physiological conditions, and notice that the arrow is reversed from the arrow that we see over here. And so essentially, what we're seeing is that, a hydrogen ion from the environment is being accepted and incorporated into the R group. And so that means that it's acting as a base, and this is a basic reaction here. And so it accepts the hydrogen ion, and notice that its amino group becomes charged after it accepts the hydrogen ion. And so essentially, what we're seeing is that this is the structure that exists at physiological pH, and this is the reaction that occurs under physiological pH. And, this structure over here that is uncharged is the structure that, would only occur at higher pH's. But again, we are specifically grouping the amino acids under physiological conditions, and how they behave under physiological conditions. And so, essentially, the main take away here is that the negatively charged acetic amino acids are grouped as acids because of this reaction that occurs to create negative charges at physiological pH. And the basic amino acids are, positive positively charged, or the positively charged amino acids are basic because they undergo basic reactions to accept hydrogens under physiological conditions. And so, essentially, that is it for this lesson, and we'll be able to move on and, get some more practice in our next couple of videos. So I'll see you guys there.
5
Problem
Problem
Draw in the R-groups from memory for each of the charged amino acids at physiological pH.
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Problem
Problem
Fill-in the missing R-groups for the following peptide from memory: H-E-K. Circle the acidic amino acids.
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7
Problem
Problem
Which of the following amino acids does not have a basic R-group?
A
H
B
S
C
R
D
K
8
Problem
Problem
Circle all the following amino acids with a basic R-group?