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Biochemistry

Learn the toughest concepts covered in Biochemistry with step-by-step video tutorials and practice problems by world-class tutors

3. Amino Acids

Charged Amino Acids

1

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Charged Amino Acids

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in this video, we're going to begin our discussion on our fourth and final amino acid group, the charged amino acids. So the charged amino acids all have our groups that are electrically charged, but they're not always charged, and it turns out that their charges depends on the pH of the solution that they're sitting in. But we'll talk about the Ph Is and the charges of our 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 seven. And so this group of charged amino acids can actually be broken up into two smaller subgroups. And so there are two 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 pneumonic to help you guys memorized not only the five charged amino acids, but also how these five 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 pneumonic is just dragons eat nights riding horses. And so we kind of already knew that right back in the medieval times there were dragons. They were eating nights, riding horses, whatever. And so what you'll see here is that our image is broken up into two parts, and so it's really breaking it up into our smaller categories of the negatively charged acidic amino acids on the left and the positively charged basic amino acids on the right. And so each of these letters here, uh, the capital letters of these words. So the d, the E and the k R N h r representing the one letter amino acid codes for those five charged amino acids. And we have all five of those one letter codes on the left over here. And so, essentially, what you'll see is that the D represents a Spartak acid Theis for glue. Tannic acid. K is for licensing. R is for Argentine and H is for history. And so this means that a spark acid and glue tannic acid are the two 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 fired acid out of their mouth is a negative thing. And so that means that Spartak acid and glue tannic acid are negatively charged, acidic amino acids. And the dragon is shooting acid out of its mouth. And that's why they're acidic. Now, looking at our image over here on the right, with the knights riding horses, you could see that we have a night riding a horse, and that is something that is very noble and positive. And so these amino acids here licensing Argentine history in our the positively charged amino acids. And so because these nights and the 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 could even imagine our night carrying a pumpkin spice latte and our horse marching into battle with Cem Ugg boots. So super basic. And so hopefully this will help you guys remember the five charged amino acids and how they could 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 negatively charged amino acids of a Spartak acid and glue tannic acid. So I'll see you guys in that video.
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Charged Amino Acids

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So now that we understand this pneumonic appear a little bit better to memorize the five charged amino acids, we're going to focus on the negatively charged, acidic amino acids or this particular group that's boxing up here. And so, with these acidic amino acids, it turns out that all the are groups actually donate ah, hydrogen ion, or H plus. And so when the are groups donate in H plus, that results in a negative charge. And again, there are only two amino acids that fall into this group, negatively charged in acidic amino acids. And they are, ah, Spartak acid and glue tannic acid. And really, it's the presence of car box Cilic acids that render these amino acids acidic in the first place. And so you really wanna be making this association between negatively charged and aesthetic amino acids. And so let's jump into our example where we can look at the actual structure. Our group structure of the, uh, these two amino acids. And so our first amino acid is a spar tick acid, and so a Spartak acids three letter code is just a S P, and it's one letter code is gonna be D because it fits in phonetically at this position here for a Spartak acid. Now it turns out that aligning, aligning once again is gonna be a leader for this amino acid. And so a Spartak acid is really just aligning with you guessed it a car boxing group. It's literally just outing with a car boxful group. And so all we need to do to get a Spartak acid structure is to start off drawing a winning so a ch and we know the hydrogen numbers they're gonna change. It's gonna end up being, too. And then we just draw a car boxing group. So a C double bond Oh, and O H group. And it turns out that this h on this, uh, 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 car boxer group, and it's aligning with a car box work. That's it. That's a Sparta Gasset structure. Now again, a Spartak acid is an acid so it can donate its hydrogen. That's what we're seeing in this process. Here. It's donating. It's acidic hydrogen. And so when that process happens, when Spartak acid donates its hydrogen ion, It actually becomes, uh, Asper Tate. It becomes Asper Tate and so we can see that right here. And so all we need to do to draw Asper Tate structure is to redraw a Spartak acid without this acidic hydrogen. And so what we can do is just draw it in ch two. It's gonna be see double Bond. Oh, 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 a Spartak acid is a negatively charged, acidic amino acid. And really, it's, uh, Asper Tate that holds that negative charge. So over here are naked our next. Our second amino acid in this group is glue tannic acid and glue tannic acids. Three letter code is G l U. And it's one letter code is E because it fits in phonetically at glue. 10 Mac acid. And so we've seen this glute here before, right? We've seen gluten and gluten we saw with glutamine, so you can really associate these glutes with one another. So we've got glutamine and glue tannic acid, and so really, what you'll see is that glue tannic acid is really just glued A mean with you guessed it a car boxful group instead of an A My group. So if you remember Glutamine, then you could also get glue tannic acid structure. So it's gonna be the same thing, so they'll have to ch two, and it will also have a car boxer group. So it'll have a C double bond, O and O. And then I'll put the h the acidic H in a different color h. So what we've got is a car boxer group here instead off an AM I group for gloomy for glue. Tannic acids are group. Now there's a second way toe also memorized glue tannic 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 but 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 glue tannic acid obviously has the gluten here, it's going to be a little bit longer. And so the second way that you could think of this is glue. Tannic acid structure is just building off of a Spartak acid structure. And so it's just a little bit taller. Noticed that. It just has ah, little bit. Mawr has a ch to an extra ch two, that Theus part a Sparta gas it doesn't have. And so that's how you memorize school. Tannic acid structure and again, blue tannic acid is an acid so it can donate. Ah, hydrogen. Okay. And it will donate this acidic hydrogen here. And so when it does, that glue tannic acid actually becomes glutamate. So it becomes glutamate and we could see glutamate right here. And so for glutamate structure, all we need to do is redraw glue, tannic acid. So we'll have the CH two ch two again the C double bond. Oh, 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 ascetic amino acids. We've got to 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 going to focus on the positively charged basic amino acids. And with these basic amino acids they all contain are groups that are capable of accepting a positively charged hydrogen ion. And so, of course, that's going to result in the our group having a positive charge and recall that there are only three amino acids that fall into this group. And those are license Argentine and history in and so are pneumonic for remembering those three amino acids is nights riding horses. And so license One letter code is K for nights, Argentines is our for riding and historians is h for horses. And so really, it's the presence of these ionized herbal nitrogen atoms or these ionized able nitrogen in the are 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 are groups themselves and our first amino acid is licensing and recall license. Three letter code is just l Y s And again it's one letter code is K and in our pneumonic uh, listen is represented by a night and so appear in the top left corner. We have our night and really license are looks like a night's stored It really looks like a knight sword. So here we have a sword to represent that. And just like with a sword, you try toe poke somebody with the pointy end you can think about are one letter code for licensing And ask yourself how many pointy ends could I try toe poke somebody with with this K here? And so when you count them up there are 1234 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 four pointy ends, and just like the Letter K has four pointy ends, there's going to be a four carbon start to the chain of license our group. And so let's go ahead and draw that in so we can draw on our first carbon. So ch two, our second siege to third and fourth Perfect. So now we have a four 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 in 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 in NH three because it's gonna be positively charged and really again. It's the presence of thes nitrogen in the are groups that make them basic and positively charged. All right, so our next one is Argentine and actually, what we're gonna do is we're gonna skip Argentine. We're gonna do history in first and then once we're done with, his sitting will go back and we'll finish Argentine. So let's jump on over to history. So recall hitting three letter code is just h i s. And it's one letter code is H and our pneumonic the H stands for a horse. And so up here in the top, right, we have our horse. And really, all history is it's Alan s. So it's our leader aligning with ah five member ID ring branching off of it. So let's go ahead and draw that in right here. So we've got Alan. So it's gonna be C H. And we know the hydrogen zehr gonna change. It's gonna end up being, too. And then there's a five member dring branching off. So let's draw that end. So we've got one side to side three side, four side, five side. Perfect. There's Allan E with our five member drink. So the next part is to remember, history means one letter code. So histamines one letter code is an H. And just like the letter H has two parallel lines. So here's one. And here's the other parallel line. Just like the H has two parallel lines. The ring in history is our group is gonna have to double bonds and to nitrogen atoms. And so the next thing to remember is that just like the h in history in in our pneumonic stands for a horse, Really, uh, historians are chain or our 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 air the back legs, these are the front legs of the 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 back legs. Here are 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 the hydrogen so we could do the same over here, drawing our little tail in the back of 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 that's gonna be positively charged. So what we could do is is draw in our extra h here and make this next year positively charged. And so the last step is just to remember that the horse here is actually not stepping on the second nitrogen atoms. So at this point, we have to double bonds, which is great, and we only have one 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, uh, the other nitrogen Adam. 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 in the the horse would also be stepping on it. So I can't go there. And the nitrogen is not gonna be in the tail. So that means that the only place the nitrogen could go is in this position here, and then we just fill in our extra hydrogen and that's it. That's the structure of history ing. So if you can remember these memory tools, hopefully that will help you remember the structure of history in our group. So now that we're done with history and we're gonna go back and we're going to complete Argentine and so Argentines, three letter code is gonna be a r G. And it's one letter code is just gonna be our for Argentina. And remember that the R and R pneumonic stands for writing and the writing is or the Argentines are group. It's kind of a mixture of the sword or listens. Our group and the horse or history into our group. It's like a mixture of the two. It's got a little bit of features of both, and so that's what we can put in here. That the our group for Argentines are. 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, whether it's one letter code. So if we were to draw on our here, you would see that there's really only three pointy ends that you could try to poke somebody with. You could try to poke somebody with this point in this point in or this point in, and you can't really use this one because it's kind of blocked off. So there's only three pointy ends, and just like there's three pointy ends in the are, there's going to be a three carbon start to the chain. So let's go ahead and drawing are three carbon start. So we got our CH two ch two and ch two perfect. So now we've got our three carbon start. The next part is to remember that, just like there are three pointy ends on the are, there's also going to be a triangular, so a triangle has three sides to it. There's gonna be a triangular nitrogen structure at the bottom of our sport 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 bonnet 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 are triangular nitrogen structure. And so what you'll see is that all you need to do is fill in the hydrogen is at this point. So, uh, this one's going to have to our one hydrogen. This one is going to have to hydrogen. And then this one up here, the one that's what the double bond is actually going to have to hydrogen isas. Well, it's gonna have NH two, and this is the one that is going to be positively charged the one that has the double bomb. And so you can kind of imagine that if you wanna have a horse. So this is how the horse comes into play. If you have a horse and then you would have a guy, let's say the guys riding the sideways horse, he's gonna be up here. His two legs would kind of straddle down and be on top of the horse. And so that's what I think about when I see this double bonds here thes two double bonds or like the guy's legs straddling the horse riding the horse, and so that can help you remember. So are for riding has that features of the sword. But it's also got this triangular nitrogen structure at the bottom that somewhat resembles, ah, person writing. Ah, horse. And so this is it for Argentine structure. And again we'll be able to utilize all of these memory tools and our practice problems. So I'll see you guys in those videos
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Charged Amino Acids

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So in our previous videos, we've said that the five charged amino acids can be further split into two smaller sub categories. The negatively charged acidic amino acids and the positively charged basic amino acids. So in this video, we're going to try to clear up any confusion that you might have about how to group the charged amino acids as either acids or basis. And so it 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 pneumonic for memorizing the charged amino acids. And that is dragons eat nights riding horses where a Spartak acid and glue tannic acid are the negatively charged, acidic amino acids and lacing Argentine and history 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 lice in Argentina and history grouped as being acidic if they have these extra hydrogen. If they have extra hydrogen, shouldn't they be able to donate those hydrogen and be categorized as assets and not as basis? Well, it turns out that this confusion has to do with the fact that we're not realizing that acid based groupings of amino acids are defined by the behaviors of the are groups under physiological conditions. And so recall that physiological pH is right around a ph of seven. 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 pH is later in our course. For now, let's take a look at our example down below. And what I want you guys to realize is on the left image. Over here. What we have is a Spartak acid and Asper Tate, which we know is a negatively charged, acidic amino acid from our pneumonic. And so the one letter codes are just D for both a Spartak acid and for Asper Tate. And we know that, uh, Asper Tate has this extra hydrogen here that is capable of being acidic, and Asper Tate notice is missing that hydrogen, and it has a negative charge on it. And so what you'll see here is that at lower pH is this amino acid exists as a Spartak acid with this extra hydrogen on its car boxful group. But as the pH changes from low, Ph is up to physiological pH right around a ph of seven. 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 car box, Late group. And so, essentially, this structure here for Asper Tate is the structure that exists at physiological pH. And so, under physiological conditions, noticed that a Spartak acid is acting as an acid. And that's why we group it as an asset because of its behavior specifically at physiological pH. Now, over here on the right hand image, what we have is listen and listen, we know is a positively charged amino acid that is basic and listens. One letter code is just okay and notice that even when it's our group does not have a charge, its name doesn't change. It's still license and it's the one letter code is still okay. 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 Ah, hydrogen ion from the environment is being accepted and incorporated into the our 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 noticed that it's 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 Onley occur at higher pH is. But again, we're 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 acidic amino acids are grouped as assets. 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 hydrogen 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

Draw in the R-groups from memory for each of the charged amino acids at physiological pH.

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6
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

Which of the following amino acids does not have a basic R-group?

8
Problem

Circle all the following amino acids with a basic R-group?

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