Acid-Base Properties of Amino Acids - Video Tutorials & Practice Problems
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Amino acids aren't always represented as neutral structures. It's time to represent them appropriately.
At physiological pH (7.4), amino acids exist as zwitterions. Let's take a deeper look.
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Why Amino Acids Exist as Zwitterions
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up to this point. We've been representing amino acids as thes neutral structures. But it turns out that at physiological pH, meaning the pH inside of your body, these amino acids don't usually look neutral. They're usually charged. So how are we going to know what types of charges to place on them? Well, that's what we're gonna focus on in this video when we talk about the acid base properties of amino acids. So at physiological pH, which is around, you know, people say seven, but it's actually like 7.4. If you're if you're Ph. Seven, you're gonna be in the hospital. That's not good. You need to be, Ah, little bit basic. 7.4 is the body's pH. And at that pH amino acids exist in this state called sweeter ions. You've probably heard the words Twitter iron before. Maybe not, but what it means is just It's a net neutral molecule with separation of charges. Let's write that in separation of charges. So that means that overall, the net charge is zero. But there's a positive and the negative or multiple positives and multiple negatives that all cancel out. Okay, so why does it exist like that because it's counterintuitive, like this is the actual equilibrium. What it looks like the amino acid starts off the way that we drew it, that we've been doing it this whole time. It has a regular car books like acid. It has a regular mean, and then at physiological pH, the equilibrium shifts so that you get an an eye on on the, uh oh, and a cat ion on the positive. If you think about it from chemistry perspective, that doesn't make a whole lot of sense at first, because you always are taught to think that the neutral structure is the most stable. So wouldn't it be more stable for it to stay over in that side, then for it to spontaneously turn into this? Why would charges be a good thing? Why would it want to look like this? Well, the explanation goes back all the way back to our acid base chemistry in organic chemistry, and in a topic called determining acid based equilibrium, we learned that the side of a equilibrium that is favored is the one with the highest peak. A. So we learned. If you have an acid base reaction the side with the has the acid with the highest peak. A is gonna be the weakest acid, and that's gonna be the one that's the most favored. Well, that's what's happening here because it turns out that all that's happening is that this hydrogen, which I'm highlighting in red and I'm also gonna highlighting yellow, is moving locations. It's getting off of the O and instead it's joining this nitrogen as being one of the three h is on that nitrogen. So it's basically moving over. Okay, if you were to think of it as a mechanism, the end is actually grabbing the H and giving electrons to the oh, does that kind of makes sense? Well, why would that so why would that make sense? Well, because that hydrogen has to choose which acid does it wanna be on? Does it want to be on a carb oxalic acid, which is a pretty steep, you know, which is a pretty moderate, decently strong acid? Or does it want to be on an ammonium, which isn't as strong of Nassib going back to organic chemistry? Do you guys remember the PKK that we memorize for carb oxalic acids? It was around five. Okay. And it turns out that amino acids are a little bit more city because they have extra groups around like nitrogen that stabilize the anti on. So actually, the P K A of most carb oxalic acids in amino acids is around two. So it's right that in the PK is roughly two of that hydrogen. Okay, once the hydrogen moves over and joins the nitrogen we learned in organic chemistry one that a nitrogen with a positive charge 10 some of p k of around 10. Okay. And actually turns out that that we're very close. It's usually around nine for amino acids. So basically the hydrogen has a choice. Does it stay on the acid that has a PK of two? Or does it move to the acid with the PKK of nine? And the answer is clear. From our acid based equilibrium video, you pick the side with the highest peak A. So that's why the hydrogen doesn't wanna be over here. It prefers to be over here because it wants to be on the acid with the highest peak. A. Because that's gonna be the one that's the most favorite. It's the weakest acid. So that is why that's the chemistry explanation for why amino acids exist in sweeter islands. Okay, so how are we going to know what types of whether it ends to draw? And it turns out that the ph differences in the PH will actually change the charges. So how we're going to do that? We're gonna find out in the next video when you talk about predominant forms.
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Determining Predominant Forms
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like water. Amino acids are AMFA, Terek and AMFA. Terek is just a fancy word for a molecule that can react either as an acid or as a base, depending on the situation. And the reason I mentioned water is because water is the most famous example of an AMFA Terek molecule. Remember that water could either accept a proton or it could donate a proton based on its surroundings based on the Pekka and the pH of the solution. Well, the same thing is true of amino acids, because amino acids have an acidic carve oxalic acid group and a basic amine group. So we're gonna need toe figure out when it's directing as an acid when it's correcting as a base. And for that, we're going to be using exact PK A values. So we use exact PK, a values given to us on a table toe figure out at a certain pH. Does that amino acid exists in a charge state or is a neutral state in a positive or negative. Now I've gone ahead and provided all these P ks for you in your amino acid breakdown sheet. We're not gonna look at it right now, But I just want to remind you remember all those numbers you saw next to the amino acids? This is what we're using them for. We're gonna use them to determine the charges of the amino acids at different pH is Okay. So before we look at an example, I want to remind you about kind of the theory behind this. Remember that in Gen. Cam, there was an equation that we learned called the Henderson Hasselbach equation. Now we're not gonna have to or what I call the H H equation. We're not gonna have to use that equation in this lesson. But there is just this idea from it that you should be aware of, which is that what the Henderson Hasselbach equation tells us is that when ph of the solution is exactly equal to the Pekka oven acid, then exactly half of that functional group is going to be ionized. Okay, so what that means is that if you're pH and your pkr exactly equal to the same amount, that means that that group that functional group will exist as a 50% neutral molecule and as a 50% charged molecules may be positive, maybe negative. It depends on the situation that says neutral in charge. I'm sorry. It's a little bit off of the screen. Okay, So what that means is that when there at equilibrium like that, the neutral and charge forms are even with each other. But once you make the ph a little bit lower than the peak A what's gonna happen? Well, now you're going to get a more pro protein ated form That predominates, because now there's gonna be more acid around. So you're gonna get more charges, more positives. And if the ph is higher than the peak A then it's gonna be more basic in the solution. So the deep rotated form is going too deep is going to predominate. Okay, So I want to show you guys an example of what this could look like, cause I know it doesn't sound very tangible, but hopefully this diagram will make it clear. Okay, so this is what we're starting off from. This is what I already told Todd. Told you guys is the sweeter ion of fennel. Allan E. Okay. And it turns out that if you look at the peak a table for federal Allan E what you'll realize is that PK one or the PK of the carb oxalic acid it's not actually to. It's close to two is 1.83 You actually need to look that up, okay? You can't just say to the PKK the exact p k two or the PKK of the nitrogen is not nine. It's 9.13 Very similar, but just a little bit higher. Okay, so what that means is that at physiological ph of 7.4, like we already discussed, it's going to exist a sweeter I on It's going to exist where the oxygen gives up its proton to the nitrogen so that the oxygen is negative and so that the nitrogen is positive. Okay. And actually, this is gonna be true for any pH. All the way from 1.83 all the way to 9.13 So basically, for like, eight numbers, almost like eight numbers of pH, it's gonna look like this because in all these situations, the sweeter ionic form is the most stable, because in all these situations, the pH hasn't become a greater number than the PK or lesser number than the PK. Okay, but what starts to happen once you reduce the pH of the solution below 1.83? Well, when you let's just think of it conceptually, if the pH is 1.83 is that acidic or basic? Super acidic? Right. So it means there's protons everywhere, right? So this negative charge has been holding on. It's been negative for a while, but what happens if I start slamming it with protons like I keep making the making it more and more acidic? Right? What if I drop it to 1.83? But if I drop it to 1.5, What if I drop it toe one? What if I drop it 2.5? You get what I'm saying. You keep throwing protons at that thing. Eventually, it's gonna get protein ated eventually. At some point, if I add enough protons to it, I'm going to get a proton there. Does that make sense now? You might be saying, Well, how do I know when it's going to add the proton or not? That's what 1.83 is any pH below 1.83 You add the proton so That means that at Ph. 1.83 or below, the pH is less than the peak. A one right PK one is 1.83 And that means that protein ated form is major predominates. That's what predominates means. Okay, Does that make sense when the pH is so low, you can't hold on to that negative charge anymore. It's going to get protein ated. Okay, Now I'm going to remove myself out of the screen to talk about this one. So same thing is this is the case of the nitrogen. So what happens if I start raising the Pete the peak? Each of the solution all the way to, like 10 all the way to 11 right? So this thing is getting super basic. There's hydroxide molecules everywhere, and at some 110.1 of these hydroxide molecules is gonna come and take away this H it's gonna come and remove it because it's positively charged. So you might be saying, Well, how do I know when the hydroxide is going to take away that h you look at the PKK to value the PKK to value is 9.13 That means that any pH that is higher than 9.13 There's gonna be so much based around that that nitrogen won't be able to hold on to that proton and eventually it's gonna lose that proton. Now it doesn't become negatively charged. That's a different idea. But it now it used to be positive. And now it goes into the neutral because it starts off positive. And now you're trying to remove a proton. Does that make sense? So how could I, like, actually say this according to our definition of here? Well, when Ph is greater, then p k A two, which is 9.13 then D protein ated form predominates is major Does that make sense? And the deep rotated form? In this sense, it doesn't dip. Rotated, by the way, doesn't mean that it always has a negative and protein ate. It doesn't always mean that it has a positive because actually, my protein ated version didn't have a positive either. It just depends on the molecule that you're starting with. But deep rooted means that I lost a proton and protein ated met that I gained a proton. Does that make sense? Cool. So this is the way that we're gonna be thinking about predominant forms we're gonna have to compare. PK is using the sheet, and then we're gonna use this simple formula to figure out what form A should be in. So let's it for this video. Let's move on to the next one.
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The 7 Ionizable Amino Acids
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So you think you're getting the hang of this? This is kind of making sense. And now I'm going to throw a wrench into the whole thing because it turns out that there's an extra complication. Which is that seven of the 20 amino acids that you learned actually also have ionized herbal side chains. And what that means is that when you are planning out the sweeter ionic form, if it has positive negatives et cetera you need to also look at the side chain and you have to figure out is the side chain going to be pro rated? Is it going to be depreciated et cetera On top of that? Some professors, some universities make you memorize these seven P. K. S. So I'm gonna give them to you and I don't really have the best memory tools for them. It's gonna be up to you to figure out if you need to memorize these or if they're going to be given to you most of the time, 90% of the time they're given to you, just like the others. So you don't have to worry. But if you happen to have a professor that once you memorize them then you're gonna need to figure out a way to memorize them. Okay so let's go ahead and move to the next page. I'm gonna move to basically back to the amino acid breakdown page. Okay so this is back to the amino acid breakdown. And now we're going to be filling in these boxes over here and the seven ionized little P. K. S. Or side chains are the ones that have white boxes so we're gonna be filling in numbers here. Okay. Cool. Another disclaimer. It turns out that not only does not everyone have to memorize them. Some people do. Some people don't but there are also differing values depending on your professor depending on what website you look at. Some will say 8.3 and some will say 8.4. It's like really stupid. So I personally don't think it's worth memorizing unless your professor makes you because No one really fully agrees. I'm going to go ahead and give you the values that I found were the most popular ones. But if your professor or textbook require you to memorize a slightly different one, use that one. Okay so 8.18. Okay, I'm not gonna give you ways to memorize this. I'm just gonna write them down and you figure that out. If you need to. Tyrosine is 10.07. Spartak acid is 3.65. Glue. Tannic acid is 2.4 not two. Sorry is 4. By the way. That kind of makes sense. Right? That Spartak would be more acidic than glue tannic because it's closer than nitrogen. So it's going to have a stronger inductive effect and this one's further away. It kind of makes sense. Um listen is 10.53. Histamine is exactly six. That one seems to be pretty universally agreed on. It's almost always six. And then arginine is 12.48. Okay so just I'm not going to help you memorize these, you probably don't even need to but just have them written down so we can use them in the following problems. We're going to be referring to this sheet a lot because we're gonna need to get all our P. K. Values from here. Okay. Now I happen to know that the next example is with listening. So let's get these let's write down these numbers now so that we can use them on the next page and I'm actually gonna write them down myself so that I can use them on the next page. So licensing the carbolic acid is 2.18. The amine is 8.95. As you can see again they're close to two and nine but they're a little bit off. And then the licensing side chain is 10.53. So now let's go over to the example, figure out What the predominant form of listen looks like and what's the net charge at a ph of 8.5. Cool. So actually just do this together. Okay. Um Actually okay no, I'll let you guys try it first. So you guys try it first and then in the next video I will solve it for you
As mentioned, 7 of the 20 amino acids have ionizablesidechains. The 7 are:Cysteine (C), Tyrosine (Y), AsparticAcid (D), GlutamicAcid (E), Lysine (K), Histadine (H), and Arginine (R).
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example
Predicting Predominant Form of Lysine
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So let's write in r P. K s. This one PK one was 2.18 This one was 8.95 And then finally the sun was 10.53 Also notice that I didn't include any hydrogen because the hydrogen, they're going to depend on the charge. Okay, so let's just go PK by PK. Okay, so the first one. So remember, the pH is 8.5. So for PK one is ph less than or greater than 2.18 It's greater than right. So pH is greater than PK one. Does that make sense? And I'm just gonna write in the numbers. Just you guys can see Ph is 8.5. PK one is 2.18 Which one's bigger? Ph. Right. So what does that mean? Well, when the pH is greater, that means protein ated. Well, no, that means deep rotated, right. We have to look at our rules. Deep protein ated predominates, right? Let's just make sure deep when it's greater deep rotated predominates, right? Because it's basic. So I'm gonna put here deep protein needed. And for this speedy protein aided, that means it needs a negative charge. Cool. So we figured out the first charge already. Awesome. So let's look at the next one. So is the pH greater than or less than P K two? It's actually less than right because P K two is 8.95 So in this case, pH is less than P K two. And once again just toe make it really clear what I'm saying is that 8.5 is a lower number than 8.95 Correct? So since it's lower, that means that it's more acidic. That means protein ated predominates. All right, let me avoid writing over the life seen. Okay, so that means that the protein aid form of this mean is NH three positive, right? So, actually, we've got ours with her eye on a to this ph 8.5. We've got ours Witter ion, by the way, I could have already known that because 8.5 is in between the two ph is PKS, right? Remember we said any pH that's between the two p. K. S will form the Twitter. I am so 8.5 makes sense that it does. Then finally, 10.53 So pH is less than Piquet a three. And just to be super clear, that means that 8.5 is less than the number 10.53 right? So since it's less, I mean, it's more acidic, which means that the protein ated form should predominate, and the protein ated form of a mean is an NH three. So that means that this should also be N H three positive. Cool. So now we figured out the predominant form at this specific pH. What is the Net charge? Well, the net charge is just summing all the charges. So I have two positives and one negative. So that means that net charge is equal to one positive. Okay? Or you could just put a bracket around and just say that it's positive. Okay, cool. So now you guys get the fact that predominant forms aren't just with the backbone. You also may have to include the side chain, and you may need to memorize your PKK's for the seven invisible amino acids if your professor wants you to. But for right now, we'll just be looking at the reference sheet every time. Okay, so let's go ahead and move on to the next video
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Problem
Problem
Predict the predominant form and net charge of tyrosine (Y) at pH 10. What is the net charge?
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Problem
Determine the net charge of the dipeptide R-C at pH 4.3. (Hint:Peptide bonds do not count)
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