Before we memorize the 20 standard amino acids, let's devote some time categorizing them into structural and functional categories.
Play a video:
Was this helpful?
I am so sorry to break this to you, but a really big part of learning proteins is memorizing your 20 amino acids. This is no easy task. It takes a lot of work. And in this video, what we're gonna do is we're gonna kind of set up our game plan for the way we're going to think about these amino acids so that when you start categorizing them, we're all on the same page. So let's go ahead and get started. So, like I said at the beginning, you're likely going to need to memorize your 20 standard amino acids that are derived from proteins. Now, you might get lucky, and maybe you don't need to memorize all of these things. But I'm just gonna prepare you to memorize all these different fax just in case. And what are the things that you're likely going to be responsible to know your response so well to know the names of the 20 amino acids the structure so actually be able to draw them from scratch There three letter abbreviations. So the abbreviations of those names, the one letter symbols of those names so the 20 amino acids are represented by different letters of the alphabet. You're probably gonna need to know that as well. Their structural categories like what type of functional groups They have their functional categories. How did they react in water crazy and maybe even their P. K s, which has to do with the acidity of these amino acids. Guys, it is so much to know. And a lot of people just resort to using flash cards. But I'm gonna help you through this process so that you're not just making flashcards from scratch. You have a strong foundation to start from. Okay, so just you know, this video is not about memorizing the acids, because we're going to do that on the next page in what's called the clutch prep amino acid breakdown, where we're going to devote a bunch of time just toe learning them. But in this video, let's just talk about how to categorize them. So it turns out that part of what sucks about learning your mental acids is that there is no universally agreed upon method of categorization. What that means is that you may ask your friend for their notes. Let's say you have ah, friend, that's one year ahead of you. It's in school and you ask them for your notes for their notes and amino acids. And let's say that they're having to learn in biochemistry and you learned it in organic chemistry. Let's say, Well, it turns out that based on your textbooks or based on your professors, your you may actually have toe learn slightly different things. You may need to categorize them slightly differently, which makes things really hard. Imagine that you wanna learn them and you go to YouTube and you look at a video and that video is gonna be a little bit different than potentially what you need to know for your class. So what I want to do is talk about the different systems of categorization and then coach you through which one we're gonna use here. A clutch prep. Okay, so the two most common methods are structural classification and functional classifications. Okay, so the first one that we're gonna talk about is structural categorization. So what does it mean to have a structural categorization? It means that you're basing the categorization of these amino acids on structural similarities. Okay, between the immuno acids. So what? You're looking at is you're looking at the actual atoms or the side chains, and you're saying these two side chains kind of looks similar? These two side chains kind of look similar. So we're going to group them into these categories very common categories that your sea of structural are categories like Alif attic. Al emphatic means that it's hydrocarbon without any aromatics in it. Okay, aromatic. So it has these rings with alternating single double bonds, sulfur containing does it have sulfur in it? There's more like oxygen containing nitrogen containing instead of like you can keep going, but basically just has to do with looking for patterns in the atoms and trying to match the atoms into groups. Okay, now, this is actually problematic, though, because some amino acids are actually gonna fit into more than one category because they're gonna have maybe two structural features that are shared with other groups. So let's just do an example to show how this is a little problematic. So I want us to together proposed structural categories for the following amino acids. So that means you don't even know your categories yet, But if you had to make some up What would you make up? Okay, so let's just go ahead and start off with this first one. Fennel, Alan. I mean, what I notice is that first of all, like, keep in mind that all of the backbones of the amino acids are the same. They all have this going on, right? They all have carb, oxalic acid. I mean, so all we're doing is we're comparing the side chains, right? We're comparing all these guys here. So when we categorize thes, we wanna be looking at the blue part and we want to be saying, you know, what's how could we kind of group these together? So federal Alan, I notice has an aromatic ring. So let's go ahead and group that as an aromatic, um, amino acid, which it is in that sense, searing has, um, and alcohol. So let's say this is alcohol containing valley ing is just a hydrocarbon. It's just, you know, carbon and hydrogen. So we could say this is Al emphatic. That's actually the definition of Aleph attic. Okay, so so far, so good struck this structural colorization. Seems you working history, Dean. So this is actually a hetero cycle, but it's still aromatic. It has those all training single bonds sold once. So this one actually also go into the aromatic category high five. It looks like we're grouping these. Well, now, let's get to tire scene. Hm. How would you group this? Well, it looks aromatic for sure. It has that benzene ring, but notice that there's a problem. It also has an alcohol. Right. So how would you categorize this? Would you categorize it as aromatic? Would you categorize it as alcohol containing the answer is that it's actually both. And that's why this system is kind of tricky, because sometimes you're gonna have overlap and you're gonna try to memorize Oh, these are my aromatics. And then you're gonna have this. These are my alcohol's. But then, like the same amino acid is in both groups. So I just wanna let us know that for the purposes of clutch prep, we're not going to be using this method one, because it's not really that accurate, right? I'm proving to you that sometimes there is overlap. But second of all, because this is actually pretty easy, like as long as you know, your amino acids, you could figure out these categories on your own just by looking at it, right? I don't need to teach you this a whole lot. I don't need to teach you what alcohol looks like or what an aromatic looks like. You can figure that out on your own. So if you're Professor, if your textbook, if your homework wants you to categorize in this way, it's all you I'm giving you permission to just look at the groups and try to figure it out that way and do your best. Okay, But we're gonna be focusing on a lot more here. A clutch prep is the functional categorization because it's a lot harder to understand, and it's the one that we're gonna need more practice on. So in the next video, we're gonna talk about functional categorization.
Play a video:
Was this helpful?
So even though I kind of just bashed the structural categorization system, I hope that one point that I got across is that it's pretty straightforward. You don't need to practice it a whole lot, just kind of look at the functional groups and use your or go knowledge to figure out what groups they belong in. And that's that's the end of it. So even though it's not the best system, at least it's pretty easy to use now. The second one is not easy to use, and this is the one we're gonna be focusing on because actually the most popular. And that has to do with functional categorization, meaning that we're gonna be looking at the similarities and differences between amino acids reacting in an aqueous environment. We want to figure out How are these immuno acids going to react in water? And that's actually going to be how we are going toe, learn to categorize the amino acids. Okay, so just, you know, how do you know we're talking about functional or structural? Well, you're gonna be looking for these types of words. You're gonna be looking for words like non polar polar neutral, acidic, basic hydrophobic Hydra Filic. All of these words, even though they don't seem toe, have to do with water. They actually do because what it's talking about is it non polar compared toa water? Is it acidic compared toa water? Is it neutral compared to water? Is it hydrophobic? Which means it's actually afraid of water is trying toe remove itself from the water. So what we're gonna be doing is we're gonna be learning how to categorize or amino acids with respect to how they react in water. And if you know this, this is first of all, it's it's the harder one to memorize, But it's also probably the more helpful because the one that's the most commonly tested Okay, now I do have one note here, which is that this one is also problematic for specific reason, which is that different sources categorize slightly differently, so they don't all use the same words. Sometimes there's overlap between the words. Sometimes they use synonyms. Okay, so what? I'm gonna be going over here a clutch prep. We're gonna be using two systems. Okay? And these were the two most common systems, and I want you to understand what they are. One of them is the neutral and charged system. Okay, so sometimes you're just going to see you may have to just memorize that these air, your neutral amino acids and these air. You're charged amino acids, so we're gonna learn that. But beneath that, there's another category, which is sometimes it's like a It's like an extra level of complexity, which you may also be required to know, and that has to do with the exact polarity of each one. So in the neutral category, there's too, so it's kinda like neutrals, the umbrella term. But within neutral. There's two sub categories, and those sub categories are non polar and polar. Okay, so if I say non polar amino acid, that means neutral. If I say polar, that means neutral. Maybe you don't even have to use the word neutral. But I'm just letting you know if you have to use whichever word you have to use. Now you're kind of understanding how they're related to each other. Same thing with charged. There's two types of charged. There's acidic charged, and there's basic charged, so you might need to memorize them all together as charged, or you might need to memorize them separately as the too acidic amino acids in the three basic amino acids. Okay, most likely you're gonna have to memorize the two and the three because they're pretty different from each other. But I'm just letting you know that if you see the term charge, it's just referring to those five. Okay, So what's actually going on in this diagram? Well, guys, remember, I talked about thes one letter symbols that represent that are used to represent amino acids. These are all 20 symbols. And what I've done here is I've ordered them. I've grouped them according to what type of category they're in. Okay, So, starting all the way from the left hand side, imagine that we have a protein. Okay, This is actually like a big protein I'm gonna draw here. Don't do this on your own page, but I'm just gonna draw like a big protein. And outside of that protein is water. And these air, all water molecules, blue, blue. They're all kind of like, floating around. And then that's the center of the protein all the way towards the left of the page. Okay, well, all the way towards the left. We have the most hydrophobic proteins or amino acids. Thes amino acids hate water because they can't hydrogen bond. They're not polar, their non polar. Right? And remember that when we learned about soluble ity a long time ago like dissolves like Is water polar or is it non polar? Do you remember? Water is very polar, So that means that according to the solid ability rules of like dissolves, like which amino acids want to be the closest toe water, the polar ones. The ones that have charges the ones that have died polls, etcetera. Which ones want to be as far away from the water is possible. The non polar ones. Because non polar and polar don't mix. It's like oil and water. Okay? It's exactly like oil and water. Okay, The charge ones are like the water, and the non polar ones are like the oil trying to stay away from the water. Okay, so we have nine amino acids that are non polar. These air going to be super hydrophobic. They're gonna wanna be as far inside of the protein is possible. They'll do whatever they can tow fold inside the protein so they're removed from the water. Then we have still in the neutral category. They're not charged, but we have slightly more polar or slightly more Hydro Filic. Um, polar groups. So these six amino acids are going to have either partial positives or partial negatives that allow them to be a little bit more comfortable around water. But they're still they still don't want to be like submerged in water. But they're right in the middle, you know, like they could be kind of on the outside of the protein. They're a little bit more hydro Filic, but they're not fully charged. Okay? And then finally, we have our charged proteins are charged amino acids. These guys have can hydrogen bond. They can have full charges potentially. And what that means is that they're gonna They're water loving these air hydro filic. They love to be out in the water, hydrogen bonding with their buddies, all these water molecules around. That's exactly what they want. They want to do whatever they can to be on the outside of the protein so that the water molecules around in the acquis environment are interacting with them. Okay, so when we talk about when we start memorizing are amino acids. We're gonna be memorizing them in this order, we're gonna be memorizing from the most hydrophobic, the non Poehler's. Then we're gonna talk about the pollers, and then we're gonna talk about our ascetics and are basics. Alright, so I hope that this makes sense. This is gonna be the system that we use here. A clutch prep. It's also the most common. Um, but if your professor or your textbook uses a slightly different system, then it will be up to you to kind of pick and choose which parts of this to keep and which parts to replace with the way that your professor wants you to learn it. But this is gonna work, I'd say 80% of the time. Okay, so let's go ahead and move on to the next video