Polar Amino Acids - Online Tutor, Practice Problems & Exam Prep

Structural Classification

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 going to do is we're going to kind of set up our game plan for the way we're going to think about these amino acids so that when we start categorizing them, we're all on the same page. So let's go ahead and get started. 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 going to prepare you to memorize all these different facts just in case. And what are the things that you're likely going to be responsible to know? You're responsible to know the names of the 20 amino acids, the structures, so actually be able to draw them from scratch. There are 3-letter abbreviations. So the abbreviations of those names, the one-letter symbols of those names. So the 20 amino acids are represented by 20 different letters of the alphabet. You're probably going to need to know that as well. Their structural categories, like what type of functional groups they have. Their functional categories, how do they react in water? Crazy. And maybe even their pKa'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 flashcards, but I'm going to 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 so 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 to 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 amino acids is that there's 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 a friend that's 1 year ahead of you. It's in school and you ask them for their notes and amino acids. And let's say that they're having to learn it in biochemistry and you learned it in organic chemistry, professors, you may actually have to learn slightly different things. You may need to categorize them slightly differently which makes things really hard. Imagine that you want to learn them and you go to YouTube and you look at a video and that video is going to be a little 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 going to use here at Clutch Prep, okay? So the two most common methods are structural classification and functional classification. So the first one that we're going to 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 amino acids. So what you're looking at is you're looking at the actual atoms or the side chains and you're saying, these 2 side chains kind of look similar. These 2 side chains kind of look similar. So we're going to group them into these categories. Very common categories that you'll see of structural are categories like aliphatic. Aliphatic means that it's a 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, etc. Like you can keep going but, basically, it 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 going to fit into more than one category because they're going to have maybe 2 structural features that are shared with other groups. So let's just do an example...

Functional Classification

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 organic knowledge to figure out what groups they belong in and 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 going to be focusing on because it's actually the most popular. And that has to do with functional categorization, meaning that we're going to be looking at the similarities and differences between amino acids reacting in an aqueous environment. We want to figure out how these amino acids are going to react in water. And that's actually going to be how we are going to learn to categorize the amino acids. Okay? So just so you know, how do you know we're talking about functional or structural? Well, you're going to be looking for these types of words. You're going to be looking for words like nonpolar, polar, neutral, acidic, basic, hydrophobic, hydrophilic. All of these words, even though they don't seem to have to do with water, they actually do. Because what it's talking about is, is it nonpolar compared to water? Is it acidic compared to water? Is it neutral compared to water? Is it hydrophobic which means it's actually afraid of water. It's trying to remove itself from the water. So what we're going to be doing is we're going to be learning how to categorize our amino acids with respect to how they react in water. And if you know this, this is, first of all, it's the harder one to memorize, but it's also probably the more helpful because it's 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 a 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 going to be going over here at Clutch Prep, we're going to be using 2 systems. Okay? And these are 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 are your neutral amino acids and these are your charged amino acids. So we're going to learn that, but beneath that there's another category which is sometimes 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 are 2 subcategories and those subcategories are nonpolar and polar. Okay? If I say nonpolar 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 charge. There are 2 types of charge. There's acidic charge and there's basic charge. So you might need to memorize them altogether as charged or you might need to memorize them separately as the 2 acidic amino acids and the 3 basic amino acids. Okay? Most likely, you're going to have to memorize the 23 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 5. Okay? So what's actually going on in this diagram? Well, guys, remember I talked about these 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 going to draw here. Don't do this on your own page, but I'm just going to draw like a big protein. And outside of that protein is water, and these are all water molecules. Bloop, bloop, bloop. 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. These amino acids hate water because they can't hydrogen bond, they're not polar, they're nonpolar. Right? And remember that when we learned about solubility a long time ago, like dissolves like. Is water polar or is it nonpolar? Do you remember? Water is very polar. So that means that according to the solubility rules of like dissolves like, which amino acids want to be the closest to water? The polar ones. The ones that have charges, the ones that have dipoles, etcetera. Which ones want to be as far away from the water as possible? The nonpolar ones. Because nonpolar and polar don't mix. It's like oil and water. Okay? It's exactly like oil and water. Okay? The charged ones are like the water, and the nonpolar ones are like the oil trying to stay away from the water. Okay? So we have 9 amino acids that are nonpolar. These are going to be super hydrophobic. They're going to want to be as far inside of the protein as possible. They'll do whatever they can to 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 hydrophilic polar groups. So these 6 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 still they still don't want to be, like, submerged in water, but they're right in the middle. You know, like, they can be kind of on the outside of the protein. They're a little bit more hydrophilic, but they're not fully charged. Okay? And then finally, we have our charged proteins, or our charged amino acids. These guys can hydrogen bond, they can have full charges potentially, and what that means is that they are going to they're water-loving. These are hydrophilic. 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 aqueous environment are interacting with them. Okay? So when we talk about when we start memorizing our amino acids, we're going to be memorizing them in this order. We're going to be memorizing from the most hydrophobic, the nonpolar, then we're going to talk about the polar, and then we're going to talk about our acidic and our basic. Alright? So I hope that this makes sense. This is going to be the system that we use here at Clutch Prep. It's also the most common, 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 going to work, I'd say 80% of the time. Okay? So let's go ahead and move on to the next video.