 Hello everybody, if you could have a seat, that would be great. We have a silly number of slides today, so I want my time in. Welcome to biochemistry. I've been out of this class for a year. Professor Gervold and Professor Mowry are taking a well-deserved break, so it's just us this year. So let's jump right into it. I'm the only professor, captain. And you have wonderful TAs in this class. Sarah Taylor, you must know Sarah. Yeah, maybe a better arrangement would be for me to switch places, but Sarah is wonderful. And she's organizing another set of wonderful TAs. If they could stand the ones without laptops, maybe, so that everybody could know. So turn around so everybody can see it. So these are your TAs. They are superstars, and they took the class previously. So they did incredibly well, and they'll be leading your conference sections. So Alex is our sole graduate TA. Alex has the responsibility of being in charge of a lot of the grading functions in the class as well as the section. So we have a lot of technology in this class, and I just forward email. So if you have any problems, a more efficient way to get your problems solved is just contact Alex directly. And so he's doing the clicker grading. So we'll be doing a test of the clicker today for those that hopefully brought them. And if your grades don't show up in Canvas grade function, then Alex would be the one to contact. Alex also is very handy with computers. So if you're having problems asking for any of the material, Alex can help you with that. Alright, so the course is centered around the Canvas webpage. And so let's go through that. So this is the basic layout of the Canvas site. There's all kinds of features, announcements on the front page. If you click the calendar link up top, you can actually subscribe to the calendar so that it'll add it to your Google calendar and you'll get happy reminders. It's time to wake up for class at 1 o'clock. So just click the calendar feed. Or if you don't want to come, don't click the calendar feed. But we have all the various assignments. This year there's problem sets. So the due dates for those are on there. There's exams and everything is on the calendar. Alright, so if you click the course info link, you have information about office hours, the TAs, like email addresses. If I'm on Skype, feel free to call me. I did that with some students last year and it's a little weird. But I'm available. If I don't pick up, I'm probably sleeping. It's okay. I'll try to be decent. Okay, syllabus. If you click the syllabus link, you get information about the grading in the course. We'll go through that in a moment. But you have a list, a day-by-day list, of all the things that we're doing. So the clicker, which clicker we're on, what the topic of the lecture is. So that's a handy thing. Alright, so exams. I know perhaps some of you are most interested in the grade in the class. And so this is one of the ways in which you're evaluated in the exam. And so we have three midterms. These midterms are given during class hours. And the reason is because the registrar won't let you register for this class unless you're available during class hours. So you can't have conflicting classes. So all of these are given during class. Now the location, obviously, we're not going to take an exam like this. And it's just impossible. You're all on top of each other. It's very uncomfortable. You can't spread out. So we'll have some sort of, perhaps, a split of the class by last name. And we'll make an announcement. The registrar likes to be suspenseful and she won't tell me, like, where we're going to be. But it's actually, for those in the back, if you want to hear uncomfortable, there's seats sort of towards the periphery. I don't know if anybody. Feel free to come in. So these exams, these are the dates of the exams. Again, it's during class hours. And we have a comprehensive final exam and that's on May 12th, which is a Monday at 2 p.m. So we have conference sections. Now, the registrar forced you to be confused. They said register for a section. You're probably thinking, oh, okay, that means I need to go to that section. That's actually not true. We just need you to register so we get a room, get some sense of what the volume of people will be. You can go to any section. You can go to no section. Not the choice I suggest, but perhaps some of you won't be able to go to a section. You can go to multiple sections. You can switch sections at any time. These TAs are available to you in the sections to help you with the material. So if you feel like you're doing okay, you know, maybe you don't go to more than one section, I should say. Now, the sections don't start until Wednesday. And so we need something to talk about. You can go and say hello, how are you? But we just have very little material until next Wednesday. Okay, so let's see. Next is old exams. So you don't have to be a member of a fraternal organization with a nice filing cabinet of exams. We provide that. You're all initiated. You're in the fraternity of biochemistry. And here are some old exams for you to review. We provide two formats of these exams, a blank format and a key, an answer key. So a useful way to study is prepare as if you're about ready to take the exam. Take the blank out. Get your iPhone or your device out. Put the timer on and go. After you're done, grade yourself. How did you do? If you did how you want to do in the class, then maybe just brush up right before the exam. If you didn't, well, there's another exam. You can study some more and take the simulated exam again. And so we'll post the key to the exam here within hours after each exam. So you can also quickly understand how well you're doing in the class. All right, so the grading. There's a lot of things that are graded in the class. And so we have the three midterm exams. Each exam, each midterm is 100 points. And the final is 200 points. It's comprehensive. We have had students not realizing that till they arrived at the final. It covers all the lectures. So it's important to study for all of them. We have clicker questions. So we'll talk about the grading of those, but those are for a total of 60 points. And then this year we have sapling problem sets, which are meant for review. Those will count for 40 points. We have two chances for you to get extra credit. So these are participation and discussion form. We'll talk about that in a moment. So that's for a total of 10 possible extra credit points. This is the distribution of grades, so we will not change this. So there's no curve, so if a lot of people drop on the last day and the average goes way up and your grade would go way down, and that would not be good. So you go into each exam knowing exactly what you need to do to get whatever grade you want. So these are the percentage of total points that you would need. So across the course, I believe it's 600. I don't know if it's right in here. Yeah, 600 points total. So any questions so far on grades? Okay. All right. And also after each assignment is graded, the points will go into the grade features. If you click grade, you'll see each of your clicker points. All the different points will show up there. So you have clickers. So I'll go back. You need to click here, and that brings you to the clicker registration site. If you haven't already done this, be sure to do this immediately after class because we'll be putting the points up in Canvas. So please use your banner ID for this. Sometimes you have a clicker that you use in more than one class, and if the other professor makes you put something else there, that's fine. But we prefer banner ID because this is a second point of information beyond your name. So in a group such as this, there's sometimes two people with the exact same name. And so we need to have banner IDs there as well. And you put your remote ID. So if you look on the back of your clicker is a little number. And when you vote, the clicker receiver receives that number and associates it with your choice. So it's important to put the correct remote ID. You are responsible for your clicker. They're available for checkout at the Friedman circulation desk at the SILI. So you need to get that. You're responsible for providing fresh batteries in your clicker. Today we'll have a test, and there's actually feedback on your clicker whether the receiver has received the vote. So you get a chance to test it. But it's a good idea to put new batteries because the students last year surely did not refresh the batteries at the end of the year. And I'm not sure that Brown did as well. Okay, so here's the quickers. So you have at least one question per class. There's 23 classes. And so you get half the points for fogging a mirror and clicking, I guess. So being alive and clicking, you get half the points. The other half the points is if you get the answer right. And we do this open book, open laptop, open discussion. So feel free to debate with your neighbors what you feel is the best choice for each question. Now the one thing you cannot do is click somebody else's clicker. So if you have a nice, bolding pocket and you start rubbing it, the TAs will notice this. So do not vote for other people. We have referred unfortunately cases of people voting for other people to deans in the past for honor code violation. So please don't do that. So there's a maximum of 60 points. You say, well, wait a minute, three points each, 23 chances. That's more than 60 points. Well, you can drop your lowest three scores. So no need for a makeup. Whatever reason you're not able to come, well, we dropped the three lowest scores. It's almost exclusively the case that the clicker points elevate the percentage or higher than the normal percent of your points in the class. So they're going to help your grade out. And also if you change your vote so maybe you click something and then later click something else, your last vote is the vote of record. So that's going to be your final vote. And there's no makeup. All right. So we have discussions. Remember, these are for extra credit. So we have two of them. One is up to from today, up to the first exam, the date of the first exam. And you may ask any question. But the question has to be academic. It can't be, you know, what's going to be on the exam? What's my favorite color? So actually, Sarah is going to be screening these questions and she'll give you feedback if she feels that maybe you need to post another question. The other thing that often happens is this wonderful thing called search the forum. So you might check if your question has already been asked. And so people keep asking the same question again and again and again just to get points. That's not really fair. The point here is to either ask a question or to answer somebody else's question. So you get points for teaching other people. It's a great deal. So five points possible for extra credit, up to exam one. And from after exam one all the way up to the day of the final you get another chance for five points of extra credit. Any questions so far? All right. So sapling. So you might have tried sapling problem sets in organic chemistry or other chemistry classes. So this is a new thing this year. The TAs have actually looked through all the sapling questions and they said, wow, I wish I had this when I was a student. They felt like it was a great way to review the material. So based on their advice we are going ahead with sapling. So it will be a total of nine problem sets. And each of them will be available for a fixed amount of time indicated on this webpage. And each one will cover either two to three lectures. So this is sapling. Remember it's only 40 points and there's nine of them. But you get five points each. So again there's one extra in case you're just ill for like the four days that the problem sets are available or you just can't do it. Well there's one extra and you can drop that. So they're available for at least four days. One of the problem sets is available longer because there's a nice long spring break and we thought it was unfair that that's time that you have on your own. There's four days in addition to the days of spring break for that one. There's no time limit for each question. After you respond to each question it will give you feedback. It will give you hints if you didn't get it right. And there will only be a 10% point reduction each time you select an incorrect choice. And so the material on the problem sets will have already been covered in class. So it's just for review. It's not to make sure you read the book ahead of time or something awful like that. It's to review so that you can say okay it's another way you can set. Am I ready for this exam? So you get the best eight of nine. It's very important that you work on these problem sets independently. Our expectation is that it's your work. And if you have any questions Sarah is running the show. So she is able to, if you have problems with the question or technical glitches with the system, she's the person to contact. Now Alex will be the one transferring the points from the sapling system into Canvas. And so he would be the one if there's some kind of problem in the transfer of your points. So it's sapling problem sets. Alright so this is an unfortunate slide but it's important that we be crystal clear about our expectations for you. And so we have an academic code and so you're not allowed to cheat on exams or quizzes so you can't click other people's clicker. You can't take a sapling quiz for other people. You cannot sneak stuff into the exam room. So actually there's a camera there and that's on during the exam. And so two years ago we had hours and hours of video of somebody doing naughty things and it didn't end well for that person. So the point is, and last year, the point is just don't bother with that. It's so much easier just to study. And also if a TA comes up and sits on the row and like stares at you, just stop doing what you're doing. So I know that the gross majority of you are honest test takers but for those who study we need to make it fair and we need to make sure that people aren't copying us of each other. So you cannot go to the bathroom and put books in the stall. You have a Krebs cycle hanging out there. We know that. So we were undergraduates at one point as well. And don't change a regrade. So we actually scan all the exams. So you're crazy if you change an exam and say, hey, I got it right and they're like, wow, it's changed miraculously. And we don't even deal with it. We might not even contact you. Dean will be in touch because it's not our role. Our role is to teach you biochemistry. Any questions on the academic code? Wonderful. So next is Facebook. We have everything. This has never been really used. So last year they used it for putting a beer song. It went through, I think, is a Krebs cycle. Or perhaps there's better uses that you could come up with. So whatever. If you want to talk to other people about the class, perhaps that would be one way to do it. We also have a YouTube channel. So throughout the semester we'll have lots of videos. Here's one of the former professors dancing for you. But we also have biochemistry videos. And these will also be on the lecture web pages. So each lecture has its own web page. On that web page are recommended readings. So this year we're using a Leninger's Sixth Edition. There's all kinds of different formats available to you. You can get the paper version from Amazon or the bookstore. There's an online version, two different online versions. One you can link directly to. The other you go through sapling to get at it. So we don't require you to do these readings, but we require you to understand the lecture PowerPoints. And if I'm a lousy teacher and don't teach you well the PowerPoints, or if you're confused by the PowerPoints, it's your responsibility to learn that. Yes. Hi. There is some. It's not major. Yes. So yes, sometimes people have different versions. Again, we see it as something that's helpful. For example, I think it probably would be okay, but the one difficulty you'll have is the page numbers are all different in the section and the figure numbers are different. So it might be a little bit confusing. One temptation I had as a student was to just read through all this stuff. And it's very overwhelming. Perhaps a more effective way to use the textbook is to go through the PowerPoints and for the things that you're just not clicking that I didn't explain well, jump into the textbook and see if you can understand it. We actually link to other authors, biochemistry textbooks as well, some of which are free on the Internet. So Berg makes a good textbook. Voight and Voight makes a good textbook. So these are really supplemental. So you could maybe get away with the fifth edition. So we also post all the PowerPoints in different formats on this site. These files might change up to the day of the lecture because I might add something, but they probably won't change that much. So you might want to wait towards maybe the beginning of the week to print out those materials if you want to print them out. And then we have a lot of supplemental materials, animations and movies and so forth. Okay, any other questions on lectures? Okay. So the Leninger has a website that's linked up. It's very hard to see. It's easier to see on your computer. But it has lots of different animations as well, of things that you might find helpful, of course not required. So all of these lectures are recorded. So the VGA feed from the laptop is being captured and there's a camera back there capturing me. So if you're ever ill or something, you really don't need to email me. So make sure you watch the lecture video. So that's a great way to review the material. The slides are sort of synced up. They have sort of an index of slides. So you can jump to a certain place in the lecture if you want to take a break once in a while. So there's two different formats, a rich media format and a vodcast. So vodcast, you could actually download the video and you could put it on a device if you so choose. Okay, so that's that. I think we're coming to the end. There's podcasts, so if you want to use the osmosis method for biochemistry, you can load up your, I guess it would be an iPhone now, not my iPad, and just go to sleep and listen to me. And it's a little weird, but perhaps it's easier than reading and being awake. So yep, podcasts and instructions. It's a little wonky in how to hook your iTunes up. So there's a little video there to show you how to do that. All right, so in class, sometimes, I mean, this is insane. There's a lot of people here. So you might be legitimately confused along with many other people about a particular topic I bring up in class. It's intimidating to say, I'm not a genius or I don't know everything. But, you know, probably the majority of people also don't know the answer to that question. But to get around that weirdness, we've created these online discussion forums. So you can click this in class discussion forum link. And then for each lecture, there's a separate link. And those will only be active when that lecture is in session. You can go there, post a question. Alex is monitoring that forum in real time. He's got a mic. And so he'll wait for a convenient time to interrupt. And he'll raise his hand and ask the question. And also, it might be another way to aggregate. Maybe people have similar questions. So if you see a question that you want to ask because they're already up there, you say, okay, well, Alex will get to that. So please use it. All right, so you have to register properly for the class. There's both a conference section and the F section. And you have to register for the class to get a grade, right? It's pretty obvious. You can't just register for a conference section, okay? I think that's it. Okay, so sometimes people get extra time on exams. It's important to know. And that's usually a very small number, maybe about 10 people in a class of this size. And it's important to know that you need to register for the ability to do that for every class every semester. So like for Bio28, you have to go contact the SEAS group and they'll set you up. You cannot contact them after the exam. We can't help. And so this is just for those that need extra time. Perhaps they have something that prevents them from doing the exam and the amount of time that we have allotted, okay? Any questions on that? Again, this doesn't apply to the gross majority here. All right. All right, so that's it. Any other questions on the organization of the class? All right, so we actually have a silly number of fly to first class. So we're going to get right into it. So first we're going to have an introduction and then we're going to start talking about our first topic, which is amino acids. So what is biochemistry? The way I look at it is biochemistry is just organic chemistry of really large molecules. So you can see it as organic chemistry semester three. You just think, oh no, I was done with this. Well, you know, perhaps we're a little bit more loving than in those classes. Generally, people do a little bit better in terms of grades in biochemistry. But what we're taking is that sort of non-biological knowledge that you may already have and say, well, how does that apply to biological systems? And so, you know, concepts like thermodynamics, kinetics, catalysis, organization of biomolecules within the cell, these are all important things. So I think, no. Let me go back. But ultimately what we're saying is what is the difference between this and this? So these are actually little hamsters that are going around a circle holding the wheel. It's very cute. It's not working right now. Disappointing. So what we're going to do is we're going to look at the organic chemistry of large molecules. So you have these puny little organic molecules in 35 and 36. Some of the molecules in biochemistry, it means adults. And so these are massive molecules and there's just tons of chiral centers. It's just amazing natural organic chemistry that goes on. And so we'll look at the first part of the class is sort of looking at fundamentals, learning languages of biochemistry, amino acids, sugars, nucleosides, things like this. And then the middle part of the class is perhaps the most daunting. How do the pathways, how do the tabillites get processed in a cell? How does energy get produced? In the last part of the class, we're looking more at sort of the biochemistry of molecular biology. So how does transcription, translation work? A lot of these subjects might be familiar to you, but we're going to look at it at perhaps a little bit more of a chemical perspective, a little bit more detail. So this is an example of one of these organic molecules. So this is the F0F1 ATP synthase, but ultimately what's going on here is just simple chemical reactions. So these large monsters are very precisely orchestrating chemical transformations. So here we're making a molecule called the ATP. We're using energy provided in the form of movement of ions across the membrane. This thing literally rotates like a ratchet, like a machine you'd see in an auto factory. It's just amazing. So this is the type of large molecules that we'll be looking at this semester. So this is everything, right? So this is the whole semester here. It's actually really hard to see, but I lied, it's only half of what we're like. So this is the other half. Now, it's a bit daunting, but I don't know a lot of the reactions there. There's certain core sort of the skeleton of all these pathways that you really have to know. And these other pathways feed off of that. And so a big challenge in this class is, jeez, by the way, what don't I have to know? Because obviously you can't know everything. So you have to look at everything. What are the fundamentals? How is the process regulated? Where is the process occurring? There are certain things. I'll tell you, this is really, really important. So like crab cycle and glycolysis, these are really important. You have to know the little details. But other places, perhaps like amino acid metabolism, they say, well, there's a lot here. And here's what you need to know. Here's what the important parts are. So there's a lot of material, but we'll go through it slowly. And the way you can remember is to see how it's connected, how everything is connected. And to think, why is this set up like this? And the logic of why this pathway exists in the way that it does. So we'll go through that. That will be our semester. So here's the textbook. What is that? Is that kilos? Maybe. I don't know. It's heavy. It's a lot of material. Reading the textbook cover to cover. Not a good idea. You're just going to glaze over. It's sort of like reading the dictionary, right? But what we're learning here is similar to reading the dictionary. In some aspects, we're learning a language. We cannot communicate with each other unless you know the words. The words are certain amino acids, nucleicides, fats, and sugars. We have to first know the words until we can put those words together in larger sentences. So the first part is going to feel a bit like A is for Ardvark. But it'll begin to come together with transition from learning vocabulary to learning sentences and paragraphs and putting them together in stories. But fundamentally, it's just organic chemistry of really big molecules. The elements that are important, carbon, oxygen, nitrogen, and hydrogen. The rest of these elements are involved in some cases, but often times they provide important chemical functionality. But really, it's all about organic molecules. So that is that. Periodic table. Organic chemistry is carbon. Carbon is bonded to other carbons. So we know a singly bonded carbon atom has this tetrahedral configuration. And then when you attach two carbon atoms together with a single bond, they freely rotate. That's going to be important in today's lecture. But if you have a double bond or a triple bond between carbons, they don't freely rotate. So there's stereo chemistry. If we have different substituents at each of the four positions here on this carbon, there's stereo chemistry. There's an anatomers. There's chiral carbon. And here we have orientation of substituents about the double bond. Nothing surprising. You've seen this before. You can have trans and cis configuration of substituents. So you'll see that throughout the semester. So these are the words of the language we're going to learn. So today we're going to learn a whole language. The language of amino acid. And so the words of this language are amino acids. The language is proteins. And so these amino acids are going to come together to form sentences, proteins. So these are polymers of amino acids. We'll also be looking at nucleicides, fats, and sugars in other lectures. So generally, we'll have a separate lecture for each of these languages. But where the biochemistry occurs is critical. So you can think of things in terms of the words, the sentences for the biopolymers, how these aggregate into the big picture and how they're organized into the cell. And throughout the semester, we're going to be looking at biochemistry from all of these perspectives. Like where do these biochemical reactions occur and why is it necessary that they occur in this way in these locations? So this is the typical cell. It's pretty simple. So it's an E. coli cell. Looks like a nice, tasty sausage. It's mostly water. So actually, so about 70% of an E. coli cell is water. So 70% of you is water. So when you all came in the room today, that's how much water you brought in, about 3,000 gallons, about 10 gallons each. It's a little creepy, huh? That's all you are is a big vat, right? You're more than that because you have other things. You have proteins, nucleic acids, polysaccharides, lipids. But mostly it's water. There's a lot of diversity. So different types of languages have different diversities. So you have proteins. There's thousands, about 3,000, tens of thousands, approaching 100,000 different proteins in a human cell, for example. DNA, there's not that much to that language. It's just a really big, complex polymer. RNA, there's thousands of different RNA molecules. So there's a lot of diversity. But in terms of weight, it's mostly just water. So that's what you are, you're here. Okay, so this is a overview of the general way we're going to be approaching biochemistry. And so today we're going to learn our first language, amino acids. So I put on the sideboards like every five minutes it sleeps. It's driving me nuts. But these are the words that we're going to be learning today. So these are the 20 amino acids. Okay, so let's jump into that. So an amino acid has some characteristics. It has an amino group. And it has an acid group. And it has something called alpha carbon. It's like the main carbon, right? And it's got this red R. So it has some sort of substituent. This R is, there's 20 different side, these are called a side chain. And there's 20 different types of side chains of amino acids listed on the board here. There's stereochemistry. So there's four different substituents around this alpha carbon. So we need a way to talk about the stereochemistry of that. And so we'll see that we have, in general, we try to just do things that are different than in orgo by tradition. And so this is not called an R or S amino acid. It's called an L amino acid. So what is it? You can learn something else. Well, you'll see why in a second. So there's four different substituents that makes it a, the alpha carbon is a chiral carbon. If there's four different substituents, if two of the substituents are the same, then it's not, it's a chiral. It's superimposable upon its mirror image. So these are themes that you've already seen in organic chemistry, rearing their ugly head again. So here we have the two different forms, stereoisomers of a particular amino acid. So one of the most simple amino acids is alanine. It's side chain as a methyl group. Okay, so here's the side chain. And we can have these two opposite orientations. And this is called L alanine. The L designation applies only to the alpha carbon. So I remember when you had R and S, you would say like two R, three S, you know, each chiral center you would lift. When you say D or L, by convention, arbitrary convention, it applies just to this alpha carbon. If you arrange the amino acid in this way with the carboxylase here, the side chain here, the amino group here and the hydrogen atom here, you have L is when the amino group is on the left. And D is when the amino group is on the not left. It's Latin, but I don't know Latin. So D, naturally occurring amino acids, are with the stereoconfiguration and the L configuration with the amino group on the left. And so you remember these fissure projections. These are one ways to represent, typically it's used with sugars, but you can also be used with amino acids. So why do we call this? Where did this garbage come from? It's just why are you doing this to us? Another useless thing. Well, it's because these amino acid molecules look very similar to glyceraldehyde. So glyceraldehyde has an oxidized carbon here. It has some kind of functionality here. And it has a hydroxyl group and a hydrogen atom. And so it's sort of similar to an amino acid. And so this is L glyceraldehyde has to do with the way it rotates light in a confusing way. And this is D glyceraldehyde. Okay, these are sort of similar. So we're naming it after, arbitrarily naming the stereochemistry after glyceraldehyde. Right, I'm like, okay. Why are we doing this? Why not use ROS? Well, because if we used ROS, the one of the 20 amino acids would seemingly have an inverted stereochemistry because of the priority rules on the side chains. And so I'll let you tell me which one it is as we go through which one would have a different RS convention, but they're all L. So it's just to make things uniform perhaps. Okay, these are just simple little molecules. Molecules have physical characteristics. One of the characteristics is its chiral. And because it's chiral, it rotates something called plain polarized light. I'm like, what is that? Well, you know, light is a wave, and that orientation of that wave can be in any direction. But if you pass that light through a filter, you can capture waves of light that are only in a single orientation. And then you can measure the rotation of that plane that passes through a chiral molecule, such as an amino acid. So the light plane, or wave, can be rotated either to the left or to the right. And you don't have to memorize, all you have to know is that it does rotate light. Like which one is D or L, and which one is plus or minus, not important in your world. These are chiral molecules, and they rotate light. Just because it's an L amino acid doesn't mean it rotates light in a certain direction. It could rotate it one way or the other. An equal mixture of an L and a D configuration of a particular molecule would cancel out, and there would be no rotation of light. So racemic mixture would not rotate light. But here we have some amino acids. They rotate light in one way. And here's another L amino acid that rotates light the other way. So it just rotates light. We're cataloging the chemical characteristics of these words that we're about to learn. Any questions so far on that? We have our first question. More of a comment on the charts on the sideboard of the amino acids. They say they see arginine aspartate twice. I didn't notice that. Arginine. They don't see arginine, and they see aspartate twice. Yeah. Well, that's not good. It's missing. I'll have it on the front slides in a moment. Any other questions? So these are L amino acids, and you're going to tell me which one would have a different R or S configuration. All right. So now we have to learn the words. We have grouped these words into, based on chemical properties. So the first group is the nonpolar aliphatic. R groups are side chains. The simple, the most simple side chain is hydrogen. Alginine. So for all of these, we're learning language. If we want to communicate with each other, we have to use words. Not just grunt. We need to use words. So you need to know the structures of these amino acids, all 20. You need to know the names. This is a tradition. Every undergraduate in biochemistry learns these things. You need to know the full name, the three-letter abbreviation, and the one-letter abbreviation. These are our vocabulary lesson for today. So glycine symbol is G-L-Y. Okay, that's easy. And its one-letter symbol is G. Cool. That's easy. We're just using the letters in the word. Alginine. Again, we have the three-letter symbol is ALLA, and the one-letter symbol is A. And it's just a methyl group. Now, proline, that's a little more interesting, right? So that's the only amino acid where you have a second bond to the amino group. So here it's a secondary amine. And when it's incorporated into proteins, it would be a tertiary amine. So here we have the alpha carbon, beta, gamma, delta carbon is attached to the amino group. So proline and P. Cool, still easy. Valine is easy to remember. The symbol is the structure, right? So it makes this V-shape. Lucene, sort of valine on steroids, one methylene extension of valine is lucene. Again, the symbols are easy to remember. Isoleucine is the conceivable isomer of lucene, where you've shifted a methyl group up here. Now, this molecule has two stereocenters, right? But the L or D designation only applies to the alpha carbon, not to any other stereocenters that might be in there. We give that the isomer that has inversion at the second stereocenter, a totally different name. Okay, just to be cute, I suppose. And then we have mysionine, it has a sulfur containing a side chain here. And so which of these molecules or these amino acids is achiral glycine? It has two identical substituents, and this one has two centers. So the stereoisomer, so that's glycine, yes, happy glycine. The stereoisomer here, when you inverted this stereocenter, is called allo-isoleucine, right? So L specifies its amino group is on the left, and allo specifies that this methyl group is on the other side. But the naturally occurring variant of isoleucine is isoleucine, right? Not allo-isoleucine. Okay, so nonpolar allophatic. We have the negatively charged side chains, aspartate, right? So it's carboxylate functionality similar to carboxylate attached to the alpha carbon, it has this methylene extension. And glutamate is just, again, a one-methylene extension of aspartate. So now we've got a little bit of confusion with these letters. The letter D is not in the word aspartate. So the way I remember it is aspartated, it's maybe a little weird. Okay, the letter E. So G, remember, is already used for glycine. So we have to pick another letter, and we pick the letter at the end of that word. So dipeptide of aspartate and phenylalanine is equal sweetener. You say, well, wait a minute, that's not sugar. Yes, that's true. Your tongue perceives it as being sweet. So dipeptide of aspartate and phenylalanine is equal. So those are the negatively charged pessimistic amino acids. The optimistic amino acid positively charged side chains are lysine. So you have an epsilon amino group on that side chain. So remember the naming alpha, beta, gamma, delta, epsilon, methylene, and then the amino group is positively charged at neutral pH. And then you have this guanidinium group on arginine. That's also positively charged. And then you have this imidazole side chain. This one's a little bit more complicated, but histidine is a very important amino acid because of its chemical property of the pKa at this position. The pKa is right around six. And so at physiological pH, which is where a lot of biochemical reactions occur, you can mess around with the protonation of histidine to affect catalysis. So these are the symbols. Lysine, again, whether it's a cute name for lysine, comes after K. Yeah, it comes after K. So K is the symbol for lysine. Lysine comes after K. Maybe that's helpful, or maybe not. Any questions so far? So we're just going through vocabulary lessons. So the polar side chains, we have alcohol-containing side chains, one of them, or actually three, two shown here. Serine, and three inane. You have these structures. Cysteine is here. Asparagine, you have a carboxymid side chain with one or two methylanes. Glutamine symbol is really impossible. I haven't come up with an amonic yet for Q. It's a queen, I don't know. So asparagine was actually the first amino acid ever discovered, and the reason is because people that eat this generate a certain smell a couple hours later. And people are like, what's that smell? And so they isolate the molecule and say, ah, asparagine, maybe there's other things that are similar than that. So the smell prompted its discovery, asparagine. Asparagine has tons of asparagine. Okay, so which of these has inverted RRS stereochemistry? At the alpha carbon, I should be more sure. Yes, do you see that? Because of the priority rules, remember. Sulfur is a little higher. But that's, I suppose, why we name it D or L. So these are all in the L configuration. So that's polar amino acids. Cysteine can do some cool chemistry. You'll see that. It can become oxidized, lose electrons to a disulfide bond. Cysteine. So if you have two cysteines in a protein, they can provide structural limitations of the protein by making a covalent bond to each other. So it's oxidation chemistry going on here. We have aromatic amino acids. So the wonderful diversity of organic molecules is used in this repertoire of amino acids. We have phenylalanine. F is a symbol because pH sounds like F, I suppose. Tyrosine is Y. So tyrosine is phenylalanine with a hydroxyl group in the para position. And then you have this tryptophan. This is heterocycle. And its letter is W. So twyptophan. Elmer Fudd helps you to remember that twyptophan is a W. So actually turkeys have a bum rap. They don't have high levels of tryptophan. All poultry has the same level of tryptophan. It's not the tryptophan that's making you sleepy and Thanksgiving. It's eating too much food, carb load. That's why you go into hibernation. So if you look it up, it's a myth. They do not have too much tryptophan. All right. So one of the characteristics of an aromatic amino acid is absorbance in the UV range. So here's the absorbance spectra of tryptophan, tyrosine, and phenylalanine. And they absorb right around 280 nanometer. And this is because they have an aromatic ring so that absorbs light. And so this characteristic of these particular amino acids, these are the only amino acids that absorb in that 280 range. So the other amino acids absorb around 220, just from the AMI amino group. But this is aromatics or a 280. And we can use this chemical characteristic of these amino acids to ascertain useful information about a protein, in particular the concentration of a protein in solution. So you guys know what absorbance is. So we have light coming into a sample. We have a cuvette of a certain fixed length. Remember this from probably lab. You did some spectrophotometry. So you have light coming in, and you measure the light coming out. And so there's a nonlinear relationship between transmission. The emitted light divided by the incident light is nonlinearly related to the absorbance. And it's basically the log of one over the transmission, which is defined here. And so this is nonlinear. So as you increase the transmission, you only slowly increase the absorbance. So if 90% of the incident light is absorbed, then you have an absorbance of one. If 99% is absorbed, you just have an absorbance of two. You're like, okay, so what? Okay, well, get into that. You got the most powerful thing you learned in all of general chemistry. Beer's Law. So Lambert Beer Law. And it's a simple relationship of absorbance to the concentration of the molecule you're measuring. So we have, let's define the symbols. You have an extension coefficient. It depends on the wavelength that you're looking at and the particular molecule that you're looking at. The concentration and the temperature, obviously, pressure. And the concentration is the concentration of the molecule. And L is the path length. It's fixed at one centimeter. Extension coefficient usually has units per molar per centimeter. So one centimeter path length is convenient because it just is a one. So L is generally one. So the concentration is equal to this absorbance divided by the extension coefficient and one. And so here we can make a very simple assumption. If you look at a protein, a particular protein probably has a certain percentage of the amino acids in the protein sequence that are aromatic. And surprisingly, this percentage doesn't vary that much between protein to protein. So that means that we can use one extension coefficient to generally approximate the extension coefficient of any protein. So on average, it's about 4% of the amino acids are tyrosine or phenylalanine, the ones that have this large extension coefficient. And so we can just use that knowledge to calculate. You just measure the absorbance of any protein solution and you can calculate the actual concentration. So this is a chemical property that leads to the useful ability to measure the concentration of a wide variety of diverse molecules that by chance have a similar percentage of aromatic amino acids. Now, it's not perfect. Some proteins are going to have a little bit more aromatic amino acids. They would have a different extension coefficient, but it's a first approximation. Another important characteristic of an amino acid is that there's acid-base chemistry going on here. You can donate or receive protons. And so we have something called a zwitterionic form of amino acid. So it's physiological pH. There's both a positive charge on the amino group and a negative charge on the carboxylate group. You're like, wow, that has a lot of anxiety, right? So these can be referred to as amphoteric amphylites. So amphoteric meaning they're both acids and bases. Amphylites meaning they conduct electricity. They're charged molecules. And so because we can change the ionization state of amino acids, we can do something very painful, which is to tighter those and determine pKa's, right? And so do you guys remember this? Maybe, yeah, if you could see the pain in everybody's eyes. So here's the titration curve. Remember, you had the burette thing. You got the acid going on, drip, drip, drip. You're measuring the pH while you're doing this. So you're measuring the pH as you tighter in hydroxide ion. And you'll notice it's not just a linear relationship between the amount of hydroxide ion and the pH. That you have these two sort of inflection points. So you have, let's think about the structure of a very simple amino acid glycine. So glycine side chain is just this hydrogen. So it's just this methylene group here. And so there's total three different charge states of this molecule. One where the amino group is positively charged. A zero net charge state where you have a positive charge on the amino group and a negative charge on the carboxylate. And a negative one charge state where you have just a negative charge on this carboxylate. So between each of these charge states, we can define a pKa. Who remembers what a pKa is? Anybody remember? What can you say about molecules at a pH equal to the pKa? So to help you out, here's a little equation. Jog the memory. What can you say about molecules at the pKa? Exactly. Well, whatever the two charge states are, there's an equal concentration. So pH equals pKa. pH minus pKa is zero. Zero equals the log of some ratio. Ten times ten to the first power is zero, right? So the ratio of one is when the pH equals the pKa. In other words, when the concentration of these two molecules is the same, that's at the pKa. So we have a pKa describing these two charge states, the plus one and the zero. We also have a pKa for these two charge states, the zero and the minus one. And then we can think about the molecule more holistically in terms of all the charge groups. And you can think about what is the pH at which there's no net charge on the molecule, right? So you have to look at the different charge states when you're thinking about this, and you say, okay, which of those, when I add up all the charges, do I get a zero? Well, that would be this one. And so the PI can be calculated, the isoelectric point is the pH at which there's no net charge on the molecule. And this PI can be calculated as the average of the pKa's that give rise to the zero net charge state. So for glycine, it's simple. There's only two pKa's, right? We don't have an ionizable side chain. So the PI is the average of these two pKa's. So it's 5.97. If you had a pH of 5.97, there would be no net charge on the molecule, okay? This is often a little bit confusing. Are you with me? Discussion form, okay. You got it? We're gonna do another one. Maybe that'll help, or maybe it won't help clarify. Let's do one more. So what about something where we have an ionizable side chain? We have to put your chemistry cap on and say what might the order of ionization be? So here we have three ionizable groups. The amino group, the carboxylate, attached to the alpha carbon, and the carboxylate in the side chain. Which of these two carboxylates would ionize first and why? I know this whole lecture is painful. Painful remembrances. I got out of that. Which would ionize first? I mean, the answer is there, but why? Why does that one ionize first? Say a little bit louder. Well, so what about, what's nearby to this one? An electron withdrawing group, right? So it helps to stabilize the formation of that negative charge. This one is more distant from an electron withdrawing group, right? So this one ionizes first. So the pKa is lower. And so here we have four different charge states. So three different groups, means four different charge states. The difference between each charge state is just a single functionality changing its charge. So here we have, for example, the carboxylate in the alpha carbon becomes negatively charged. And then this other carboxylate becomes negatively charged. And the carboxylate group becomes unprotonated. So these are the four, so it's important. When you look at these molecules, I often just say draw this on an example, just a little hand. So you've got to look at these molecules. You can memorize it, which is one approach. I could just think about it. What makes sense? What could all the ionization states be? And then you can define, between each ionization state is going to be a pKa, a pH at which there's an equal concentration of two molecules for this pKa, these two molecules for this pKa, these two molecules for this pKa. And then we can also define, well, what about this isoelectric point? So that's, remember, the pH at which there's no net charge on the entire molecule. So to figure that out, you have to look at all the four possible charge states. Which one has zero net charge? So it's this one. There's a positive and a negative charge. The total net charge is zero. So the pI can be calculated as the average of the pKa's leading to the zero net charge state. So it's the average of these two pKa's, right? Not the average of these two. Not the average of these two. The two pKa's leading to the zero net charge state is, the average of that is the isoelectric point. And you can think of isoelectric point for these simple little molecules, but also for proteins. When you combine lots of amino acids, you can calculate an isoelectric point. Okay? So this is a painful memory lane of titration. Drip, drip, drip. Okay, any questions on this? It's... Okay? That's me so far? Okay. So we're going to change topics if it's okay. Yeah. Yeah. Make it end. All right. So now we've learned all the words. We're on our way to a language, but now we can just have a random combination of these words. We have to make meaningful sentences. And so think about the chemical functionality in amino acid. It has two... What you could perceive as sticky patches. Two places where it could make a covalent bond with another amino acid. So you've got a carboxylate group, and that can condense with loss of water. Think of frosty beverage. To make an amide bond. How does that work? You've got the two electrons here. Attack, electrons up, back down. Oh, God. Thought I was done with the word go. So that's the condensation reaction to form an amide bond. Or it's also referred to as a peptide bond. This is the covalent bond that lengths amino acids to each other. Every amino acid has both an amino group and a carboxylate group. So every amino acid can make a covalent bond to two other amino acids. So it can form a polymer, right? Just go on forever. So if we can bring these two groups together, condense them to make an amide bond, we can also hydrolyze this bond to make the free carboxylate and the amino group. So there's a set of enzymes that break these bonds apart that happen to be proteins. And a set of enzymes that put them together that happen to be RNA molecules that will learn way at the end of the course. So there's catalysts. This doesn't happen spontaneously. If it did, we'd all just turn them mush. We'd just flow onto the ground. These proteins, these covalent bonds, they're actually really hard to break without some sort of catalyst going on. So there's a peptide bond. So we can begin to think about synthesis of a polymer of amino acids. We can call this, for example, an oligoprop peptide. So here we have aspartic acid, glycine, alanine, valanine, methionine, isoleucine. Each of those has two functional groups that can make a bond to one other amino acid. So we can make covalent bonds, the imide bonds, and make a new peptide. And this peptide is called Asgly-Alleval-Met-Iso by the three-letter symbol. Let's look at some of the features of this side chain. It has a polypeptide backbone. So here you have a line of covalent bonds and a straight line. This is called the polypeptide backbone. You have the carbonyl groups sticking out, the amino groups intercalating with the alpha carbons here. Each oligopeptide has, it's sided, it's directional. Do you see that? So this has a free amino group. There's only one free peptide backbone amino group and one free carboxylate group on the peptide backbone. So this is called the interminous, and this is called the C-terminus. Side chains might have those kinds of functionalities, but when we say interminous and C-terminus, we're referring to the polypeptide backbone and the free amino group on the polypeptide backbone or the carboxylate. So it's the C-terminus. So the molecules are named starting a convention alert, starting from the interminous going to the C-terminus. Okay, so this molecule is called As-Gly-Ala-Val-Met-Iso. It is not Isomet-Val-Ala-Gly-As. That's a completely different molecule with different properties. That molecule would have isoleucine at the interminous. So the naming by convention is going from the interminous to the C-terminus. Often it's typical for us to write this starting from the left, having the amino terminus on the left and the C-terminus on the right. Okay? So these are conventions, but how could we name them if we didn't have a convention? They could be either direction. Let's look at some more examples. So here's another oligopeptide. This one's written up and down. And so the interminous is here and the C-terminus is here, right? Because they're colorful, right? No, because they're the peptide backbone, the amino group and the carboxylate and the peptide backbone. So we're talking about this carboxylate when we say N and C-terminus. So what's the name of this molecule? L, glue. Is this a very participatory? That's how I am. I'm sorry. I'm going to torch you with questions all year long. L, glue, gly, lice. It's not gly, glue, gly, glue, lice. That would be a completely different molecule with a lysine at the interminous. Okay? So we're naming polymers. This word in the English language, if you Google longest word, there's a wonderful movie, someone for three hours is saying the Titan amino acid sequence. And he just gets up after three hours and walks out of the room. It's wonderful. But he starts from the interminous when he does this. Pointless activity. Okay. So you're with me so far. So we've made a polymer. We've taken these words. We've formed covalent bonds with other words. And now we have a polymer. And that has orientation from the end to the C terminus. There's also an amide bond. And that amide bond, what kind of feature is left out from this picture here? What thing have organic chemists said, yeah, you know any toys write that? Loam tears, right? So there's two, there should be two little dots here. And why is that? Well, because you can form a resonance structure. So who cares? Well, resonance, because there's partial double bond character, that means there's not free rotation. It's not just a single bond. It's partial double bond. Because there's partial double bond character here, because of those long pairs, you can think of these things as inflexible. They're planar. So you can define a plane here. And this plane doesn't rotate because of the partial double bond. The amide bonds are critical to provide some limitations on the structure of proteins. So those proteins, those amino acids, when they come together into proteins, they're not completely flexible. It'd be hard to achieve a structured protein. You have planes rotating relative to each other around an alpha carbon. So the alpha carbon here, you can see is at the corner of the plane. That's the swivel joint between the planes. So the only degree of rotation that we have is between neighboring planes of amino acids at the alpha carbon. And we'll spend a whole lecture, the next lecture, talking about this kind of structure. But this is a primer, beware of the partial double bond character of this amide bond. So because there's two different, because this is not truly a single bond, it's a partial double bond, you can think of the substituents as in the trans or as configuration, right? Because there's hindered rotation about this bond. And so this is one feature that you'll see manipulated within proteins to give certain structural aspects. Okay? So here's, we can define the angles between these planes. Like conceptually, you could just say one angle, right? Because there's two planes. They rotate with each other. But we say how about two? Two's better than one. So instead of having one angle describing the orientation of these planes relative to each other, going from zero to 360, which might have been logical, we instead define two angles going from zero to 180. So we have an angle phi and an angle psi. And you're not gonna be able to know what these mean or how they're defined until we get to the next lecture. But just be aware, this is how we define the orientation of the planes formed by these amide bonds. Fine psi angles. So we can think of different levels of organization of structures. The primary sequence is just the letters of amino acids from N-terminus to C-terminus. The secondary structure are these structural elements. So you'll see corkscrews. You'll see planes. You'll see turns. You'll see segments of amino acids that are just random and very flexible. That's called secondary structure. But we can attach each of these structural elements to each other in a particular orientation. That's called tertiary structure. So for example, you can have a helix, a turn, and then another helix. And so the way that those orient with each other is the tertiary structure. Now tertiary structure refers to only a single polypeptide. If you have more than one polypeptide coming together to make a particular structure, that's called a quartinary structure. So not all proteins have more than one polypeptide. So a polypeptide is defined as one molecule that has just a bunch of amide bonds. If you have two polypeptides, they have non-covalent interactions between them. Okay, that's the introduction to that. All right, so we can take those polypeptides and we can cut them into pieces. We can cleave amino acids using a protein catalyst called a peptidase or protease. And these proteases are useful tools that we have in the lab for cutting at specific locations within proteins. And so we have a whole lecture talking about the mechanism of this particular protease, chymotrypsin. So chymotrypsin cuts C-terminally to phenylalanine tryptophantiracy. You're like... So that means you cut on the... So if you draw it in the normal orientation, you go along the sequence, so you get to one of those aromatic amino acids and you cut to the right, the amide bond on the right after that amino acid. That specificity is provided by a particular enzyme holding that peptide such that the scissors are exactly positioned where they need to cut. So each of these proteases can cut at a specific point. You're like, so what? Why are we learning this? Well, this is a useful tool that allows us to determine the primary sequence of a protein. So we can cut, for example, here's a polypeptide. We can use trips to cut it into pieces. And then we could sequence this peptide. There's an ancient way to do this and a modern way. So we'll talk about the modern way. So we can use something called a mass spectrometer to measure the sequence of these small peptides that come from cleaving a protein into pieces with peptidase called trypsin. So what the instrument is going to do is it takes these peptides and causes them to fall apart and measures the mass of the pieces. Each amino acid except for two has unique masses. Which two have the same mass? Yep, the isomers. Solucine, isolucine. So what we're going to do, let me show you a little bit more detail about this. This might be a bit overwhelming but I'm available in office hours. So first what we have to do is get the molecule, the peptide molecule into the instrument. We have to make it fly and put a charge on it, right? So we take all the liquid away and then we have peptide molecules floating in space and they are drawn into the instrument using a charge that's placed on them. Inside of the instrument, we have them collide against some kind of helium atom or nitrogen atoms or nitrogen molecules and that collision causes them to break apart and they break apart in predictable ways at the amide bond. This partial double bond. These are charged ions. So let's look at this. So here we have a polypeptide and when we collide that with helium we can break the bond, the amide bond. You're like, wait a minute, shouldn't that be the strongest bond in a polypeptide? Yes, a polypeptide in solution but a polypeptide flying in space that has been passed through an acidic solution is going to have a charge and where is that charge going to land? It's going to land at those amide bonds. You're going to protonate those amide bonds. So that's where you're going to fragment. So all we do in sequencing by mass spectrometry is to cut the amide band and measure the mass of the fragments and then we compare that list of masses to our amino acid table and we say, okay, we know what each amino acid weighs so we could just measure the shift between peaks and read off the sequence and so we can sequence about 20,000 peptides per hour using this method. They're fast. So that's probably going to be confusing. If I were to ask any questions on mass spec and the exam I'd be very merciful and loving and would not ask about the nitty details this is a general idea of what we're doing here. We're breaking peptides apart into pieces measuring the mass of the pieces and using our table of amino acids to figure out which amino acid the sequence of amino acids there. So I think we have a clicker. So we have five minutes left. So if you take your clicker out there is an on-off button. You can start the polling. There's an on-off button. When you click the on button do you see a light come on? That would be good news. So I think the devices you guys have should have two lights. One light indicates power. The other light indicates whether your vote has been received and so if you click and your vote has been received. So people are voting already probably. So try to click a button. Do you see the other light light up on your clicker? So it goes like green I think. Green is good. Okay. All right. So there's only one correct answer to today's clicker question. I sort of put it up. Only one. And we're recording your name. Only one right answer. All right. So just to reduce the anxiety I will be generous and accept any answer to today's quiz. The main purpose is to make sure it's functional. But when you go home please check to make sure that you got the answer that you voted for. And you must register your clicker. Okay. All right. Let's see. Let's see what the vote is. Ha! So what do you think's the top? But you said the top is good. It's over a half of you just want to be here. This is good semester. All right.