in this video, we're gonna talk about amino acid configuration, so we're calling our previous lesson videos. We refresh our memories on configuration Kyra Ality and Fisher projections from your old organic chemistry courses. And so if you don't remember much about those three topics, be sure to go back and re watch those older videos from our organic chemistry topic before you continue here. Especially since the information in this video directly feeds off of the information from those older videos. And so that being said, Let's get started. And it's important to note that pretty much all of the Alfa amino acids are Kyrill, except for just one amino acid. And that exception is glazing. And so glazing is the Onley, a Cairo amino acid and moving forward when we're talking about amino acid configuration. Were Onley referring to the Cairo amino acids, and we're not referring to glazing now. Biochemist actually use a different convention other than the RNs convention to refer to amino acid Chire ality, and the convention that they use is called Fisher's Convention, which is named after the scientist Emile Fisher, who used the two letters L and D, rather than R and s to refer to the configuration of the Carol Carbon. Now it's important to note that life has a preference for l amino acids and life almost exclusively uses L amino acids to build their proteins, and that applies to pretty much all domains of life. And so, if you had to guess and take a shot in the dark at the configuration of any random amino acid in any random protein, guess the L amino acid. But that's not to say that D amino acids are completely irrelevant, because there are some rare exceptions. For instance, some bacteria used D amino acids toe build their cell walls, and that gives them some advantages in some scenarios. But again, the major take away here is that life almost exclusively uses L amino acids. Now all l amino acids having s configuration, except for just one l amino acid. And that is L Sistine. And so L Sistine is the on li l amino acid that does not have an s configuration, and instead it has our configuration. And the reason for this exception here has to do with the Cairo Center priorities, which we're very familiar with because we know that when determining the configuration of a Cairo carbon, the first step is to assign priorities to the four different groups around that Cairo carbon. And so when it comes to amino acids, the our group is always priority number three. And the exception is, of course, Sistine. Our group, who is priority number two. And so essentially this bullet point here explains why Sistine is an exception, and it's also going to be important down below in Method Number two of our example. And so, in our example, we're going to talk about two different methods to determine the Ellen de Configurations of amino acids. On the left, we have Method number one for standard Fisher projections. And on the right, we have Method number two for non standard Fisher projections. So we'll start with the image on the left and notice. What we have here is a standard fisher projection for an L amino acid. And so method number one is pretty much all about how to recreate this image here, uh, to create a standard fisher projection for an l amino acids. And so the first step in method number one is to make sure that our car Boxer group is on top. And so over here we can put our car Boxley and I on on top Pretty easy, right? So the second step is to essentially make sure that the longest carbon chain is vertical and so we haven't yet talked about the are groups of all of these amino acids. We'll do that later in our course. But as you'll see later in our course, the our group of every Cairo carbon is the first. Adam is a carbon atom. And so, essentially, in order to make sure that the longest carbon chain is vertical, we have to make sure that the our group is on bottom. And then, of course, our last step here, the third and last step, is if we're drawing an l amino acid, all we need to do is make sure that the amino group is on the left, and so you can think l is for left and so we can put our amino group on the left. And of course, that means that our last group is going to be the hydrogen and it's gonna be on the right, and so that's essentially the three steps that allows to draw a standard Fisher projection of an L amino acid. Now, if we wanted to draw a D amino acid instead, all we have to do is make sure that our amino group is not on the left. And so essentially, all we would have to do to draw a D amino acid is to take this amino group and swap places with the hydrogen. And when we do that, we would have ourselves a D amino acid. And so, essentially, you want to use Method number one if you're ever being asked to draw a standard Fisher projection, because it's pretty much the easiest method. But Method Number two over here is pretty much on lee gonna be used if you're given a nonstandard Fisher projection of an amino acid. And so notice down below. We have these two Fisher projections that air given to us, and both of them are non standard. And the way that we can tell is because noticed that the car boxer group is not on top. Instead, we have our car Boxley and ions on the bottom also notice that our longest carbon chain is not vertical, since our car boxer group and the are groups which are blue over here are not in a vertical line and then also noticed that the amino group is neither on the left nor on the right. The amino group is at the top, So this is definitely a nonstandard fisher projection. And so, with method number two, the first step is to essentially determine the R and the S configuration of the Cairo all of the Alfa Carbon. And so recall, uh, in our previous lesson videos that we covered and refresh our memories on how to determine the configuration off a Fisher projection. And so the second step in method number two is essentially to just remember that all of the elements amino acids haven't asked configuration and the Onley exception here is L Sistine and so down below to apply method number to notice on the left. Here, what we have is a very specific amino acid, and this is actually a winning because it has this particular our group, which is a metal group. And again, we haven't talked about the are groups of the amino acids just yet. We'll talk about those later in our course. For now, you can just think that we have Allen in over here on the left. But you can pretty much think of any amino acid here on the left. Any Kyrill amino acid? Uh, except Sistine. So this amino acid here is representing any Cairo amino acid except Sistine. And over here on the right, what we have is assisting our groups. Insisting is the exception here. And we know that if we want to determine the R. N s configuration, all we need to do is a sign priority. So let's assign priorities to this, uh, amino acid over here on the left first. So we know from our previous lesson videos how to do this will be assigned priorities. And we know that the nitrogen has the greatest atomic number. So it's going to get the first priority, and we know that the hydrogen have the lowest priority. So it's going to get the fourth priority. And so now we need to determine the priorities between these two groups here, and so recall up above we said that the our group is always priority number three for all amino acids. Except for Sistine, who is priority number two. And so that means that they are group here in blue is gonna be priority number three. And this is going to be priority number two. And so all we need to do is draw arrows from 1 to 2, 2 to 3 and three back toe one skipping priority number four here. And this looks like a clockwise rotation of, uh, priorities 12 and three. And a clockwise rotation would indicate an R configuration. But recall from our previous lesson videos that even though standard Fisher projections typically have these flat lines here that don't have any wedges or dashes that we have to imagine the vertical lines as being on dash is going away from us into the page. And we have to imagine the horizontal lines and a Fisher projection to be popping out out of the page, coming out as wedges. And so essentially, what's important to note here is that our fourth priority here is on a wedge, and so we can go ahead and imagine it here, being on a wedge. And remember that when our fourth priority is on a wedge, we always need to flip the configuration. And so, even though this looks like a clockwise are configuration. It's actually an s configuration. And so recall that up above we said that all l amino acids haven't s configuration except l assisting. And since this is not, this is any amino acid except Sistine, and it has an s configuration. What we're saying is that this is also an l amino acid, and this is El Alamein. Now, if we were to work out the same logic over here on the right, we know that to determine the configuration we assigned priorities, the nitrogen here is still gonna have the first priority. So priority number one, the hydrogen is still gonna have priority number four. And essentially, the Onley difference here is that the our group of Sistine, which you can see here, actually gives it the second priority. And that's exactly what we set up above. That Sistine Czar Group is the Onley one that actually changes the priority from priority number three toe priority number two. So now it has priority number two instead of priority number three like it did previously. And so that means that the car Boxley and I and of course, is gonna be priority number three And so again we draw our arrows from to 2. 2 to 3 and three back toe one. And essentially, this looks like a counterclockwise s configuration. But again, we have to remember that our fourth priority here is on a wedge. And so that's gonna flip the configuration. And even though it looks like it's gonna be an s configuration, it's actually gonna be in our configuration. And so what we have is a cyst ing within our configuration. And remember that cyst ing else assisting eyes going toe have is not gonna have an s configuration. Else assisting has an R configuration. And because we have our configuration for the Sistine, that means that it is l. Sistine. And so, essentially, what we've done is we've used Method number Two to identify that both of these amino acids shown r l amino acids and so moving forward, we'll be able to get some practice utilizing these concepts and skills. And so I'll see you guys in our next video
Which of the following statements is true?
Life predominantly uses D-amino acids to build proteins.
Except for Ser, life predominantly uses S-amino acids to build proteins.
All L-amino acids have an S configuration.
Life almost exclusively uses L-amino acids to build proteins.
L-Amino Acid Representations
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So now that we know that life predominantly uses l amino acids, we have to be able to recognize other representations of l amino acids. And there are several ways to represent l amino acids, and we have some of the more common ones down below. In our example. Now, in our last lesson video, we talked about two different methods to determine the l and D configuration of an amino acid. And if worse comes to worst, you can always fall back to Method number two and just determine the R and S configuration. But sometimes determining R N S is just time consuming, and we want a quicker, faster way to be able to just look at something and determine if it's l or De. And so that's really what this video is all about. And so over here on the far left noticed that what we have is a Fisher projection, and this is a standard Fisher projection for an amino acid. And we know because we have the car boxing group on top. We have our longest carbon chain vertical, meaning that our our group is on the bottom and it's an l amino acid because the amino group is on the left. And so this is just one representation of an L amino acid. And we can actually get all of these other representations of the l amino acids just by simply rotating the molecule in a specific way and rotating the bonds of the molecule in a specific way. And so it's not really that important for you guys to understand the rotations. It's more so important that, you know, thes important other, uh, l amino acid representations. But just to get you guys a little bit oriented over here, what we have is our amino group. And over here, what we have is our hydrogen and notice that in this orientation they're both popping out at you at the page. So we've got our amino group here and we've got our hydrogen over here. They're both popping out at you. And so if we were to take this molecule when we were to simply just rotated on its side so that the amino group is up top and the hydrogen is on bottom, that's exactly what we have over here. So we've got our hydrogen on bottom and army no group on top And so if we take this amino group on top and hydrogen on bottom and we were to just rotate it like this so that the hydrogen is in the back and the amino group is going down and popping out at you in a wedge, that's exactly what we've got in this representation here. So notice that our amino group is popping out at you in a wedge and the hydrogen, which isn't shown here. It's going in the back like that. And so this is one representation of an L amino acid. When you can see we just got it by simply doing rotations. And so if you notice that we have the Amin or the amino group going down and on a wedge, so that's a quick way. To be able to recognize an L amino acid is just to say, If the amino group is going down on the wedge, it's an L amino acids. Now, if we were to take this particular bond right here and we were to rotate that bond, then what we can get is this other amino acid representation this other l amino acid representation. So now notice that instead of the amino group going down. We have the our group going down and the our group is going down and on a dash, not a wedge. So that is one representation of l Amino as what? L amino acid as well, our group going down and dashed. And so if we were to take this molecule again here and we were to flip the molecule so you can imagine taking a spatula and just sliding the spatula right underneath of this car box group like this and just flipping this molecule just like you would flip a pancake. And what you'll see is that the car boxer group, the Carbonnel Group here, is going up. But down here, it's going down. Then what you'll see is that we've got this other l amino acid representation just by simply flipping it. And now the our group is going up. But the our group is on a wedge going up. So that's our last representation, the our group going up, but on a wedge. And so really, when it comes to these representations, you really want to familiarize yourself with this one in the middle, the our group going down and dash So this is the amino acid representation that we're gonna be using when we talk about each of the individual are groups for each of the individual amino acids. So really, familiarize yourself with this one. And so, if you know that the our group is going down and dash, if it's going up, it must be going on a wedge, not a dash. And then if the amino group is going down, it's gotta be on a wedge. And so hopefully this little strategy of just being able to recognize that our group going down Dash will save you guys a little bit of time on determining R and S configuration And so we'll be able to get some practice utilizing and recognizing these representations in our practice video, so I'll see you guys there.