Amino Acid Configuration - Online Tutor, Practice Problems & Exam Prep

Amino acids are primarily chiral, with glycine as the only achiral exception. Biochemists use Fisher's convention (L and D) to denote chirality, favoring L amino acids in life forms. Most L amino acids have an S configuration, except L cysteine, which has an R configuration due to priority differences in its R group. Recognizing L amino acids can be simplified through various representations, such as standard Fischer projections, where the amino group is on the left. Understanding these configurations is crucial for amino acid analysis and protein structure comprehension.

L & D Amino Acid Configurations

In this video, we're going to talk about amino acid configuration. So recall in our previous lesson videos, we refreshed our memories on configuration, chirality, 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 rewatch those older videos from our organic chemistry topic before you continue here, especially since the information in this video directly feeds off the information from those older videos. And so that being said, let's get started. It's important to note that pretty much all of the alpha amino acids are chiral, except for just one amino acid, and that exception is glycine. And so glycine is the only achiral amino acid. Moving forward, when we're talking about amino acid configuration, we're only referring to the chiral amino acids, and we're not referring to glycine. Now, biochemists actually use a different convention, other than the RNS convention, to refer to amino acid chirality. The convention that they use is called Fisher's convention, which is named after the scientist, Emil Fisher, who used the two letters L and D, rather than R and S, to refer to the configuration of the chiral carbon. It's important to note that life has a preference for L amino acids, and life almost exclusively uses L amino acids to build its proteins, and that applies to pretty much all domains of life. 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 use D amino acids to build their cell walls, and that gives them some advantages in some scenarios. But again, the major takeaway here is that life almost exclusively uses L amino acids. Now all L amino acids have an S configuration, except for just one L amino acid, and that is L Cysteine. And so L Cysteine is the only L amino acid that does not have an S configuration, and instead, it has an R configuration. The reason for this exception here has to do with the chiral center priorities, which we're very familiar with because we know that when determining the configuration of a chiral carbon, the first step is to assign priorities to the 4 different groups around that chiral carbon. And so when it comes to amino acids, the R group is always priority number 3. The exception is, of course, cysteine's R group, who is priority number 2. And so, essentially, this bullet point here explains why cysteine is an exception. It's also going to be important down below in method number 2 of our example. In our example, we're going to talk about 2 different methods to determine the L and D configurations of amino acids. On the left, we have method number 1 for standard Fisher projections, and on the right, we have method number 2 for nonstandard 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. Method number 1 is pretty much all about how to recreate this image here, to create a standard Fisher projection for an L amino acid. The first step in method number 1 is to make sure that our carboxyl group is on top. Over here, we can put our carboxylate anion on top. Pretty easy. Right? The second step is to essentially make sure that the longest carbon chain is vertical. We haven't yet talked about the R 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 R group of every chiral carbon is the first atom 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 R group is on the 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 going to be on the right. And so that's essentially the 3 steps that allow us to draw a standard Fischer 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. When we do that, we would have ourselves a D amino acid. You want to use method number 1 if you're ever being asked to draw a standard Fisher projection because it's pretty much the easiest method. However, method number 2 over here is pretty much only going to be used if you're given a nonstandard Fisher Projection of an amino acid. And so notice down below, we have these 2 Fischer projections that are given to us, and both of them are nonstandard. And the way we can tell is because notice that the carboxyl group is not on top. Instead, we have our carboxylate anions on the bottom. Also, notice that our longest carbon chain is not vertical since our carboxyl group and the R groups, which are in blue over here, are not in a vertical line. And then also, notice 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 Fischer projection. With method number 2, the first step is to essentially determine the R and the S configuration of the chiral, alpha-carbon. Recall from our previous lesson videos that we covered and refreshed our memories on how to determine the configuration of a Fisher projection. The second step in method number 2 is essentially to just remember that all of the L amino acids have an S configuration. The only exception here is L Cysteine. Down below to apply method number 2, notice on the left here, what we have is a very specific amino acid, and this is actually alanine because it has this particular R group, which is a methyl group. And again, we haven't talked about the R 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 alanine over here on the left, but you can pretty much think of any amino acid here on the left, any chiral amino acid, except cysteine. So this amino acid here is representing any chiral amino acid except cysteine. And over here on the right, what we have is cysteine's R groups, and cysteine is the exception here. And, we know that if we want to determine the RNS configuration, all we need to do is assign priorities. So let's assign priorities to this amino acid over here on the left first. So we know from our previous lesson videos how to do this, so we assign 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 hydrogens have the lowest priority, so it's going to get the 4th priority. And so now we need to determine the priorities between these two groups here. Recall up above, we said that the R group is always priority number 3 for all amino acids, except for cysteine, who is priority number 2. And so that means that the R group here in blue is going to be priority number 3, and this is going to be priority number 2. And so all we need to do is draw arrows from 1 to 2, 2 to 3, and 3 back to 1, skipping priority number 4 here. This looks like a clockwise rotation of priorities 1, 2, and 3, 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, we have to imagine the vertical lines as being on dashes going away from us into the page. And we have to imagine the horizontal lines in a Fischer projection to be popping out of the page, coming out as wedges. And so essenti

Which of the following statements is true?

• A. Life predominantly uses D-amino acids to build proteins.
• B. Except for Ser, life predominantly uses S-amino acids to build proteins.
• C. All L-amino acids have an S configuration.
• D. Life almost exclusively uses L-amino acids to build proteins.

L-Amino Acid Representations

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 2 different methods to determine the L and D configuration of an amino acid, and if worse comes to worse, you can always fall back to method number 2 and just determine the R and S configuration. But sometimes determining R and 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 D. And so that's really what this video is all about.

And so over here on the far left, notice that what we have is a Fischer Projection, and this is a standard Fischer Projection for an amino acid. And we know because we have the carboxyl group on top, we have our longest carbon chain vertical, meaning that our R 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 important other, L-amino acid representations. And so it's not really that important for you guys to understand the rotations, it's more so important that you know these important other, 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 and we were to simply just rotate it 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 our amino 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's in the back and the amino group is going down and popping out at you on a wedge, that's exactly what we've got in this representation here. So notice that our amino group is popping out at you on 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, and you can see we just got it by simply doing rotations. And so, if you notice that we have the amine 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 a wedge, it's an L-amino acid.

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 R group going down. And the R group is going down and on a dash, not a wedge. So that is one representation of an L-amino acid as well, R 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 carboxyl group like this and just flipping this molecule just like you would flip a pancake, and what you'll see is that the carboxyl group, the carbonyl 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 R-group is going up, but the R group is on a wedge going comes to it comes to these representations, you really want to familiarize yourself with this one in the middle, the R group going down and dash.

So this is the amino acid representation that we're going to be using when we talk about each of the individual R groups for each of the individual amino acids. So really familiarize yourself with this one. And so if you know that the R group is going down and dashed, 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 got to be on a wedge. And so, hopefully, this little strategy of just being able to recognize the R group going down in 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.

Which of the following shows an L-amino acid?

• A.
• B.
• C.
• D.

Here’s what students ask on this topic:

What is the difference between L and D amino acids?

L and D amino acids refer to the chirality of the amino acid molecules. This chirality is determined using Fischer's convention, named after Emil Fischer. In this system, L (levo) and D (dextro) denote the configuration of the chiral carbon. For L amino acids, the amino group is on the left in a standard Fischer projection, while for D amino acids, it is on the right. Life predominantly uses L amino acids to build proteins, although D amino acids are found in some bacterial cell walls. Most L amino acids have an S configuration, except for L cysteine, which has an R configuration due to the priority of its R group.

Why is glycine considered an achiral amino acid?

Glycine is considered an achiral amino acid because it lacks a chiral center. In other words, its alpha carbon is bonded to two hydrogen atoms, making it symmetrical. Chirality arises when a carbon atom is bonded to four different groups, creating non-superimposable mirror images. Since glycine does not meet this criterion, it does not exhibit chirality and is the only achiral amino acid among the standard amino acids.

How do you determine the configuration of an amino acid using Fischer projections?

To determine the configuration of an amino acid using Fischer projections, follow these steps: 1) Ensure the carboxyl group is on top. 2) Make sure the longest carbon chain is vertical, with the R group at the bottom. 3) For L amino acids, place the amino group on the left; for D amino acids, place it on the right. If given a non-standard Fischer projection, determine the R/S configuration by assigning priorities to the groups around the chiral center. Most L amino acids have an S configuration, except for L cysteine, which has an R configuration.

Why does L cysteine have an R configuration?

L cysteine has an R configuration due to the priority of its R group. In amino acids, the R group typically has the third priority when assigning configurations. However, cysteine's R group contains a sulfur atom, which has a higher atomic number than the oxygen in the carboxyl group, giving it the second priority. This change in priority results in an R configuration for L cysteine, unlike other L amino acids, which have an S configuration.

What are the common representations of L amino acids?

Common representations of L amino acids include standard Fischer projections, where the carboxyl group is on top, the longest carbon chain is vertical, and the amino group is on the left. Other representations involve rotating the molecule to show different perspectives. For example, the amino group can be shown going down on a wedge, or the R group can be shown going down on a dash. These representations help quickly identify L amino acids without determining the R/S configuration each time.