Drawing a Peptide - Video Tutorials & Practice Problems
On a tight schedule?
Get a 10 bullets summary of the topic
1
concept
Drawing a Peptide
Video duration:
4m
Play a video:
Video transcript
In this video, we're gonna talk about how to draw a peptide. So a lot of times your professors expect you guys to know how to draw a peptide, and really the structure of a peptide can be drawn simply from its primary protein structure. And really, there are 3 basic steps to draw any protein. And we'll talk about step number 1 in this video, and in our next videos, we'll talk about steps 2 and steps 3. So for step number 1, the very first step in drawing a peptide is just to draw the peptide backbone and also to identify the alpha carbons. And recall that the alpha carbons is just the central carbon atom where the R group is attached. And so, the backbone actually consists of repeated atoms for each residue residue that's present. And so those repeated atoms are actually just a nitrogen, a carbon, and a carbon. And so for each residue, there's going to be a nitrogen carbon carbon. And so that means that if there are 2 residues, then there's gonna be 2 sets of ncc's. If there are 3 residues, then that means there's gonna be 3 sets of ncc's. And so it turns out that this middle c here is always going to be the alpha carbon, and this last c over here is going to be the carbonyl group carbon. And remember, the carbonyl group is just a C double bond O. And so also recall from our previous videos that only the very first and the last residues in a chain actually have free or ionizable amino groups or carboxyl groups respectively in the backbone. So what that means is that the very first amino acid residue has a free amino group, but it lacks a free carboxyl group. But the very last amino acid residue has a free carboxyl group, but it lacks a free amino group. And then, all the internal residues lack both free amino and free carboxyl groups in their backbone. And so let's take a look at our example so we can, see visualize the very first step in drawing a peptide, which again is to draw the backbone and identify alpha carbons. And so, what you'll see is that we're gonna be drawing a peptide which has 3 amino acid residues. So we're only going to draw an amino acid with 3 residues, so write that here. And so because we have 3 residues, what that means is that we're going to have 3, sets residues, what that means is that we're gonna have 3, sets of the ncc's. So, let's go ahead and let's start drawing in our ncc's. So we're gonna have, be n c c. Alright. Perfect. So, now, residue, so it's gonna be n c c. Alright. Perfect. So now we've got our 3 n c c sets in there for each of our 3 residues. And so, we know that the very first amino group over here is gonna be free and ionizable. So we can go ahead and draw in our n h three plus, because we know that it's gonna be, ionized at physiological pH. And then, at the very end over here, what we can do is draw in our carboxyl group which is also going to be free. And so we can draw it as a carboxylate anion with a negative charge. And so, the next part to do, now that we've drawn in the, the backbone, is to identify the alpha carbons. So recall that the alpha carbons are gonna be the middle c. So here's our n c c, so it's gotta be the middle c here. So this is gonna be our alpha carbon. So now let's check for the next one. N c c, it's gotta be the middle one, so it's it's this one here. And then for our last one, n c c, it's this one here. So this is our alpha carbon. So now we've identified the alpha carbons and we've drawn in the backbone. And the last step here, what we're going to do is just realize that over here what we have is the n terminal end and over here what we have is the c terminal step finished step number 1. And so, I'll see you guys in our next video, where we'll talk about the second step to drawing a peptide.
2
concept
Drawing a Peptide
Video duration:
3m
Play a video:
Video transcript
So now that we've finished the first step in drawing a peptide, let's move on to the second step. And in the second step of drawing a peptide, consider amino acid chirality. And by considering amino acid chirality, all I really mean is that I want you guys to recall that life almost exclusively uses l amino acids. And remember the way that we recognize and draw l amino acids is to remember R group is going up when the r group is going up, it must be on a wedge. And that's all I really mean. So let's take a look at our example where we'll be able to see step number 2 of drawing a peptide, which again is gonna be to draw the carbonyl groups and consider amino acid chirality. And so as you can see, we've already got our steps filled in from step number 1 of drawing the peptide. And so again, remember that each amino acid residue is gonna have a nitrogen, carbon carbon set, an n c c. And it's the middle c here that's gonna be the alpha carbon. And so this c over here is gonna be the carbonyl group carbon, and so we know that we're gonna put the carbonyl group on this carbon over here. So let's go ahead and draw in the carbonyl group. Perfect. So now, we got to do the same thing for the next residue because remember, we have a total of 3 residues. And so here's our next NCC set. The middle one is gonna be the alpha carbon here, and so that means that this other carbon over here must be the carbonyl group carbon. So we can draw it and we can draw it facing down this time since this carbon is kind of going down. And then we have our last NCC. And guess what? The carbonyl group is already there from our carboxyl group being present, so we don't need to draw that one. So now we've drawn all the carbonyl groups, the next step is to consider the, chirality. And so, for the chirality, remember, if the R group is going down, it has to be dashed. And remember, the R groups come off of the alpha carbons, so let's go to each of our alpha carbons, so we know this is an alpha carbon here and it's already kind of going down. Notice that it's it's like moving downwards already. And so because it's already down, we just need to draw our R group down and dash, so it's gotta be on a dash. Let's just draw a dash here. Perfect. There's our our chirality. So this is gonna be an L amino acid already. Now, let's consider the next residue and here's our next alpha carbon over here. So that's where we know our r group is going to be. So, this one is kind of going up, notice that it's going up in an upwards fashion, so that means our r group is going to be going up. And when the r group is up, it's got to be on a wedge. And so, of course, that means that we're going to draw a wedge here. So we'll draw our wedge. Perfect. There's our wedge. Alright. That's it. And then on our last, alpha carbon over here, it's going down again. Notice that it's kind of coming down. And because of that reason, our r group group is gonna be down and dashed, so that means that we're gonna put a dash over here on this alpha carbon where our r group is gonna go. And that's it. That's all we need to do. That's step number 2. Pretty easy. Right? So now that we finished step number 2, I'll see you guys in our video where we'll do our last and final step, step number 3. See you guys there.
3
concept
Drawing a Peptide
Video duration:
2m
Play a video:
Video transcript
So now that we've covered both the first and second steps for drawing a peptide, in this video, we're gonna focus on the 3rd and final step for drawing a peptide. And in this 3rd step, all we need to do is fill in the remaining hydrogens on the nitrogen atoms. And so all we need to do is add nitrogen here and add a hydrogen here. And so essentially the hydrogens on the nitrogen atoms can't be assumed. So we have to draw them in, but the hydrogens that are on carbon atoms they can be assumed so we don't need to draw those in. And so in addition to filling in the remaining hydrogens on the nitrogen atoms, all we need to do is draw in the r groups for each of the amino acid residues. And so in the example below, it says to draw in the R groups for the peptide, alanine, valine, and leucine. And so, over here near our n terminal n, we have our first amino acid residue and our first r group, and that will be the R group of alanine. And so we know that because a is the first letter of the alphabet and that's easy to remember, alanine's R group is also easy to remember because it's literally just a methyl group, a CH three group. And so that's it for alanine and next what we have is valine and, that would be v and recall that valine is literally just like alanine, except it, it's going to have a v shape to it. So essentially, all we need to do is draw an alanine, so c h with a v shape to it, so 2 methyl groups branching off and that is it for valine structure. Now, last but not least, what we have is l and l is for leucine and leucine is really just a loose extension of valine. So, it's exactly the same as valine except it's gonna have an extra c h 2. So it'll have the, c h 2 and then it will have the veiling at the end. So it's an extended loose version of valine. And so that is it for the peptide alanine, valine and leucine, and that completes this, process on drawing a peptide and we'll be able to get practice utilizing these three steps for drawing a peptide in our next couple of practice videos. So I'll see you guys there.
4
Problem
Problem
Draw the following peptide given its primary protein structure: D-R-A-W.
Video duration:
8m
Play a video:
Was this helpful?
5
Problem
Problem
Strive for greatness and draw the chemical structure of the following peptide: S-T-R-I-V-E.
Video duration:
7m
Play a video:
Was this helpful?
6
Problem
Problem
Aim high and draw the following peptide: A-I-M-H-I-G-H.
Video duration:
8m
Play a video:
Was this helpful?
7
Problem
Problem
Be a boss & draw the chemical structure of the following peptide: P-C-Y-N-F-Q-K.