Draw a two-stranded antiparallel β-sheet with appropriate hydr...

Question

Draw a two-stranded antiparallel β-sheet with appropriate hydrogen bonding between the following peptides:

1) L-A-D-Y.

2) G-A-G-A.

Accepted Answer

So this practice problem wants us to draw a 2 stranded antiparallel beta sheet with appropriate hydrogen bonding between the following peptides, Lady Gaga. So we're drawing a Lady Gaga antiparallelbeta sheet here. And so first, what we're gonna do is draw the lady, peptide. And recall that the steps for drawing a peptide, we first need to draw the backbone and identify alpha carbons. So for this lady here, remember the way that we draw the peptide backbone, it is by drawing an n c c set for each amino acid residue. So we have 4 amino acid residues in this lady peptide over here, which means that we're gonna have 4 NCC sets. So let's go ahead and draw that over here. So let's put in our nitrogen, here's our carbon, carbon, and, that's one set, so then we can do that again. Nitrogen, carbon, carbon, 2 sets, nitrogen, carbon, carbon, that's 3, and then nitrogen, carbon, carbon. Perfect. That's 4 sets. So now we need to identify alpha carbons and remember that the n c c, the middle one's going to be the alpha carbon. So we can put the the alpha carbon for this middle ncc. So ncc, the middle one's alpha carbon. Ncc, middle one's an alpha carbon. Ncc, middle one's an alpha carbon. Alright. Great. So, now that we have this strand, lady going from left to right in this direction, what we need to do is consider drawing the Gaga peptide, but going in the opposite direction. So remember, if this one's going from left to right, N terminal or C terminal, the other one, Gaga, needs to go from right to left, n terminal to c terminal. So then we can go ahead and draw in our Gaga peptide. We can go ahead and draw the same backbone. So it backbone. So it also has 4 residues, so we'll we're gonna need 4 NCC sets, but this time, we're gonna go in the opposite direction. And so, what we wanna do is since we started up, over here with this nitrogen, we'll start up over here with this nitrogen. So we'll have a nitrogen, it'll come down, and then n c c. Then we'll have n c c, n c c, and n c c. Perfect. Alright. So now what I'm gonna do is I'm going to, shift these guys down a little bit and give us some a little bit more space and move this up. Move this guy back down. Here, let's just get rid of him and draw him back in. Alright. So now what we've got is we've got our 2 peptides and now we need to identify the alpha carbons here and we know it's gonna be the middle, carbon. So n c c, the middle one's alpha carbon. Ncc, middle one's an alpha carbon. Ncc, middle one's an alpha carbon. Ncc, middle one's an alpha carbon. Alright. So now that we've got these, we can move on to our 2nd step for drawing a peptide, which is just to draw in the carbonyl groups and to identify amino acid chirality. So, when we're drawing in the carbonyl groups, it's just gonna be on the ones that do not have an alpha carbon on them. So, this c over here is gonna be a carbonyl group. And we know that it's going to also be the last residue is gonna have a free carboxyl group, so we'll put an o and we'll make it charge, so an o minus. Then we can draw in the other carbonyl groups, so for all of them that do not have an alpha carbon on them. So top peptide's done. Now we can do the bottom one. So here we have 1. Here we have 1 going down. Here's one going up. And then here's one going down. And again, this is gonna be the end, so it's going to have, carboxyl anion. It's gonna be free since it's the last residue. And so we know that the, first residue is gonna have a free amino group, so let's go ahead and put in n h three plus from both of these. And so okay. So now we're done with step number 2. We we need to move on to identify amino acid chirality. And so all the chirality is saying is that if the r group if the r group is going down, then it should be on a dash, But if the r group is going up, then it should be on a wedge. And so, we can take a look at each of our, alpha carbons here and we can say, okay, well, this one's going up. This alpha carbon here, it's kind of going up, so its r group is going to go up. When the r group is going up, it has to be on a wedge. So, this is going to be on a wedge here and then down on a dash. Up on a wedge, down on a dash. Perfect. Alright. So we can do the same for the bottom one. So down on a dash, up on a wedge. Down on a dash, up on a wedge. Alright. So now we've got our chirality. The last step is to just draw in the r groups. So, for, the first peptide, which is on the bottom, so this is peptide number 1, this is peptide number 2 up here. So, for peptide number 1, that's lady. So l here is for leucine. Remember that leucine's r group is literally just a, it's just a loose extension of valine, so it's essentially just going to be CH 2. It's gonna be valine with an extra CH 2, so it'll be CH 2 and then CH, and then 2 methyl groups coming off. So there is Leucine's R group. Next, what we have is A, and A is for alanine, and alanine's first letter is, its one letter code is just an a. And just like a is the first letter of the alphabet, alanine's R group is pretty easy to remember just like a is the first letter of the alphabet and that's easy to remember. So it's literally just gonna be a methyl group, so it's just gonna be a CH3. So there's alanine right there. D is for aspartic acid and aspartic acid is literally just alanine with a carboxyl group. So all we need to do is redraw alanine and we know the hydrogens are gonna change, it's gonna end up just having 2, and then we just draw a carboxyl group, and we can make it a carboxyl anion, make it charged. And then, so that is aspartic acid, and then y is is gonna be tyrosine, and tyrosine is literally just phenylalanine with a hydroxyl group baby. So phenylalanine is literally just alanine with a phenyl group. So group baby. So there is our, lady peptide. So lady peptide is completely done being drawn. So now, we can move on to Gaga. And so remember, gaga is, this is the end terminal end and this is the c terminal end. And over here, here's our end terminal end, so we have to put our, g over here on the right side. So g is for glycine and glycines, our group is literally just a hydrogen atom, so we can just put in a hydrogen over here. So the next one is a and a is literally just alanine, which is just a methyl group, so it's just methyl group, so it's just gonna be a CH3. Then we have g again, which is literally just glycine, which is just a hydrogen, and then we have alanine again. So alanine is literally just going to be a methyl group, c h 3. So now we've got our peptide completely drawn. The last step is to draw in the appropriate hydrogen bonds. So we wanna draw in the appropriate hydrogen bond stabilizing this anti parallel beta sheet. And so all we need to do is take a look at the r groups I'm sorry, take a look at the carbonyl groups, and the amino groups of the backbone, and we can really ignore all of the r groups because the r groups are not gonna be involved with hydrogen bonding. So here's our 1st carbonyl group and here's an amino group. And these 2 are facing towards each other, so there's gonna be a hydrogen bond forming between these 2. So we can draw our hydrogen bond in green, a green dotted line. So here's one hydrogen bond that will form. Then over here, we have a second hydrogen bond that will form. So each of these nitrogens is gonna have a hydrogen on them. And so with each of these, nitrogens that have a hydrogen, they're going to form a, hydrogen bond. So here's another hydrogen. And so, okay, so now we've got our hydrogens in there. We're going to fill in here a hydrogen bond that forms between these 2. And then this next residue, notice that the carbonyl groups and the amino groups are facing the opposite direction. So, again, with this one, so they do not form hydrogen bonds. But these 2 are facing the right direction, so they are gonna form a hydrogen bond and so is this one. And then over here, notice that they're facing the opposite directions. They're going away from each other. And so, because these groups are going away from each other, they do not form hydrogen bonds. And so, these hydrogen bonds that are highlighted here are the only 4 hydrogen bonds that are stabilizing our anti parallel beta sheet. And so this concludes our practice, and I'll see you guys in our next video.

Difficoltà con Biochemistry?

Draw a two-stranded antiparallel β-sheet with appropriate hydrogen bonding between the following peptides:
1) L-A-D-Y.
2) G-A-G-A.

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