Draw the following peptide given its primary protein structure...

Question

Draw the following peptide given its primary protein structure: D-R-A-W.

Accepted Answer

Alright. So this practice problem wants us to draw the following peptide given its primary protein structure of d r a w or just draw. And so when we're drawing a peptide, we're going to follow our 3 steps for drawing a peptide. And in our first step, we need to draw the peptide backbone and identify alpha carbons. And so when we're drawing the peptide backbone, we know that we're going to draw these NCC sets or these nitrogen carbon carbon sets. And we know that there's going to be an ncc set for each amino acid residue that we have. And so since we have a total of 4 amino acid residues, we're going to have a total of 4 ncc sets. And so, down below we can start to draw that. And so, we have our nitrogen over here, and then we know that it can go either up or with a carbon here, or it can go down with a carbon, and it doesn't matter which way we go. So I'm gonna go up here with a carbon and down with another carbon. So here's our n c c set and we know that the middle carbon in this n c c set is gonna be the alpha carbon. So we can label it with the alpha carbon symbol here and so that's our 1st n c c set and that covers our first residue of aspartic acid here. So, we need to keep drawing n c c sets, so we have another n c c set, and of course the middle carbon is the alpha carbon, and that is for our next residue arginine. So we need to continue drawing n c c sets. So now we have another n c c set, and again our middle carbon is the alpha carbon, alpha carbon, and then that covers alanine. And last but not least, what we have is our next 'n' c c set', and again the middle carbon is going to be the alpha carbon. And then we already know that at the end terminal end, we're going to have a free amino group, so we can put an NH 3+ over here. And at the c terminal end, we're going to have a free carboxylate group, we can put a COO- over there. And so that is it for the first step and we can move on to the second step where we're going to draw in the carbonyl groups and consider amino acid chirality. And so the carbonyl groups are going to be on the carbons that are not labeled as alpha carbon. And so any carbon that's labeled as the alpha carbon is not gonna have a carbonyl group. So we can put the carbonyl groups in for all of these carbons shown here. And then by considering amino acid chirality, all we really mean is to remember that life predominantly uses proteins with 'l' amino acids. And so all of our, carbons, our alpha carbons, have to have an 'l' configuration. And the way that we, can confirm that is that if the 'r' group is going down, then the 'r' group has to be on a dash. And then if the 'r' group is going upwards, then the 'r' group has to be on a wedge. And so looking at our 1st alpha carbon over here, notice that it's kind of pointing up in an upwards direction, and so that means that our r group is going to be going up. And when our our group is going up, it's going to be on a wedge. And so we can draw a wedge over here. Perfect. And then this alpha carbon over here is pointing in a downwards direction, so it's going to be on a dash. This one's going up and on a wedge and this one's going down and on a dash. And so that is it for the amino acid chirality and we're done with step number 2. And so in step number 3, all we need to do is draw in the hydrogens on the nitrogen atoms. So drawing in hydrogens on these nitrogen atoms here, and then all we need to do is draw in the r groups for each amino acid residue. And so starting over here with the d here, we know that the d is for aspartic acid and aspartic acid is an acid, so it has a carboxylic acid group and its 'r' group is literally just alanine with a carboxylic acid group. And so alanine is CH3, but we know that the number of hydrogens are gonna change for aspartic acid. It's gonna end up being 2. And then it's gonna have a carboxylic acid group, so c double bond o with a o minus on it. And so because it is charged here with this carboxylate group, it's referred to as aspartate. And so that is it for our first amino acid residue and we can move on to our arginine. And so arginine, essentially is going to have features of the knight's sword or lysine's r group and features of the horse or histidine's r group. And because it has features of the Night's Sword, we can count up how many points it has that you could try to poke somebody with just like you poke somebody with a Night's Sword. And so, it has a total of 1, 2, 3 pointy ends that you could try to poke somebody with, which reminds us that there's a 3 carbon start to our r group here. So 1, 2, 3 carbon start to the r group, and then, just like there's a 3 carbon start to the r group, there's a triangular nitrogen structure that has 3 points, in the r group as well. And so, the way that this triangular nitrogen structure works is that there's a nitrogen, a carbon, and a nitrogen, and then this carbon is double bonded to a nitrogen. And so all we need to do now is draw in all the hydrogens, so this one will have 1, this one will have 2, and this one will also have 2, and it's going to have a positive charge on it. And so, that is it for arginine's R group. Now moving on to our next amino acid, A, A is for alanine and just like it's easy to remember that a is the first letter of the alphabet, alanine's R group is also really easy to remember. And so, it's literally just a methyl group or a CH three group. And so that is it for alanine. And then last but not least, what we have is w and w is for tryptophan because the way that Bugs Bunny would say it is twitophan with a w, so it's phonetic. And so tryptophan is literally just alanine with 2 joined rings. The first ring is a 5 membered ring and the second ring is a 6 membered benzene ring. But the benzene ring goes below the structure, so we're gonna draw it last. So we can draw alanine first. So we have ch 2, because we know the number of hydrogens are gonna change, and then it's gonna be a 5 membered ring that we're drawing first. So here's our 1, 2, 3, 4, 5 membered ring. Alright, great. So now the next part is to figure out where does this nitrogen go because we know that tryptophan structure, r group, has a single nitrogen atom in it. And so the way that we remember where the nitrogen goes is that tryptophan trips on a tripod and tripods have 3 legs so that reminds us that there's a 3 carbon start to the nitrogen. And so notice that there's 1, 2, 3 carbon start, which means that we could put our nitrogen here. And so let's go ahead and get rid of these dots and put our nitrogen in here like that. Perfect. So now that we know where our nitrogen is, the next part is to realize that the nitrogen is not part of the benzene and we know that the benzene has to be below the structure, which means that the benzene can't go on this side of the joined ring or on this side because either otherwise it would be above and we want it to be below the structure. And then it can't be on this side or on this side either because then the nitrogen would be part of the benzene ring and that can't be the case. So that means that only this side is available for the benzene to be joined to the ring, and so we can go ahead and draw in our benzene ring here And what you can see is that our benzene ring is below, it's got the lowest point in our r group. And so the last part here is to remember that the double bond is not touching the nitrogen or the benzene ring, and so the double bond goes here because that's the only place that it can go where it does not touch the nitrogen or the benzene ring, and then of course we fill in our hydrogen, and that is it for tryptophan structure. And so here we've drawn the entire, structure, the peptide of d r a w or draw, and that concludes this practice. So I'll see you guys in our next video.

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Draw the following peptide given its primary protein structure: D-R-A-W.

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