Drawing a Peptide: Study with Video Lessons, Practice Problems & Examples

Drawing a Peptide

In this video, we're going to 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 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 are just the central carbon atom where the R group is attached. And so, the backbone actually consists of repeated atoms for each 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 going to be 2 sets of NCCs. If there are 3 residues, then that means there's going to be 3 sets of NCCs. 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 going to 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 going to have 3, sets of the NCCs. So, let's go ahead and let's start drawing in our NCCs. So we're going to have, be N C C. Alright. Perfect. So, now, residue, so it's going to be N C C. Alright. Perfect. So now we've got our 3 NCC sets in there for each of our 3 residues. And so, we know that the very first amino group over here is going to be free and ionizable. So we can go ahead and draw in our NH3⁺, because we know that it's going to 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 going to be the middle c. So here's our N C C, so it's got to be the middle c here. So this is going to be our alpha carbon. So now let's check for the next one. N C C, it's got to 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 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.

Drawing a Peptide

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 the 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 going to 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 going to have a nitrogen, carbon, carbon set, an N-C-C. And it's the middle C here that's going to be the alpha carbon. And so this C over here is going to be the carbonyl group carbon, and so we know that we're going to 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 going to 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 moving downwards already. And so because it's already down, we just need to draw our R group down and dashed, so it's got to be on a dash. Let's just draw a dash here. Perfect. There's our chirality. So this is going to 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 is going to be down and dashed, so that means that we're going to put a dash over here on this alpha carbon where our R group is going to 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.

Drawing a Peptide

So now that we've covered both the first and second steps for drawing a peptide, in this video, we're going to focus on the 3rd and final step for drawing a peptide. In this 3rd step, all we need to do is fill in the remaining hydrogens on the nitrogen atoms. Essentially, the hydrogens on the nitrogen atoms can't be assumed, so we have to draw them in, but the hydrogens that are on the carbon atoms can be assumed, so we don't need to draw those in. 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.

In the example below, it says to draw in the R groups for the peptide, alanine, valine, and leucine. Over here, near our N-terminal N, we have our first amino acid residue and our first R group, which will be the R group of alanine. 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 CH₃ group.

Next, we have valine, denoted as "V", and recall that valine is literally just like alanine, except it has a V shape to it. So essentially, all we need to do is draw an alanine with a V shape to it, so 2 methyl groups branching off, and that is it for valine’s structure.

Last but not least, we have leucine, denoted as "L", and leucine is really just a loose extension of valine. So, it's exactly the same as valine except it's going to have an extra CH₂. So it'll have the CH₂, and then it will have the valine at the end. It's an extended loose version of valine. That is it for the peptide alanine, valine, and leucine, and that completes this process on drawing a peptide.

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.

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

Alright. So this practice problem wants us to draw the following peptide given its primary protein structure of draw or just draw. And so when we're drawing a peptide, we're going to follow our 3 steps for drawing a peptide. In our first step, we need to draw the peptide backbone and identify alpha carbons. When drawing the peptide backbone, we know that we are going to draw these NCC sets, or these nitrogen carbon carbon sets. Since we have a total of 4 amino acid residues, we are going to have a total of 4 NCC sets. We have our nitrogen over here, and then it can go either up with a carbon here, or it can go down with a carbon, and it doesn't matter which way we go. I'm going to go up here with a carbon and, down with another carbon. Here's our NCC set and we know that the middle carbon in this NCC set is going to be the alpha carbon, so we can label it with the alpha carbon symbol here. That's our first NCC set and that covers our first residue of aspartic acid. We need to keep drawing NCC sets, so we have another NCC set and of course, the middle carbon is the alpha carbon for our next residue, arginine. We continue drawing NCC sets. Now we have another NCC set, and again our middle carbon is the alpha carbon, covering alanine. Last but not least, we have our next NCC set, and again the middle carbon is going to be the alpha carbon. At the N-terminal end, we are going to have a free amino group, so we can put an NH₃⁺ over here. At the C-terminal end, we are going to have a free carboxylate group, so we can put a COO⁻ over there. That is it for the first step and we can move on to the second step where we are going to draw in the carbonyl groups and consider amino acid chirality. The carbonyl groups are going to be on the carbons that are not labeled as the alpha carbon. By considering amino acid chirality, we remember that life predominantly uses proteins with L-amino acids. If the R group is going down, then the R group has to be on a dash. If the R group is going upwards, then the R group has to be on a wedge. Looking at our first alpha carbon, it is pointing up, so its R group is going up and will be on a wedge. This alpha carbon is pointing downwards, so it is on a dash. This one goes up and on a wedge, and this one goes down and on a dash. That completes the amino acid chirality. For step number three, we draw in hydrogens on the nitrogen atoms. Next for aspartic acid, which is an acid, it has a carboxylic acid group in its R group, literally just alanine with a carboxylic acid group. Alanine is CH₃, but the number of hydrogens changes for aspartic acid. It ends up with 2 hydrogens and a carboxylic acid group: COO⁻. Because it is charged, it's referred to as aspartate. Next is arginine, which has features of a knight's sword (Lysine's R group) and features of a horse (Histidine's R group). It has a total of 3 pointy ends, which reminds us that there's a 3-carbon start to our R group. Just like there's a 3-carbon start to the R group, there's a triangular nitrogen structure with 3 points in the R group as well. The triangular nitrogen structure works with nitrogen, carbon, and nitrogen, and this carbon is double bonded to a nitrogen. Draw in all the hydrogens: this one has 1, this one and this one also have 2. It is going to have a positive charge on it. Alanine's R group is just a methyl group, CH₃. Finally, tryptophan is just alanine with two joined rings. The first ring is a 5-membered ring, and the second ring is a 6-member benzene ring, but the benzene ring goes below the structure. Alanine starts as CH₂, leading to our 5-membered ring. Tryptophan's structure has a single nitrogen atom situated after a 3-carbon start, reminding us that tryptophan "trips on a tripod," and tripods have 3 legs. The nitrogen must be placed away from points where it could join the benzene, ensuring it is not part of the benzene ring. The available side for the benzene to join the ring is defined, and we can draw our benzene ring below, marking the lowest part of the R group. We observe that double bonds do not touch the benzene ring and fill in our hydrogen. That is it for the tryptophan structure. Here we’ve drawn the entire structure of the peptide of DRAW or draw, and that concludes this practice.

Strive for greatness and draw the chemical structure of the following peptide: S-T-R-I-V-E.

Alright. So this practice problem wants us to strive for greatness and draw the chemical structure of the following peptide, strive. And so we're going to follow our 3 steps for drawing a peptide. And in the first step, we're going to draw the peptide backbone and identify alpha carbons. Now when we're drawing the peptide backbone, we know that we draw an NCC set or a nitrogen carbon carbon set for each amino acid residue that's in the peptide. And since we have a total of 6 amino acid residues in the peptide, we're going to have a total of 6 NCC sets, or nitrogen carbon carbon sets. And so let's go ahead and draw that in first. So over here we have a nitrogen and we know that we're going to have NCC, so that's one set right there, then we have another NCC set, that's 2, then we have NCC that's 3, NCC that's 4, NCC, that's 5, and then NCC, that's 6, NCC sets. And so, essentially we know that, we need to identify alpha carbons, and the alpha carbon is going to be the middle carbon within each of these, NCC sets. So here's our middle alpha carbon right here. Here's the next NCC, so it's going to be the middle alpha carbon. NCC, middle carbon. NCC, middle carbon. NCC, middle carbon. And NCC, middle carbon. Alright. So now that we've got all of our middle carbons, alpha carbons labeled, we can quickly tell if we've got the right number of NCC sets if we count the number of alpha carbons. So we have a total of 5, 6, alpha carbons, which means that we have 6 amino acid residues accounted for and the appropriate amount of NCC sets. And so, we know that at the end terminal, there's going to be a free and ionizable amino group, so an NH₃⁺. And then at the opposite end, the carboxyl end, we know that there's going to be a free and ionizable carboxylate group. And so that is it for the first step, and in the second step, we can draw in the carbonyl groups and consider amino acid chirality. And so the carbonyl groups are going to be on all the carbons that are not labeled with the alpha carbon symbol. And so it'll be on all of these indicated carbons here. And so, that is it for the carbonyl groups. And now all we need to do is consider amino acid chirality, which is just remembering that if the R group is going down, then it has to be on a dash, but if the R group is going up, then it has to be on a wedge. And so looking at our first amino acid alpha carbon over here, notice that it's pointing in an upward direction with these bonds here, which means that our R group is going to be going up, and when our R group is going up, it's going to be on a wedge, and so up here we can draw a wedge. And then this alpha carbon is going down, so we can draw it on a dash. This one's going up, so we can put it on a wedge. This one's going down, so we can put it on a dash. This one going up so we can put it on a wedge, and this one's going down so we can put it on a dash. And that is it for step number 2. So in step number 3, all we need to do is fill in the hydrogens on the nitrogen atoms. So essentially just drawing in hydrogens at these nitrogens indicated here, and then we need to fill in the R groups for each amino acid residue. And so our first amino acid residue is S, which is for serine, and the next one is T, which is for threonine. And we know that alcohol is a serious threat, and so the serious is for serine and the threat is for threonine. So we know that serine and threonine have alcohol groups in their R groups. And so serine is literally just alanine with an alcohol group, and alanine we know is CH₃, but we know that the number of hydrogens are going to change for serine and it's going to end up being just 2, and then it's going to have an alcohol group branching off of it. So, that is it for serine structure and we can move on to threonine. And really, threonine structure is branching right off of serine. So, what you'll see is that we have a carbon and an OH group coming off just like what we have over here. But with threonine structure it has 3 different parts around its central carbon atom in its R group, and those three parts are a hydrogen, an alcohol group or a hydroxyl group, and a methyl group, a CH₃ group. And so that is it for the threonine structure and we can move on to our next one which is R and that's for arginine. And we know that arginine has features of a night sword or lysine's R group, and because knight's swords are used to poke people with, we can count the number of pointy ends that the R group, that the, one letter code R here has that we could try to poke somebody with, and since it has 3 pointy ends that we could try to poke somebody with, that means that there's a 3 carbon start to our chain here. So we have a 3 carbon start, CH2, CH2, CH2, and then that also reminds us that there's a triangular nitrogen structure at the end of the R group. And the way that that triangular nitrogen structure works is that there's a nitrogen, a carbon, and a nitrogen, and then the carbon is double bonded to another nitrogen. And then we fill in the hydrogens, so this one's going to have 1, this one's going to have 2, and then this one will also have 2, and it's going to have a positive charge. And so that is it for arginine structure. And then next what we have is the 'I' and the 'I' is for isoleucine, and isoleucine is an isomer of leucine, which means it has the same chemical atoms, but just a different arrangement of those chemical atoms. And that arrangement we can get from comparing it to valine since, isoleucine is a lopsided valine. And so, all we need to do is draw valine, so valine is alanine with a V shape like that, and then we make the valine lopsided by drawing an extra methyl group, and that is it for isoleucine. So then, next what we have is valine, and we know that valine is literally alanine with a V shape, so it's just going to be CH with 2 methyl groups branching off making a V shape like that. And then last but not least, what we have is E which is for glutamic acid. And so because it has the GLUT in it, we know that it's going to have an extra butt section and extra CH₂ in comparison to aspartic acid. And so, all we need to do is draw in an extra CH₂ in comparison to aspartic acid, and aspartic acid is just alanine with a carboxyl group. And so, we draw in CH₂, we draw in an extra CH₂, and then we draw in the carboxyl group that makes it an acid. So we know that it's glutamic acid, so it has to have a carboxylic acid. And so, it's going to be ionized like this as a carboxylate group, so we have a carboxylate group here. We have an extra CH₂ butt section, if you will, that is accounted for by the glut. And so this is glutamic acid's R group, and because it's ionized it's actually going to be glutamate. And so, essentially, that is it for our peptide here and we've drawn the peptide STRIDE, the chemical structure for it. So, that concludes this practice problem and I'll see you guys in our next one.

Aim high and draw the following peptide: A-I-M-H-I-G-H.

Alright. So this practice problem wants us to aim high and draw the following peptide, aim high. And so what we're going to do is follow our 3 steps for drawing a peptide. In the first step, we're going to draw the peptide backbone and identify the alpha carbons. When we're drawing the peptide backbone, we're going to draw an NCC set or a nitrogen carbon carbon set for each amino acid residue in the peptide. Since there's a total of 7 amino acid residues in the peptide, there's going to be a total of 7 NCC sets. So let's get started with drawing those 7 NCC sets. What we have is a nitrogen, carbon, carbon, that's 1 NCC set. Then we need more of those, so NCC, that's 2, NCC that's 3, NCC that's 4, NCC that's 5, NCC that's 6, and NCC that's 7. So now we have all 7 of our NCCs. The next step is going to be to identify the Alpha Carbons, which will be the middle carbon in each of these NCC sets. Here's an Alpha Carbon here, here's an Alpha Carbon, here's an Alpha Carbon, here's an Alpha Carbon here, here's an Alpha Carbon, here's an Alpha Carbon, and finally here's an Alpha Carbon. Remember, at the N-terminal end, there's going to be a free ionizable amino group, so it's going to be an NH3+, and at the opposite end, the carboxyl end, there's going to be a free and ionizable carboxylate group, COO-. And so, essentially that is it for step number 1. In step number 2, we're going to draw in all of the carbonyl groups and consider amino acid chirality. When drawing the carbonyl groups we draw them on the carbons that are not labeled as Alpha Carbon. We can draw them on all of these carbons as indicated, and we are almost done. Now we need to consider amino acid chirality, which is just remembering that life predominantly uses L-amino acids in their proteins. We need to make sure that our amino acids have the L-configuration, and the way that we do that is by remembering that when the R-group is going down, it should be on a dash, and when the R-group is going up, it should be on a wedge. Looking at our first Alpha Carbon over here, which we know is going to have an R-group, notice that it's pointing in the upwards direction here. That means this Alpha Carbon is going to have an R-group that's going up, and when the R-group is going up, it's going to be on a wedge. Over here, this Alpha Carbon is going down, so it's going to be on a dash. This one's going up, so it's going to be on a wedge. This one's down and on a dash, up and on a wedge, down and on a dash, and up and on a wedge. And so that is it for step number 2. In step number 3, all we need to do is fill in the hydrogens on the nitrogen atoms, so essentially just drawing in hydrogens on all of these nitrogen atoms shown here. We need to draw in the R-groups for each of the amino acid residues. The first amino acid residue that we have is A, and A is for alanine. Alanine's R-group is easy to remember because it's just a methyl group or a CH3 group. Next, we have I, and I is for isoleucine, which is an isomer of Leucine. To draw isoleucine, we know valine is just alanine with a V shape with these 2 methyl groups. And to draw isoleucine we just need to make valine lopsided. Moving on, what we have is M and M is for methionine. Methionine has a methylthiol group and its R-group forms a sideways M shape. It has a carbon going down and then coming up, and then at this point, it has a methyl thiol group, so it has a sulfur and a methyl group coming off. Next, we have H, and H is for histidine. Histidine's R-group is alanine with a 5-membered ring coming off of it. All we need to do is draw alanine here, and the ring branching off alters the number of hydrogens. Our 5-membered ring is going to look like this. Histidine's R-group looks like a sideways horse due to its structure with 2 nitrogens in the R-group and 2 double bonds. The next amino acid is I again for isoleucine, so it's just a lopsided valine. Then we have G, and G is for glycine, whose R-group just glides right on through because it's so small; it's just a single hydrogen atom. The last amino acid is H again for histidine, so the structure is the same as described earlier. This concludes our peptide for 'aim high' here, and we have indeed aimed high. This concludes this practice problem. See you guys in our next video.

Be a boss & draw the chemical structure of the following peptide: P-C-Y-N-F-Q-K.

Alright. So this practice problem wants us to draw the chemical structure of the following peptide, pcynfqk. This peptide is not a word like our previous practice problems, but after drawing this peptide, we would have drawn all 20 of the alpha amino acids in a peptide, which is a good thing. And so we're going to follow our 3 steps for drawing a peptide. And in the first step, we're going to draw the peptide backbone and identify the alpha carbons. We know that, when we're drawing the peptide backbone, we're going to draw an NCC set, or a nitrogen carbon carbon set, for each of the amino acid residues in the peptide. And because we have 7 amino acid residues in our peptide, we're going to draw 7 NCC sets. Let's go ahead and get started with that process. Start with a nitrogen, carbon, carbon, that's 1 NCC set. Nitrogen, carbon, carbon, 2. Nitrogen, carbon, carbon, 3. But not least, nitrogen carbon carbon 7. Now that we've got all of our NCC sets, we need to identify the alpha carbon, and the alpha carbon is going to be the middle carbon in the NCC set. So, it'll be this alpha carbon here. At the end terminal end, we're going to have a free and ionizable amino group for most of our linear peptide. So we're going to have an NH3+ over here. And then at the other end, we're going to have a c terminal end with a free carboxylate group or COO-. In step number 2, we need to draw in all of 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 the Alpha carbons. And so, it'll be all of these indicated carbons that are shown here. And then we need to consider amino acid chirality, remembering that life predominantly uses L amino acids to build their proteins. To ensure that our amino acids have the L configuration, we need to make sure that our R groups that are going down are going to be on a dash and the R groups that are going up are going to be on a wedge. In step number 3, we need to draw in all of the hydrogens on the nitrogen atoms and the R groups for each of the amino acids. Our first amino acid is P for proline, whose R group forms a pentagon loop connecting back to the nitrogen atom, changing the number of hydrogens on that nitrogen. Next, C is for cysteine, which incorporates a SH group. Y is for tyrosine, characterized by a phenyl group finished with a hydroxyl group. N is for asparagine, symbolized by an amide group coming off its side chain. F represents phenylalanine, which strictly has a phenyl group branching off. Q for glutamine resembles asparagine but includes an extra CH2 in its side chain. Lastly, K, representing lysine, features a 4-carbon alkyl chain terminating in an amine group. And with that, we have successfully drawn our peptide here. That confirms that we are definitely bosses and we accomplished this problem. I'll see you guys in our next video.

Here’s what students ask on this topic:

What are the steps to draw a peptide?

To draw a peptide, follow three essential steps. First, create the peptide backbone by connecting nitrogen, carbon, and carbon (NCC) for each amino acid residue, identifying alpha carbons. Second, incorporate carbonyl groups and consider amino acid chirality, ensuring L amino acids are represented correctly with R groups on wedges or dashes. Finally, add hydrogen atoms to nitrogen and draw the specific R groups for each amino acid, such as alanine (methyl), valine (branched), and leucine (extended). Understanding these steps is crucial for visualizing peptide structures and their functions.

How do you identify the alpha carbon in a peptide backbone?

In a peptide backbone, the alpha carbon is the central carbon atom in the repeated nitrogen-carbon-carbon (NCC) sequence for each amino acid residue. Specifically, it is the middle carbon in the NCC sequence. For example, in a peptide with three residues, you will have three sets of NCC, and the middle carbon in each set is the alpha carbon. Identifying the alpha carbon is crucial as it is the point where the R group (side chain) is attached.

What is the significance of amino acid chirality in drawing peptides?

Amino acid chirality is significant because life predominantly uses L amino acids. When drawing peptides, it is essential to represent L amino acids correctly. This is done by ensuring the R group is on a wedge if it is going up or on a dash if it is going down. Correctly representing chirality ensures the peptide's structure is accurate, which is crucial for understanding its function and interactions.

How do you add R groups to a peptide structure?

To add R groups to a peptide structure, first identify the alpha carbons in the peptide backbone. Each alpha carbon will have an R group attached. For example, alanine has a methyl group (CH₃), valine has a branched structure (similar to alanine but with an additional methyl group forming a V shape), and leucine has an extended structure (similar to valine but with an extra CH₂ group). Draw these R groups at the appropriate alpha carbons to complete the peptide structure.

Why is it important to add hydrogen atoms to nitrogen in peptide structures?

Adding hydrogen atoms to nitrogen in peptide structures is important because these hydrogens cannot be assumed and must be explicitly drawn. This ensures the peptide structure is complete and accurate. Hydrogens on carbon atoms can be assumed and do not need to be drawn. Properly adding hydrogen atoms to nitrogen helps in visualizing the peptide's structure and understanding its chemical properties and interactions.