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.
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Drawing a Peptide - Online Tutor, Practice Problems & Exam Prep
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.
Drawing a Peptide
Video transcript
Drawing a Peptide
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 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
Video transcript
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.
Problem Transcript
Strive for greatness and draw the chemical structure of the following peptide: S-T-R-I-V-E.
Problem Transcript
Aim high and draw the following peptide: A-I-M-H-I-G-H.
Problem Transcript
Be a boss & draw the chemical structure of the following peptide: P-C-Y-N-F-Q-K.
Problem Transcript
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.