Drawing a Peptide

in this video, we're gonna talk about how to draw peptide. So a lot of times your professors expect you guys to know how to draw peptide. And really, the structure of a peptide could be drawn simply from its primary protein structure. And really, there are three basic steps to draw any protein, and we'll talk about Step number one in this video and our next videos. We'll talk about steps. Two steps. Three. So for step number one, the very first step and drawing a peptide is just to draw the peptide backbone and also toe identify the Alfa carbons and recall that the Alfa Carbons is just the central carbon atom where the our 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 two residues, then there's gonna be two sets of N. C. C. S. If there are three residues, then that means there's gonna be three sets of N. C. C. s. And so it turns out that this middle c here is always going to be the Alfa Carbon. And this last see over here is going to be the Carbonnel group carbon. And remember, the Carbonnel Group is just a C double bond. Oh, and so also recall from our previous videos that Onley, the very first and the last residues and a chain actually have free or ionized able ionized able amino groups or car boxing 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 car boxing group. But the very last amino acid residue has a free car box a group, but it lacks a free amino group. And then all the internal residues lack both free amino and free car box of groups in their backbone. And so let's take a look at our example. So we can, uh, see visualized the various first step in drawing a peptide, which again is to draw the backbone and identify Alfa carbons. And so what you'll see is that we're gonna be drawing ah peptide, which has three amino acid residues. So we're only gonna draw an amino acid with three residues. So right that here And so because we have three residues, what that means is that we're gonna have three sets of the N C c. So let's go ahead and let's start drawing in R N C c. So we're gonna have a nitrogen here and N C c. That's for one residue. Now, our next residue is gonna be N C c. Perfect. And then we have our third residue. So it's gonna be N c. See? All right, Perfect. So now we've got our three NCC sets in there for each of our three residues. And so we know that the very first amino group over here is gonna be free and ionized well, so we can go ahead and draw in our NH three plus because we know that it's gonna be, uh, ionized at physiological pH and then a two very end over here. What we could do is drawing our car boxful group, which is also gonna be free, and so we can draw it as a car. Boxley and I am with a negative charge. And so the next part to do now that we've drawn in the backbone is to identify the Alfa Carbon. So recall that the Alfa 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 Alfa 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 Alfa Carbon. So now we've identified the Alfa Carbons and we've drawn in the backbone and the last step here, What we're gonna do is just realized that over here, what we have is the end terminal end, and over here, what we have is the C terminal end, and that's it. So we have finished that number one, and so I'll see you guys in our next video where we'll talk about the second step to 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, all we need to do is fill in the Carbonnel groups. So draw in the Carbonnel groups and consider amino acid Cairo ality. And by considering amino acid chi rally, 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 that when the our group is going down, it's gotta be on a dash. And then when the our group is going up, when the our 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 two of drawing a Peptide, which again is gonna be to draw the Carbonnel groups and consider amino acid Kyra ality. And so, as you can see, we've already got our steps filled in from step number one 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 Alfa Carbon. And so this see over here is gonna be the carbonnel group carbon. And so we know that we're gonna put the Carbonnel group on this carbon over here, So let's go ahead and drawing the car bottle group Perfect. So now we got to do the same thing for the next residue because remember, we have a total three residues. And so here's our next n C C set. The middle one is gonna be the Alfa Carbon here. And so that means that this other carbon over here must be the Carbonnel group carbon so we can draw it and we can draw facing down this time since this carbon is kind of going down and then we have our last N c c. And guess what? The Carbonnel group is already there from our car boxes group being present so we don't need to draw that one. So now we've drawn all the carbonnel groups. The next step is to consider the consider Chire ality And so for the choir ality remember, if the our group is going down, it has to be dashed and remember that our groups come off of the Alfa Carbon. So let's go to each of our Alfa Carbon. So we know this is an Alfa Carbon here, and it's already kind of going down. Notice that it z like moving downwards already. And so because it's already down, we just need to draw our our group down and dash, so it's got to be on a dash. Let's just draw a dash here. Perfect. There's our Kyra ality. So this is gonna be an l amino acid already. Now let's consider the next residue. And here's our next Alfa carbon over here. So that's where we know our our group is gonna be. So this one's kind of going up notice that it's going up in upwards fashion, so that means our our group is gonna be going up. And when the our group is up, it's gotta 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. All right, that's it. And then on our last Alfa carbon over here. It's going down again. Notice that it's kind of coming down. And because of that reason are our group is gonna be down and dashed. So that means that we're gonna put a dash over here on this Alfa Carbon where our group is gonna go and that's it. That's all we need to do. That's step number two Pretty easy, right? So now that we've finished Step number two, I'll see you guys in our next video or we'll do our last and final step Step number three. See you guys there.

So now that we've covered both the 1st and 2nd steps for drawing a peptide in this video, we're going to focus on the third and final step for drawing a peptide. And in this third step, all we need to do is fill in the remaining hydrogen on the nitrogen atoms. And so all we need to do is add nitrogen here and at a hydrogen here. And so essentially, the hydrogen on the nitrogen atoms can't be assumed, so we have to draw them in. But the hydrogen is that air 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 hydrogen on the nitrogen atoms, all we need to dio is draw in the are groups for each of the amino acid residues. And so, in the example below, it says to draw on the are groups for the peptide allen in veiling and loosen. And so over here near our N terminal. And we have our first amino acid residue in our first our group. And that will be the our group of Allan E. And so we know that because a is the first letter of the alphabet, and that's easy to remember. Alan into our group is also easy to remember because it's literally just a metal group, a CH three group. And so that's it for outing. And next. What we have is veiling and, uh, that would be V and recall that bailing is literally just like Alan ing accept it. Um, it's gonna have a V shape to it. So essentially all we need to do is drawing a winning so C h with a V shape to it. So to metal groups branching off and that is it for veiling structure now, Last but not least, what we have is l and L is for losing. And losing is really just a loose extension of veiling. So it's exactly the same as veiling, except it's gonna have an extra CH two so it will have the CH two, and then it will have the veiling at the end. So it's an extended loose version of veiling. And so that is it for the peptide Alinea unveiling and losing. And that completes this, um, process on drawing a peptide and we'll be able to get practice utilizing these three steps were drawing a peptide and our next couple of practice video, so I'll see you guys there.