Peptide Group

So now that we know about the peptide bond and primary protein structure, before we get to secondary protein structure, we're going to talk about the peptide group. So recall that the peptide bond is an, um, I'd covalin linkage. And the atoms that are around the peptide Bond exhibit special characteristics and these special characteristics that they display are critical to the overall shape of a protein. And so these atoms that are around the peptide bond are part of the peptide group. And so again, the peptide bond is a specific Covalin bond. But the peptide group is referring to specific atoms that air around the peptide bond. And so the specific atoms of the peptide group are the two peptide bond atoms, or the two atoms that air directly involved in the peptide bond, as well as therefore, neighbors or the four atoms that these two, um, atoms are bonded to. And so there is a total of six atoms that are a part of the peptide group, and those six Adams include the Carbonnel Group, Adams, the Amino group Adams and the two adjacent Alfa Carbons. And so we'll be able to see that in our example down below. So in this example, what we're gonna do is consider the peptide group. We're going to circle all of the Alfa carbons and draw the residents arrows for the bonds of the peptide group. And so what you'll see is that what we have is a dye peptide. So it has to amino acid residues. And you could see that because we've got these two are groups which are in blue. So we've got this our group here, which is just a hydrogen, so it must be a glistening residue. And then over here we have a methyl group, so it's gotta be an Allen in residue. And these two residues are joined by the peptide bond here, which is in red and so we can see our peptide bond is in red. Now, notice that the atoms that are in pink here are part of the peptide group. And again, the atoms of the peptide group include the Carbonnel Group, which is these two atoms right here. It includes the atoms of the amino group which are these two atoms right here. And it includes the two Alfa carbons which are right here so we can go ahead and circle these Alfa carbons, which are again connected to the our groups. And so what you'll notice is that there's actually some resonance that's present between some of these bonds of the peptide group. And so this particular lone pair that's right here on the nitrogen will actually come down to the peptide bond. And then this double bond that's on the Carbonnel Group will go up to the oxygen. And so we've got our residents brackets here and our residents arrows. And over here we have our other residents structure. So notice with this resident structure, we now have a double bond that's present on the, uh, peptide bond and then on either side over here, what we have is a negative charge on our carbonnel group oxygen and a positive charge on the nitrogen. And so across this peptide bond, there's actually a die poll moment, so you can see that it is a polarized, uh, peptide bond. So essentially, what happening if we draw the dipole moment, you could see that there's electron density over here and less electron density over here because it's positive. And so that makes there are peptide bond, a uh ah, Polar peptide bond. And that's important to keep in mind. And also because it has double bond character here. It's gonna have some partial double bond character as well, and so recall that the best way to represent resonance is by drawing a hybrid, resonant structures so down below. What we have is the hybrid resident structure, which is more accurate depiction of the resonance that's occurring. And so notice that for our peptide bond here we have partial double bond character, not a full double bond, just a partial double bond character. And then the same applies for our Carbonnel group double bond and then on the Carbonnel group oxygen. There's a partial negative charge, and on the amino group, uh, nitrogen, there's a partial positive charge. And so these features here of the polarization of the peptide bond and the double bond character of the peptide bond are gonna be very important as we move along and we'll talk more about them throughout our different lessons. So I'll see you guys in our next practice problem where we'll be able to apply some of these concepts

So now that we know what the peptide group is, we can talk about the confirmations of the peptide group and so recall that the peptide bond actually displays partial double bond character because of the resonance. And really, it's this partial double bond nature of the peptide bond that's responsible for two things. The first thing that is responsible for is keeping the atoms of the peptide group in the same plane. And the way that it does that is that the double bond nature actually limits peptide bond rotation. And so recall from your previous organic chemistry courses that double bonds are not able to rotate. And so because the peptide bond has partial double bond character, its bond rotation is limited and really again. It's this limited bond rotation that keeps the atoms of the peptide group in the same plane. So the second important thing that the double bond nature is responsible for is restricting the peptide group Adams toe, one of two possible confirmations either the trans confirmation or the CIS confirmation. And so the thing is, is that the vast majority of most of the peptide groups are going to be in the Trans confirmation. And so the Onley exception to this is gonna be the peptide group on the end terminal side of a pro lean residue. And so you guys should know that the exception the Onley exception is going to be, ah, pro lean residue. And this is because pro lean, we know has a big, cyclic, bulky, our group and so really pro leans. Our group encounters about the same amount of Starik hindrance in both the Trans and the cyst confirmation, so it doesn't prefer one confirmation over the other. And so you tend to find pro leans in both confirmations. But again, pro Lien is the exception, and the vast majority of peptide groups are in the trans confirmation. So normally the CIS confirmation is going to be less favorable, and it's less favorable normally, because it encounters mawr, stared hindrance between the are groups and will be able to see that down in our example below. So in our example, what we're going to do is labeled the peptide group confirmations. And so over here on the left, noticed that are peptide. Bond is in red here, shown with a partial double bond character, and so what we know is that if we can imagine a new imaginary line going through this double bond the peptide bomb, which will see, is that the two groups that are bulky. So the two bulky groups, this group over here and this group over here are on opposite sides of the double bond. And because they're on opposite sides of the double bond, that makes this confirmation on the left a trans confirmation. So this is the trans confirmation. Now, this group on the right must be this cyst confirmation. And so what you'll notice is that if we do the same thing, here's our peptide bond here. If we imagine an imaginary line going through our peptide bond like this, notice that both of our bulky groups this one over here and this one over here Oops, wrong color. This one over here are on the same side of the double bond. And so notice that these two bulky groups here are gonna encounter a lot of Starik hindrance between each other. And so this assist confirmation is normally going to be less favorable and so thes air the two confirmations of the peptide bond. And it's important to keep these in mind. As we move forward, we'll be able to get some practice understanding and applying these concepts, so I'll see you guys in those practice videos.

So now that we've talked about the peptide group, the peptide group confirmations and the double bond nature of the peptide bond, let's zoom out a little bit and talk about the effects of all of these things on the protein. And it turns out that the result is really just limited flexibility of the peptide backbone. And so each internal amino acid residue is actually flanked with a peptide group, and we know that the atoms of the peptide group are all in the same plane. And so if we take a look at our example below notice that each of these green squares represents the peptide group and the plane of the atoms in the peptide group, and so together all of the peptide groups make the protein backbone. And collectively, the double bond nature of all of the peptide bonds in the backbone end up limiting the flexibility of the backbone, and that ends up limiting the possible, um, peptide structures. And so, if we look at our example down below, the red dots represent oxygen's the blue represent. Nitrogen and the white represent either Alfa carbons or the our groups. And again, thes green squares represent the peptide groups in the plane of the atoms of the peptide groups. And so, with these peptide groups here, each square Green Square represents a different peptide group and noticed that this peptide group that square that we have, you cannot rotate and break that square in half. So what we're saying is that this bond right here, which is the peptide bond in the middle of each square, cannot be rotated. So essentially, these squares have to stay in the same plane. You can rotate neighboring squares, but the squares themselves cannot be broken in half. And so that it has to do with the the double bond nature of the peptide bond. But even though this square can't be broken in half, the other bonds that are around it can rotate. So this bond right here can rotate. And, uh, this bond over here can rotate. It's just the middle one, this green one, the peptide bond that cannot rotate. So again, you can think of the peptide bond being limited in its flexibility because the again the cubes cannot be broken in half, but the cubes that air neighboring can rotate, and so it's very interesting and together all of these peptide groups again, they limit the flexibility of the backbone and the peptide structure, so that's important to keep in mind. And so this concludes our lesson here, and I'll see you guys in our practice video where we'll be able to apply some of these concepts.