Peptide Group: Videos & Practice Problems

The peptide bond, an amide covalent linkage, exhibits partial double bond character, limiting rotation and maintaining the peptide group's planar conformation. This results in two possible configurations: trans and cis, with trans being predominant except for proline residues. The rigidity of the peptide backbone restricts protein flexibility, influencing overall protein structure. Understanding these characteristics is crucial for grasping protein dynamics and interactions, as they play a significant role in the formation of secondary and tertiary structures, ultimately affecting protein function.

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. Recall that the peptide bond is an amide covalent linkage. The atoms that are around the peptide bond exhibit special characteristics, and these characteristics are critical to the overall shape of a protein. These atoms around the peptide bond are part of the peptide group. The peptide bond is a specific covalent bond, but the peptide group refers to specific atoms surrounding the peptide bond. These specific atoms of the peptide group are the 2 peptide bond atoms, or the 2 atoms that are directly involved in the peptide bond, as well as their 4 neighbors or the 4 atoms to which these 2 atoms are bonded. There's a total of 6 atoms in the peptide group. These 6 atoms include the carbonyl group atoms, the amino group atoms, and the 2 adjacent alpha carbons. We'll be able to see this in our example below.

In this example, we're going to consider the peptide group. We will circle all of the alpha carbons and draw the resonance arrows for the bonds of the peptide group. What we have is a dipeptide, having 2 amino acid residues. You can identify this by the 2 R groups, which are in blue. This R group here is just a hydrogen, indicating a glycine residue. The other group, a methyl group, indicates an alanine residue. These two residues are joined by the peptide bond, which is in red. Notice that the atoms in pink are part of the peptide group. The atoms of the peptide group include the carbonyl group, which are these two atoms here, the atoms of the amino group, these 2 atoms here, and the 2 alpha carbons connected to the R groups. There's resonance present between some of these bonds of the peptide group. A lone pair on the nitrogen comes down to the peptide bond, and the double bond on the carbonyl group shifts up to the oxygen. We've included our resonance brackets and arrows here, showing another resonance structure. In this resonance structure, there is a double bond on the peptide bond, and on either side, there is a negative charge on the carbonyl group oxygen and a positive charge on the nitrogen. Across this peptide bond, there's actually a dipole moment, showing it as a polarized peptide bond. Drawing the dipole moment, you can see an electron density shift from the nitrogen to the oxygen, emphasizing the polar nature of the peptide bond. Additionally, it has partial double bond character. The best way to represent resonance is by drawing a hybrid resonance structure. Below, we present the hybrid resonance structure, a more accurate depiction of the resonance occurring. Here, our peptide bond has partial double bond character. Similarly, the carbonyl group double bond and the partial negative charge on the carbonyl oxygen, and a partial positive charge on the amino group nitrogen are highlighted. These features, the polarization of the peptide bond and the double bond character, will be important as we move along. We'll talk more about them throughout our lessons. See you guys in our next practice problem where we will apply some of these concepts.

Which atoms are not part of the peptide group?

• A. Carbonyl group atoms
• B. First R-group atom
• C. Amide group atoms
• D. α-carbons

Answer: (B)

Peptide Group

So now that we know what the peptide group is, we can talk about the conformations of the peptide group. Recall that the peptide bond displays partial double bond character because of resonance. This partial double bond nature of the peptide bond is responsible for two things. The first thing it's responsible for is keeping the atoms of the peptide group in the same plane. The double bond nature limits peptide bond rotation. Double bonds are not able to rotate. Because the peptide bond has partial double bond character, its bond rotation is limited. This limited bond rotation keeps the atoms of the peptide group in the same plane. The second important thing the double bond nature is responsible for is restricting the peptide group atoms to one of two possible conformations: either the trans conformation or the cis conformation. The vast majority of peptide groups are in the trans conformation. The only exception is the peptide group on the N-terminal side of a proline residue. Proline has a big cyclic bulky R group, which encounters the same amount of steric hindrance in both the trans and cis conformations. So, it does not prefer one conformation over the other. You tend to find prolines in both conformations. But again, proline is the exception, and the vast majority of peptide groups are in the trans conformation. Normally, the cis conformation is less favorable because it encounters more steric hindrance between the R groups. We will be able to see that down in our example below.

In our example, we are going to label the peptide group conformations. Over here on the left, notice that our peptide bond is shown in red with partial double bond character. An imaginary line going through this double bond indicates that the peptide bulky groups, this group over here and this group over here, are on opposite sides of the double bond. Because they are on opposite sides of the double bond, this makes this conformation a trans conformation. If we do the same thing here with our peptide bond, notice that both bulky groups are on the same side of the double bond. These two bulky groups encounter a lot of steric hindrance between each other, which makes the cis conformation normally less favorable. These are the two conformations of the peptide bond, and it is important to keep these in mind as we move forward. We will be able to get some practice understanding and applying these concepts. I'll see you guys in those practice videos.

Why are atoms of the peptide group planar?

• A. Bulky side chains prevent the trans conformation & free rotation around a peptide bond.
• B. Peptide bonds are double bonds that prevent bond rotation.
• C. Hydrogen bonding between the N-H and C=O groups stabilizes cis conformation & limits bond rotation.
• D. Peptide bonds contain partial double bond character, preventing free bond rotation.

Answer: (D)

For each figure, highlight each bond with limited rotation & determine the conformation of each peptide group.
A. 
B. 
C. 

So this practice problem says, for each of the figures below, highlight each bond with limited rotation and determine the conformation of each of the R1, R2, and R3. And so, because we have 3 different R groups with R1, R2, and R3, that means that we have 3 different residues in this peptide. And when we have 3 residues, that tells us that we have 2 peptide bonds. We know we only have 2 peptide bonds because the number of peptide bonds is always going to be one minus the number of residues. And so, if we have 3 residues and subtract 1, that tells us there are 2 peptide bonds. And we know that peptide bonds have limited rotation, so let's go and find these peptide bonds. Recall, a quick way to be able to find the peptide bonds is to look for the carbonyl groups because they kind of stand out. And so the carbonyl groups are C double bond O, and so here we have a carbonyl group. And we know that peptide bonds are amide linkages, and so that means that the carbonyl group has to link to a nitrogen atom. So here's our nitrogen atom. And so, what you can see is that this link between them right here must be a peptide bond, and indeed it is. And so here's our first peptide bond. So now, we check our next carbonyl group and here it is over here and the carbonyl group again has to be linked to another nitrogen. And so that means that this bond right here has to be a peptide bond. So now, let's check our last carbonyl group which is right here, and notice that it is not linked to a nitrogen, so that means that this is not a peptide bond. And so these are our 2 peptide bonds right here. And so now that we found our peptide bonds, we know that they're going to have limited rotation and let's determine the conformation of the peptide group. Remember that the way we determine the conformation is we imagine an imaginary line going through it and then we look at the 2 bulky groups. And so we've got a bulky group on this side going this way and on this side, our bulky group is going this way. So this whole thing would be the bulky group. And so notice that these bulky groups are on opposite sides of the double bond going away from each other. And this is a type of trans conformation. So this is a trans conformation. So what we can do is we can label this conformation as trans. So now let's check this double bond over here and we can do the same thing. We can put an imaginary line through this and look at its bulky groups. Notice that it has one bulky group going this way and then it has another bulky group, which is this one going this way. And so these 2 bulky groups again are on opposite sides of the double bond, which means that they are also in the trans conformation. So we can label this double bond this peptide bond as well as being in the trans conformation. So both of these are in the trans. And then also recall that any bond that has a double bond is going to have limited rotation. So really, the carbonyl group double bonds are also going to have limited rotation. And so, all of the other bonds that are not highlighted here are going to be able to have more rotation. They're not limited in their rotation, and so they have free rotation. So now, let's check B over here. And what we have with B, what you'll notice is that we have a proline amino acid residue. So you can see here that we've got this, NCC, so it goes NCC. And, we know that the middle C here is going to be an alpha carbon. And notice that this alpha carbon, the R group, goes out, goes out, back, and connects back to the nitrogen. So this is a proline residue here. And so with this proline residue, we can see that the way that we identify the peptide bond is to look for the carbonyl group. So here's a carbonyl group and we know that the carbonyl group is going to be bonded to a nitrogen, so that means that this bond in between these two must be a peptide bond, and indeed it is. And so, what we can see here is that this peptide bond right here, when we draw the imaginary line through it like this, and we know that the R here represents the rest of the molecule, so this R here is a big bulky group. Opposite this is the big bulky group. And so these 2 big bulky groups are on opposite sides of the peptide bond. So this means that this peptide bond is going to be in a trans conformation. So what we can do is say that this peptide bond here is in a trans conformation. So now, if we check this one over here, notice that, again, we have another proline residue, and this is the alpha carbon here. And this time, again, what we see is, here's our carbonyl group and here's our nitrogen. So this time, what we see is this is the peptide bond. And with this peptide bond, what we'll see is that if we draw our imaginary line through it like this, what you'll see is that our big bulky groups, so this R group here, which is the rest of the molecule, and this group over here, this group over here is also the other bulky group. They are both on the same side of the peptide bond, which means that this is in the cis conformation. And so recall that proline residues are the ones that can be in the cis conformation. They do not have a preference for the trans or the cis conformation. And this is the exception that can take on either conformation. So what we've done here is we've highlighted all of the bonds that have limited rotation except for these bonds right here, which we know all double bonds are going to have limited rotation. And so now, we've completed this practice problem. We've highlighted all the bonds with limited rotation and we've determined the conformation for each of the peptide groups that are shown. So that concludes this practice problem and I'll see you guys in our next video.

Peptide Group

So now that we've talked about the peptide group, the peptide group conformations, 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 the double bond nature of all of the peptide bonds in the backbone ends up limiting the flexibility of the backbone and that ends up limiting the possible peptide structures. And so if we look at our example down below, the red dots represent oxygens, the blue represent nitrogens, and the white represent either alpha carbons or the R groups. And again, these 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 notice 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 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, 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 cubes cannot be broken in half, but the cubes that are neighboring can rotate. And so, it's very interesting. 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.

In the diagram below, the square plane drawn behind the protein molecule indicates the:

• A. Plane of the peptide group due to absence of rotation & partial double-bond nature of the Cα-N bond.
• B. Region of steric hindrance determined by the large C = O group.
• C. Absence of rotation around the C-N bond because of its partial double-bond character.
• D. Region of the peptide bond that contributes to a Ramachandran plot.

Answer: (C)

Here’s what students ask on this topic:

What is a peptide group in biochemistry?

A peptide group in biochemistry refers to the specific set of atoms surrounding a peptide bond. The peptide bond itself is an amide covalent linkage between the carboxyl group of one amino acid and the amino group of another. The peptide group includes six atoms: the carbonyl carbon and oxygen, the amide nitrogen and hydrogen, and the two adjacent alpha carbons. These atoms exhibit special characteristics, such as partial double bond character due to resonance, which restricts rotation and maintains the planar conformation of the peptide group. This rigidity is crucial for the overall shape and function of proteins.

Why does the peptide bond exhibit partial double bond character?

The peptide bond exhibits partial double bond character due to resonance between the lone pair of electrons on the nitrogen and the double bond of the carbonyl group. This resonance creates a situation where the peptide bond has characteristics of both a single and a double bond. The partial double bond character restricts rotation around the peptide bond, keeping the atoms of the peptide group in the same plane. This rigidity is essential for maintaining the structural integrity of proteins and influences their secondary and tertiary structures.

What are the possible conformations of the peptide group?

The peptide group can adopt two possible conformations: trans and cis. In the trans conformation, the bulky groups attached to the alpha carbons are on opposite sides of the peptide bond, minimizing steric hindrance. This is the predominant conformation for most peptide groups. In the cis conformation, the bulky groups are on the same side of the peptide bond, leading to increased steric hindrance and making this conformation less favorable. The exception is the peptide group involving proline residues, which can adopt both cis and trans conformations due to similar steric hindrance in both forms.

How does the partial double bond character of the peptide bond affect protein structure?

The partial double bond character of the peptide bond significantly affects protein structure by limiting the rotation around the peptide bond. This restriction keeps the atoms of the peptide group in a planar conformation, reducing the flexibility of the protein backbone. As a result, the overall flexibility of the protein is limited, which influences the formation of secondary structures like alpha helices and beta sheets. This rigidity is crucial for the proper folding and function of proteins, as it helps maintain the specific three-dimensional shape necessary for their biological activity.

Why is the trans conformation of the peptide group more common than the cis conformation?

The trans conformation of the peptide group is more common than the cis conformation because it minimizes steric hindrance between the bulky groups attached to the alpha carbons. In the trans conformation, these groups are on opposite sides of the peptide bond, reducing the likelihood of clashes and allowing for a more stable structure. In contrast, the cis conformation places the bulky groups on the same side, leading to increased steric hindrance and making this conformation less favorable. The exception is the peptide group involving proline residues, which can adopt both cis and trans conformations due to similar steric hindrance in both forms.