Peptides - Online Tutor, Practice Problems & Exam Prep

Peptides Concept 1

Now here we're going to say that peptides are formed when 2 or more amino acids bond with each other through a peptide bond. Now here we're going to say the peptide bond, also known as an amide bond, is when we have the carboxyl group of 1 amino acid covalently bonds with the amino group of another amino acid. Now pay attention here. We have the carboxyl group here in its anionic form, so its negatively charged forme, and we have the amino group in its positive charge form. Now if we come down here, we're talking about the formation of a peptide bond. We've kind of seen this before when we talked about the formation of an amide bond. Remember, that happens through a condensation reaction. We have the loss of water. So here we have alanine, which is our amino acid, and we have threonine here. We're going to say we're going to have the loss of water. So if we look at this, the loss of water, we would lose this oxygen here, and we'd lose 2 hydrogens here from the NH₃ group. Right. So we have the loss of water here. Here we show this arrow. This arrow that's pointing up shows that we have the loss of water, so it's leaving the two structures. What's left behind combine together give us our peptide bond. So we lost this oxygen, we lost 2 hydrogens. Meaning that nitrogen still has 1 H on it. So that's why it's still here. We didn't touch anything in terms of this carbonyl group, so it's still intact. The bond they form is a result of them losing water. So now we have a dipeptide and we show this by giving the 3 letter code for each amino acid connected to each other by a hyphen. This hyphen here can represent this peptide bond between the two amino acids. Now here we're going to say that the number of amino acids and peptides is indicated by prefixes. So we know dí, tri, tetra. Here we're going to say that a polypeptide is a peptide consisting of a larger number of amino acid residues. And remember, a residue is just an individual amino acid contained within a peptide. Here, we call this a dipeptide, dí because it's 2 amino acids connected by 1 peptide bond. If we have 3 amino acids, then it would be a tripeptide. If we have 4 amino acids, it would be a tetra peptide. If we have beyond that, then we can start talking about it being a more complicated chain of amino acids connected by peptide bonds. Right. But just remember, we've seen something like this before when we talked about the formation of amide in earlier chapters. Now we're relating it to the connection of 2 different amino acids to one another. Right. So just remember, a peptide is 2 aminos connected by a peptide bond.

Peptides Example 1

Circle all peptide bonds and amino residues in the following tetrapeptide. Alright. So remember, a peptide bond is basically an amide bond. So we're going to look for where we have a carbonyl single bonded to a nitrogen. If we take a look, here goes one of them. This is an amide bond. Here goes a carbonyl carbon connected to a nitrogen. There goes another one. And then there goes our last one here. So we have 3 peptide bonds. They say that it's a tetrapeptide, so that means we have 4 peptides connected to one another. So remember, this would represent one peptide. Remember, the amide bond is what connects 2 different peptides or 2 different amino acids to one another. So this is 1. Here goes a second one. We're going to cut the amide bond. That's a second. Then here, this is another one. There goes another one. We should be circling it, but just for us to see me tracing where the peptide is. And then finally, we have this last one here. So this represents our 4 peptides involved.

Drawing & Naming Peptides Concept 2

Now, when it comes to drawing and naming peptides, remember that every peptide has directionality. What we mean by that is that we look at it from the N terminus to the C terminus end. Now, when we say N terminus, this is just the residue with the free amino group. And when we say C terminus, this is the residue with the free carboxyl group. When drawing or naming, always arrange from left to right and have it in N terminus to C terminus when looking at a peptide. If we take a look here, we have our N terminus on the left and that's because the free amino group is on the left side here on that end, and then they're connected to another amino acid through this peptide bond here. And this is the C terminus because the carboxyl group is on this end. Right. So we're looking at this structure, this peptide, two amino acids connected by a peptide bond and we're looking on the left side, we have our N terminus end and on the right side, we have our C terminus end. Keep this directionality in mind whenever you're naming or writing a peptide.

Peptides Example 2

Draw a dipeptide structure consisting of given amino acids in the following order. Next, we have to name the dipeptide using the three-letter codes separated by hyphens. Alright. So here, remember, we have to write this in terms of N terminus to C terminus. This means that the amino acid on the left side will have its carboxyl group interacting with the amino group of the amino acid on the right. This is a condensation reaction where we're going to have the loss of water. So, we're going to lose the oxygen from the carboxyl group and two hydrogens from the amino group. This is where water is being lost. After that, everything left behind will come together to form our dipeptide structure.

We have our benzene ring with an OH group connected to this CH₂, which is connected to this carbon with the NH₃⁺. Next, we have our carboxyl group. Here, I'm going to draw the peptide bond in red. It's connected now to this nitrogen, which still has one of its hydrogens. It's still connected to all this stuff here. So CH₂, and then we have SH here, and then we have the carboxyl group here. So this will be our dipeptide structure.

Now what we need to do is we need to basically give the three-letter code. So if we take a look at this, this amino acid on the right is easy to spot because it has an SH group which is unique to cysteine. We know cysteine's three-letter code is Cys, based on its first three letters. This one here has an OH group, it is a polar group, so remember this one is tyrosine. Its three-letter code is Tyr, again based on its first three letters. So that means that this dipeptide that we have here would be Tyr-Cys. So this would be the dipeptide name using our three-letter code. And this would be the dipeptide structure.

Draw a tripeptide structure consisting of following amino acids in following order. Name tripeptide using 3 letter codes.

• A.
• B.
• C.
• D.

Here’s what students ask on this topic:

What is a peptide bond and how is it formed?

A peptide bond, also known as an amide bond, is a covalent bond that forms between the carboxyl group of one amino acid and the amino group of another amino acid. This bond is created through a condensation reaction, which involves the loss of a water molecule. Specifically, the carboxyl group (COOH) of one amino acid loses an OH group, and the amino group (NH2) of another amino acid loses a hydrogen atom (H), resulting in the formation of water (H2O) and the peptide bond. This process links the amino acids together, forming a dipeptide, tripeptide, or longer polypeptide chain.

What is the significance of the N terminus and C terminus in peptides?

The N terminus and C terminus are crucial for understanding the directionality of peptides. The N terminus is the end of the peptide with a free amino group (NH2), while the C terminus is the end with a free carboxyl group (COOH). When drawing or naming peptides, it is essential to arrange them from the N terminus on the left to the C terminus on the right. This directionality is important for the proper identification and function of peptides, as it determines the sequence and orientation of the amino acids within the peptide chain.

How are peptides classified based on the number of amino acids?

Peptides are classified based on the number of amino acids they contain. A dipeptide consists of two amino acids connected by one peptide bond. A tripeptide contains three amino acids, and a tetrapeptide has four amino acids. When the peptide chain contains more than four amino acids, it is referred to as a polypeptide. These classifications help in understanding the complexity and length of the peptide chains, which are essential for studying protein structure and function.

What is the role of condensation reactions in peptide bond formation?

Condensation reactions play a crucial role in peptide bond formation. During a condensation reaction, two amino acids are joined together by a peptide bond, and a molecule of water (H2O) is released. This reaction involves the carboxyl group (COOH) of one amino acid losing an OH group and the amino group (NH2) of another amino acid losing a hydrogen atom (H). The resulting bond between the carbon of the carboxyl group and the nitrogen of the amino group forms the peptide bond, linking the amino acids together in a peptide chain.

Why is understanding peptide structure important for studying proteins?

Understanding peptide structure is essential for studying proteins because peptides are the building blocks of proteins. The sequence and arrangement of amino acids in a peptide determine the protein's primary structure, which in turn influences its secondary, tertiary, and quaternary structures. These structures are critical for the protein's function, stability, and interactions with other molecules. By understanding how peptides form and their directional properties, researchers can better comprehend how proteins are synthesized, folded, and how they perform their biological functions.