A) Consider both the peptide Gly—Pro—Ser—Glu—Thr (in a li...

Question

A) Consider both the peptide Gly—Pro—Ser—Glu—Thr (in a linear chain) and a cyclic peptide of the same exact sequence Gly—Pro—Ser—Glu—Thr (with a peptide bond linking the Thr & Gly). Are these peptides chemically the same? Explain.

B) Can you expect to separate the peptides above by Native-PAGE? Why or why not?

B) Can you expect to separate the peptides above by Native-PAGE? Why or why not?

Accepted Answer

Alright. So here's a 2 part practice problem broken up into part a up above and part b down below. And part a wants us to consider both the peptide, glycine, proline, serine, glutamate, and threonine in a linear chain, as well as a cyclic peptide of the same exact sequence, glycine, proline, serine, glutamate, and threonine, except with an additional peptide bond linking the threonine and glycine amino acid residues, which are the last and the first residue, making it a cyclic peptide. And then it asks, are these peptides chemically the same? And explain. And so just to be able to visualize these proteins, on the left, we have the linear peptide. And it turns out that most proteins in nature are actually linear in nature, which is why we've only really talked about linear peptides. But the, the cyclic peptide over here, even though they are very, very rare, they do exist and some bacteria can actually create these cyclic peptides here. And so, cyclic peptides here. And so, here, it's asking us if these peptides are chemically the same. Now we know that with linear peptides on the n terminal end, there's a potentially ionizable amino group, which is being shown over here. And on the opposite end, the c terminal end, there's a potentially ionizable carboxylate group. Now in the cyclic peptide over here, notice it has this additional peptide bond between the last and the first amino acid residue. And so, this is an additional peptide bond that's lacking in the linear peptide over here. And so essentially what happens to create this peptide bond is the carboxylate group of threonine is reacting with the amino group of glycine. And so we know that when peptide bonds form, they form via dehydration synthesis reactions. And so this arrow here could represent the dehydration synthesis reaction. And we know that dehydration synthesis reactions produce a side product of H two O, a water molecule, as they produce the new peptide bond. And so literally, the cyclic peptide over here here is missing a water molecule that the linear peptide actually has stored in its carboxyl, group and its amino group. And so, essentially, when it's asking us if these peptides are chemically the same, we can, clearly see that the answer is no. They are not chemically the same because they literally don't have the same atoms. The cyclic peptide is missing an H two O molecule. So we could say, no, because the cyclic peptide lacks an H two O molecule, and it also lacks, free or ionizable amino and carboxyl groups. So that means it has less ionizable groups available. So that's something important to keep in mind. So this is the answer for part a as to are they chemically the same and explain. So now moving on to part b down below, it's asking us, can you expect to separate these peptides above by native PAGE or native polyacrylamide gel electrophoresis? Why or why not? Now from our previous lessons, we know that native PAGE separates proteins based on their native properties. So the proteins maintain their native shapes, their native masses, and their native charges. And so, clearly looking at the cyclic peptide over here and the linear peptide over here, we can see that they definitely differ in their shape. So that's already one factor that will allow us to separate these 2 peptides via native page. So can we expect to separate the, peptides via native page? The answer their shape, but they don't only differ in their shape. Notice again that the cyclic peptide over here is lacking a water molecule. It lacks an H two o. And so it literally has less atoms than the linear peptide, peptide. And less atoms, of course, is gonna mean less mass. So they also differ in their mass. Now, what you'll also notice is that the linear peptide on the left over here has more ionizable groups. It has this amino group and it has this carboxylate group. So depending on the pH, then they could also differ in their charges. And so what we can do is, we can, add and charge. So they differ in their shape, their mass, and their charge, but only depending on pH. So we can add depending on pH. And so, this here concludes this practice problem for part b. And so I'll see you guys in our next video.

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