Answer the following questions (A, B & C) relating to the ...

Question

Answer the following questions (A, B & C) relating to the 4 tripeptides.

i) Tyr-Lys-Met ii) Asp-Trp-Tyr iii) Asp-His-Glu iv) Leu-Val-Phe

A. Which tripeptide is most negatively charged at pH = 7? _________

B. Which tripeptide contains the largest number of nonpolar R groups? __________

C. Which tripeptide contains sulfur? ____________

Accepted Answer

So this practice problem wants us to answer the following questions a, b, and c, which are below, which relate to the 4 tripeptides, which are labeled with Roman numerals 1, 2, 3, and 4. And so question a asks, which tripeptide is most negatively charged at pH 7? And so we're gonna need to, consider all of the ionizable groups and recall that there are 7 amino acids with an ionizable r group, and the mnemonic to help us memorize those 7 amino acids is just yucky crazy dragons eat knights riding horses. So if it's not one of these 7 amino acids, then we're not gonna be interested in its r group because the r group is not gonna contribute to the net charge of the peptide. And so, let's take a look by starting with the amino groups. So the amino groups, on all of these far ends over here are going to have a potential ionization. So let's let's take a look and consider that for all of these peptides here. We'll do it all at once in one go. And so let's go up and take a look at our pKa chart to see what the, pKa is of the amino group. So notice that the pKa of the amino group is 8. And so, a pKa of 8 is actually greater than the pKa, I'm sorry, a pKa of 8 is greater than the pH of 7. And so that means that the conjugate acid form is gonna predominate and the amino group is gonna contribute a positive charge because the conjugate acid form has a positive charge. So we can put a positive charge for the amino group for all of the peptides. So next, let's check the our, the carboxyl group. And the carboxyl group for all of the peptides, we can also do all at once because we know that this end is gonna have a carboxyl group that could be potentially ionized. So if we go up and check the, p k a of the carboxyl group, the c terminus, notice that it's 3.5. And a p k a of 3.5 is less than the pH of 7. When the p k a is less than the pH, that means the conjugate base is gonna predominate and the conjugate base is gonna have a negative charge. So this is gonna have a negative charge for all of these, carboxyl groups. Alright. So now, what we can do is focus on the I r groups that are ionized. And so, tyrosine over here is going to have an r group that could potentially ionized. And methionine does not fall into this group, so it doesn't have an ionizable R group. So there's only 2 charges we need to consider here. Let's start with tyrosine. And so when we look at tyrosine, you can see that its, p k a is 10.5 and a p k a of 10.5 is greater than the pH of 7, which means it's gonna be protonated, it's gonna be in its conjugate acid form. And the conjugate acid form of tyrosine is just gonna have a neutral net charge of 0. It's gonna be 0. And so, let's check lysine, and you can see lysine's, pKa is also 10.5. And so that means that the conjugate acid form is gonna predominate, but the conjugate acid form of lysine has a positive charge. So it's gonna be a positive charge. So that means that the total net charge on this peptide over here is going to be a sum of all of these charges. So these, these two charges here cancel each other out, this one and this one. And so the only thing that's left is this positive charge. So this one's gonna have a plus one charge, which we'll do in a different color. Let's do it in green, just to say this one's got a plus one charge. So now we can check aspartic acid over here or the next peptide number 2, and we know aspartic acid could potentially have a negative charge. Tryptophan is non ionizable it's not one of these 7, so we don't care about its R group. Tyrosine, again, could potentially contribute a negative charge. And so we already did tyrosine, we know it's gonna contribute a net charge of 0 we just checked it. But let's go up and check aspartic acid. And aspartic acid is right here, and you can see it has a pKa of 3.9. And so a pKa of 3 point 9 is less than the pH of 7. And when the pKa is less than the pH, that means that the conjugate base is gonna predominate and the conjugate base of aspartic acid is gonna have a negative charge. So we can put a negative charge in here. So the total net charge on this peptide here is going to be, you can see that this, charge and this charge cancel each other out. So the only charge that's available is this one, and that's going to make it a negative one charge. So this peptide has negative one charge. So now we've got these 2 peptides. Let's check this one over here. And so the good thing is we already did aspartic acid over here and so we know it's gonna have a negative charge. Histidine could potentially have a positive charge, so we'll put it in blank here. And glutamic acid could potentially have a negative charge. And glutamic acid could potentially have a negative charge. And so let's go up and check histidine first. So as you can see, histidine up here has a pKa of 6 and the pKa of 6 is less than the pH of 7. And so that means that the conjugate base form is gonna predominate and the conjugate base of histidine has a neutral net charge of just 0. And so glutamic acid, we can check that, and glutamic acid has a pKa of 4.1. And so a pka of 4.1 is less than the pH of 7. And when the pka is less than the pH, that means the conjugate base predominates and the conjugate base of glutamic acid is gonna have a negative charge on it. And so, when we total the net charges on this guy, what we'll see is that these two charges cancel each other out. So the only 2 charges that are available are this one and this one. So this one's going to have a negative two charge. So it's gonna be negative 2. We'll put that in green. And then this last one over here, notice that leucine, valine and phenylalanine do not have ionizable R groups. They're not part of these 7. And so that means that their total net charge is just going to be 0. It's just gonna be 0 because this positive charge here cancels out with this negative charge over here. So then, that makes it pretty clear. For a, it says, which tripeptide is most negatively charged at pH 7? That makes it pretty clear that 3 here is the one that's most negatively charged, so we can put peptide 3 here for our answer. Now, b says, which tripeptide contains the largest number of non polar r groups? And so recall that our mnemonic to mem to memorize the non polar r groups is just GAV LIMP. So GAV LIMP. These are our non polar r groups. So if we take a look and count them up, what we'll see is that this first one over here, what we'll do is we'll highlight them in blue if they are nonpolar. Methionine here is the m, so you can see that this one does have one non polar r group, but the other 2 are not considered in this non polar group. So there's only one over here. Over here in this peptide number 2, there are none that fall into the non polar group, so this one has 0. This one over here also has 0 that fall into the non polar group, and then this one over here actually has leucine and valine that both fall in here. So leucine and valine are both right here. So this one has 2 peptides that fall into the non group. So that means that b here is gonna be peptide number 4. So peptide number 4 has the most the largest number of nonpolar r groups. And then c asks, which tripeptide contains sulfur? And we know there are only 2 amino acids that contain a sulfur atom, and those are gonna be methionine with the methyl thiol group and cysteine with the SH group, the SH group, so the sulfhydryl group. So there are none of these amino acids have cysteine in them, but there is one that has a methionine and that's this one over here. And so that means that peptide 1 contains a sulfur, so we can put peptide 1 over here. And so this, concludes this practice problem and I'll see you guys in our next one.

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