Would you expect to find this segment at the center or at the ...

Question

Would you expect to find this segment at the center or at the surface of a protein? Why?

Accepted Answer

Hi, everyone. Lets look at our next problem. Where would you most likely find this peptide segment? And we have three amino acids by their three letter abbreviations, pheile and TRP in a protein. And Y select the best answer. A, the amino acid segment is found at the surface of the protein because it has side chains that are hydrophilic and interact well with the aqueous environment. B the amino acid segment is located at the surface of the protein because it has cy genes that are large and non polar allowing them to interact with hydrophobic environments. See, the amino acid segment is positioned in the interior of the protein because it has side chains that are large non polar and hydrophobic, which favors interactions away from the aqueous environment or D the amino acid segment is found in the interior of the protein because it stabilizes the core structure. So we know we'll be focusing on the nature of the side chains of these three amino acids to explain their location. And the biggest key will be recall that proteins in a biological context are in an aqueous environment. So we'll find hydrophilic side chains most likely on the outside of the protein and hydrophobic side chains on the interior of the protein away from the aqueous environment. So just by logic, we can rule out choice B because its reasoning is that the amino acid segment will be located at the surface because the side chains are large and nonpolar. So even without looking at what our remembering what our side chains are, this wouldn't make sense. So we can rule out choice B and then choice D which says they're in the interior because it stabilizes the core structure. This would not be correct. Remember that, you know, I'm not sure what this question wants to mean by a core structure. But we know interactions between the backbone of the amino acids are what gives us our secondary structure, things like our beta sheets and alpha helices. So our next step is we need to remember what the side chains are or look them up and analyze whether we're looking at hydrophilic or hydrophobic side chains. So let's take a look at our amino acids. So our first one is phe or phenylalanine and it has an side chain that is CH two. So one bridging carbon atom and then a benzene ring. So that's an easy one aromatic nonpolar. Now, if I were on a test, so I needed to want to wanted to go quickly, I would go ahead and choose charge C, choose choice C which says the side chains are large nonpolar and hydrophobic. I've already got one that's a benzene ring that's obviously nonpolar. So I can bet that the others will be as well since I am stuck between two choices, hydrophilic and hydrophobic. So that would lead me to choose C and move on. But this is a practice question. So let's just be thorough. And in the interest of that, let's think about our other side chains. So then we have ile or ISO, it's, it's our group. But these are our groups, not the entire amino acid, obviously. So the R group of Iselin is we've got ach with a methyl group and then two more carbons. So essentially a sec beetle group and you can see this is, you know, somewhat bulky, this sort of bow shape and it's also nonpolar. So we've got a non nonpolar hydrocarbon chain there. So as we expected, another hydrophobic sighed Ching are and then our final one trip to fan, it's our group. This is actually the largest of the amino acids. It has an indo our group. So a branching ch two group and then this double ring structure with a pure ring that contains ac C double bond and a nitrogen and then an attached benzene ring. So there is a nitrogen in there. So at first you might think polar, but when we look at this overall structure, which is these, you know, aromatic rings and mostly hydrocarbon is just the one nitrogen overall, this is going to be a bulky and nonpolar group. So we've got three pretty bulky nonpolar groups and that's going to make them likely to be found in the interior away from the aqueous environment. So choice C is indeed our answer and we can cross out choice. A since the side chains are definitely not hydrophilic and our answer to where we'd most likely find the peptide segment, phenylalanine, isoleucine tryptophan in a protein. And why is choice C that it would be positioned in the interior of the protein because it has side chains that are large nonpolar and hydrophobic which favors interactions away from the aqueous environment. See you in the next video.

Would you expect to find this segment at the center or at the surface of a protein? Why?

Key Concepts

Protein Structure

Hydrophobic and Hydrophilic Interactions

Protein Folding

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