Consider the amino acids lysine, valine, and aspartate in an e...

Question

Consider the amino acids lysine, valine, and aspartate in an enzyme. State which of these amino acids have R groups that would:

b. be found in hydrophilic regions

Accepted Answer

All right. Hello everyone. So this question is asking us, given the following amino acids, crw and F, which ones have our groups most likely to be found in the hydrophilic regions of an enzyme? Option A is C, option B is R, option C is W and option D is F. Now, starting off here, recalled in biochemistry, the amino acids that we study can be represented either as three letter abbreviations or one letter abbreviations. These abbreviations are standardized to have a specific meaning. So, C for example, represents cysteine, R represents origin, W represents trip to fame or chip. The fan and F represents phenyl allen. And because these are different amino acids, of course, they all are going to be characterized by their unique side chain. And so depending on the properties of the side chains, we can go ahead and classify amino acids in several different ways. For example, we can talk about non polar amino acids with hydrocarbon side chains, we can talk about polar neutral amino acids and we can also talk about acidic or basic amino acids, which generally speaking, have a charge to them. So starting off here with our amino acids, tryptophan and phenylalanine recall that both of these would be classified as nonpolar amino acids. This is because both of these side chains include relatively large aromatic rings that are mostly hydrocarbon, right. The exception is tryptophan, which does have a nitrogen atom inside of the ring. However, the rest of the side chain is very nonpolar and therefore hydrophobic. Now, on the other hand, both cysteine and arginine can be classified as polar. But before we talk about what sets them apart from each other, let's talk about what it means for an amino acid to be in the hydrophilic region of an enzyme. And just for the sake of demonstration here, let's say I have this enzyme that's an oval and this particular enzyme is interacting or is present in something like the cytozole right side is all and body fluids in general are aqueous, right? Which means that they're composed of what? So because of their aqueous, right, that fluid is going to be polar. And so when we discuss the properties of those amino acids that make up the enzyme that are closest to that aqueous environment, we want them to mesh well with the solvent, right, we want those amino acids to have favorable interactions with the aqueous environment so that the enzyme dissolves well. So because of this hydrophilic amino acids should be on the outside. On the other hand, hydrophobic amino acids tend to be found on the inside of an enzyme three dimensional structure, that way they can be shielded, so to speak from the aqueous environment and not have to interact with the polar fluid. So, because we're talking about the, the hydrophilic region of an enzyme, which is most likely the exterior, given that most fluids tend to be aqueous, we can eliminate tryptophan and phenylalanine as options. So now we have to decide between cysteine and arginine. And so the difference lies in their side chain, right? Because both of these are polar, that's true. But that doesn't quite tell the full story, so to speak, Sistine, for example, is polar, but its only polar element of the side chain is a file group or s group. It's polar and it does form hydrogen bonds, but these hydrogen bonds are relatively weak and cysteine is better known for the formation of disulfide bonds. So, cysteine is more often associated with the tertiary structure of a protein and more specifically in internal disulfide bonding. So not quite the best candidate for the hydrophilic region. This leads us now to arginine, which is one of those acidic or basic amino acids that I mentioned towards the beginning of the video arginine if you recall is a basic amino acid and it's going to have a positive charge at physiological Ph now it's the charge that's going to make an amino acid like arginine, more hydrophilic still. So the more hydrophilic, the more favorable interactions it's going to have with that eight week environment. So option B which is R for Arginine is going to be the best answer here and there you have. So with that being said, thank you so very much for watching and I hope you found this helpful.

Consider the amino acids lysine, valine, and aspartate in an enzyme. State which of these amino acids have R groups that would:
b. be found in hydrophilic regions

Key Concepts

Amino Acid Properties

Hydrophilicity vs. Hydrophobicity

Enzyme Structure and Function

Watch next