What's inside the enzyme?

[Deepa100]

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Which of the following amino acids would most likely be present in the interior of the tertiary structure of a globular enzyme?
A. Cysteine
B. Asparagine
C. Lysine
Correct Answer D. Valine

Can some one refresh me on why the inside of an enzyme is hydrophobic?

 

[sleepy425]

ok, so it's just so that they hydrophobic residues are as far away from the water as possible.

the simplest explanation (which is entirely correct, it's not an oversimplification or anything, and it's as deep as you'll need on the mcat and really, for any purpose except physical chemistry) is that the hydrophilic residues group to the outside so that they can interact with the aqueous environment. water does not penetrate deeply beyond the surface of the protein, so this is a convenient place for hydrophobic molecules to locate since they are reasonably shielded from the water. that's really all there is to it. it's the same way micelles work with fatty acids. the polar carboxyl groups orient to the outside of the micelle while the hydrophobic alkyl chains orient towards the inside of the micelle.

that's why valine, which just has an isopropyl group for its R group, generally is found in the interior of the protein.

so just remember, inside is hydrophobic because there's very little water in the inside of the protein, whereas there's a ton of water on the surface (since it's dissolved in water) so hydrophilic residues will be more common on the surface

 

[nikeshp]

do we really need to know all of the amino acids?

 

[JA Prufrock]

do we really need to know all of the amino acids?

That's what I was wondering, and I doubt it. This kind of question would either be passage-based with information reguarding the residues included, or it might be a discrete with structures included. I think sleepy's explanation is the logic we need to be familiar with.

 

[Deepa100]

That's what I was wondering, and I doubt it. This kind of question would either be passage-based with information reguarding the residues included, or it might be a discrete with structures included. I think sleepy's explanation is the logic we need to be familiar with.

I think you need to know the types- basic polar, acidic, hydrophobic.

 

[Vihsadas]

I think you need to know the types- basic polar, acidic, hydrophobic.

I agree. This is good information to have at the ready.

 

[Kaustikos]

That's what I was wondering, and I doubt it. This kind of question would either be passage-based with information reguarding the residues included, or it might be a discrete with structures included. I think sleepy's explanation is the logic we need to be familiar with.

Not true. I have seen questions arise where they ask you something about an amino acid by name and you're expected to answer the question based on YOUR knowledge of amino acids.

 

[engineeredout]

I was going through the EK 1001 bio questions, and for one of them they specifically state in the answer that you should know for the MCAT that glycine is the smallest amino acid.

The question had to do with which amino acid was going to best fit into a sterically hindered spot.

 

[JA Prufrock]

wow well that's news to me since characteristics of amino acids doesn't seem like introductory bio material. Thanks for the heads up.

 

[engineeredout]

Adding a few more from the EK book:

Know that cystine is the only amino acid capable of forming covalent disulfide bonds.

Know the three basic and two acidic amino acids

Also be aware that glycine is the only optically INactive amino acid.

 

[ballofnerves]

Yeah, there are quite a few of EK questions that require knowledge of specific amino acids. Not too sure if this is specific to EK or if this comes up in the AAMC practice tests, etc. Hopefully somebody can shed some light on this.

 

[unsung]

Which of the following amino acids would most likely be present in the interior of the tertiary structure of a globular enzyme?
A. Cysteine
B. Asparagine
C. Lysine
Correct Answer D. Valine

Can some one refresh me on why the inside of an enzyme is hydrophobic?

It's like a micelle (think soaps, bile, what have you).

 

[unsung]

Adding a few more from the EK book:

Know that cystine is the only amino acid capable of forming covalent disulfide bonds.

Know the three basic and two acidic amino acids

Also be aware that glycine is the only optically INactive amino acid.

To add to that, methionine is the a.a. coded by the start codon AUG, meaning it's at the start of each protein.

Proline is a helix breaker because of its unique structure- an "imino acid" with its disubstituted nitrogen.

 

[HolyGrail]

At some point in time you should just memorize these... it is pretty useful. I'm not actually being sarcastic.🙂