do I REALLY have to memorize every pKR, pl, pks of amino acids?

[paul2752]

I know that amino acids have become a huge part of biochem questions in MCAT, and am already memorizing the side chains.

But, do we really have to know the individual side chain pK, pk(1,2,3), and pl? If we do, that sounds extremely impractical to rote learn them.

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[Professional Student]

No, that would be ridiculous. Just know what amino acids are basic/acid, and know the general pK and pI for the acidic side chains (~2 and ~5), and the general pK and pI for the basic side chains (~12 and ~10). That's all.

 

[aldol16]

Move this to the MCAT discussion forum, please. Other people on there will find the answers useful.

Here's what I think you should know. You should know the side chain structures well enough that you can answer a reasoning question from that knowledge. For example, replacement of valine with which of the following would least affect protein folding? A) P B) E C) W D) I. You should know that the pKa of the carboxy terminus is around 2 and the pKa of the amino terminus is around 9. The side chain pKas you should also be familiar with for the ones that have pKas that are relevant under normal conditions. So definitely D, E, H, K, and R since these are most often used in biology as ion-pairs and/or catalytic residues. Y and C are useful to know as well.

So if I asked you what the net charge of the following peptide is at pH 7, you should be able to calculate it: DEPGVILWYCMKRIGAH.

You don't have to memorize pIs but you should be able to calculate it if you're given the relevant equilibria and pKa values.

 

[paul2752]

Thanks. THat sounds better.

 

[Lost in Translation]

Good news is that very little of this information is relevant in medical school.

Or bad news, depending on your perspective.

 

[paul2752]

Then why are they tested..lol

 

[Dochopeful13]

Move this to the MCAT discussion forum, please. Other people on there will find the answers useful.

Here's what I think you should know. You should know the side chain structures well enough that you can answer a reasoning question from that knowledge. For example, replacement of valine with which of the following would least affect protein folding? A) P B) E C) W D) I. You should know that the pKa of the carboxy terminus is around 2 and the pKa of the amino terminus is around 9. The side chain pKas you should also be familiar with for the ones that have pKas that are relevant under normal conditions. So definitely D, E, H, K, and R since these are most often used in biology as ion-pairs and/or catalytic residues. Y and C are useful to know as well.

So if I asked you what the net charge of the following peptide is at pH 7, you should be able to calculate it: DEPGVILWYCMKRIGAH.

You don't have to memorize pIs but you should be able to calculate it if you're given the relevant equilibria and pKa values.

Sorry to hijack the thread but how exactly can you tell what amino acid affects protein folding the least when three out of the four amino acids are nonpolar like valine? What am I missing?

 

[deleted600623]

Sorry to hijack the thread but how exactly can you tell what amino acid affects protein folding the least? I assume it is glumatic acid because it has a charged side chain. Do these amino acids with charged side chains not affect protein folding?

Basically the question is asking which AA is just like valine. If you changed valine to something else, the AA that is most like it will have the least affect.


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[Dochopeful13]

Basically the question is asking which AA is just like valine. If you changed valine to something else, the AA that is most like it will have the least affect.


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Maybe I'm wrong but aren't threr of the four choices nonpolar like valine? So how do you know which non polar amino acid is closest to valine?

 

[deleted600623]

Maybe I'm wrong but aren't threr of the four choices nonpolar like valine? So how do you know which non polar amino acid is closest to valine?

I may be wrong in my thinking or misinterpreting the question but Proline and Tryptophan are both bulky AAs whereas Isoleucine is much more similar in structure with valine.


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[aldol16]

Sorry to hijack the thread but how exactly can you tell what amino acid affects protein folding the least when three out of the four amino acids are nonpolar like valine? What am I missing?

You have to know more properties than only which ones are polar and not. You should know that proline is oddly shaped so it introduces kinks into the folding structure. This is because the nitrogen is conformationally restricted by the rigidity of the five-membered ring. Glutamate is acidic so not a good choice. Tryptophan is hydrophobic but not the best answer because it's aromatic whereas valine is a simple aliphatic chain. Tryptophan is also much much bigger than valine so it'll mess up local structure. Isoleucine is also a simple aliphatic chain and looks most similar to valine out of the choices so it's the best choice.

 

[Dochopeful13]

You have to know more properties than only which ones are polar and not. You should know that proline is oddly shaped so it introduces kinks into the folding structure. This is because the nitrogen is conformationally restricted by the rigidity of the five-membered ring. Glutamate is acidic so not a good choice. Tryptophan is hydrophobic but not the best answer because it's aromatic whereas valine is a simple aliphatic chain. Tryptophan is also much much bigger than valine so it'll mess up local structure. Isoleucine is also a simple aliphatic chain and looks most similar to valine out of the choices so it's the best choice.

Thank you. Kaplan does not really touch on individual amino acid structures. Is there a particular resource you recommend?

 

[aldol16]

Thank you. Kaplan does not really touch on individual amino acid structures. Is there a particular resource you recommend?

Just Google "amino acid structures and properties." Look at some of the images. There are some good figures floating around. Print one out and tape it above your desk - you'll want to know their structures (roughly - you don't need to reproduce it - just be able to recognize it) and properties. And one- and three-letter codes as well.

 

[Lawpy]

Thank you. Kaplan does not really touch on individual amino acid structures. Is there a particular resource you recommend?

Just Google "amino acid structures and properties." Look at some of the images. There are some good figures floating around. Print one out and tape it above your desk - you'll want to know their structures (roughly - you don't need to reproduce it - just be able to recognize it) and properties. And one- and three-letter codes as well.

I would ignore selenocysteine since it's a complicated case and isn't universal. I don't recall seeing it in any passage and any full length exam.

Another good image:

 

[aldol16]

I would ignore selenocysteine since it's a complicated case and isn't universal. I don't recall seeing it in any passage and any full length exam.

Excellent graphics! One of those was actually taped to my wall at some point in time. Anyway, I agree with ignoring selenocysteine, but it's actually a very interesting case. Selenocysteine is actually very important because it is, in some cases, a better version of the sulfur-containing enzyme and can protect the enzyme against oxidative damage, which allows the enzyme to do many more challenging oxidation reactions. With sulfur, the enzyme will inactivate because the sulfur will get oxidized to sulfoxide or something whereas the selenocysteine variants retain catalytic activity. Here are two examples:

https://www.nature.com/nchembio/journal/v13/n5/full/nchembio.2335.html
Selenocysteine Confers Resistance to Inactivation by Oxidation in Thioredoxin Reductase: Comparison of Selenium and Sulfur Enzymes

 

[paul2752]

Wow thanks for the detailed info. I sure will read over them