Polar vs Nonpolar Amino Acids

[xkb89]

Hello, everyone. I am creating flashcards for the 20 amino acids, and I notice there is a discrepancy on whether Proline, Cysteine, and Tyrosine are polar or nonpolar. I have seen multiple "charts" where they are listed differently. Could someone please confirm which category AAMC would determine each would be in? Thank you!

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[kraskadva]

Proline is generally considered nonpolar. While there is some electronegativity imbalance (i.e. polarity) in the R group, it cannot be charged under physiological conditions, is pretty much never involved in catalytic regions of proteins (mainly structural, in kinks/turns), and the R group tends not to participate in Hydrogen bonds (b/c often prevented by stereochemistry), and is therefor listed with nonpolar aa's.

Cysteine and Tyrosine are both polar, but uncharged. Any source that tells you otherwise on these two is not to be trusted, as they're clearly polar. Tyrosine can be listed with hydrophobic aa's sometimes (and it is that also) but it's still polar as well.

 

[kraskadva]

Also, generally I think the best way to memorize groups like this is mnemonics. Mine for the amino acids is a bit rude, but I find it memorable (made it up 4 years ago and still can't forget it)

It's below the spoiler tag, just as a warning for the rudeness. One letter codes are capitols, explanations in lowercase.

Spoiler

non-polar: the LIMP F A G VW has no pole (if you don't get this one... well then it won't seem rude)
{edit: sdn thinks it's rude too and tried to *** the F A G}
polar, uncharged: the QueeN CYST isn't charged (she's the queen, so she doesn't pay for things)
polar, charged: HaRK i have good news (for the positively charged), and ED is always negative (for the negative ones...i know a guy named ed, who's very salty, but you could pick a different interpretation)

 

[xkb89]

Perfect. Thanks for clarifying!


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[aldol16]

Cysteine and Tyrosine are both polar, but uncharged. Any source that tells you otherwise on these two is not to be trusted, as they're clearly polar. Tyrosine can be listed with hydrophobic aa's sometimes (and it is that also) but it's still polar as well.

It's actually not as simple as textbooks make it out to be. When in doubt, always return to the science. (But for MCAT purposes, cysteine and tyrosine are polar). I just want to make the point that one shouldn't immediately discount a source - especially if the science is actually there.

This is actually a good resource if you're interested in the scientific rationale for assigning hydrophobicity (take a look at Table 2): http://www.sciencedirect.com/science/article/pii/0022283682905150

By this measure, cysteine is actually more hydrophobic than alanine. So whether you consider it "polar" depends on your definition, but it's quite oily. Tyrosine doesn't like water, but if you look at the hydropathy index, it's not that averse to it. I mean, it's less averse to it than proline. This is mainly due to the oily phenyl ring of tyrosine. Again, how you define polarity will change your answer as to whether it's polar, but it only likes water a little bit.

The MCAT tends to define polar as a "large enough" dipole moment in the side chain, which is mainly limited to heteroatoms. I don't believe you'll ever have to rank amino acids in order of polarity - definitely not when the science is ambiguous. Most of the time, the questions will be based on some central property of the amino acid (e.g. specific charge, presence of hydroxyl group for phosphorylation, presence of sulfur for disulfide bonds, etc.).

 

[kraskadva]

It's actually not as simple as textbooks make it out to be. When in doubt, always return to the science. (But for MCAT purposes, cysteine and tyrosine are polar). I just want to make the point that one shouldn't immediately discount a source - especially if the science is actually there.

This is actually a good resource if you're interested in the scientific rationale for assigning hydrophobicity (take a look at Table 2): http://www.sciencedirect.com/science/article/pii/0022283682905150

By this measure, cysteine is actually more hydrophobic than alanine. So whether you consider it "polar" depends on your definition, but it's quite oily. Tyrosine doesn't like water, but if you look at the hydropathy index, it's not that averse to it. I mean, it's less averse to it than proline. This is mainly due to the oily phenyl ring of tyrosine. Again, how you define polarity will change your answer as to whether it's polar, but it only likes water a little bit.

The MCAT tends to define polar as a "large enough" dipole moment in the side chain, which is mainly limited to heteroatoms. I don't believe you'll ever have to rank amino acids in order of polarity - definitely not when the science is ambiguous. Most of the time, the questions will be based on some central property of the amino acid (e.g. specific charge, presence of hydroxyl group for phosphorylation, presence of sulfur for disulfide bonds, etc.).

Oh, for sure. I will certainly bow to this chemical logic.
For the purposes of the MCAT/UG Biochem (and Med School Biochem AFAIK), though, it can be simplified. Especially in the context of a polypeptide, not as stand-alone amino acids.