Accepted
at 11:18 p.m. Feb, 16, 2024
by
Michael_B
Bulk Suggestion
Bulk ID:
Brian_BH/02.12.24-01:35AM
Type of change:
New Tags
Rationale for change
QID: 400365.
Question specifies the breakage of a thiol group, and requires the recognition that, compared to other answer options available, cysteine is the only likely candidate based on its containing sulfur.
No changes in fields
Text
{{c2::
}}
}}This amino acid is {{c1::Cysteine::Full Name}}, {{c1::CYS::3 Letter Name}}, {{c1::C::1 Letter Name}}: {{c1::Polar Uncharged Aliphatic::Side Chain Characteristic}}.
Extra
Photo credit: Magnus Manske, CC BY-SA 3.0, Via Wikimedia Commons
Cys, C
Polar Neutral
Important Discrepencies To Keep In Mind Amongst Some Amino Acids
Reasoning: TL/DR: these are borderline, complicated cases. There is no broad consensus on whether cysteine and tyrosine should be considered hydrophobic or polar. Proline is clearly nonpolar though.
The reason for the confusion is that are there several ways to define and measure polarity and hydrophobicity for amino acids. First, the polarity and hydrophobicity of the free amino acid is very different from that of the amino acid side chain in the context of a peptide (protein). I assume you are interested in the latter.
Proline is a bit special in that it does not have an -NH3 group; the amine nitrogen binds to the side chain -- it is more of a "loop" than a chain -- and the peptide bond is different. But this "side loop" clearly has no polar group, and I think there is good agreement that proline should be considered nonpolar. The Khan Academy page is probably mistaken on this one. Proline is intermediate in hydrophobicity.
Tyrosine: As mentioned, polarity of the tyrosine side chain is unclear since it is quite large and has both polar and nonpolar groups. Tyrosine is somewhat hydrophobic, but among the amino acids, it places itself near the middle on most hydrophobicity scales. So tyrosine is a borderline case, which explains why different sources disagree.
→ Note that it is more polar than Phenylalanine if that was to come up, and if comparison had to be made.
Cysteine is special in the context of proteins, since cysteine residues often pair up via disulfide bonds, and this changes its properties. By itself, the -SH group is polar (although less so than an -OH group) so the cysteine side chain is somewhat polar. It is intermediate in hydrophobicity as measured by solvent partitioning. Cysteine was considered hydrophobic based on the observation that cysteine is often found in the interior of proteins, away from the water solvent; but this is largely due to its ability to form disulfide bonds.
From Reddit → Here part of the confusion comes from cysteine (AA with S-H R group vs cystine (a cysteine which has formed an S-S bond with another cysteine is called cystine). So here the bare AA, cysteine, is modestly polar and not to bulky, so thus hydrophilic when you see it in a simple polypeptide. However, biologically there is very little free cysteine, it is moslty found without its -H bound to another cysteine as cystine. This S-S disulfide bond is no longer polar, and fairly hydrophobic.
This is even further complicated by the fact that protein folding studies show that even unbound cysteine (with -H) tend to behave in protein folding experiments more like a hydrophobic AA than expected. So traditionally cysteine has been considered polar on the basis of predicted chemistry, however experimental data in poly peptides shows it to be more similar to the hydrophobic AAs. I suppose we can consider this aspect similar to the issue with Tyrosine. Simply put Hydrophobicity is a continuum, not a binary.Photo credit: Magnus Manske, CC BY-SA 3.0, Via Wikimedia Commons
Lecture Notes
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Missed Questions
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Pixorize
Sketchy
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Additional Resources
Note: Though the following visual is helpful, it is misleading to label methionine under the 'polar, uncharged' category. Also do not condone the 'ass***' mnemonic.
Important Discrepencies To Keep In Mind Amongst Some Amino Acids
Reasoning: TL/DR: these are borderline, complicated cases. There is no broad consensus on whether cysteine and tyrosine should be considered hydrophobic or polar. Proline is clearly nonpolar though.
The reason for the confusion is that are there several ways to define and measure polarity and hydrophobicity for amino acids. First, the polarity and hydrophobicity of the free amino acid is very different from that of the amino acid side chain in the context of a peptide (protein). I assume you are interested in the latter.
Proline is a bit special in that it does not have an -NH3 group; the amine nitrogen binds to the side chain -- it is more of a "loop" than a chain -- and the peptide bond is different. But this "side loop" clearly has no polar group, and I think there is good agreement that proline should be considered nonpolar. The Khan Academy page is probably mistaken on this one. Proline is intermediate in hydrophobicity.
Tyrosine: As mentioned, polarity of the tyrosine side chain is unclear since it is quite large and has both polar and nonpolar groups. Tyrosine is somewhat hydrophobic, but among the amino acids, it places itself near the middle on most hydrophobicity scales. So tyrosine is a borderline case, which explains why different sources disagree.
→ Note that it is more polar than Phenylalanine if that was to come up, and if comparison had to be made.
Cysteine is special in the context of proteins, since cysteine residues often pair up via disulfide bonds, and this changes its properties. By itself, the -SH group is polar (although less so than an -OH group) so the cysteine side chain is somewhat polar. It is intermediate in hydrophobicity as measured by solvent partitioning. Cysteine was considered hydrophobic based on the observation that cysteine is often found in the interior of proteins, away from the water solvent; but this is largely due to its ability to form disulfide bonds.
From Reddit → Here part of the confusion comes from cysteine (AA with S-H R group vs cystine (a cysteine which has formed an S-S bond with another cysteine is called cystine). So here the bare AA, cysteine, is modestly polar and not to bulky, so thus hydrophilic when you see it in a simple polypeptide. However, biologically there is very little free cysteine, it is moslty found without its -H bound to another cysteine as cystine. This S-S disulfide bond is no longer polar, and fairly hydrophobic.
This is even further complicated by the fact that protein folding studies show that even unbound cysteine (with -H) tend to behave in protein folding experiments more like a hydrophobic AA than expected. So traditionally cysteine has been considered polar on the basis of predicted chemistry, however experimental data in poly peptides shows it to be more similar to the hydrophobic AAs. I suppose we can consider this aspect similar to the issue with Tyrosine. Simply put Hydrophobicity is a continuum, not a binary.Note: Though the following visual is helpful, it is misleading to label methionine under the 'polar, uncharged' category. Also do not condone the 'ass***' mnemonic.
One by one
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