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I'm looking at amino acid abbreviations and on every site I visit, asparagine and glutamine have two different abbreviations. Is there a reason for this? Do they represent different forms of the amino acid that may have different properties?

I'm looking at the abbreviations on this site as an example: http://www.hgmd.cf.ac.uk/docs/cd_amino.html

On the page, asparagine has an abbreviation of 'N' and an abbreviation of 'B'. The abbreviation 'B' doesn't correspond to a codon so why is it there?

Glutamine also has two abbreviations ('Q' and 'Z'). The abbreviation 'Z' doesn't correspond to a codon either.

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    $\begingroup$ Welcome to Bio. Are you askinh whether Arg and Gln are different amono acids?? $\endgroup$ – AliceD Dec 8 '15 at 20:33
  • $\begingroup$ Great edit - @Roland has given the right answer - see the official IUPAC website $\endgroup$ – AliceD Dec 10 '15 at 21:24
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The abbreviation Asx (B) is used if it is uncertain whether the amino acid at a given position in a peptide sequence is Asparagine or Aspartate. Similarly, Glx (Z) is used when there is uncertainty between Glutamine / Glutamate.

These two pairs of amino acids can be ambiguous in peptide sequences because Asp/Asn and Glu/Gln differs only by a terminal amide (-NH2) group in the side chain, and this amide group can be spontaneously lost from proteins by a deamidation reaction. When this occurs, asparagine is converted to aspartate/isoaspartate, and glutamine to glutamate/glutamate. These cannot be distinguished from "real" aspartate or glutamate by classic peptide sequencing, nor by mass spectrometry, since their mass is identical. Hence, protein sequences obtained directly from protein frequently contains Asx/Glx entries.

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Asparagine (Asn) and glutamine (Gln) are derived forms of the amino acids aspartic acid (Asp) and glutamic acid (Glu). Both amino acid pairs (Asn/Asp, Gln/Glu) consist of the same carbon backbone, their side chains only differ in their functional group. Aspartic and glutamic acid include a carboxylic acid (-COOH), whereas asparagine and glutamine are carboxamides (-CO-NH2).

Here you can see asparagine and aspartic acid as example:

Asparagine (Asn) Asparagine (Asn)

Aspartic acid (Asp) Aspartic acid (Asp)

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The reason is simple: These are two different amino acids with different side chains. They look very similar, but they are not:

enter image description here

This is L-Glutamine, its chemical formula is C5H10N2O3.

enter image description here

This is L-Asparagine, its chemical formula is: C4H5N2O3. This shows that L-Asparagine has one CH2 less than L-Glutamine.

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From the reference in the question, the query seems to be asking "Why does an amino acid have two abbreviations, such as Asn and N for asparagine, and Gln and Q for glutamine?"

This is because both abbreviations are commonly used in the scientific literature. The longer, 3-letter, abbreviation is useful because it is a recognizable shortening of the amino acid's name. The 1-letter abbreviation tends to be very arbitrary (e.g. Q for glutamine), so it is not very mnemonic. However, the single letter form is much easier to make use of for long sequences of amino acids, as in giving the sequence of a particular protein.

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NCBI Amino Acid Abbreviations (IUPAC): http://www.ncbi.nlm.nih.gov/Class/MLACourse/Modules/MolBioReview/iupac_aa_abbreviations.html

Glutamine and asparagine are converted into glutamic acid (Gln) and aspartic acid (Asn) by a simple hydrolysis of the amide group, so they are slightly different from each other. In general the amino acids Glutamine and asparagine's amide group (CONH2) are changed to a carboxyl group (COOH).

A good answer to this question was also given in this forum, with visualization: https://www.quora.com/Whats-the-difference-between-asparagine-and-aspartic-acid

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  • $\begingroup$ No, Asx (B) and Glx (Z) are the abbreviations used when there is uncertainty abous Aspartate/Asparagine or Glutamate/Glutamine, respectively. $\endgroup$ – Roland Dec 8 '15 at 21:00
  • $\begingroup$ Okay - In a way that makes more sense. But just because I am curious: I generally trust the NCBI webpage - so why does it refer to them as this in the table? It seems as though the standardized way of writing them (if you have to differentiate between e.g. Glutamine and glutamic acid is Glx and Gln).. What about the one letter code ( B and Z) because that is very specific for glutamine and asparagine, or is it the same with that as well? $\endgroup$ – CuriousTree Dec 8 '15 at 21:55
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    $\begingroup$ Look at the NCBI table again. It says that Q is the specific code for glutamine (Gln), and N is the specific code for asparagine (Asn). Asx (B) and Glx (Z) are the abbreviations used for the ambiguous (unspecific) cases. See also my answer above for an explanation of why this occurs. $\endgroup$ – Roland Dec 8 '15 at 22:00

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