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Since polypeptides are a linear chain of twenty amino acids, each having a single letter abbreviation (e.g. Alanine = A). So can a polypeptide be represented as just the sequence (say: ADN for an Alanine, Aspartic acid, Asparagine polypeptide)?

This method of classifying polypeptides would lead to a possible 8000 (20**3) variations just for 3-amino-acid-polypetides (3200000 for 5-amino-acid-polypeptides, etc.) and that there would be many variations; and for longer polypeptides - that is, proteins - there would be even more variations.

Or are only the important polypeptides and proteins named, since not every variation of polypeptides and proteins are found in the body? I would've thought that many proteins (and enzymes, etc.) are incredibly specific and so they could be classified in some methodological way, as opposed to just 'lipase' or 'carbohydrase' which provides no structural information (though it would have a long methodological name).

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You can certainly refer to short peptides by their sequence. I don't know of any exact boundaries, but I've seen tripeptides referred to by either their three letter codes (Ala-Asp-Asn) or even the chemical name (alanylaspartylasparagine) although obviously that gets ridiculous pretty quickly.

As the largest known protein, titin also has the longest IUPAC name of a protein. The full chemical name of the human canonical form of titin, which starts methionyl... and ends ...isoleucine, contains 189,819 letters and is sometimes stated to be the longest word in the English language, or any language. However, lexicographers regard generic names of chemical compounds as verbal formulae rather than English words

For more than around 5 amino acids, just the sequence makes more sense. It would be interesting to analyse scientific paper abstracts to see how many have the sequence as the 'name', but anyway.

When we get to proteins, it would be unhelpful to refer to them by their sequence. They usually have names - enzymes are often named by what they act on (like 'alcohol') and how they act on them (like 'dehydrogenase'). In addition, there are structured names called E.C. numbers - sarcosine dehydrogenase is 1.5.8.2, for example.

As you point out, there are a very large number of sequences that do not correspond to proteins found in an organism. To name one of these is tricky, and if someone synthesises one then they would have to come up with some naming scheme to refer to it.

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    $\begingroup$ Not to mention that referring to a full protein by sequence alone starts to become redundant because the primary structure becomes slightly less interesting when compared with 2/3/4-ary structure. While a peptide is still short (say less than 10 AA) it probably doesn't have much structure, so its sequence becomes responsible for its chemical activity primarily, and referring to it like that still makes sense. $\endgroup$ – Joe Healey Jan 6 '17 at 19:46
  • $\begingroup$ Thank you, that all makes sense, but if single letters for the abbreviations of amino acids are only used not name polypeptides of length <5 amino acids, then what's the point in abbreviation it. Surely a 'ALRDNNA' polypeptide would have similar chemical properties (and/or functions) to a 'ALRDNL' polypeptide. If that's not what would categorise families of polypeptides, then how else? $\endgroup$ – Lucas Dyson-Diaz Jan 6 '17 at 20:52
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    $\begingroup$ I think you may need to clarify what you mean by polypeptide 'family'. The only polypeptides that are generally assigned names beyond just their sequence are ones which demonstrate particular functions or where someone has contracted the name for convenience. For example, I did some work on poly-glutamine and polyproline. They were stretches of 10,20,30,40,50 amino acids, but we're all proline or glutamine. It wouldn't make sense to refer to them as PPPPPPPPPPPPPPPPPPP when polyP(20) is easier. $\endgroup$ – Joe Healey Jan 7 '17 at 9:01

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