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Why do we choose a grammar from a lot of grammars that can describe structure of proteins? Usually, there are a lot of (maybe infinite) grammars that can describe one language. Why do we choose a specific one? Especially the language of proteins of gene just has finite sentences or words.

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Are you talking about protein nomenclature or what? –  Miguel Ángel Naranjo Ortiz Sep 3 '13 at 22:34
    
@MiguelÁngelNaranjoOrtiz,no,what I am talking about is the description of the protein structure by formal language,it is research that tries to predict the structure by DNA or RNA –  XL _at_China Sep 3 '13 at 22:47
    
Actually when describing the 3D structure of a protein you only need the angles formed by the peptidic bond of every aminoacid, and the aminoacidic sequence. This is the kind of data yyou obtain when proteins are resolved by X-ray diffraction. Those are raw data thought, and they usually describe protein structure by different nomenclatures, such as domain organization or secondary structure prediction. In this case, you describe regions of the protein with a particular structure, often related with its function. –  Miguel Ángel Naranjo Ortiz Sep 3 '13 at 22:56
    
@MiguelÁngelNaranjoOrtiz You also need the sidechain orientations for a complete structure. The raw data for X-ray is the electron density, though in NMR torsion-angle space is often used for structure calculation. –  Mad Scientist Sep 4 '13 at 6:04
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1 Answer

I did not understand your question completely but this is what I guess you want to know:

  1. Why genetic code evolved to be what it is ?
  2. How the sequence of the protein coded by a mRNA give rise to a particular structure ?

Answer to first question cant be definitive. The textbook explanation for why a 3-letter code exists is because a 2-letter code cannot describe all the 22 amino acids, with all its permutations. But then comes another question: why only 22 amino acids. I can't even speculate the answer to this question; the simple amino acids are fine but for an example why lysine and not a similar amino acid with a shorter side chain - no idea.

So, given 22 amino acids, a 3-letter code and 4 nucleotides, the multiple codons for an amino acid are similar in sequence (usually the first two bases are conserved in accordance with the wobble hypothesis. The last base usually doesnt base pair strongly with the tRNA and is of minimal importance).


The answer to second question is somewhat straightforward. The sequence can give rise to infinitely many structures but in a given environment (consisting of the solvent, other solutes etc), the sequence adopts a particular structure in accordance with the free energy minimization principle. There is a possibility that given an environment a protein can have two different optimal structures and can switch between these two structures.

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Good,thank you for your answer,but I don't know why somebody voted down my question. –  XL _at_China Sep 5 '13 at 0:44
    
well.. i didnt vote it down :P Perhaps they did because you are not really clear with what you want to ask. I kinda understood the point but rather than giving an analogy with grammar you can ask the question using scientific terminology. –  WYSIWYG Sep 5 '13 at 11:01
    
,thank you,I know you did not.To tell the truth,I am not a biologist,and I am not familiar with bioinformation. –  XL _at_China Sep 5 '13 at 11:37
    
perhaps you can restate your question based on the comments and the answer. even if your query is answered it will be better for someone who looks up an existing answer. –  WYSIWYG Sep 5 '13 at 11:46
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