Degenerate code

Several hypotheses have been developed in order to interpret the paradox of a degenerate code and the specific synthesis of proteins. The wobble theory of Crick (1966 a) postulates the possibility of alternate ways of pairing between the bases of the w-RNA and -RNA. Within the framework of this theory it is assumed that the pairing for the two first positions of each codon-anticodon pair is normal, A <—>TJ, C <—>G. But in order to explain the multiple correspondence it is necessary to assume other possibilities of pairing for the third position. The postulated rela-... 

It follows that the technique is useful to identify (1) point mutation (a single different nucleotide) that may be a silent mutation (also known as a synonymous mutation due to degenerate coding), resulting in a codon that codes for the same amino acid or a missense mutation (type of non-synonymous mutation) producing a codon that codes for a different amino acid the resulting protein may be non-functional but certain missense mutations can be quiet since the protein may stiU function polymorphisms, (3) insertions, and deletions. 

Incorporation of amino acids into a polypeptide chain occurs through the involvement of a class of small RNA molecules known as transfer RNA or tRNA. For each codon in mRNA, there is a corresponding tRNA to which the amino acid specified by the codon is covalently attached. Since multiple codons specify the same amino acid (degenerate code), a given amino acid may be linked to a set of tRNAs. 

As we noted, a three-letter genetic code contains sixty-four words, called codons, but there are only twenty amino acids. Thus there are forty-four more codons than are required to specify all of the amino acids found in proteins. Three of the codons—UAA, UAG, and UGA—specify termination signals for the process of translation. But this still leaves us with forty-one additional codons. What is the function of the "extra" code words Francis Crick (recall Watson and Crick and the double helix) proposed that the genetic code is a degenerate code. The term degenerate is used to indicate that different triplet codons may serve as code words for the same amino acid. 

A degenerate code is one in which more than one triplet can specify a given amino acid. 

Due to isosemantic substitutions, there probably is more evolutionary history inscribed in the base sequence of nucleic acids than in the amino-acid sequence of corresponding polypeptide chains. By its implications, a degenerate code thus emphasizes the role of nucleic acids as master molecules over polypeptides, (a role still doubted by some (Commoner, 1962)). even though polypeptides may interact with nucleic acids to regulate the rate of synthesis of both polypeptides and nucleic acids. All the potentialities of an individual may be assumed to be inscribed in polypeptide chains that are actually synthesized, or could be synthesized, by the cells under certain circumstances, and in the structures that control the actual and potential rates of this synthesis. Yet it appears conceivable, since equal rates of synthesis under the control of distinct but isosemantic codons are possible, that the individual... 

Lysine (AAA, AAG), glutamine, and cysteine have two codons isoleucine, leucine and phenylalanine have three threonine, glycine, alanine, valine, proline, and tyrosine all have four and serine and arginine have six. Consequently, in many cases more than one codon is able to dictate the position of a given amino acid. The code is therefore referred to as a degenerate code. As a result, many mutations occur which are not accompanied by alterations in the amino acid sequence. It would therefore appear that a degenerate code constitutes an evolutionary advantage, and even if all 64 triplets existed in the RNA template, all triplets need not function in transcription. The choice of a triplet could also be restricted by the number of available transfer RNA s. But if 60 sequences can be used... 

Hydrophobic cluster analysis (HCA) is a very efficient method to analyse and compare protein sequences. Schematically, HCA uses a highly degenerated code for the sequences, where only two main states are initially considered hydrophobic andhdrophilic. 

If a code word consisted of oidy two letters then 4 = 16 combinations would result evidently not enough. But three symbols per combination brings it up to 4 = 64 possibilities—more than enough to provide each of the twenty amino acids with one codon. Probably there are two or even three codons for each of several amino acids. This situation is called a degenerate code, which means that several combinations stand for the same thing. Other combinations probably are nonsense, i.e., they do not stand for any amino acid. 

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