DNA actually has multiple codes (Introduction)

by David Turell , Thursday, August 28, 2014, 02:09 (3740 days ago)

Redundant codons are not evolutionary degeneration of the DNA but create another coding level providing another layer of information to be followed, in this case related to protein folding:-"Redundancy in the primary genetic code allows for additional independent codes. Coupled with the appropriate interpreters and algorithmic processors, multiple dimensions of meaning, and function can be instantiated into the same codon string. We have shown a secondary code superimposed upon the primary codonic prescription of amino acid sequence in proteins. Dual interpretations enable the assembly of the protein's primary structure while enabling additional folding controls via pausing of the translation process. TP [transitional pausing] provides for temporal control of the translation process allowing the nascent protein to fold appropriately as per its defined function. This duality in the coding function acts to reduce the redundancy in the genetic code when viewed holistically. The functionality of condonic redundancy denies the ill-advised label of “degeneracy.” When simultaneously combined with other coding schemas such as intron/exon boundary conditions, and overlapping and oppositely oriented promoters, multiple dimensions of independent coding by the same codon string has become apparent. (my bold)
 
"The ribosome can be thought of as an autonomous functional processor of data that it sees at its input. This data has been shown to be PIo in the form of prescribed data (D'Onofrio et al., 2012), not just probabilistic combinatorial data. Choices must be made with intent to select the best branch of each bifurcation point, in advance of computational halting.
 
"The arrangement of codons has embodied in it a prescribed sequential series of both amino acid code and time-based TP code necessary for protein assembly and nascent pre-folding that defines protein functionality. We have shown that the TP coding schema follows distinct and consistent rules. We have demonstrated that these rules are logical and unambiguous. The actual hexanucleotide “word” selection is dependent upon the next adjacent codon. This conditional selection is shown in the algorithm section. Such an iterative process nicely lends itself to an algorithmic process should geneticists experiment with writing their own genetic code. Understanding the dual mappings between the amino acid and TP code will allow algorithmically computed solutions to simultaneously fulfilling the this dual requirement using the same written code.
 
"It has been shown that both the genetic code and TP code are decoupled allowing simultaneous decoding and dual functionality within the ribosome using the same alphabet (nucleotides) but different languages. With other languages such as French, we share the same alphabet, but employ different semantic and grammatical rules. The same is true of the codon alphabet being used by the cell to generate more than one language.
 
"The TP code exhibits distinct meaning in relation to mappings between codons and pausing units. The TP code also exhibits a syntax or grammar that obeys strict codon relationships that demonstrate language properties. Because of the redundancy of the genetic code, it could be argued that the TP language is a subset of the genetic language. The subspace of the TP language resides, and thus appears to have a dependency on, the primary genetic code. Within this subspace, however, we argue that the TP language is decoupled from and remains independent of the protein-coding language.
 
"Hypothetically, in a non-redundant codon to amino acid mapping, once the codon sequence is selected, thereby defining the prescribed amino acid chain, this prescription would preclude additional information from occupying the same space (ORF) to prescribe TP. The only way the physical constraints could be removed from formal PIo instantiation of additional TP controls using the same code would be to build redundancy into the genetic language. Thus, having redundant contingency in the genetic code is both a necessary and sufficient condition to represent multiple languages using the same alphabet of the genetic code.
 
"Amino acid sequence, by necessary consequence, points to mRNA sequences. We further posit that the interactions with translation pausing can be traced back to the specific arrangements of redundant codons in the mRNA, and ultimately to the genome. We propose that the pausing functions are facilitated by first generating a pause state in the translation of the mRNA codons within the ribosome. This gives protein factors, trigger factors and other chaperones the necessary time to mechanically perform folding operations.-Taken from the conclusion:-http://journal.frontiersin.org/Journal/10.3389/fgene.2014.00140/full