Gene:
> > Information loss for eucaryotic cells (for all I know about it) seems
> > to not occur until the mRNA is generated. At this point the introns
> > are removed and the 5' and 3' regions which govern the RNA polymerase
> > action are cut off. How you could possibly reconstruct them is not known
> > to me. I would say the lesser information loss occurs at mRNA
> > translation to protein. You could, in theory, duplicate the codons since
> > you have a limited number of selections. How you would replace the
> > control regions and introns is harder. Codon usage is specific for
> > individual creatures and the wrong codon choice could doom your coded
> > protein in certain instances. I work on Entamoeba histolytica and it
> > has never yet been seen to use 4 codons and another 6 are quite rare.
> > E. histolytica is a very AT rich organsim. Certain thermophilic organisms
> > are very GC rich.
Sorry I was wrong here. Upon further discussion, there are three places
that information seems to be lost. When the DNA goes to the initial RNA
transcript, you lose the information contained in the 5' and 3' control
regions--that is upstream and downstream of the DNA there are elements
which tell RNA polymerase where to bind and (I think) how tenaciously.
These are not included in the RNA transcript. I don't know how they
could be retrieved.
Next, the introns are lost when RNA goes to mRNA. HOw this could be
reconstructed is also a mystery to me.
Lastly, the information about the specific codons used is lost in the
degeneracy of the genetic code when mRNA is translated to protein.
> > As I mentioned above, in certain instances, certain codon choices might
> > spell doom if you ever wanted a functional protein to be made again. They
> > aren't sure why this is, as far as I know (not far) but too many Gs and Cs
> > in Entamoeba are thought to gum up the RNA polymerase machinery if they
> > occur in certain spots, so the RNA strand prior to mRNA doesn't get made.
> > Certain codons in certain organisms might also harm the ability of the
> > mRNA to be made from the splicing machinery. And lots of As and Ts in
> > thermophilic organisms would result in the DNA being denatured (AT-rich
> > regions melt more readily than GC rich regions since ATs are held together
> > by two hydrogen bonds while GC pairs have three) at the temperatures at
> > which they exist.
>
> Fascinating. So there are 'higher-level' constraints on relative
> abundances on the bases?
Yes, certain molecules of the DNA or RNA duplicating machinery seem to
have different tolerances for stretches of particular bases depending on
the organism.
____________________________________________________________
Gene D. Godbold, Ph.D. Lab: 804 924-5167
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