There are a slew of DNA binding proteins which need to bind to the
promoter in order to generate an RNA transcript. They specifically
recognize areas of DNA as well as previously bound proteins.
There are other proteins, downstream and upstream
(3' and 5', respectively) which *can* (they aren't always present as I
understand) either enhance the generation of the RNA transcript or inhibit
the generation of the transcript. Other proteins help determine the rate
at which the RNA polymerase bebops along the DNA strand. This is
necessary for some proteins which need to be turned on (and off) quickly.
There are also thought to be signals that regulate the stability of the
RNA transcript in the 3' noncoding end of the RNA.
The information of the enhancers would be transformed from
the interaction of the protein with the DNA sequence to the number of RNA
transcripts, I think, but I don't know how you would work backwards. The
stability information would be lost after translation of the protein from
mRNA. The information regarding how fast the RNA polymerase transcribes
the RNA from the DNA, while vital for certain regulatory proteins, is not
amenable to retrieval either once the RNA transcript is made.
> OK, this last sounds like what my idea of the coding process was. I'm
> not very familiar with introns and why they'd be lost. Would my
> molbio textbook talk about this? I understand introns are fairly new
> on the scene (at least as far as textbooks might be concerned).
Your textbook should definitely talk about them; they aren't exceptionally
new. Prokaryotes don't have introns. Even some eukaryotes don't have
many introns (Entamoeba doesn't anyway, and neither does yeast)
> > Certain molecules of the DNA or RNA duplicating machinery seem to
> > have different tolerances for stretches of particular bases depending on
> > the organism.
>
> That is interesting. As you may know, in coding theory such codes sound
> like NRZ codes (non-return-to-zero). That is, your code can't allow more
> than a certain number of zeroes in a row, otherwise the timing will drift
> on the readout device. For example, in a CD player, I think the max number
> of zeroes in a row is like 4 or 5. This makes it necessary to pick an
> ECC which doesn't have the possibility of concatenating more than the
> critical number of zeroes. i.e. you can't have one codeword with 101000
> and another of 000101110 because if the two come in order, you have 6
> zeroes--too many.
I'm not really up on coding theory, though it seems like it wouldn't be
that foreign to molecular biology. I wonder why they don't teach us any?
(Not that I'm a molecular biologist; I just sometimes play one at work.
:-) Why is the NRZ rule used in CD players?
Gene
____________________________________________________________
Gene D. Godbold, Ph.D. Lab: 804 924-5167
Research Associate Desk: 804 243-2764
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