Chemistry/DNA Question?

[Puzzler]

What does it mean when a messenger RNA has several A's on the 3 prim end? ie. AAAAAA

Edited August 14, 2009 by Puzzler

[Theophrastus]

A, is simply an abbreviation for adenine, one of the four bases, in RNA (adenine (A), Cytosine ©, Guanine (G) and (U) Uracil). As for the 3' (3 prime) and 5' (5 prime) (given the first, you should be familiar with the second), these define the direction of the RNA strand. 3', is the hydroxyl group, bonded to the third (or gamma) carbon of the ribose sugar, that lies at one end of the chain, while 5' is the hydroxyl group, bonded to the 5th (or epsilon) carbon of the ribose sugar, at the opposite end of the chain.

 

This has particular relevance in DNA which has two antiparallel strands, and thus defines, the strand's direction, and in doing so, its identity. (Here's a link showing a dinucleotide; it's nice to have visuals )

 

http://journals.iucr.org/c/issues/2005/08/00/hj1051/hj1051scheme1.gif

 

So, finally what this means is that the first several nucleotides, moving from the 3' end, are AMP (adenosine monophosphate)

Edited August 14, 2009 by Theophrastus

[UC]

http://en.wikipedia.org/wiki/Polyadenylation

[CharonY]

It should be added that polyadenylation of mRNAs is primarily found in eukaryotes.

[Theophrastus]

It should be added that polyadenylation of mRNAs is primarily found in eukaryotes.

 

That's interesting. Why so? If I'm not mistaken, three A's code for a lysine residue. Why do eukryotic proteins show a greater tendency to form numerous consecutive lysine residues?

[CharonY]

The polyadenylation is outside the coding area. I.e. it will not get translated.

[Theophrastus]

Ah, thanks for the info.

 

Interestingly enough, I was looking through a biochem text I was given (I've been searching through a variety, as when you are planning to waste hundreds of dollars, you might as well do so contented by the content), and I found a chart comparing several bacteria, animals, and of course human beings, in terms of the (molar) percent fraction of the organism's total DNA content, that each of the four residues takes up (on average).

 

I found that particularly in mammalian cells (which for reasons unkown to me, were the only examples of eukryotic cells, given in the text) the percentage taken up by guanine and cytosine was exactly equal (given rounding to the closest 0.1 percent), while there always seemed to be slightly more adenine than thymine. For example, in humans, 30.1% of the DNA content is thymine, while 30.4% is adenine, resulting in a difference of (about) 0.3%. Or similarly, in cows, there is a 0.3% difference in terms of adenine versus thymine content. (A= 29%, T= 28.7%) Pigs on the other hand, had a adenine surplus of an even larger 0.7%. (A= 29.8%, T= 29.1%)

 

Can polyadenylation, be seen as a rational explanantion for this, in DNA, just as in RNA, apart from the slight deviations, due to simple experimental variation, or is it only part of the explanation? Or more broadly, how is the excess adenine channeled, in DNA, and why is it present?

 

[edit]

 

Had to remove further, "why questioning," following examination of UC's link.

Edited August 23, 2009 by Theophrastus

[CharonY]

It should not be as DNA exists stably as a double helix (except during events like replication and transcription that is). To evaluate the apparent discrepancy it is necessary to know how this values were generated. E.g. it could be that it was just a measurement of the individual bases (e.g. by chromatography) of different cells. So both experimental as well as intra-individual differences may account for that. However one would also expect slight variability for the individual G and C content. Or you could have extract from cells that are in the process of replication and so that you could get unequal yields.

What is clear is that it is not based on sequence data as automatically A would be equal to T. And the AT would add up with GC to 100%.

Polyadenylation happens after transcription. It is not encoded within the genome. And even if it was, the anti-parallel strand would carry polyTs in that case.

[jesus]

aren't the extra adenines on the end to protect the rna code from degrading?

 

or am i thinking of something else? its been awhile since i did bio.