5' end of gene

Mark D. Garfinkel garfinkl at iitmax.iit.edu
Tue Mar 15 15:53:11 EST 1994

sac5001 at tamuts.tamu.edu (Scott Alexander Coonrod) writes:

>I have a simple question that no one to date has been able
>answer adequately. When one talks about the 5' end of a gene
>they are referring to the end at which the promoter and other
>regulatory regions are located. It is the starting point for
>transcription. When you look at any freshman biology book it
>clearly shows that both DNA and RNa polymerases can only
>bind to the 3' end and move in the 5' direction on the template.
>It therefore makes a transcript in the 5' ---> 3' direction.
>Why then do we not refer to the front of the gene as the
>3'end because thats where transcription starts. Im sure
>there must be a simple answer to this question but I havent
>found it yet. Any help would be appreciated.

	You answer your own question. Since DNA is an anti-parallel
double helix, it is easy for confusion to arise. Indeed, some
research journals (Journal of Biological Chemistry, and the various
American Society for Microbiology titles) give excruciatingly
detailed instructions for authors regarding the appropriate
terminology. Even professional scientists need guidance out of the
morass of jargon.

	Consider that one workable definition of a gene is "a segment
of DNA that is transcribed." The resulting RNA has a 5'->3' polarity,
and is the *functional product* of that gene (whether it is a ribosomal,
transfer, or messenger RNA is beside the point). The gene has two strands,
of course: one strand is "RNA-congruent," by which I mean it has the same
5'->3' polarity as the RNA product and except for thymine-uracil and
deoxyribose-ribose is essentially identical to the RNA product (excision
of introns notwithstanding); the other strand has anti-parallel orientation,
complementary base sequence, and serves as the template strand. We chose
to name the orientation of a transcribed segment of DNA in terms of the
*polarity of the functional RNA product* and not the polarity of the
template strand. Thinking in terms of the RNA product makes this a
non-arbitrary choice. The wisdom of this choice is reinforced by the
special case of mRNA, the biological function of which is to serve as
template for translation, a process that begins at/near the mRNA's 5'
end and continues towards its 3' end.

Mark D. Garfinkel (e-mail: garfinkl at iitmax.acc.iit.edu)
My views are my own, which is why they're copyright (c) 1994

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