How does RNA polymerase tell the difference between (+) sense

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>>16039
I-I think You're better off asking /sci/.

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>>16042
Ha. Maybe if I wanted to hear about how I'm worthless, should have known this since age 8, and will never go anywhere in STEM. :P

>>16051
http://online.stanford.edu/course/molecular-foundations-medicine
I don't know if this is what your looking for, as I haven't tried this course, but here it is just in case.
The courses are free, they use them to test how well their teaching methods work.

It would do with the 5' 3' directionality of each nucleotide.

The protein (or protein complex) in question that is binding to nucleotide would attach in a way where the 5' end is in one space, and the 3' in another.

This would be the same for all organisms with the ATCG genetic code.

>>16324
Oh, and I forgot to mention.

As far as searching through genetic databases is concerned. The sequencing machines will record the read direction if they can and are instructed to do so. In cases where the direction isn't indicated, that information may not be needed, or if it is needed, then the read without a direction can be compared to its complement (which hopefully you have, and have a direction for as well), and if it matches over a certain threshold you can claim the reads are complements and are opposite directions. I'm pretty sure you can also search a sequence for known genetic patterns. So if you find the subsequence ZYX in sequence ABC, and you know ZYX is read in a certain direction, then you can guess the direction of the read.

I'm a bioinformatics student, and haven't gotten too far in this field, so sorry if my answer is shakey. It should be generally correct.

>>16332
This is pretty much the right answer.

Fact is that transcriptional complexes are forming and falling apart all the time - it's a stochastic event. The energetics work lot more favourably for real genes than for some random pseudopromoter. RNA pol and interaction between all the various factors required for full initiation are more stable for a "real" gene. The energetics work for the correct sense regardless of what strand it's on.

Of course abortive transcription from pseudogenes or pseudopromoters happens at some low level, but presumably this is selected against over time to keep it from becoming an issue (actually not 100% certain how much cleanup is required by the cell on this end, but it happens).