[tuhin (OP)]

Hello,
I got some thoughtful answers to the previous questions posted. Here are some new ones -
1. Talking about RNA transcription , why is the  need to form the transcription bubble  when the template strand can be accessed from the outside ( this is my thinking ). In other words, why is the new RNA that is being synthesized forms inside  the transcription bubble?

For DNA replication , that the lagging and the leading strands are synthesized inside the replication bubble , there is atleast one logic.
They need to lie side by side so that H bonds can form between the complementary bases of the lagging and the leading strand. This is not the case in case of RNA transcription.

2.When a gene is being transcribed from the 3'--->5' template strand what lies in the exactly opposite part of the  5'--->3' non template strand ? That part of the non template strand should contain the allele  of the gene that is being transcribed in the template strand ?!

3. What determines which particular allele of a gene present on both strands of DNA would be transcribed?

I ask question 2&3 because a diploid cell with TT genotype would have two homologous chromosomes  each with T. Again each chromosome would have a double stranded DNA. If T lies in a particular strand of the DNA , what lies on the exactly opposite other strand of the DNA. The other T should lie in the other homologous chromosome ?

So ?! Time to scratch head few times?
tuhin 
                 
                 
         
                   
   

[genegenie]

Hi tuhin. These are my thoughts on your Q's
1. The so-called 'transcription bubble' is required as the DNA strands must be separated to allow for synthesis of the RNA from the nucleoside triphosphates that have been exposed. The 'bubble' relates to the unwound DNA as well as the associated RNA pol complex. With regards to your question about outside access, the bound RNA/DNA duplex is 8-9 nts and each pair rotates about 36 degrees in relation to the next. Therefore the new duplex would have completed almost a complete turn, appearing both 'inside and otside'.

2. & 3. The RNA polymerase complex moves along the DNA, locates and binds to the promotor, causing RNA pol to unwind the strands for transcription etc. I imagine that the direction of movement of the RNA Pol complex, and then the particular promotor sequence to which it binds, would direct which strand is the template.

I'm not sure if I really answered your Q's. Can anyone elaborate?

[tuhin (OP)]

Hello genegenie,
I also think that transcription bubble needs to be formed because  probably it is the only  way by which nitrogenous bases of the template strand can be accessed ( because bases lie inside of the strand ?!) by the RNA polymerase to form the complimentary bases of the RNA. Since bases of the template strand lie inside , I presume, because of this the new RNA can not be formed accessing the template DNA strand from outside.
My second question was that if a particular segment of DNA was being transcribed , what lies on  exactly the opposite part of the template strand ,ie, on the non template strand ? Should it carry the allelic form of the gene that is being transcribed?
tuhin

[genegenie]

Hi tuhin
On the non-template strand would be the complementary sequence which, even if read 3' to 5', would read differently to the sequence on the template strand.

[tuhin (OP)]

Hello genegenie,
the allele of the gene should be present on the other homologue , but the non template strand carries also genes, is not it? So if a particular gene is being transcribed on a template strand , exactly on the opposite part ,ie  on the non template strand , that part should also carry some other gene which has no relation to the gene that is being transcribed ?!! Genes are present on both the strands !!
tuhin

[genegenie]

Hi tuhin
Considering that so much of a genome (certainly in eukaryotes)is non-transcribed DNA, I would imagine it unlikely that a gene would exist on the complementary strand. If this was the case, then a single base pair mutation would in effect, alter 2 genes, which would not be a good thing. But honestly, I'm not certain of this. Perhaps someone else knows...?

[Ians Daddy]

Hmmmm, another "love connection"? How far is India from Australia?

[genegenie]

And more to the point, what would my husband say!!!![]

[Ians Daddy]

Ooops! I just thought I'd play Cupid for a moment. Love to see compatibles mix. []

[genegenie]

That's OK Ians Daddy. But I'm not sure about compatibles....two genetics nerds together is a frightening thought, they'd probably try to clone each other.[]

[Ians Daddy]

Hahahaha! Guess that is frightening.

[janetkissho]

Great answers submitted by all of you thanks for helping.

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