DNA Random Access: Can Cells Access Any Gene?

[cam875]

this is similar to how a computer processor can access any part of memory at any time. I was just wondering if things in cells can access any gene at any time sort of like, ok we need this protein let's jump to this gene and begin reading it off or is it all sequentially all the time.

 

[JonMoulton]

Initiation of transcription from genes is in parallel. The bases in each gene sequence are read out sequentially, but many genes are being transcribed at the same time. Whether transcription is starting at a gene or not is determined by which proteins are stuck to the DNA in the promoter/operator regions. Regions of DNA can be activated or inactivated by the state of the histone spools around which the DNA can be wound.

However, the analogy with random access in a computer has a problem: single-processor computers access only one memory location per clock cycle, while genes are not "clocked" but can transcribe simultaneously (let's not quibble about relativistic effects here, you know what I mean).

 

[cam875]

but what i am trying to ask is that if the cell needs to get gene 1000 does it have to go through 1-999 first even if they are parallel that is wasted time and energy is it not?

 

[JonMoulton]

To begin transcription of gene 100, the cell does not need to first transcribe genes 1-99. The required proteins just bind to the promoter/operator region of gene 100 and transcription starts there (while other genes are also being transcribed).

 

[cam875]

but other genese are still being transcribed and they are not needed to is my point if it was a computer, and therefore it would be wasted energy right?

 

[Ygggdrasil]

Each gene can be transcribed basically independently of other unrelated genes.

 

[JonMoulton]

At a given time, perhaps genes 23, 42 43 61 and 100 are being transcribed. Only those genes are being transcribed which have the appropriate complement of proteins interacting with their unique promoter-operator regions. Thanks to the optimization due to natural selection, it will generally be just those genes needed for fitness that are being transcribed. Thus energy is not being wasted in the manner that you propose.

 

[Q_Goest]

Hi JonMoulton,
Interesting discussion. I wonder if there is a surplus of protiens being created by the nucleus or if transcription is regulated. And if regulated, can you describe in a nutshell how that happens?

 

[JonMoulton]

Some proteins are produced constitutively, that is, without regulation. Others have feedback from sensor proteins, sometimes through multiple-step signaling pathways, that control the configuration of the regulatory proteins bound to the gene's promoter/operator region. A classic case study is the lac operon. Look in the index of any senior-level biochem book or microbiology book for a description of that operon, which involves feedback regulation.

A new area of study in biology is the microRNA system, which regulates gene expression (that is, regulates manufacture of protein) by suppressing translation of mRNA. Briefly, a short strand of RNA (itself regulated at the transcriptional level) is bound to a protein complex, binds to partially-complementary regions in the 3'-untranslated region of mRNAs (usually, though targets in other locations have been found) and suppresses the formation of an active initiation complex (formation of this complex is the first step in the translation of a protein from an RNA template).

That's about all I can cram into a nutshell. There are chapters on gene regulation in molecular biology texts. I've not touched on related topics like alternative splicing, attenuation, ribozymes, natural antisense transcripts, bending of DNA by proteins like the E.coli integration host factor (IHF) to bring distant regions of DNA into proximity and allow DNA-bound proteins to interact, histone protein modifications that change the tightness of DNA winding on histone spools ... this could go on and on. At least this list can provide a few keywords/phrases to lead you into the subject.

 

[Q_Goest]

Thanks Jon!