DNA - mutation - 'silent’ gene

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DNA - mutation - 'silent’ gene

Postby tess on December 15th, 2007, 3:32 pm 

Genes can be lost in many ways. This study focused on losses caused by mutations that disrupt the open reading frame (ORF-disrupting mutations). These are either point mutations, where events such as the insertion or substitution of a DNA base alter the instructions delivered by the DNA, or changes that occur when a large portion of a gene is deleted altogether or moves to a new place on the genome.

Could somebody explain to me in the simple words what does it mean?

Moves to a new place on the genome.

Does it mean it becomes a ‘silent’ gene If not , does it still have power to interact and as such - send instructions?

And one more question:

Even if we don’t know function of ‘silent’ genes’ – they have to be there for the reason or are they just a rubbish which evolution would clean?
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Postby BioWizard on December 15th, 2007, 3:50 pm 

All genes have some basic features which allow them to produce protein. Forgetting about introns and exons for now, all genes must have an initiation codon (which allows translation of the mRNA by the ribosome to be initiated), body codons (which translate to the corresponding amino acids), and a termination codon, which as the name indicates, terminates translation.

So after the genes gets transcribed, it will produce an mRNA that has the basic structure:

initiation codon - body codon - termination codon

The nucleotide sequence from the initiation codon (which translates to methionine) to the last codon before the termination codon is referred to as the open reading frame or ORF. This means that this is the part of the nucleotide sequence that is open for translation into protein by the ribosomes.

So if a mutation occurs somewhere at the beginning of the gene and causes one of the reading codons to become a termination codon, you will have termination much earlier in the open reading frame, and instead of producing the whole protein, you will produce only a short part of it towards the beginning. This is what is meant by "disruption of the ORF".

Another way of disrupting genes is DNA translocations which cause part of the gene to be chopped off its proper location and moved somewhere else on the genome. This means that the gene will have lost part of it's ORF, and from the location it was cut onwards, it will now code for something else, or maybe nothing. The most interesting case I know is of a gene that got chopped in two, and each half got located to a different part of the chromsome, but the two halves are still able to come together and form a single functional enzyme after they are expressed from the two separate half-genes. It's too complicated to explain here though. Most genes that get parts of them translocated aren't so lucky though.

Finally, silent genes can arise in a number of ways, but all boil down to the fact that the gene is no longer undergoing selection for it's role. See genes mutate all the time, but the reason why they are preserved is that mutants that disrupt it's function get selected out. If there were no selection, no DNA sequences would be preserved. It is the continuous selection of the functional sequences that keeps genes evolving towards their function. Now say you have a gene that undergoes a duplication event. You will have two functional genes within the cell, but the cell only needs one. So if one of the two gets a mutation that disrupts it's activity, it will not be selected out, because it still has a functional copy. The mutated gene will now continue to mutate further, because it is no longer undergoing selection (the selection will now be restricted to the copy that is still functional at that point). As time goes by, the gene will stop being expressed, because it's not serving any important role anyway, and in fact it's using up expression resources which can be better used for genes that do serve a role. The gene is then said to have gone silent, and will continue to mutate into a "gene fossil". As enough time passes, it's sequence will change to the point where you can no longer recognize that it was a gene at all.

I hope that helps.
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Postby Removed user on December 15th, 2007, 3:55 pm 

Hmm, simple… Well, perhaps:

The cell has various biochemical repair mechanisms, if it did not life would have long ago ceased to exist (i.e., no maintenance men). These repair mechanisms are not 100% efficient, which is a good thing as if they were life would have long ago ceased to exist (i.e., no evolution). One of these repair mechanisms (perhaps as much accidental as purposeful) is to sequester the “broken” DNA where it can do little harm (i.e., “go play in your room, be quiet, and stop bothering me”).
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Postby tess on December 16th, 2007, 3:20 pm 

Thank you very much.
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