Genome Length

Michael Coyne mcoyne at argo.net
Sat Oct 21 10:56:33 EST 1995

Agschultz wrote:
> On October 6, 1995, Mary Kuhner writes,
> > In many organisms another substantial portion of the junk (DNA) consists
> of
> > thousands of copies of sequences which have the ability to duplicate
> > themselves.  These may or may not be useful in some way to the organism;
> > they could survive even if they are not useful, as a sort of genetic
> > parasite, because of that copying ability.

Okay, now I'm confused.  By what critera is DNA classified as "junk"?  I would 
have assumed that junk DNA would imply DNA which, when examined at the sequence 
level, shows no evidence of a function.  Even this is not enough of a 
definition, since many (most?) eucaryotic genes have exons, which are "useless" 
bits of DNA (in as much as they don't code for anything) but still perform a 
vital function as "spacers", if you will.  DNA which has the ability to 
duplicate itself (presumably unlinked to the replication of the chromosome) 
must therefore have some genes and therefore is not junk.  How does this DNA 
duplicate itself (most DNA codes for proteins, which in turn do the work)?  If 
these pieces of DNA excise themselves and form replicons which then 
re-integrate into the chromosome, they are behaving much like plasmids or 
viruses, and therefore probably were introduced to the genome by outside 
acquision.  These pieces of DNA could be integrated viruses or plasmids, and 
could serve as a source of plasticity to the genome by adding a mechanism of 
introducing mutations.

> Secondly, some speculation on the subject by the experts may prove helpful
> in my understanding of genetics. For example, what purpose might they
> serve?
> What triggers them to duplicate?
> Do they encode RNA compliments?
> Do they have start and stop condons? If so, how are they regulated?

If these pieces of DNA had start and stop codons, they would be genes, and 
would code for an mRNA (codons are elements of mRNA, not of DNA).

> Also, from the above description, it is not clear if they are encoded
> within the genome or are they just segments of DNA?
> Thanks in advance for your replys.
> Allen.
> Allen Schultz

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