| |
| Junk DNA |
« View previous topic :: View next topic » |
| Author |
Message
|
| weknowtheword |
 Posted: Fri Feb 23, 2007 10:23 pm Post subject: Junk DNA |
 |
|
Forum Sophomore
Joined: 10 Dec 2006
Posts: 168
|
|
| Back to top |
|
 |
| Robbie |
| Posted: Sat Feb 24, 2007 7:48 am Post subject: |
|
|
Moderator
Joined: 08 Aug 2006
Posts: 828
Location: Dublin, Ireland
|
| Junk DNA is DNA which doesnt code for anything. A huge amount of our DNA is simply "spare DNA". It's worth nothing as far as we know since it has no use. |
|
| Back to top |
|
|
| anand_kapadia |
| Posted: Sat Feb 24, 2007 8:27 am Post subject: |
|
|
Forum Senior
Joined: 16 May 2006
Posts: 312
Location: India
|
| is a stem cell the same having no fuction. |
|
| Back to top |
|
|
| FaTaL_eRRoR |
| Posted: Sat Feb 24, 2007 8:35 am Post subject: |
|
|
Forum Freshman
Joined: 24 Feb 2007
Posts: 21
Location: The Netherlands
|
| Robbie wrote: |
| Junk DNA is DNA which doesnt code for anything. A huge amount of our DNA is simply "spare DNA". It's worth nothing as far as we know since it has no use. |
That's not entirely true...
I'll try to explain, but I'm no expert on this(yet).
The "Junk" DNA indeed does not code for any proteins or anything else, as far as we know.
But it has other uses...
As you might know, the human genome is limited, and, compared to some other organisms, relatively small..
The weird thing is, we only have 30,00 genes, however we produce about 90,000 proteins. Only 1 percent of our DNA actually codes for proteins..
However, we make up for it by having that "Junk DNA".
This Junk DNA has probably had a great effect on our evolution, and these parts of DNA are also called alu sequences.
How this works is pretty difficult to explain, but when DNA is transcribed into RNA(which eventually is "turned" into substances(proteins) which may be needed in our body), this DNA is essentially "copied", in this process, sequences from our genes are cut and pasted from different parts of our DNA.
These alu elements can "move around" in your DNA(through alternative splicing), which causes us to create different proteins from the same part of "useful" DNA, while the old DNA is saved as well. Also, alu sequences can "create" new points from which you will start transcribing DNA into RNA, which makes for even more combinations.
It comes down to the fact, that without this junk DNA, our race wouldn't even exist, and because we have it we can use much less DNA for much more proteins:)
ps. every detail may not be exactly right, plz correct me if i'm wrong...only learned this in school 2 weeks ago 
[EDIT]
| anand_kapadia wrote: |
| is a stem cell the same having no fuction. |
hehe, stem cells are a whole other story, and i know alot less about those..
I do, however know that they do have a very important funtion in our body.
Stem cells can be used(or rather modified) to create a variety(alot) of new cells(don't know exactly which cells, but most of em) in our body, that wouldn't regenerate without them...
_________________
grtz.
-FaTaL_eRRoR |
|
| Back to top |
|
|
| AlexP |
| Posted: Sat Feb 24, 2007 9:17 am Post subject: |
|
|
Moderator
Joined: 01 Jul 2006
Posts: 1698
Location: NY
|
i would think that mutations in junk DNA wouldn't really affect us, so the more junk DNA there is, the less the chance of getting a mutation in DNA that matters more. seems like that'd be right. of course i'm not saying that's why we have junk DNA, but it's a benefit of it.
FaTaL_eRRoR, i think you did a good job explaining that, i just learned about that too...
_________________
"There is a kind of lazy pleasure in useless and out-of-the-way erudition." -Jorge Luis Borges |
|
| Back to top |
|
|
| FaTaL_eRRoR |
| Posted: Sat Feb 24, 2007 9:21 am Post subject: |
|
|
Forum Freshman
Joined: 24 Feb 2007
Posts: 21
Location: The Netherlands
|
| Chemboy wrote: |
| i would think that mutations in junk DNA wouldn't really affect us, so the more junk DNA there is, the less the chance of getting a mutation in DNA that matters more. seems like that'd be right. of course i'm not saying that's why we have junk DNA, but it's a benefit of it. |
i guess, however a mutation in the junk dna could actually un-junk it(make it code for an amino-acid)...small chance, but it's probably possible, and pretty bad as well.
however, keep in mind not every mutation has to be bad, mutations can also change things for the better...
_________________
grtz.
-FaTaL_eRRoR |
|
| Back to top |
|
|
| AlexP |
| Posted: Sat Feb 24, 2007 9:31 am Post subject: |
|
|
Moderator
Joined: 01 Jul 2006
Posts: 1698
Location: NY
|
| FaTaL_eRRoR wrote: |
| Chemboy wrote: |
| i would think that mutations in junk DNA wouldn't really affect us, so the more junk DNA there is, the less the chance of getting a mutation in DNA that matters more. seems like that'd be right. of course i'm not saying that's why we have junk DNA, but it's a benefit of it. |
i guess, however a mutation in the junk dna could actually un-junk it(make it code for an amino-acid)...small chance, but it's probably possible, and pretty bad as well.
however, keep in mind not every mutation has to be bad, mutations can also change things for the better... |
yeah, i wasn't thinking of that. but if a segment of junk DNA wasn't normally transcribed, would it be after it was mutated to form an amino acid-coding codon?
_________________
"There is a kind of lazy pleasure in useless and out-of-the-way erudition." -Jorge Luis Borges |
|
| Back to top |
|
|
| FaTaL_eRRoR |
| Posted: Sat Feb 24, 2007 9:51 am Post subject: |
|
|
Forum Freshman
Joined: 24 Feb 2007
Posts: 21
Location: The Netherlands
|
| Chemboy wrote: |
| FaTaL_eRRoR wrote: |
| Chemboy wrote: |
| i would think that mutations in junk DNA wouldn't really affect us, so the more junk DNA there is, the less the chance of getting a mutation in DNA that matters more. seems like that'd be right. of course i'm not saying that's why we have junk DNA, but it's a benefit of it. |
i guess, however a mutation in the junk dna could actually un-junk it(make it code for an amino-acid)...small chance, but it's probably possible, and pretty bad as well.
however, keep in mind not every mutation has to be bad, mutations can also change things for the better... |
yeah, i wasn't thinking of that. but if a segment of junk DNA wasn't normally transcribed, would it be after it was mutated to form an amino acid-coding codon? |
not sure what you mean here...junk DNA isn't transcribed at all, it's removed from the DNA, and does not appear in the RNA in any form after transcription
if the junk DNA was mutated, it wouldn't be junk DNA anymore, and would either code for a protein when transcribe, or do nothing..
_________________
grtz.
-FaTaL_eRRoR |
|
| Back to top |
|
|
| Crabby |
| Posted: Sat Feb 24, 2007 12:49 pm Post subject: Junk DNA and mariner elements |
|
|
Forum Freshman
Joined: 04 Jan 2007
Posts: 24
Location: Puget Sound
|
| FaTaL_eRRoR wrote: |
| Robbie wrote: |
| Junk DNA is DNA which doesnt code for anything. A huge amount of our DNA is simply "spare DNA". It's worth nothing as far as we know since it has no use. |
The "Junk" DNA indeed does not code for any proteins or anything else, as far as we know...This Junk DNA has probably had a great effect on our evolution, and these parts of DNA are also called alu sequences. |
If I am not mistaken, some of this Junk DNA may be endosymbiotic or even parasitic to the extant human genome. We are known to carry around and pass on to our children all sorts of sequences that go unexpressed in our phenotypes. Tsetse fly genes (mariner elements), for example, have found their way into the human genome (but nobody yet has taken on those symptoms portrayed by Jeff Goldlum in the movie The Fly).
—Crabby |
|
| Back to top |
|
|
| Robbie |
| Posted: Sat Feb 24, 2007 1:18 pm Post subject: |
|
|
Moderator
Joined: 08 Aug 2006
Posts: 828
Location: Dublin, Ireland
|
Yeah, well its' thought that viruses have a role to play in the evolution of junk DNA (or indedd just evolution) as they are known to cause DNA exchanges when they interact with DNA during their replication.
fatal error; what you are saying about alternative spligcing is sort of right.
that's bascially where different parts of the transcribed RNA are removed. Some "exons" are removed as well as the introns and depending on the exons retained, different proteins are formed.
I dont think that exons which are not used in the coding for a certain protein count as junk DNA but this is where the idea of junk DNA gets a bt clouded.
There is still junk DNA which is not used under any circumstance and which is never transcribed into mRNA. |
|
| Back to top |
|
|
| FaTaL_eRRoR |
| Posted: Sat Feb 24, 2007 1:42 pm Post subject: |
|
|
Forum Freshman
Joined: 24 Feb 2007
Posts: 21
Location: The Netherlands
|
| Robbie wrote: |
Yeah, well its' thought that viruses have a role to play in the evolution of junk DNA (or indedd just evolution) as they are known to cause DNA exchanges when they interact with DNA during their replication.
fatal error; what you are saying about alternative spligcing is sort of right.
that's bascially where different parts of the transcribed RNA are removed. Some "exons" are removed as well as the introns and depending on the exons retained, different proteins are formed.
I dont think that exons which are not used in the coding for a certain protein count as junk DNA but this is where the idea of junk DNA gets a bt clouded.
There is still junk DNA which is not used under any circumstance and which is never transcribed into mRNA. |
right, I forgot the part about introns and exons  , thx for reminding me, will help me with my exams 
guess i should look my textbook over once more instead of trying to learn everything from 1 lesson
_________________
grtz.
-FaTaL_eRRoR |
|
| Back to top |
|
|
| Robbie |
| Posted: Sat Feb 24, 2007 1:48 pm Post subject: |
|
|
Moderator
Joined: 08 Aug 2006
Posts: 828
Location: Dublin, Ireland
|
You're doing this in school! I'm in med school and I'm only doing this!
That's worrying!!! |
|
| Back to top |
|
|
| FaTaL_eRRoR |
| Posted: Sat Feb 24, 2007 2:09 pm Post subject: |
|
|
Forum Freshman
Joined: 24 Feb 2007
Posts: 21
Location: The Netherlands
|
well, it's not like i'm in high school or anything, don't know where you're from, but here in holland we call it HBO, i'm in the first year after high school, hoping to get my bachelor in 3 years and master in 5
completely off-topic now:p, but I guess the question's been answered
_________________
grtz.
-FaTaL_eRRoR |
|
| Back to top |
|
|
| Kevin |
| Posted: Mon Mar 05, 2007 5:23 am Post subject: |
|
|
New Member
Joined: 02 Feb 2007
Posts: 2
|
| FaTaL_eRRoR wrote: |
| The "Junk" DNA indeed does not code for any proteins or anything else, as far as we know. |
Not exactly - certain studies suggest that certain intergenic areas are responsible for regulatory mechanisms (such as gene expression) and that they even code for proteins in the case of pseudogenes (about which I will say a bit more below) - it may be, however, that the proteins they encode are of no use to their host genome.
| FaTaL_eRRoR wrote: |
| The weird thing is, we only have 30,00 genes, however we produce about 90,000 proteins. Only 1 percent of our DNA actually codes for proteins.. |
We have about 21,000 functional genes and nearly an equal amount of non-functional pseudogenes.
| FaTaL_eRRoR wrote: |
| This Junk DNA has probably had a great effect on our evolution, and these parts of DNA are also called alu sequences. |
Alu sequences constitute about 10 % of the entire "junk DNA", but not more. Other retrotransposons make up about another 25 %. I'll state what else this junk DNA presumably contains a bit further on.
| FaTaL_eRRoR wrote: |
| How this works is pretty difficult to explain, but when DNA is transcribed into RNA(which eventually is "turned" into substances(proteins) which may be needed in our body), this DNA is essentially "copied", in this process, sequences from our genes are cut and pasted from different parts of our DNA. |
I take it that you are attempting to explain how Alu sequences are inserted into the genome and you're sort of tying yourself up in knots Alu sequences are retrotransposons which are able to transcribe themselves into RNA, avail themselves of an enzyme called Alu endonuclease to open the DNA double helix between G and C which allows the transcript to insert itself via reverse transcription, thereby compromising the DNA sequence. This is copy and paste, but not cut and paste (which is an important difference as transposons use the latter, while retrortansposons always use the former mechanism).
| FaTaL_eRRoR wrote: |
| These alu elements can "move around" in your DNA(through alternative splicing), which causes us to create different proteins from the same part of "useful" DNA, while the old DNA is saved as well. Also, alu sequences can "create" new points from which you will start transcribing DNA into RNA, which makes for even more combinations. |
The Alu sequences, being retrotransposons, don't move per se once they have been inserted into the genome (as opposed to transposons), but an Alu sequence may transcribe itself once again, target another DNA sequence and then that transcript inserts itself via reverse transcription (as I explained above) and with the ramifications you outlined, but the original sequence from which the transcript was made remains where it was.
| FaTaL_eRRoR wrote: |
| It comes down to the fact, that without this junk DNA, our race wouldn't even exist, and because we have it we can use much less DNA for much more proteins:) |
Well at the very least the amount of junk DNA prevents genomic viruses and other (retro)transposons/mutations from specifically targeting protein-coding gene sequences when there is enough intergenic material where they can work on and insert themselves - therefore, the probability of the insertion of Alu sequences (or comparable sequences stemming from other sources) into protein-coding genetic material is much less than it would be without junk DNA.
| Robbie wrote: |
| Junk DNA is DNA which doesnt code for anything. A huge amount of our DNA is simply "spare DNA". It's worth nothing as far as we know since it has no use. |
Actually these are much deeper waters, and there are a lot of hypotheses with regard to the actual purpose of “junk DNA”.
Apart from having the obvious advantage of “warding off” mutations, “junk DNA” contains "pseudogenes", which are incapacitated genes that have been disabled in the course of our evolution. Pseudogenes are generated in three distinct ways which I won’t expound here in-depth (unless you ask nicely ), suffice it to say that they stem from (1) duplicates of genes made prior to cell division which are spread across the genome, (2) from genes that became obsolete and are no longer maintained by gene repair mechanisms and (3) from mRNA that is scooped up my genomic viruses that insert themselves into DNA via retrotransposition. These pseudo-genes have all lost their former function and do not code for the proteins the genes encode from which they originated since they have been modified by mutations which are allowed to occur unchecked by gene repair mechanisms. These pseudogenes may have at least three distinct uses:
1. It is believed that some of the pseudogenes, actually *do* perform a specific task, e.g. they carry out a process that regulates the manner in which the transcript (mRNA) of the gene from which the pseudogene originated is translated.
2. Pseudogenes - which are non-functional genes - may spring to life again (i.e. if they were dead, which is the case when they do not code for anything, neither their original protein nor a modified one) on account of a mutation and actually code for novel proteins which may or may not be useful - this process contributes to genetic evolution.
3. Pseudogenes, which are either disabled duplicates of still existing genes or of earlier versions of these genes or are genes that became defunct when they ceased to be of importance provide a record of how our genome has evolved and give us an insight into how this evolution works, what circumstances are required, etc. Well, strictly speaking this is not of use to the organism per se, but to us scientists it is exceedingly so
As for the remainder of junk DNA which does not contain pseudogenes, there are various surmises as to its end:
- It protects protein-coding genes by making mutations less probable (s.a.)
- It is important for genetic evolution; it constitutes a breeding ground for mutations which may turn out to be of use and thus contribute to genetic diversity / underlie genetic evolution (s.a.)
- It may perform regulatory mechanisms and thus govern gene expression, cellular behaviour etc.
- It may simply ensure that genes are spaced apart far enough from each other so that transcription enzymes may set to work without interfering with each other
- It may contain genes that have been "deactivated" because they are no longer of use but are kept to be re-activated if need be (e.g. if the environment changes and the organism needs to re-adapt to earlier conditions ...)
These are all just conjectures, though, but certain studies have indicated that they may not be far off the truth.
Still, it might also be that junk DNA is only allowed to exist because new stuff is constantly being added to the DNA (e.g. Alu sequences, transposons) in so rapid a fashion that it is impossible for DNA repair mechanisms to eliminate it instantly, though I deem that even though this may have been the cause for much of the junk DNA to come into being in the first place, junk DNA has since been employed by organisms and assumed several invaluable functions, which is often the case in evolution: If an inconvenience/nuisance can't be rectified, it may be turned into an advantage instead |
|
| Back to top |
|
|
| Guest |
| Posted: Mon Mar 05, 2007 7:20 am Post subject: |
|
|
|
| Can anybody tell me why evolution should remove 'junk DNA' or any other part? - I can see no reason for a mechanism to evolve to serve such a purpose. 'Housecleaning' is a human term only. |
|
| Back to top |
|
|
|
|
|
  |
Goto page 1, 2 Next |
Page 1 of 2 |
|
You cannot post new topics in this forum
You cannot reply to topics in this forum
You cannot edit your posts in this forum
You cannot delete your posts in this forum
You cannot vote in polls in this forum
|
|
|
|
