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Thread: Junk DNA

  1. #1 Junk DNA 
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    Hi,

    I was just wondering what is junk DNA, and what is it worth?

    Thanks... :-D :-D


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  3. #2  
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    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.


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  4. #3  
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    is a stem cell the same having no fuction.
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  5. #4  
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    Quote Originally Posted by Robbie
    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]

    Quote Originally Posted by anand_kapadia
    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.
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  6. #5  
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    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
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    Quote Originally Posted by Chemboy
    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.
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  8. #7  
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    Quote Originally Posted by FaTaL_eRRoR
    Quote Originally Posted by Chemboy
    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
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  9. #8  
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    Quote Originally Posted by Chemboy
    Quote Originally Posted by FaTaL_eRRoR
    Quote Originally Posted by Chemboy
    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.
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  10. #9 Junk DNA and mariner elements 
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    Quote Originally Posted by FaTaL_eRRoR
    Quote Originally Posted by Robbie
    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
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    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.
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  12. #11  
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    Quote Originally Posted by Robbie
    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 :P , 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.
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  13. #12  
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    You're doing this in school! I'm in med school and I'm only doing this!
    That's worrying!!!
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  14. #13  
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    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, but I guess the question's been answered
    grtz.
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  15. #14  
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    Quote Originally Posted by FaTaL_eRRoR
    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.

    Quote Originally Posted by FaTaL_eRRoR
    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.

    Quote Originally Posted by FaTaL_eRRoR
    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.

    Quote Originally Posted by FaTaL_eRRoR
    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).

    Quote Originally Posted by FaTaL_eRRoR
    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.

    Quote Originally Posted by FaTaL_eRRoR
    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.

    Quote Originally Posted by Robbie
    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
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  16. #15  
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    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.
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  17. #16  
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    Kevin: interesting stuff alright, a lot sounds uite plausible however, some of it still involves the DNA being passive and not actually doing anything, eg protecting from potential mutation, the DNA still doesnt actually DO anything.
    ... but interesting stuff nonetheless

    Megabrain: dont unerstsnd the question, are you saying evolution should be resulting in more/less DNA?
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  18. #17  
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    Robbie: Thank you As far as I know, the cell features DNA repair mechanisms (in the form of enzymes) that try to remedy mutations in protein-coding genes, e.g. base pairs that have been removed or interchanged - this is an active process.

    As for the junk DNA - yes, it is generally passive in its protection, but that does not clash with the hypothesis that junk DNA actually has a purpose, even if it had been just rubbish in the first place, it proved to be of use to the organism and was kept, having assumed a function. Also, note that apparently, some areas of junk DNA do influence regulatory mechanisms, which they do actively, not passively.

    Megabrain: It is very obvious why evolution should dispose of rubbish: This rubbish is duplicated everytime a cell divides. This requires energy and resources. Using energy and resources for something that is superfluous is highly ineffective, and evolution generally tends to favour those who do not waste anything and are more effective than other organisms. Since cells are part of an organism which serves as their environment, though, and do not directly compete with, say, unicellular organisms, saving energy and resources by throwing out "genetic garbage" may not have been necessary for them from a competitive point of view. Still, evolution generally tends to have organisms dispose of obsolete aspects in order to be more competitive, and therefore it is even more likely that "junk" DNA is not junk after all.
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