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Can DNA be interpreted differently?

  1. Sep 3, 2006 #1

    Q_Goest

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    Is it possible to create a type of life form using DNA which doesn't match the DNA of that life form as we know it? For example, could we artificially create some type of DNA for a "cocker spanial" that didn't match a cocker spanial's DNA, but would produce a matching life form that looked and acted just like a cocker spanial? Alternatively, could the genes be interpreted differently such that the DNA of a cocker spanial produced a mushroom instead?

    Perhaps a less dramatic question might be, can a gene be interpreted in some different way than it presently is? A gene for example, that encodes the instructions to make cones in the eye might be interpreted as being the gene to make a kidney instead. Thus, by having different DNA entirely, the body's (ribosome's?) interpretation would be such that despite the different genes, the end result is a cocker spanial.

    The flip side of this is to suggest that genes or DNA constitute very specific and unique instructions for life which can not be interpreted differently.

    I can see some potential problems with this idea of multiple genetic interpretation. For example it may be the animal's digestive system could no longer digest the same foods because the enzymes used to digest food might no longer be the same. The properties of molecules are made up by the properties of the atoms, so those properties are fixed, but does that fact forbid nature from interpreting genes/DNA in more than one way?
     
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  3. Sep 3, 2006 #2
    Well, you and I have human DNA and hopefully look and act like humans but our two DNA profiles do not "match" perfectly--it is why you are you and I am I. Is this what you ask--why two individual cocker spanials are not identical to each other yet each is classified as a cocker spanial ?:confused: Now, as to relationship between cocker spanials and mushrooms, while it is true that they must share certain genes with respect to basic metabolism (such as Krebs Cycle), it would not be possible to just cut and paste the cocker spanial genes and then artificially make a mushroom out of them. Not sure this answers your questions.
     
  4. Sep 3, 2006 #3

    Q_Goest

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    Hi Rade:
    Sorry, that's not what I meant. Humans and chimps have about 99% of the same genes, and you and I have even more of the same ones. What I conclude from that is the human DNA is essentially identical, with minor variations which result in different eye color, skin color, etc. The question I have is much more hypothetical than that.

    I think of DNA as being a code which is interpreted by all living things in a consistant way. The gene for an eye cone cell for a monkey is the same as the gene in my DNA. We claim it's that way because we evolved from similar animals, and that's not incorrect. However, I wonder if a gene (say the one for the eye cone cell) is the only possible series of molecules that can produce the given feature. After all, the series of molecules we call a gene is just a section of DNA which must be interpreted in some way by the ribosome. If we had a different ribosome, it might interpret the eye cone color gene as the kidney gene and make a kidney cell instead. Same gene, different interpretation. For example, the word "boot" has two different meanings depending on what language you're speaking. In the US, we consider a boot as footwear, but in England they may consider a boot as the trunk of a car. Same word, different interpretation.

    If genes and DNA must be interpreted in order to create some biological feature, then I ask, can the genes be interpreted in some different way completely, and yet still create the same biological feature? If that's true, we can create the same type of animal out of any random series of genes, simply by modifying the ribosome which interprets them. We could even take the DNA of a mushroom and by changing how the genes are interpreted, we could create a cocker spanial, or a monkey out of it. Is that possible? If not, then genes can't be thought of as just codes. They aren't simply the information needed to create something. If a gene can only do one thing, and can't be interpreted as something else, then genes have fundamental properties akin to molecular properties. But then again, genes are molecules, so I wouldn't be surprised to find genes can only be interpreted in a single way. If genes can only be interpreted in one way, it's as if nature is saying a "boot" is only ever considered to be a type of footwear, and nothing else. A "boot" can't be the trunk of a car.
     
  5. Sep 3, 2006 #4

    DaveC426913

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    The encoding/decoding mechanism (the base pairs in the DNA and the RNA that "reads" them) and the building team (creation of enzymes and proteins) are highly interlinked and follow little pattern.

    A given gene (sequence of base pairs) could, with little effort or messing about, easily create a completely different set of enzymes and proteins, which would lead to a completely different thing being built. Of course, as usual, 99.9% of the time this has useless or lethal results, which would be seen as a cancer.

    As usal, the blueprints are arbitrary, and interpretation depends on your decoding scheme. Notepad will read a .gif file, but the results won't make a lot of sense.

    A gene could produce a set of proteins, but if the body is missing important trace nutrients, it will either not make them, or make flaws.
     
  6. Sep 3, 2006 #5
    To answer your first question above, each protein is made of amino acids and each amino acid has a "unique" triplet codon made of nucleotides (in DNA we have A,T,C,G, in RNA we replace T with U). Now, all amino acids (except Tryptophan) have more than one triplet mRNA codon--so for example, the mRNA codon for tyrosine amino acid could be UUA, UAU, AUU. So, as to your first question (if I read it correct), yes, a given feature (such as tyrosine) can have different gene codes that produce it. As to your second question, which I take to be "can any of the total possible 64 triplet codes form more than one amino acid"--the answer is no. So, from above example, UUA codon NEVER forms any amino acid except for tyrosine. Thus, the ribosome really has no role to "interpret" UUA any way other than UUA = tyrosine. So, think of tyrosine as being your "boot" that you refer to--it can come in different boot forms (UUA, UAU, AUU), but a boot (UUA) can NEVER be a coat, the coat has a different set of codons.
     
  7. Sep 4, 2006 #6

    Q_Goest

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    Hi DaveC,
    Sounds like you're suggesting the interpretation of a gene can be as variable as a computer program such that mushroom DNA can be reinterpreted as cocker spanial DNA. Is that right?

    Regarding errors in how genes are processed, let's ignore that for the sake of this thread.

    Hi Rade,
    I figured this discussion would quickly get in over my head. Are you suggesting that only the amino acids are fundamental in some way, and that genes are not?

    Could you expand on this? My understanding is mRNA is interpreted by the ribosome, but not sure what exactly it does with this information.

    Any good references would be appreciated.
     
  8. Sep 4, 2006 #7

    selfAdjoint

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    Living things like us are made of proteins, and other proteins (enzymes) mediate the chemical reactions that we call "life". This is oversimplified but is a major picture of what is going on.

    Now each protein is made of amino acids strung together in a chain; a particular sequence of amino acids. That sequence is unique to the particular protein; any other sequence would constitute some other protein. So if you know the sequence, you know the protein, although to acually build one you would have to solve the incredibly difficult folding problem. For the only other thing a protein has bbesides its amino acid sequence is its complicated pattern of folding up. Much research on this going on right now.

    How are the amino acid sequences constructed in the cell? Molecules of RNA contain the a chemical ID for each desired amino acid, in triplet code just like the DNA, but with a chemical difference in the triplets. Sequences of RNA place in a beaker withe amino acid solutions will assembled bits of protein - not complete proteins excpt in veryspecial cases. In the cell there are little bodies called Ribosomes, whre RNA assembeles the cell's proteins.

    And where does the RNA come from? It is what is produced from DNA! DNA makes messenger RNA molecules (mRNA) which go to the ribosomes and are copied to transfer RNA (tRNA) and the ribosome uses the tRNA as a template to add amino acids together to make a protein.

    Once again this explanation captures the big picture that covers most of what happens, but modern research has shown some exceptions and variantions on the patterns.
     
    Last edited: Sep 4, 2006
  9. Sep 4, 2006 #8
    No, the genetic DNA--->mRNA triplet codons are "fundamental"--they are [as explained in above post by selfAdjoint] the blueprint that the ribosome uses to form the protein.
    When I say that the ribosome does not "interpret" the genetic code, we have to ask what is meant by the word interpret. In order for the ribosome to interpret the mRNA code it would need to have the ability to modify it--it has no such ability. What the ribosome "does with the mRNA information" is make proteins, exactly as provided by the sequence of the triplet codons.
    See this for explanation of ribosome function and structure and relationship to mRNA:http://en.wikipedia.org/wiki/Ribosome
     
  10. Sep 5, 2006 #9

    Q_Goest

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    Thanks for the quicky tutorial, selfAdjoint and Rade. After some reading on this subject, it occurred to me that a gene might be better described as a protein with a start codon at one end and a stop codon at the other. Is that correct?

    From this and Rade's comments, I'm under the impression the ribosome simply copies that portion of the gene which represents the protein, so there is no 'interpretation'. The gene is just making copies of it's protein which is that part of the gene between the start and stop codon.

    Now I'm confused as to how the body makes new cells. I was under the impression we have a gene with the blueprint to manufacture "blue eyes" or "a kidney cell" or any other feature of the body. The genes must orchestrate this some how, as they alone have the "code" with which to create new cells during development. I take it that's not the job of the ribosome then?

    When a cell divides, what tells the new cell to become a nerve cell or a muscle cell? I guess that's where I wonder if there could be some 'interpretation' or deciphering going on by the cells - a process whereby genes instruct the new cell to become a specific type of cell.
     
  11. Sep 5, 2006 #10

    chroot

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    Many proteins can suffer a small code change without completely failing to function. Many common diseases like sickle-cell anemia are caused by a single protein failure. Such anomalies don't always kill the organism, but the misshapen proteins are often less efficient than the normal counterparts.

    Other proteins, like haemoglobin, have undergone many, many subtle evolutionary changes over time. The human haemoglobin is somewhat different from that of other creatures, but accomplishes basically the same task and is only marginally better.

    Keep in mind that most of our DNA is 'junk' which does not actually code any active proteins. You could shuffle around various pieces of active DNA without affecting the overall organism. On the other hand, some genes, like those with promoters, need to be laid down in a particular order.

    The vast majority of single-point mutations do not cause any malfunction in the organism, which is evidence that there are a very large number of distinctly different DNA strands, all of which would encode something we'd call 'human.'

    - Warren
     
  12. Sep 5, 2006 #11

    selfAdjoint

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    A traditional gene is not a protein. Once again, proteins are chains of chemically linked amino acids; A standard gene is made of up of four types of chemicals (bases) strung together on a sugar skeleton into the famous double helix. When I said some proteins that are inherited and affect the expression of normal genes might be called genes, I did not intend to subsume genes into proteins or proteins into genes.
     
  13. Sep 6, 2006 #12

    arildno

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    It should be remembered that some forms of RNA is a lot more active than just being "messengers".

    Furthermore, when a protein is configurated, protein chains with the same amino acid sequence may be configurated slightly differently (and, hence, somewhat different functioning).
     
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