Wobble - doesn't make sense

Discussion in 'Health and medical' started by Tomhendricks474, Feb 19, 2004.

  1. Something doesn't ring true here -

    "(Crick's) proposal, termed the wobble hypothesis suggested that whereas the steric requirement
    between the anticodon of the tRNA and the codon of the mRNA may be very strict for the first two
    positions, it may be more flexible at the third... allowing two codons that specify the same amino
    acid and differ only at the third position to use the same tRNA in protein synthesis."

    True as far as it goes but why is it so?

    "(Gamov) reasoned that it would require at least 3 nucleotides for each amino acid to have its own
    unique codon... Since there are 20 different amino acids that have to be specified, codons must
    contain at least 3 successive nucleotides."

    But that is backward reasoning. It seems to accept the fact that life demanded 20 aa's and 19 or 21
    would not do. To me that is ridiculous reasoning. It's reasoning that fills in the facts to fit the
    future goal - or what we think is the future goal. But codons were NOT building for the future.

    Wobble only seems to make sense if you turn the argument around. I suggest this: Imagine a strand of
    unpaired RNA bases sticking out from some paired bases. Its these 'naked' bases that would most
    likely bond with other molecules. Example : note number = the most important positions of codon on
    each end of a folded molecule

    3 - 1 - 2- folded molecule - 2-1-3

    a. I suggest there had to be at least 3 positions to have a center one. The center one was protected
    by being in the center with at least a base on either side and at least it is sticking 2 bases
    outside of the fold so it is accesible. Thus the center one should be the most important in
    coding = #1

    b. To expand coding another positons was included. It was the position nearest the folded molecule.
    Or rather I would call it the 2nd most protected and at the same time the most easily accessible
    base position = #2

    c. More coding is needed and in this case all that is necessary in the #3 position - or the out on a
    limb position - is fit of the 3rd position base. Thus it is in almost every case either an A/G
    purine OR a C/U pyrimidine

    Also base stacking plays an important part with it favoring middle for most stability then the other
    two in the same order as above.

    The wobble IMO is not to fit someone's preconceived notion of how many aa's we need. It is there as
    the last step in expanding an h-bonding code of 3 positions - at the least protected and most
    vulnerable spot. And that vulnerability of being the position way out on a limb, and the fact that
    it is not needed to code other than as a purine or pyrimidine, and it's lesser base stacking; is why
    it wobbles

    Now look at a tRNA and you see these 2 naked ends clear as day. The acceptor stem from the molecule
    out is molecule - discriminator base 73 - C - C - A to adapt to aa

    The anti codon from the 3' - 5' end molecule - purine base 37 - [anticodon 36 - 35 - wobble} then
    imagine a cut to make this end a single strand instead of a loop.

    Both ends are evolved versions of the same thing

    Comment?
     
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  2. << . I suggest there had to be at least 3 positions to have a center one. The center one was
    protected by being in the center with at least a base on either side and at least it is sticking 2
    bases outside of the fold so it is accesible. >>

    Perhaps too the center one would hold with h-bonds under certain conditions, if it was protected on
    both sides with other bases, and had base stacking etc. Perhaps the key number of 3 base pairs has
    to do with what was necessary to have this h- bond with any other molecule

    If this is so then it suggests the first connection between RNA and Amino acids. If they could
    bond together they would be less likely to be denatured in the high heat of this early period on
    hot Earth.
     
  3. Larry Moran

    Larry Moran Guest

    On Sat, 21 Feb 2004 06:31:00 +0000 (UTC),
    TomHendricks474 <[email protected]> wrote:

    >Someone else wrote:
    >> I suggest there had to be at least 3 positions to have a center one. The center one was protected
    >> by being in the center with at least a base on either side and at least it is sticking 2 bases
    >> outside of the fold so it is accesible. >>
    >
    > Perhaps too the center one would hold with h-bonds under certain conditions, if it was protected
    > on both sides with other bases, and had base stacking etc.

    The interaction between two trinucleotides (3 "bases") is governed almost entirely by stacking
    interactions. The hydrogen bonds play an insignificant role in the overall stability of the double-
    stranded molecule. The hydrogen bonds are necessary for complementarity but that's a different
    matter altogether.

    You need to have three nucleotides in order to have stacking interactions.

    > Perhaps the key number of 3 base pairs has to do with what was necessary to have this h- bond with
    > any other molecule

    No, you need three nucleotides in order to get stacking interactions that make the formation of double-
    stranded molecules thermodynamically favorable.

    > If this is so then it suggests the first connection between RNA and Amino acids. If they could
    > bond together they would be less likely to be denatured in the high heat of this early period on
    > hot Earth.

    The melting point of a double-stranded trinucleotide is probably less than room temperature.

    Larry Moran
     
  4. Irr

    Irr Guest

    > "(Gamov) reasoned that it would require at least 3 nucleotides for each
    amino
    > acid to have its own unique codon... Since there are 20 different amino acids that have to be
    > specified, codons must contain at least 3 successive nucleotides."
    >
    > But that is backward reasoning. It seems to accept the fact that life demanded 20 aa's and 19
    > or 21 would not do. To me that is ridiculous reasoning. It's reasoning that fills in the facts
    > to fit the
    future
    > goal - or what we think is the future goal. But codons were NOT building
    for
    > the future.

    The ideas of Gamow, Crick, and others were not concerned about evolution, but rather how DNA->RNA-
    >protein coding took place. They were arguing based on known data, namely the 4 base composition of
    DNA and the known 20 amino acids that biochemistry was built on. No teleology required.
     
  5. << The ideas of Gamow, Crick, and others were not concerned about evolution, but rather how DNA->RNA-
    >protein coding took place. They were arguing based on known data, namely the 4 base composition of
    DNA and the known 20 amino acids that biochemistry was built on. No teleology required. >>

    Agreed. But in talking about the origin, we've got to look at wobble in a new way and re-examine it
    -not as a means to getting to an end, but as a way that some chemical variants were able to survive
    that day's heat cycle, while others could not.
     
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