T
Tomhendricks474
Guest
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?
"(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?