Dear Theresa,
a nicely written explanation from Wikipedia :
The Central dogma of molecular
biologyhttp://en.wikipedia.org/wiki/Central_dogma_of_molecular_biology
describes the process of
translationhttp://en.wikipedia.org/wiki/Translation_(biology) of a
Hi Theresa,
To add to Anat's comments: Although the AUG codon for the first methionine and
all other methionines in a protein coding sequence look the same, they are read
in a very different way by the ribosomal machinery. The first AUG is recognized
by the initiation complex, which includes
Opher Gileadi wrote:
Hi Theresa,
To add to Anat's comments: Although the AUG codon for the first methionine and
all other methionines in a protein coding sequence look the same, they are read
in a very different way by the ribosomal machinery. The first AUG is recognized
by the initiation
Never one to shrink from philosophizing, I wonder generally why the codon
conventions are the way they are? Is it like the QWERTY keyboard--basically
an historical accident--or is there some more beautiful reason? One might
argue that since basically all organisms share the convention (are there
Just search for genetic code evolution in pubmed and you will find tons of
literature on it. The main driving force appears to have been to minimize
physico-chemical changes in amino acid properties for frequent mutations.
In other words, if you take mutation rates at the single-nucleotide level
On 03/19/13 10:34, Jacob Keller wrote:
Never one to shrink from philosophizing, I wonder generally why the
codon conventions are the way they are? Is it like the QWERTY
keyboard--basically an historical accident-
QWERTY didn't just happen. It was designed. Don't kids today know how
to use
I never said QWERTY just happened-- I said it was an accident of
history, based on the belief that some people nowadays have stopped using
manual typewriters, and they nevertheless still use the QWERTY keyboard.
I.e., because of the way history unfolded, we are now locked into using a
non-ideal
On Tue, Mar 19, 2013 at 9:34 AM, Jacob Keller
j-kell...@fsm.northwestern.edu wrote:
One might argue that since basically all organisms share the convention
(are there exceptions, even?), that it must be the best of all possible
conventions.
There are actually lots of exceptions. For example
I believe that the reason all organisms share the convention (more or
less) is that it dates back to LUCA - the Last Universal Common Ancestor of
all extant life. LUCA must have had the basic transcription and translation
machinery that we now see somewhat divergently-evolved versions of in all
I don't understand this argument, as it would apply equally to all features
of the theoretical LUCA (protein and DNA sequences, etc). To make it
logically sound, I think you have either to include some kind of super-high
boundary to getting to other possible conventions (you probably imply this)
why doesn't initiation occur also at methionines in the middle of proteins?
It can and does. I can show you expression gels where I make full-length
protein and a fragment from an internal initiation.
Why use a big expensive amino acid instead of choosing one of the glycine
codons?
I
On 03/19/2013 02:41 PM, Jacob Keller wrote:
I don't understand this argument, as it would apply equally to all
features of the theoretical LUCA
No it won't. Different features would have different tolerance levels
to modifications.
Philosophically, one is wrong to expect that living
I don't understand this argument, as it would apply equally to all features
of the theoretical LUCA
No it won't. Different features would have different tolerance levels to
modifications.
Yes, this tolerance is the second (hidden or implicit) principle I
referred to. So you'd have to explain
It is so intolerant to change because reassigning a codon to a different
amino acid type or stop codon affects thousands of proteins that use that
codon simultaneously. The probably that none of those mutations are
deleterious is extremely small.
Genetic code changes are more common in the
Why use a big expensive amino acid instead of choosing one of the glycine
codons?
I can't quickly track anything down in the literature to back this up, but
expensive could be part of it. The cell
doesn't want to start translation if there isn't ample resources to finish
the job.
You may want to read:
Evolutionary conservation of codon optimality reveals hidden signatures of
cotranslational folding
Nature structural molecular biology VOLUME 20 NUMBER 2 FEBRUARY 2013 237
Here they suggest that the codon bias is such it allows translation to pause
and folding of the
Jacob,
So you'd have to explain why the codon convention is so
intolerant/invariant relative to the other features--it seems to me
that either it is at an optimum or there is some big barrier holding
it in place.
Because altering codon convention will result in massive translation errors.
On 03/19/13 14:41, Jacob Keller wrote:
I don't understand this argument, as it would apply equally to all
features of the theoretical LUCA (protein and DNA sequences, etc). To
make it logically sound, I think you have either to include some kind
of super-high boundary to getting to other
Dear all
I have a somewhat philosophical question. Why do all protein sequences start
with a methionine (not referring to mature/processed form)? What is so special
about methionine and cannot be replaced by other amino acids?
Second, how does the ribosome know the first start codon is for
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