Re: News: Without enzyme, biological reaction essential to life takes 2.3 billion years
- From: dk@xxxxxxxxxxxxxxxxxxxxxxxxx (DK)
- Date: Mon, 1 Dec 2008 13:43:04 -0500 (EST)
In article <ggt8qo$17h7$1@xxxxxxxxxxxxxxxxxxx>, "Robert Karl Stonjek" <rstonjek@xxxxxxxxxxxxxx> wrote:
Without enzyme, biological reaction essential to life takes 2.3 billion
years
Maybe. But maybe not. That this reaction is slow spontaneously
was known. The point of the paper is to provide quantitative
estimate and I beliive that it fails to do so convincingly.
http://www.pnas.org/content/105/45/17328
1. The big number that is supposed to awe everyone is
based on *extrapolation* of the experimentally derived
spontaneous rate.
2. That extrapolation was derived from a linear fitting for the
Arrhenius plot (Fig.3, legend). This is a common and severe
mistake - equal weights were applied to the data spanning
3 orders of magnitude. But there is no way variance of the
experimental signal was the same throughout the entire
range. Jeez, and I thought these days every Biochem 101
student is taught to NOT ever derive anything from linearized
plots! That no estimated standard deviations of the fit's
parameters are mentioned anywhere in the paper is only
all too telling. Thus, it's anyone guess how close to reality
the extrapolation from >180C down to 25C is.
3. The assumption was made that Arrhenius plot remains linear
from 180-250C down to 25C - which may not be true; life is
full of nonlinear Arrhenius plots.
4. The study did not use the actual sustrate. It used a much
smaller compound that is part of the porphyrinogen. While this
had to do with obvious experimental limitations (porphyrinogen
is unstable for other reasons), no attempt was made to prove
that the spontaneous rates of decarboxylation are expected to
be identical for pyrrolyl-3-acetate and porphyrinogen. That the
macrocycle ring has absolutely no influence on the chemistry
of pyrroles is a very dubious assumption. At a minimum, a full
quantum mechanics calculation should have been carried out
to prove that it is reasonable to assume the near equivalence.
(That's not difficult to do these days but it was evidently not done).
All in all, a shaky ground for any quantitative claims.
All biological reactions within human cells depend on enzymes. Their power
as catalysts enables biological reactions to occur usually in milliseconds.
But how slowly would these reactions proceed spontaneously, in the absence
of enzymes - minutes, hours, days? And why even pose the question?
One scientist who studies these issues is Richard Wolfenden, Ph.D., Alumni
Distinguished Professor Biochemistry and Biophysics and Chemistry at the
University of North Carolina at Chapel Hill. Wolfenden holds posts in both
the School of Medicine and in the College of Arts and Sciences and is a
member of the National Academy of Sciences.
Which explains why the work was published in PNAS with a
turnaround of three weeks.
"Without catalysts, there would be no life at all, from microbes to humans,"
he said. "It makes you wonder how natural selection operated in such a way
as to produce a protein that got off the ground as a primitive catalyst for
such an extraordinarily slow reaction."
Evidently, it does not take much to catalyse this reaction.
Authors' own results show that simple protonation of the carboxyl
results in ~ 1,000X enhanced rate at 200C (and estmated
100,000X when extrapolated to 25C).
DK
.
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