---

The biochemical motors and machines found in the cell’s interior
reveal a diversity of form and function that mirrors the diversity of
designs produced by human engineers, and thus they pose a serious
challenge to the random
mutation and selection concept of evolution theory. It is an easy to
understand argument that the machine will work as a complete whole
only when all the necessary components are assembled, but when
defective or missing some parts, it will be non-functional or useless.

One of the most compelling argument for design is found in the example
of cyanobacteria’s biomachines with amazingly complex and precise
timekeeping devices.

A physiological black box is to a biologist what an ornately decorated
package is to a small child: a mysterious treasure that promises
delightful toys within. With fitting elan, a small community of
scientists has ripped open the
packaging of the cyanobacterial circadian clock, compiled the parts
list, examined the gears, and begun to piece together the mechanism.
Over the past 2 years, the 3D molecular structures have been solved
for the core components of the cyanobacterial circadian clock: KaiA,
KaiB, and KaiC. In a surprisingly literal analogy to mechanical
timepieces, the protein that seems to be at the heart of the clock
mechanism, KaiC, forms a hexameric ring that even looks like a cog:
the escape wheel, perhaps. Previous work has shown that KaiC has an
autophosphorylation activity, and that the presence of KaiA and KaiB
modulates the extent to which KaiC is phosphorylated. In this issue of
PNAS, Nishiwaki et al. biochemically identify two amino acid residues
on KaiC to which phosphoryl groups covalently attach, and show the
necessity in vivo of a phosphorylation-competent residue at these
positions. By searching the crystal structure for evidence of
phosphorylated sites, Xu et al. pinpoint a third residue that may
“borrow” the phosphoryl group dynamically. Together, their work
contributes richly to our understanding of what makes the gears mesh
and turn to crank out a 24-h timing
circuit....

Because each of these components (at minimum) is a dimer [composite of
two molecular chains], KaiC is known to be a hexamer [composite of six
chains], and other proteins may be present as well, the cyanobacterial
clock can be thought of as an organelle unto itself: a “periodosome”
that assembles and disassembles during the course of a day, defining
the circadian period.[1]

“Periodosome” means “time-keeping body” – i.e., clock.


In the article by Johnson, Egli and Stewart published recently in the
Science magazine there is a similar, somewhat more detailed
description of cyanobacteria’s circadian clock:

An endogenous circadian system in cyanobacteria exerts pervasive
control over cellular processes, including global gene expression.
Indeed, the entire chromosome undergoes daily cycles of topological
changes and compaction. The biochemical machinery underlying a
circadian oscillator can be reconstituted invitro with just three
cyanobacterial proteins, KaiA, KaiB, and KaiC. These proteins
interact to promote conformational changes and phosphorylation events
that determine the phase of the in vitro oscillation. The high-
resolution structures of these proteins suggest a ratcheting mechanism
by which the KaiABC oscillator ticks unidirectionally. This
posttranslational oscillator may interact with transcriptional and
translational feedback loops to generate the
emergent circadian behavior in vivo. The conjunction of structural,
biophysical, and biochemical approaches to this system reveals
molecular mechanisms of biological timekeeping.[2]

According to Johnson et al each cell has 10,000 KaiC proteins. Each
of the KaiC protein is a barrel mechanism with two donut-shaped rings,
each made of six toothed parts that make it look like a gear wheel.
The clock runs on ATP energy[3] pellets. It accumulates hydrogen
bonds through phosphorylation events that force it to “tick” like a
ratchet in one direction. It keeps an accurate 24-hour cycle,
releasing its energy for the next round in conjunction with feedback
loops from the nucleus and cytoplasm.

As obvious from the complexity described above, it is very reasonable
to suggest that even one simplest, efficient molecular machine for
example the KaiC protein could not appear without being designed and
what to say about
10,000 of them that harmoniously tick together i.e the 10,000 proteins
in each particular cell.

NOTES:
1. Susan S. Golden, “Meshing the gears of the cyanobacterial circadian
clock,“ Proceedings of the National Academy of Sciences USA, 10.1073/
pnas.0405623101.
2. 1. Johnson, Egli and Stewart, “Structural Insights into a
Circadian Oscillator,” Science, 31 October 2008: Vol. 322. no. 5902,
pp. 697-701, DOI: 10.1126/science.1150451.
3. ATP or adenosine triphosphate is a high energy phosphate compound
found in the body; one of the major forms of energy available for
immediate use in the body.


http://krishnascience.com
http://harinam.net