Biology Reference
In-Depth Information
the average rate of compaction per step is about 10
2
. This would mean that on
average, each chunking process reduces the motional degree of freedom of DNA
components by a factor of about 10
2
. Thus, we can conclude that “chunking” is
synonymous with “constraining” and hence the acronym, C & C, can be interpreted
to mean either “chunking-and-constrain” or “chunking-and-control.”
The “chunking” phenomenon depicted in Fig.
2.9
is a highly organized process
and thus requires dissipating free energy catalyzed by enzymes. Therefore, it
wouldbereasonabletopredictthatfivedifferent classes of enzyme complexes
catalyzing each of the five chunking (or coding, or renormalizing) operations
shown in the figure will be discovered. I coined the term “chunkase” around 2005
while teaching “Theoretical Aspects of Pharmacology” to Pharm D students at
Rutgers. Each chunkase is probably as large as ribosomes or spliceosomes, whose
orderly motions would be driven by conformons derived from chemical reactions
(Sect.
8.4
).
As already alluded to, one of the main reasons for the “chunking operations”
found in the eukaryotes is most likely to facilitate self-replication of the cell
which entails replicating DNA. In principle, DNA replication can be achieved in
two ways
1.
Replication without chunking
- First replicate n DNA molecules into 2n DNA
molecules, separating them into two identical groups by transporting only one of
the sets across a membrane through an active transport mechanism.
2.
Replication with chunking
- Replicate n DNA molecules into 2n molecules, each
chunked into smaller, more compact particles, which can be more easily
counted
and
sorted
than the original, unchunked DNA double helices.
It is intuitively clear that Mechanism (1) would be much more difficult to
implement than Mechanism (2) in agreement with von Neumann who also consid-
ered similar mechanisms of cell divisions (von Neumann 1966). In fact it should be
possible to compute the two different efficiencies of cell divisions (or mitosis)
based on the two mechanisms of DNA replications described above. Such
chunking-based cell division may not be necessary for prokaryotes but becomes
important as the number of chromosomes to be replicated increases in eukaryotes.
Chunking is reversible: What gets chunked must get “de-chunked” at some point
during a cell cycle, catalyzed by enzyme complexes distinct from associated
chunkases. The enzyme complexes postulated to catalyze de-chunking operations
may be referred to as “i-
>
j de-chunkase,” where i and j refer to the adjacent levels
of chunking with i
j.
The purpose of chunking the (n
>
1)th level components of a network into a
node at the nth level may be construed as producing a new function at the nth level
that is not available on the (n
1)th level (see Fig.
2.10
). The function at the nth
level may be viewed as a chunked version of
(structure, processes, and
mechanisms) at the (n
