Biology Reference
In-Depth Information
DNA double helix
Level 5
Problem-oriented language
2 nm
Translation (compiler)
Assembly language level
Beads-on-a-strong
Level 4
11 nm
Translation (assembler)
30 nm-Chromatin
Level 3
Operating system machine level
30 nm
Partial interpretation
(operating system)
Instruction set architecture level
Extended chromosome
Level 2
300 nm
Interpretation (microprogram) or direct
Condensed section of
metaphase chromosome
Microarchitecture level
Level 1
700 nm
Hardware
Entire chromosome
Level 0
Digital logic level
1400 nm
Fig. 11.14 (
Left
) The multilevel structural organization of the computer (Adapted from
Tanenbaum 2003). Digital logic
¼>
Microarchitecture
¼>
Instruction set architecture
¼>
Operating system machine
Problem-oriented language. (
Right
)
Multistep chunking of DNA into chromosome. DNA double helix
¼>
Assembly language
¼>
¼>
beads-on-a-string form of
chromatin
¼>
30-nm chromatin fiber
¼>
300-nm section chromosome
¼>
700-nm section
chromosome
¼>
1,400-nm section metaphase chromosome
Many mathematical models have been proposed to account for the results of the
single-molecule enzymological measurements on COx (Lu et al. 1998; Kurzynski
2006; Qian and Xie 2006; Prakash and Marcus 2007), but they are all rooted in
the conventional Michaelis-Menten mechanisms as applied to individual molecules
of enzyme and couched in the language of physics- and chemistry-based continuous
mathematical functions such as Eq.
11.25
shown in Sect.
11.3.3
. The main objective
of this section is to propose an alternative theory of single-molecule enzymology
that is based on the concept of
conformons
(i.e., the packets of conformational
energy
and genetic
information
stored at sequence-specific sites within biopolymers
that are postulated to drive all goal-directed molecular processes in the cell includ-
ing catalysis; see Chap.
8
). The concept of conformons was originally developed
to account for the energy-coupled processes of the living cell such as oxidative
phosphorylation, muscle contraction, and active transport (Green and Ji 1972a, b;
Ji 1974b, 1985a, b, 2000) but has also been found to provide a reasonable explana-
tion for the mechanistic isomorphism (or similarity) between
blackbody radiation
and
enzymic catalysis
(see Fig.
11.24
) as found in Ji (2008b). If the conformon-
based explanation for single-molecule enzymological data on COx proves to be
correct, it would be possible to conclude that the single-molecule enzymological
