Biology Reference
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(also called Brownian motions or thermal fluctuations) play in living systems.
But thermally excited states of biopolymers can last only briefly, in the order of
10
12
-10
13
s, and hence very difficult to study unlike stable structures or ground-
state structures or conformations (see nodes B and C in Fig.
14.7
). The transition from
the ground-state conformation of a biopolymer to its excited state requires thermal
excitation which corresponds to Step 2 in Fig.
14.7
. According to the generalized
Franck-Condon principle (GFCP) (Sect.
2.2.3
), the thermally excited states of proteins
must release heat rapidly enough to pay back, within the lifetime of the excited states,
the thermal energy “borrowed” by enzymes from their environment to reach excited
states. When a sufficient number of thermally excited enzymic processes are
coupled properly in space and time, self-organized processes are thought to emerge
called Intracellular Dissipative Structures (IDSs) or dissipatons, capable of carrying
biocomplexity
can be identified with the many-to-one mappings between the lower
nodes and their higher counterparts in Fig.
14.7
. For example, many different amino
acid sequences of proteins (node A) are known to fold into similar three-dimensional
conformations (node B), leading to what is known as the “designability of a structure,”
defined as the number of sequences folding into the same structure (Zeldovich and
Shakhnovich 2008). There are almost infinite number of amino acid sequences for a
finitely sized protein (e.g., 20
100
10
107
different sequences of proteins with
100 amino acid residues), but there are only several thousand known protein folds. The
single-molecule enzymological data provided by Lu et al. (1998) and analyzed in Sect.
11.3.3
indicate that many ground-state conformations of cholesterol oxidase are
The mapping between thermally excited states of enzymes (node C) and exer-
gonic chemical reactions (node D) may be one-to-one due to the fact that these two
nodes are
coupled
through the mechanism constrained by the generalized
Franck-Condon principle (Sect.
2.2.3
).
It is here suggested that the mapping between exergonic chemical reactions (node
D) and IDSs (node E) (see Step 4 in Fig.
14.7
) is similar to the mapping between
ground-state conformations of proteins (node B) and their excited states (node C),
since both these mappings involve thermal excitations as discussed in Sect.
12.12
.
In other words, it is here postulated (1) that there are more exergonic chemical
reactions (each catalyzed by an enzyme) than there are cell functions and (2) that
two or more different sets of exergonic chemical reactions can support an identical
intracellular function
or an
intracellular dissipaton
.
¼
1.27
17.7 The Quality-Quantity Duality and Biocomplexity
The duality of
quality
versus
quantity
is a well-established topic in philosophy.
Spirkin (1983) states that the quality of an object is “the sum-total of its properties”
and that the quantity of an object “is expressed by numbers.” Table
17.5
lists some
examples of the quantity-quality dualities that occur in molecular and cell biology.
