Biology Reference
In-Depth Information
Fig. 8.2
A general
mechanism of redox reaction
satisfying the generalized
Franck-Condon principle and
the Principle of Microscopic
Reversibility
generalized Franck-Condon principle (GFCP) (Sect.
2.2.3
) and the principle of
microscopic reversibility (PMR), which Hine (1962) describes as follows:
...
the mechanism of a reversible reaction is the same, in microscopic detail (except for the
direction of reaction,
.), for the reaction in one direction as in the other under a given set
of conditions. (8.15)
A close examination will reveal that the mechanism given in Fig.
8.2
obeys
PMR. Please note that, in the Franck-Condon state, (
b
), indicated by [
...
]
{
, two
electrons can be associated with either A or B with an equal probability. We assume
that water molecules equilibrate rapidly within the enzyme active site, reacting with
anion to form a hydroxide ion, OH
-
, or with a cation to form a hydronium ion,
H
3
O
+
, written simply as H
+
.
...
8.3 Experimental Evidence for Conformons
The idea that biological properties of enzymes may depend on the mechanical
(i.e., conformational) energy stored in proteins was first seriously considered by
R. Lumry and others in the 1950s and 1960s (Lumry 1974, 2009; Lumry and
Gregory 1986) (reviewed in Ji 1979, 2000), but the first direct experimental
evidence for such a possibility did not emerge until the mid-1960s when the so-
called “supercoiled” DNA was observed under electron microscope (Stryer 1995,
p. 795). When a circular DNA duplex is cut through both strands and the resulting
ends are twisted around the long duplex axis (called the helical axis)
n
times in
the direction of increasing the distance between the paired bases (referred to as the
negative direction) and then resealed, the circular form twists in space so that the
helical axis itself coils into a helix, a phenomenon known as “supercoiling.” To
undo each helical turn, about ten hydrogen bonds must be broken between the
complementary base pairs along the DNA double helix, requiring a total of about
15 kcal/mol of free energy. Thus, a circular DNA duplex which was negatively
twisted around the helical axis, say, 20 times would store approximately 15
20
¼
300 kcal/mol of mechanical energy in the form of conformational deformations
or strains. Therefore, a supercoiled DNA duplex can be interpreted as providing
a
direct experimental evidence for the concept of conformons.
That is, the supercoiled
DNA duplex stores conformons.
