Biology Reference
In-Depth Information
1
2
3
O
(
E
)/
C
(
D
)
/
C'
(
T
) [
OC'
(
E,T
)
/
CO
(
D,E
)
/
C'C
(
T,D)
]
‡
C'
(
T
)
/
O
(
E
)
/
C
(
D
)
4
[
CO
(
D,E)
/
C'C
(
T,D
)
/
OC'
(
E,T
)]
‡
[
C'C
(
T,D)
/
O
C'
(
E,T
)
/
C
O
(
D,E
)]
‡
6
5
C
(
D
)
/
C'
(
T
)
/
O
(
E
)
Fig. 7.4 The
pre-fit
molecular mechanism of the rotary catalysis of the F
1
-ATPase (in the
direction of ATP hydrolysis) based on the generalized Franck-Condon principle (GFCP) or the
mational states of the F
1
stator ring and the
blue
letters indicate the ligands bound to the
b
subunits.
The
square brackets
indicate the high-energy transition state or activated states called the
Franck-Condon state (Reynolds and Lumry 1966). The mechanism obeys the Principle of Micro-
scopic Reversibility (see Sect.
3.3
)
so that it can be driven forward (from
left
to
right
) or backward
(from
right
to
left
), depending whether the Gibbs free energy change,
D
G, accompanying ATP
hydrolysis is negative or positive, respectively
1
to 3 in that they obey both the generalized Franck-Condon principle and the
principle of microscopic reversibility.
7.2 Enzymic Catalysis
7.2.1 Enzymes as Molecular Machines
Chemical engineers can control chemical reactions at the macroscopic (or bulk) level,
but it is only enzymes that can (or have both
energy
and
information
to)
control
chemical reactions on the microscopic (or molecular) level. Since (1) the living
properties of the cell can be exhibited only if driven by exergonic (i.e., free energy-
releasing) chemical reactions and (2) since most, if not all, chemical reactions inside
the cell are catalyzed by enzymes, it would follow that enzymes provide the immedi-
ate mechanisms for controlling living processes in cells. So, to understand life on the
most fundamental level, it is necessary first to understand how individual enzymes
(as networks of atoms) work and how they work as groups (as nodes of metabolic
networks) to accomplish results that are beyond the capabilities of individual
enzymes (such as space- and time-dependent expressions of select genes).
Enzymes may be viewed as the most basic bionetworks whose nodes are atoms
and whose links are of two principal types -
covalent bonds
and
non-covalent
bonds
. The former involves sharing of one or more pairs of electrons between two
atomic nuclei (with interaction energies in the range of 50-100 kcal/mol), while the
latter involves much weaker bonds such as electrostatic bonds, hydrogen bonds,
hydrophobic bonds, and van der Waals interactions (with interaction energies in the
range of 1-3 cal/mol).
