Biology Reference
In-Depth Information
as the “electronic-conformational interactions” (Volkenstein 1986). A molecule has a
unique
configuration
(as defined by the set of covalent bonds it possesses) and many
conformations
(as defined by the three-dimensional arrangements of the covalently
bound atoms in a molecule which can be altered without breaking or forming any
covalent bonds) (Sect.
3.2
). Some of the simplest examples of molecules having
different configurations are provided by isomers. Thus, cis- and trans-1-chloro-2-
bromo-ehtylene have an identical set of atoms, i.e., C
2
H
4
BrCl, and yet have two
different
configurations
(or arrangements of these atoms in the Euclidean space),
namely, cis- and trans-isomers which cannot be interconverted without breaking at
least one of the covalent bonds of C
¼
C, C-H, C-Cl, and C-Br.
A given
configuration
of a set of atoms can assume numerous
conformations
(also called
conformers
). For example, 1-chloro-2-bromo-ethane, the product of
reducing the C
C double bond in 1-chloro-2-bromo-ethylene, can exist in two
conformations, one in which the chlorine and bromine atoms are located farthest
apart and the other in which they are located nearest to each other, and these two
conformations can be interconverted through rotations around covalent bonds. One
crucial difference between
configurations
and
conformations
is that the activation
free energy barrier separating one
configuration
from another is much higher
(
50-100 kcal/mol
) than that separating one
conformation
from another within a
given configuration (
1-3 kcal/mol
). Therefore, the thermal energy available under
physiological conditions (about 0.6 kcal/mol) is usually not large enough to change
configurations but sufficient to cause appreciable conformational changes, leading
to the following general statement:
Configurations
of molecules are too robust to be altered but
conformations
of a molecule
are labile enough to be interconverted, through thermal fluctuations.
¼
(11.18)
According to the cell language theory (Ji 1997a, 1999b), Statement 11.18 is
ultimately responsible for the phenomenon known as “rule-governed creativity”
(Sect.
6.1.4
), namely, the ability of biopolymers (and cells) to generate indefinitely
large numbers of states within the constraints of a finite number of components and
syntactic rules. The relationship between
configurations
and
conformations
can be
diagrammatically represented as shown in the first two columns in Fig.
11.21
. Note
that the energy separations between configurations are greater than those between
conformations.
In discussing biochemistry, molecular biology and biophysics, it is useful to
differentiate between
small molecules
(which may be referred to as
“micromolecules” (e.g., glucose, ATP, NADH, and FAD) and
large molecules
(
or macromolecules
) including proteins, RNA, and DNA. What characterizes
biological macromolecules vis-a`-vis micromolecules
of organic chemistry is that
biological macromlecules (or
biomacromolecules
) are the product of a long
biological evolution and hence carry biological (also called evolutionary or genetic)
information, whereas micromolecules do not. In other words, biomacromolecules
possess an extra degree of freedom not available to micromolecules, i.e., the
