Chemistry Reference
In-Depth Information
Chapter 3
Structural and Molecular Biology
for Chemists
Introduction
35
The Structural Building Blocks of Proteins
37
Primary, Secondary, Tertiary, and Quaternary Structure of Proteins
41
Secondary and Tertiary Structures of Nucleic Acids
50
INTRODUCTION
In the previous chapter we introduced readers from a more biological background to some notions of inorganic
chemistry and, in this chapter, we explain to readers from a more chemical and physical background the
fundamental concepts of structural and molecular biology, which will be necessary to follow our path through the
diverse roles of metals in biological systems. For more information concerning the content of this Chapter see
Branden and Tooze, 1991; Berg et al., 2002; Campbell et al., 2005; Creighton, 1993; Fersht, 1999; Voet and Voet,
2004.
Our introduction to structural and molecular biology begins with a sharp reminder that life must function in an
aqueous environment. We believe that terrestrial life originated in some kind of primordial sea, and, as the fossil
record suggests, it is only quite recently that it ventured onto dry land. It might puzzle a few readers as to how it
came about that this aquatic life managed to survive during periods of extensive glaciation. There is a very simple
explanation
the density of ice is 0.9167 g/cm
3
at 0
C,
and is lower than that of water, which has a maximum density of 1.000 at 4
C.
1
This means that water freezes
from the top down, allowing aqueous life to remain viable underneath the ice. Water is a polar solvent: the large
difference in electronegativity between O and H means that the O
e
liquid water, unlike most liquids, expands on freezing
e
H bond has 33% ionic character, reflected in
the dipole moment of water (1.85 Debye units). An immediate consequence of this is that H
2
O molecules associate
through hydrogen bonds. In the highly ordered structure of ice, each water molecule is hydrogen bonded to four
neighbours in a tetrahedral arrangement (
Figure 3.1
)
. Even at the physiological temperature of 37
C, water
molecules still form an extensive network of hydrogen bonds, accounting for the highly cohesive nature of liquid
water. In common with the other two kinds of noncovalent bonds, electrostatic interactions, and van der Waal's
interactions, hydrogen bonds are transient. Like the lights on a Christmas tree flickering on and off, continually
being formed and broken, switching partners, these weak noncovalent forces play essential roles in biology.
Whether it is the folding of proteins into elegant predetermined three-dimensional forms, the faithful replication of
huge DNA molecules, the specific molecular recognition of substrates by enzymes, or of signalling molecules by
their receptors, these myriad weak interactions are at the heart of the biological action. All biological structures
e
1. Which is why cold rooms are maintained at this temperature.
