Biophysical Chemistry
By Alan Cooper
The Royal Society of Chemistry
Copyright © 2011 A. Cooper
All rights reserved.
ISBN: 978-1-84973-081-5
Contents
1 Biological Molecules,
2 Spectroscopy,
3 Mass Spectrometry,
4 Hydrodynamics,
5 Thermodynamics and Interactions,
6 Kinetics,
7 Chromatography and Electrophoresis,
8 Imaging,
9 Single Molecules,
Answers to Problems,
Subject Index,
CHAPTER 1
Biological Molecules
You don’t need to know any biology in order to study biological molecules, but it does help to have some background.
1.1 Introduction
This book is mainly about the experimental methods used to understand the physical properties and function of the molecules that make up living systems.
These molecules — proteins, polynucleotides, polysaccharides, lipids — are not necessarily any different from molecules we study in other branches of chemistry. But there are some additional factors, arising from their biological origin, which we need to be aware of.
Biological macromolecules are large molecules formed from many smaller units and are (usually) polymers of precise length and specific sequence.
They (usually) fold or associate into specific conformational assemblies stabilized by non-covalent interactions.
This (usually) happens in water.
The molecules are the (usually) successful outcomes of biological evolution.
It is this last point that makes things so exciting for the biophysical chemist. The molecules we see today are the results of countless random (more or less) experiments over millions of years during which living systems have evolved to take advantage of subtle principles of physical chemistry that we barely yet understand. By studying such systems we can learn much about physical chemistry in general, with potential for applications in other areas.
1.2 Proteins and Polypeptides
Proteins are polymers made up of specific sequences of L-amino acids linked together by covalent peptide (amide) bonds (Figure 1.1). Amino acids are chosen from a basic set of 20 building blocks differing in side chain (Figure 1.2), with occasional special purpose side chains made to order (e.g. hydroxyproline).
D-amino acids are encountered only in special instances such as bacterial cell walls and peptide antibiotics.
Typical proteins range in polypeptide chain length from around 50 to 5000 amino acids. The average relative molecular mass of an amino acid is around 110, so proteins can have RMMs from 500 to 500 000 (0.5–500 kDa) or more — especially in multi-subunit proteins consisting of specific aggregates (see Table 1.1).
The term ‘molecular weight’ is not strictly accurate (why?) but is commonly used, especially in the older (biochemical) literature. The more correct terms are ‘relative molecular mass (RMM)’ (no units) or ‘molar mass’ (kg mol1 or g mol1). One dalton (1 Da) is equal to 1 amu (atomic mass unit).
Proteins function as enzymes (biological catalysts), antibodies, messengers, carriers, receptors, structural units, etc. Their chemical structure and molecular conformation are commonly described in terms of:
Primary structure: the sequence of amino acids in the polypeptide chain (see Figure 1.3). This is unique to each protein, and is determined (primarily) by the genetic information encoded in the DNA of the relevant gene.
Secondary structure: regular, repeating structures such as α-helix, β-sheets, etc. (see
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