of a cell is referred to as the genome, and the study of the structure and function of this
DNA is called genomics. By analogy, the proteome is defined as the total protein
component of a cell, and the study of the structure and function of these proteins is
called proteomics. The ultimate aim of proteomics is to catalogue the identity and
amount of every protein in a cell, and determine the function of each protein.
Earlier sections of this chapter and Chapter 11 describe the traditional, but still very
valid approach to studying proteins, where individual proteins are extracted from
tissue and purified so that studies can be made of the structure and function of the
purified proteins. The subject of proteomics has developed from a different approach,
where modern techniques allow us to view and analyse much of the total protein
content of the cell in a single step. The development of these newer techniques has
gone hand-in-hand with the development of techniques for the analysis of proteins by
mass spectrometry, which has revolutionised the subject of protein chemistry. The
cornerstone of proteomics has been two-dimensional (2-D) PAGE (described in
Section 10.3) and the applications of this technique in proteomics are described below.
However, although 2-D PAGE remains central to proteomics, the study of proteomics
has stimulated the development of further methods for studying proteins and these
will also be described below.
8.5.1 2-D PAGE
2-D PAGE has found extensive use in detecting changes in gene expressions between two
different biological states, for example comparing normal and diseased tissue. In this case,
a 2-D gel pattern would be produced of an extract from a diseased tissue such as a liver
tumour and compared with the 2-D gel patternsof an extract from normal liver tissue.
The two gel patterns are then compared to see whether there are any differences in the two
patterns. If it is found that a protein is present (or is absent) only in the liver tumour
sample, then by identifying this proteinwe are directed to the gene for this protein and
can thus try to understand why this gene is expressed (or not) in the diseased state. In this
way it is possible to obtain an understanding of the molecular basis of diseases. This
approach can be taken to studyanydisease process where normal and diseased tissue can
be compared, for example arthritis, kidney disease, or heart valve disease.
Under favourable circumstances up to 5000 protein spots can be identified on a
large format 2-D gel. Thus with 2-D PAGE we now have the ability to follow changes
in the expression of a significant proportion of the proteins in a cell or tissue type,
rather than just one or two, which has been the situation in the past. The potential
applications of proteome analysis are vast. Initially one must produce a 2-D map of
the proteins expressed by an organism, tissue or cell under ‘normal’ conditions. This
2-D reference map and database can then be used to compare similar information
from ‘abnormal’ or treated organisms, tissues or cells. For example, as well as
comparing normal tissue with diseased tissue (as described above), we can:
- analyse the effects of drug treatment or toxins on cells;
- observe the changing protein component of the cell at different stages of tissue
development;
341 8.5 Proteomics and protein function
