Biochips – fundamentals and applications - Electrochemical Sensors, Biosensors and Their Biomedical Applications - page 330

11.3 PROTEINCHIPS
11.3.1 Protein array and proteome
Protein arrays (or chips), in comparison to DNA chips, represent a great technical
advance, allowing thousands of proteins to be studied in a single experiment for the
understanding of biological systems or system biology, in which protein plays a central
role as most biological functions in organisms are mainly executed by protein. In addi-
tion, proteins are extremely important in human physiology and in medicine because
most diseases occur at the level including those which are considered genetic or heritable.
Therefore, when we wish to identify specifi c protein functions, various diseases in diag-
nostics or discover new drugs in medicine, we should eventually focus on the proteome.
Proteins are created, or translated on the basis of the information contained in genes,
namely, the DNA sequence of genes. While gene expression data provide important
information regarding the underlying proteins, they cannot necessarily predict the
myriad changes that occur to a protein subsequent to translation. This inability to accu-
rately characterize proteins based on gene expression data is a result of protein control
mechanisms that occur after the protein is synthesized from the gene. Consequently,
there is no direct way at present to correlate the genomic sequence and protein func-
tion although protein components are encoded by gene (DNA or sometimes RNA).
Compared with genome, proteome is much more complicated and thus more dif-
fi cult to explore. First, proteins are composed of 20 amino acids while genes contain
only fi ve nucleic acids. Moreover, proteins possess complex 3D structure (primary,
secondary, tertiary, and quaternary) and their functionality is often dependent on the
state of proteins, such as post-translational modifi cations, partnership with other pro-
teins, protein subcellular localization, and reversible covalent modifi cations. As a
result, there might be as many as 1 million different human proteins compared with
only 30 000 or so genes. Second, proteins require more delicate handling than DNA,
because they can easily unfold and get denatured when coming in contact with the
improper surface or environment. Third, strand complementarity makes identifi cation
of DNA a simple task, whereas proteins must be detected using mass spectrometric
analysis in conjunction with sophisticated software or using molecules (such as anti-
bodies) that specifi cally recognize their molecular structure. Fourth, protein detection
should be highly sensitive for the lack of an effective amplifying technology such as
PCR. All these make proteome far from the level of precision available to users and
purveyors of genomic technology.
Proteome may help biologists to study basic cell functions and molecular organiza-
tions, another big fi eld in microbiology for various research areas. Proteomics is also
applicable to plant research for many different purposes such as breeding plants against
higher bacterial, heat, cold, drought, and other resistances, increasing the yield of
crops, and many more. In such fi elds, proteomes are usually combined with genomes.
Traditional methodologies such as 2D-gel electrophoresis and mass spectrometry
have been considerably improved to resolve thousands of proteins in a single experi-
ment. However, these approaches are both time consuming and unsuitable for the