Environmental Engineering Reference
In-Depth Information
mutagenesis may be used to probe the structure-function relationships among the amino
acids.
In one approach to this technique, 10 to 15 base pair oligonucleotides are inserted into the
gene sequence at random; alternatively, the mutagenesis may be designed such that internal
deletions occur as well. Insertions or deletions that disrupt the function of the protein are
assumed to occur in regions essential to the correct folding of the protein, while those that are
tolerated are assumed to occur on the surface or in less-essential regions. In this way, the
functional regions of an enzyme can be mapped with high resolution [1, 21, 31, 37].
Variations on the above-mentioned analytical mutagenesis methods are numerous, highly
specialized, and evolving rapidly; for current and detailed information, the reader is referred
to Current Protocols in Molecular Biology, updated quarterly [1].
2.6. Proteomics
The cellular proteome is the complete set of proteins found in a particular cell type under
a specific set of conditions. The complete proteome, in turn, is the complete set of proteins
that may be synthesized by the set of cellular proteomes, or the approximate protein analog of
the genome. A cell's proteome typically possesses a much larger number of elements than
does its genome, due to alternative processing of gene products and post-translational
modifications such as glycosylation and phosphorylation. It is also more complex than the
genome, in that it incorporates functional interactions among distinct proteins, and it is
dynamic, in comparison to the generally static genome [38].
Proteomics is the study of proteomes, particularly including proteome structure and
function, and includes protein separation, identification, quantification, and analysis of
protein sequences, structures, modifications, and interactions. It therefore encompasses the
development of technologies used in protein separation and structural analysis, such as two-
dimensional (2D) electrophoresis and mass spectrometry, as well as the study of protein-
protein and protein-DNA interactions that influence the synthesis of other proteins [38].
Proteomics is a recent addition to the landscape of biological research and represents an
expansion in biological thought from concentration upon individual proteins and protein
assemblages to large systems of interacting proteins. Proteomics is directly related to
metabolic engineering, discussed below, in that it considers systems of enzymes interacting in
metabolic pathways, as well as those interacting to govern cell division, cell signaling and
response to environmental conditions, and transcriptional regulation that in turn determines
the composition of the proteome itself [39, 40].
Like genomics, proteomics has emerged from the rapidly expanding set of databases, for
example, Swiss-Prot, http://us.expasy.org/sprot/; Protein Data Bank, http://www.rcsb.
org/pdb/) and data-mining tools as an application of bioinformatics that demands powerful
computational resources and promises insights on greater scales of cellular complexity than
have previously been possible [40, 41].
Since biotechnology relies directly upon the ability to control a cell's proteome,
particularly including optimization of the balance between metabolic pathways that
synthesize desired products and other pathways that maintain cell vigor, advances in
proteomics will directly benefit all bioengineering endeavors.
