By Bernhard Ø. Palsson
Genome sequences at the moment are on hand that permit us to figure out the organic parts that make up a mobilephone or an organism. the recent self-discipline of platforms biology examines how those parts have interaction and shape networks, and the way the networks generate entire mobilephone services similar to observable phenotypes. This textbook describes find out how to version networks, ascertain their houses, and relate those to phenotypic services. a few wisdom of linear algebra and biochemistry is needed, because the booklet displays the irreversible development of accelerating mathematical content material in biology schooling.
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Extra info for Systems Biology: Properties of Reconstructed Networks
Sample text
R Genomic data include DNA sequences and the location and functional annotation of genes. Transcriptional regulatory models also account for many of the intragenic regions where RNA polymerase and transcription factors bind. r Extensive biochemical information is contained in reconstructions. The L and D forms of compounds are accounted for separately. A molecule’s charge can be determined from its pKa value and network-scale proton balancing. All reactions must elementally and 49 50 Metabolic Networks charge balanced.
The first basic feature of biological networks is that they evolve; they change with time. They are time variant. Principally, such changes occur through the kinetic properties of the links in the network and the changing of the available or active links in the network at any given point in time. The number of available links can be manipulated by regulation of gene expression, by horizontal gene transfer, and by other mechanisms. The second feature that has to be taken into account is the fact that they have a sense of purpose.
2). Catabolism carries out the degradation of substrates via a series of converging pathways that lead to a set of 11 metabolites of central importance, called the biosynthetic precursors. Anabolism is a set of diverging pathways that originate from these central metabolites to form monomers or 32 Metabolic Networks CO2, H2O O2 (or other electron acceptors) substrates (reduced compounds) ETS c a t a b o l i s m ATP ADP NADPH NADP+ sugarphosphates PEP Pyruvate AcCoA α-KG SuccCoA OA a n a b o l i s m specialty products energy input from catabolism amino acids nucleotides fatty acids g r o w t h proteins RNA/DNA membranes organelles etc.