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systems_bioloy_ch_3systems_biology_ch_3systems_biology_ch_3systems_biology_ch_3.ppt

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systems_bioloy_ch_3systems_biology_ch_3systems_biology_ch_3systems_biology_ch_3

Systems Biology Study GroupChapter 3 Walker Research Group Spring 2007 Overview Review Biochemical Network reconstruction Metabolic Networks Basic Features Hierarchy Reconstruction Methods Genome-scale Metabolic Reconstructions Multiple Genome-scale Networks Summary Review Systems Biology: Process of genome scale network reconstruction, followed by synthesis of in silico models describing their functionalities Enumeration of biological components Identification of links connecting processes Modeling Hypothesis generation and testing Review Roots of Systems Biology Biology Molecular biology High throughput sequencing Genome scale analysis Systems Analog simulations Large scale simulations of metabolic networks Genome scale models and analysis Systems Biology constrained by: Chemical transformation properties Stoichiometry Relative and absolute rates Functional states Physiochemical nature Orientation Biochemical Network Reconstruction Network reconstruction: Process of identifying all reactions that comprise a network Networks are not separate and independent of each other Metabolic Networks Metabolism – Biochemical modification of chemical compounds within living cells. Metabolic networks are the collection of pathway through which this is accomplished Source: Feigenson, G. 2006 BIOBM 331 Basic Features Intermediary metabolism: chemical “engine” Converts raw materials into energy, building blocks for biological structures Obeys laws of physics and chemistry Elaborate regulatory structure Source: Feigenson, G. 2006 BIOBM 331 Hierarchy Simplify conceptualization of network functions Level 1 – Cellular Inputs and Outputs Coarse description of overall activity First published experiments in human metabolism Italian physician Santorio Santorio in 1614 Used a steelyard balance to weigh himself after eating, sleeping, working etc. Found that most of food intake was lost through “insensible perspiration” Source: Metabolism. Wikipedia, public domain art. 18 July 2005