c06_netw_prop_bio_handout - The structure of molecular...

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1 The structure of molecular & cellular networks To be able to construct and analyze a cellular network, we need to clearly define what we identify as a node and what we represent with an edge. The nodes and edges have to be at least similar to each other, e.g. represent the same type of cellular component (protein, chemical) or the same type of interaction (mass transfer, regulation). We can, and often need to, define different types of nodes and edges. Life at the cellular level • Cellular functions rely on the coordinated action of interacting components. • Proteins – provide structure to cells and tissues – work as molecular motors – sense chemicals in the environment – drive chemical reactions – regulate gene expression • Interconnections between components are the essence of a living process. David Goodsell/ Science Photo Library receptor proteins , enzymes , ribosomes , DNA gene regulatory network protein-protein interaction network Frequently defined molecular interaction networks external signals Citrate Cycle bio-chemical reaction network signal transduction network Examples of intracellular networks 1. Protein interaction networks nodes: proteins edges: protein-protein interactions (binding), modification of a protein 2. Biochemical reaction networks nodes: reactants (substrates) or products of the reactions enzymes – catalyze the reactions reactant-enzyme complex (“reaction node”) edges: reactions catalysis (regulation)
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c06_netw_prop_bio_handout - The structure of molecular...

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