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Extra resources for An introduction to metabolic and cellular engineering
The information-carrying networks are shown in a different layer just for the sake of clarity and its presence on top does not imply hierarchy. On the contrary, cross-talk connections existing between the two layers are emphasized by arrows (activatory, with arrowheads, or inhibitory, with a crossed line). g. the nodes on the top layer are proteins or second messengers. The proteins are continuously synthesized through transcription, translation mechanisms of gene expression, and exert feed-back regulation (eg.
A view of cells as multilayered mass-energy-information networks of reactions. Metabolic reactions embedded in the cytoplasmic scaffolds are shown diagrammatically with each chemical species represented by a filled circle (bottom layer). Central catabolic pathways (glycolysis and the TCA cycle) are sketched. The chemical reaction network for the synthesis of a microorganism, (eg. , 1989) (see text for further explanation). A typical mammalian cell synthesizes more than 10,000 different proteins, a major proportion of which are enzymes that carry out the mass-energy transformations of the bottom-layer network.
The occurrence of at least one process that exhibits a kinetic non-linearity. g. g. substrate) inhibition, feedforward (product) activation, cross-activation or cross-inhibition. In the case of chemical reactions, they may be arranged in linear, branched, cyclic pathways or as combinations of these basic configurations. Within this framework, metabolic pathways with different topologies (linear, circular) and sources of non-linear kinetics (allostery, stoichiometric autocatalysis) were compared as energy converters for thermodynamic efficiency (Fig.