Mittenthal, Jay E., Bertrand Clarke, and Mark Levinthal. “Designing bacteria.” In Thinking about Biology , pp. 65-103. CRC Press, 2018.
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There are at least two justifications for using a design approach to understand the organization of molecular pathways in bacteria. First, any systems that undergo selection for a long time in competition with alternatives will often show favorable features of design because they meet performance criteria better than the alternatives. Second, plausible arguments suggest that since bacteria perform metabolism and self-reproduction, they meet performance criteria. The resources available to a bacterium are limited. Thermodynamics imposes fundamental limits; mass and energy are conserved, and the free-energy changes in chemical reactions are limited. The macromolecular net uses the key metabolites to synthesize macromolecules, which perform the activities that enable bacteria to survive. In bacteria a single regulator, called a repressor, activator, antiterminator, or proterminator, can regulate an entire operon. The operons of a bacterial chromosome are complexes that increase the speed of Deoxyribonucleic acid (DNA) handling.