Abstract
In this chapter, we briefly introduce the basic concept of molecular biology and also biological information processing in general. As a detailed example of the information processing phenomena (signal recognition, transformation, and biological response) in a living system, we explain the diauxie (two phase) growth of Escherichia coli in glucose and lactose mixed medium and show the mechanistic simulation of the system according to the systems biology approach. In addition, we introduce epigenetic mutation as another example for the information processing in a living system.
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References
Yamato, I.: From structure and function of proteins toward in silico biology. Quantum Bio-Informatics V. (From Quantum Information to Bio-Informatics). In: Accardi, L., Freudenberg, W., Ohya, M. (eds.) Proceedings of the International Symposium of Quantum Bio-Informatics Research Center 2011, Chiba, pp. 473–485. World Scientific, Singapore (2013)
Bassham, J., Benson, A., Calvin, M.: The path of carbon in photosynthesis. J. Biol. Chem. 185, 781–787 (1950)
Krebs, H.A., Johnson, W.A.: Metabolism of ketonic acids in animal tissues. Biochem. J. 31, 645–660 (1937)
Fiske, C.H., Subbarow, Y.: Phosphorus compounds of muscle and liver. Science 70, 381–382 (1929)
Szent-Györgyi, A., Banga, I.: Adenosinetriphosphatase. Science 93, 158 (1941)
Huxley, H., Hanson, J.: Changes in the cross-striations of muscle during contraction and stretch and their structural interpretation. Nature 173, 973–976 (1954)
Watson, J.D., Crick, F.H.C.: Molecular structure of nucleic acids: a structure for deoxyribose nucleic acid. Nature 171, 737–738 (1953)
Crick, F.: Central dogma of molecular biology. Nature 227, 561–563 (1970)
Yamato, I., Ando, T., Suzuki, A., Harada, K., Itoh, S., Miyazaki, S., Kobayashi, N., Takeda, M.: Toward in silico biology (from sequences to systems). Quantum Bio-Informatics (From Quantum Information to Bio-Informatics). In: Accardi, L., Freudenberg, W., Ohya, M. (eds.) Proceedings of the International Symposium of Quantum Bio-Informatics Research Center 2007, Chiba, pp. 440–455. World Scientific, Singapore (2008)
Gilbert, W.: The RNA world. Nature 319, 618 (1986)
Anfinsen, C.B.: Principles that govern the folding of protein chains. Science 181, 223–230 (1973)
Gibson, D.G., Benders, G.A., Andrews-Pfannkoch, C., Denisove, E.A., Baden-Tillson, H., Zaveri, J., Stockwell, T.B., Brownley, A., Thomas, D.W., Algire, M.A., Merryman, C., Young, L., Noskov, V.N., Glass, J.I., Venter, J.C., Hutchison 3rd, C.A., Smith, H.O.: Complete chemical synthesis, assembly, and cloning of a Mycoplasma genitalium genome. Science 319, 1215–1220 (2010)
Levinthal, C.: How to fold graciously. Mossbauer Spectroscopy in Biological Systems: Proceedings of a Meeting Held at Allerton House, pp. 22–24. Monticello, Illinois (1969)
Bryngelson, J.D., Wolynes, P.G.: Spin glasses and the statistical mechanics of protein folding. Proc. Natl. Acad. Sci. USA 84, 7524–7528 (1987)
Bryngelson, J.D., Onuchic, J.N., Socci, N.D., Wolynes, P.G.: Funnels, pathways, and the energy landscape of protein folding. Proteins: Struct., Funct., Bioinform. 21, 167–195 (1995)
Shaw, D.E., Maragakis, P., Lindorff-Larsen, K., Piana, S., Dror, R.O., Eastwood, M.P., Bank, J.A., Jumper, J.M., Salmon, J.K., Shan, Y., Wriggers, W.: Atomic-level characterization of the structural dynamics of proteins. Science 15, 341–346 (2010)
Basieva, I., Khrennikov, A., Ohya, M., Yamato, I.: Quantum-like interference effect in gene expression: glucose-lactose destructive interference. Syst. Synth. Biol. 5, 59–68 (2011)
Jacob, F., Monod, J.: Genetic regulatory mechanism in the synthesis of proteins. J. Mol. Biol. 3, 318–356 (1961)
Asano, M., Basieva, I., Khrennikov, A., Ohya, M., Tanaka, Y., Yamato, I.: Quantum-like model of diauxie in Escherichia coli: operational description of precultivation effect. J. Theor. Biol. 314, 130–137 (2012)
Khrennikov, A.: Classical and quantum mechanics on information spaces with applications to cognitive, psychological, social and anomalous phenomena. Found. Phys. 29, 1065–1098 (1999)
Ohya, M.: Adaptive dynamics and its applications to chaos and NPC problem. QP-PQ: quantum probability and white noise analysis. Quantum Bio-Inform. 21, 181–216 (2007)
Beckwith, J.R., Zipser, D.: The Lactose Operon. University of Tokyo Press, Tokyo (1971)
Beckwith, J.R.: The lactose operon in Escherichia coli and Salmonella typhimurium. In: Neidhardt, F.C., Ingraham, J.L., Low, K.B., Magasanik, B., Schaechter, M., Umbarger, H.E. (eds.), pp. 1444–1452. ASM, Washington (1987)
Loomis Jr., W.F., Magasanik, B.: Glucose-lactose diauxie in Escherichia coli. J. Bacteriol. 93, 1397–1401 (1967)
Inada, T., Kimata, K., Aiba, H.: Mechanism responsible for glucose-lactose diauxie in Escherichia coli challenge to the cAMP model. Genes Cells 1, 293–301 (1996)
Postma, P.W.: Phosphotransferase system for glucose and other sugars in Escherichia coli and Salmonella typhimurium. In: Neidhardt, F.C., Ingraham, J.L., Low, K.B., Magasanik, B., Schaechter, M., Umbarger, H.E. (eds.), pp. 127–141. ASM, Washington (1987)
Kitano, H.: Systems biology: a brief overview. Science 295, 1662–1664 (2002)
Tomita, M., Hashimoto, K., Takahashi, K., Shimizu, T.S., Matsuzaki, Y., Miyoshi, F., Saito, K., Tanida, S., Yugi, K., Venter, J.C., Hutchison 3rd, C.A.: E-CELL: software environment for whole-cell simulation. Bioinformatics 15, 72–84 (1999)
Mendes, P.: GEPASI: a software for modeling the dynamics, steady states and control of biochemical and other systems. Comput. Appl. Biosci. 9, 563–571 (1993)
Albert, J., Rooman, M.: Dynamic modeling of gene expression in prokaryotes: application to glucose-lactose diauxie in Escherichia coli. Syst. Synth. Biol. 5, 33–43 (2011)
Asano, M., Basieva, I., Khrennikov, A., Ohya, M., Yamato, I.: A model of epigenetic evolution based on theory of open quantum systems. Syst. Synth. Biol. (2013). doi:10.1007/s11693-013-9109-2
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Asano, M., Khrennikov, A., Ohya, M., Tanaka, Y., Yamato, I. (2015). Fundamentals of Molecular Biology. In: Quantum Adaptivity in Biology: From Genetics to Cognition. Springer, Dordrecht. https://doi.org/10.1007/978-94-017-9819-8_3
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DOI: https://doi.org/10.1007/978-94-017-9819-8_3
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