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Reactions With Disinfectants
Published in Richard A. Larson, Eric J. Weber, Reaction Mechanisms in Environmental Organic Chemistry, 2018
Richard A. Larson, Eric J. Weber
The reactions of aqueous solutions of free chlorine with nucleic acid bases has been studied by many groups of workers. They are generally very complex. The free pyrimidine base uracil (54), for example, gave a variety of products when chlorinated. The initial product, 5-chlorouracil (55: Hayatsu et al., 1971: Hoyano et al., 1973), was converted by excess HOCl to di- and trichloro derivatives, to chlorohydrins, and finally to ring destruction products including CO2, NCl3, and Cl3CCOOH. At high pH, significant quantities of CHCl3 were produced. Formaldehyde and formic acid were not observed, and the mechanism of the ring cleavage remains obscure (Dennis et al., 1978). The closely related compound, uridine monophosphate (56), was surprisingly unreactive toward HOCl relative to the other RNA nucleoside monophosphates. Cytidine and adenosine monophosphates (57,58) were most reactive as measured by UV spectroscopic changes. Products of the reactions were not determined (Dennis et al., 1979). Cytosine (59) and cytidine appeared to chlorinate more or less cleanly at the 5-position (Hayatsu et al., 1971); other mono- and dichloro isomers have been identified depending on chlorine dose and pH (Reynolds et al., 1988). The side-chain N-chloro adduct may be an intermediate, and chlorohydrins derived from double-bond HOCl addition arise at high concentrations of HOCl (Patton et al., 1972).
Metabolism
Published in Markus W. Covert, Fundamentals of Systems Biology, 2017
How do we mathematically represent such an objective? Scientists have measured the chemical composition of certain cells, including E. coli, from which we can determine the biomass maximization objective. For example, we know that, under certain conditions, E. coli is 70% water and that the remaining dry E. coli biomass consists of 55% protein, 20.5% RNA, 3.1% DNA, 9.1% lipid, 3.4% lipopolysaccharide, 2.5% murine, 2.5% glycogen, and 3.9% polyamines, metabolites, cofactors, and ions (by weight), and thus we also know that the metabolic network needs to produce these biomass components in these amounts to make cells. Several of these components can be specified further; for example, 1 g of E. coli DCW contains 0.205 g RNA, which has 165 µmol AMP (adenosine mono-phosphate), 203 µmol GMP (guanosine monophosphate), 126 µmol CMP (cytidine monophosphate), and 136 µmol UMP (uridine monophosphate).
Saccharomyces cerevisiae
Published in Shakeel Ahmed, Aisverya Soundararajan, Pullulan, 2020
Orotidine-5-monophosphate (OMP) is involved in pyrimidine synthesis [4, 25, 32]. Decarboxylation of orotidine-5-monophosphate to uridine monophosphate is often used as a selection marker for the URA3 gene [3, 7, 18]. The orotidine-5-monophosphate (OMP) enzyme is thought to be a single function enzyme, and mutations can lead to autotrophy of uracil [32]. Thus, OMP decarboxylase enzyme activity can be quantitated, and 5-fluoro-orotic acid (5-FOA) can be added to agar to select for mutant revertants [7, 36, 46].
Assembly of nucleobases into rings and cages via metal ions
Published in Journal of Coordination Chemistry, 2022
Bernhard Lippert, Pablo J. Sanz Miguel
An alternative to intramolecular chelation of a metal ion by a nucleotide, which provides the mentioned macrochelate, is intermolecular metal binding, leading to a dinuclear complex. [Pt(en)(5′-CMP)]2 (with 5′-CMP = 5′-cytidine monophosphate) [17] is a typical example. In it, both PtII ions bind to N3 of the cytosine and an oxygen of the phosphate group each, thereby producing a head-tail dinuclear species. There is even the possibility of having exclusive metal binding to two bridging phosphate groups, with the nucleobases not involved in metal binding at all, such as in [Cu(L)(H2O)(5′-UMP)]2 [17] (with L = o-phenanthroline and 5′-UMP = 5′-uridine monophosphate), but of course, this pattern is phosphate—rather than nucleobase—specific. Related to this pattern are dinuclear nucleobase complexes with other bridging ligands such as hydroxide [18] or halide [19], and terminal nucleobases, which we likewise will not discuss further. The more typical 2:2-complexes are those, in which both metal ions cross-link donor sites of the heterocyclic rings. Examples today include virtually all common nucleobases.