Bases, biochemistry

Can the carbon-based biochemistry of life as we know it function in organic solvents Certainly, many enzymes function in organic solvents, and many organic reactions fundamental to biochemistry can occur in nonaqueous solvents.31,32 However, even enzymes that are active in organic solvents need some bound water to maintain their active structure. Moreover, water is important in other vital biochemical reactions during metabolism and biosynthesis, and water is a product of metabolic reactions. Scientists infer that carbon-based life is not likely to be able to adapt to a pure-solvent milieu unless it has some mechanism to form water from such solvents as alcohols or to produce all the necessary water de novo from biochemical reactions. Are those mechanisms possible, and is there evidence that bacteria could grow in some organic solvent, with or without trace levels of water ... 

Itoh N, Izumi Y, Yamada H (1987) Haloperoxidase-catalyzed halogenation of nitrogen-containing aromatic heterocycles represented by nucleic bases. Biochemistry 26 282-289... 

McGhee, J., von Hippel, P., formaldehyde as a probe of DNA structure. I. Reaction with exocyclic amino groups of DNA bases. Biochemistry 1977, 14, 1281-1303. 

Courtois E, Ploux O. Escherichia coli cyclopropane fatty acid synthase is a bound bicarbonate ion the active-site base Biochemistry 2005 44 13583-13590. 

It has been argued that the development of a sugar-based biochemistry might have been an early evolutionary iimovation [3] and that sugar catabolism may have been one of the first successful energy-conversion processes. Therefore, I have chosen to consider central metabolism in two parts (a) the conversion of glucose and other sugars to pyruvate, and... 

By structure is meant not only the disposition of covalent bonds, but also conformation, at the small molecule and at the macromolecular level. By mechanism is meant a description of reactive intermediates and transition states - evidence-based curly arrows. It is with some reservation that the word carbohydrate is in the title, as strictu sensu carbohydrate biochemistry includes much of primary metabolism, such as glycolysis or the Calvin cycle. These reactions are in general not covered there are several excellent curly-arrow-based biochemistry texts available. 

Dolinnaya NG, Braswell EH, Fosella JA, Klump H, Fresco JR (1993) Molecular and thermodynamic properties of d(A -G)10, a single-stranded nucleic acid helix without paired or stacked bases. Biochemistry 32 10263-10270... 

In recent years it has become increasingly apparent that more highly reduced phosphorus compounds (i.e. phosphonic and phosphinic acids) also play prominent roles in life science [245-247]. The mechanisms which have driven the chemical evolution of phosphate-based biochemistry are stiU under discussion [248]. Alternative prebiotic mechanisms for polyphosphate formation using reduced phosphorus species and particularly //-phosphinates (H2PO2 ) are emerging as probable explanations. 

Seek, F. and Kehne, A, OHgomers with alternating thymidine and 2 -deoxytubercidin duplex stabilization by a 7-deazapurine base, Biochemistry, 24,7556,1985. 

The ability to form chains is one of the most important characteristics of a carbon-based biochemistry. The complexity of life depends upon repeating imits that can be formed into structures capable of carrying out complex functions from information storage to cell membrane formation. Carbon fulfils this need. 

Y. Cao, G. Varo, M. Chang, B. Ni, R. Needleman, and J.K. Lanyi, Water is required for proton transfer from aspartate-96 to the bacteriorhodopsin Shiff base. Biochemistry 30 10972 (1991). 

Enzymes are classified in terms of the reactions which they catalyse and were formerly named by adding the suffix ase to the substrate or to the process of the reaction. In order to clarify the confusing nomenclature a system has been developed by the International Union of Biochemistry and the International Union of Pure and Applied Chemistry (see Enzyme Nomenclature , Elsevier, 1973). The enzymes are classified into divisions based on the type of reaction catalysed and the particular substrate. The suffix ase is retained and recommended trivial names and systematic names for classification are usually given when quoting a particular enzyme. Any one particular enzyme has a specific code number based upon the new classification. 

In Chapter 1 we saw that a major achievement of the first half of the twentieth cen tury was the picture of atomic and molecular structure revealed by quantum mechan ICS In this the last chapter we examine the major achievement of the second half of that century—a molecular view of genetics based on the structure and biochemistry of nucleic acids... 

PVDF-based microporous filters are in use at wineries, dairies, and electrocoating plants, as well as in water purification, biochemistry, and medical devices. Recently developed nanoselective filtration using PVDF membranes is 10 times more effective than conventional ultrafiltration (UF) for removing vimses from protein products of human or animal cell fermentations (218). PVDF protein-sequencing membranes are suitable for electroblotting procedures in protein research, or for analyzing the phosphoamino content in proteins under acidic and basic conditions or in solvents (219). 

Immunoassay is a method that identifies and quantifies unknown analytes usiag antibody—antigen reactions. Techniques are based ia immunochemistry, analytical chemistry, and biochemistry, with a history of development paralleling advances ia microbiology and immunology (see also Immunotherapeutic agents). 

A system based partly on historical names, partly on the substrate, and partly on the type of reaction catalyzed is far from satisfactory. In 1956, the International Union of Biochemistry set up a Commission on Enzymes to consider the classification and nomenclature of enzymes. The Commission presented a report in 1961 whose recommendations for naming and classifying enzymes were subsequently adopted (12). Enzymes are classified on the basis of the reactions they catalyze. Despite its apparent complexities, the system is precise and very descriptive, accommodating existing enzymes and serving as a systematic basis for the naming of new enzymes. AH enzymes are placed in one of the six principal classes. 

Auramine O (4,4 -bis-dimethylaminobenzophenone imine hydrochloride) [2465-27-2] M 321.9, pK 10,71 (free base), 9.78 (carbinolamine). Crystd from EtOH as hydrochloride, very slightly soluble in CHCI3, UV 434 (370) nm. The free base has m 136 after crystn from benzene. [J Chem Soc 1724 1949 Biochemistry 9 1540 1970]. 

Monte Carlo search methods are stochastic techniques based on the use of random numbers and probability statistics to sample conformational space. The name Monte Carlo was originally coined by Metropolis and Ulam [4] during the Manhattan Project of World War II because of the similarity of this simulation technique to games of chance. Today a variety of Monte Carlo (MC) simulation methods are routinely used in diverse fields such as atmospheric studies, nuclear physics, traffic flow, and, of course, biochemistry and biophysics. In this section we focus on the application of the Monte Carlo method for... 

S Modi, MI Paine, MI Sutcliffe, L-Y Lian, WU Pnmi-ose, CR Wolfe, GCK Roberts. A model for human cytochrome P450 2d6 based on homology modeling and NMR studies of substrate binding. Biochemistry 35 4540-4550, 1996. 

The first dynamical simulation of a protein based on a detailed atomic model was reported in 1977. Since then, the uses of various theoretical and computational approaches have contributed tremendously to our understanding of complex biomolecular systems such as proteins, nucleic acids, and bilayer membranes. By providing detailed information on biomolecular systems that is often experimentally inaccessible, computational approaches based on detailed atomic models can help in the current efforts to understand the relationship of the strucmre of biomolecules to their function. For that reason, they are now considered to be an integrated and essential component of research in modern biology, biochemistry, and biophysics. 

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