Energetics of abiogenic chemical systems

After recalling the energy consumption necessary to produce the main categories of biochemicals from the equilibrium state of an hydrogenated atmosphere, the primary processes by which energy can be absorbed in a mixture of methane and ammonia in the presence of aqueous solutions are defined. From the very first excitations, unsaturated products are formed. In fact, this formation of atmospheric precursors is the primordial state of a photochemically induced redox dismutation.The evolution of solutions obtained from the dissolution of these atmospheric precursors in aqueous media is described from experimental data and analysed on energetic grounds. The relaxation of energy accumulated in such solutions involves non enzymic archetypes of the main categories of metabolic processes; in particular some unsaturated atmospheric precursors must be looked upon as primordial representatives of biochemical dehydrating agents.Absorption of light energy in the solutions obtained from the evolution of precursors happens near the visible range and should govern their further evolution. In fact, biochemicals which were proviously detected as products of model experiments are not present in these solutions. They were probably obtained during analytical procedures from products of the evolution of atmospheric precursors which are unstable against decreases of pH.Cyclic autocatalytic effects must be involved in the further evolution of the models of the first aqueous solutions. Their possible role in the appearance of optical dissymmetry is emphasized on theoretical grounds.     

Before programs: the physical origination of multicellular forms

By examining the formative role of physical processes in modern-day developmental systems, we infer that although such determinants are subject to constraints and rarely act in a "pure" fashion, they are identical to processes generic to all viscoelastic, chemically excitable media, non-living as well as living. The processes considered are free diffusion, immiscible liquid behavior, oscillation and multistability of chemical state, reaction-diffusion coupling and mechanochemical responsivity. We suggest that such processes had freer reign at early stages in the history of multicellular life, when less evolution had occurred of genetic mechanisms for stabilization and entrenchment of functionally successful morphologies. From this we devise a hypothetical scenario for pattern formation and morphogenesis in the earliest metazoa. We show that the expected morphologies that would arise during this relatively unconstrained "physical" stage of evolution correspond to the hollow, multilayered and segmented morphotypes seen in the gastrulation stage embryos of modern-day metazoa as well as in Ediacaran fossil deposits of approximately 600 Ma. We suggest several ways in which organisms that were originally formed by predominantly physical mechanisms could have evolved genetic mechanisms to perpetuate their morphologies.     

Solvent-tolerant bacteria for biotransformations in two-phase fermentation systems

Product removal from aqueous media poses a challenge in biotechnological whole-cell biotransformation processes in which substrates and/or products may have toxic effects. The assignment of an additional liquid solvent phase provides a solution, as it facilitates in situ product recovery from aqueous media. In such two-phase systems, toxic substrates and products are present in the aqueous phase in tolerable but still bioavailable amounts. As a matter of course, adequate organic solvents have to possess hydrophobicity properties akin to substrates and products of interest, which in turn involves intrinsic toxicity of the solvents used. The employment of bacteria being able to adapt to otherwise toxic solvents helps to overcome the problem. Adaptive mechanisms enabling such solvent tolerant bacteria to survive and grow in the presence of toxic solvents generally involve either modification of the membrane and cell surface properties, changes in the overall energy status, or the activation and/or induction of active transport systems for extruding solvents from membranes into the environment. It is anticipated that the biotechnological production of a number of important fine chemicals in amounts sufficient to compete economically with chemical syntheses will soon be possible by making use of solvent-tolerant microorganisms.     

Native chemical ligation of hydrophobic [corrected] peptides in lipid bilayer systems

The covalent modification of water-insoluble membrane polypeptides incorporated into lipid bilayers by native chemical ligation is described. The key feature of this strategy is the use of cubic lipidic phase (CLP) matrixes as reaction media. The CLP-matrix consists of a lipid bilayer into which hydrophobic polypeptides and folded membrane proteins can be inserted and two unbounded aqueous channels that give the aqueous phase access to both sides of an infinite lipid bilayer and thus ensure that modification of solvent-exposed sites is independent of the topology of membrane incorporation. The enzymatic removal of an N-terminal proteolytic cleavage sequence from the membrane polypeptide exposes an N-terminal cysteine residue. Subsequently, a C-terminal thioester peptide is joined to the N-terminus of the polypeptide by a native chemical ligation reaction. By use of this approach, incorporation of a variety of molecular tools, such as spectroscopic probes, unnatural amino acids, and molecular markers into membrane proteins that cannot be easily solubilized in detergent or denaturant solutions, may be achieved.     

Redox and addition chemistry of quinoid compounds and its biological implications

The overall biological activity of quinones is a function of the physico-chemical properties of these compounds, which manifest themselves in a critical bimolecular reaction with bioconstituents. Attempts have been made to characterize this bimolecular reaction as a function of the redox properties of quinones in relation to hydrophobic or hydrophilic environments. The inborn physico-chemical properties of quinones are discussed on the basis of their reduction potential and dissociation constants, as well as the effect of environmental factors on these properties. Emphasis is given on the effect of methyl-, methoxy-, hydroxy-, and glutathionyl substituents on the reduction potential of quinones and the subsequent electron transfer processes. The redox chemistry of quinoid compounds is surveyed in terms of a) reactions involving only electron transfer, as those accomplished during the enzymic reduction of quinones and the non-enzymic interaction with redox couples generating semiquinones, and b) nucleophilic addition reactions. The addition of nucleophiles, entailing either oxidation or reduction of the quinone, are exemplified in reactions with oxygen- or sulfur nucleophiles, respectively. The former yields quinone epoxides, whereas the latter yields thioether-hydroquinone adducts as primary molecular products. The subsequent chemistry of these products is examined in terms of enzymic reduction, autoxidation, cross-oxidation, disproportionation, and free radical interactions. The detailed chemical mechanisms by which quinoid compounds exert cytotoxic, mutagenic and carcinogenic effects are considered individually in relation to redox cycling, alterations of thiol balance and Ca++ homeostasis, and covalent binding.     

Bioavailability of organic chemicals in the aquatic environment.

1. Bioavailability in the aquatic environment can be defined as the external availability of a chemical to an organism. The availability of sediment-sorbed chemicals to organisms is a particularly important aspect of this phenomena. 2. Various experiments described in the literature, such as toxicity and accumulation experiments, have investigated the influence of suspended sediment in the aqueous phase on bioavailability. 3. The bioavailability of a chemical appears to be influenced by the chemical, the sediment, and the organism being examined. Thus, describing "the bioavailability" of a chemical in the aquatic environment is not a simple process.     

Electrochemical methods of evaluating the van't Hoff enthalpy in reactions involving biological macromolecules

We highlight conditions under which coincidence of van't Hoff and calorimetric enthalpies can be experimentally verified for reactions of biochemical interest. First, we clarify that, often, chemical equations in condensed phase do not explicitly contain information on all processes involved. Second, we underline that the accuracy of electrochemical methods is much higher than that of other non-calorimetric techniques. Electrochemical data on the binding of ethidium ion to DNA are re-examined to verify that the entropy evaluated as the temperature derivative of the free energy agrees in full with the calorimetric one. Third, we point out that unfolding or self-association enthalpies of redox proteins can be reliably obtained by electromotive force measurements, taking advantage of their linkage to redox enthalpies. Thermodynamic cycles coupling biochemical transformations to redox systems are briefly discussed.     

A paradoxical effect of hydrated C60-fullerene at an ultralow concentration on the viability and aging of cultured Chinese hamster cells

The effect of an aqueous solution of hydrated C₆₀-fullerene (HyFn) on the growth and “stationary phase aging” (accumulation of “age-related” changes in cultured cells during the slowing down of their proliferation within a single passage and the subsequent “aging” in the stationary phase of growth) of transformed B11-dii FAF28 Chinese hamster cells was studied. The final calculated concentration of HyFn in the growth medium was 10^?19 M. A paradoxical result contrasting the available data on the absence of HyFn cytotoxicity at higher concentrations was obtained in our experiments: namely, HyFn decelerated cell proliferation (estimated by the growth of mass culture, as well as by the efficiency of colony formation) and accelerated the “stationary phase aging” of the cell culture. Moreover, repeated addition of an aqueous solution of HyFn (to the final calculated concentration of 10^?19 M) to the cells that had already reached the stationary phase of growth caused a rapid (within no more than 24 h) death of a significant part of the cell population. The observed effect of HyFn at ultralow concentration is supposed to arise from the alterations in the properties of the water surrounding the fullerene molecule: namely, water becomes a donor and acceptor of electrons and regulates redox processes (especially those involving oxygen) in aqueous systems. This effect of HyFn at an ultralow concentration may be specific for transformed cells, and, therefore, experiments on normal fibroblasts with limited mitotic potential are planned as a continuation of the present study. It is also possible that the reported antiaging effect of HyFn in experimental animals is due to its anticancer, immunostimulatory, antiviral, and antibacterial properties manifested only at the whole-organism level.     

Formation of plastocyanin and cytochrome c-553 in different species of blue-green algae

Fifteen species from different genera of blue-green algae have been examined for their formation of plastocyanin (PC) and cytochrome c-553 (cyt c-553) in high or low Cu media. In addition to species which contain only cyt c-553 and those which completely exchange their cyt c-553 by PC, a new regulatory type was detected in which this exchange was incomplete. By comparing different species, it could be shown that either this incomplete exchange of cyt c-553 by PC as well as lack of PC in some other blue-green algae is not caused by restricted Cu uptake but is due to different biosynthetic and regulatory properties. Occurrence of PC and cyt c-553 cannot be used as a taxonomic criterium to classify blue-green algae. However, formation of either one or both of these redox components fits well into a line of evolution of the photosynthetic apparatus from the blue-green algae via green algae to higher plants.Abbreviations PC plastocyanin; cyt c-553, cytochrome c-553     

Enhancement of hydrolytic activity of sphingolipid ceramide N-deacylase in the aqueous-organic biphasic system

Lysoglycosphingolipids were produced from glycosphingolipids by using sphingolipid ceramide N-deacylase, which cleaves the N-acyl linkage between fatty acids and sphingosine bases in various glycosphingolipids. The enzyme reaction was done in a biphasic media prepared with water;-immiscible organic solvent and aqueous buffer solution containing the enzyme. We investigated the effects of organic solvents and detergents on lysoglycosphingolipid production in the biphasic system. Among the organic solvents tested, n-butylbenzene, cumene, cyclodecane, cyclohexane, n-decane, diisopropylether, n-heptadecane, and methylcyclohexane promoted hydrolysis of GM1, whereas benzene, chloroform, ethyl acetate, and toluene inhibited GM1 hydrolysis. Hydrolysis of asialo GM1, GD1a, GalCer, and sulfatide was also enhanced by the addition of n-decane. The hydrolytic activity of the enzyme was enhanced by the addition of 0.8% sodium taurodeoxycholate or sodium cholate to the aqueous phase. The most effective hydrolysis of various glycosphingolipids by the enzyme was thus obtained in the aqueous-n-decane biphasic system containing 0.8% sodium taurodeoxycholate. Under this condition, the fatty acids released from GM1 by the action of the enzyme were trapped and diffused into the organic phase, while lysoGM1 remained in the aqueous phase.Thus the almost complete hydrolysis of GM1 was achieved using the biphasic system, while at most 70% of hydrolysis was obtained using normal aqueous media possibly due to the inhibition of hydrolysis reaction by accumulation of fatty acids in the reaction mixture.     

Theory of iron-sulfur center N-2 oxidation and reduction by ATP.

The data of Ohnishi (1975) and of Gutman and coworkers on iron-sulfur center N-2 in mitochondria and submitochondrial particles are examined in as much quantitative detail as possible from the standpoint of both chemiosmotic theory and of chemical intermediate (transductase) theory.A method of examination of the behavior of an energy transduction site by plotting its properties as a function of both the high and low redox potentials on either side of the site is described in some detail.That adding ATP causes center N-2 to go oxidized when buffered redox-wise on the low potential side and reduced when buffered on the high potential side can be explained by both chemiosmotic and chemical intermediate theory.Chemiosmotic explanations consistent with the data exclude location of N-2 at the inside of the mitochondrial membrane, but location at the out side or the middle or mobile across the membrane cannot be ruled out by present data.All four abridged transductase models of chemical intermediate theory can be fitted to the data by choice of parameters.That center N-2 is a simple redox couple located at either side of energy transduction site 1 is ruled out.Further experiments needed to clarify present ambiguities are shown to be: (i) Adding ATP while buffering (redox-wise) the NAD⁺-NADH inside whole mitochondria; (ii) mapping the apparent midpoint potential or, alternatively, the redox state as a complete function of the redox potentials on both the high and low sides; (iii) determination of differences that may be caused by sidedness of the preparation (mitochondria or submitochondrial particles); and (iv) determining effects of changing the partitioning of the proton motive force between ΔpH and membrane potential.     

早期地球的环境变化和生命的化学进化

生命起源是当代最大的科学疑谜之一,也是历来人类普遍关注的一个焦点。在地球上最早的生物出现之前,有机物经历了漫长而复杂的化学进化过程,称为生命的化学进化。地球上生命的化学进化与非生物部分的早期演化过程,是密切地相互关联、相互作用并相互制约的。文章着重阐述与生命的化学关系最为密切的冥古宙和太古宙的地球演化历史,指出这两个阶段所形成的还原性原始大气和古海洋条件在生命的化学进行中起了极其重要的作用,并且从宇宙形成、太阳系演化和地球环境早期演化的角度,探讨地球生命的化学进化历程;以地球形成初期发生了一系列复杂的有机化学反应过程,由无机分子生成生物小分子,再进一步生成生物大分子,直至最后产生原始细胞。此外,文章评述当前国际上最流行的生命化学进化学说,对早期地球的化学进化是发生在地球表面的原始海洋、粘土矿物、火山喷发等,或是来源于地球之外的宇宙空间进行了综合的阐述。     

Bioavailability of organic chemicals in the aquatic environment

• 1.1. Bioavailability in the aquatic environment can be defined as the external availability of a chemical to an organism. The availability of sediment-sorbed chemicals to organisms is a particularly important aspect of this phenomena.
• 2.2. Various experiments described in the literature, such as toxicity and accumulation experiments, have investigated the influence of suspended sediment in the aqueous phase on bioavailability.
• 3.3. The bioavailability of a chemical appears to be influenced by the chemical, the sediment, and the organism being examined. Thus, describing “the bioavailability” of a chemical in the aquatic environment is not a simple process.

     

Micron-scale phase segregation in lipid monolayers induced by myelin basic protein in the presence of a cholesterol analog

It was previously shown that myelin basic protein (MBP) can induce phase segregation in whole myelin monolayers and myelin lipid films, which leads to the accumulation of proteins into a separate phase, segregated from a cholesterol-enriched lipid phase. In this work we investigated some factors regulating the phase segregation induced by MBP using fluorescent microscopy of monolayers formed with binary and ternary lipid mixtures of dihydrocholesterol (a less-oxidable cholesterol analog) and phospholipids. The influence of the addition of salts to the subphase and of varying the lipid composition was analyzed. Our results show that MBP can induce a dihydrocholesterol-dependent segregation of phases that can be further regulated by the electrolyte concentration in the subphase and the composition (type and proportion) of non-sterol lipids. In this way, changes of the lipid composition of the film or the ionic strength in the aqueous media modify the local surface density of MBP and the properties (phase state and composition) of the protein environment.     

Diffusion of hydrophilic probes in bicontinuous lipidic cubic phase

The lipidic cubic phase was prepared by mixing monoolein (monooleoyl-rac-glycerol, MO) with water in 64:36% ratio and applied to the solid support-glassy carbon or platinum electrodes. Highly viscous, homogeneous and transparent cubic phase film remained stable and firmly attached to the electrode surface. In order to describe the efficiency of transport of small hydrophilic molecules within the film, we studied the diffusion of selected redox mediators along the network of aqueous channels present in the cubic phase structure. Loading times, diffusion coefficients and concentrations of the mediators in the layer were determined by voltammetry and chronocoulometry using two types of electrodes: a normal size electrode working in the linear diffusion regime and an ultramicroelectrode working under spherical diffusion conditions. In addition to the well-defined order, transparency and viscosity, the fast transport of small redox mediators through the aqueous channels of the cubic phase and along the interfacial water-lipid region is another important property of this matrix. The diffusion of the hydrophilic probes in the cubic phase was found to be more efficient than in the Nafion layers. Efficient transport of small redox mediators within the cubic phase means that not only enzymes and synthetic catalysts can be incorporated into the phase but also their fast communication with electrode surface will be enabled thanks to the simultaneous incorporation of small mobile redox mediators. This property of the cubic liquid crystalline phases based on lipids makes them especially interesting from the point of view of practical applications in biosensing and bioelectrocatalysis.     

Structure for energy cycle: a unique status of the second law of thermodynamics for living systems

Distinguishing things from beings, or matters from lives, is a fundamental question. Extending E. Schr?dinger's neg-entropy and I. Prigogine's dissipative structure, we propose a chemical kinetic view that the earliest "live" process is embedded essentially in a special interaction between a pair of specific components under a particular, corresponding environmental conditions. The interaction exists as an inter-molecular-force-bond complex(IMFBC) that couples two separate chemical processes: one is the spontaneous formation of the IMFBC driven by a decrease of Gibbs free energy as a dissipative process; while the other is the disassembly of the IMFBC driven thermodynamically by free energy input from the environment. The two chemical processes coupled by the IMFBC originated independently and were considered non-living on Earth, but the IMFBC coupling of the two can be considered as the earliest form of metabolism: the first landmark on the path from things to a being. The dynamic formation and disassembly of the IMFBC, as a composite individual, follows a principle designated as "… structure for energy for structure for energy…", the cycle continues; and for short it will be referred to as "structure for energy cycle". With additional features derived from this starting point, the IMFBC-centered "live" process spontaneously evolved into more complex living organisms with the characteristics currently known.     

The evolving redox chemistry and bioavailability of vanadium in deep time

The incorporation of metal cofactors into protein active sites and/or active regions expanded the network of microbial metabolism during the Archean eon. The bioavailability of crucial metal cofactors is largely influenced by earth surface redox state, which impacted the timing of metabolic evolution. Vanadium (V) is a unique element in geo–bio‐coevolution due to its complex redox chemistry and specific biological functions. Thus, the extent of microbial V utilization potentially represents an important link between the geo‐ and biospheres in deep time. In this study, we used geochemical modeling and network analysis to investigate the availability and chemical speciation of V in the environment, and the emergence and changing chemistry of V‐containing minerals throughout earth history. The redox state of V shifted from a more reduced V(III) state in Archean aqueous geochemistry and mineralogy to more oxidized V(IV) and V(V) states in the Proterozoic and Phanerozoic. The weathering of vanadium sulfides, vanadium alkali metal minerals, and vanadium alkaline earth metal minerals were potential sources of V to the environment and microbial utilization. Community detection analysis of the expanding V mineral network indicates tectonic and redox influence on the distribution of V mineral‐forming elements. In reducing environments, energetic drivers existed for V to potentially be involved in early nitrogen fixation, while in oxidizing environments vanadate () could have acted as a metabolic electron acceptor and phosphate mimicking enzyme inhibitor. The coevolving chemical speciation and biological functions of V due to earth's changing surface redox conditions demonstrate the crucial links between the geosphere and biosphere in the evolution of metabolic electron transfer pathways and biogeochemical cycles from the Archean to Phanerozoic.     

Kinetic models for enzymic cellulose degradation in aqueous two-phase systems

Cellulose materials can readily be degraded into cellobiose and glucose by hydrolysis of the enzymes cellulase and beta-glucosidase in aqueous media. Product inhibition does, however, retard the reaction rate and reduce productivity. This may be avoided by carrying out the degradation of cellulose in an aqueous two-phase system, which permits the enzymes and the substrate to be partitioned to one phase and the products to be extracted into a second phase. In addition, two-phase systems also allow recycling of the enzymes. Here, three models previously developed for "one-phase" enzymic degradation are compared to data from enzymic degradation in an aqueous two-phase system. The models tested agreed relatively well with batch experiments during a period of 200 h. For one of the models tested, continuous degradation also gave accurate agreement.     

Influence of auxins on alkaloid accumulation by a transgenic cell line of Catharanthus roseus

The transgenic cell line of Catharanthus roseus (L.) G. Don S10 was used to study the effect of the presence of the synthetic auxins naphthalene acetic acid and 2,4-dichlorophenoxyeacetic acid in the culture medium on the accumulation of terpenoid indole alkaloids. Line S10 carries a recombinant, constitutively over-expressed version of the endogenous strictosidine synthase gene. The experiments were carried out using a two-stage culture system, consisting of a growth phase of 7 to 10 days and a production phase of 14 or 30 days. The hormonal composition was a crucial factor when formulating both the growth and the production media. It was determined that the presence of naphthalene acetic acid during the production phase led to lower levels of alkaloid accumulation. The presence of 2,4-dichlorophenoxyacetic acid in the growth medium reduced culture aggregation and repressed secondary metabolism. Cultures grown in medium containing 2,4-dichlorophenoxyacetic acid showed reduced capacity to supply biosynthetic precursors, which resulted in low levels of accumulation of terpenoid indole alkaloids. Cultures grown in 2,4-D-containing medium showed reduced capacity to supply biosynthetic precursors and higher rates of catabolic activity, which resulted in low levels of TIA accumulation. The expression of the gus and strictosidine synthase transgenes, measured at the enzyme level, was similarly high under all conditions tested. This revised version was published online in June 2006 with corrections to the Cover Date.