An elementary kinetic model of energy coupling in biological membranes

The purpose of this work is to contribute to the understanding of the fundamental kinetic properties of the processes of energy coupling in biological membranes. For this, we consider a model of a microorganism that, in its plasma membrane, expresses two electrogenic enzymes (E(1) and E(2)) transporting the same monovalent cation C and electrodiffusive paths for C and for a monovalent anion A. E(1) (E(2)) couples transport C to the reaction S(1)<-->P(1) (S(2)<-->P(2)). We developed a mathematical model that describes the rate of change of the electrical potential difference across the membrane, of the internal concentrations of C and A, and of the concentrations of S(2) and P(2). The enzymes are incorporated via two-state kinetic models; the passive ionic fluxes are represented by classical formulations of electrodiffusion. The microorganism volume is maintained constant by accessory regulatory devices. The model is utilized for stationary and dynamic studies for the case of bacteria employing the electrochemical gradient of Na(+) as energetic intermediate. Among other conclusions, the results show that the membrane potential represents the relevant kinetic intermediate for the overall coupling between the energy donor reaction S(1)<-->P(1) and the synthesis of S(2).     

Role of water in some biological processes.

The state of intracellular water has been a matter of controversy for a long time for two reasons. First, experiments have often given conflicting results. Second, hitherto, there have been no plausible grounds for assuming that intracellular water should be significantly different from bulk water. A collective behavior of water molecules is suggested here as a thermodynamically inevitable mechanism for generation of appreciable zones of abnormal water. At a highly charged surface, water molecules move together, generating a zone of water perhaps 6 nm thick, which is weakly hydrogen bonded, fluid, and reactive and selectively accumulates small cations, multivalent anions, and hydrophobic solutes. At a hydrophobic surface, molecules move apart and local water becomes strongly bonded, inert, and viscous and accumulates large cations, univalent anions, and compatible solutes. Proteins and many other biopolymers have patchy surfaces which therefore induce, by the two mechanisms described, patchy interfacial water structures, which extended appreciable distances from the surface. The reason for many conflicting experimental results now becomes apparent. Average values of properties of water measured in gels, cells, or solutions of proteins are often not very different from the same properties of normal water, giving no indication that they are averages of extreme values. To detect the operation of this phenomenon, it is necessary to probe selectively a single abnormal population. Examples of such experiments are given. It is shown that this collective behavior of water molecules amounts to a considerable biological force, which can be equivalent to a pressure of 1,000 atm (1.013 x 10(5) kPa). It is suggested that cells selectively accumulate K+ ions and compatible solutes to avoid extremes of water structure in their aqueous compartments, but that cation pumps and other enzymes exploit the different solvent properties and reactivities of water to perform work of transport or synthesis.     

Analysis of information content for biological sequences.

Decomposing a biological sequence into modular domains is a basic prerequisite to identify functional units in biological molecules. The commonly used segmentation procedures usually have two steps. First, collect and align a set of sequences that are homologous to the target sequence. Then, parse this multiple alignment into several blocks and identify the functionally important ones by using a semi-automatic method, which combines manual analysis and expert knowledge. In this paper, we present a novel exploratory approach to parsing and analyzing such kinds of multiple alignments. It is based on a type of analysis-of-variance (ANOVA) decomposition of the sequence information content. Unlike the traditional change-point method, this approach takes into account not only the composition biases but also the overdispersion effects among the blocks. The new approach is tested on the families of ribosomal proteins and has a promising performance. It is shown that the new approach provides a better way for judging some important residues in these proteins. This allows one to find some subsets of residues, which are critical to these proteins.     

Information content of chemical structures and some possible biological applications

The purpose of this paper is to calculate the amount of information contained in a chemical or biological structure, and to estimate the energy needed for obtaining an organization unit. The first problem is solved by applying H. J. Morowitz's reasoning (Bull. Math. Biophysics,17, 81–86, 1955) and, for the second one, calculations based upon bond formation heat are carried out.Information content theoretical physical entropy, real physical entropy, informational entropy or negentropy entropic information or neginformation, heat amount, as well as relationships between these system parameters, are defined and used. The investigation covers 63 chemical substances (inorganic and organic compounds). The numerical results should show that common organized systems happen to be between two extreme kinds of systems: highly disordered systems and ideally organized systems. Some speculative numerical applications are carried out regarding chlorophyllian photosynthesis and information amount accumulated through biological growth. It seems that Information Theory may predict some biocalorimetric results.     

Chemical constituents and energy content of some latex bearing plants

The latex bearing plants Plumeria alba, Calotropis procera, Euphorbia nerrifolia, Nerium indicum and Mimusops elengi were evaluated as potential renewable sources of energy and chemicals. Plant parts (leaf, stem, bark) and also whole plants were analyzed for elemental composition, oil, polyphenol, hydrocarbons, crude protein, alpha-cellulose, lignin and ash. The dry biomass yields were between 4.47 and 13.74 kg/plant. The carbon contents in whole plants varied from 38.5% to 44.9%, while hydrogen and nitrogen contents varied from 5.86% to 6.72% and 1.26% to 2.34%, respectively. The bark of the plants contained the highest amount of hydrocarbons (1.78-3.93%) and the leaves contained the lowest amounts (0.26-1.82%). The unsaponifiable materials and fatty acids in the oil fractions of whole plants ranged from 22.8% to 56.4% and 24.7% to 58.7%, respectively. The highest gross heat value was exhibited by C. procera (6145 cal/g) and the lowest by N. indicum (4405 cal/g). Hydrocarbon fractions were characterized by IR and (1)H-NMR and by thermogravimetric analyses. The activation energy (E(a)) in the third stage of decomposition was the greatest in the hydrocarbon fraction obtained from M. elengi (16.40 kJ mol(-1)) and the lowest for C. procera (3.96 kJ mol(-1)). The study indicated that the plant species might be suitable as alternative source of hydrocarbons and other phytochemicals.     

On some properties of stochastic information processes in neurons and neuron populations

The information in the nervous spike trains and its processing by neural units are discussed. In these problems, our attention is focused on the stochastic properties of neurons and neuron populations. There are three subjects in this paper, which are the spontaneous type neuron, the forced type neuron and the reciprocal inhibitory pairs.

1. The spontaneous type neuron produces spikes without excitatory inputs. The mathematical model has the following assumptions. The neuron potential (NP) has the fluctuation and obeys the Ornstein-Uhlenbeck process, because the N P is not so perfectly random as that of the Wiener process but has an attraction to the rest value. The threshold varies exponentially and the NP has the constant lower limit. When the NP reaches the threshold, the neuron fires and the NP is reset to a certain position. After a firing, an absolute refractory period exists. In discussing the stochastic properties of neurons, the transition probability density function and the first passage time density function are the important quantities, which are governed by the Kolmogorov's equations. Although they can be set up easily, we can rarely obtain the analytical solutions in time domain. Moreover, they cover only simple properties. Hence the numerical analysis is performed and a good deal of fair results are obtained and discussed.
2. The forced type neuron has input pulse trains which are assumed to be based on the Poisson process. Other assumptions and methods are almost the same as above except the diffusion approximation of the stochastic process. In this case, we encounter the inhomogeneous process due to the pulse-frequency-modulation, whose first passage time density reveals the multimodal distribution. The numerical analysis is also tried, and the output spike interval density is further discussed in the case of the periodic modulation.
3. Two types of reciprocal inhibitory pairs are discussed. The first type has two excitatory driving inputs which are mutually independent. The second type has one common excitatory input but it advances in two ways, one of which has a time lag. The neuron dynamics is the same as that of the forced type neuron and each neuron has an identical structure. The inputs are assumed to be based on the Poisson process and the inhibition occurs when the companion neuron fires. In this case, the equations of the probability density functions are not obtained. Hence the computer simulation is tried and it is observed that the stochastic rhythm emerges in spite of the temporally homogeneous inputs. Furthermore, the case of inhomogeneous inputs is discussed.

     

Restoration of some energy linked processes lost during the ageing of rat liver mitochondria

Some energy linked processes partially lost during the ageing of rat liver mitochondria, such as respiratory control index, ADP:O ratio and the Ca⁺⁺ and K⁺ uptake were restored to approximately the original level prior to ageing by addition of dithioerythritol to aged mitochondria.It is suggested that the maintenance of mitochondrial energy linked processes may depend upon the integrity of specific pairs of vicinal thiol groups of the membrane.     

Storing energy crops for methane production: effects of solids content and biological additive

The effect of storage on chemical characteristics and CH4 yield (taking into account loss of VS during storage) of a mixture of grasses and ryegrass, ensiled as such (low solids content) and after drying (medium and high solids) with and without biological additive, were studied in field and laboratory trials. Up to 87% and 98% of CH4 yield was preserved with low solids grass (initial TS 15.6%) and high solids ryegrass (initial TS 30.4%), respectively, after storage for 6months, while under suboptimal conditions at most 37% and 52% of CH4 yield were lost. Loss in CH4 yield was mainly due to VS loss, presumably caused by secondary fermentation as also suggested by increasing pH during storage. Biological additive did not assist in preserving the CH4 yield.     

Using lanthanide-based resonance energy transfer for in vitro and in vivo studies of biological processes

This review describes key directions in the development of different probes based on complex compounds of lanthanides for in vitro and in vivo researches. The role of microsecond fluorescence of lanthanides for overcoming problems of background fluorescence is considered. The basic classes of synthetic and genetically encoded complex compounds of lanthanides are summarized. Main principles of designing lanthanide-based molecular sensors, including FRET sensors based on lanthanides and colored fluorescent proteins are described. Their applications in bioanalytical research and cellular bioimaging are described. The main principles of cellular bioimaging using lanthanides are formulated, questions of their delivery into cells are considered, and the problem of their potential toxicity for living organisms is discussed. A technique using multiphoton excitation of lanthanides is described.     

Enzyme kinetics and the rate of biological processes

It is found empirically that a simple modification of the usual theoretical kinetic formulation (in which a transformation in the temperature scale is made) describes the temperature dependence of a wide variety of biochemical processes with a greater accuracy than hitherto achieved. Used in conjunction with the formulation of the theory of absolute reaction rates this empirical relation facilitates the determination of the thermodynamic functions. The results of applying these relations to biochemical processes support the contention that in the lower temperature range of enzyme activity a thermodynamic equilibrium exists between catalytically active and inactive forms of the enzyme. It is suggested that at low temperatures the formation of intramolecular hydrogen bridges converts reactive enzyme particles to a catalytically inactive condition, in which the active centers either lose their specific configuration or are no longer exposed to the substrate. Upon the basis of this interpretation, values of the entropy changes that are calculated theoretically are found to be in agreement with those calculated from the experimental data. The reactive configuration of the enzyme is apparently possessed in only a relatively narrow temperature band, being lost at both high and low temperatures. The kinetics of biological processes appear to differ only quantitatively from those of in vitro enzyme-catalyzed reactions. In both cases the non-linearity of the Arrhenius plots appears to be due to the fact that in the lower temperature range of enzyme activity a series of reactions are involved in the formation of the activated complex. These include reactions which lead to the formation of the catalytically reactive form of the enzyme followed by that which leads to the formation of the activated complex. The conversion of enzymes to the catalytically inactive form is essentially completed at temperatures of –10–0°C. in living systems, whereas in in vitro experiments with purified enzyme preparations this condition is not attained until temperatures 30–60°C. lower have been reached.     

Pre-enzymic origin of metabolic redox processes and of the energy storage processes

A treatment of the energetic conditions which regulate the non-equilibrium occurrence of metabolic redox processes associated with degradations of carbon chains or formations of condensed bonds shows that such processes are conditioned by the nature of the substrates and not by the preexistence of enzymic catalysts or cellular ultrastructures. An experimental program has been initiated to spectrophotometrically, electrochemically and chemically detect which redox components appear during model, studies of chemical evolution, operating from simple mixtures of CH₄, NH₃, H₂ and water and from the same mixtures with added phosphorus or sulfur derivatives and metal cations.