On the evolution of the photosynthetic pigments

During the course of terrestrial evolution, some organisms developed the capability of capturing and utilizing solar radiation. Colored compounds were undoubtedly incorporated within living forms from the earliest times, but during the transition from heterotrophic to a photoautotrophic metabolism only those pigments were selected that were components of the evolving photosynthetic apparatus and were able to catalyze reactions involving storage of light energy in chemical bonds. In this communication, some properties of tetrapyrroles with a closed porphyrin ring containing a metal ion in the center are discussed. These compounds are present in all principal contemporary photosynthetic pigments, and their synthesis has been demonstrated from simpler compounds under prebiotic conditions. It is probable that during intermediate stages in the evolution of photosynthesis, pigments with oxidizing potentials lower than that of chlorophyll were utilized to store light energy although they were not capable of removing electrons from water. The evolution and function of multiple forms of a given photosynthetic pigmentin vivo are discussed. ‘Accessory’ pigments may be regarded as rudiments of the evolutionary development of the photosynthetic apparatus.     

On the evolution of the photosynthetic pigments.

During the course of terrestrial evolution, some organisms developed the capability of capturing and utilizing solar radiation. Colored compounds were undoubtedly incorporated within living forms from the earliest times, but during the transition from heterotrophic to a photoautotrophic metabolism only those pigments were selected that were components of the evolving photosynthetic apparatus and were able to catalyze reactions involving storage of light energy in chemical bonds. In this communication, some properties of tetrapyrroles with a closed porphyrin ring containing a metal ion in the center are discussed. These compounds are present in all principal contemporary photosynthetic pigments, and their synthesis has been demonstrated from simpler compounds under prebiotic conditions. It is probable that during intermediate stages in the evolution of photosynthesis, pigments with oxidizing potentials lower than that of chlorophyll were utilized to store light energy although they were not capable of removing electrons from water. The evolution and function of multiple forms of a given photosynthetic pigment in vivo are discussed. 'Accessory' pigments may be regarded as rudiments of the evolutionary development of the photosynthetic apparatus.     

Excited flavin and pterin coenzyme molecules in evolution

Excited flavin and pterin molecules are active in intermolecular energy transfer and in photocatalysis of redox reactions resulting in conservation of free energy. Flavin-containing pigments produced in models of the prebiotic environment are capable of converting photon energy into the energy of phosphoanhydride bonds of ATP. However, during evolution photochemical reactions involving excited FMN or FAD molecules failed to become participants of bioenergy transfer systems, but they appear in enzymes responsible for repair of UV-damaged DNA (DNA photolyases) and also in receptors of blue and UV-A light regulating vital functions of organisms. The families of these photoproteins (DNA-photolyases and cryptochromes, LOV-domain- and BLUF-domain-containing proteins) are different in the structure and in mechanisms of the photoprocesses. The excited flavin molecules are involved in photochemical processes in reaction centers of these photoproteins. In DNA photolyases and cryptochromes the excitation energy on the reaction center flavin is supplied from an antenna molecule that is bound with the same polypeptide. The role of antenna is played by MTHF or by 8-HDF in some DNA photolyases, i.e. also by molecules with known coenzyme functions in biocatalysis. Differences in the structure of chromophore-binding domains suggest an independent origin of the photoprotein families. The analysis of structure and properties of coenzyme molecules reveals some specific features that were significant in evolution for their being selected as chromophores in these proteins.     

Photosystem II reaction centre quenching: mechanisms and physiological role

Dissipation of excess absorbed light energy in eukaryotic photoautotrophs through zeaxanthin- and DeltapH-dependent photosystem II antenna quenching is considered the major mechanism for non-photochemical quenching and photoprotection. However, there is mounting evidence of a zeaxanthin-independent pathway for dissipation of excess light energy based within the PSII reaction centre that may also play a significant role in photoprotection. We summarize recent reports which indicate that this enigma can be explained, in part, by the fact that PSII reaction centres can be reversibly interconverted from photochemical energy transducers that convert light into ATP and NADPH to efficient, non-photochemical energy quenchers that protect the photosynthetic apparatus from photodamage. In our opinion, reaction centre quenching complements photoprotection through antenna quenching, and dynamic regulation of photosystem II reaction centre represents a general response to any environmental condition that predisposes the accumulation of reduced Q(A) in the photosystem II reaction centres of prokaryotic and eukaryotic photoautotrophs. Since the evolution of reaction centres preceded the evolution of light harvesting systems, reaction centre quenching may represent the oldest photoprotective mechanism.     

Metastability of microtubules induced by competing internal forces

Recent modeling efforts to estimate energies of tubulin-tubulin bonds shed light on a delicate balance between competing mechanical forces maintaining microtubule walls. Here we formulate two important refinements to the explanation of bond energetics. First, energy surface calculations in the elastic filament approximation reveal a finite stabilizing barrier assumed a simple Lennard-Jones-like potential for protein bonds. The presence of a guanosine triphosphate (GTP) cap represented by straight segments is necessary, as it is predicted for a long time. In the lack of such a cap, the protofilaments are either in an absolutely stable or absolutely unstable state. Second, our calculations show that this barrier appears only if the mechanical energy associated with the conformational change after GTP hydrolysis (curling energy) is larger than the strength of lateral bonds. The overall energy balance we propose supports continuous assembly of GTP dimers, a metastable state in the presence of a finite GTP cap and energetically driven disassembly of guanosine diphosphate protofilaments.     

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.     

Modeling rupture of growing aneurysms

Growth and rupture of aneurysms are driven by micro-structural alterations of the arterial wall yet precise mechanisms underlying the process remain to be uncovered. In the present work we examine a scenario when the aneurysm evolution is dominated by turnover of collagen fibers. In the latter case it is natural to hypothesize that rupture of individual fibers (or their bonds) causes the overall aneurysm rupture. We examine this hypothesis in computer simulations of growing aneurysms in which constitutive equations describe both collagen evolution and failure. Failure is enforced in constitutive equations by limiting strain energy that can be accumulated in a fiber. Within the proposed theoretical framework we find a range of parameters that lead to the aneurysm rupture. We conclude in a qualitative agreement with clinical observations that some aneurysms will rupture while others will not.     

Reduction of Canine Plasminogen Leads to an Expanded Molecule which Precipitates

Canine plasminogen is made up of seven domains. In each domain there are several cysteines that are linked by disulfide bonds. Reduction of a limited number of the cystines destabilizes the protein such that it precipitates. The bond or bonds that are broken provide about 14 kcal of stabilization energy. Circular dichroism and dynamic light scattering indicate that there is probably an intermediate that is formed prior to precipitation and that the intermediate is somewhat larger than the compact form of plasminogen.     

Effects of Nanoanatase TiO2 on Photosynthesis of Spinach Chloroplasts Under Different Light Illumination

With a photocatalyzed characteristic, nanoanatase TiO₂ under light could cause an oxidation–reduction reaction. Our studies had proved that nano-TiO₂ could promote photosynthesis and greatly improve spinach growth. However, the mechanism of nano-TiO₂ on promoting conversion from light energy to electron energy and from electron energy to active chemistry energy remains largely unclear. In this study, we report that the electron transfer, oxygen evolution, and photophosphorylation of chloroplast (Chl) from nanoanatase-TiO₂-treated spinach were greatly increased under visible light and ultraviolet light illumination. It was demonstrated that nanoanatase TiO₂ could greatly improve whole chain electron transport, photoreduction activity of photosystem II, O₂-evolving and photophosphorylation activity of spinach Chl not only under visible light, but also energy-enriched electron from nanoanatase TiO₂, which entered Chl under ultraviolet light and was transferred in photosynthetic electron transport chain and made NADP⁺ be reduced into NADPH, and coupled to photophosphorylation and made electron energy be transformed to ATP. Moreover, nanoanatase h⁺, which photogenerated electron holes, captured an electron from water, which accelerated water photolysis and O₂ evolution.     

Promotion of Energy Transfer and Oxygen Evolution in Spinach Photosystem II by Nano-anatase TiO<Subscript>2</Subscript>

Being a proven photocatalyst, nano-anatase is capable of undergoing electron transfer reactions under light. In previous studies we had proven that nano-anatase improved photosynthesis and greatly promoted spinach growth. The mechanisms by which nano-anatase promotes energy transfer and the conversion efficiency of the process are still not clearly understood. In the present paper, we report the results obtained with the photosystem II (PSII) isolated from spinach and treated by nano-anatase TiO₂ and studied the effect of nano-anatase TiO₂ on energy transfer in PSII by spectroscopy and on oxygen evolution. The results showed that nano-anatase TiO₂ treatment at a suitable concentration could significantly change PSII microenvironment and increase absorbance for visible light, improve energy transfer among amino acids within PSII protein complex, and accelerate energy transport from tyrosine residue to chlorophyll a. The photochemical activity of PSII (fluorescence quantum yield) and its oxygen-evolving rate were enhanced by nano-anatase TiO₂. This is viewed as evidence that nano-anatase TiO₂ can promote energy transfer and oxygen evolution in PSII of spinach.     

The first living systems: a bioenergetic perspective.

The first systems of molecules having the properties of the living state presumably self-assembled from a mixture of organic compounds available on the prebiotic Earth. To carry out the polymer synthesis characteristic of all forms of life, such systems would require one or more sources of energy to activate monomers to be incorporated into polymers. Possible sources of energy for this process include heat, light energy, chemical energy, and ionic potentials across membranes. These energy sources are explored here, with a particular focus on mechanisms by which self-assembled molecular aggregates could capture the energy and use it to form chemical bonds in polymers. Based on available evidence, a reasonable conjecture is that membranous vesicles were present on the prebiotic Earth and that systems of replicating and catalytic macromolecules could become encapsulated in the vesicles. In the laboratory, this can be modeled by encapsulated polymerases prepared as liposomes. By an appropriate choice of lipids, the permeability properties of the liposomes can be adjusted so that ionic substrates permeate at a sufficient rate to provide a source of monomers for the enzymes, with the result that nucleic acids accumulate in the vesicles. Despite this progress, there is still no clear mechanism by which the free energy of light, ion gradients, or redox potential can be coupled to polymer bond formation in a protocellular structure.     

A photoacoustic study of water infiltrated leaves

Photoacoustic measurements of photosynthetic energy storage were conducted on water infiltrated pea and sugar maple leaves. The samples were vacuum infiltrated with pure water or with a suitable buffer. The use of such methodology permitted an accurate determination of the energy storage parameter at low modulation frequencies, where in non-infiltrated leaves oxygen evolution dominates the photoacoustic signal and does not allow energy storage measurements. Differences between infiltration media were not essential, however the use of pure water as infiltration medium sometimes caused instability of the measured energy storage, particularly at longer experimental time. Values of energy storage in individual samples ranged mostly between 0.2 to 0.35. Measured as a function of the modulation frequency, energy storage was found to be constant from about 10 to 200 Hz for pea leaves. In sugar maple leaves, the energy storage slightly increased between 100 and 500 Hz. Obtaining an accurate value for energy storage also allowed an accurate estimation of the O₂ evolution contribution to the photoacoustic signal of an unfiltrated leaf. In a maple leaf its frequency dependence showed only the effect of diffusion in the entire frequency range (10–500 Hz). Energy storage transients were observed after long periods (ca. 1/4-2 hrs) of dark adaptation upon the transition to light. In this case the initial energy storage was roughly about 1/2 that of the steady state value indicating strong PS I activity, while PS II was transiently incompetent. Energy-storage increased during illumination in a way to correspond to photosynthetic induction events as previously measured by fluorescence and O₂ evolution. Transients in energy storage were also found following high light to low light transitions (i.e., switch off of the saturating background light), that paralleled similar transients in oxygen evolution, showing initial transient inactivation followed by progressive reactivation of PS II.Abbreviations ES energy storage - PA photoacoustic(s) - PTR photothermal radiometry     

Origins of life: conformational energy calculations on primitive tRNA nestling an amino acid

We report conformational energy calculations on our proposal of a molecular interaction theory for the origin of the nucleic acid-directed, adaptor-mediated synthesis of proteins that links the phenomena of chemical and biological evolution. A particular conformation of a pentanucleotide turns out to be a double-sided template for a primitive decoding system. It is able to neatly nestle an amino acid via hydrogen bonds, and this complex is found to be an energetically favourable conformation. The total potential energy of the complex is calculated using semi-empirical potential energy functions. A local-minimum conformation is obtained and its features are reported. The template conformation of the pentanucleotide is found to have an energy value far lower than a regular helical conformation. When the amino acid is nestled in the cleft of the template-conformation through specific hydrogen bonds, the energy is further lowered. A D-amino acid nestled into the PIT (Primitive tRNA) is found to be less stable than its L counterpart, as revealed by energy calculations.     

Coherent phenomena in photosynthetic light harvesting: part two—observations in biological systems

Considerable debate surrounds the question of whether or not quantum mechanics plays a significant, non-trivial role in photosynthetic light harvesting. Many have proposed that quantum superpositions and/or quantum transport phenomena may be responsible for the efficiency and robustness of energy transport present in biological systems. The critical experimental observations comprise the observation of coherent oscillations or “quantum beats” via femtosecond laser spectroscopy, which have been observed in many different light harvesting systems. Part Two of this review aims to provide an overview of experimental observations of energy transfer in the most studied light harvesting systems. Length scales, derived from crystallographic studies, are combined with energy and time scales of the beats observed via spectroscopy. A consensus is emerging that most long-lived (hundreds of femtoseconds) coherent phenomena are of vibrational or vibronic origin, where the latter may result in coherent excitation transport within a protein complex. In contrast, energy transport between proteins is likely to be incoherent in nature. The question of whether evolution has selected for these non-trivial quantum phenomena may be an unanswerable question, as dense packings of chromophores will lead to strong coupling and hence non-trivial quantum phenomena. As such, one cannot discern whether evolution has optimised light harvesting systems for high chromophore density or for the ensuing quantum effects as these are inextricably linked and cannot be switched off.     

The Foundation of Kinship

Men's hunting has dominated the discourse on energy capture and flow in the past decade or so. We turn to women's roles as critical to household formation, pair-bonding, and intergenerational bonds. Their pivotal contributions in food processing and distribution likely promoted kinship, both genetic and affinal, and appear to be the foundation from which households evolved. With conscious recognition of household social units, variable cultural constructions of human kinship systems that were sensitive to environmental and technological conditions could emerge. Kinship dramatically altered the organization of resource access for our species, creating what we term "kinship ecologies." We present simple mathematical models to show how hunting leads to dependence on women's contributions, bonds men to women, and bonds generations together. Kinship, as it organized transfers of food and labor energy centered on women, also became integrated with the biological evolution of human reproduction and life history.     

Structure-function investigations of bacterial photosynthetic reaction centers

During photosynthesis light energy is converted into energy of chemical bonds through a series of electron and proton transfer reactions. Over the first ultrafast steps of photosynthesis that take place in the reaction center (RC) the quantum efficiency of the light energy transduction is nearly 100%. Compared to the plant and cyanobacterial photosystems, bacterial RCs are well studied and have relatively simple structure. Therefore they represent a useful model system both for manipulating of the electron transfer parameters to study detailed mechanisms of its separate steps as well as to investigate the common principles of the photosynthetic RC structure, function, and evolution. This review is focused on the research papers devoted to chemical and genetic modifications of the RCs of purple bacteria in order to study principles and mechanisms of their functioning. Investigations of the last two decades show that the maximal rates of the electron transfer reactions in the RC depend on a number of parameters. Chemical structure of the cofactors, distances between them, their relative orientation, and interactions to each other are of great importance for this process. By means of genetic and spectral methods, it was demonstrated that RC protein is also an essential factor affecting the efficiency of the photochemical charge separation. Finally, some of conservative water molecules found in RC not only contribute to stability of the protein structure, but are directly involved in the functioning of the complex.     

Effect of light intensity and thickness of culture solution on oxygen production by algae

Data from a small cylindrical culture unit with variable annular culture chambers indicate that (i) the rate of oxygen evolution by an algal culture in the linear phase of growth is a logarithmic function of light intensity, and (ii) the rate of oxygen evolution per unit volume of suspension is linearly related to the reciprocal of culture thickness. These two relationships have been combined in an empirical equation which gives the expected variation of the oxygen production rate with light intensity, culture thickness, and suspension volume. The applicability of this equation has been tested on a larger, multilight culture unit in this laboratory. The agreement between the experimental and calculated oxygen production rates was very satisfactory, suggesting that the equation is not limited to a particular culture unit but may have wide applicability. The efficiency of the culture unit from the standpoint of oxygen output (chemical energy) relative to electrical energy to supply the light source has been calculated, and the maximum value of 0.51% was obtained. The energy to run auxiliary equipment was not a factor in these calculations. The maximum efficiency in converting light energy to chemical energy was approximately 12%. An extrapolation of the experimental results suggests that approximately 2 ft³ and 30 kw would be required to provide the oxygen needs of one man.     

Stepwise molecular evolution of bacterial photosynthetic energy conversion

The concept of continuity in molecular evolution implies a stepwise formation of metabolic systems and processes. In this manner, chemical and biological evolution have given rise, step by step, to such complicated systems as the photosynthetic apparatus and thus, such elaborate processes as photosynthesis in the living cell. Among currently living organisms, the bacteria contain a much less complex photosynthetic system than the algae and higher plants, which uniquely are capable fo splitting H2O. But also the bacterial system is a very highly evolved and sophisticated, membrane-bound apparatus for the transformation of light energy to other biologically useful energy forms. The study of its molecular evolution is here undertaken by the method of attempting to break down the system into its main components and functions in order to elucidate how they had originated and evolved, and how, by divergent and convergent evolutionary steps, the stage was set for the arrival of bacterial photophosphorylation.     

Light energy conservation processes in Halobacterium halobium cells.

In Halobacterium halobium, proton pumping driven by light or by respiration generates an electrochemical potential difference across the membrane. Energy storage in this form is only transient. Cellular energy transducers competing with proton leaks stabilize this free energy as high energy phosphate bonds, electrochemical potential of other ions, and chemical potential of amino acids and possibly other chemical species. The pH changes induced by light or by respiration in cell suspensions are complicated by proton flows associated with the functioning of the cellular energy transducers. Dominant is the proton inflow coupled to the synthesis of ATP, which has been kinetically resolved. A proton-per-ATP ratio of about 3 is calculated from simultaneous measurements of photophosphorylation and the proton inflow. This value is compatible with the chemiosmotic coupling hypothesis. The time course of the light-induced changes in membrane potential indicates that light-driven pumping increases a dark preexisting potential of about 130 mV only by a small amount (20-30 mV). The complex kinetic features of the membrane potential changes do not closely follow those of the pH changes, indicating that flows of ions other than protons are involved. A qualitative model consistent with the available data is presented. A salient feature of this model is a sudden relaxation of the protonmotive force by a proton inflow through the ATPase when the preexisting protonmotive force is increased by light or respiration and reaches a critical value. The trigger could be either the proton-motive force, the pH gradient, or possibly the internal pH.     

Light Energy Dissipation under Water Stress Conditions: Contribution of Reassimilation and Evidence for Additional Processes

Using ¹⁴CO₂ gas exchange and metabolite analyses, stomatal as well as total internal CO₂ uptake and evolution were estimated. Pulse modulated fluorescence was measured during induction and steady state of photosynthesis. Leaf water potential of Digitalis lanata EHRH. plants decreased to −2.5 megapascals after withholding irrigation. By osmotic adjustment, leaves remained turgid and fully exposed to irradiance even at severe water stress. Due to the stress-induced reduction of stomatal conductance, the stomatal CO₂ exchange was drastically reduced, whereas the total CO₂ uptake and evolution were less affected. Stomatal closure induced an increase in the reassimilation of internally evolved CO₂. This `CO<sub>2</sub> recycling' consumes a significant amount of light energy in the form of ATP and reducing equivalents. As a consequence, the metabolic demand for light energy is only reduced by about 40%, whereas net photosynthesis is diminished by about 70% under severe stress conditions. By CO<sub>2</sub> recycling, carbon flux, enzymatic substrate turnover and consumption of light energy were maintained at high levels, which enabled the plant to recover rapidly after rewatering. In stressed D. lanata plants a variable fluorescence quenching mechanism, termed `coefficient of actinic light quenching,' was observed. Besides water conservation, light energy dissipation is essential and involves regulated metabolic variations.