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Theory of Intelligent Design, the best explanation of Origins » Photosynthesis, Protozoans,Plants and Bacterias » Light harvesting complex of photosynthesis

Light harvesting complex of photosynthesis

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1 Light harvesting complex of photosynthesis on Sat Mar 01, 2014 3:49 pm

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Light-harvesting complex

A light-harvesting complex is a complex of subunit proteins that may be part of a larger supercomplex of a photosystem, the functional unit in photosynthesis. It is used by plants and photosynthetic bacteria to collect more of the incoming light than would be captured by the photosynthetic reaction center alone. Light-harvesting complexes are found in a wide variety among the different photosynthetic species. The complexes consist of proteins and photosynthetic pigments and surround a photosynthetic reaction center to focus energy, attained from photons absorbed by the pigment, toward the reaction center using Förster resonance energy transfer.


http://www.ks.uiuc.edu/Research/chromatophore/

http://www.cryst.bbk.ac.uk/PPS95/course/9_quaternary/lhc.html



LIGHT HARVESTING COMPLEX II

The complex is formed from nine protomers each consisting of an alpha and beta polypeptide, three bacteriochlorophyll a (Bchl a) molecules, one rhodopin glucoside and one beta-octylglucoside molecule. The structure has precise 9 fold symmetry and comprises two concentric rings of trans-membrane helices. A continuous ring of 18 Bchl a molecules are situated between these helices. A further 9 Bchl a molecules are found between beta peptide helices at a distance of 18.0Å from the first ring. The two rings of molecules are linked through the intertwining of their phytol chains and the contacts of rhodopin glucoside molecules.

The structure explains many of observed spectral transfer processes between the various chromaphores within the complex. The peripheral antenna complexes aggregate into two dimensional arrays, incorporating the core complex comprising LH1 and the Reaction Centre. The homology of the LH1 subunit and that of LH2 suggests that the 850nm bacteriochlorin molecules from LH2 and the 870nm absorbers in LH1 are at the same point in the membrane. Thus efficient energy transfer within these arrays occurs without special relative orientations of the light harvesting molecules.

Förster resonance energy transfer
Förster resonance energy transfer (FRET), Fluorescence resonance energy transfer (FRET), resonance energy transfer (RET) or electronic energy transfer (EET), is a mechanism describing energy transfer between two chromophores. A donor chromophore, initially in its electronic excited state, may transfer energy to an acceptor chromophore through nonradiative dipole–dipole coupling.The efficiency of this energy transfer is inversely proportional to the sixth power of the distance between donor and acceptor making FRET extremely sensitive to small distances.

Measurements of FRET efficiency can be used to determine if two fluorophores are within a certain distance of each other. Such measurements are used as a research tool in fields including biology and chemistry.

FRET is analogous to near field communication, in that the radius of interaction is much smaller than the wavelength of light emitted. In the near field region, the excited chromophore emits a virtual photon that is instantly absorbed by a receiving chromophore. These virtual photons are undetectable, since their existence violates the conservation of energy and momentum, and hence FRET is known as a radiationless mechanism. Quantum electrodynamical calculations have been used to determine that radiationless (FRET) and radiative energy transfer are the short- and long-range asymptotes of a single unified mechanism.




See more :

http://zeiss-campus.magnet.fsu.edu/articles/spectralimaging/spectralfret.html

Ancient Bacteria Use Quantum Mechanics



The light-harvesting antenna complex of purple bacteria



The quantum world is a strange one. In a process called “quantum tunneling,” particles can pass through barriers as if they aren’t there at all. As a result of a process called “perturbation,” empty space can give rise to virtual particles that “blip” into and out of existence. Because of a phenomenon known as “quantum coherence,” a particle can be in several different places at once. These ideas defy common sense, but they have been experimentally verified in many different ways.

It turns out that photosynthesis (the process by which some organisms convert the energy in sunlight into energy that they can use) exploits quantum coherence in an incredible way. When light strikes a photosynthetic organism, its energy must be captured so that it can be used in an amazingly complex process that will convert it from radiant energy into chemical energy.

http://www2.estrellamountain.edu/faculty/farabee/BIOBK/biobookps.html

It has long been known that photosynthesis is about 95% efficient when it comes to the first step of capturing light’s energy.1 Until now, however, scientists have not understood how photosynthesis could be that efficient.

After all, harvesting light in a biological environment is difficult. Even though photosynthetic organisms have a well-designed “antenna” system for capturing that light (an example is given above), a living organism is usually in motion. Its environment is also constantly stimulating it in different ways. As a result, even though the antenna system is well designed, it will be distorted and deformed as the organism moves and responds to its environment. This means there should be times when the antenna system is well-aligned, producing very efficient transfer of energy, but there should also be times where it is misaligned, reducing its efficiency. Nevertheless, photosynthesis stays very efficient, regardless of how the antenna complex is distorted.

How does the antenna complex stay efficient? The answer is incredible.

Richard Hildner and his colleagues studied the antenna complex of purple bacteria, single-celled organisms that perform photosynthesis.

http://www.earthlife.net/prokaryotes/proteo.html#1

Richard Hildner and his colleagues studied the antenna complex of purple bacteria, single-celled organisms that perform photosynthesis. Unlike plants and many other photosynthetic organisms, they do not produce oxygen as a byproduct of their photosynthesis, and they are generally considered to have very “simple” photosynthetic machinery. As Chandler, Hsin, and Gumbart of the University of Illinois write:

http://www.ks.uiuc.edu/Training/CaseStudies/pdfs/lh2.pdf

Among all photosynthetic organisms, purple bacteria are considered to have the oldest and simplest photosynthetic apparatus, making them ideal candidates for photosynthetic studies.

What Dr. Hildner and his colleagues found, however, was anything but “simple.” They found that the light-collecting antennae of purple bacteria exploit quantum coherence when they absorb a particle of light (which is called a photon). Because of this, the photon can essentially be everywhere in the antennae at once. What does this mean? It means that regardless of the current state of the antenna, the photon can explore all possible pathways in the absorption process. The most efficient pathway can then be chosen, regardless of how distorted or deformed the antenna might be! As the authors state:

…long-lived coherences contribute to the necessary robustness against external perturbations and disorder that are ubiquitous in biological systems at physiological temperatures. In this respect, the biological function of these complexes, light absorption and energy funneling toward the reaction center, is optimized for each individual aggregate, and long-lived quantum coherences herein play an important role.

Without exploiting quantum coherence, then, the photosynthesis of purple bacteria would not be as robust. It would vary depending on the specific external perturbations and disorder that happen to be occurring at the time.


Now think about this for a moment. Purple bacteria are supposed to have “simple” photosynthetic machinery. However, even this “simple” machinery is sophisticated enough to exploit quantum mechanics – an esoteric aspect of nature that even most scientists don’t understand. In fact, from an evolutionary point of view, purple bacteria were the first to evolve the process. Nevertheless, they use quantum mechanics!

Now, of course, it is always possible that earlier photosynthetic machinery in purple bacteria was simple and that evolution “tinkered” with the process for billions of years to come up with the ability to exploit quantum mechanics. However, there is no evidence for this. The fact is that the simplest, most “primitive” version of photosynthesis that currently exists in nature has already mastered quantum mechanics. As far as I’m concerned, this provides even more evidence that photosynthesis is the product of an Incredible Designer.



Non-classicality of the molecular vibrations assisting exciton energy transfer at room temperature


Light-gathering macromolecules in plant cells transfer energy by taking advantage of molecular vibrations whose physical descriptions have no equivalents in classical physics, according to the first unambiguous theoretical evidence of quantum effects in photosynthesis published today in the journal Nature Communications.

The majority of light-gathering macromolecules are composed of chromophores (responsible for the colour of molecules) attached to proteins, which carry out the first step of photosynthesis, capturing sunlight and transferring the associated energy highly efficiently.

Previous experiments suggest that energy is transferred in a wave-like manner, exploiting quantum phenomena, but crucially, a non-classical explanation could not be conclusively proved as the phenomena identified could equally be described using classical physics.

Often, to observe or exploit quantum mechanical phenomena systems need to be cooled to very low temperatures. This however does not seem to be the case in some biological systems, which display quantum properties even at ambient temperatures.

Now, a team at UCL have attempted to identify features in these biological systems which can only be predicted by quantum physics, and for which no classical analogues exist.

 We found that the properties of some of the chromophore vibrations that assist energy transfer during photosynthesis can never be described with classical laws, and moreover, this non-classical behaviour enhances the efficiency of the energy transfer.

Alexandra Olaya Castro

“Energy transfer in light-harvesting macromolecules is assisted by specific vibrational motions of the chromophores,” said Alexandra Olaya-Castro (UCL Physics & Astronomy), supervisor and co-author of the research. “We found that the properties of some of the chromophore vibrations that assist energy transfer during photosynthesis can never be described with classical laws, and moreover, this non-classical behaviour enhances the efficiency of the energy transfer.”

Molecular vibrations are periodic motions of the atoms in a molecule, like the motion of a mass attached to a spring.  When the energy of a collective vibration of two chromphores matches the energy difference between the electronic transitions of these chromophores a resonance occurs and efficient energy exchange between electronic and vibrational degrees of freedom takes place.

Providing that the energy associated to the vibration is higher than the temperature scale, only a discrete unit or quantum of energy is exchanged. Consequently, as energy is transferred from one chromophore to the other, the collective vibration displays properties that have no classical counterpart.

The UCL team found the unambiguous signature of non-classicality is given by a negative joint probability of finding the chromophores with certain relative positions and momenta. In classical physics, probability distributions are always positive.

“The negative values in these probability distributions are a manifestation of a truly quantum feature, that is, the coherent exchange of a single quantum of energy,” explained Edward O’Reilly (UCL Physics & Astronomy), first author of the study. “When this happens electronic and vibrational degrees of freedom are jointly and transiently in a superposition of quantum states, a feature that can never be predicted with classical physics.”

Other biomolecular processes such as the transfer of electrons within macromolecules (like in reaction centres in photosynthetic systems), the structural change of a chromophore upon absorption of photons (like in vision processes) or the recognition of a molecule by another (as in olfaction processes), are influenced by specific vibrational motions. The results of this research therefore suggest that a closer examination of the vibrational dynamics involved in these processes could provide other biological prototypes exploiting truly non-classical phenomena.

Spatial propagation of excitonic coherence enables ratcheted energy transfer

Experimental evidence shows that a variety of photosynthetic systems can preserve quantum
beats in the process of electronic energy transfer, even at room temperature. However, whether
this quantum coherence arises in vivo and whether it has any biological function have remained
unclear. Here we present a theoretical model that suggests that the creation and recreation of
coherence under natural conditions is ubiquitous. Our model allows us to theoretically demonstrate
a mechanism for a ratchet e ect enabled by quantum coherence, in a design inspired by an energy
transfer pathway in the Fenna-Matthews-Olson complex of the green sulfur bacteria. This suggests
a possible biological role for coherent oscillations in spatially directing energy transfer. Our results
emphasize the importance of analyzing long-range energy transfer in terms of transfer between
inter-complex coupling (ICC) states rather than between site or exciton states

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Design principles of photosynthetic light-harvesting 1

http://reasonandscience.heavenforum.org/t1547-light-harvesting-complex-of-photosynthesis#5463

Photosynthetic organisms are capable of harvesting solar energy with near unity quantum efficiency. Even more impressively, this efficiency can be regulated in response to the demands of photosynthetic reactions and the fluctuating light levels of natural environments. We discuss the distinctive design principles through which photosynthetic light-harvesting functions. These emergent properties of photosynthesis appear both within individual pigment–protein complexes and in how these complexes integrate to produce a functional, regulated apparatus that drives downstream photochemistry. One important property is how the strong interactions and resultant quantum coherence, produced by the dense packing of photosynthetic pigments, provide a tool to optimize for ultrafast, directed energy transfer. We also describe how excess energy is quenched to prevent photodamage under high-light conditions, which we investigate through theory and experiment. We conclude with comments on the potential of using these features to improve solar energy devices.

In light-harvesting organisms, these conditions lead to a general architecture of pigment–protein complexes were large, dense arrays of chromophores serve as antennae or the sites of initial absorption events. The excitation then migrates quickly, without losses from relaxation to the ground state, to a location, the reaction center, where a photochemical reaction traps the excitation and initiates an electron transfer chain that converts the light energy into usable chemical energy. Once the excitation reaches the reaction center, it must be converted irreversibly into chemical energy. Charge separation must be ultrafast with little or no back flow of charge,
while metal-based catalysts must be made from earth-abundant materials to allow plants to flourish across the planet.


The complexity of the chemistry initiated in the photosynthetic reaction centers suggests that they are metabolically expensive to make and should be diluted with respect to the number of light absorbers. This leads to the concept of an efficient antenna system that matches the rate of light absorption and transfer to the reaction center to the maximum possible rate of downstream electron and proton transfer and subsequent chemical steps of carbon fixation and ATP production

At low light levels, most photosynthetic systems operate with near unity quantum efficiency. At high light levels, the rate of solar absorption can significantly exceed the turnover frequency of the PSII reaction center. This creates the possibility of system damage via reactive oxygen species such as singlet oxygen. To minimize damage, plants and algae have evolved feedback mechanisms to control the efficiency of light harvesting
in response to external factors such as light intensity and the solar spectrum.

Question: When did the repair mechanisms evolve? If they evolved AFTER the system was fully setup, high light levels would have damaged photosystem II complexes without being repaired, and the process could not have perpetuated.  In order to exist, had the repair mechanism not have to be fully setup right from the start ? 

However, damage to PSII, the site of the water splitting reaction, does occur. In the event of damage, plants have a remarkable and, as yet, imperfectly understood repair mechanism for PSII reaction centers In this article, we discuss how certain aspects of photosynthesis have been optimized for effective natural light-harvesting and may have utility for the design of artificial systems. We focus on two major features of photosynthetic light-harvesting, as these characteristics are critical to creating devices that are both efficient at light-harvesting and robust under natural conditions. Photosynthetic organisms exhibit efficient, directional energy transfer, and we examine how the molecular structures are designed to give rise to ultrafast energy flow. We also discuss the ability of algae and higher plants to regulate light-harvesting by safely dissipating excess energy. We finish with more comments on what we think is necessary to know in order to design an efficient photosynthetic device.



Antenna design
Antenna structural motifs show a great deal of variety in natural photosynthetic systems. Fig. 2 gives examples of three very different-looking antenna systems from plants and two types of photosynthetic bacteria. Despite their different architectures, all the antenna systems share both high quantum efficiency and two structural characteristics: first, they have very densely packed chromophores (e.g., the antenna of Photosystem I has a chlorophyll concentration of about 0.9 M. This dense packing, required for the effective absorption of sunlight, produces strong interactions between the component molecules, modifying their electronic and dynamic properties and introducing new functions significantly different from their components. In other words, they exhibit emergent properties. Second, most, if not all, antenna systems contain carotenoid molecules, which serve as both secondary light harvesters and photoprotective agents.

These two features can be examined from an engineering design standpoint. From this perspective, what are the control parameters available within the molecular machinery of photosynthetic light harvesting systems? The most obvious are the choice of pigments. We will confine our comments to systems with chlorophyll (Chl), bacteriochlorophyll (BChl), and carotenoid (Car) optical components; although other light harvesting molecules are found, nature is remarkably parsimonious in its use of different chemical species in photosynthesis.

Instead of constructing many different chromophores, nature has preferred to manipulate the properties of specific components by means of: (1) variations in their individual protein environments, which introduce differences in transition energies and in the strength and timescales of coupling of the excited states to the nuclear motion of the protein; and (2) electronic coupling to neighboring chromophores. These interactions are able to introduce changes to the functional behavior of the pigments because of the dense packing found in photosynthetic complexes, as mentioned above.

So nature has preferences? 

Dynamics of light harvesting
Speed is essential to efficient light harvesting. As noted above, at low light levels, energy transfer processes in photosynthetic organisms can show a >90% quantum efficiency, which is defined as the percentage of absorbed photons that undergo charge separation at the reaction center.2 Fig. 1 presents a sample trajectory of excitation energy through a model of the photosynthetic apparatus. This translocation of the excitation must be achieved before the energy is lost through fluorescence or nonradiative relaxation.  Nature uses a variety of sophisticated methods to achieve the necessary speed and directionality of energy flow. One
such method that has gathered much recent attention is the use of intrinsically quantum mechanical phenomena to optimize energy flow

This is evidence that an intermediate evolutionary stage would have been non-functional. The system had to be fully setup, just right, from the beginning, in order to function. And even more amazing, it uses quatum mechanics to reach the goal of energy transfer. 

A balance between coherent and incoherent transfer is required to achieve the optimal rate of energy transfer. The formally exact quantum dynamic calculations of Ishizaki and Fleming show that the rate of energy transfer in a dimer system has a maximum when calculated as a function of the reorganization energy. Too little decoherence and the system simply oscillates; too much, as a result of environmental relaxation on the initial site, and the excitation is trapped there.


So we have a nice example of fine tuning here. 

To prevent damage and avoid repair, PSII contains feedback mechanisms, collectively called nonphotochemical quenching (NPQ), that trigger the redirection of energy transfer to quenching sites where the excitations can be harmlessly dissipated as heat. 
The response of PSII to variations in the intensity of sunlight can be viewed as a feedback control system involving a negative feedback controller that stabilizes the photosystem by quenching singlet excitation of excess light

1. http://pubs.rsc.org.sci-hub.cc/en/content/articlelanding/2012/fd/c1fd00078k#!divAbstract

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