Light harvesting complex of photosynthesis

Light-harvesting complex

https://reasonandscience.catsboard.com/t1547-light-harvesting-complex-of-photosynthesis

A light-harvesting complex has 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. 14

Blankenship, Photosynthesis, page 62:
All chlorophyll-based photosynthetic organisms contain light-gathering antenna systems. These systems function to absorb light and transfer the energy in the light to a trap, which quenches or deactivates the excited state. In most cases, the trap is the reaction center itself, and the excited state is quenched by photochemistry with energy storage. In some cases, however, the quenching is by some other process, such as fluorescence or internal conversion. The antenna pigments are arranged in well-defined, three-dimensional structures, so that only a few energy transfer steps are required to connect any two pigments in the array.

If chlorophylls would be arranged so that the energy had to diffuse along a linear, or one-dimensional, array of chlorophyll pigments, then the concept of energy transfer in photosynthesis would not be feasible. One-dimensional diffusion is very inefficient because many, many transfers are required to move the excitation from one point in the array to another.

Question: How could the right arrangement have emerged in a gradual, stepwise, evolutionary fashion, if only the arrangement in well-defined, three-dimensional structures, where only a few energy transfer steps are required to connect any two pigments in the array is feasible? 


One-dimensional and three-dimensional antenna organization models.
In the one-dimensional model, excitation must be transferred by many steps before encountering a trap where photochemistry takes place. In the three-dimensional model, the trap is always no more than a few energy transfer steps from any of the pigments in the antenna complex.

A chlorophyll molecule, which is roughly square with dimensions of ∼10 Angstroms per side, will be illuminated by approximately 1100 photons per second, although not all of these photons will be absorbed. Calculating the target size that a chlorophyll molecule presents to this incoming rain of photons determines how many photons will actually be absorbed. 

The target concept is schematically illustrated in Figure below:



A photon is a strange combination of particle and wave, with a physical size that is roughly similar to the wavelength of the photon, which in the visible region is much larger than a molecule. The photon interacts with a molecule and has its energy deposited in the molecule, whereupon the photon ceases to exist and the molecule is left in an excited state. Even with full sunlight, there is approximately a tenth of a second between photons being absorbed by any given chlorophyll molecule, and it can easily be several orders of magnitude longer under most conditions. A tenth of a second is an eternity on the molecular scale.

Even in full sunlight, a chlorophyll molecule only absorbs a few photons each second. If a reaction centre had no antenna pigments then it would be active only a small percentage of the time. However, if there is a large antenna
complex, energy absorbed by a large number of pigments can be channelled to the reaction centre increasing the efficiency of the photochemistry.


If every chlorophyll had associated with it the entire electron transfer chain and enzymatic complement needed to finish the job of photosynthesis, then these expensive components would sit idle most of the time, only occasionally springing into action when a photon is absorbed. This would obviously be wasteful, and ultimately such an arrangement would be unworkable. It is as if a factory were to have a number of expensive manufacturing machines sitting idle most of the time while a key raw material is being brought in at a slow pace. It makes more sense to buy only a few expensive machines and somehow to improve the delivery system of raw materials. This is what antennas do for photosynthetic organisms.

My comment: Did you observe the language employed? " It makes more sense". This is teleology. Goal orientation. Why would unguided evolutionary mechanisms produce chlorophylls wherein an inadequate arrangement and chaotic position would be of no use at all? - but only, in a workable arrangement? This is once again a formidable example where only intelligent setup explains rationally the setup of the biological system in question. 

In addition, in all cases, photochemistry produces unstable initial products that will be lost if a second photochemical event does not take place in a relatively short time. If all pigments were functionally independent, most of these unstable products would be lost. All these factors demand that photons be collected and their energy delivered to and used in a central place. Because of these considerations, every
known photosynthetic organism has an antenna of some sort associated with it. 



However, it appears that in many cases the size of the antenna system is larger than what might be expected to be the most efficient in terms of conversion of solar energy. Many organisms, especially those that live in full sunlight, must dissipate much of the energy that the antenna system collects or risk photodamage. 

An antenna complex is composed of numerous molecules of chlorophylls and carotenoids connected by proteins. PSII antenna complexes can be divided into

1. Internal antennae composed of protein and chlorophyll complexes, such as CP43 (43 kDa) and CP47 (47 kDa) proteins, which contain chlorophyll a and β - carotene molecules
2. Trimeric external antennae composed of LHCII, which contain chlorophyll a , chlorophyll b , and xanthophylls
3. Monomeric proteins CP29 (29 KDa), CP26 (26 kDa), and CP24 (24 kDa) binding chlorophyll a , chlorophyll b , and xanthophylls

The Light harvesting antenna is located peripherally with respect to reaction centers and is specialized in harvesting light and in transferring excitation energy to the reaction center, thus increasing the amount of photons absorbed per photosystem. 12

Despite the existence of a variety of models and theoretical methods that complement the experimental results, to our knowledge, there is currently no method that can describe the photophysics of individual photosynthetic pigments as well as the dynamical evolution of their coupled excitations when embedded within a proteic environment from an atomistic, time dependent perspective. The main problem lies in that due to the large size of the antenna complex, i.e. a few thousand atoms, this entire system cannot be simulated with the present computational methods found in literature 13

Most of the photons that are converted to biochemical energy and biomass through photosynthesis are harvested by the major light-harvesting chlorophyll a/b binding antenna complex light-harvesting complex II (LHCII), which is one of the most abundant proteins on earth. 10   Light harvesting is important for the function of photosynthesis8 — for a variety of reasons — so exploring the operation of natural light-harvesting complexes provides an excellent platform for understanding how photo-excitation can be directed and amplified using assemblies of light-absorbing molecules [url=https://sci hub.bz/http://www.nature.com/nchem/journal/v3/n10/full/nchem.1145.html?wt..]11[/url] This extraordinary chain of events is started and regulated by light harvesting. Energy from sunlight is captured by complexes that subsequently funnel it to reaction centers on a 10–100 picosecond timescale ( A picosecond is one trillionth (10 -12 ) of a second ).  More specifically, light harvesting relies on the process of electronic energy transfer moving electronic excitation energy — which is stored fleetingly (nanoseconds - a nanosecond (ns) is  equal to one billionth of a second (10⁻⁹ or ¹/_{1,000,000,000} s)  by molecules in excited states — within networks of light-absorbing molecules (chromophores) to a target chromophore or trap. 

Natural solar-energy conversion in photosynthesis is one of the most important biological processes in which electronic energy-transfer plays a decisive role. 7  The initial capture of light energy is a kinetic challenge. Chlorophylls (Chls) and bacteriochlorophylls (BChls), the workhorse pigments of photosynthesis, will dissipate their absorbed light energy as fluorescence in 3–6 ns! Even the fastest enzymes, such as carbonic anhydrase, cannot keep up, they operate in kinetic regimes that are at least an order of magnitude slower . In this respect, the light-harvesting (LH) antennas of photosynthetic organisms are some of the most impressive proteins developed by Nature. Created by God 8 Matter’s capacity to transform radiation energy into an electron flow is probably one of nature’s most fundamental ways to actualize life on earth. 9

A photon – a particle of light – after a journey of billions of kilometres hurtling through space, collides with an electron in a leaf outside your window. The electron, given a serious kick by this energy boost, starts to bounce around, a little like a pinball. It makes its way through a tiny part of the leaf’s cell, and passes on its extra energy to a molecule that can act as an energy currency to fuel the plant.  4 The trouble is, this tiny pinball machine works suspiciously well. Classical physics suggests the excited electron should take a certain amount of time to career around inside the photosynthetic machinery in the cell before emerging on the other side. In reality, the electron makes the journey far more quickly. What’s more, the excited electron barely loses any energy at all in the process. Classical physics would predict some wastage of energy in the noisy business of being batted around the molecular pinball machine. The process is too fast, too smooth and too efficient. It just seems too good to be true.

Then, in 2007, photosynthesis researchers began to see the light. Scientists spotted signs of quantum effects in the molecular centres for photosynthesis. Tell-tale signs in the way the electrons were behaving opened the door to the idea that quantum effects could even be playing an important biological role. This could be part of the answer to how the excited electrons pass through the photosynthetic pinball machine so quickly and efficiently. One quantum effect is the ability to exist in many places at the same time – a property known as quantum superposition. Using this property, the electron could potentially explore many routes around the biological pinball machine at once. In this way it could almost instantly select the shortest, most efficient route, involving the least amount of bouncing about. Quantum physics had the potential to explain why photosynthesis was suspiciously efficient – a shocking revelation for biologists.

Quantum phenomena such as superposition had previously been observed mostly under highly controlled conditions. Typical experiments to observe quantum phenomena involve cooling down materials to bitingly cold temperatures in order to dampen down other atomic activity that might drown out quantum behaviour. Even at those temperatures, materials must be isolated in a vacuum – and the quantum behaviours are so subtle that scientists need exquisitely sensitive instruments to see what’s going on.

The first step in photosynthesis is the capture of a tiny packet of energy from sunlight that then has to hop through a forest of chlorophyll molecules to makes its way to a structure called the reaction center where its energy is stored. The problem is understanding how the packet of energy appears to so unerringly find the quickest route through the forest. An ingenious experiment first carried out in 2007 in Berkley, California, probed what was going on by firing short bursts of laser light at photosynthetic complexes. The research revealed that the energy packet was not hopping haphazardly about, but performing a neat quantum trick. Instead of behaving like a localized particle traveling along a single route, it behaves quantum mechanically, like a spread-out wave, and samples all possible routes at once to find the quickest way. 5



Quantum biology 6
One of the simplest and most well-studied examples is the light-harvesting apparatus of green-sulphur bacteria (Fig. 1)



These have a very large chlorosome antenna that allows them to thrive in low-light conditions. The energy collected by these chlorosomes is transferred to the reaction centre through a specialized structure called the FennaMatthewsOlson (FMO) complex. Owing to its relatively small size and solubility in water, the FMO complex has attracted much research attention and as a result has been well characterized. What is remarkable is the observed efficiency of this and other photosynthetic units. Almost every photon (nearly 100%) that is absorbed is successfully transferred to the reaction centre, even though the intermediate electronic excitations are very short-lived (1 ns). In 2007, Fleming and co-workers demonstrated evidence for quantum coherent energy transfer in the FMO complex12, and since then the FMO protein has been one of the main subjects of research in quantum biology. The FMO complex itself normally exists in a trimer of three complexes, of which each complex consists of eight bacteriochlorophyll a (BChl-a) molecules. These molecules are bound to a protein scaffold, which is the primary source of decoherence and noise, but which also may assist in protecting the coherent excitations in the complex and play a role in promoting high transport efficiency. The complex is connected to the chlorosome antenna through what is called a baseplate. Excitations enter the complex from this baseplate, exciting one of the BChl molecules into its first singlet excited state. The molecules are in close proximity to one another (roughly 1.5 nm), enabling the excitation energy to transfer from one BChl molecule to another, until it reaches the reaction centre.


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.



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.

One of its remarkable features is the efficiency with which energy is transferred within the light-harvesting complexes comprising the photosynthetic apparatus. Suspicions that quantum trickery might be involved in the energy transfer processes at the core of photosynthesis are now confirmed by a new spectroscopic study.This wavelike characteristic of the energy transfer process can explain the extreme efficiency of photosynthesis 13 This wavelike characteristic of the energy transfer within the photosynthetic complex can explain its extreme efficiency, in that it allows the complexes to sample vast areas of phase space to find the most efficient path. 


Förster resonance energy transfer  1
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.





Ancient Bacteria Use Quantum Mechanics



The light-harvesting antenna complex of purple bacteria 2
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.

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. The energy transfer efficiency between chlorophyll molecules is close to 100%, and it is lower when the transfer occurs from carotenoids to chlorophyll (Hall and Rao 1999).

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. 3 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.

“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.[/quote]

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 eect 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

1. http://zeiss-campus.magnet.fsu.edu/articles/spectralimaging/spectralfret.html
2. http://www2.estrellamountain.edu/faculty/farabee/BIOBK/biobookps.html
3. http://www.earthlife.net/prokaryotes/proteo.html#1
4. http://www.bbc.com/earth/story/20160715-organisms-might-be-quantum-machines
5. https://www.theguardian.com/science/2014/oct/26/youre-powered-by-quantum-mechanics-biology
6. http://www.nature.com.sci-hub.cc/nphys/journal/v9/n1/full/nphys2474.html
7. https://sci-hub.tw/http://www.nature.com/nchem/journal/v3/n10/full/nchem.1145.html?WT.mc_id%3DTWT_NatureChemistry
8. https://sci-hub.tw/http://www.biochemj.org/content/474/13/2107
9. http://www.vision-in-cichlids.com/ophtomolecules.htm
10. http://www.plantcell.org/content/26/9/3646
11. https://sci-hub.tw/http://www.nature.com/nchem/journal/v3/n10/full/nchem.1145.html?wt..
12. http://www.sciencedirect.com/science/article/pii/S0005272811001460
13. https://uncommondescent.com/intelligent-design/is-photosynthesis-irreducibly-complex/#more-2255
14. https://en.wikipedia.org/wiki/Light-harvesting_complex


More readings: 
http://www.ks.uiuc.edu/Research/chromatophore/
http://www.cryst.bbk.ac.uk/PPS95/course/9_quaternary/lhc.html

Design principles of photosynthetic light-harvesting 1

https://reasonandscience.catsboard.com/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

we're going to start our talk of the biochemistry of plants by talking of course about photosynthesis now the general makeup of photosynthesis consists of light dependent reactions and another set code light independent reactions the light dependent reactions as they sound are dependent on photons of energy from the Sun okay the light independent reactions used to not too long ago we called the dark reaction that's not necessarily true because they don't have to occur in the dark they are just independent of lights they don't have to have it so we're going to refer to them as the light independent reactions the light dependent reactions are divided into two phases those are going to be photosystem 2 and photosystem 1 now you might notice it's unusual that I said two before one that's because literally in physiological conditions that we're going to look at photosystem 2 occurs first

The reason that its main photosystem two is out of the two photosystems it was discovered last okay so the system one was discovered first but unfortunately for the naming system it occurred second to photosystem 2 light dependent reactions must occur in the daylight and we're going to see that we're going to look hopefully and understand that they're very dependent on energy from the Sun in the form of UV photons photosystems who has what we call a reaction center a reaction center from the context of plant is a part of the plant particularly in the thylakoid which we talked about previously that is really good at being electronically excited and also donating electrons in photosystem to that particular reaction center is turned p680 in photosystem 1 that reaction center is termed p700 the p and the number indicates their pigments and that they absorb light of that particular wavelength for example p680 absorbs light at about six hundred and 80 nanometers and when these reacton centers give up electrons to an acceptor that's nearby as well look at they initiate something called the photosynthetic electron transport chain

You may have heard of electron transport chain in the context of mitochondria and in all of biology that is by no means the only one there are many of them this is one of them that we're going to call the photosynthetic electron transport chain.  The light dependent reactions ultimately are going to generate two main things that are going to be used by the light independent reactions those two products are NADPH and ATP and specifically they will be used in something referred to as the Calvin cycle.  Before we get into most of the biology and biochemistry we need to understand how these things work and to do that we're going to look at what's called a pigment molecule this one is called chlorophyll this is one of the chlorophyll sources by no mean the only one the chlorophyll is what we call a light-absorbing pigment now if you took biochemistry one you probably did a study of a molecule referred to a heme. derived from a molecule actually directly called protoporphyrin 9 this is made in plants and mammals and it turns out the protoporphyrin 9 has two main pathways it can go it can either go through team synthesis which is done in plants or it can go towards chlorophyll synthesis a much more drawn-out pathway from that point but still team is derived from the same molecule as chlorophyll and you can see it hopefully in the ring structured there that macro cyclic structure but one difference you should know this is the following in heem the ion in the center of the ring is iron two-plus in the case of all chlorophylls it's magnesium

It turns out that magnesium is going to allow the chlorophyll to have some special properties particularly drastically going up in energy and then also donating electrons it's very important that that magnesium be the eye on there and not the iron one of those properties specifically is what we're going to be referring to as resonance and energy transfer now what is resonance energy transfer to do this we need to look at this diagram here which if you take in any kind of analytical chemistry this is called a Jablonski diagram what it shows are various electronic States from low energy at the bottom to high energy at the top and any kind of electronic energy dissipation that we have you see on the far right we have phosphorescence and we have fluorescence absorption right things that you've probably heard of okay you may have seen some of this quantum mechanical phenomenon before but not make me in the context of biology or biochemistry

Now there's a process I want to talk about and you can see it right here internal conversion now knowing exactly what it is is really not important don't worry about the s2 over there in the s-1 I don't really care about that in fact you don't really need to understand much of that what you should notice is we start out here at the bottom in some sort of ground state UV light particularly from the Sun strikes these light absorbing pigments such as this and that causes electrons to go up in energy you see electrons can be up in energy up here now what is internal conversion I'm just going to read off of here even though you know I hate reading off of powerpoints internal conversion is a conversion between electronic energy states in which energy is transferred between a donor and acceptor in vibrational resonance that's a fancy way of saying that it's a transfer of energy between two different electronic energy states that are really close and energy alright hopefully you see that this blue line that goes completely horizontally from left to right which represents internal conversion you're getting a switch or conversion between electronic energy states all right

In other words the electron can switch apparently from s2 to s1 we don't really care about that so much all right now generally internal conversion is used to describe conversion within one molecule however if we talk about it with respect to transfer between two molecules that are different we call it resonance energy transfer all right here I see an electron that's in an excited state up here designated by the asterisk it turns out that if I put another molecule over here aka the acceptor molecule whereas this is the donor it turns out that for this for this energy state with this electron there's another whole energy state in this molecule that's equal to this energy state it's equal energy it's in what we call vibrational resonance and it turns out that this electron is in exactly the same energy state as this state over here now very important point we are not talking about electron transfer there are things that transfer electrons later in photosynthesis we're talking about energy transfer not electron transfer which is kind of an unusual concept here

It turns out that this electron once it gets excited can all of a sudden relax down to the ground state in this blue line right here just all of a sudden relax back down however it doesn't just relax back down and do nothing it actually dissipates that energy but where does that energy go well it turns out the energy is transferred to the in acceptor over here and when that energy is transferred not the electron when this electron relaxes down to this energy state down here at the ground state the dissipated energy causes an electron over here to go up in energy okay in other words what we have is a sequential process of light striking a molecule a pigment that is an electron goes up in energy and then it relaxes back down but in doing so when it relaxes it dissipates and releases a lot of energy and it just so happens there are nearby other pigments that can accept that energy and though their electrons go up in energy and then those electrons are going to relax and release some energy that's going to cause another nearby molecule to have an electron that goes up

This is what we call resonance energy transfer okay electron goes up in energy relaxes back down this concept is resonance energy transfer all right this is not electron transfer these are not redox reactions that we're going to see later initially in photosynthesis as we talked about before we have first of all energy transfer and then electron transfer later so the basic idea once again you have light that strikes an electron in one of the pigments electron goes up in energy but it relaxes back down okay and when it relaxes down it releases energy that activates an electron of another nearby pigment and you see an electron go up here and then that one's going to relax down release energy and excite another electron so you're going to have a continuous process from pigmented pigment of electron excitation electron relaxation and excitation of the next electron and then that one's going to relax so it's excite relax excite relax excitement lacks but it propagates energy transfer from one pigment to the next but the really important concept okay often times this energy transfer is referred to as exit on transfer okay this is a piece of terminology

now why is this important well it turns out that light does not directly strike what we call the reaction center briefly earlier in this video we talked about the reaction center of the photosystems okay in photosystem two we're going to see that's called reaction center p680 and in photosystem one it's p700  the light does not necessarily directly strike p680,  in fact the light energy has to strike an outside pigment perhaps this one out here and it turns out that from this process that we've just been talking about where an electron gets excited it relaxes and releases energy to excite the next electron it's actually going to occur in a chain  whether we're talking about the photosystems the reactions that happen later on that we're going to talk about in future videos or the mitochondrial electron transport chain that generally we have what we call unidirectional transfer of electrons all right the antenna complex in plants that occurs before the electron transport chain you could sort of think of as an energy transport chain  we have excitation of an electron relaxation of an electron which causes the excitation of another electron in the nearby molecule so light strikes this pigment right here follow my mouse excitation relaxation excites the electron here this excited electron relaxes excites the electron here this excited electron relaxes excites the next one here this excited electron relaxes excites the next one here and so on and so forth and it turns out that later on we're going to have unidirectional electron flow here we have unidirectional energy flow



and it turns out that the light energy is transferred from pigments on the outside of the reaction center and it's transformed or transferred unidirectionally along a specific path usually to the reaction center where this dark green dot is representative more p680 the reaction center a photosystem -  I just want to be clear that when light strikes these pigments out here it's not actually electron transfers its energy transfers it's only until we get to the reaction center that we get an electron transfer  now all of these sort of lightish green pigments out here even the ones that are not involved in this chain right here  all of these up here these are what we termed the antenna complex okay the antenna complex is function basically is to transfer energy from the outside of the photosystem directly to the reaction center and it turns out it's very efficient it's also unidirectional let me read these light energy is absorbed by pigment 1 and P 1 becomes or pigment 1 becomes excited once excited P 1 or pigment 1 relaxes to the ground state and the emitted energy excites the next pigment P 2 in a repetitive process of excitation followed by relaxation or emission energy flows from p1 to p2 to p3 to p4 up until the energy excites the special pair of chlorophyll in p680 and that's going to be the subject of another video

don't worry so much about what the special pair of course goals are suffice to say they're part of the p680 reaction center and they can actually donate electrons and the antenna complex a series of light absorbing pigments accepts UV photons and transfers them rapidly to a special pair of chlorophyll molecules in p680 s reaction center all right and it really technically isn't transferring the UV photon it's transferring the energy of the UV photon now you see this little arrow right here that says decreasing energy going down all right that's because every one of these energy transfers it's going from high energy to low energy come back and look over here alright this is just a general diagram but increasing energy is going up notice how overall the energies are going down so the next molecule will have this higher energy state maybe right here and the next one have higher energy state down here and so forth in other words energy is being transferred from high energy to low energy to lower energy and lower and lower and lower and let me ask you a question what's the Gibbs free energy of that kind of energy transfer it's spontaneous it's negative its spontaneous to transfer from high energy to low energy in other words plants are more or less designed to be able to transfer this energy that's very high UV energy from the light down in energy in a spontaneous fashion to the reaction center however even though the energy transfer from this pigment right here to the reaction center is a lower energy than of UV photons it's still enough to excite the special pair in p680 s reaction center and that's going to lead us into talking about p680 and a lot of this may not make a lot of sense right now but if you keep watching the videos we're going to piece together all the pieces and hopefully it will make sense

An antenna is required to capture light 1

In order to excite a photosynthetic reaction center, a photon with defined energy content has to react with a chlorophyll molecule in the reaction center. The probability is very low that a photon not only has the proper energy, but also hits the pigment exactly at the site of the chlorophyll molecule. Therefore efficient photosynthesis is possible only when the energy of photons of various wavelengths is captured over a certain surface by a so-called antenna (Fig. 2.8 ).


Figure 2.8 Photons are collected by an antenna and their energy is transferred to the reaction center. In this scheme the squares represent chlorophyll molecules. The excitons conducted to the reaction center cause a charge
separation

The antennae of plants consist of a large number of protein-bound chlorophyll molecules that absorb photons and transfer their energy to the reaction center. Only a few thousandths of the chlorophyll molecules in the leaf are constituents of the actual reaction centers; the remainder are contained in the antennae. Observations made as early as 1932 by Robert Emerson and William Arnold in the United States indicated that the large majority of chlorophyll molecules are not part of the reaction centers. Analysis of the chlorophyll content of the algae suspension showed that under saturating conditions only one molecule of O2 was formed per 2,400 chlorophyll molecules. About 300 chlorophyll molecules are associated with one reaction center. These are constituents of the antennae.

How is the excitation energy of the photons captured in the antennae and transferred to the reaction centers?

The physical mechanism by which excitation energy is conveyed from the chlorophyll that absorbs the light to the reaction center is thought to be resonance transfer. By this mechanism the excitation energy is transferred from one
molecule to another by a nonradiative process. Auseful analogy for resonance transfer is the transfer of energy between two tuning forks. If one tuning fork is struck and properly placed near another, the second tuning fork
receives some energy from the first and begins to vibrate. As in resonance energy transfer in antenna complexes, the efficiency of energy transfer between the two tuning forks depends on their distance from each other and their relative orientation, as well as their pitches or vibrational frequencies. Energy transfer in antenna complexes is very efficient: Approximately 95 to 99% of the photons absorbed by the antenna pigments have their energy transferred to the reaction center, where it can be used for photochemistry. There is an important difference between energy transfer among pigments in the antenna and the electron transfer that occurs in the reaction center: Whereas energy transfer is a purely physical phenomenon, electron transfer involves chemical changes in molecules.

The Antenna Funnels Energy to the Reaction Center

The sequence of pigments within the antenna that funnel absorbed energy toward the reaction center has absorption maxima that are progressively shifted toward longer red wavelengths (Figure 7.19).



This red shift in absorption maximum means that the energy of the excited state is somewhat lower nearer the reaction center than in the more peripheral portions of the antenna system. As a result of this arrangement, when excitation is transferred, for example, from a chlorophyll b molecule absorbing maximally at 650 nm to a chlorophyll a molecule absorbing maximally at 670 nm, the difference in energy between these two excited chlorophylls is lost to the environment as heat. For the excitation to be transferred back to the chlorophyll b, the energy lost as heat would have to be resupplied. The probability of reverse transfer is therefore smaller simply because thermal energy is not sufficient to make up the deficit between the lower-energy and higher energy pigments. This effect gives the energy-trapping process a degree of directionality or irreversibility and makes the delivery of excitation to the reaction center more efficient. In essence, the system sacrifices some energy from each quantum so that nearly all of the quanta can be trapped by the reaction center.


Question: Could  a natural selection process have selected chlorophyll b's which absorbs maximally at 650nb and so higher energy, and placed them more distant from the reaction center, and selected chlorophyll a molecules, and placed them more close to the reaction center, envisage the advantage the energy-trapping process a degree of directionality or irreversibility, which makes the delivery of excitation to the reaction center more efficient ? 

Many Antenna Complexes Have a Common Structural Motif

In all eukaryotic photosynthetic organisms that contain both chlorophyll a and chlorophyll b, the most abundant antenna proteins are members of a large family of structurally related proteins. Some of these proteins are associated primarily with photosystem II and are called light-harvesting complex II (LHCII) proteins; others are associated with photosystem I and are called LHCI proteins. These antenna complexes are also known as chlorophyll a/b antenna proteins. The structure of one of the LHCII proteins has been determined by a combination of electron microscopy and electron crystallography (Figure 7.20).



The protein contains three α-helical regions and binds about 15 chlorophyll a and b molecules, as well as a few carotenoids. Only some of these pigments are visible in the resolved structure. The structure of the LHCI proteins
has not yet been determined but is probably similar to that of the LHCII proteins. All of these proteins have significant sequence similarity and are almost certainly descendants of a common ancestral protein.


The transfer of energy in the antennae via electron transport from chromophore to chromophore in a sequence of redox processes, as in the electron transport chains of photosynthesis or of mitochondrial respiration, could be excluded, since such an electron transport would need considerable activation energy. When chromophores are positioned very close to each other, the quantum energy of an irradiated photon is transferred from one chromophore to the next. One quantum of light energy is named a photon, one quantum of excitation energy transferred from one molecule to the next is termed an exciton. A prerequisite for the transfer of excitons is a specific positioning of the chromophores. 

How did evolutionary mechanisms manage to create such an antenna complex, and bring the chlorophylls together into the right distance, in order for the quantum energy being able to irradiate from one chromophore to the next ?

This is arranged by proteins, and therefore the chromophores of the antennae always occur as protein complexes. The antennae of plants consist of an inner part and an outer part (Fig. 2.10).



The outer antenna, formed by the light harvesting complexes (LHCs), collects the light. The inner antenna, consisting of the core complexes, is an integral constituent of the reaction centers; it also collects light and conducts the excitons that were collected in the outer antenna to the photosynthetic reaction centers. The LHCs are composed of polypeptides, which bind chl-a, chl-b, xanthophylls, and carotenes. These proteins, termed LHC polypeptides, are encoded in the nucleus. A plant contains many different LHC polypeptides.

The function of an antenna is illustrated by the antenna of photosystem II

The antenna of the PS II reaction center contains primarily four LHCs termed LHC-IIa–d. The main component is LHC-II b; it represents 67% of the total chlorophyll of the PS II antenna and is the most abundant membrane
protein of the thylakoid membrane, and has therefore been particularly thoroughly investigated. LHC-IIb occurs in the membrane, most probably as a trimer. The monomer consists of a polypeptide to which four xanthophyll molecules are bound. The polypeptide contains one threonine residue, which can be phosphorylated by ATP via a protein kinase. Phosphorylation regulates the activity of LHC-II.

There has been a breakthrough in establishing the three-dimensional structure of LHC-IIb by electron cryomicroscopy at a temperature of 4 K of crystalline layers of LHC-IIb-trimers (Fig. 2.11).


Figure 2.11 Sterical arrangement of the LHC-IIb monomer in the thylakoid membrane, viewed from the side. Three alpha -helices of the protein span the membrane. Chlorophyll-a (black tetrapyrrole ring) and chlorophyll-b (red
tetrapyrrol ring) are oriented almost perpendicularly to the membrane surface. Two lutein molecules (black carbon chain) in the center of the complex act as an internal cross brace. 

The LHC-IIb-peptide forms three transmembrane helices. The two lutein molecules span the membrane crosswise. The other two molecules are not visible in the isolated LHC complex. The chl-b-molecules, where the absorption maximum in the red spectral region lies at a shorter wavelength than that of chl-a, are positioned in the outer region of the complexes. Only one of the chl-a molecules is positioned in the outer region; the others are all present in the center. Figure 2.12 shows a vertical projection of the arrangement of the monomers to form a trimer. 


Figure 2.12 The LHCII- trimer viewed from above from the stroma side. Within each monomer the central pair of helices forms a left-handed super coil, which is surrounded by chlorophyll molecules. The chl-b molecules (red)
are positioned at the side of the monomers.

The chl-a positioned in the outer region mediates the transfer of energy to the neighboring trimers or to the reaction center. The trimers are arranged in the membrane as oligomers forming the antenna for the conductance of the absorbed excitons. The chl-a/chl-b ratio is much higher in LHC-IIa and LHC-IIc than in LHC-IIb. Most likely LHC-IIa and LHC-IIc are positioned between LHC-IIb and the reaction center.

1. Plant Biochemistry Fourth edition, page 60

We must ask what concentration of chromophores is optimum  1

Are there ideal arrangements of molecules with respect to each other, and how can chromophores with different absorption energies best be organized to capture a broad spectral cross-section of light and funnel energy through space to the final energy acceptor? The answers to these questions define the spatial and energetic landscape of the antenna. Studies of the fluorescence emission from solutions of organic dyes showed that the fluorescence quantum yield is drastically reduced at high dye concentration. For example, in the case of chlorophyll-a in ether solvent, the fluorescence is almost completely quenched at a concentration of 0.1 M. Nevertheless, chlorophyll is present in LHCII at a concentration of approximately 0.25 M and up to 0.5 M in photosystem I (PSI). Clearly it is remarkable that no concentration quenching is found for these antenna complexes. As already suggested by Beddard and Porter, the organization of these molecules in the protein scaffold is not random and must be a crucial factor in obviating concentration quenching in photosynthetic complexes while enabling the chromophores to be employed at high local concentration to optimize energy transfer.  The arrangement and choice of chromophores also needs to avoid quenching by charge transfer. For example, reaction centers and antenna systems are constructed from the same basic chromophores, but the molecular dimer in reaction centers, the special pair, is a potent electron donor. 

Energy transfer is extremely distance-dependent. Typical interchromophore center-to-center distances of neighboring molecules are consequently close (~6 to 25 Å) — so energy-transfer rates are fast in light-harvesting complexes.

Here, the relevant question is: How was this setup of the correct chromophore ( chlorophyll ) distances achieved? How did it emerge? Were natural mechanisms capable of evolving the right distances from one chromophore to the next? Was a step by step process possible? The energy transfer to the reaction center would only be achieved if the chain was fully developed and setup with the molecules all placed reaching the reaction center, with the right distances in place. A light harvesting complex without all chlorophylls in place would have no function.

If the chromophores are positioned too close to each other in certain orientations, then non-fluorescent dimers can serve as excitation sinks that deplete excitations. Hence, while a crude optimization of light harvesting involves maximizing the concentration of chromophores in the volume of a light-harvesting complex, a critical consideration is how to avoid concentration quenching.

So not any distance will do, but only the just right distance between each molecule. That is a task of fine-tuning and achieving high precision. How did non-intelligent mechanisms achieve this precision? trial and error? there is no stepwise build-up possible. It's an either everything or nothing.

In the quest for discovering the design principles guiding chromophore arrangement for optimal light-harvesting, it has been thought that long-range molecular ordering can be important.

Is it not remarkable, that the author writes about " design principles " ?

Natural antennas are regulated, photoprotected and robust
Photosynthesis is highly regulated. Reaction rates need to be juggled to cope with daily and seasonal light variation as well as environmental stresses that limit CO2 fixation. The solar irradiance can change by orders of magnitude during the day. At low light conditions photosynthesis can be limited, thus light harvesting is crucial. But under bright sunlight — or even quite moderate light flux — excitations are harvested much faster than the frequency that reaction centers ‘reset’ after doubly reducing the final electron acceptor in the reaction center that stores the photogenerated potential (in type-II reaction centers a quinone serves this function). The excess excitations could form triplet states and, in turn, singlet oxygen that devastates biological molecules. It is not surprising, then, that various mechanisms have evolved to dissipate excess excited states (both singlets and triplets).

How could the system survive, if the regulatory mechanisms and to dissipate excess excited states were not present right from the beginning?  

First of all, in virtually all photosynthetic light-harvesting complexes, the chlorophylls occur in combination with carotenoids. For instance in LHCII, each monomeric subunit contains two luteins in the center, a neoxanthin and a violaxanthin (see Fig. 3) 



in addition to the chlorophylls. The carotenoids in the complex fulfil multiple functions: 

(1) the two central luteins constitute an essential structural element; 
(2) caratenoids have an essential function in light-harvesting; photons absorbed by the allowed visible transition (the S2 state) are transferred mainly to chlorophyll-a on a femtosecond timescale 
(3) triplets formed on the chlorophylls (predominantly on chlorophyll-a) are quenched very efficiently by the carotenoids
(4) the carotenoids in most light-harvesting complexes play a role in a process called non-photochemical quenching that operates under high light conditions, and which allows the light-harvesting antenna to switch into a state in which most of the excitation energy is dissipated as heat

These functions, and certainly (3) and (4), are essential in natural photosynthesis.

Which indicates that carotenoids were required right from the start.

These functions, and certainly (3) and (4), are essential in natural photosynthesis. A protein-based photosynthetic apparatus does not survive when chlorophyll triplets accumulate. The reason is simple: chlorophyll triplets react very effectively with oxygen to produce singlet oxygen, an extremely reactive species. In contrast, carotenoid triplets are too low in energy to produce singlet oxygen, and as a consequence triplet–triplet energy transfer from chlorophyll to carotenoid protects the photosynthetic apparatus. This protection is extremely efficient: in all plant light-harvesting systems it is almost impossible to detect a chlorophyll triplet at room temperature even under conditions in which the excited state lifetime is long and a substantial amount of carotenoid triplet is being formed.

Uncovering Quantum Secret in Photosynthesis - June 20, 2013


Excerpt: Photosynthetic organisms, such as plants and some bacteria, have mastered this process: In less than a couple of trillionths of a second, 95 percent of the sunlight they absorb is whisked away to drive the metabolic reactions that provide them with energy. The efficiency of photovoltaic cells currently on the market is around 20 percent.,,,


Van Hulst and his group have evaluated the energy transport pathways of separate individual but chemically identical, antenna proteins, and have shown that each protein uses a distinct pathway. The most surprising discovery was that the transport paths within single proteins can vary over time due to changes in the environmental conditions, apparently adapting for optimal efficiency. "These results show that coherence, a genuine quantum effect of superposition of states, is responsible for maintaining high levels of transport efficiency in biological systems, even while they adapt their energy transport pathways due to environmental influences" says van Hulst.

http://www.sciencedaily.com/releases/2013/06/130620142932.htm


1. https://sci-hub.bz/http://www.nature.com/nchem/journal/v3/n10/full/nchem.1145.html?wt..

Light-harvesting Complexes, a marvel of molecular engineering

Photosynthesis is one of the most fascinating biosynthesis pathways in nature. Every leaf does photosynthesis and produces oxygen as a waste product, and at the same time, fixes carbon dioxide from the air through the most abundant protein in nature, Rubisco:

Rubisco's amazing evidence of design  
https://reasonandscience.catsboard.com/t1554-the-rubisco-enzymes-amazing-evidence-of-design

You would not be in front of your screen, reading my line, without this marvel of molecular engineering. There are many aspects worth to give a closer look. All 26 protein complexes used in the pathway are irreducible. That is, all are ESSENTIAL and must be there, fully setup. But not any arrangement will do.

Chlorophyll must be inserted in just the right way in so-called Light-harvesting Complexes. Imagine a Photovoltaic solar energy station, where many solar panels are arranged circularly, capturing light, and transmitting the energy to the central point of the circle.

Light-harvesting complexes do basically the same, but in a far far more sophisticated manner, than humans could ever imagine, invent, and set up. My following write-up exemplifies how life is depending on many millions of essential factors, where if just ONE is missing, no life. In our case, if Chlorophylls are not ordered in a functional way around the reaction center of photosystem two, no function, no advanced life would exist on earth. But let's give a closer look.

Following article is best read at my library:

Light-harvesting complex
https://reasonandscience.catsboard.com/t1547-light-harvesting-complex-of-photosynthesis

A light-harvesting complex has 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. 14

Blankenship, Photosynthesis, page 62:
All chlorophyll-based photosynthetic organisms contain light-gathering antenna systems. These systems function to absorb light and transfer the energy in the light to a trap, which quenches or deactivates the excited state. In most cases, the trap is the reaction center itself, and the excited state is quenched by photochemistry with energy storage. In some cases, however, the quenching is by some other process, such as fluorescence or internal conversion. The antenna pigments are arranged in well-defined, three-dimensional structures, so that only a few energy transfer steps are required to connect any two pigments in the array.

If chlorophylls would be arranged so that the energy had to diffuse along a linear, or one-dimensional, array of chlorophyll pigments, then the concept of energy transfer in photosynthesis would not be feasible. One-dimensional diffusion is very inefficient because many, many transfers are required to move the excitation from one point in the array to another.

Question: How could the right arrangement have emerged in a gradual, stepwise, evolutionary fashion, if only the arrangement in well-defined, three-dimensional structures, where only a few energy transfer steps are required to connect any two pigments in the array is feasible?

One-dimensional and three-dimensional antenna organization models.

In the one-dimensional model, excitation must be transferred by many steps before encountering a trap where photochemistry takes place. In the three-dimensional model, the trap is always no more than a few energy transfer steps from any of the pigments in the antenna complex.

A chlorophyll molecule, which is roughly square with dimensions of ∼10 Angstroms per side, will be illuminated by approximately 1100 photons per second, although not all of these photons will be absorbed. Calculating the target size that a chlorophyll molecule presents to this incoming rain of photons determines how many photons will actually be absorbed.

A photon is a strange combination of particle and wave, with a physical size that is roughly similar to the wavelength of the photon, which in the visible region is much larger than a molecule. The photon interacts with a molecule and has its energy deposited in the molecule, whereupon the photon ceases to exist and the molecule is left in an excited state. Even with full sunlight, there is approximately a tenth of a second between photons being absorbed by any given chlorophyll molecule, and it can easily be several orders of magnitude longer under most conditions. A tenth of a second is an eternity on the molecular scale. If every chlorophyll had associated with it the entire electron transfer chain and enzymatic complement needed to finish the job of photosynthesis, then these expensive components would sit idle most of the time, only occasionally springing into action when a photon is absorbed. This would obviously be wasteful, and ultimately such an arrangement would be unworkable. It is as if a factory were to have a number of expensive manufacturing machines sitting idle most of the time while a key raw material is being brought in at a slow pace. It makes more sense to buy only a few expensive machines and somehow to improve the delivery system of raw materials. This is what antennas do for photosynthetic organisms.

My comment: Did you observe the language employed? " It makes more sense". This is teleology. Goal orientation. Why would unguided evolutionary mechanisms produce chlorophylls wherein an inadequate arrangement and chaotic position would be of no use at all? - but only, in a workable arrangement? This is once again a formidable example where only intelligent setup explains rationally the very specific arrangement of the biological system in question.

In addition, in all cases, photochemistry produces unstable initial products that will be lost if a second photochemical event does not take place in a relatively short time. If all pigments were functionally independent, most of these unstable products would be lost. All these factors demand that photons are collected and their energy delivered to and used in a central place. Because of these considerations, every
known photosynthetic organism has an antenna of some sort associated with it.

Designed or not designed? You decide.