Photosynthesis

Photosynthesis

https://reasonandscience.catsboard.com/t1555-photosynthesis

1. In photosynthesis, 26 protein complexes and enzymes are required to go through the light and light-independent reactions, a chemical process that transforms sunlight into chemical energy, to get glucose as an end product.  The pathway must go all the way through, and all steps are required, otherwise, glucose is not produced, and advanced life would not be possible on earth.
2. Photosynthesis is an interdependent and irreducible complex system, that could not have evolved since all parts had to be in place right from the beginning. It contains many interdependent systems composed of parts that would be useless without the presence of all the other necessary parts. In these systems, nothing works until all the necessary components are present and working.
3. Therefore, the photosynthetic pathway is not likely due to evolution, but intelligent design and setup. 

Is photosynthesis irreducibly complex?
https://www.youtube.com/watch?v=ktXnLnUA8XA&t=149s

Oxygenic photosynthesis is itself the most complex metabolic machine known in nature. 10

“The process of photosynthesis is a very complex set of interdependent metabolic pathways “How it could have evolved is a bit mysterious.”
Robert Blankenship, professor of biochemistry at Arizona State University  

The origin of the oxygen evolving complex ( OEC )  is an enigma.
Oxygen evolving complex in Photosystem II: Better than excellent Mohammad Mahdi Najafpour*a and Govindjeeb 

Mystery Microorganism May Have Been the First to Produce Oxygen
However, much remains unknown about when and how cyanobacteria evolved oxygenic photosynthesis. "The whole question of the origin of cyanobacteria has long been a mystery because they kind of just appeared out of the tree of life with this very advanced capability to do oxygenic photosynthesis without any apparent forebears," said biochemist Robert Blankenship at Washington University in St. Louis, Missouri.
https://www.insidescience.org/news/mystery-microorganism-may-have-been-first-produce-oxygen

How Cyanobacteria went green
Robert E. Blankenship

The evolutionary origin of the Cyanobacteria and how they developed the ability to oxidize water, which poses extreme energetic and mechanistic constraints, have long been enigmatic. Until recently, all known members of the cyanobacterial phylum were capable of oxygenic photosynthesis, and no evolutionary precursors or sister taxa had been identified, although there were hints of cyanobacterial relatives in such unlikely places as the human gut microbiome.   Shih et al. have used molecular clocks to date the divergence of the photosynthetic from the nonphotosynthetic Cyanobacteria at 2.5 billion to 2.6 billion years ago; this date is much closer to the great oxidation event. The origin of oxygenic photosynthesis may thus be described as resulting from the horizontal gene transfer of information needed for this metabolic process to a previously nonphotosynthetic line of organisms (see the figure). This group became the photosynthetic Cyanobacteria, which went on to develop the ability to oxidize water and changed the world.
brushysci-hub.tw/http://science.sciencemag.org/content/355/6332/1372

My comment: One cannot overlook the ad-hoc explanation given by Blankenship, without any evidence whatsoever. Horizontal gene transfer is basically a gap filler for naturalism. Can't explain it by evolution ? Say, Horizontal gene transfer did it. 

Why Do We Need to Teach the Evolution of Photosynthesis?
Robert E. Blankenship1 and Arlene L. M. Haffa2
The teaching of evolution in schools has long been a controversial societal issue, especially in secondary school education in the USA. In recent years, repeated attempts to rewrite science standards and modify textbooks to downplay evolution or present alternatives have been made. The most visible of these recent efforts has been spearheaded by the Intelligent Design (ID) movement, which has its origins in the creationist movement. ID proposes that certain biological systems are “irreducibly complex”, in that they are so complicated that it is impossible that they arose via the gradual accumulation of mutations and therefore must have been created by an “intelligent designer”. Conversely, if a process follows physical laws and logic that are understood, it also must have been created by this intelligent designer according to a “master plan”. The identity of the intelligent designer is usually not explicitly stated but is meant to be God. Photosynthesis is a process that has been portrayed in ID literature as irreducibly complex in those aspects that are not well understood, and elegant by design in those that are. It thus becomes a central issue in this larger societal debate. It is important that scientists clearly articulate the existing evidence relating to the origin and evolution of photosynthesis and communicate this information to the community at large in a way that is both accessible and scientifically valid.

Photosynthesis is an extremely complex biological process that has been studied extensively by a multitude of scientific disciplines. Its evolutionary origins and trajectory are still not well understood. Many aspects of photosynthesis that have been studied in detail show elegance and symmetry. Photosynthesis is thus a natural candidate to be included in some ID writings as an example of an irreducibly complex system on the one hand, and as part of the master plan on the other.

Photosynthesis is indeed an extremely complex process whose origin and evolutionary development is still not well understood. It is thus a natural candidate to be used as an example of an irreducibly complex designed biological system.

With regard to the field of photosynthesis, the ID community has used the concept that photosynthetic pigments harvest the solar energy that is available to them. In regard to the matching of light-harvesting pigments to the solar irradiance in the environment the ID movement seeks this “evidence of fine-tuning” as proof of an intelligent purposeful force and that this “approach is both quite natural and scientifically fruitful” (Wiker 2003).

Does Science Point to God? The Intelligent Design Revolution
https://www.crisismagazine.com/2003/does-science-point-to-god-the-intelligent-design-revolution

The ID community has also decided that because the surface temperature of the earth is just right for photosynthesis this is further proof of a designer, as part of the “Anthropic Principle” (Corey 1993). The argument is made that even if other molecules besides chlorophyll had evolved to harvest solar energy they would have similar quantum states, and thus require similar temperatures.

Fallacies of the ID movement
Argument: As responsible scientists concerned about scientific literacy, it is relevant and urgent that we convey to the general public clear and accurate knowledge about photosynthesis so that it is not used to buttress faulty arguments that would lead scientific education in our public schools backwards. One type of faulty reasoning is called a “bifurcation” or a “false dilemma”. This if often referred to as the either/or fallacy when someone claims that there are only two alternatives, and usually one alternative is not desirable. In this case ID advocates claim that the order and symmetry of the universe must be either the result of blind chance or a master designer.
Response: Blankenship, rather than refute the claimed dichotomy, moves to the next argument, without responding to the claim. I agree with the claim: 

Comparing worldviews - there are basically just two
https://reasonandscience.catsboard.com/t2793-worldviews-there-are-basically-just-two-in-regards-of-origins#6492

There are basically just two worldviews

(a) time, chance, and the natural properties of matter; or 
(b) design, creation, and the undeniable properties of organization and mind.

Either the order was imposed upon matter, or it naturally resides within matter.

The ID movement also maintains mutually premises. When science has yet to explain a natural process it is deemed irreducibly complex.

Argument: The ID movement also maintains mutually contradictory premises. When science has yet to explain a natural process it is deemed irreducibly complex. Conversely, when science does offer accessible explanations of natural phenomena this becomes evidence of the master plan.
Response: This is the common " God of the gaps" argument. The problem is that proponents of intelligent design do not formulate their arguments based on lack of knowledge and gaps, but based on what is known. On the contrary, this is precisely what is frequencly observed. The trajectory of development of phenomena X is not well understood and is responded by proposing evolution. That is a naturalism  of the gaps argument. 

Blankenship failed entirely to enter into the real issues, by demonstrating that photosynthesis is not irreducibly complex, and how evolution did the Job. By not doing it, indirectly and implicitly admits the strength of the design inference. 

https://link.springer.com/chapter/10.1007%2F978-1-4020-6709-9_346





In photosynthesis, 26 protein complexes and enzymes are required to go through the light and light-independent reactions, a chemical process that transforms sunlight into chemical energy,  to get glucose as an end product, a metabolic intermediate for cell respiration.  A good part of the protein complexes is uniquely used in photosynthesis. The pathway must go all the way through, and all steps are required, otherwise, glucose is not produced. Also, in the oxygen-evolving complex, which splits water into electrons, protons, and CO2, if the light-induced electron transfer reactions do not go all the five steps through, no oxygen, no protons, and electrons are produced, no advanced life would be possible on earth. So, photosynthesis is an interdependent system, that could not have evolved, since all parts had to be in place right from the beginning. It contains many interdependent systems composed of parts that would be useless without the presence of all the other necessary parts. In these systems, nothing works until all the necessary components are present and working. So how could someone rationally say, the individual parts, proteins and enzymes, co-factors and assembly proteins not present in the final assemblage,  all happened by a series of natural events that we can call ad hoc mistake "formed in one particular moment without the ability to consider any application." , to then somehow interlink in a meaningful way, to form electron transport chains, proton gradients to " feed " ATP synthase nanomotors to produce ATP, and so on?  Such independent structures would have not aided survival. Consider the light-harvesting complex,  and the electron transport chain, that did not exist at exactly the same moment--would they ever "get together" since they would neither have any correlation to each other nor help survival separately? Repair of PSII via turnover of the damaged protein subunits is a complex process involving highly regulated reversible phosphorylation of several PSII core subunits. If this mechanism would not work starting right from the beginning,  various radicals and active oxygen species with harmful effects on photosystem II (PSII) would make it cease to function.  So it seems that photosynthesis falsifies the theory of evolution, where all small steps need to provide a survival advantage.


Essential parts of oxygenic photosynthesis

The photosynthesis pathway is interdependent and irreducible. Take any of the individual parts out, and the process ceases to function. Neither do most individual parts and proteins have any function, unless in this remarkable pathway. We can, therefore, infer that design explains best the origin of photosynthesis through a creator.

1. Lipid bilayer membranes are critical to the early stages of energy storage, such that photosynthesis must be viewed as a process that is at heart membrane-based. 4
2. Chlorophyll is an essential component of photosynthesis, which helps plants get energy from light. 1
3. The light-harvesting complexes, also called antenna complexes,  are essential for collecting sunlight and regulating photosynthesis 2
4. Photosystem II (PSII) is a key component of photosynthesis 2
5. The oxygen-evolving is responsible for catalyzing the oxidation of water to molecular oxygen in plants, algae, and cyanobacteria. 3
6. The cytochromeb6 f complex  is an essential player in noncyclic and cyclic electron flow 4
7. Plastocyanin is an essential member of photosynthetic electron transport and functions near PS I.  5
8.  PSI is necessary to provide the energy to reduce NADP+ to NADPH  6
9. Ferredoxin (Fd) proteins are required for the electron transfer process  from the bound Fe–S centers in the Photosystem I reaction center to NADP+. 4
10. Ferredoxin—NADP(+) reductase same as 9
11. In plants and photosynthetic bacteria ATP synthase is essential for solar energy conversion and carbon fixation.


In a photovoltaic system, each part of the system has a specific function, which is essential and contributes to the whole system to achieve its pre-established goal, in this case, to produce electric energy. Solar panels play a central ingredient in the system. Neither do Solar panels have function by their own, nor all other parts without Solar panels. They are interdependent. Nobody in its sane mind, would construct a factory to produce Solar panels with no use, and without making all other parts, and a system map, a blueprint, how to bring all parts together to have a functional whole. 

In photosynthesis, 26 protein complexes and enzymes are required to go through the light and light-independent reactions, a chemical process that transforms sunlight into chemical energy, to get glucose and fixed carbon to make glucose, its food of the organism as end products. A good part of the protein complexes are uniquely used in photosynthesis. The pathway must go all the way through, and all steps are required, otherwise glucose is not produced. Also, in the oxygen evolving complex, which splits water into electrons, protons, and oxygen, if the light-induced electron transfer reactions do not go all the five steps through, no oxygen, no protons and electrons are produced, and no advanced life would be possible on earth.

So, photosynthesis is an interdependent system that could not have evolved, since all parts had to be in place right from the beginning. It contains many interdependent systems composed of parts that would be useless without the presence of all the other necessary parts. In these systems, nothing works until all the necessary components are present and working. So how could someone rationally say, the individual parts, proteins and enzymes, co-factors and assembly proteins not present in the final assemblage -- all happened by a series of natural events that we can call ad hoc mistakes "formed in one particular moment without ability to consider any application," to then somehow interlink in a meaningful way, to form electron transport chains, proton gradients to "feed" ATP synthase nano motors to produce ATP, and so on? Such independent structures would have not aided survival.



Photosynthesis is the most vital bioenergy-generating process, without which life on earth and the existence of our biosphere would be impossible. 7 Photosynthesis, the basic process that feeds the world, begins when the pigments in the antenna complex capture the sunlight and transfer the energy to the pair of chlorophyll molecules that make up the reaction center of a photosystem. 8
Establishing the overall chemical equation of photosynthesis required several hundred years and contributions by many scientists. The chemical reactions of photosynthesis are complex. In fact, at least 50 intermediate reaction steps have now been identified. It is not surprising that working out how nature has mastered the efficient capture of the Sun’s energy has been the subject of research for over a century 5
In plants, photosynthesis occurs in chloroplasts, large organelles found mainly in leaf cells. During photosynthesis, chloroplasts capture the energy of sunlight, convert it into chemical energy in the form of ATP and NADPH, and then use this energy to make complex carbohydrates out of carbon dioxide and water. The principal carbohydrates produced are polymers of hexose (six-carbon) sugars: sucrose, a glucose-fructose disaccharide.  9

Natural solar-energy conversion in photosynthesis is one of the most important biological processes in which electronic energy-transfer plays a decisive role. 6  The objective of photosynthesis is to produce biological energy, which is generated in direct ratio to photoinduced charge-separation reactions occurring in reaction-centre complexes.  Notably, however, reaction centres are surrounded by many chromophores (often ~200) that are bound in light-harvesting complexes; these complexes contain a high concentration of molecular chromophores that absorb solar photons. The energy, stored in electronic excited states of the chromophores, is then transferred within and among light-harvesting proteins until it reaches a reaction center



Teleological explanations have played a central role throughout the history of the life sciences. Biological textbooks invariably suggest that teleological explanations were expunged from the physical sciences in the seventeenth century and finally, thanks to Charles Darwin, from the biological sciences in the nineteenth. And yet the same textbooks often explain adaptations by reference to natural selection in language that sounds suspiciously teleological. “That color pattern is present in the males of that population of fish because it increases their attractiveness to female mates without increasing their visibility to predators.” Moreover, explanations that at least appear to be teleological are not restricted to the observable, phenotypic adaptations of vertebrate behavior. Notice the explanatory structure implicit in the following quotation from
Albert Lehninger’s Bioenergetics: The Molecular Basis of Biological Energy Transformations (1971, 110; emphasis added).

Thus photo-induced cyclic electron flow has a real and important purpose, namely, to transform the light energy absorbed by chlorophyll molecules in the chloroplast into phosphate bond energy. 4


At the base of virtually every food chain on Earth, today is a photosynthetic organism – a tree, a plant, an algal cell or a cyanobacterium. Virtually every living thing on the planet today is ultimately powered by sunshine. Every mouthful of every meal has its origins in the Sun, from the fruit and vegetables created by plants that absorb sunlight directly, to the meat and fish that deliver their sunshine second- or third-hand as part of the complex food chain. It appears today as if the Sun is a truly fundamental ingredient for life, a provider without which life couldn’t exist. Yet this intimate relationship with our nearest star is not a simple one. The Sun is a far from benevolent companion. Its radiant rain has a dark side that is as dangerous as it is nourishing, and early in the development of life on Earth it is likely that the Sun was a presence to be avoided rather than cherished. To understand how life transformed its relationship with light, we have to go back to a time when life sheltered in the darkness. For many biologists, life on Earth didn’t begin in the light, but rather in the darkness of the deep oceans. The transformation of light from threat to food required one of life’s most extraordinary inventions: oxygenic photosynthesis. The evolution of this biological process ultimately resulted in the capture of carbon and the release of large amounts of oxygen into the atmosphere, which in turn played a key role in triggering the explosive evolution of life from the simple to the complex and conscious. Photosynthesis uses carbon dioxide and water to produce sugars and oxygen in a process powered by the energy of the Sun. The purpose of photosynthesis, if you are a plant, is twofold. One is clearly visible in the famous equation: it is to make sugars, which is done by forcing electrons onto carbon dioxide. The other, which is hidden in the detail, is to capture energy from the Sun and store it in a usable form. All life on Earth stores energy in the same way, as a molecule called adenosine triphosphate, or ATP. This suggests strongly that ATP is a very ancient ‘invention’, and the details of its production and function could provide clues as to life’s origin.




The molecular machinery of oxygenic photosynthesis in constructed from three distinct components known as photosystem I, photosystem II, and the Oxygen Evolving Complex, linked together by two electron transport chains. This linked molecular machine is known as the Z scheme. Photosystem I takes electrons and, using energy from the Sun collected by the pigment chlorophyll, forces them onto carbon dioxide to make sugars. Photosystem II functions in a different way. It uses another form of chlorophyll and, rather than forcing its energised electrons onto carbon dioxide, it cycles them around a circuit somewhat like a battery, siphoning off a little of the Sun’s captured energy and storing it in the form of ATP. In order to make sugars and ATP, therefore, the plant needs sunlight, carbon dioxide and a supply of electrons. It doesn’t ‘care’ where those electrons come from. The plant may not care, but we certainly do, because plants get their electrons from water, splitting it apart in the process and releasing a waste gas (oxygen) into the atmosphere. This is the source of all the oxygen in the atmosphere of our planet, and so understanding the evolution of the Z scheme is of paramount importance if we are to understand how Earth came to be a home for complex animals like us.

In photosynthesis, 26 protein complexes and enzymes are required to go through the light and light-independent reactions, a chemical process that transforms sunlight into chemical energy, to get glucose and fixed carbon to make glucose, its food of the organism as end products. A good part of the protein complexes are uniquely used in photosynthesis. The pathway must go all the way through, and all steps are required, otherwise glucose is not produced. Also, in the oxygen evolving complex, which splits water into electrons, protons, and oxygen, if the light-induced electron transfer reactions do not go all the five steps through, no oxygen, no protons and electrons are produced, and no advanced life would be possible on earth.

So, photosynthesis is an interdependent system that could not have evolved, since all parts had to be in place right from the beginning. It contains many interdependent systems composed of parts that would be useless without the presence of all the other necessary parts. In these systems, nothing works until all the necessary components are present and working. So how could someone rationally say, the individual parts, proteins and enzymes, co-factors and assembly proteins not present in the final assemblage -- all happened by a series of natural events that we can call ad hoc mistakes "formed in one particular moment without ability to consider any application," to then somehow interlink in a meaningful way, to form electron transport chains, proton gradients to "feed" ATP synthase nano motors to produce ATP, and so on? Such independent structures would have not aided survival.

Consider the light harvesting complex, and the electron transport chain, that did not exist at exactly the same moment--would they ever "get together" since they would neither have any correlation to each other nor help survival separately? Repair of PSII via turnover of the damaged protein subunits is a complex process involving highly regulated reversible phosphorylation of several PSII core subunits. If this mechanism would not work starting right from the beginning, various radicals and active oxygen species with harmful effects on photosystem II (PSII) would make it cease to function. So it seems that photosynthesis falsifies the theory of evolution, where every small step needs to provide a survival advantage.



1) http://www.newworldencyclopedia.org/entry/Chlorophyll
2) http://www.nature.com/nature/journal/v421/n6923/full/nature01344.html
3) http://www.sciencedirect.com/science/article/pii/S0010854507001877
4) Blankenship: Molecular mechanisms of photosynthesis
5) http://www.esalq.usp.br/lepse/imgs/conteudo_thumb/24-Katoh.pdf
6) http://www.nature.com/nsmb/journal/v8/n7/full/nsb0701_577.html
7) http://www.atpsynthase.info/Basics.html

Fun and games with Otangelo Grasso about photosynthesis
http://sandwalk.blogspot.com.br/2016/04/fun-and-games-with-otangelo-grasso.html



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

The oxygen evolving complex (OEC) of photosystem II is irreducible complex.
https://reasonandscience.catsboard.com/t1583-the-oxygen-evolving-complex-oec-of-photosystem-ii-is-irreducible-complex

The biosynthesis pathway of Chlorophyll, essential for advanced life, is irreducible complex
https://reasonandscience.catsboard.com/t1546-chlorophyll-biosynthesis-pathway


“The process of photosynthesis is a very complex set of interdependent metabolic pathways “How it could have evolved is a bit mysterious.”
Robert Blankenship, professor of biochemistry at Arizona State University  

The origin of the oxygen evolving complex ( OEC )  is an enigma.
Oxygen evolving complex in Photosystem II: Better than excellent Mohammad Mahdi Najafpour*a and Govindjeeb 

Deep in the heart of this nest of proteins lies the manganese cluster, whose precise arrangement of atoms remains one of biology's outstanding problems.
One of the outstanding questions concerning the early Earth is how ancient phototrophs made the evolutionary transition from anoxygenic to oxygenic photosynthesis, which resulted in a substantial increase in the amount of oxygen in the atmosphere.
Light-driven oxygen production from superoxide by Mn-binding bacterial reaction centers, James P. Allen 

Perhaps the most widely discussed yet poorly understood event in the evolution of photosynthesis is the invention of the ability to use water as an electron donor, producing O2 as a waste product and giving rise to what is now called oxygenic photosynthesis.
Transition from Anoxygenic to Oxygenic Photosynthesis in a Microcoleus chthonoplastes Cyanobacterial Mat.  Jørgensen BB1, Cohen Y, Revsbech NP.

......and type II reaction center apoproteins is still unresolved owing to the fact that a unified evolutionary tree cannot be generated for these divergent reaction center subunits
Complex evolution of photosynthesis. Xiong J1, Bauer CE.

While the rise of oxygen has been the subject of considerable attention by Earth scientists, several important aspects of this problem remain unresolved.
Manganese-oxidizing photosynthesis before the rise of cyanobacteria  Jena E. Johnsona, Samuel M. Webbb

Although several hypotheses have been proposed to explain the origin of water oxidation and the Mn₄CaO₅ cluster (Blankenship and Hartman 1998; Dismukes et al. 2001;Sauer and Yachandra 2002; Rutherford and Faller 2003; Johnson et al. 2013), it is still unclear how an ancestral bacterium evolved the capacity to split water.
Origin and Evolution of Water Oxidation before the Last Common Ancestor of the Cyanobacteria


Early Evolution of Photosynthesis1 Robert E. Blankenship

To understand the origin and early evolution of photosynthesis, we need to consider mechanisms and evolution of all these subsystems and processes:

Evolutionary origins of oxygen evolution center and linked photosystems are important unsolved problems.
Pigments ( Chls , carotenoids, bilins )
Reaction centers (including O2  Evolution Center)
Antenna complexes
Electron transfer pathways
Carbon fixation pathways
Photoprotection mechanisms
Integration into cellular metabolism
No single branching diagram can represent the complex path of evolution of photosynthesis. 
The evolution of PS2 proteins has been partially by gene recruitment and partially by gene duplication, but most of the proteins are orphans, with no known source.

Origin and Evolution of Photosynthesis- Remaining Challenges

Nature of the earliest PS systems not known
Significance of gene duplications in RC evolution not understood
Evolutionary origin of the oxygen evolving complex not known
No good understanding of how two photosystems were linked in series



The argument of photosynthesis
1. One article in New Scientist magazine about green leaves under the bright sun states: “Catching up with nature’s innovation,” remains tantalizing but frustrating.  “Take sunlight, add water, and there you have it: free energy,” the article teased.  “Plants have been doing this for quite some time, splitting water’s hydrogen apart from its oxygen, but our efforts to turn water into a source of free hydrogen fuel by mimicking them have borne no fruit.”
2. A team led by Dr. Sun who is at work in Stockholm, Sweden is experimenting with different kinds of electrodes that produce more-desirable hydrogen gas instead of hydrogen ions.  Unfortunately, “the efficiency is abysmal” for these and all other electrodes tested so far, said rival John Turner in Colorado at the National Renewable Energy Laboratory.  Dr. Sun would be happy to get 10% efficiency – far below the near-100% efficiency plants get from the sun. Turner has achieved 12% efficiency, but his electrodes are only stable for a few days.  (The best solar cells achieve 27% efficiency.)
3. The great difficulty of imitating the marvelous structures of the nature is indicative of very complex design.
4. And even if the scientists ever succeed to mimic nature they will only prove intelligent design to account for the exquisite engineering we observe in living things.
5. Hence the supreme scientist and designer who is impossible to be imitated exists.
6. Photosynthesis is a extraordinary evidence of God's creative power.




http://www.genome.jp/kegg/pathway/map/map00195.html




All animals and most microorganisms rely on the continual uptake of large amounts of organic compounds from their environment. These compounds provide both the carbon-rich building blocks for biosynthesis and the metabolic energy for life. It is likely that the first organisms on the primitive Earth had access to an abundance of organic compounds produced by geochemical processes, but it is clear that these were used up billions of years ago. Since that time, virtually all of the organic materials required by living cells have been produced by photosynthetic organisms, including plants and photosynthetic bacteria. The core machinery that drives all photosynthesis appears to have evolved more than 3 billion years ago in the ancestors of present-day bacteria; today it provides the only major solar energy storage mechanism on Earth. The most advanced photosynthetic bacteria are the cyanobacteria, which have minimal nutrient requirements. They use electrons from water and the energy of sunlight to convert atmospheric CO2 into organic compounds—a process called carbon fixation. In the course of the overall reaction nH2O + nCO2 → (light) (CH2O)n + nO2, they also liberate into the atmosphere the molecular oxygen that then powers oxidative phosphorylation. In this way, it is thought that the evolution of cyanobacteria from more primitive photosynthetic bacteria eventually made possible the development of the many different aerobic life-forms that populate the Earth today.

Chloroplasts use chemiosmotic mechanisms to carry out their energy interconversions in much the same way that mitochondria do. Although much larger than mitochondria, they are organized on the same principles. They have a highly permeable outer membrane; a much less permeable inner membrane, in which membrane transport proteins are embedded; and a narrow intermembrane space in between. Together, these two membranes form the chloroplast envelope. The inner chloroplast membrane surrounds a large space called the stroma, which is analogous to the mitochondrial matrix. The stroma contains many metabolic enzymes and, as for the mitochondrial matrix, it is the place where ATP is made by the head of an ATP synthase. Like the mitochondrion, the chloroplast has its own genome and genetic system. The stroma therefore also contains a special set of ribosomes, RNAs, and the chloroplast DNA. An important difference between the organization of mitochondria and chloroplasts is highlighted in the Figure below:



The inner membrane of the chloroplast is not folded into cristae and does not contain electron-transport chains. Instead, the electron-transport chains, photosynthetic light-capturing systems, and ATP synthase are all contained in the thylakoid membrane, a separate, distinct membrane that forms a set of flattened, disc-like sacs, the thylakoids. The thylakoidmembrane is highly folded into numerous local stacks of flattened vesicles called grana, interconnected by nonstacked thylakoids. The lumen of each thylakoid is connected with the lumen of other thylakoids, thereby defining a third internal compartment called the thylakoid space. This space represents a separate compartment in each chloroplast that is not connected to either the intermembrane space or the stroma.

Chloroplasts Capture Energy from Sunlight and Use It to Fix Carbon

We can group the reactions that occur during photosynthesis in chloroplasts into two broad categories:

1. The photosynthetic electron-transfer reactions (also called the “light reactions”) occur in two large protein complexes, called reaction centers, embedded in the thylakoid membrane. A photon (a quantum of light) knocks an electron out of the green pigment molecule chlorophyll in the first reaction center, creating a positively charged chlorophyll ion. This electron then moves along an electron-transport chain and through a second reaction center in much the same way that an electron moves along the respiratory chain in mitochondria. During this electron-transport process, H+ is pumped across the thylakoid membrane, and the resulting  electrochemical proton gradient drives the synthesis of ATP in the stroma. As the final step in this series of reactions, electrons are loaded (together with H+) onto NADP+, converting it to the energy-rich NADPH molecule. Because the positively charged chlorophyll in the first reaction center quickly regains its electrons from water (H2O), O2 gas is produced as a by-product. All of these reactions are confined to the chloroplast.

2. The carbon-fixation reactions do not require sunlight. Here the ATP and NADPH generated by the light reactions serve as the source of energy and reducing power, respectively, to drive the conversion of CO2 to carbohydrate. These carbon-fixation reactions begin in the chloroplast stroma, where they generate the three-carbon sugar glyceraldehyde 3-phosphate. This simple sugar is exported to the cytosol, where it is used to produce sucrose and many other organic metabolites in the leaves of the plant. The sucrose is then exported to meet the metabolic needs of the nonphotosynthetic plant tissues, serving as a source of both carbon skeletons and energy for growth.

Thus, the formation of ATP, NADPH, and O2 (which requires light energy directly) and the conversion of CO2 to carbohydrate (which requires light energy only indirectly) are separate processes



A summary of the energyconverting metabolism in chloroplasts. Chloroplasts require only water and carbon dioxide as inputs for their lightdriven photosynthesis reactions, and they produce the nutrients for most other organisms on the planet. Each oxidation of two water molecules by a photochemical reaction center in the thylakoid membrane produces one molecule of oxygen, which is released into the atmosphere. At the same time, protons are concentrated in the thylakoid space. These protons create a large electrochemical gradient across the thylakoid membrane, which is utilized by the chloroplast ATP synthase to produce ATP from ADP and phosphate. The electrons withdrawn from water are transferred to a second type of photochemical reaction center to produce NADPH from NADP+. As indicated, the NADPH and ATP are fed into the carbonfixation cycle to reduce carbon dioxide, thereby producing the precursors for sugars, amino acids, and fatty acids. The CO2 that is taken up from the atmosphere here is the source of the carbon atoms for most organic molecules on Earth. In a plant cell, a variety of metabolites produced in the chloroplast are exported to the cytoplasm for biosyntheses. Some of the sugar produced is stored in the form of starch granules in the chloroplast, but the rest is transported throughout the plant as sucrose or converted to starch in special storage tissues. These storage tissues serve as a major food source for animals.

However, they are linked by elaborate feedback mechanisms that allow a plant to manufacture sugars only when it is appropriate to do so. Several of the chloroplast enzymes required for carbon fixation, for example, are inactive in the dark and reactivated by light-stimulated electron-transport processes.

Carbon Fixation Uses ATP and NADPH to Convert CO2 into Sugars

Animal cells produce ATP by using the large amount of free energy released when carbohydrates are oxidized to CO2 and H2O. The reverse reaction, in which plants make carbohydrate from CO2 and H2O, takes place in the chloroplast stroma. The large amounts of ATP and NADPH produced by the photosynthetic electron-transfer reactions are required to drive this energetically unfavorable reaction.



Figure above illustrates the central reaction of carbon fixation, in which an atom of inorganic carbon is converted to organic carbon: CO2 from the atmosphere combines with the five-carbon compound ribulose 1,5-bisphosphate plus water to yield two molecules of the three-carbon compound 3-phosphoglycerate. This carboxylation reaction is catalyzed in the chloroplast stroma by a large enzyme called ribulose bisphosphate carboxylase, or Rubisco for short. Because the reaction is so slow (each Rubisco molecule turns over only about 3 molecules of substrate per second, compared to 1000 molecules per second for a typical enzyme), an unusually large number of enzyme molecules are needed. Rubisco often constitutes more than 50% of the chloroplast protein mass, and it is thought to be the most abundant protein on Earth. In a global context, Rubisco also keeps the amount of the greenhouse gas CO2 in the atmosphere at a low level. Although the production of carbohydrates from CO2 and H2O is energetically unfavorable, the fixation of CO2 catalyzed by Rubisco is an energetically favorable reaction. Carbon fixation is energetically favorable because a continuous supply of the energy-rich ribulose 1,5-bisphosphate is fed into the process. This compound is consumed by the addition of CO2, and it must be replenished. The energy and reducing power needed to regenerate ribulose 1,5-bisphosphate come from the ATP and NADPH produced by the photosynthetic light reactions. The elaborate series of reactions in which CO2 combines with ribulose 1,5-bisphosphate to produce a simple sugar—a portion of which is used to regenerate ribulose 1,5-bisphosphate—forms a cycle, called the carbon-fixation cycle, or the Calvin cycle



Each turn of the cycle converts six molecules of 3-phosphoglycerate to three molecules of ribulose 1,5-bisphosphate plus one molecule of glyceraldehyde 3-phosphate. Glyceraldehyde 3-phosphate, the three-carbon sugar produced by the cycle, then provides the starting material for the synthesis of many other sugars and all of the other organic molecules that form the plant.

Photosynthesis at the forefront of a sustainable life 1

The development of a sustainable bio-based economy has drawn much attention in recent years, and research to find smart solutions to the many inherent challenges has intensified. In nature, perhaps the best example of an authentic sustainable system is oxygenic photosynthesis. The biochemistry of this intricate process is empowered by solar radiation influx and performed by hierarchically organized complexes composed by photoreceptors, inorganic catalysts, and enzymes which define specific niches for optimizing light-to-energy conversion. The success of this process relies on its capability to exploit the almost inexhaustible reservoirs of sunlight, water, and carbon dioxide to transform photonic energy into chemical energy such as stored in adenosine triphosphate. Oxygenic photosynthesis is responsible for most of the oxygen, fossil fuels, and biomass on our planet.

Sugars Generated by Carbon Fixation Can Be Stored as Starch or Consumed to Produce ATP

The glyceraldehyde 3-phosphate generated by carbon fixation in the chloroplast stroma can be used in a number of ways, depending on the needs of the plant. During periods of excess photosynthetic activity, much of it is retained in the chloroplast stroma and converted to starch. Like glycogen in animal cells, starch is a large polymer of glucose that serves as a carbohydrate reserve, and it is stored as large granules in the chloroplast stroma. Starch forms an important part of the diet of all animals that eat plants. Other glyceraldehyde 3-phosphate molecules are converted to fat in the stroma. This material, which accumulates as fat droplets, likewise serves as an energy reserve. At night, this stored starch and fat can be broken down to sugars and fatty acids, which are exported to the cytosol to help support the metabolic needs of the plant. Some of the exported sugar enters the glycolytic pathway, where it is converted to pyruvate. Both that pyruvate and the fatty acids can enter the plant cell mitochondria and be fed into the citric acid cycle, ultimately leading to the production of large amounts of ATP by oxidative phosphorylation



How chloroplasts and mitochondria collaborate to supply cells with both metabolites and ATP. (A)The inner chloroplast membrane is impermeable to the ATP and NADPH that are produced in the stroma during the light reactions of photosynthesis. These molecules are therefore funneled into the carbon-fixation cycle, where they are used to make sugars.The resulting sugars and their metabolites are either stored within the chloroplast—in the form of starch or fat—or exported to the rest of the plant cell. There, they can enter the energy-generating pathway that ends in ATP synthesis linked to oxidative phosphorylation inside the mitochondrion. Unlike the chloroplast, mitochondrial membranes contain a specific transporter that makes them permeable to ATP . Note that the O2 released to the atmosphere by photosynthesis in chloroplasts is used for oxidative phosphorylation in mitochondria; similarly, the CO2 released by the citric acid cycle in mitochondria is used for carbon fixation in chloroplasts. (B) In a leaf, mitochondria (red) tend to cluster close to the chloroplasts (green), as seen in this light micrograph.

Plants use this ATP in the same way that animal cells and other nonphotosynthetic organisms do to power a variety of metabolic reactions. The glyceraldehyde 3-phosphate exported from chloroplasts into the cytosol can also be converted into many other metabolites, including the disaccharide sucrose. Sucrose is the major form in which sugar is transported between the cells of a plant: just as glucose is transported in the blood of animals, so sucrose is exported from the leaves to provide carbohydrate to the rest of the plant.

The Thylakoid Membranes of Chloroplasts Contain the Protein Complexes Required for Photosynthesis and ATP Generation

We next need to explain how the large amounts of ATP and NADPH required for carbon fixation are generated in the chloroplast. Chloroplasts are much larger and less dynamic than mitochondria, but they make use of chemiosmotic energy conversion in much the same way. As we saw in Figure 14–38, chloroplasts and mitochondria are organized on the same principles, although the chloroplast contains a separate thylakoid membrane system in which its chemiosmotic mechanisms occur. The thylakoid membranes contain two large membrane protein complexes, called photosystems, which endow plants and other photosynthetic organisms with the ability to capture and convert solar energy for their own use. Two other protein complexes in the thylakoid membrane that work together with the photosystems in photophosphorylation—the generation of ATP with sunlight— have mitochondrial equivalents. These are the heme-containing cytochrome b6-f complex, which both functionally and structurally resembles cytochrome c reductase in the respiratory chain; and the chloroplast ATP synthase, which closely resembles the mitochondrial ATP synthase and works in the same way.


Photosynthesis is one of the most efficiently cycled and sustainable processes we know in Nature. This deceivingly simple process forms the basis for all the energy sources essential to life, from the intake of food to the burning of fossil fuels, and more recently, for the industrial production of value-added chemicals or bio-energy.

Blankenship: Molecular mechanisms of photosynthesis pg.206:

All known existing photosynthetic organisms are highly sophisticated cells, far removed from the first forms.

Another apparent paradox is the discovery that enzyme systems that either use O2, such as various oxidases, or protect against its reactive byproducts, such as superoxide or hydrogen peroxide, are found widely distributed throughout the tree of life. This suggests that these enzyme systems were present in the last common ancestor, which we earlier argued was not even photosynthetic, let alone oxygenic.

This is indeed a paradox, and finds hardly a convincing explanation through naturalistic , gradualistic early earth and life scenarios. Why would LUCA evolve these protective enzymes at all, if they were not required before oxygen arose in the atmosphere ?

So the ability to use or protect against oxygen appears on the surface to have been present prior to the ability to make oxygen . There are two possible explanations for this apparent paradox. First, low levels of O2 and other reactive oxygen species were almost certainly produced on the early Earth by nonbiological processes such as UV photolysis of water, so even the earliest cellsmay have needed protection from these toxic species.

Photolysis of water vapor and carbon dioxide produce hydroxyl and atomic oxygen, respectively, that, in turn, produce oxygen in small concentrations. This process produced oxygen for the early atmosphere before photosynthesis became dominant. 2

So it is questionable if UV photolysis would yield enough oxygen in order to provoke the first cells to evolve these extraordinary complex protective enzymes. Furthermore, would these enzymes not have to evolve in a very short period of time , in order to protect the cells before they would die ?

What was the nature of the earliest form of photosynthesis andwhatmight have been its evolutionary antecedents? Unfortunately, there is little definitive information to constrain our thinking on this question.

How do metabolic pathways originate and evolve? This is an issue that goes well beyond photosynthesis, but certainly includes photosynthesis as an example of a metabolic pathway, albeit an extraordinarily complex one.

Photosynthesis Also Produces Reduced Nitrogen and Sulfur Compounds 3

Photosynthesis encompasses more than carbon dioxide fixation and carbohydrate synthesis. In plants and algae, the ATP and NADPH generated by photosynthetic energy transduction reactions are consumed by a variety of other anabolic pathways found in chloroplasts. Carbohydrate synthesis is only one example of carbon metabolism; the synthesis of fatty acids, chlorophyll, and carotenoids also occurs in chloroplasts. Moving beyond carbon metabolism, several key steps of nitrogen and sulfur assimilation are localized in chloroplasts. The reduction of nitrite ( ) to ammonia , for example, is catalyzed by a reductase enzyme in the chloroplast stroma, with reduced ferredoxin serving as an electron donor. The ammonia is then channeled into amino acid and nucleotide synthesis, portions of which also occur in chloroplasts. Furthermore, much of the reduction of sulfate to sulfide is catalyzed by enzymes in the chloroplast stroma. In this case, ATP and reduced ferredoxin provide energy and reducing power. The sulfide, like ammonia, may then be
used for amino acid synthesis.




Photosynthesis Web Resources
Photosynthesis Journals
Internet chemistry Photosynthesis great resource
Photosynthesis
Photosynthesis Web Resources
Photophosphorylation video
Bio 231 - Cell Biology Lab animation
Photosynthesis
Photosynthesis
Photosynthesis  , Arizona Education
THE PHOTOSYNTHETIC PROCESS
twinkle toes, greate site about photosynthesis
Videos about photosynthesis
Photosynthesis Biociclopedia
Light harvesting complex of photosynthesis
Z-Scheme
Chlorophyll Biosynthesis in Bacteria: The Origins of Structural and Functional Diversity
Photosynthetic reaction centre
Evolution of photosynthesis
Chlorophyll biosynthesis pathway
Slideshare on Photosynthesis
Photosynthesis and the Transition to an Aerobic World


Books :

Oxygenic Photosynthesis: The Light Reactions

1. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4054791/
2. http://www.globalchange.umich.edu/globalchange1/current/lectures/Perry_Samson_lectures/evolution_atm/
3. Beckers world of the cell pg.315
4. The Cambridge Encyclopedia of Darwin and Evolutionary Thought, page 153
5. https://sci-hub.bz/http://www.nature.com/nchem/journal/v3/n10/full/nchem.1145.html?wt..
6. https://sci-hub.bz/http://www.nature.com/nchem/journal/v3/n10/full/nchem.1145.html?wt..
7. Chlorophyll Fluorescence Understanding Crop Performance— Basics and Applications, page 1
8. Handbook of Photosynthesis, third edition, page 8
9. Lodish, Molecular Cell Biology, Eight edition, page 560
10. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2606772/#fn2
11. https://www.scientificamerican.com/article/timeline-of-photosynthesis-on-earth/

Photosynthesis (supposedly) evolved early in Earth’s history.
The rapidity of its emergence suggests it was no fluke and could arise on other worlds, too. 11 
4.6 billion years ago -- Formation of Earth
3.4 billion years ago -- First photosynthetic bacteria

There is suggestive evidence that photosynthetic organisms were present in the younger sequences of the Kaapvaal and Pilbara cratons (~3.4–3.2 Ga) in the form of stromatolites and microfossils, which are inferred from morphology or geological context (Javaux et al. 2010; Noffke et al. 2006; Westall 2004). Though closely related, the two forms of photosynthetic bacteria, primitive anoxygenic and advanced oxygenic organisms, differ in their metabolism (Blankenship 2010; Schopf 1999). The primitive photosynthetic bacteria (such as green sulfur bacteria and purple bacteria) absorbed near-infrared rather than visible sunlight and produced sulfur or sulfate compounds rather than oxygen. They differ from oxygenic photosynthesis in the nature of the terminal reactants (e.g., hydrogen sulfide rather than water) and in the by-product generated (e.g., elemental sulfur instead of molecular oxygen). Therefore, water is not used as an electron donor. Anoxygenic phototrophs use molecules such as H2S, as opposed to H2O. Their pigments (possibly bacteriochlorophylls) were predecessors to chlorophyll. H2S is supplied in the vent environment by geothermal activity, and the metabolism of anoxygenic phototrophs produces sulfur as a by-product and builds glucose, the universal cellular fuel.

The origin and evolution of photosynthesis have long remained enigmatic, owing to a lack of sequence information of photosynthesis genes across the entire photosynthetic domain. Xiong and co-worker obtained new sequence information from the green sulfur bacterium Chlorobium and the green nonsulfur bacterium Chloroflexus and demonstrated conclusively for the first time that the major lineages of pigment (bacteriophyll) involved in anoxygenic photosynthesis arose before the development of oxygenic photosynthesis (chlorophyll) (Xiong et al. 2000) There are many examples of living anoxygenic phototrophs such as Chloroflexus, Rosieflexus, Thermochromatium, and Chlorodium, which are adapted to thermophilic habitat.

By the late Archean, a more complicated form of photoautotrophy, the oxygenic photosynthesis, evolved, as manifested by cyanobacteria associated with their stromatolites.
Handbook of Astrobiology  page 290

That is the claim. Where is the evidence ??!!

Further readings:
Mechanism for photosynthesis found in primeval, non-photosynthetic microbe

Out of thin air
The invention of oxygenic photosynthesis was a small step for a bacterium, but a giant leap for biology
and geochemistry. So when and how did cells first learn to split water to make oxygen gas?
https://sci-hub.wf/10.1038/445610a

Green power (photosynthesis) God’s solar power plants amaze chemists

hem impossible to form in the first place. But if oxygen is as old as the oldest rocks, there is no geological evidence to support the hypothetical oxygen-free atmosphere required.

Photosynthetic mechanisms

Our research aim at understanding the regulatory pathways that govern the biogenesis, performance and acclimation of the photosynthetic protein complexes in the thylakoid membrane.

Most attension so far has been put on Photosystem II composed of nearly 30 different protein subunits encoded by both the chloroplast and the nuclear genomes. Identification and role of translocon components, molecular chaperones and other folding factors in the thylakoid membrane, in stroma and in the thylakoid lumen during translation, insertion and assembly of chloroplast-encoded thylakoid membrane proteins are being addressed. As chloroplasts have developed from prokaryotic progenitors, we investigate in parallel the regulation and assembly of both the cyanobacterial and chloroplast thylakoid membrane complexes.


In addition to the harvesting of sunlight, the chloroplasts also function as "receptors" of environmental signals. We aim at system biology view on the chloroplast-derived regulation of nuclear gene expression by environmental cues, including redox and metabolite signaling. Redox signalling from chloroplasts to the nucleus is likely to be an important component in various stress responses and acclimation of plants but also metabolites derived from CO2 fixation are important regulators of nuclear gene expres​sion(Piippo et al, 2006). Information on global redox regulation of nuclear genes by chloroplast signals is obtained by transcript profiling and proteomics approaches.

Fig 2. Redox and metabolite control of nuclear gene expression in photosynthetic cells. Both environmental and metabolic cues modulate the function of chloroplasts, which in turn is likely to be involved in the relay of information to the nuclear compartment, finally leading to plant acclimation to prevailing conditions.

One of the least characterised thylakoid protein complexes is the NDH-1 complex. In chloroplast thylakoids it has been suggested to have a crusial role in plant acclimation to adverse environmental contditions whereas in cyanobacterial membranes there are multiple NDH-1 complexes with distinct functions in respiration, cyclic electron transfer around PS I and in Ci acquisition. We have recently started a project for functional, proteomic and structural characterisation of these different cyanobacterial NDH-1 complexes.

Subproject 1: Biosynthesis, assembly and turnover of chloroplast encoded thylakoid proteins

D1 protein turnover in photosystem II. The D1 protein of Photosystem II undergoes rapid light-dependent turnover. Upon degradation of the damaged D1 protein the new D1 copy is co-translationally incorporated into PSII (Zhang et al. 1999).

Usingin organello chloroplast translation system we have shown that the translation of chloroplast-encoded D1 protein is regulated by (i) a redox component activated by photosystem I, by (ii) trans-thylakoid proton gradient and by (iii) thiol reactants (Zhang et al., 2000; Zhang and Aro, 2002).

The role of photosystem II photodamage-repair-cycle and the heterogeneity of PS II in the grana and stroma thylakoids have been extensively studied (Aro et al., 2005; Danielson et al., 2006) Further the role of small proteins in the assembly of PS II and the oxygen evolving complex (OEC) has been addressed in the project (Baena-Gonzalez and Aro, 2002; Suorsa et al., 2004; Rokka et al., 2005; Suorsa et al., 2006)
Different steps involved in the turnover of the PSII D1 protein are depicted in a scheme below.

Fig 4. Turnover of D1 protein.
Chloroplast transformants:
The role of orf62 (psbZ) in chloroplast genome was resolved by tobacco transformants. Deletion of this gene revealed an important regulatory role for ORF62 protein in thylakoid electron transfer, in dissecting electrons from PSII to various pathways including the NDH complex and the terminal oxidase, PTOX. (Mäenpää et al., 2000, Baena-Gonzalez et al., 2001).Collaboration with P. Mäenpää, University of Turku, Finland.
Deletion of the psbA gene, encoding the D1 protein, from chloroplast genome resulted in complete absence of the PSII complex from the thylakoid membrane. This, in turn, was shown to induce a highly elevated level of the NDH and PTOX complexes in the thylakoid membrane, thereby partially compensating for the lack of PSII and making the chloroplasts to maintain proper redox poise (Baena-Gonzalez et al., 2003). Such alternative electron transfer pathways are supposed to function as "safety valves" during severe environmental stress on PSII, e.g. under photoinhibitory conditions (Allahverdiyeva et al, 2005). Collaboration with Prof. P. Maliga, Waksman Institute, Rutgers University, USA and P. Mäenpää, University of Turku, Finland.

Yet another set of chloroplast transformants, the deletion mutants of the genes in the psbEFLJ operon, one at the time, have been characterized and the roles of these 4 genes in the assembly of PSII were investigated. None of the mutants is capable of autotrophic growth. Both the pbsE and psbF gene products are imperative for synthesis and assembly of the D1/D2 heterodimer.

PsbL protein turned out to be a prerequisite for stable assembly of CP43 and dimerization of PSII and finally the PsbJ protein is an absolute requirement for the attachment of the peripheral LHCII to the PSII core complex. Proper assembly of the oxygen evolving complex also reguires both PsbL and PsbJ (Suorsa et al., 2004). Collaboration with Prof. R. Herrmann, Ludwig-Maximilians Universität, Muenchen, Germany.

Subproject 2: PSII core and LHCII protein phosphorylation
We have demonstrated that LHCII protein accumulation and acclimation of plants to various environmental conditions is, at least partially self-regulating (Pursiheimo et al., 2001). This was demonstrated to occur via redox signalling and activation/deactivation of the thylakoid LHCII kinase. LHCII kinase is known to be under complex redox regulation; activation occurring via reduction of plastoquinone and occupation of the Qo site in the cytb6f complex. At high light intensities, however, a superimposed inactivation of the kinase by thiol reductants takes place in the chloroplasts (Rintamäki et al., 2000). We have further studied this intriguing regulation mechanism of thylakoid protein phosphorylation. An important result is a strong metabolic control of LHCII protein phosphorylation (Hou et al., 2003). It was shown that under in vivo conditions cells favor state 2 and transition to state 1 protects against excess light induced "oxidative stress" (Tikkanen et al, 2006).Collaboration with Prof. Eevi Rintamäki, University of Turku, Finland.
We have also addressed the regulation of thylakoid protein dephosphorylation by immunophilin TLP40 located in thylakoid lumen. It was of particular interest to note the TLP40-mediated acceleration of PSII core protein dephosphorylation as a response to a sudden heat shock to the plants (Rokka et al., 2000). Physiological implication of this regulation is likely to allow fast degradation of damaged D1 protein copies. Further investigations on TLP40 and other thylakoid phosphoproteins are in progress in collaboration with prof. Henrik Vibe Scheller, KVL, Copenhagen, Denmark and Dr. A. Vener, Linköping University, Sweden.

Subproject 3: Chloroplast-mediated regulation of nuclear genes
Chloroplast signaling involves mechanisms to relay information from chloroplasts to the nucleus, to change nuclear gene expression in response to environmental cues. Aside from reactive oxygen species (ROS) produced under stress conditions, changes in the reduction/oxidation state of photosynthetic electron transfer components or coupled compounds in the stroma and the accumulation of photosynthesis-derived metabolites are likely origins of chloroplast signals. We attempted to investigate the origin of the signals from chloroplasts in mature Arabidopsis leaves by differentially modulating the redox states of the plastoquinone pool and components on the reducing side of photosystem I, as well as the rate of CO2 fixation, while avoiding the production of ROS by excess light. Differential expression of several nuclear photosynthesis genes, including a set of Calvin cycle enzymes, was recorded. These responded to the stromal redox conditions under prevailing light conditions but were independent of the redox state of the plastoquinone pool. The steady-state CO2 fixation rate was reflected in the orchestration of the expression of a number of genes encoding cytoplasmic proteins, including several glycolysis genes and the trehalose-6-phosphate synthase gene, and also the chloroplast-targeted chaperone DnaJ. Clearly, in mature leaves, the redox state of the compounds on the reducing side of photosystem I is of greater importance in light-dependent modulation of nuclear gene expression than the redox state of the plastoquinone pool, particularly at early signaling phases. It also became apparent that photosynthesismediated generation of metabolites or signaling molecules is involved in the relay of information from chloroplast to nucleus. (Piippo et al 2006).
Fig 5. Clustering of all 2,027 genes that showed significant changes in expression in at least 1 of the light treatments (red, upregulated; green, downregulated; gray, missing value). Control sample treated with growth light served as a baseline reference for each treatment. Three independent biological replicates, starting from the growth of a new set of plants, are shown for each light treatment for comparison of the repeatability of the biological replicates. Each biological replicate measurement is an average of technical replicates that were obtained by spotting each DNA fragment 3 times on a single slide, producing 3 technical replicates for each measurement. For detailed data analysis procedure, see Piippo et al 2006. Light conditions are darkness (D), PSI light (PSI; 30 µmol·m-2·s-1), low light (LL; 20 µmol·m-2·s-1), PSII light (PSII*, 150 µmol·m-2·s-1; PSII, 50 µmol·m-2·s-1) and high light (HL; 450 µmol·m-2·s-1).

Subproject 4: Transcriptional regulation of PSII and PSI genes
Our first studies on regulation of chloroplast gene transcription have been conducted in collaboration with prof. G. Link in Bochum (Baena-Gonzalez et al., 2001). When plants were subjected to higher irradiances we notified a global enhancement of chloroplast gene transcription. Isolation of plastid specific RNA polymerase revealed a phosphorylation of specific protein subunits, which was interpreted to be responsible, together with enhanced thiol reduction state, of the accelerated polymerase activity.
In the cyanobacterium Synechocystis 6803, the expression of the psb genes encoding the various subunits of PSI and PSII was studied in more detail (Herranen et al., 2001; Herranen et al., 2005). The PSII genes fell into two distinct regulation groups. psbA and psbD genes formed their own group being under regulation of the repressor protein in darkness. Rapid upregulation of these two genes upon exposure of cells to light is likely to guarantee a flexible synthesis of the D1 and the D2 proteins, respectively. Other psb genes require protein synthesis for activation upon exposure of cells to light and are likely to be regulated via activator proteins. Common to both gene groups is a regulation of the mRNA stability by the redox state of the plastoquinone pool (Herranen et al., 2001).
Action spectrum of psbA gene expression interestingly revealed a maximum of transcripts in blue light, similar to the action spectrum of photoinhibition, thus suggesting a causal relationship between the two processes (Tyystjärvi et al., 2002).
Another cyanobacterium, Synechococcus PCC7942, clearly uses a different strategy for regulation of psbA gene expression as a response to environmental cues (Sippola and Aro, 2000). In this species the thiol redox state of the cell determines the transcriptional activation or repression of various members of the psbA gene family encoding two distinct forms of the D1 protein. The so-called stress form (D1 form 2) is only transiently expressed if the cell metabolism can be acclimated to changed environmental conditions and the redox balance to be regained.
Both in Synechocystis (Tyystjärvi et al., 2001) and in Synechococcus (Sippola and Aro, 2000) the novel discovery was an obvious translational regulation of psbA genes, in addition to a generally recognized transcriptional regulation. This regulation mechanism is typical in chloroplasts but in cyanobacteria it might be specific only for the psbA genes and synthesis of the rapidly turning-over D1 protein.

Subproject 5: Cyanobacterial NDH-1 complexes
Upon decision to acquire a proteomic view of cyanobacterial thylakoid membrane complexes in order to understand the acclimation strategies of the photosynthetic machinery to varying environmental conditions, we made a discovery of novel NDH-1 complexes (Herranen et al., 2004). We were able to identify two distinct NDH-1 complexes, to show the functional roles for these complexes in respiration and cyclic electron flow around PSI and also to show a huge dynamics in the expression of these complexes and in their co-operation with the NdhD3/NdhF3/CupA/Sll1735 complex, according to a multitude of environmental cues (Zhang et al., 2004). This study was followed by detailed mass spectrometric analysis of the 15 protein subunits of the largest NDH-1 complex (Battchikova et al., 2005). We then developed the isolation methods for the NDH-1 complexes using a His-tag approach (Zhang et al., 2005) and have so far resolved the EM structure by single particle electron microscopy in collaboration with Prof. E. Boekema (Arteni et al., 2006). Several membrane protein complexes in cyanobacteria are presently under investigation.

Fig. 6. Hypothetical scheme of the assembly of multiple NDH-1 complexes in cyanobacteria. Letters refer to corresponding ndh gene products.

http://www.genome.jp/kegg/pathway/map/map00195.html

In photosynthesis, 26 protein complexes and enzymes are required to go through the light and light independent reactions, a chemical process that transforms sunlight into chemical energy,  to get glucose as end product, a metabolic intermediate for cell respiration. The protein complexes are uniquely used in photosynthesis. The pathway must go all the way through, and all steps are required, otherwise, glucose is not produced. Also, in the oxygen-evolving complex, which splits water into electrons, protons, and CO2, if the light-induced electron transfer reactions do not go all the five steps through, no oxygen, no protons and electrons are produced, no advanced life would be possible on earth. So, photosynthesis is a interdependent system, that could not have evolved, since all parts had to be in place right from the beginning. So it seems that photosynthesis falsifies the theory of evolution, where all small steps need to provide a survival advantage.

Photosynthesis is a process used by plants and other organisms to convert light energy, normally from the sun, into chemical energy that can be later released to fuel the organisms' activities. This chemical energy is stored in carbohydrate molecules, such as sugars, which are synthesized from carbon dioxide and water – hence the name photosynthesis, from the Greek φῶς, phōs, "light", and σύνθεσις, synthesis, "putting together". Oxygen is generally released as a waste product, although anoxic photosynthesis is possible. Most plants, most algae, and cyanobacteria perform photosynthesis. Photosynthetic organisms are called photoautotrophs. Photosynthesis maintains atmospheric oxygen levels and supplies all of the organic compounds and most of the energy necessary for life on Earth.


http://creationsafaris.com/crev201105.htm#gene499

The particular part of the reactor that splits water molecules and combines oxygen atoms into the O2 gas we breathe they said is

“one of nature’s most fascinating and important reactions.”

Scientists unlock some key secrets of photosynthesis

"The photosynthetic system of plants is nature's most elaborate nanoscale biological machine,"

"It converts light energy at unrivalled efficiency of more than 95 per cent compared to 10 to 15 per cent in the current man-made solar technologies.
"Photosystem II is the engine of life," Lakshmi said. "It performs one of the most energetically demanding reactions known to mankind, splitting water, with remarkable ease and efficiency."

http://www.ks.uiuc.edu/History/photosynthesis/PhotoPart4.html

But this current work on coherence draws from some 30-plus years of Schulten and collaborators labouring to understand the story of how nature has fashioned photosynthesis to make it an efficient and elegant process. And Schulten's objective still remains to uncover the many steps of photosynthesis and clearly explain the findings to the research community. “There was a lot of work done, methodological developments and theory and so on, but the goal was to explain how nature effectively harvests sunlight,” summarizes Schulten on his last 35 years. “It's maybe still not complete, but I figured it out to a large degree.”


Scientists unlock some key secrets of photosynthesis

The photosynthetic system of plants is nature’s most elaborate nanoscale biological machine,” said Lakshmi. “It converts light energy at unrivaled efficiency of more than 95 percent compared to 10 to 15 percent in the current man-made solar technologies.,, “Photosystem II is the engine of life,” Lakshmi said. “It performs one of the most energetically demanding reactions known to mankind, splitting water, with remarkable ease and efficiency.”,,, “Water is a very stable molecule and it takes four photons of light to split water,” she said. “This is a challenge for chemists and physicists around the world (to imitate) as the four-photon reaction has very stringent requirements.”

In order for advanced life to be possible, the distance of the earth from the sun, the carbon dioxide level in the atmosphere, Oxygen quantity in the atmosphere, Nitrogen quantity in the athmosphere, atmospheric pressure, atmospheric transparency, stratospheric ozon quality, amongst other parameters, must be in a very tiny, limited range.

How could it be better explained, than through intentional design ?

The frequency distribution of electromagnetic radiation produced by the sun is also critical, as it needs to be tuned to the energies of chemical bonds on earth. If the photons of radiation are too energetic (too much ultraviolet radiation), then chemical bonds are destroyed and molecules are unstable; if the photons are too weak (too much infrared radiation), then chemical reactions will be too sluggish. The radiation produced is dependent on a careful balancing of the electromagnetic force (alpha-E) and the gravity force (alpha-G), with the mathematical relationship including (alpha-E)12, making the specification for the electromagnetic force particularly critical. On the other hand, the chemical bonding energy comes from quantum mechanical calculations that include the electromagnetic force, the mass of the electron, and Planck's constant. Thus, all of these constants have to be sized relative to each other to give a universe in which radiation is tuned to the necessary chemical reactions that are essential for life.

Another interesting fine tuning coincidence is that the emission spectrum for the sun not only peaks at an energy level which is idea to facilitate chemical reaction but it also peaks in the optical window for water. Water is 107 more opaque to ultraviolet and infrared radiation than it is to radiation in the visible spectra (or what we call light). Since living tissue in general and eyes in particular are composed mainly of water, communication by sight would be impossible were it not for this unique window of light transmission by water being ideally matched to the radiation from the sun. Yet this matching requires carefully prescribing the values of the gravity and electromagnetic force constants as well as the Planck's constant and the mass of the electron.

Visible light is  incredibly fine-tuned for life to exist 
Though visible light is only a tiny fraction of the total electromagnetic spectrum coming from the sun, it happens to be the "most permitted" portion of the sun's spectrum allowed to filter through the our atmosphere. All the other bands of electromagnetic radiation, directly surrounding visible light, happen to be harmful to organic molecules, and are almost completely absorbed by the atmosphere. The tiny amount of harmful UV radiation, which is not visible light, allowed to filter through the atmosphere is needed to keep various populations of single cell bacteria from over-populating the world (Ross; reasons.org). The size of light's wavelengths and the constraints on the size allowable for the protein molecules of organic life, also seem to be tailor-made for each other. This "tailor-made fit" allows photosynthesis, the miracle of sight, and many other things that are necessary for human life. These specific frequencies of light (that enable plants to manufacture food and astronomers to observe the cosmos) represent less than 1 trillionth of a trillionth (10^-24) of the universe's entire range of electromagnetic emissions. Like water, visible light also appears to be of optimal biological utility (Denton; Nature's Destiny).

Distance of the earth from the sun : Malcolm Bowden says, "If it were 5% closer, then the water would boil up from the oceans and if it were just 1% farther away, then the oceans would freeze, and that gives you just some idea of the knife edge we are on."

The carbon dioxide level in atmosphere  If greater: runaway greenhouse effect would develop.  If less: plants would be unable to maintain efficient photosynthesis

Oxygen quantity in atmosphere If greater: plants and hydrocarbons would burn up too easily.  If less: advanced animals would have too little to breathe

Nitrogen quantity in atmosphere If greater: too much buffering of oxygen for advanced animal respiration; too much nitrogen fixation for support of diverse plant species.  
If less: too little buffering of oxygen for advanced animal respiration; too little nitrogen fixation for support of diverse plant species.

Atmospheric pressure: If too small: liquid water will evaporate too easily and condense too infrequently; weather and climate variation would be too extreme; lungs will not function. If too large: liquid water will not evaporate easily enough for land life; insufficient sunlight reaches planetary surface; insufficient uv radiation reaches planetary surface; insufficient climate and weather variation; lungs will not function

Atmospheric transparency:If smaller: insufficient range of wavelengths of solar radiation reaches planetary surface . If greater: too broad a range of wavelengths of solar radiation reaches planetary surface

stratospheric ozone quantity:If smaller: too much uv radiation reaches planet’s surface causing skin cancers and reduced plant growth . If larger: too little uv radiation reaches planet’s surface causing reduced plant growth and insufficient vitamin production for animals


Photosynthesis is a process used by plants and other organisms to convert light energy, normally from the sun, into chemical energy that can be later released to fuel the organisms' activities. This chemical energy is stored in carbohydrate molecules, such as sugars, which are synthesized from carbon dioxide and water – hence the name photosynthesis, from the Greek φῶς, phōs, "light", and σύνθεσις, synthesis, "putting together". Oxygen is also released, mostly as a waste product. Most plants, most algae, and cyanobacteria perform the process of photosynthesis, and are called photoautotrophs. Photosynthesis maintains atmospheric oxygen levels and supplies all of the organic compounds and most of the energy necessary for all life on Earth.

Light Absorption for Photosynthesis

Photosynthesis depends upon the absorption of light by pigments in the leaves of plants. The most important of these is chlorophyll-a, but there are several accessory pigments that also contribute.

Principles of Spectrophotometry

Quantum Yield

The quantum yield (Φ) of a process in which molecules give up their excitation energy (or "decay") is the fraction of excited molecules that decay via that pathway (Clayton 1971, 1980).

The value of Φ for a particular process can range from 0 (if that process is never involved in the decay of the excited state) to 1.0 (if that process always deactivates the excited state). The sum of the quantum yields of all possible processes is 1.0.

In functional chloroplasts kept in dim light, the quantum yield of photochemistry is approximately 0.95 ( 95% efficient ) , the quantum yield of fluorescence is 0.05 or lower, and the quantum yields of other processes are negligible. The vast majority of excited chlorophyll molecules therefore lead to photochemistry.

The quantum yield of formation of the products of photosynthesis, such as O2, can be measured quite accurately. In this case the quantum yield is substantially lower than the value for photochemistry, because several photochemical events must take place before any O2 molecules form. For O2 production the measured maximum quantum yield is approximately 0.1, meaning that 10 quanta are absorbed for each O2 molecule released. The reciprocal of the quantum yield is called the quantum requirement. The minimum quantum requirement for O2 evolution is therefore about 10 (see textbook Figure 7.11). Quantitative measurements of the absorption of light and the fate of the energy contained in the light are essential to an understanding of photosynthesis.

"Information is information, not matter or energy. No materialism which does not admit this can survive at the present day."
Norbert Weiner - MIT Mathematician - Father of Cybernetics

Materialists have tried to get around this crushing evidence for the sudden appearance of life by suggesting life could originate in extreme conditions. Yet they are betrayed once again by the empirical evidence:

Refutation Of Hyperthermophile Origin Of Life scenario
Excerpt: While life, if appropriately designed, can survive under extreme physical and chemical conditions, it cannot originate under those conditions. High temperatures are especially catastrophic for evolutionary models. The higher the temperature climbs, the shorter the half-life for all the crucial building block molecules, http://www.reasons.org/LateHeavyBombardmentIntensityandtheOriginofLife

Chemist explores the membranous origins of the first living cell:
Excerpt: Conditions in geothermal springs and similar extreme environments just do not favor membrane formation, which is inhibited or disrupted by acidity, dissolved salts, high temperatures, and calcium, iron, and magnesium ions. Furthermore, mineral surfaces in these clay-lined pools tend to remove phosphates and organic chemicals from the solution. "We have to face up to the biophysical facts of life," Deamer said. "Hot, acidic hydrothermal systems are not conducive to self-assembly processes."
http://currents.ucsc.edu/05-06/04-03/deamer.asp

The evidence scientists have discovered in the geologic record is stunning in its support of the anthropic hypothesis. The oldest sedimentary rocks on earth, known to science, originated underwater (and thus in relatively cool environs) 3.86 billion years ago. Those sediments, which are exposed at Isua in southwestern Greenland, also contain the earliest chemical evidence (fingerprint) of “photosynthetic” life [Nov. 7, 1996, Nature]. This evidence had been fought by materialists since it is totally contrary to their evolutionary theory. Yet, Danish scientists were able to bring forth another line of geological evidence to substantiate the primary line of geological evidence for photo-synthetic life in the earth’s earliest sedimentary rocks (U-rich Archaean sea-floor sediments from Greenland - indications of +3700 Ma oxygenic photosynthesis (2003). Thus we now have conclusive evidence for photo-synthetic life in the oldest sedimentary rocks ever found by scientists on earth. The simplest photosynthetic bacterial life on earth is exceedingly complex, too complex to happen by accident even if the primeval oceans had been full of pre-biotic soup.

The Miracle Of Photosynthesis - electron transport - video
https://www.youtube.com/watch?v=hj_WKgnL6MI

Evolution vs ATP Synthase - Molecular Machine - video
http://www.metacafe.com/watch/4012706/evolution_vs_atp_synthase_molecular_machine/

Electron transport and ATP synthesis during photosynthesis - Illustration
http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=cooper.figgrp.1672

Evolutionary biology: Out of thin air John F. Allen & William Martin:
The measure of the problem is here: “Oxygenetic photosynthesis involves about 100 proteins that are highly ordered within the photosynthetic membranes of the cell." http://www.nature.com/nature/journal/v445/n7128/full/445610a.html

Estimating the prevalence of protein sequences adopting functional enzyme folds: Doug Axe:
Excerpt: Starting with a weakly functional sequence carrying this signature, clusters of ten side-chains within the fold are replaced randomly, within the boundaries of the signature, and tested for function. The prevalence of low-level function in four such experiments indicates that roughly one in 10^64 signature-consistent sequences forms a working domain. Combined with the estimated prevalence of plausible hydropathic patterns (for any fold) and of relevant folds for particular functions, this implies the overall prevalence of sequences performing a specific function by any domain-sized fold may be as low as 1 in 10^77, adding to the body of evidence that functional folds require highly extraordinary sequences. http://www.ncbi.nlm.nih.gov/pubmed/15321723

Evolution vs. Functional Proteins - Doug Axe - Video
http://www.metacafe.com/watch/4018222/evolution_vs_functional_proteins_where_did_the_information_come_from_doug_axe_stephen_meyer/

Of note: anoxygenic (without oxygen) photosynthesis is even more of a complex chemical pathway than oxygenic photosynthesis is:

"Remarkably, the biosynthetic routes needed to make the key molecular component of anoxygenic photosynthesis are more complex than the pathways that produce the corresponding component required for the oxygenic form."; Hugh Ross

also of note: Anaerobic organisms and most viruses are quickly destroyed by direct contact with oxygen.

"There is no question about photosynthesis being Irreducibly Complex. But it’s worse than that from an evolutionary perspective. There are 17 enzymes alone involved in the synthesis of chlorophyll. Are we to believe that all intermediates had selective value? Not when some of them form triplet states that have the same effect as free radicals like O2. In addition if chlorophyll evolved before antenna proteins, whose function is to bind chlorophyll, then chlorophyll would be toxic to cells. Yet the binding function explains the selective value of antenna proteins. Why would such proteins evolve prior to chlorophyll? and if they did not, how would cells survive chlorophyll until they did?" Uncommon Descent Blogger

Interestingly, while the photo-synthetic bacteria were reducing greenhouse gases and producing oxygen, and metal, and minerals, which would all be of benefit to modern man, "sulfate-reducing" bacteria were also producing their own natural resources which would be very useful to modern man. Sulfate-reducing bacteria helped prepare the earth for advanced life by detoxifying the primeval earth and oceans of poisonous levels of heavy metals while depositing them as relatively inert metal ores. Metal ores which are very useful for modern man, as well as fairly easy for man to extract today (mercury, cadmium, zinc, cobalt, arsenic, chromate, tellurium and copper to name a few). To this day, sulfate-reducing bacteria maintain an essential minimal level of these heavy metals in the ecosystem which are high enough so as to be available to the biological systems of the higher life forms that need them yet low enough so as not to be poisonous to those very same higher life forms.

Bacterial Heavy Metal Detoxification and Resistance Systems:
Excerpt: Bacterial plasmids contain genetic determinants for resistance systems for Hg2+ (and organomercurials), Cd2+, AsO2, AsO43-, CrO4 2-, TeO3 2-, Cu2+, Ag+, Co2+, Pb2+, and other metals of environmental concern.
http://www.springerlink.com/content/u1t281704577v8t3/
http://www.int-res.com/articles/meps/26/m026p203.pdf

Even this recent "evolution friendly" article readily admits the staggering level of complexity required for the "first" cell:

Was our oldest ancestor a proton-powered rock? - Oct. 2009
Excerpt: “There is no doubt that the progenitor of all life on Earth, the common ancestor, possessed DNA, RNA and proteins, a universal genetic code, ribosomes (the protein-building factories), ATP and a proton-powered enzyme for making ATP. The detailed mechanisms for reading off DNA and converting genes into proteins were also in place. In short, then, the last common ancestor of all life looks pretty much like a modern cell.”
http://www.newscientist.com/article/mg20427306.200-was-our-oldest-ancestor-a-protonpowered-rock.html

Journey Inside The Cell - DNA to mRNA to Proteins - Stephen Meyer - Signature In The Cell - video
https://www.youtube.com/watch?v=1fiJupfbSpg

Signature in the Cell - Book Review - Ken Peterson
Excerpt: the “simplest extant cell, Mycoplasma genitalium — a tiny bacterium that inhabits the human urinary tract — requires ‘only’ 482 proteins to perform its necessary functions…(562,000 bases of DNA…to assemble those proteins).” ,,, amino acids have to congregate in a definite specified sequence in order to make something that “works.” First of all they have to form a “peptide” bond and this seems to only happen about half the time in experiments. Thus, the probability of building a chain of 150 amino acids containing only peptide links is about one chance in 10 to the 45th power.
In addition, another requirement for living things is that the amino acids must be the “left-handed” version. But in “abiotic amino-acid production” the right- and left-handed versions are equally created. Thus, to have only left-handed, only peptide bonds between amino acids in a chain of 150 would be about one chance in 10 to the 90th. Moreover, in order to create a functioning protein the “amino acids, like letters in a meaningful sentence, must link up in functionally specified sequential arrangements.” It turns out that the probability for this is about one in 10 to the 74th. Thus, the probability of one functional protein of 150 amino acids forming by random chance is (1 in) 10 to the 164th. If we assume some minimally complex cell requires 250 different proteins then the probability of this arrangement happening purely by chance is one in 10 to the 164th multiplied by itself 250 times or one in 10 to the 41,000th power.
http://www.spectrummagazine.org/reviews/book_reviews/2009/10/06/signature_cell

"No man-made program comes close to the technical brilliance of even Mycoplasmal genetic algorithms. Mycoplasmas are the simplest known organism with the smallest known genome, to date. How was its genome and other living organisms' genomes programmed?" - David L. Abel and Jack T. Trevors, “Three Subsets of Sequence Complexity and Their Relevance to Biopolymeric Information,” Theoretical Biology & Medical Modelling, Vol. 2, 11 August 2005, page 8
http://www.biomedcentral.com/content/pdf/1742-4682-2-29.pdf

First-Ever Blueprint of 'Minimal Cell' Is More Complex Than Expected - Nov. 2009
Excerpt: A network of research groups,, approached the bacterium at three different levels. One team of scientists described M. pneumoniae's transcriptome, identifying all the RNA molecules, or transcripts, produced from its DNA, under various environmental conditions. Another defined all the metabolic reactions that occurred in it, collectively known as its metabolome, under the same conditions. A third team identified every multi-protein complex the bacterium produced, thus characterising its proteome organisation.
"At all three levels, we found M. pneumoniae was more complex than we expected,"
http://www.sciencedaily.com/releases/2009/11/091126173027.htm

Intelligent Design or Evolution? Stuart Pullen
The chemical origin of life is the most vexing problem for naturalistic theories of life's origins. Despite an intense 50 years of research, how life can arise from non-life through naturalistic processes is as much a mystery today as it was fifty years ago, if not more.
http://www.arn.org/arnproducts/php/book_show_item.php?id=106

On The Origin Of Life And God - Henry F. Schaefer, III PhD. - video
http://www.metacafe.com/watch/4018204/the_origin_of_life_and_god_henry_fritz_schaefer_phd/

By the way, there is a one million dollar "Origin-of-Life" prize being offered:

"The Origin-of-Life Prize" (hereafter called "the Prize") will be awarded for proposing a highly plausible mechanism for the spontaneous rise of genetic instructions in nature sufficient to give rise to life.
http://www.us.net/life/index.htm

Is Photosynthesis Irreducibly Complex?

From Nature magazine:
“Knowing how plants and bacteria harvest light for photosynthesis so efficiently could provide a clean solution to mankind’s energy requirements. The secret, it seems, may be the coherent application of quantum principles.
 
Photosynthesis provides the primary energy source for almost all life on Earth. 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. The study reveals electronic quantum beats characteristic of wavelike energy motion within the bacteriochlorophyll complex from the green sulphur bacterium Chlorobium tepidum. This wavelike characteristic of the energy transfer process can explain the extreme efficiency of photosynthesis, in that vast areas of phase space can be sampled effectively to find the most efficient path for energy transfer.

Photosynthetic complexes are exquisitely tuned to capture solar light efficiently, and then transmit the excitation energy to reaction centres, where long term energy storage is initiated. The energy transfer mechanism is often described by semiclassical models that invoke ‘hopping’ of excited-state populations along discrete energy levels. Spectroscopic data clearly document the dependence of the dominant energy transport pathways on the spatial properties of the excited-state wavefunctions of the whole bacteriochlorophyll complex. Here we obtain direct evidence for remarkably long-lived electronic quantum coherence playing an important part in energy transfer processes within this system. The quantum coherence manifests itself in characteristic, directly observable quantum beating signals among the excitons within the Chlorobium tepidum FMO complex at 77 K. 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. Evidence for wavelike energy transfer through quantum coherence in photosynthetic systems Gregory S.
Engel et al Nature 446, 782-786 (12 April 2007) | doi:10.1038/nature05678″


Conclusion? Obviously this is a brilliant piece of design by someone who even knows how quantum mechanics works. Well not exactly …
Photosynthesis Analysis Shows Work Of Ancient Genetic Engineering 


Science Daily 2002  The development of the biochemical process of photosynthesis is one of nature’s most important events, but how did it actually happen? This is a question that molecular biology has first posed, and now perhaps answered.

“The process of photosynthesis is a very complex set of interdependent metabolic pathways,” said Robert Blankenship, professor of biochemistry at Arizona State University. “How it could have evolved is a bit mysterious.”


Photosynthesis is one of the most important chemical processes ever developed by life — a chemical process that transforms sunlight into chemical energy, ultimately powering virtually all the living things and allowing them to dominate the earth. The evolution of aerobic photosynthesis in bacteria is also the most likely reason for the development of an oxygen-rich atmosphere that transformed the chemistry of the Earth billions of years ago, further triggering the evolution of complex life. After decades of research, biochemists now understand that this critical biological process depends on some very elaborate and rapid chemistry involving a series of enormously large and complex molecules a set of complex molecular systems all working together.

“We know that the process evolved in bacteria, probably before 2.5 billion years ago, but the history of photosynthesis’s development is very hard to trace,” said Blankenship.
In a paper in the November 22 2002 issue of Science, Blankenship and colleagues partially unravel this mystery through an analysis of the genomes of five bacteria representing the basic groups of photosynthetic bacteria and the complete range of known photosynthetic processes.


The analysis revealed clear evidence that photosynthesis did not evolve through a linear path of steady change and growing complexity but through a merging of evolutionary lines that brought together independently evolving chemical systems — the swapping of blocks of genetic material among bacterial species known as horizontal gene transfer.


“We found that the photosynthesis-related genes in these organisms have not had all the same pathway of evolution. It’s clear evidence for horizontal gene transfer,” said Blankenship.
Blankenship performed a mathematical analysis of the set of shared genes to determine possible evolutionary relationships between them, but they arrived at different results depending on which genes were tested
“We did a kind of tree analysis of all 188 genes to determine what the best evolutionary tree was. We found that a fraction of the genes supported each of the different possible arrangements of the tree. It’s clear that the genes themselves have different evolutionary histories,” Blankenship said.


Blankenship argues that different pieces of the system evolved separately in different organisms, perhaps to serve purposes different from their current function in the photosynthesis. Brought together either by fusion of two different bacteria or by the “recruitment” of blocks of genes, the new combination of genes resulted in a new combined system.
“This kind of evolution in bacteria is kind of like what happens at a junk dealer,” said Blankenship.


“Bits and pieces of whatever there is out in the yard get hauled back and welded together and made into this new thing. All these metabolic pathways get borrowed and bent a bit and changed.”
Blankenship points out that nature’s way of creating useful and complicated chemical systems through horizontal gene transfer also points to how human-directed biodesign might co-opt the process.
“This work gives us some insights into how complex metabolic pathways originated and evolved, so this might give some ideas about how to engineer new pathways into microorganisms,” he said. “These organisms could be designed to carry out new types of chemistry that may benefit mankind, such as multi-step synthesis of drugs.”


How exactly did all those different organisms, who donated parts of the photosynthesetic process, get their energy while they were doing all that evolving of the components of the Irreducibly Complex looking system ready to be put together by the Blind Watchmaker?


1) http://www.uncommondescent.com/intelligent-design/is-photosynthesis-irreducibly-complex/

Oxygen, the molecule that made the world

Nick Lane, page 131
The hitch-hiker’s guide to the galaxy describes the Earth as an utterly insignificant blue-green planet, orbiting a small and unregarded yellow sun in the uncharted backwaters of the western spiral arm of the galaxy. In deriding our anthropocentric view of the Universe, Douglas Adams left the Earth with just one claim to fame: photosynthesis. Blue symbolizes the oceans of water, the raw material of photosynthesis; green is for chlorophyll, the marvellous transducer that converts light energy into chemical energy in plants; and our little yellow sun provides all the solar energy we could wish for, except perhaps in England. Whether Adams intended it or not, his scalpel was sharp — photosynthesis defines our world. Without it, we would miss much more than the grass and trees. There would be no oxygen in the air, and without that, no land animals, no sex, no mind or consciousness; no gallivanting around the galaxy. The world is so dominated by the green machinery of photosynthesis that it is easy to miss the wood for the trees — to overlook the conundrum at its heart. Photosynthesis uses light to split water, a trick that we have seen is neither easy nor safe: it amounts to the same thing as irradiation. A catalyst such as chlorophyll gives ordinary sunlight the destructive potency of x-rays. The waste product is oxygen, a toxic gas in its own right. So why split a molecule as robust as water to produce toxic waste if you can split something else much more easily, such as hydrogen sulphide or dissolved iron salts, to generate a less toxic product? The immediate answer is easy. For living organisms, the pickings from water-splitting photosynthesis are much richer than those from hydrothermal activity, the major source of hydrogen sulphide and iron salts.

Today, the total organic carbon production deriving from hydrothermal sources is estimated to be about 200 million tonnes (metric tons) each year. In contrast, the amount of carbon turned into sugars by photosynthesis by plants, algae and cyanobacteria is thought to be a million million tonnes a year — a 5000-fold difference. While volcanic activity was no doubt higher in the distant geological past, the invention of oxygenic (oxygen-producing) photosynthesis surely increased global organic productivity by two or three orders of magnitude. Once life had invented oxygenic photosynthesis, there was no looking back. But this is with hindsight. Darwinian selection, the driving force of evolution, notoriously has no foresight. The ultimate benefits of a particular adaptation are completely irrelevant if the interim steps confer no benefit. In the case of oxygenic photosynthesis, the intermediate steps require the evolution of powerful molecular machinery that can split water using the energy of sunlight. From a biological point of view, if you can split water, you can split anything. 

Such a powerful weapon must be caged in some way lest it run amok and attack other molecules in the cell. If, when the watersplitting device first evolved, it was not yet properly caged, as we might postulate for a blindly groping first step, then it is hard to see what advantage it could offer. And what of oxygen? Before cells could commit to oxygenic photosynthesis, they must have learnt to deal with its toxic waste, or they would surely have been killed, as modern anaerobes are today.  But how could they adapt to oxygen if they were not yet producing it? An oxygen holocaust, followed by the emergence of a new world order, is the obvious answer; but we have seen that there is no geological evidence to favour such a catastrophic history In terms of the traditional account of life on our planet, the difficulty and investment required to split water and produce oxygen is a Darwinian paradox.

The usual solution presented is selective pressure. Perhaps, for example, the stocks of hydrogen sulphide and dissolved iron salts eventually became depleted, putting life under pressure to adapt to an alternative, such as water. Perhaps, but on the face of it there is a difficulty here — the argument is circular. For the large geochemical stocks of hydrogen sulphide and iron to have become depleted in this way, they must have been oxidized by something, and the most likely, if not the only, candidate for oxidation on this scale is oxygen itself. The trouble is that there was no free oxygen before photosynthesis. Only photosynthesis can produce free molecular oxygen (O2) on the scale required. Thus, it seems that the only way to generate enough selective pressure for the evolution of photosynthesis is through the action of photosynthesis.

This argument is not just circular, it is also demonstrably false. We know from biomarkers diagnostic of cyanobacteria that oxygenic photosynthesis evolved more than 2.7 billion years ago. Despite this early evolution, we know that iron was still being precipitated from the oceans in vast banded iron formations a billion years later. In no sense were oceanic iron salts depleted. Similarly, stagnant conditions, in which deep ocean waters are saturated with hydrogen sulphide, seem to have persisted until the time of the first large animals, the Vendobionts, and recur sporadically even today. When these dates are taken together, we are forced to conclude that oxygenic photosynthesis evolved before the exhaustion of iron and hydrogen sulphide, at least on a global scale.

Why, and how, then, did oxygenic photosynthesis evolve? 
In the light of the last chapter, you may have guessed the answer already. There is good circumstantial evidence that oxidative stress, produced by solar radiation as on Mars, lies behind the evolution of photosynthesis on the Earth. The details are fascinating but also reveal just how deeply rooted is our resistance to oxygen toxicity: part and parcel, it seems, of the earliest known life on Earth. The earliest known bacteria did not produce oxygen by photosynthesis, but they could breathe oxygen — in other words they could apparently generate energy from oxygen-requiring respiration before there was any free oxygen in the air. To understand how this could be, and why it is relevant to our health today, we need to look first at how photosynthesis works, and how it came to evolve.

Of the different types of photosynthesis carried out by living organisms, only the familiar oxygenic form practised by plants, algae and cyanobacteria generates oxygen. All other forms (collectively known as anoxygenic photosynthesis) do not produce oxygen and pre-date the more sophisticated oxygenic form. Despite our anthropocentric interest in oxygen, plants are not much concerned with the gas — what they need from photosynthesis is energy and hydrogen atoms. The different forms of photosynthesis are united only in that they all use light energy to make chemical energy (in the form of ATP) needed to cobble hydrogen onto carbon dioxide to form sugars. They differ in the source of the hydrogen, which might come from water, hydrogen sulphide or iron salts, or indeed any other chemical with hydrogen attached. Overall, plant photosynthesis converts carbon dioxide (CO2) from the air into simple organic molecules such as sugars (general formula CH2O). These are subsequently burnt by the plant in its mitochondria to produce more ATP, and also converted into the wealth of carbohydrates, lipids, proteins and nucleic acids that make up life. We met the enzyme that cobbles hydrogen onto carbon dioxide in Chapter 5 — Rubisco, the most abundant enzyme on the planet. But Rubisco needs to be spoon-fed with its raw materials — hydrogen and carbon dioxide. Carbon dioxide comes from the air, or is dissolved in the oceans, so that is easy. Hydrogen, on the other hand, is not readily available — it reacts quickly (especially with oxygen to form water) and is so light that it can evaporate away into outer space. Hydrogen therefore needs a dedicated supply system of its own. This is, in fact, the key to photosynthesis, but for many years the lock resisted picking. Ironically, the mechanism only became clear when researchers finally understood where the oxygen waste came from.

In oxygenic photosynthesis, the hydrogen can only come from water, but the source of the oxygen is ambiguous. If we look at the overall chemical equation for photosynthesis, we see that it could come from either carbon dioxide or water: 

CO2 + 2H2O  (CH2O) + H2O + O2

At first, scientists guessed that the oxygen came from carbon dioxide — a perfectly reasonable and intuitive assumption, but quite wrong as it turned out. The fallacy was first exposed in 1931, when Cornelis van Niel showed that a strain of photosynthetic bacteria used carbon dioxide and hydrogen sulphide (H2S) to produce carbohydrate and sulphur in the presence of light— but did not give off oxygen:

CO2 + 2H2S  (CH2O) + H2O + 2S

The chemical similarity between H2S and H2O led him to propose that in plants the oxygen might come not from carbon dioxide at all, but from water, and that the central trick of photosynthesis might be the same in both cases. The validity of this hypothesis was confirmed in 1937 by Robert Hill, who found that, if provided with iron ferricyanide (which does not contain oxygen) as an alternative to carbon dioxide, plants could continue to produce oxygen even if they could not actually grow. Finally, in 1941, when a heavy isotope of oxygen (18O) became available, Samuel Ruben and Martin Kamen cultivated plants with water made with heavy oxygen. They found that the oxygen given off by the plants contained only the heavy isotope derived from water, proving conclusively that the oxygen came from water, not carbon dioxide. In oxygenic photosynthesis, then, hydrogen atoms (or rather, the protons (H+) and electrons (e–) that constitute hydrogen atoms) are extracted from water, leaving the ‘husk’ — the oxygen — to be jettisoned into the air. The only advantage of water is its great abundance, for it is not easy to split in this way. The energy required to extract protons and electrons from water is much higher (nearly half as much again) than that needed to split hydrogen sulphide. Controlling this additional energy
requires special ‘high-voltage’ molecular machinery, which had to evolve from the ‘low-voltage’ photosynthetic machinery previously used to split hydrogen sulphide. To understand how and why this voltage jump was made, we need to look at the structure and function of the machinery in a little more detail.

Whatever the source of hydrogen atoms — hydrogen sulphide or water the energy for their extraction is supplied by the electromagnetic rays that we know as sunlight. All electromagnetic rays, including light, are packaged
into discreet units called photons, each of which has a fixed quantity of energy. The energy of a photon is related to the wavelength of the light, which is measured in nanometres (a billionth of a metre). The shorter the wavelength, the greater the energy. This means that ultraviolet photons (wavelength less than 400 nanometres) have more energy than red photons (wavelength of 600 to 700 nanometres), which have more energy than infrared photons (wavelength above 800 nanometres). The interaction of light with any molecule always takes place at the level of the photon. In photosynthesis, chlorophyll is the molecule that absorbs photons. It cannot absorb any photon — it is constrained by the structure of its bonds to absorb photons with very particular quantities of energy. Plant chlorophyll absorbs photons of red light, with a wavelength of 680 nanometres. In contrast, the anoxygenic purple photosynthetic  bacterium Rhodobacter sphaeroides has a different type of chlorophyll, which absorbs less-energetic infrared rays with a wavelength of 870 nanometres. When chlorophyll absorbs a photon, its internal bonds are energized. The energetic vibrations force an electron from the molecule, leaving the chlorophyll short of one electron. Loss of an electron creates an unstable, reactive form of chlorophyll. However, the newly reactive molecule cannot simply take back its missing electron. That is snatched by a neighbouring protein and is whipped off down a chain of linked proteins, putting it beyond reach, like a rugby ball being passed across the field by a line of players. On the way, its energy is used to power the synthesis of ATP in a manner exactly analogous to that in mitochondrial respiration.

The theft of an electron is half way to stealing an entire hydrogen atom, as hydrogen consists of a single proton and a single electron. Little extra work is needed to steal the proton. Electrostatic rearrangements draw a positively charged proton (from water in the case of oxygenic photosynthesis) after the negatively charged electron. The proton and the electron are eventually reunited by Rubisco as a hydrogen atom in a sugar molecule. What happens to the chlorophyll? Having lost an electron, it becomes far more reactive, and will snatch an electron from the nearest suitable source. Reactive chlorophyll is constrained in the same way as a mediaeval dragon which is fed with virgins to stop it ravaging the neighbourhood. The source of suitable virgins — electrons in the case of chlorophyll — includes any plentiful sacrificial chemical, such as water, hydrogen sulphide or iron. Devouring an electron settles the chlorophyll back into its normal equable state, at least until another photon sets the whole cycle in motion again.

Which electron donor is used in photosynthesis — hydrogen sulphide, iron or water — ultimately depends on the energy of the photons that are absorbed by the chlorophyll. In the case of purple bacteria, their chlorophyll can only absorb low-energy infrared rays. This provides enough energy to extract electrons from hydrogen sulphide and iron, but not from water. To extract electrons from water requires extra energy, which must be acquired from higher-energy photons. To do this requires a change in the structure of chlorophyll, so it can absorb red-light photons instead of infrared light. The evolutionary question is this: why did the structure of chlorophyll
change, allowing it to absorb red light and split water, when the existing chlorophyll of purple bacteria could already extract electrons from hydrogen sulphide and iron salts, which were plentiful in the ancient oceans? More specifically, what environmental pressure could have led to the evolution of a new and more potent chlorophyll, capable of oxidizing water and much else in the cell, when the old chlorophyll was less reactive and less dangerous — and yet still sufficiently strong to oxidize hydrogen sulphide? Technically, the answers to these questions are surprisingly simple.

According to Robert Blankenship of Arizona State University and Hyman Hartman, of the Institute for Advanced Studies in Biology at Berkeley, California, tiny changes in the structure of bacterial chlorophylls can lead to large shifts in their absorption properties. Two small changes to the structure of bacteriochlorophyll a (which absorbs at 870 nm) are all that it takes to generate chlorophyll d, which absorbs at 716 nanometres. In 1996, an article in Nature by Hideaki Miyashita and colleagues of the Marine Biotechnology Institute in Kamaishi, Japan, reported that chlorophyll d is the main photosynthetic pigment in a bacterium called Acaryochloris marina, which splits water to generate oxygen. Thus, an intermediate between bacteriochlorophyll and plant chlorophyll is not only plausible: it actually exists. From chlorophyll d another trifling change is all that is required to produce chlorophyll a, the principal pigment in plants, algae and cyanobacteria, which absorbs light at 680 nanometres.

Technically, then, the evolutionary steps required to get from bacteriochlorophyll to plant chlorophyll are simply achieved. The question remains, why? A chlorophyll that absorbs light at 680 nanometres is less good at absorbing light at 870 nanometres. It is therefore less efficient at splitting hydrogen sulphide, and so bacteria carrying it are at a competitive disadvantage compared with the bacteria that kept their original chlorophyll. Even worse, switching chlorophylls to split water poses the problem of what to do with the toxic oxygen waste, as well as any leaking free-radical intermediates — the same as those produced by radiation.Without foresight, how did life manage to cope with its dangerous new invention? Chlorophyll extracts electrons from water one at a time. To generate oxygen from water, it must absorb four photons and lose four electrons in succession, each time drawing an electron from one of two water molecules. The overall water-splitting reaction is:

2H2O  O2 + 4H+ + 4e–

Only in the final stage is oxygen released. The rate at which chlorophyll extracts electrons depends on how quickly the photons are absorbed. As the successive steps cannot take place instantly, a series of potentially reactive free-radical intermediates must be produced, if only transiently. For plants, this whole system is precarious in the extreme. Reactive oxygen intermediates are produced from water as it is stripped of electrons one by one to form oxygen. Some of these reactive intermediates might escape from the reaction site to devastate nearby molecules. Even if they don’t escape, in the final step molecular oxygen is released into the cell in large quantities. Inside a modern plant leaf the oxygen concentration can reach three times atmospheric levels. Tiny cyanobacteria pollute themselves and their immediate surroundings in a similar fashion. This would have happened even in ancient times before there was any oxygen in the surrounding air. Some of this excess oxygen inevitably steals stray electrons to form superoxide radicals. The risks are huge. Chaos could break out at any moment. The closest analogy is a nuclear power station. If the reactors are sealed properly it is safe enough, but if a leak develops we face a disaster on the scale of Chernobyl. In both nuclear power and oxygenic photosynthesis the safety margins are slim, but the potential benefits — unlimited energy — are huge.

If photosynthesis is to work at all, the reactive intermediates from water must be sealed inside a structure that immobilizes them, preventing them from escaping before oxygen is released. Needless to say, they are sealed in such a cage, this is how photosynthesis works. The cage is made of proteins and is called the oxygen-evolving complex (or sometimes the water-splitting enzyme). Water is bound tightly inside the protein cage while the electrons are extracted one at a time. But this is no ordinary cage. Its structure conceals a secret that is much older than the hills, which transports us back to the time before oxygenic photosynthesis evolved, to a time more than 2.7 billion years ago, before there was any oxygen in the atmosphere. This structure is the key to life on Earth, for without it the Earth would have remained as sterile as Mars.

The structure of the oxygen-evolving complex is very similar to that of an antioxidant enzyme called catalase. In fact, the oxygen-evolving complex looks as if it evolved from two catalase enzymes lashed together.

The evidence is not compelling, but is certainly intriguing. First, there is a broad similarity in reaction mechanisms. Both catalase and the oxygen-evolving complex bind two identical molecules (either 2H2O2 or 2H2O), which are then reacted together to generate oxygen, via a strikingly similar sequence of steps. Second, both contain clusters of manganese atoms at their core. Hyman Hartman and others have noted that the manganese core of catalase is structurally very similar to half that of the oxygen-evolving complex, implying that the latter may have evolved by the lashing together of two catalase units. ( Why would and should natural mechanisms have done this ? ) However, it is possible that the structural similarities between catalase and the oxygen-evolving complex are no more than coincidence, or a case of convergent evolution towards a similar endpoint, like
the development of wings from very different structures in insects, birds and bats. Even if the similarity is authentic evidence of genetic relatedness, we cannot rule out the possibility that catalase evolved from the oxygen-evolving complex rather than the other way round.

If so, then catalase must have evolved before the oxygen-evolving complex. If so, the chronology must be as follows. Catalase evolved on the early Earth, in an atmosphere devoid of oxygen. One day, two catalase molecules became bound together to form a cage that enabled the safe splitting of water: the oxygen-evolving complex. This cage allowed the evolution of oxygenic photosynthesis. As a result, the atmosphere filled with oxygen.

Wow. The guess work and just so story is remarkable. 

Life was put under serious oxidative stress. Luckily it could cope: it already had at least one antioxidant enzyme that could to protect it — catalase. How convenient! But wait a moment. If catalase came before photosynthesis, then even if there was no atmospheric oxygen, there must have been oxidative stress. Is this plausible? To answer this question, we must take a look at how catalase works. Catalase is responsible for getting rid of hydrogen peroxide. This is a potential killer for bacteria. Virtually all aerobic organisms possess a form of this enzyme, and even some anaerobic bacteria, which try to avoid oxygen like the plague, retain some catalase just in case. It works extraordinarily quickly. Without catalase, and in the absence of iron, hydrogen peroxide takes several weeks to break down into water and oxygen. Dissolved iron, of course, catalyses the breakdown of hydrogen peroxide into hydroxyl radicals, and eventually water, via the Fenton reaction. If iron is incorporated into a pigment molecule such as haem (the pigment in haemoglobin) the rate of decomposition is increased 1000-fold. If the haem pigment is embedded in a protein, as is the case with catalase, then hydrogen peroxide is broken down directly and safely into oxygen and water, at a rate that is estimated to be 100 million times faster than the rate in the presence of iron alone. There are several different types of catalase. Most animal cells have a form that has four haem molecules embedded in its core. In contrast, some microbes have a different sort of catalase, which contains manganese instead of haem at its core. Despite their different structures, both enzymes are equally fast, and are correctly called catalase, in the sense that they work in the same way — they both catalyse the reaction of two molecules of hydrogen peroxide with each other to form oxygen and water:

2H2O2  2H2O + O2

This simple reaction mechanism reveals a great deal about conditions on the Earth 3.5 billion years ago. It is the exact equivalent of the natural reaction between two molecules of hydrogen peroxide, but is speeded up 100 million times by the enzyme. The need for two molecules of hydrogen peroxide means that catalase is extremely effective at removing hydrogen peroxide when concentrations are high, when it is easy to bring two molecules together. It works less well at low concentrations of hydrogen peroxide, when it is harder to find two molecules close together. Catalase is thus swift to remove high concentrations of hydrogen peroxide, but is poor at mopping up trace amounts or at maintaining a stable low-level equilibrium. Today, most aerobic organisms have a second group of enzymes, known as the peroxidases, which can dispose of trace amounts of hydrogen peroxide. These enzymes work better at low levels of hydrogen peroxide because they act in a fundamentally different way. Rather than bringing two molecules of hydrogen peroxide together, they use antioxidants such as vitamin C to convert a single molecule of hydrogen peroxide into two molecules of water, without generating any oxygen. Most aerobic cells have both sets of enzymes, and break down hydrogen peroxide using both mechanisms. Catalase is used for bulk removal, peroxidase for subtle adjustments. We might infer that any cell using catalase would need to cope with large fluxes of hydrogen peroxide, at least occasionally. Catalase is highly specialized: it has no other known target and works at an extraordinary speed. 

Such tremendous efficiency does not appear out of the blue by chance: we might as well believe that the eighteenth-century theologian Tom Paley stumbled across a nuclear reactor, rather than his celebrated watch, and instead of inferring the hand of a designer, ascribed it to an accidental arrangement of the elements. There is nothing accidental about catalase. If it was present on the early Earth, before photosynthesis, then there must have been hydrogen peroxide too, and in abundance. This is counter-intuitive, to say the least. Is it really credible that the early Earth could have been so rich in hydrogen peroxide that there was a selective pressure for the evolution of catalase? As we have seen, Mars is rich in iron peroxides; but their abundance in Martian soils tells us nothing about how quickly they were formed on the early Earth. While they were almost certainly formed on Earth (which is, after all, closer to the Sun, and so more drenched in ultraviolet rays), the abundance of hydrogen peroxide on Earth would have depended on its rate of formation and destruction — and these in turn are dependent on atmospheric and oceanic conditions. While the existence of catalase implies that hydrogen peroxide was indeed abundant, the story is suggestive but far from conclusive. Luckily, there are other ways to answer the question, and they not only support the notion that photosynthesis evolved in response to oxidative stress, but they also explain a few other long-standing paradoxes.

One of the most respected atmospheric scientists of recent decades is James Kasting, now at Pennsylvania State University, and during the 1980s at the NASA Ames Research Centre in California. In the mid-1980s, peroxide might have been on the early Earth. He was not really aiming to answer questions about the evolution of photosynthesis but rather to look at the time-line for oxygen production. A surrogate measure for the accumulation of
oxygen in the air is the extent of iron-leaching from fossil soils. Because iron is soluble in the absence of oxygen, it can be washed out of soils by rainfall on an oxygen-free planet. As oxygen builds up in the atmosphere,
it reacts with iron in the soil to produce insoluble rusty iron deposits, which cannot be leached out by rainfall in the same way. In theory, then, fossil soils preserve a record of atmospheric oxygen levels in their iron content — the more oxygen there is in the air, the more iron is left in the soil. The trouble is that the fossil-soil record can be read to imply that oxygen began to accumulate in the air well over 3 billion years ago (long before the major rise 2 billion years ago). This early date does not tally with the sulphur-isotope measurements, or with the larger-scale deposits, such as banded iron formations, red-beds and uranium ores. Kasting was interested in the discrepancy. Earlier studies of fossil soils had tacitly assumed that the most important oxidant dissolved in rainwater had always been oxygen itself. Kasting queried this assumption and set out to compute the possibility that hydrogen peroxide had been the most important oxidant in rainwater before the advent of atmospheric oxygen. In a detailed theoretical paper, Kasting, working with Heinrich Holland and Joseph Pinto at Harvard, calculated the rate at which water is split by ultraviolet rays under a variety of conditions. They then took into consideration the solubility of the degradation products (such as hydrogen peroxide) in rain droplets, to calculate their likely steady-state concentrations in rainwater and in lakes on the early Earth. Under the most likely conditions 3.5 billion years ago — high carbon dioxide levels, a trace of oxygen (less than 0.1 per cent of present atmospheric levels) and virtually no ozone screen — Kasting calculated that there should have been a continuous flux (based on the rate of formation and removal by reaction or rainfall) of about 100 billion
molecules of hydrogen peroxide per second per square centimetre. Although this number sounds fantastically big, we should bear in mind the inconceivably large number of molecules that make up matter. There are said to be more molecules in a single glass of water than there are glasses of water in all the oceans. We should not be too surprised to discover, then, that 100 billion molecules of hydrogen peroxide weigh about 56 thousand billionths of a gram.

To put these numbers into some sort of perspective, Kasting calculates that dissolved hydrogen peroxide, which is much more soluble than oxygen, accounts for between 1 and 6 per cent of the total oxidant concentration in rainwater today. There is no reason why the amount of hydrogen peroxide in rainwater should have been any less 3 billion years ago, and it may well have been higher, as the intensity of ultraviolet radiation was more than 30 times greater. Such a large flux of hydrogen peroxide must have placed the first cells under oxidative stress. The level of stress would have been exacerbated by the reactivity of hydrogen peroxide in comparison with oxygen. In particular, hydrogen peroxide reacts quickly with dissolved iron, to produce hydroxyl radicals, whereas oxygen reacts much more slowly. In today’s well-oxygenated oceans, the reactivity of hydrogen peroxide is limited by the low availability of dissolved iron (which long ago reacted with oxygen and precipitated out as banded iron formations), but during the early Precambrian, the oceans were so full of dissolved iron that hydrogen peroxide must have been continuously reacting with iron to produce hydroxyl radicals via the Fenton reaction. Thus, not only was there more hydrogen peroxide on the early Earth, it was also more likely to react to produce oxidative stress. The effect that hydrogen peroxide had on the environment must have depended on the amount of iron available. In the deep oceans there was such a vast amount of dissolved iron that any hydrogen peroxide dissolved in rainwater could never have altered the overall chemical balance. In the shallow seas and freshwater lakes, however, there was much less iron. These low levels of iron could plausibly have been depleted, or exhausted, by a steady drizzle of hydrogen peroxide. With the loss of iron and hydrogen sulphide, such secluded environments would have grown steadily more oxidized. According to the mathematical models of Hyman Hartman and his colleague Chris McKay, at the NASA Ames Research Center, the sheltered lakes and sea basins may well have become oxidizing enough to stimulate the evolution of antioxidant enzymes such as catalase. Once this had happened, bacteria living in shallow-water environments would have been pre-conditioned to the appearance of free oxygen.

Thus, there are good grounds for thinking that there was indeed plentiful hydrogen peroxide on the early Earth, and that it built up in sheltered environments. The oxidation of such environments by hydrogen peroxide was probably a strong enough selective pressure to stimulate the evolution of the antioxidant enzyme catalase. Catalase itself seems to have been the basis of the oxygen-evolving complex, enabling the evolution of oxygenic photosynthesis. So far the story makes sense, but we are left with one difficult question. Why would oxygenic photosynthesis evolve from catalase? Catalase would presumably have been present in the photosynthetic bacteria that generated energy by splitting hydrogen sulphide or iron salts in the era before oxygenic photosynthesis. In fact, hydrogen peroxide has some parallels with these early photosynthetic fuels. To remove electrons from hydrogen peroxide requires a similar input of energy to that required to remove electrons from hydrogen sulphide, and so could have been achieved using the same bacteriochlorophyll. Hydrogen peroxide would therefore have been a good source of hydrogen for photosynthesis. And, while far less plentiful than hydrogen sulphide and iron salts, it was nonetheless formed most readily in the surface waters, closest to the full power of the Sun. If this scenario is true, then catalase could have doubled as a photosynthetic enzyme. Because splitting hydrogen peroxide generates oxygen, this recruitment of catalase to photosynthesis also bridges the evolutionary gap between anoxygenic and oxygenic photosynthesis. If catalase was acting as a photosynthetic enzyme, then it would be natural for a number of catalase molecules to cluster around the photosynthetic apparatus. In these circumstances, it would be simple for two catalase molecules to became associated as a complex: the prototype oxygen-evolving complex. At first it would have continued to use hydrogen peroxide as an electron donor, but given the right energy input, this complex could split water. We know that three small changes in the structure of bacteriochlorophyll can transform its properties, enabling it to absorb high-energy light at a wavelength of 680 nm. We now have a prototype oxygen-evolving complex (the nut-cracker that can physically split water) and a chlorophyll that can provide enough energy for it to do so (or the hand that presses the nut-cracker). Thus, with no foresight and no disadvantageous steps, we have taken a path leading from anoxygenic photosynthesis to oxygenic photosynthesis. The evolution of oxygenic photosynthesis, then, seems practically inevitable, as long as three conditions are met: a selective pressure to use water; a mechanism for splitting water; and a tolerance to the oxygen waste. The selective pressure to use water was the loss of iron and hydrogen sulphide from sheltered environments. The mechanism for splitting water was a simple binding together of two catalase molecules. Tolerance for oxygen was imparted by catalase, and probably several other antioxidant enzymes which had evolved in response to oxidative stress from ultraviolet radiation. These conditions could never have been fulfilled in the deeper oceans. They were full of iron and hydrogen sulphide, and shielded from the effects of ultraviolet radiation. Life there would have had no need to tolerate oxygen. In these places, even if given enough light, any mutations that produced chlorophyll from bacteriochlorophyll would have been eliminated by natural selection as worse than useless. They would have slashed the light-capturing capacity of bacteria without any gainful return.

The explanatory power of an ‘oxidative stress before free oxygen’ hypothesis is strong. If true this reverses received wisdom. The hypothesis implies that photosynthesis would not have been possible without the oxidative stress generated by ultraviolet radiation. Far from cowering away at the bottom of the oceans, in sulphurous hydrothermal vents (or black smokers), life embraced the surface oceans very early, and dealt with the conditions there through the evolution of potent antioxidant enzymes such as catalase. Without these radiation-scorched conditions, watersplitting photosynthesis could never have evolved. Even more significantly, the evolution of oxygenic photosynthesis hangs by a single thread: the accidental association of two catalase molecules.

If this hypothesis seems to be over-reliant on a single lucky chance, it is worth remembering that, unlike flight or vision, which evolved independently many times, oxygenic photosynthesis only ever evolved once. All algae, all plants, the entire green planet, use exactly the same system. All of them inherited it from the cyanobacteria, which invented it once, perhaps 3.5 billion years ago. No other cells on Earth ever learnt to split water. All known water-splitting complexes are related in structure, and all are similar to catalase. Perhaps life once existed on Mars, but found another way of dealing with the less-intense solar radiation. Catalase never evolved. Without catalase, oxygenic photosynthesis never evolved. Without photosynthesis, free oxygen never accumulated in the air. And without oxygen, there was no multicellular life, no little green Martians, no war of the worlds.

Convinced? Perhaps not, but there is more. To my mind, the most conclusive evidence comes not from atmospheric modelling, or structural and functional similarities, but from comparative genetics. Not the
genetics of photosynthesis, which are still rather murky, but the genetics of respiration: how life came to use free oxygen as a means of extracting energy from food in the first place. Again, intuition is turned on its head. It seems impossible for oxygen-respiring organisms to have evolved before there was any free oxygen in the air. Surely they could not have evolved before oxygenic photosynthesis! We may have to think again. According to another iconoclastic viewpoint, put forward and backed with increasingly strong evidence by José Castresana and Matti Saraste of the European Molecular Biology Laboratory in Heidelberg, this is exactly what happened.6 Respiration using oxygen evolved before photosynthesis, oxygen breathers before there was any free oxygen in the air. The arguments of Castresana and Saraste hinge on the identity of a singlecelled creature named LUCA, the Last Universal Common Ancestor.

Essential parts of oxygenic photosynthesis

The photosynthesis pathway is interdependent, and irreducible. Take any of the individual parts out, and the process ceases to function. Neither do most individual parts and proteins have no function , unless in this remarkable pathway.
We can therefore infer that design explains best the origin of photosynthesis through a creator.

1. Lipid bilayer membranes are critical to the early stages of energy storage, such that photosynthesismust be viewed as a process that is at heart membrane-based. 4
2. Chlorophyll is an essential component of photosynthesis, which helps plants get energy from light. 1
3. The light harvesting complexes, also called antenna complexes,  are essential for collecting sunlight and regulating photosynthesis 2
4. Photosystem II (PSII) is a key component of photosynthesis 2
5. The oxygen evolving is responsible for catalyzing the oxidation of water to molecular oxygen in plants, algae, and cyanobacteria. 3
6) The cytochromeb6 f complex  is an essential player in noncyclic and cyclic electron flow 4
7) Plastocyanin is an essential member of photosynthetic electron transport and functions near PS I.  5
8  PSI is necessary to provide the energy to reduce NADP+ to NADPH  6
9) Ferredoxin (Fd) proteins are required for the electron transfer process  from the bound Fe–S centers in the Photosystem I reaction center to NADP+. 4
10) Ferredoxin—NADP(+) reductase same as 9
11) In plants and photosynthetic bacteria ATP synthase is essential for solar energy conversion and carbon fixation.



1) http://www.newworldencyclopedia.org/entry/Chlorophyll
2) http://www.nature.com/nature/journal/v421/n6923/full/nature01344.html
3) http://www.sciencedirect.com/science/article/pii/S0010854507001877
4) Blankenship: Molecular mechanisms of photosynthesis
5) http://www.esalq.usp.br/lepse/imgs/conteudo_thumb/24-Katoh.pdf
6) http://www.nature.com/nsmb/journal/v8/n7/full/nsb0701_577.html
7) http://www.atpsynthase.info/Basics.html

Bacteria Shared Photosynthesis Genes. Really ?! 1

Five groups of bacteria use light as an energy source. To understand how photosynthesis genes could have evolved multiple times in these bacteria, Blankenship and others spent years studying the individual genes. But when bacterial genome sequences began pouring into public databases, they decided to take a global approach. In the summer of 2001, graduate student Jason Raymond and his colleagues began to analyze the genome sequences of one organism from each of the five photosynthetic groups:

a cyanobacterium,
a filamentous green bacterium,
a purple bacterium,
a green sulfur bacterium,
and a heliobacterium.

Comparing the five genomes using several computer programs, including one called BLAST, they found 200 genes that were common to all.

This is an ad hoc speculation, based on evolutionary assumptions, to explain away a lack of evidence for evolution.  Even if these bacteria did swap genes, It still doesn’t explain how photosynthesis, an immensely complicated set of processes, proteins, genes, and regulators, could ever evolve even once in the first place.  This idea is falsified by an observation mentioned in a lecture this past weekend by Dr. George Howe, retired botanist at The Master’s College in California.  He noted that CAM photosynthesis, a different variety of light-gathering food production used by the saguaro cactus, appears in up to 30 widely-scattered families of flowering plants.  Some species in a family will have the usual kind, and some will have the CAM kind, with no phylogenetic rhyme or reason.  It is inconceivable that such a complex set of hardware and software could have arisen independently even once, let alone 30 times. 2

The process of photosynthesis in desert plants has evolved mechanisms to conserve water. Plants that use crassulacean acid metabolism (CAM) photosynthesis fix CO2 at night, when their stomata are open.
Plants that use C4 carbon fixation concentrate carbon dioxide spatially, using "bundle sheath cells" which are inundated with CO2. 3

1. http://science.sciencemag.org.sci-hub.cc/content/298/5598/1538.2.full
2. http://creationsafaris.com/crev1102.htm
3. https://www.boundless.com/biology/textbooks/boundless-biology-textbook/photosynthesis-8/the-light-independent-reactions-of-photosynthesis-82/cam-and-c4-photosynthesis-1005-17182/

Small One-Helix Proteins Are Essential for Photosynthesis in Arabidopsis 1

Assembling the photosynthetic complexes in the thylakoid membrane requires a tight coordination of protein synthesis and folding with pigment synthesis and delivery. Failures of this coordination can lead to protein misfolding or accumulation of uncoupled pigments that initiate deleterious processes rather than funneling the absorbed energy to the photosynthetic reaction centers . Recent studies on cyanobacteria demonstrated that the family of High Light Induced Proteins (HLIPS) plays important functions as carriers of newly synthesized pigments during the assembly of photosystem II and potentially also photosystem I. As their name implies, HLIPs were identified by their up-regulation during high light stress, when photo-damaged photosystems have to be degraded and replaced. In this process, HLIPs may additionally function in the recycling of pigments from damaged photosystems or antennae . 

For cyanobacterial HLIPs, homodimer or heterodimer formation has been postulated as a prerequisite of pigment binding. Binding of HLIPs to photosystem II reaction centers has been clearly demonstrated.

Another class of three-helix proteins, the Early Light Induced Proteins (ELIPs) are almost exclusively expressed during light stress and de-etiolation of proplastids. They do not contribute to light harvesting but may act as pigment carriers during the assembly of photosynthetic complexes.  

The One-helix proteins (OHPs) resemble most closely the ancestral cyanobacterial HLIPs and almost all photosynthetic eukaryotes contain at least one member of each of the two sub-classes OHP1 and OHP2.  In a similar manner a complex comprising both OHP1 and OHP2 may be formed in higher plants, depending on either protein for functionality. Such a complex might not interact strongly with the structural photosystem components but might be essential for pigment delivery to both reaction centers during biogenesis or repair, which would explain the severe mutant phenotype.

OHP proteins fulfill a crucial function in either assembly or maintenance of photosynthetic reaction center complexes, similar to their evolutionary ancestors, the cyanobacterial HLIPs.

PSI and PSII reaction centers are affected by depletion of OHP proteins

The similar regulation of OHP1 and OHP2 expression and the nearly identical mutant phenotypes indicated that OHP1 and OHP2 are required for PSII function and that both proteins might be functionally linked. 

1. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5253381/

Cytochrome b6f: Proton Pumping and ATP Synthesis



we've mentioned at this point that p680 transfers electrons one at a time to feel fighting and then it transfers electrons to plasticquinone to plasticquinone B and so on and so forth now some of these electron transfers are too
for example plastoquinone transfers to electrons to plastic window and be plastic when will be transfers to electrons it's very complicated it's not really so much important to understand how many electrons are transferred what's the mechanism of the enzymes but the cytochrome b6f complex is going to be very critical and now we're going to talk about

it the thylakoid has two main areas a stroma and a lumen all right cytochrome b6f pumps protons from the stroma into the thylakoid lumen here is something that's very important this is creates a proton gradient all right it turns out that not only do you mitochondria have ATP synthase chloroplasts particularly the thylakoids also have ATP synthase in fact this proton gradient is actually going to function analogously and completely homologousy I should say to the AT synthase in mitochondria it's very interesting so this cytochrome b6f remember it's receiving electrons ultimately from p680 but it's going through these series of electronic and donors and then finally it donates electrons society chrome b6d it's basically for all intents and purposes going to use the energy from those electrons to pump the protons okay and by pumping protons from the stroma into the thylakoid lumen you create a proton gradient and just like in the mitochondria that you've learned about in the past that proton gradient powers ATP synthase and if you don't remember what ATP synthesis it's the one of the most important enzymes will ever talk about if the enzyme that makes the majority of ATP okay this process right here has a special name it's called photophosphorylation uses the power of photosynthesis to phosphorylate adp to make ATP and that's catalyzed by ATP synthase if you want more detail on ATP synthase we have a whole video on that here's the key point that most people forget ATP is made by both chloroplasts and mitochondria in plants

here's the ATP that's produced ultimately by ATP synthase but it's powered by the cytochrome b6f complex alright the ATP is one of the first important products that we get from the photosystems particularly from this is basically photosystem 2 alright that ATP is going to go to what we call the Calvin cycle over here which is part of what we call the light independent reactions photosystem 1 and 2 are light dependent reactions alright and now we're going to basically get into a discussion of photosystem 1 and we're going to find it's basically identical in function or at least very very similar to the function of photosystem 2 now the electrons from cytochrome b6f they don't just stop there you can see it here if you look but ultimately those electrons are transferred into what's called an electron carrier that's actually identical to what we saw on the electron transport chain in the mitochondria ubiquinone it turns out there is a Q cycle in here just like there is in the mitochondria particularly in complex 3 there's a queue cycle and this ubiquinone is going to reduce to Ubiquinol ultimately this ubiquinol is going to transfer its electrons to a protein called plastocyanin and it turns out you can see plastic sign in right here classify an ins function is to take the electrons that were given to the cytochrome b6f complex and transfer them to photosystem one.

Photosystem I Functions: Electron Flow and Function



here's where we're going to have something analogous to photosystem 2 in photosystem 2 light struck p680 in photosystem 1 light strikes p700 the same thing we saw and talked about in the other video for charge separation if you want more detail on this for p700 go back and watch this video in the context of p680 it is the same thing however there's one key difference that you need to understand when p700 goes up in energy it's still going to donate an electron in the excited state to an electron acceptor all right you're still going to have an electron hole that needs electrons to fill it just like in p680 over here but there's one key difference that's very important once filled the electron hole in p680 from photosystem 2 it was the oxygen-evolving complex it's split water and gave the electrons to p680 to fill the electron hole well we have an electron hole in p700 once we donate the electron to these exceptors so what fills the hole in photosystem 1 p700 a good question would be true or false it's the oxygen-evolving complex and the answer is false it's plastocyanin remember plastocyanin took those electrons from the cytochrome b6f complex and its function plastocyanin is to fill the electron holes produced by p700 excitation and subsequent electron transfer all right and we're just going to more or less gloss over these electron acceptor and donors all these unidirectional electron flow but suffice it to say suffice it to say these electrons are going to travel to a modified chlorophyll a called a knot or a zero and then to file a quinone and then to an iron-sulfur protein and then to ferredoxin and ultimately those electrons from ferredoxin are going to go on to nadp+

Ferredoxin:NADP+ Reductase: Generation of NADPH



we're now going to talk about NADPH we've talked about one important molecule that plants make and that's ATP there's another one called NADPH we have NADPH where we have a very different way of making it humans involve the pentose phosphate pathway and malic enzyme plants do it through a very different mechanism they're actually going to do it through an enzyme that you can't really see over here but it's through ferredoxin and nadp+ and the enzyme is called ferredoxin nadp+ reductase all right then the actual mechanism of this is less important but suffice it to say electrons are going to transfer be transferred from ferredoxin one at a time and then they're ultimately going to both go on to nadp+ and you're going to get NADPH all right it turns out that this electron acceptor nadp+ is the final electron acceptor in photosynthesis all right this brings up an interesting point all right between photosynthesis and cellular respiration which is what you talked about in the mitochondria you have often heard and probably more in general biology that photosynthesis is the reverse of cell respiration now look at this picture is it really the exact opposite is it were the exact opposite then you would literally see just the reverse reactions well you don't see that but something that's interesting to note what was the initial electron donor in cell respiration it was NADH go back and watch the playlist look in your bio chem textbook and you'll see that the initial electron donor was NADH that reduction with catalyzed by NADH dehydrogenase

nadh is the initial electron donor there nadp a nadp is the final electron acceptor all right let's reverse it what is the initial electron donor in photosynthesis water what is the final electron acceptor in cell respiration oxygen they basically are sort of reverses of each other all right in cell respiration we go from oxygen to water in photosynthesis we go from water to oxygen in cell respiration we go from NADH to nad and then photosynthesis we go from nadp to NADPH although there is that difference between nad and nadp it's basically just the reverse okay compare the structure of nadh and nadph they're basically identical exceptors for a phosphate so mechanistically in the middle of the pathway it's not though just the reverse of cell respiration but overall the net reactions are almost exactly opposite now here's the key fnr or ferredoxin nadp reductase reduces nadp+ to NADPH this NADPH right here is going to be used ultimately by the Calvin cycle which is a part of the light independent reactions and I'm going to end with it with this slide right here we saw in another video that ATP is produced through ATP synthase through photophosphorylation that fuels the calvin cycle ferredoxin nadp reductase forms NADPH which fuels the calvin cycle the whole purpose of the light-dependent reactions is to make ATP and NADPH so that the light independent reactions idea the calvin cycle can make sugar so in the next set of videos we're going to look at the light independent reactions and see that their major function is to make sugar

Calvin Cycle: Carbon Fixation, Rubisco, and Rubisco Activase



all right so I know what I do is sort of non-conventional when we look at the Calvin cycle generally our first step is carbon fixation and then we have reduction of 3-pga and then we have regeneration of rubp rubp as we know it's regulus 1/5 bisphosphate however I always prefer to do steps two and three first and that's because first of all it really doesn't matter what order you do it in it's a cycle but Rubisco is kind of the more subtle concept it's a very important thing to understand in plants and it's going to lead us into talking about c3 c4 and cam plants so I do this last alright this right here is ribulose 1/5 bisphosphate or rubp the enzyme rubisco Rubisco is really an acronym what it really stands for is ribulose 1/5 bisphosphate carboxylase oxygenase it turns out that this enzyme as we'll go in more detail later can act as a carboxylase and an oxygenation carboxylase is an enzyme that adds carbon to some molecule usually in the form of carbon dioxide so ordinarily carboxylase is add carboxyl groups an oxygen ace is an enzyme that uses a lot of times molecular oxygen and the adds oxygen to a molecule most certainly the carboxylase is the desired function because we're Disco's main function is supposed to be carbon fixation ok so it turns out that rubp is a five carbon molecule and we need to get it initially to a six carbon molecule so we can split it in half and get to three carbon molecules but you can't split a five carbon molecule into two three carbons it doesn't make sense you have to add a carbon to this five carbon rubp to make it a six carbon molecule and then you can split it in half so our rubp is going to be carboxylated by Rubisco and the net reaction is we Rubisco the net reaction is we carboxylate rubp and then split it into two molecules of 3 phosphoglycerate and as we mentioned in the previous video those two 3 phosphoglycerates have the potential to be turned back into glucose

so general information about Rubisco it has a turnover number about 3 molecules per seconds this is a very slow enzyme it's one of the slowest end lines you'll ever run across i'm compare it to some enzymes like catalase which has a turnover of 40 million per second and compare that to 3 okay so Rubisco is very slow so how on earth are plant able to maintain their metabolism with such a slow enzyme well they just simply make a lot of the enzyme the turnover is low but the v-max doesn't have to be low they could just make a lot of this enzyme it turns out Rubisco is thought to be the most abundant protein in the world the plants just have to make a ton of it in order to satisfy their metabolic requirements in terms of carbon fixation and it turns out that Rubisco is a very tightly regulated enzyme the ability to do the calvin cycle is largely regulated by the actual regulation of Rubisco and we're going to talk a little bit about the new regulation certain parts of it and the three main ways it's regulated are by the pH of the environment that's in an enzyme called Rubisco activase and then an allosteric if you want to call it that modulator called to carboxy di Rabbinate all one phosphate which we're just going to abbreviate CA 1p

now in terms of the pH we're not going to go much into that but suffice to say it has a pH optimum which is going to be around 9 or greater okay if the pH is less than that Rubisco activity drops a lot okay I mean it turns out that we'll go into this in another video later but understand that whenever those of the proton pump is activated remember back to the light-dependent reactions the cytochrome b6f complex that pumps protons to power ATP synthase protons affect pH right and so depending on how active that proton pump is that changes the pH and it also changes Rubisco activity we're going to look at that in a separate video all right but CAC a one p and Rubisco activase strongly modulate this than done alright so Rubisco normally is going to be inactive at night okay so at night there's a molecule of rubp that does what we call clogs the active site after removal of a critical carbonate group alright some things about Rubisco that you have to understand to make this make sense Rubisco active site has an unusual functional group in it alright and this is this diagram up here it's kind of confusing go let's go through it there has to be a critical carbamate group inorder for this enzyme to work a carbamate group what it is is it's essentially a carboxyl group but instead of being attached to a carbon is attached to a nitrogen and if there's any amino acid that has a good nitrogen to do that it's lysine so in other words a carboxyl group is attached to a lysine r group and that makes the carbonate and it turns out this enzyme is only activated when you have that carbonate group this right here is the carbonate group in sort of a formula form there's the enzyme itself here's the lysine attached to a co2 the enzyme is only activated whenever that carbonate group is present it can't be the free lysine okay and the catalytic cycle in general involves a magnesium chelated to the carbot to the carbonate group and then the rubp a key Lakes to the magnesium so you have this this indirect linkage of the carbonate to the magnesium to the rubp and only when Rubisco is where basically active site has this form is it able to function

now what if that carbonate group is not there as it is over here okay in other words this is a free lysine it does not have the co2 attached is not a carbamate all right it turns out that the enzyme is inactivated and it turns out also this generally occurs at night but instead of having a carbonate group in the magnesium there's a free lysine but an rubp is there instead all right it's just a free lysine not attached to anything and it's coordinated to rubp all right some people call this rubp a storage rubp and I would certainly agree with that but it's mostly considered an inhibitory rubp all right even though rubp is the substrate through this Co its absolutely dependent on this carbonate group so if that carbonate group is not there in the rubp is there its inhibitory so there is an enzyme called Rubisco activase and ultimately what Rubisco activase does is it catalyzes the removal of that rubp and the insertion of the co2 that allows formation of the carbonate group in other words what Rubisco activase does is it does two things removes the inhibitory or storage rubp and it carbonates or allows the formation of the carbonate residue in the active site two things that are required for Rubisco is function key here carbonate is essential for Rubisco function now to go back to the previous slide we mentioned there's another regulator called two carboxy di Rabbinate all one phosphate CA 1p it turns out the CA 1 P also which is shown right here can actually strongly regulate the function of Rubisco it turns out that CA 1p inhibits the function of Rubisco also so sometimes plants need to regulate Rubisco in other ways so they will start making CA 1 P is shown here which can get into the active site and inhibit Rubisco okay in other words Rubisco is a very strongly regulated enzyme because it really controls the entry into the light independent reactions even though we look at it last in the calvin cycle it's what really controls the entry into glucose synthesis

REPAIR AND REGULATION OF THE PHOTOSYNTHETIC MACHINERY 1

http://reasonandscience.heavenforum.org/t1555-photosynthesis#5702

Plants have to deal with seasonal changes. The radiation strongly varies (by orders of magnitude) in biotopes like tropical rainforests or marine systems at different levels of the oceans. Therefore, suitable adaptation mechanisms are required to cope with these conditions. Essentially, two functional demands have to be satisfied:

(i) at weak irradiations the few quanta have to be collected and efficiently transferred to the photoactive pigment PRC and
(ii) at exposure to strong light the organism must be protected from destruction due to deleterious side reactions, in particular by the formation of very reactive singlet oxygen. Most of the regulatory processes take place at the level of electronically excited states that are formed by light absorption of the antenna pigments. The number and spectral properties of the PA molecules permit an optimal adaptation of the photosynthetic apparatus to the irradiation conditions in the environment.

The most important reaction for most life forms on earth is oxygenic photosynthesis. Photosystem (PS) II, its core protein complex,  is “an enzyme of life” and has produced almost all oxygen in the atmosphere by splitting water. Establishing the overall chemical equation of photosynthesis required several hundred years and contributions by many scientists. The chemical reactions of photosynthesis are complex. In fact, at least 50 intermediate reaction steps have now been identified. Photosystem PSII "is one of nature's most complicated enzymes — complicated partly because it involves a four-electron oxidation process resulting in four intermediate states and the concurrent chemistry of O-O bond formation." PSII is at the heart of photosynthesis, and catalyzes the thermodynamically most demanding reaction in biological systems, the splitting of water into oxygen and reducing equivalents. The monomer of this bewilderingly complex machinery consists of 20 different protein subunits that bind 77 organic cofactors and seven metal ions. In the reaction center and light-harvesting antenna proteins, a large number of different molecules (35 chlorophyll a, 11 carotenoid, 2 pheophytin a, 2 plastoquinone, 2 heme, and 1 bicarbonate), as well as four manganese ions, two calcium ions, and an iron ion, are held at precise distances and relative orientations that are required for optimal absorption and conversion of light energy to perform efficient electron transfer.

Photosynthetic systems face a special challenge. They are designed to absorb large amounts of light energy and process it into chemical energy. At the molecular level, the energy in a photon can be damaging, particularly under unfavorable conditions. In excess, light energy can lead to the production of toxic species, such as superoxide, singlet oxygen, and peroxide, and damage can occur if the light energy is not dissipated safely. Photosynthetic organisms therefore contain complex regulatory and repair mechanisms. Some of these mechanisms regulate energy flow in the antenna system, to avoid excess excitation of the reaction centers and ensure that the two photosystems are equally driven. Although very effective, these processes are not entirely fail-safe, and sometimes toxic compounds are produced. Additional mechanisms are needed to dissipate these compounds—in particular, toxic oxygen species. Despite these protective and scavenging mechanisms, damage can occur, and additional mechanisms are required to repair the system. Figure below provides an overview of the several levels of the regulation and repair systems.


Overall picture of the regulation of photon capture and the protection and repair of photodamage.
Protection against photodamage is a multilevel process. The first line of defense is suppression of damage by quenching of excess excitation as heat. If this defense is not sufficient and toxic photoproducts form, a variety of scavenging systems eliminate the reactive photoproducts. If this second line of defense also fails, the photoproducts can damage the D1 protein of photosystem II. This damage leads to photoinhibition. The D1 protein is then excised from the PSII reaction center and degraded. A newly synthesized D1 is reinserted into the PSII reaction center to form a functional unit.

Carotenoids Serve as Photoprotective Agents
In addition to their role as accessory pigments, carotenoids play an essential role in photoprotection. The photosynthetic membrane can easily be damaged by the large amounts of energy absorbed by the pigments if this energy cannot be stored by photochemistry; this is why a protection mechanism is needed. The photoprotection mechanism can be thought of as a safety valve, venting excess energy before it can damage the organism. When the
energy stored in chlorophylls in the excited state is rapidly dissipated by excitation transfer or photochemistry, the excited state is said to be quenched.

If the excited state of chlorophyll is not rapidly quenched by excitation transfer or photochemistry, it can react with molecular oxygen to form an excited state of oxygen known as singlet oxygen (1O2*). The extremely reactive singlet oxygen goes on to react with and damage many cellular components, especially lipids. Carotenoids exert their photoprotective action by rapidly quenching the excited state of chlorophyll. The excited state of carotenoids does not have sufficient energy to form singlet oxygen, so it decays back to its ground state while losing its energy as heat. Mutant organisms that lack carotenoids cannot live in the presence of both light and molecular oxygen—a rather difficult situation for an O2-evolving photosynthetic organism.

So does it then not make carotenoids indispensable, and had they not to be present in its current state right from the beginning ? 

For non-O2-evolving photosynthetic bacteria, mutants that lack carotenoids can be maintained under laboratory conditions if oxygen is excluded from the growth medium.

Some Xanthophylls Also Participate in Energy Dissipation
Nonphotochemical quenching, a major process regulating the delivery of excitation energy to the reaction center, can be thought of as a “volume knob” that adjusts the flow of excitations to the PSII reaction center to a manageable level, depending on the light intensity and other conditions. The process appears to be an essential part of the regulation of antenna systems in most algae and plants.  Nonphotochemical quenching is the quenching of chlorophyll fluorescence  by processes other than photochemistry. As a result of nonphotochemical quenching, a large fraction of the excitations in the antenna system caused by intense illumination are quenched by conversion into heat. Nonphotochemical quenching is thought to be involved in protecting the photosynthetic machinery against overexcitation and subsequent damage. The molecular mechanism of nonphotochemical quenching is not well understood, although it is clear that the pH of the thylakoid lumen and the state of aggregation of the antenna complexes are important factors. Three carotenoids, called xanthophylls, are involved in nonphotochemical
quenching: violaxanthin, antheraxanthin, and zeaxanthin. In high light, violaxanthin is converted into zeaxanthin, via the intermediate antheraxanthin, by the enzyme violaxanthin de-epoxidase.

The Photosystem II Reaction Center Is Easily Damaged
Another effect that appears to be a major factor in the stability of the photosynthetic apparatus is photoinhibition, which occurs when excess excitation arriving at the PSII reaction center leads to its inactivation and damage . Photoinhibition is a complex set of molecular processes, defined as the inhibition of photosynthesis by excess light. Prolongued inhibition results in damage to the system such that the PSII reaction center must be disassembled and repaired. The main target of this damage is the D1 protein that makes up part of the PSII reaction center complex (see Figure
7.24). 



When D1 is damaged by excess light, it must be removed from the membrane and replaced with a newly synthesized molecule. The other components of the PSII reaction center are not damaged by excess excitation and are thought to be recycled, so the D1 protein is the only component that needs to be synthesized. 

Revisiting the photosystem II repair cycle 2

The ability of photosystem (PS) II to catalyze the light-driven oxidation of water comes along with its vulnerability to oxidative damage, in particular of the D1 core subunit. Plant survival is crucially dependent on an efficient molecular repair of damaged PSII realized by a multistep repair cycle. 3 The steady work of this photosystem depends on the balance between the rates of light-induced damage and repair of PSII, the process including partial disassembly of inactivated PSII, proteolytic degradation of the photo-damaged reaction centre protein D1 and co-translational insertion of newly synthesised D1 protein in PSII 5

Turnover of the D1 protein includes degradation of the photo-damaged polypeptide and co-translational insertion of the newly synthesized protein in the partially disassembled PSII complexes as a crucial part of the PSII repair cycle
High light stress triggers an architectural switch of the thylakoid network that is advantageous for swift protein repair.  Photodamaged PSII undergoes repair in a multi-step process involving 

(i) reversible phosphorylation of PSII core subunits 
(ii) monomerization and lateral migration of the PSII core from grana to stroma thylakoids; 
(iii) partial disassembly of PSII; 
(iv) proteolytic degradation of damaged D1; 
(v) replacement of damaged D1 protein with a new copy;
(vi) reassembly of PSII monomers and migration back to grana thylakoids for dimerization and supercomplex assembly. Here we review the current knowledge on the PSII repair cycle.

To provide access for the repair machinery to photodamaged D1 buried in PSII supercomplexes, megacomplexes or semicrystalline arrays, the latter first need to be disassembled, the thylakoid membranes unfolded, and released PSII monomers transported to stroma lamellae


Model of the PSII repair cycle. Complexes are drawn according to Nickelsen and Rengstl (2013).3 ‘P's in purple circles represent phosphate groups, red labeled D1 is photodamaged D1, light-green labeled D1 a new copy of the protein. Proteins labeled in blue represent factors that presumably are exclusively involved in PSII repair while proteins labeled in gold are factors that are likely involved in PSII de novo biogenesis and repair. Salmon-colored MPH1 was suggested to protect PSII from photodamage. See text for details.

(i) reversible phosphorylation of PSII core subunits 
To run efficiently, these processes require the light-dependent specific phosphorylation of PSII core proteins D1, D2, CP43 and PsbH. The lack of PSII core protein phosphorylation disturbs the disassembly of PSII supercomplexes at high light, which is a prerequisite for efficient migration of damaged PSII complexes from grana to stroma lamellae for repair. This results in accumulation of photodamaged PSII complexes, which in turn results, upon prolonged exposure to high light (HL), in general oxidative damage of photosynthetic proteins in the thylakoid membrane. 4 Not only LHCII but also the PSII core proteins D1, D2, CP43, PsbH and TSP9 undergo redox regulated strong and dynamic phosphorylation cycle

Two thylakoid proteases, Deg P2 and FtsH, have been implicated in proteolytic degradation of the photo-damaged D1.
6


A pigment-binding protein essential for regulation of photosynthetic light harvesting

Absorption of light that exceeds a plant's capacity for xation of CO2 results in thermal dissipation of excitation energy in the pigment antenna of photosystem II by a poorly understood mechanism. This regulatory process, termed nonphotochemical quenching, maintains the balance between dissipation and utilization of light energy to minimize generation of oxidizing molecules, thereby protecting the plant against photo-oxidative damage. 7 These results show clearly that the PsbS protein contributes to photoprotective energy dissipation rather than photosynthetic light harvesting.

A Major Light-Harvesting Polypeptide of Photosystem II Functions in Thermal Dissipation 8

In natural environments, photosynthetic organisms are exposed to a range of fluctuating light intensities. At low light intensities, an increase in photon flux density correlates with increased photosynthetic carbon fixation. However, above a certain threshold, carbon fixation becomes saturated and photosynthesis is incapable of using all of the energy absorbed by the light-harvesting complexes (LHCs). Under these conditions of excess light absorption, the chloroplast lumen becomes highly acidic, the electron transport chain becomes reduced, and excitation energy accumulates within the light-harvesting complexes of photosystem II (LHCII). Excess excitation of LHCII could result in an increase in the half-life of singlet chlorophyll a in the pigment bed and the consequent production of triplet chlorophyll a and singlet oxygen.
If not detoxified immediately, singlet oxygen can cause protein modification and lipid peroxidation. Furthermore, once initiated, lipid peroxidation becomes autocatalytic, resulting in massive membrane photodestruction (Niyogi, 1999). Excess light also depletes the NADP+ pool, causing an increase in the rate of electron flow from the donor side of photosystem I (PSI) to oxygen, generating superoxide and hydrogen peroxide (Asada, 1999).
Plants respond to the absorption of excess light with a suite of short-term and long-term photoprotective mechanisms that minimize damage. Over the short term, carotenoids have photoprotective functions in detoxifying and limiting the formation of singlet oxygen. The xanthophyll lutein occupies the L1 and L2 sites of LHC polypeptides and can quench ∼80% of the triplet chlorophyll generated within LHCII (Peterman et al., 1997). The remaining triplet chlorophyll can react with oxygen to generate singlet oxygen.
Singlet oxygen can be detoxified by lutein and neoxanthin within LHCII or by zeaxanthin and α-tocopherol in the thylakoid membranes (Croce et al., 1999b; Havaux et al., 2000). α-Tocopherol and zeaxanthin also disrupt autocatalytic membrane lipid peroxidation (Niyogi, 1999). Superoxides generated on the acceptor side of PSI are detoxified by a series of membrane-associated and stromal enzymes, including superoxide dismutase and ascorbate peroxide (Asada, 1999).

Intermediate states, produced by univalent electron transport within photosystems, are toxic and need to be scavenged, a function performed by LHC-bound xanthophylls with far enhanced efficiency with respect to lipid free carotenoids [8–11]. This activity is essential for photoprotection even at low light intensity [12,13]. 9


Triplets formed on the chlorophylls (predominantly on chlorophyll-a) are quenched very efficiently by the carotenoids; and 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,  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.

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.

Non-photochemical quenching is a protection mechanism that is switched on under high light conditions when the photosynthetic electron-transfer machinery gets saturated and the probability of recombination of charge-separated states increases. These recombinations may again lead to triplet states and cause damage. In plants, non-photochemical quenching is switched on by the build-up of a trans-membrane proton gradient that, in intense light, can happen in a few tens of seconds. Consequently, such quenching must be on account of some physical mechanism that allows one or more of the light-harvesting complexes to switch into a quenching state. 10 

Currently, two mechanisms for the quenching event are heavily discussed. The first is proposed to operate in one of the minor light-harvesting complexes of PSII, CP29, where a charge separation has been observed between a chlorophyll and the carotenoid zeaxanthin, followed by rapid recombination. In intact thylakoids under non-photochemical quenching conditions, signals reflecting the formation of carotenoid radicals have also been observed. The second is proposed to operate in LHCII, where, under conditions that mimic the quenching state, a major fraction of the chlorophyll excitons were observed to decay through energy transfer to one of the luteins in the heart of the complex, thereby populating the lutein S1 state that subsequently decays on a picosecond timescale. Two-photon fluorescence excitation experiments on LHCII and plants in different quenching states, in which the carotenoid S1 state was selectively excited, indeed demonstrated an increased interaction between the luteins and their surrounding chlorophylls with increased levels of quenching. It is not impossible that both mechanisms operate in parallel. It is remarkable that both ‘switches’ require a conformational change to modulate the interaction between the carotenoid and the chlorophyll. That interaction controls the switch between light harvesting and quenching.

A key player in adaptive processes is the LHCII photosynthetic antenna system, which is involved both in light harvesting and in the protection of the photosynthetic apparatus. Its principal roles are to efficiently collect light energy to drive the primary photochemical reactions of PSII and PSI and to provide photoprotection. To achieve this goal, photosynthetic organisms have developed two distinct strategies. The first regulates the amount of light energy used by the PSII reaction center for photochemistry, especially when this energy exceeds the capacity of the photosynthetic machinery. In this strategy, the system switches to a protective mode in which the excess absorbed energy is dissipated as heat through a process called energy-dependent nonphotochemical quenching (qE-NPQ) 11

Without this protection system, the long-living singlet chlorophyll excited states produced under excess light would undergo triplet formation and react with molecular oxygen to produce reactive oxygen species, which damage cellular components. The second strategy balances the excitation energy absorbed by the LHCII and LHCI antenna systems and readjusts the redox poise of the electron transfer chain upon strong fluctuations in irradiance to optimize photosynthetic electron flow. This readjustment of the absorption cross sections of PSII and PSI can occur in either the short term (through the redistribution of the mobile LHCII antenna, referred to as a state transition) or the long term (through transcriptional and translational regulation of LHC gene expression). In the case of qE-NPQ, the LHCII system is able to sense the state of the light-energy balance directly through the pH across the thylakoid
membrane and to respond through structural changes.

Carotenoids can intercept the excess energy from excited chlorophyll molecules by thermally deactivating them, which prevents the production of singlet oxygen, a highly reactive form of this element. Unlike chlorophylls and carotenoids, phycobilins are water soluble. 


1. Plant Physiology 3th ed., page 136
2. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5058467/
3. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3523818/
4. https://sci-hub.bz/http://www.sciencedirect.com/science/article/pii/S0005272808006579
5. http://www.sciencedirect.com/science/article/pii/S0005272806003422
6. http://emboj.embopress.org/content/20/4/713
7. https://sci-hub.bz/http://www.nature.com/nature/journal/v403/n6768/full/403391a0.html
8. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC151466/
9. http://www.sciencedirect.com/science/article/pii/S0005272811001460
10. https://sci-hub.bz/http://www.nature.com/nchem/journal/v3/n10/full/nchem.1145.html?wt.
11. https://sci-hub.bz/http://www.annualreviews.org/doi/full/10.1146/annurev-arplant-050213-040226#_i7

The orchestrated assembly of molecular machines and factories points to intelligent design

http://reasonandscience.heavenforum.org/t1555-photosynthesis#5705

Biochemical processes like photosynthesis require the assembly and interconnection of several molecular machines. Parallels can be drawn to the assembly of man-made apparatuses and factories. Both require the coordinated assembly based on the right mounting sequences; all parts must be the correct ones, correct size, shape, materials, form. Often, these parts depend on other molecular machines to make them. Most proteins use in their active site metal clusters, which by themselves require complex machines for uptake of the right materials, import into the cell, and joining different metals together in complex ways to provide biochemical function. Then, these parts must be directed to the place where they will be mounted in the right sequence and correct arrangement to produce a purposeful, goal-oriented function. The parts cannot be mounted anyhow. They must be placed at the right place, into the right position, and correctly interconnected.  

A salient thing to be outlined is that in many if not most cases, the individual parts do not find use in other biochemical machines, but be used uniquely in a given, specific pathway or molecular machine. These parts have no function by their own, so there would be no reason for evolutionary mechanisms either to produce intermediate stages or end products, which only find use for higher ends or distant goals. And the individual parts do not find use either if the whole process is not fully set up and working - if one part of the system is missing - nothing goes. In case of photosynthesis, for example, chlorophylls, carotenoids, or Rubisco are essential for the final goal - no part can be missing - or carbohydrates are not synthesized.   

Manmade assembly depends on blueprints made by intelligent engineers and instructions given to the mechanicians, electricians etc. In biochemistry, these instructions are stored either in the genome, or epigenetic codes and signals.  

Here an example and describe how it works :

A characteristic feature of the photosynthetic complexes is that they all consist of numerous chloroplast and nucleus-encoded subunits. In the case of PSII, PSI, and Cytb6f these complexes contain in addition pigments such as chlorophylls and xanthophylls as well as hemes, quinones, and iron-sulfur (Fe-S) centers that act as redox cofactors. Hence the biogenesis of the photosynthetic apparatus involves a concerted interplay between the chloroplast and nucleocytosolic genetic systems as well as a tight coordination between protein and pigment synthesis and insertion into the thylakoid membranes. 1

In photosynthesis, 26 protein complexes and enzymes are required to go through the light and light-independent reactions, a chemical process that transforms sunlight into chemical energy, to get glucose and fixed carbon to make glucose, its food of the organism as end products.

To give an example of the task, just one of these proteins complexes, Photosystem II (PSII), is a multi-subunit pigment-protein complex found in cyanobacteria and chloroplasts. 2 Its  composed of

- 17 intrinsic  sub-units
-   3 extrinsic sub-units
-    cofactors
-  35 chlorophylls
-  2   pheophytins
- 11 β-carotenes
- > 20 lipids
- plastoquinones
- 2 heme irons
- 1 non-heme iron
- 4 manganese atoms,
- 4 calcium atoms
- 3 Cl- ions per monomer

Assembly of PSII is highly co-ordinated and proceeds through a number of distinct assembly intermediates. Associated with these assembly complexes are proteins that are not found in the final functional PSII complex. Structural information and possible functions are beginning to emerge for several of these ‘assembly’ factors, notably Ycf48/Hcf136 , Psb27 and Psb28. 1)

3


A remarkable feature of photosynthetic organisms is their ability to adapt to changing light conditions, which is reflected in changes in the organization of the photosynthetic complexes.

The ability of adaptations is essential, and repair mechanisms must be fully functional right from the beginning.

A stepwise, evolutionary emergence of such highly sophisticated, regulated, precise molecular machines without intelligence is extremely unlikely, if not - impossible. This is not an argument from ignorance. We know by experience that intelligence can produce machines and factories. We have no knowledge of any other non-guided, non-intelligent mechanisms able of the feat.

1. http://www.plantphysiol.org/content/155/4/1493
2. https://academic.oup.com/aob/article/106/1/1/94944/Recent-advances-in-understanding-the-assembly-and
3. https://www.frontiersin.org/articles/10.3389/fpls.2016.00617/full

The fundamental importance of light-harvesting complexes for life

http://reasonandscience.heavenforum.org/t1555-photosynthesis#5716

It's safe to say that the existence and supposed evolution of all higher life-forms depend fundamentally on Photosynthesis - the mechanism upon which oxygen and carbohydrates are produced. If someone cannot explain the origin of Light-harvesting complexes in the photosynthesis pathway, it would even be meaningless if macro-evolution were an undisputed fact and true, and point to naturalism.  If someone wants to propose evolution and, more generally, natural processes to explain our origins, the elucidation of how photosynthesis emerged, deserves the highest priority - and without solving this question, everything else is not solved either. The treatise below touches and addresses just a SMALL aspect and questions that require being answered, but are fundamental and vital ones. 

Photosynthesis is the most vital bioenergy-generating process, without which life on earth and the existence of our biosphere would be impossible. It is the basic process that feeds the world, begins when the pigments in the antenna complex capture the sunlight and transfer the energy to the pair of chlorophyll molecules that make up the reaction center of a photosystem.  Establishing the overall chemical equation of photosynthesis required several hundred years and contributions by many scientists. The chemical reactions of photosynthesis are complex. In fact, at least 50 intermediate reaction steps have now been identified. It is not surprising that working out how photosynthesis has mastered the efficient capture of the Sun’s energy has been the subject of research for over a century.  In plants, photosynthesis occurs in chloroplasts, large organelles found mainly in leaf cells. During photosynthesis, chloroplasts capture the energy of sunlight, convert it into chemical energy in the form of ATP and NADPH, and then use this energy to make complex carbohydrates out of carbon dioxide and water. The principal carbohydrates produced are polymers of hexose (six-carbon) sugars: sucrose, a glucose-fructose disaccharide.  

Notably, reaction centers are surrounded by many chromophores (often ~200) that are bound in light-harvesting complexes; these complexes contain a high concentration of molecular chromophores that absorb solar photons. The energy, stored in electrically excited states of the chromophores, is then transferred within and among light-harvesting proteins until it reaches a reaction center.

The Right Wavelength 

Recent research indicates that sunlight has magnificent features that inspire amazement. Both light and heat are different manifestations of electromagnetic radiation. In all its manifestations, electromagnetic radiation moves through space in waves similar to those created when a stone is thrown into a lake. And just as the ripples created by the stone may have different heights and the distances between them may vary, electromagnetic radiation also has different wavelengths. The stars and other sources of light in the universe do not all give out the same kind of radiation. Instead, they radiate energy with a broad range of wavelengths. Gamma rays, which have the shortest wavelengths, are just 1 of 10^25 the length of the longest radio waves. Strangely enough, nearly all of the radiation emitted by the Sun falls into a single band that is also 1 of10^25 of the whole spectrum. The reason is that the only kinds of radiation that are necessary and fit for life fall in this narrow band. Some wavelengths are several kilometers long while others are shorter than a billionth of a centimeter and the other wavelengths are to be found in a smooth, unbroken spectrum everywhere in between. To make things easier, scientists divide this spectrum up according to wavelength and they assign different names to different parts of it. The radiation with the shortest wavelength (one-trillionth of a centimeter) for example is called "gamma rays": these rays pack tremendous amounts of energy. The longest wavelengths are called "radio waves": they can be several kilometers long but carry very little energy. (One result of this is that radio waves are quite harmless to us while exposure to gamma rays can be fatal.) Light is a form of electromagnetic radiation that lies between these two extremes. The first thing to be noticed about the electromagnetic spectrum is how broad it is: the longest wavelength is 10^25 times the size of the shortest one. A number that big is pretty meaningless by itself. Let's make a few comparisons.

For example, in 4 billion years (the estimated age of the Earth) there are about 10^17 seconds. If you wanted to count from 1 to 10^25 and did so at the rate of one number a second nonstop, day and night, it would take you 100 million times longer than the age of the earth! If we were to build a pile of 10^25 playing cards, we would end up with a stack stretching halfway across the observable universe.
This is the vast spectrum over which the different wavelengths of the universe's electromagnetic energy extend. Now the curious thing about this is that the electromagnetic energy radiated by our Sun is restricted to a very, very narrow section of this spectrum. 70% of the Sun's radiation has wavelengths between 0.3 and 1.50 microns and within that narrow band, there are three types of light: visible light, near-infrared light, and ultraviolet light. Three kinds of light might seem quite enough but all three combined make up an almost insignificant section of the total spectrum. Remember our 10^25 playing cards extending halfway across the universe? Compared with the total, the width of the band of light radiated by the Sun corresponds to just one of those cards!

Why should sunlight be limited to such a narrow range?
The answer to that question is crucial because the only radiation that is capable of supporting life on earth is the kind that has wavelengths falling within this narrow range.
In Energy and the Atmosphere, the British physicist Ian Campbell addresses this question and says "That the radiation from the Sun (and from many sequence stars) should be concentrated into a minuscule band of the electromagnetic spectrum which provides precisely the radiation required to maintain life on earth is very remarkable." According to Campbell, this situation is "staggering".

Let us now examine these "staggering features of light" more closely.
In the whole electromagnetic spectrum, there is just one little band that has the energy to cross this threshold exactly. Its wavelengths range between 0.70 microns and 0.40 microns and if you'd like to see it, you can: just raise your head and look around–it's called "visible light". This radiation causes chemical reactions to take place in your eyes and that is why you are able to see. "The radiation is known as "visible light" makes up 41% of sunlight even though it occupies less than 1/10^25 of the whole electromagnetic spectrum. In his famous article "Life and Light", which appeared in Scientific American, the renowned physicist George Wald considered this matter and wrote:
 "the radiation that is useful in promoting orderly chemical reactions comprises the great bulk of that of our sun."  That the Sun should radiate light so exactly right for life is indeed an important example of design.

Photosynthesis, the basic process that feeds the world, begins when the pigments ( Chlorophyll a and b, and carotenoids ) in the antenna complex capture the sunlight and transfer the energy to the pair of chlorophyll molecules that make up the reaction center of a photosystem.



The highest Solar energy spectrum is in the 400nm to 800nm range, from ultraviolet to red. This is also the visible spectrum, which we are able to see as colors. Without Chlorophyll, no light is absorbed, and photosynthesis cannot occur ( They exercise the same function as solar panels ). Chlorophyll pigments are essential for all advanced lifeforms on earth. They absorb photons, which are transmitted to the reaction center in photosystem II holoprotein complex. Chlorophyll appears green to our eyes because it absorbs light mainly in the red and blue parts of the spectrum, so only some of the light enriched in green wavelengths (about 550 nm) is reflected into our eyes

How does a molecule “capture” the energy of light? A photon can be envisioned as a very fast-moving packet of energy. When it strikes a molecule, its energy is either lost as heat or absorbed by the electrons of the molecule, boosting those electrons into higher energy levels. Whether or not the photon’s energy is absorbed depends on how much energy it carries (defined by its wavelength) and on the chemical nature of the molecule it hits. Electrons occupy discrete energy levels in their orbits around atomic nuclei. To boost an electron into a different energy level requires just the right amount of energy, just as reaching the next rung on a ladder requires you to raise your foot just the right distance. A specific atom can, therefore, absorb only certain photons of light—namely, those that correspond to the atom’s available electron energy levels. As a result, each molecule has a characteristic absorption spectrum, the range and efficiency of photons it is capable of absorbing. 




Molecules that are good absorbers of light in the visible range are called pigments. Organisms have  a variety of different pigments, but there are only two general types used in green plant photosynthesis: carotenoids and chlorophylls. Chlorophylls absorb photons within narrow energy ranges. Two kinds of chlorophyll in plants, chlorophylls a and b, preferentially absorb violet-blue and red light. 



Neither of these pigments absorbs photons with wavelengths between about 500 and 600 nanometers, and light of these wavelengths is, therefore, reflected by plants. When these photons are subsequently absorbed by the pigment in our eyes, we perceive them as green. Chlorophyll a is the main photosynthetic pigment and is the only pigment that can act directly to convert light energy to chemical energy. However, chlorophyll b, acting as an accessory or secondary light-absorbing pigment, complements and adds to the light absorption of chlorophyll a. Chlorophyll b has an absorption spectrum shifted toward the green wavelengths. Therefore, chlorophyll b can absorb photons chlorophyll a cannot. Chlorophyll b therefore greatly increases the proportion of the photons in sunlight that plants can harvest. An important group of accessory pigments, the carotenoids, assist in photosynthesis by capturing energy from light of wavelengths that are not efficiently absorbed by either chlorophyll.

The energy required to excite a chromophore molecule depends on the chromophore structure. A general property of chromophores is that they contain many conjugated double bonds,  in the case of the tetrapyrrole ring of chlorophyll -a. These double bonds are delocalized. Figure 2.5







Pigments have an alternating arrangement of single and double bonds in the molecule, these are conjugated bonds that share electrons.   Conjugated Bond length determines wavelength to be absorbed -  The specific wavelength of light that can be absorbed is determined by the number and structure of conjugated bonds in the pigment molecule.

Questions: Did Carbon dioxide have the inherent drive to use light energy, and transform itself into complex organic compounds to become biofuel for advanced life?
How could matter have selected the right atoms and the right conjugated bond structure to form the right pyrrole - chromophore structure in Chlorophylls and carotenoids, which permits to match the photon energy level,  to promote and boost the electrons into a different energy level, required for Foerster energy transfer to the reaction center of PSII? 
How could non-intelligent processes have selected the right materials to produce the complex structures required absorb light in the biologically relevant electromagnetic spectrum?
How could it have found out about how to structure of the substituents on the rings which define the complementary absorption spectrum?

Photosynthesis Takes Place in Complexes Containing Light-Harvesting Antennas and Photochemical Reaction Centers
How does the plant benefit from this division of labor between antenna and reaction center pigments? Even in bright sunlight, a chlorophyll molecule absorbs only a few photons each second. If every chlorophyll had a complete reaction center associated with it, the enzymes that make up this system would be idle most of the time, only occasionally being activated by photon absorption. However, if many pigments can send energy into a common reaction center, the system is kept active a large fraction of the time.

Question : How did natural mechanisms like evolution find out about this problem, and emerge with a fully functional Light-Harvesting Antenna, joining enough chlorophylls and funneling enough energy to the reaction center ? 

Chlorophylls have a long hydrophobic hydrocarbon tail that anchors them in the photosynthetic membrane. 









Question: How could the Light-harvesting Complex (LHC) have become functional without the Chlorophyll tail, which permits to anchor Chlorophylls into the membrane? Furthermore, the distance from one Chlorophyll molecule to the next had to be just right from the beginning, otherwise, energy transfer could not have happened. A stepwise manner through evolution was simply not possible. Its an either " everything or nothing" situation. 

Dynamics of light harvesting
Speed is essential to efficient light harvesting. 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 quantum 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. 

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

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?

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?

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

Intermediate states, produced by univalent electron transport within photosystems, are toxic and need to be scavenged, a function performed by LHC-bound xanthophylls with far enhanced efficiency with respect to lipid-free carotenoids. This activity is essential for photoprotection even at low light intensity.

Triplets formed on the chlorophylls (predominantly on chlorophyll-a) are quenched very efficiently by the carotenoids; and 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,  are essential in natural photosynthesis. 

Essential means, carotenoids providing that mechanisms had to be fully embedded and present in the Light-Harvesting Complex from day 1. 

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.

In addition to the chlorophylls. The carotenoids in the complex fulfill 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. Chlorophylls and Carotenoids form an interdependent system. One has no function without the other.   There is no sound explanation based on natural mechanisms, how the Light harvesting complex could have emerged by evolutionary mechanisms, in a step-wise fashion.  

What proposed mechanisms for the emergence of complex protein structures must explain :

- assembly and degradation of the complex holo-enzymes, or molecular machines
- The origin of assembly co-factor proteins, only used for assembly of these molecular complexes
- some molecular machines are super complexes - for example, Photosystem II in photosynthesis requires 40 permanent proteins, which must be assembled in the right manner, while other proteins are expressed or associated only in stress conditions or during assembly and/or degradation
- In higher plants and algae, PSII is composed of two moieties: the core complex that contains all the cofactors of the electron transport chain, and the outer antenna, which increases the light-harvesting capacity of the core
- both moieties are essential and irreducible, and the assembly of both depends on highly complex, ordered proceedings which must be correctly encoded in the genome from the beginning.
- molecular super-complexes are often composed of metallic cofactors, in their active site. Photosystem II for example, contains the oxygen-evolving complex in the core structure, that generates the redox potential required to drive water splitting. This Metal-cluster has around it a protein called D1 which provides most of the ligands to the Mn4CaO5. Both, the D1 subunit, and the ligands are essential.

 

- The assembly of this metal cluster is a light-driven process called photoactivation
- It is a highly complex process, requiring for the assembly is an oxidative process that involves removal of electrons  from the Mn ions and the formation of oxo-bridges between the metals of the cluster with the bridging oxygen  atoms.  The photoassembly process was found to have a high complexity and up to now, there is no completed model for this process.

Maintenance of the highly dynamic Mn4CaO5 cluster also requires the delivery of a constant supply of the proper levels of Mn2+ and Ca2+

New type of photosynthesis discovered
https://www.sciencedaily.com/releases/2018/06/180614213608.htm#:~:text=Acaryochloris%20lives%20underneath%20a%20green,leaving%20just%20the%20near%2Dinfrared.&text=The%20chlorophyll%2Df%20based%20photosynthesis,of%20photosynthesis%20that%20is%20widespread.