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Photosynthesis

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1 Photosynthesis on Sun Mar 02, 2014 11:53 am

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Photosynthesis

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

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 a 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.

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  
http://reasonandscience.heavenforum.org/t1554-the-rubisco-enzymes-amazing-evidence-of-design

The oxygen evolving complex (OEC) of photosystem II is irreducible complex.
http://reasonandscience.heavenforum.org/t1583-the-oxygen-evolving-complex-oec-of-photosystem-ii-is-irreducible-complex

The biosynthesis pathway of Chlorophyll, essential for advanced life, is irreducible complex
http://reasonandscience.heavenforum.org/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

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.  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 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. 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 someont 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 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 all small steps need to provide a survival advantage.


Dianne Patty has kindly " peer reviewed " the article. Below some corrections. 







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



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2 Re: Photosynthesis on Sun Mar 02, 2014 11:54 am

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Plastids

The plastid is a major organelle found in the cells of plants and algae. Plastids are the site of manufacture and storage of important chemical compounds used by the cell.  They possess a double-stranded DNA molecule, which is circular, like that of prokaryotes.

Each plastid creates multiple copies of a circular 75–250 kilobase plastome. ( The plastome is the genetic material that is found in plastids in plant cells (for example in the chloroplast). ) The number of genome copies per plastid is variable, ranging from more than 1000 in rapidly dividing cells, which, in general, contain few plastids, to 100 or fewer in mature cells, where plastid divisions have given rise to a large number of plastids. The plastome contains about 100 genes encoding ribosomal and transfer ribonucleic acids (rRNAs and tRNAs) as well as proteins involved in photosynthesis and plastid gene transcription and translation. However, these proteins only represent a small fraction of the total protein set-up necessary to build and maintain the structure and function of a particular type of plastid. Plant nuclear genes encode the vast majority of plastid proteins, and the expression of plastid genes and nuclear genes is tightly co-regulated to coordinate proper development of plastids in relation to cell differentiation.





Chloroplasts

Chloroplasts  are organelles, specialized subunits, in plant and algal cells. Their main role is to conduct photosynthesis, where the photosynthetic pigment chlorophyll captures the energy from sunlight, and stores it in the energy storage molecules ATP and NADPH while freeing oxygen from water. They then use the ATP and NADPH to make organic molecules from carbon dioxide in a process known as the Calvin cycle. Chloroplasts carry out a number of other functions, including fatty acid synthesis, much amino acid synthesis, and the immune response in plants.





Acclimation to Changing Environmental Conditions

Plants and algae are constantly subjected to changes in light quality and quantity and need to adapt rapidly to maintain a high photosynthetic yield. We are studying the underlying molecular mechanisms of this light acclimation in the mobile unicellular alga Chlamydomonas reinhardtii and in the land plant Arabidopsis thaliana using a molecular-genetic approach. Our research is mainly focused on state transitions which involve an adaptive reorganization of the light-harvesting complex within the thylakoid membrane. This process also allows algal cells to respond to the metabolic requirements for ATP. Using genetic, biochemical and systems biology approaches, we have identified and characterized some of the factors involved in this acclimation process which include the Stt7/STN7 and Stl1/STN8 protein kinases. Because Stt7/STN7 has emerged as one of the key player in chloroplast signalling, a major task is to study its activation in vivo and in vitro, and to identify its targets and signalling components both in the chloroplast and the nucleus.



[/quote]

Thylakoid

A thylakoid is a membrane-bound compartment inside chloroplasts and cyanobacteria. They are the site of the light-dependent reactions of photosynthesis. Thylakoids consist of a thylakoid membrane surrounding a thylakoid lumen. Chloroplast thylakoids frequently form stacks of disks referred to as granum (singular: grana). Granum are connected by intergranal or stroma thylakoids, which join granum stacks together as a single functional compartment.









In-Depth Analysis of the Thylakoid Membrane Proteome of Arabidopsis thaliana Chloroplasts: New Proteins, New Functions, and a Plastid Proteome Database


Altogether, 154 proteins were identified, of which 76 (49%) were α-helical integral membrane proteins. Twenty-seven new proteins without known function but with predicted chloroplast transit peptides were identified, of which 17 (63%) are integral membrane proteins. These new proteins, likely important in thylakoid biogenesis, include two rubredoxins, a potential metallochaperone, and a new DnaJ-like protein.  

We identified 83 out of 100 known proteins of the thylakoid localized photosynthetic apparatus, including several new paralogues and some 20 proteins involved in protein insertion, assembly, folding, or proteolysis. An additional 16 proteins are involved in translation, demonstrating that the thylakoid membrane surface is an important site for protein synthesis.

Chloroplasts in green algae and higher plants contain photosynthetic thylakoid membranes with four multisubunit protein complexes (photosystem I [PSI], photosystem II [PSII], ATP synthase, and cytochrome b6f complexes), each with multiple cofactors. These four complexes are composed of at least 70 different proteins that perform the photosynthetic reactions.

They require coordinated expression of the nuclear and plastid genome and coordination between protein accumulation and biosynthesis of many cofactors in addition to the formation and maintenance of the lipid bilayer.

Throughout the last decade or so, significant progress has been made in identifying and characterizing proteins involved in these processes, such as proteases

Protease

A protease (also termed peptidase or proteinase) is any enzyme that performs proteolysis, that is, begins protein catabolism by hydrolysis of the peptide bonds that link amino acids together in the polypeptide chain forming the protein. Proteases have evolved multiple times, and different classes of protease can perform the same reaction by completely different catalytic mechanisms. Proteases can be found in animals, plants, bacteria, archea and viruses.

proteolysis

Proteolysis is the breakdown of proteins into smaller polypeptides or amino acids. In general, this occurs by the hydrolysis (  Hydrolysis ( meaning "water", and lysis, meaning "separation") usually means the cleavage of chemical bonds by the addition of water ) of the peptide bond, and is most commonly achieved by cellular enzymes called proteases, but may also occur by intramolecular digestion, as well as by non-enzymatic methods such as the action of mineral acids and heat.

Proteolysis in organisms serves many purposes; for example, digestive enzymes break down proteins in food to provide amino acids for the organism, while proteolytic processing of polypeptide chain after its synthesis may be necessary for the production of an active protein. It is also important in the regulation of some physiological and cellular processes, as well as preventing the accumulation of unwanted or abnormal proteins in cells.

Pigments for Photosynthesis

A photosynthetic pigment (accessory pigment; chloroplast pigment; antenna pigment) is a pigment that is present in chloroplasts or photosynthetic bacteria and captures the light energy necessary for photosynthesis.

A pigment is a material that changes the color of reflected or transmitted light as the result of wavelength-selective absorption.


Pigments for Photosynthesis


Photosynthetic pigments



Photosynthesis in plants is dependent upon capturing light energy in the pigment chlorophyll, and in particular chlorophyll a. This chlorophyll resides mostly in the chloroplasts and gives leaves their green color. The range of light absorption in leaves is extended by some accessory pigments such as the carotenoids, but does not cover the entire visible range - that would make the leaves black!

Some plants and plantlike organisms have developed other pigments to compensate for low light or poor use of light. Cyanobacteria and red algae have phycocyanin and allophycocyanin as accessory pigments to absorbe orange light. They also have a red pigment called phycoerythrin that absorbs green light and extends the range of photosynthesis. The red pigment lycopene is found in vegetables. Some red algae are in fact nearly black, so that increases their photosynthetic efficiency. Brown algae have the pigment fucoxanthin in addition to chlorophyll to widen their absorption range. These red and brown algae grow to depths around 270 meters where the light is less than 1% of surface light.

But the most advanced plants are the land plants, which have the least advanced system for gathering light!

Biological pigment

Biological pigments, also known simply as pigments or biochromes are substances produced by living organisms that have a color resulting from selective color absorption. Biological pigments include plant pigments and flower pigments. Many biological structures, such as skin, eyes, fur and hair contain pigments such as melanin in specialized cells called chromatophores.

Pigment color differs from structural color in that it is the same for all viewing angles, whereas structural color is the result of selective reflection or iridescence, usually because of multilayer structures. For example, butterfly wings typically contain structural color, although many butterflies have cells that contain pigment as well.

  Heme/porphyrin-based: chlorophyll, bilirubin, hemocyanin, hemoglobin, myoglobin

  Light-emitting: luciferin

  Carotenoids:
  Hematochromes (algal pigments, mixes of carotenoids and their derivates)

  Carotenes: alpha and beta carotene, lycopene, rhodopsin

  Xanthophylls: canthaxanthin, zeaxanthin, lutein

  Proteinaceous: phytochrome, phycobiliproteins


There are three basic classes of pigments.

Chlorophylls are greenish pigments which contain a porphyrin ring. This is a stable ring-shaped molecule around which electrons are free to migrate. Because the electrons move freely, the ring has the potential to gain or lose electrons easily, and thus the potential to provide energized electrons to other molecules. This is the fundamental process by which chlorophyll "captures" the energy of sunlight.

There are several kinds of chlorophyll, the most important being chlorophyll "a". This is the molecule which makes photosynthesis possible, by passing its energized electrons on to molecules which will manufacture sugars. All plants, algae, and cyanobacteria which photosynthesize contain chlorophyll "a". A second kind of chlorophyll is chlorophyll "b", which occurs only in "green algae" and in the plants. A third form of chlorophyll which is common is (not surprisingly) called chlorophyll "c", and is found only in the photosynthetic members of the Chromista as well as the dinoflagellates. The differences between the chlorophylls of these major groups was one of the first clues that they were not as closely related as previously thought.

Carotenoids are usually red, orange, or yellow pigments, and include the familiar compound carotene, which gives carrots their color. These compounds are composed of two small six-carbon rings connected by a "chain" of carbon atoms. As a result, they do not dissolve in water, and must be attached to membranes within the cell. Carotenoids cannot transfer sunlight energy directly to the photosynthetic pathway, but must pass their absorbed energy to chlorophyll. For this reason, they are called accessory pigments. One very visible accessory pigment is fucoxanthin the brown pigment which colors kelps and other brown algae as well as the diatoms.

Phycobilins are water-soluble pigments, and are therefore found in the cytoplasm, or in the stroma of the chloroplast. They occur only in Cyanobacteria and Rhodophyta.

Chlorophyll



Chlorophyll biosynthesis

Chlorophyll (also chlorophyl) is a green pigment found in cyanobacteria and the chloroplasts of algae and plants. Its name is derived from the Greek words χλωρός, chloros ("green") and φύλλον, phyllon ("leaf"). Chlorophyll is an extremely important biomolecule, critical in photosynthesis, which allows plants to absorb energy from light. Chlorophyll absorbs light most strongly in the blue portion of the electromagnetic spectrum, followed by the red portion. Conversely, it is a poor absorber of green and near-green portions of the spectrum, hence the green color of chlorophyll-containing tissues.


Chlorophyll a is a specific form of chlorophyll used in oxygenic photosynthesis. It absorbs most energy from wavelengths of violet-blue and orange-red light. It also reflects green/yellow light, and as such contributes to the observed green color of most plants. This photosynthetic pigment is essential for photosynthesis in eukaryotes, cyanobacteria and prochlorophytes because of its role as primary electron donor in the electron transport chain. Chlorophyll a also transfers resonance energy in the antenna complex, ending in the reaction center where specific chlorophylls P680 and P700 are located.

Chlorophyll

Chlorophylla-a is the primary pigment for photosynthesis in plants.  It has the composition C55H72O5N4Mg. It exhibits a grass-green visual color and absorption peaks at 430nm and 662nm. It occurs in all photosynthetic organisms except photosynthetic bacteria.

Chlorophyll-b has the composition C55H70O6N4Mg, the difference from chlorophyll-a being the replacement of a methyl group with a CHO. It exhibits a blue-green visual color and absorption peaks at 453nm and 642nm. It occurs in all plants, green algae and some prokaryotes. There is usually about half as much chlorophyll-b as the -a variety in plants.






THE PHOTOSYNTHETIC PROCESS

Chlorophylls are greenish pigments which contain a porphyrin ring. This is a stable ring-shaped molecule around which electrons are free to migrate. Because the electrons move freely, the ring has the potential to gain or lose electrons easily, and thus the potential to provide energized electrons to other molecules. This is the fundamental process by which chlorophyll "captures" the energy of sunlight.

There are several kinds of chlorophyll, the most important being chlorophyll "a". This is the molecule which makes photosynthesis possible, by passing its energized electrons on to molecules which will manufacture sugars. All plants, algae, and cyanobacteria which photosynthesize contain chlorophyll "a". A second kind of chlorophyll is chlorophyll "b", which occurs only in "green algae" and in the plants. A third form of chlorophyll which is common is (not surprisingly) called chlorophyll "c", and is found only in the photosynthetic members of the Chromista as well as the dinoflagellates. The differences between the chlorophylls of these major groups was one of the first clues that they were not as closely related as previously thought.

Carotenoids are usually red, orange, or yellow pigments, and include the familiar compound carotene, which gives carrots their color. These compounds are composed of two small six-carbon rings connected by a "chain" of carbon atoms. As a result, they do not dissolve in water, and must be attached to membranes within the cell. Carotenoids cannot transfer sunlight energy directly to the photosynthetic pathway, but must pass their absorbed energy to chlorophyll. For this reason, they are called accessory pigments. One very visible accessory pigment is fucoxanthin the brown pigment which colors kelps and other brown algae as well as the diatoms.

Phycobilins are water-soluble pigments, and are therefore found in the cytoplasm, or in the stroma of the chloroplast. They occur only in Cyanobacteria and Rhodophyta.

Phycobilins are not only useful to the organisms which use them for soaking up light energy; they have also found use as research tools. Both pycocyanin and phycoerythrin fluoresce at a particular wavelength. That is, when they are exposed to strong light, they absorb the light energy, and release it by emitting light of a very narrow range of wavelengths. The light produced by this fluorescence is so distinctive and reliable, that phycobilins may be used as chemical "tags". The pigments are chemically bonded to antibodies, which are then put into a solution of cells. When the solution is sprayed as a stream of fine droplets past a laser and computer sensor, a machine can identify whether the cells in the droplets have been "tagged" by the antibodies. This has found extensive use in cancer research, for "tagging" tumor cells.

Like plants, the cyanobacteria use water as an electron donor for photosynthesis and therefore liberate oxygen; they also use chlorophyll as a pigment. In addition, most cyanobacteria use phycobiliproteins, water soluble pigments which occur in the cytoplasm of the chloroplast, to capture light energy and pass it on to the chlorophylls. (Some cyanobacteria, the prochlorophytes, use chlorophyll b instead of phycobilin.) It is thought that the chloroplasts in plants and algae all evolved from cyanobacteria.
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3 Re: Photosynthesis on Sun Mar 02, 2014 11:56 am

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Photosynthesis: C2, C3, and C4 Cycles


Photosynthesis is a necessary bridge between the sun and most organisms on earth. When light travels from the sun, the energy it contains is in packets called photons. The photons travel through the atmosphere and are absorbed by a light harvesting complex that is found in chlorophyll containing organisms or photoautotrophs. The energy is transferred adjacently by a process called resonance energy transfer.

In the presence of water and carbon dioxide, photosynthesis will ultimately produce oxygen and glucose that other organisms can use(Brooker). Neither humans nor any other mammals are capable of producing energy from sunlight. We must rely on photosynthesis in photoautotrophs. Since there is an abundance of photoautotrophs compared to other organism there is always an abundance of oxygen

The Light and Dark Cycles of Photosynthesis


Photosynthesis contains two cycles. The light cycle and the dark (Calvin/Benson) cycle. The light cycle, as it name implies, occurs when a light source is available. Light energy and water molecules are used in the light reaction to produce NADPH.

The oxygen from the water is released as a waste. The hydrogen from water molecules along with hydrogen from the stroma are used to create concentration of hydrogen protons inside the lumen. This electrochemical gradient is then used to power the phosphorylation of ADP to make ATP(Brooker). Then, that newly created ATP and NADPH are used along with carbon dioxide from the environment in the Calvin Cycle also known as the dark reaction.

Note: Plants usually store materials produced during the daytime for use during the dark cycle.

The Calvin-Benson Cycle

While the light reaction occurs along the thylakoid membrane, the Calvin cycle(C3 cycle) occurs outside of the thylakoids in the stroma. The Calvin cycle consist of the following steps:

carbon fixation–>reduction—-> carbohydrate production—>RuBP regeneration.

When the initial molecule(carbon fixation), ribulose1,5-bisphosphate (RuBP), reacts with carbon dioxide with the aid of the RuBP carboxylase enzyme(RUBISCO), the first stable molecules produced are two 3-carbon molecule called 3-phosphoglycerate(PGA). There is a non stable 6-carbon molecule that precedes PGA but it immediate breaks into 2 PGA molecules(Brooker). Once PGA is made ATP donates a phosphate group to PGA to form 1,3-bisphosphoglycerate. It now has 2 phosphate groups, one each on the first and third carbons. Now in the reduction and carbohydrate production stage 1,3-bisphosphate takes the H from an NADPH being reduced and releases its phosphate group to become 3-phosphoglceraldehyde(PGAL). PGAL can now be used to create carbohydrates for energy and regeneration of the original RuBP molecule.

The enzyme RUBISCO is such a pivotal factor in the Calvin cycle yet it is very large and unique. The amino acid sequence of the enzyme RUBISCO is identical in all species of plants(Mauseth)! For the hundreds of millions of years plants have existed every mutation, no matter how minor, must have affected the activation site and have been disadvantageous. So it can be inferred that RUBISCO must have been spontaneously or very quickly formed by natural means at the same time as all the other enzyme in the Calvin cycle. This can also be evidence for some type of intelligent design(Behe).

As complete as the C3 cycle may seem it is actually far from perfect. With the abundance of oxygen and RUBISCO’s low affinity for carbon dioxide, a phenomena known as photorespiration occurs. Oxygen is attached instead carbon dioxide. This produces 1 PGA like normal, but one irregular molecule called phosphoglycolate. The organism must take steps to convert this potentially harmful molecule into useful amino acids and CO2. The problem with photorespiration is the organism looses energy trying to convert the phosphoglycolate back into useful material.

Since for some reason the RUBISCO enzyme was unable to be evolutionarily modified to have a higher affinity for carbon dioxide, some organism have developed a separate compartment that has another enzyme called (PEP) phosphophenolpyruvate carboxylase. PEP has a high affinity for CO2 and none for oxygen. So in this compartment CO2 is rapidly picked up, and used along with PEP to form oxaloacetate. As more CO2 flows down the carbon dioxide gradient, the oxaloacetate powers the reduction of NADPH while oxaloacetate is being decarboxylated and moved into a new compartment. The decarboxylation of the molecule brings carbon dioxide into the compartment where RUBISCO is located so that only carbon dioxide is near RUBISCO(Mauseth). It would be a great advancement if PEP carboxylase could use carbon dioxide and PEP to make PGA. There would be no need for Kranz anatomy if RUBISCO could be modified to have a high affinity for carbon dioxide and none for oxygen like PEP carboxylase.

The basis of life on earth is energy in the form of light that arrives to the earth in the form of photons. The mechanism to harvest this energy is a highly ordered system and serves a highly specific purpose: conversion of light energy into a stable, transferable form of energy. While photosynthesis appears to be an irreducibly complex system(Behe), it ultimately serves it’s purpose of producing enough molecular oxygen and carbohydrates for life to survive. Photosynthesis is a complex system that it is not perfect due to oxygen binding which starts the process of photorespiration. C2 photosynthesis or photorespiration may benefit an organism in other unverified ways, but for now it is considered disadvantageous because photosynthesis occurs at a much slower rate than C3 or C4 photosynthesis. There is much debate whether photosynthesis and other complex systems are a product of design because the ordered, and interacting components serve a purpose, and can not be broken down into any less complex yet functioning system(Behe). Maybe bacteria by chance developed photosynthesis by random mutations, horizontal gene transfer, and natural selection millions of years ago and were absorbed in a symbiotic relationship by eukaryotic cells(Dawkins). “The search for truth is more precious than its possession.” -Albert Einstein

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



Even now, plants are the basis of the food chain, because they don’t require their own food but make it from sunlight via photosynthesis. In this process, they also produce the oxygen (O2) which is essential for all air-breathing life. Photosynthesis is therefore one of the most important chemical reactions on Earth. If we could duplicate it, it would probably solve all the world’s energy problems.2 But even the most ingenious chemists have yet to match the ingenious machinery of the humble plant.

The unique … arrangement … is essential … because it must be able to store the energy from four photons, and hold water molecules in just the right positions. This structure had to be complete otherwise it would not work at all …. Therefore it could not be built up gradually by small changes by natural selection … because an incomplete intermediate system is no use at all, so it would not be selected.
Water blasting problem

The key to photosynthesis is breaking up a molecule of water into hydrogen and oxygen. The hydrogen can then combine with CO2 from the air to make sugars, which the plant (and herbivores) can use for food. All this occurs in the molecules called chlorophylls, which are responsible for the greenness of plants.

But breaking up water requires an enormous amount of energy—basically the amount released when hydrogen is burned to form water in the first place.

One problem is the very nature of light itself. Light is a form of energy, but it comes in ‘packets’ called photons. If the photon energy is not large enough to break the water molecule, then it won’t matter how many of them there are (i.e. how bright the light is). But a photon that is energetic enough3 to break water would also shatter most biological molecules in the process. Yet we don’t see exploding leaves!

A few years ago, two chemists from Yale University, Gary Brudvig and Robert Crabtree, made an artificial system that managed to produce oxygen.4 However, they had not worked out how to use light energy, so instead they used the chemical energy of powerful bleaches.5 And even then, it produced only 100 O2 molecules before being destroyed. Yet it was a great achievement, by human standards, to make something that didn’t fall apart immediately.6
Ingenious solution7

It turns out that in leaves, there is a special assembly called Photosystem II (named because it was discovered second). A photon strikes this, and it is channeled into a type of chlorophyll called P680. There it knocks out an electron from an atom, and this energetic electron eventually helps make sugars from CO2. But then, the P680 must replenish the lost electron. This is a big problem for artificial photosynthesis—human chemists have also so far been unable to produce a system that replenishes the electrons knocked out by the photons. Photosynthesis would have quickly ground to a halt without this, so how are the electrons replaced?

They come from a special catalytic core, which removes the required electrons from water, again with the help of light. The light breaks two molecules of water into a molecule of oxygen, four electrons and two hydrogen ions.

The core has a unique arrangement of atoms, with an unusual cube of three atoms of Mn, one Ca and four O, attached to a single Mn [update: see Where Water Is Oxidized to Dioxygen: Structure of the Photosynthetic Mn4Ca Cluster, Science 314(5800):821–825, 3 November 2006; Learning how nature splits water]. This core builds up enough energy, in the form of redox potential,8 in stages by absorbing four photons.

The redox potential of water is +2.5 V, while each photon raises the catalytic core’s redox potential by 1 V. So after the third stage, there is enough energy for the single Mn to remove an electron from a water molecule, leaving an OH radical and H+ ion. Then the catalytic core gets to the fourth stage, and provides the Mn atom with enough power to attack the OH radical and leaves a highly reactive O atom and another H+ ion. At this moment, the Ca atom in the cube plays its essential role. It is holding another water molecule in just the right place, so it can be attacked by this O atom, producing an O2 molecule, two more H+ ions and two electrons.The unique Mn3CaO4–Mn arrangement is present in all plants, algae and cyanobacteria, which suggests that this arrangement is essential. Not surprising, because it must be able to store the energy from four photons, and hold water molecules in just the right positions. This structure had to be complete otherwise it would not work at all—in splitting water and replenishing electrons. Therefore it could not be built up gradually by small changes by natural selection. This is because an incomplete intermediate system is no use at all, so it would not be selected.


And even this core would be useless without many other coordinated features. For example, as above, the energy involved is damaging for biological molecules. Yet there are key proteins required, but must be constantly repaired, so these mechanisms must be in place too. In fact, instability of these proteins made it hard to work out the core’s structure.9

If the most intelligent human designers can’t duplicate photosynthesis, then it’s perfectly scientific to believe that photosynthesis had a far more intelligent designer.
This is especially so since Darwinian processes could not have generated photosynthesis, because there are too many intricate mechanisms necessary for it to work at all.
Plants were there right at the beginning

Recent research indicates that there was oxygen even in the ‘oldest’ rocks on earth, which evolutionists ‘date’ to 3.7 billion years old (Ga).11 This in turn suggests that there were green plants to produce it. However, evolutionists claim that the earth was being bombarded by meteorites till about 3.8 Ga.

Yet this latest research shows that life existed almost as soon the earth was able to support it. There is just no room for ‘billions and billions of years’ for life to evolve. And this life was not just the simplest type, but was advanced enough to photosynthesize.

Also, this research is devastating for chemical evolutionary theories of the origin of life.13 The famous gas discharge experiments by Stanley Miller and Harold Urey must exclude free oxygen, because oxygen destroys organic molecules, and makes t
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.

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5 Photosynthetic mechanisms on Wed Mar 12, 2014 7:15 pm

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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.

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6 Re: Photosynthesis on Sat Aug 15, 2015 7:38 am

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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.


http://reasonandscience.heavenforum.org/t1546-chlorophyll-biosynthesis-pathway


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 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."

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 laboring 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 also 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
http://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
http://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

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7 Is Photosynthesis Irreducibly Complex? on Tue Nov 10, 2015 8:51 pm

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Is Photosynthesis Irreducibly Complex?

From Nature this week. “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. Roseanne J. Sension doi:10.1038/446740a Full Text 
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 tepidumThis 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 1, 2. 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 6, 10. 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 Ã¢â‚¬â€ 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/

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8 Oxygen, the molecule that made the world on Wed May 04, 2016 4:12 pm

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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.

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9 Re: Photosynthesis on Thu May 05, 2016 4:18 am

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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

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10 Re: Photosynthesis on Sat Feb 04, 2017 7:04 pm

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Mechanism for photosynthesis found in primeval, non-photosynthetic microbe

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