Intelligent Design, the best explanation of Origins

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Intelligent Design, the best explanation of Origins » Photosynthesis, Protozoans,Plants and Bacterias » Why the biosynthesis pathway of Chlorophyll must be intelligently designed

Why the biosynthesis pathway of Chlorophyll must be intelligently designed

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Why the biosynthesis pathway of Chlorophyll must be intelligently designed

http://reasonandscience.heavenforum.org/t1546-why-the-biosynthesis-pathway-of-chlorophyll-must-be-intelligently-designed

Experiments carried out between 1905 and 1913 in Zurich and Berlin by Richard Willstätter and his collaborators led to the discovery of the structural formula of the green leaf pigment chlorophyll, a milestone in the history of chemistry. This discovery made such an impact that Richard Willstätter was awarded the Nobel Prize in Chemistry as early as 1915.

Chlorophyll is the world’s most abundant organic material, and essential for all advanced life forms. The make of chlorophyll is a formidable example of biochemical machines in action like human made machines working in a factory, and how they require intelligence for setup. As follows, I try to explain my point in a nutshell, as short and illustrative and clear as possible:

Photosynthesis is a process used by plants and other organisms to convert light energy into chemical energy used to fuel the organisms' activities Photosynthesis finds its equivalent in human-made Solar Electric Power Systems which make electricity from sunlight. In photosynthesis, 26 protein complexes are required to transform sunlight into chemical energy. Each of the protein complexes is essential. If any is missing, energy cannot be transformed. In Photosynthesis, chlorophylls are essential to absorb light, while in its human-made equivalent, Photovoltaic systems, Solar panels do the same job as chlorophylls used in photosynthesis.  Without chlorophyll, no light can be absorbed, and energy cannot be captured. All proteins of photosynthesis must be fully developed and interlinked, they are interdependent.  It would be meaningless to produce chlorophyll without the other proteins required for photosynthesis. Chlorophyll by its own, has no function, in the same manner, as it would be meaningless to produce Solar panels without the other parts required in the process to produce electrical energy. Solar panels by their own are useless. In Solar Electric Power Systems, a minimal number of five interdependent and interconnected parts is required, or the process is not functional.

Chlorophyll biosynthesis is a complex pathway of  17 irreducible sequential highly specific steps, of which eight last steps specific enzymes uniquely in this pathway are doing their manufacturing process. Unless the pathway goes all through, chlorophyll a molecules cannot be produced, and will not be functional. In a similar manner, the making of solar panels requires complex factories and machines, and at least seven processing steps, of which each requires complex machines which produce the intermediate products. The process must go all through, or functional Solar panels can not be produced. In the same manner, as chlorophyll requires complex manufacturing processes to get biologically functional, all other proteins in the photosynthesis pathway do, too. Most of these proteins require multiple sub-units, which need to fit precisely, they must be synchronized, coordinated, and be compatible each with the other parts ( like a lock and key ).
In the same manner, as Solar panels require complex manufacturing processes to get made, and to become functional, all other parts of the Solar Power Systems, to be made, require equally complex manufacturing processes. Once the individual parts are made, how to interconnect the parts must be precisely defined and instructed through precise information.  
The end function, namely producing energy, depends on ALL these steps fully setup and interlinked to become a working, functional whole.

There relies on the BIG flaw in Darwin's idea: ‘Why would evolution produce a series of enzymes that only generate useless intermediates until all of the enzymes needed for the end product exist, fully functional,  and are interlinked in a useful manner ?’
A minimal amount of precise information is required for a gene to instruct for complex functions. If a gene does not contain sufficient information for an end function, it confers no selective advantage, and no end goal is achieved. Thus, before a region of DNA contains the required information for functional multi-part protein complexes, natural selection plays no role in guiding its evolution. The step by step selective mechanism is not a sufficient nor adequate explanation for the complex molecular proceedings observed in living cells and organisms. This problem becomes even bigger in Origin of Life Scenarios, where evolution is not a possible mechanism since evolution depends on DNA replication. Therefore, intelligent design is an adequate explanation for the origin of photosynthesis, Chlorophyll, and actually all living beings.

A minimal amount of instructional complex information is required for a gene to produce useful proteins.  Thus, before a region of DNA contains the requisite information to make useful proteins, natural selection would not select for a positive trait and play no role in guiding its evolution. Moreover, natural selection would not select for components of a complex system that would be useful only in the completion of the much larger system.

Biological cell factories and molecular machines find often their equivalents in human-made artifacts. 
Chlorophyll pigment molecules are essential in photosynthesis, allowing plants and other organisms to absorb solar energy from light. Chlorophylls are vital for photosynthesis, a process to convert light energy into chemical energy that can later be released to fuel the organisms' activities (energy transformation). 

Human-made solar panels exercise the same function as chlorophyll. A solar power system is designed to supply usable solar power, using solar panels in the first step to capturing solar energy. We can draw interesting parallels between human-made solar panels and power systems, to its equivalent in nature, chlorophylls, and photosynthesis, and point out, why they provide an excellent illustration of intelligent design.

In order to gain electricity through solar power,  the installation of a solar power system is required. It consists of an arrangement of several components, including solar panels, a solar inverter, cabling,  solar tracking system, and an integrated battery solution to store the energy produced. If any of the mentioned components are missing, solar energy cannot be gained and stored. The final goal cannot be achieved. Each of the components is essential, and need to be interconnected correctly. One of the indispensable components is solar panels. 

The make of solar panels requires complex factories and machines  
The basic component of solar panels,  pure silicon,  is not pure in its natural state. It must be brought to the manufacturing site, the solar panel factory, cleaned, and prepared for the further steps. The same happens in cells, where raw material must be imported in complex mechanisms, through gates in the cell membrane.   The manufacturing process goes from Purification of silicon, Making single crystal silicon, silicon wafers, doping,  placing electrical contacts, anti-reflective coating, and finally encapsulating the cell. Finally, the panel goes through a quality control process and implantation. That's an eight step production process, which must go all the way through; each step is essential and requires also several complex machines, which are specifically designed with specific processing and manufacturing goals. 

It's evident that the whole process requires the invention and implementation by intelligence. That is, engineers, which first make a scientific research, and based on the findings and inventions, experience and collected data, elaborate the relevant blueprints of the whole production process of each single machine, interconnections, and conceptualization as how the functional whole will provide the desired outcome. Functional parts are only meaningful within a whole, in other words, it is the whole that gives meaning to its parts. The information is based on a language system wich must be pre-established. To define a specific subpart of a machine that requires a specific shape, size, material etc. the initial requirement is the language or code system, and the information based on that language to specify the part in question.In that way, the workers in the factory know how to decipher and understand the blueprint, its meaning, to produce the panels.   Intelligent agents think with an "end goal" in mind, allowing them to solve complex problems by taking many parts and arranging them in intricate patterns that perform a specific function. They need to be able to organize parts availability, synchronization, manufacturing and assembly coordination and interface compatibility of the single parts and subunits. The individual parts must precisely fit together and be correctly interconnected. The production process usually takes place in complex factories which also must be fully built, and ready for production. The raw materials are sourced, transported to the factory, selected and prepared for use at the right facility. 

What humans invented a few decades ago, was implemented much before through photosynthesis.  

Without chlorophyll, no light is absorbed, and photosynthesis cannot occur. Chlorophyll pigments are essential for all advanced lifeforms on earth. They absorb photons, which are transmitted to the reaction center in photosystem II.  In a similar process as solar panel manufacturing, its equivalents, chlorophylls,  must be made by a complex manufacturing process, similar as in a factory production line. Chlorophyll  biosynthesis requires a complex pathway of 17 highly specific steps, like in a production line, and at each step, specific molecular machines  advance in the make of chlorophyll , one step after the other,  one enzyme handing over the subproduct to the next enzyme,   by which in the eighth last steps, specific enzymes are used,  uniquely in this pathway. That is as to say, specific machines are in place, to do their job only and exclusively for that specific manufacturing step and process. The pathway must go all the way through, otherwise, chlorophyll is not produced. Any intermediate product has no biological function. 

The enzymes used in each single step use by themselves highly coordinated and complex multistep manufacturing procedures to produce the intermediate products. For example, Porphobilinogen deaminase enzyme (PBGD)  is highly complex and specified in its structure, using co-factors for catalysis, and uses 4 highly coordinated, ordered, sequenced and complex steps, forming a geometrically correct tetrapyrrole ( a part of chlorophyll ), and repeats the first two manufacturing steps in total 4 times.

The evolutionary model is day by day…step by step…we are getting better and better all the time, adding to get more complexity. But that suggested manufacturing process raises serious questions in face of the challenge to produce photosynthesis.     

Without solar panels, no energy could be captured, a solar power system would be non-functional. 
No chlorophyll, no caption of photons, no photosynthesis, no plant and no advanced life. 

Chlorophyll by its own has no function. So there would be no sense to produce it in a complex manufacturing process unless all other parts for photosynthesis would be in place. Evolution has no foresight. So let's suppose, hundreds of millions of years would produce chlorophylls.  SO WHAT ???! - by their own, there is no function for them, and if they don't have a function, natural selection would not select them. Chlorophyll by its own, without the other proteins used in the photosynthesis pathway, would have no use. It's as if someone would produce solar panels, without use.

What good would it be to make complex manufacturing machines to produce intermediate products for solar panel production, without all the other machines and a functional factory fully setup and in place? 
What good would there be for natural selection to select and produce enzymes, used in this complex manufacturing process, without all the other enzymes in place, and the whole process coordinated to get a useful end product? 

What good would it be, if solar panels would be produced, but all other parts would be missing to transform solar energy into useful energy? 
What good would there be, if the chlorophyll pathway would go all the way through the 17th step? Chlorophyll would be produced, BUT:
What good for survival would there be for chlorophyll on its own, if not fully embedded in the photosynthesis process? none.

What good would there be for photosynthesis without chlorophyll in place, capturing light, and transmitting it to the photosystem? none, since capturing light is essential for the whole process. Therefore,  Chlorophyll biosynthesis is an interdependent, irreducible pathway. A minimal number of parts is required, and any shorter version would be nonfunctional. 

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 antenana proteins. Why would such proteins evolve prior to chlorophyll and if they did not how would cells survive chlorophyll until they did? 11

The thing is, there's no driver for any of the pieces to emerge individually because single parts confer no advantage in and of themselves. The necessity for the parts of the system to be in place all at once is simply evidence of a planning organizing creative intelligence.  

Biological systems are functionally organized, integrated into an interdependent network, and complex, like human-made machines and factories. The wiring of an electrical device equals to the biosynthesis pathway of chlorophyll. For the assembly of a biological system of multiple parts, not only the origin of the genome information to produce all proteins/enzymes with their respective subunits and assembly cofactors must be explained, but also parts availability ( The right materials must be transported to the building site. Often these materials in their raw form are unusable. Other complex machines come into play to transform the raw materials into a usable form.  All this requires specific information. )  synchronization, ( these parts must be read on hand at the building site )  manufacturing and assembly coordination ( which required the information of how to assemble each single part correctly, at the right place, at the right moment, and in the right position ) , and interface compatibility ( the parts must fit together correctly, like lock and key ) . Unless the origin of all these steps is properly explained, functional complexity as existing in biological systems has not been addressed adequately.

How could the whole process have started " off the hooks " from zero without a planning intelligence? 
Why would natural, unguided mechanisms produce a series of enzymes that only generate useless intermediates until all of the enzymes needed for the end product exist, are in place and do their job?
Furthermore, the process is highly toxic for cell membranes and would destroy the surrounding molecules, if not duly protected right from the beginning. 
My conclusion is: The invention of Chlorophyll biosynthesis can only be explained by the acting agency of an intelligent mind.

An intelligent designer is a capable agent, able of planning, with the foresight of the end result, and the requirement of machines and pathways and manufacturing processes for an end goal and useful product. Mindless, unguided, random, evolutionary processes are NOT. We are granted to infer, based on positive scientific evidence and knowledge ( no ignorance ! ) that intelligent design is the best explanation for the origin of the biosynthesis pathway of chlorophyll and photosynthesis.    

More readings: Photosynthesis
http://reasonandscience.heavenforum.org/t1555-photosynthesis





Without blood, there would be no advanced life. Nor so without chlorophylls. What do both have in common?

The amazing similarity between blood and chlorophyll

Scientist already discovered that life comes from the sun. Chlorophyll contains oxygen, carbon, nitrogen, hydrogen and magnesium, whilst hemoglobin from the blood contains iron at the place of magnesium, see figure below. Both iron and magnesium are metallic atoms.



Organisms spend a lot of time acquiring energy (capacity to do work) and nutrients ( a to convey substance that an organism needs for growth and survival, but cannot make of itself). Despite the close similarity between blood and chlorophyll, plants are producers (they make their own food using energy and materials from their environment) and animals are consumers (cannot make their own food). As stressed by Jeremy Rifkin: “the first economy of the world is photosynthesis”.

Hemacyanin is another molecule which is reform conveying oxygen in hemolymph, the blood of arthropods. An arthropod are members of the phylum Arthropoda (invertebrate animal with an exoskeleton, segmented body, and jointed appendages). Insects, arachnids, crustaceans are among this group. Hemacyanin has copper at his center. It is the metallic element at the center of these molecules that give their characteristic color.

Chlorophyll, hemoglobin, and hemocyanin are three fundamental molecules of life as we know in our planet. These molecules are needed since diffusion or plasma solubility in delivering oxygen is very ineffective, and higher organisms needed to evolve in building specific proteins to transport dioxygen in the blood. These substances are able to transport oxygen in the blood through acceptance of dioxygen from a surface in contact with air (lung) or water (gill), circulate to the tissues, delivering their needed oxygen. Of course, the carrier molecule must not be irreversibly oxidized by dioxygen, and transition metals, characterized by lower oxidation states that were used to accomplish this task. Otherwise, they would be lost for further purpose. However, these metallic elements are carried, involved in a structural protein casing that protects them against irreversible oxidation (in a way not entirely known).

Oxygen may be seen as the elixir of life…and death. The name “oxygen” was bequeathed by Antoine Lavoisier (1743-1794), the revolutionary scientist and political conservative beheaded in May 1794 during the French Revolution. The great mathematician Joseph-Louis Lagrange (1736-1813) regretted the decision of the Revolutionary Tribunal and said: “it took but a moment to cut off that head, though a hundred years perhaps will be required to produce another like it”.

Life on Earth starts with an anaerobic metabolism that still nowadays persist in the form of bacteria living in oxygen-poor environments. In the early earth, nearly all oxygen was bound in compounds, like water and silicate rocks. But nearly 3 billion years ago the “invention” in nature of plant photosynthesis turned the anaerobic world into our present type of environment with aerobic life. It is clear that the introduction of oxygen into the anaerobic world obliged the organisms existing at that time to adapt since a lot of the by-products of oxygen metabolism are toxic compounds. Oxygen was essential to retain on Earth much of the hydrogen, since our planet has a relatively small mass, and can easily lose free hydrogen to the cosmic space. Without binding to oxygen, nearly all hydrogen would be lost forever.

The atomic structure dictates what an element can do, what compounds it can form, and what properties it possess. The nucleus of the common isotope of oxygen contains eight protons and eight neutrons, and is designated by 16O. Quantum mechanics tells us that electrons are not located in the nucleus as “orbitals”, but as a “cloud”, a region of space where electrons are most likely to be.


Chlorophyll biosynthesis is a complex pathway with 17 highly specific steps, of which eight last steps are used by specific enzymes uniquely in this pathway.
The pathway must go all the way through, otherwise, chlorophyll is not synthesized.
Therefore, the Chlorophyll biosynthesis pathway is irreducibly complex.

What good would there be, if the pathway would go only up to the 15th step? none
What good would there be, if the pathway would go all the way through the 17th step? Chlorophyll would be produced, BUT:
What good for survival would there be for chlorophyll on its own, if not fully embedded in the photosynthesis process? none.
What good would there be for photosynthesis without chlorophyll in place, capturing light, and transmitting it to the photosystem? none, since capturing
light is essential for the whole process.

‘Why would evolution produce a series of enzymes that only generate useless intermediates until all of the enzymes needed for the end product have evolved?’

Five following conditions would all have to be met:

the issue about the observed origin of irreducible complexity, similarly, is not to be dismissed by saying that’s Behe’s argument. Have you had an empirically warranted answer to Menuge’s  C1 – 5 criteria for exaptation  (  a shift in the function of a trait during evolution. For example, a trait can evolve because it served one particular function, but subsequently it may come to serve another.). . . the usually attempted counter? If not, then the issue of irreducible complexity is very definitely still on the table. The criteria:

For a working biological system to be built, the five following conditions would all have to be met:

C1: Availability. Among the parts available for recruitment to form the system, there would need to be ones capable of performing the highly specialized tasks of individual parts, even though all of these items serve some other function or no function.

C2: Synchronization. The availability of these parts would have to be synchronized so that at some point, either individually or in combination, they are all available at the same time.

C3: Localization. The selected parts must all be made available at the same ‘construction site,’ perhaps not simultaneously but certainly at the time they are needed.

C4: Coordination. The parts must be coordinated in just the right way: even if all of the parts of a system are available at the right time, it is clear that the majority of ways of assembling them will be non-functional or irrelevant.

C5: Interface compatibility. The parts must be mutually compatible, that is, ‘well-matched’ and capable of properly ‘interacting’: even if subsystems or parts are put together in the right order, they also need to interface correctly.

( Agents Under Fire: Materialism and the Rationality of Science, pgs. 104-105 (Rowman & Littlefield, 2004). HT: ENV.)


Let's have a look about the BEST explanation that proponents of natural mechanisms can come up with:

Blankenship: Molecular mechanisms of photosynthesis pg.208:

It is not conceivable that highly complex molecules such as chlorophylls were synthesized by prebiotic chemistry, given their very specific functional groups and multiple chiral centers. Instead, they are the end product of a progressive evolutionary development, in which simple molecules are the start of the biosynthesis chain and are then progressively elaborated in later steps. In this view, each intermediate in the modern pathway was at some point the end point in the pathway. This requires that each intermediate in the modern pathway be usable in the past as an end product. In the case of chlorophyll biosynthesis, Granick proposed that simple porphyrins or porphyrin precursors were the starting points and that successive steps were added to improve the efficiency of the pigments or to extend light absorption into new spectral ranges. This is an appealing idea and is probably at least partially true. The Granick hypothesis in the context of photosynthesis has been championed by Mauzerall (1992), as well as embraced by others (Olson and Pierson, 1987; Olson, 1999, 2006).

This is about the best explanation that proponents of naturalistic origins can come up with. All it exemplifies is baseless just so assertions in a superficial manner. Pseudo science at its best. It should be clear to any honest thinker that there is a huge gap of explanatory power between proponents of naturalism, and design.

Resumed: For the assembly of a biological system of multiple parts, following steps must be explained: the origin of the genome information to produce all subunits and assembly cofactors. Parts availability, synchronization, manufacturing and assembly coordination through genetic information, and interface compatibility. The individual parts must precisely fit together. All these steps are better explained through a super intelligent and powerful designer, rather than mindless natural processes by chance, or/and evolution since we observe all the time minds capabilities producing machines and factories, producing machines and end products.

everything *has* to be in place at once or else an organism has no survival advantage. The thing is, there's no driver for any of the pieces to evolve individually because single parts confer no advantage in and of themselves. The necessity for the parts of the system to be in place all at once is simply evidence of creation. Photosynthesis missing one piece (like chlorophylls) is like a car missing just one piece of the drive train (such as a differential); it's not that it doesn't function as well - it doesn't function at all!

Outline of chlorophyll a biosynthesis from glutamate. The enzymes that catalyze the individual numbered reactions are

(1) glutamyl-tRNA synthetase;
(2) glutamyl-tRNA reductase;
(3) glutamate 1-semialdehyde aminotransferase;
(4) porphobilinogen synthase;
(5) hydroxymethylbilane synthase;
(6) uroporphyrinogen III synthase;
(7) uroporphyrinogen III decarboxylase;
(8 )coproporphyrinogen III oxidative decarboxylase;
(9) protoporphyrinogen
IX oxidase;

following are the last eight steps :

(10) protoporphyrin IX Mg-chelatase;

http://www.genome.jp/dbget-bin/www_bget? ec:6.6.1.1
[th]Pathway[/th]
ec00860  Porphyrin and chlorophyll metabolism
ec01100  Metabolic pathways
ec01110  Biosynthesis of secondary metabolites
(11) S-adenosyl-L-methionine:Mg-protoporphyrin IX methyltransferase;

http://www.genome.jp/dbget-bin/www_bget?ec:2.1.1.11
[th]Pathway[/th]
ec00860  Porphyrin and chlorophyll metabolism
ec01100  Metabolic pathways
ec01110  Biosynthesis of secondary metabolites
(12)–(14) Mg-protoporphyrin IX monomethyl ester oxidative cyclase;

http://www.genome.jp/dbget-bin/www_bget?ec:1.14.13.81
[th]Pathway[/th]
ec00860  Porphyrin and chlorophyll metabolism
ec01100  Metabolic pathways
ec01110  Biosynthesis of secondary metabolites
(15) divinyl (proto)chlorophyllide 4-vinyl reductase;

http://www.genome.jp/dbget-bin/www_bget?ec:1.3.1.75
[th]Pathway[/th]
ec00860  Porphyrin and chlorophyll metabolism
ec01100  Metabolic pathways
ec01110  Biosynthesis of secondary metabolites
(16) light-dependent NADPH:protochlorophyllide oxidoreductase or light-independent protochlorophyllide reductase;

http://www.genome.jp/dbget-bin/www_bget?ec:1.3.7.7
[th]Pathway[/th]
ec00860  Porphyrin and chlorophyll metabolism
ec01100  Metabolic pathways
ec01110  Biosynthesis of secondary metabolites
(17) chlorophyll synthase.

http://www.genome.jp/dbget-bin/www_bget?ec:2.5.1.62
[th]Pathway[/th]
ec00860  Porphyrin and chlorophyll metabolism
ec01100  Metabolic pathways
ec01110  Biosynthesis of secondary metabolites
The assembly of chlorophyll takes seventeen enzymes. 1 
Natural selection could not operate to favor a system with anything less than all seventeen being present and functioning. What evolutionary process could possibly produce complex sophisticated enzymes that generate nothing useful until the whole process is complete? Some proponents of evolution argue that the assumed primeval organic soup had many of the simpler chemicals and that only as they were used up did it become necessary to generate the earlier enzymes in the pathway. InThe Mystery of Life’s Origin: Reassessing Current Theories, the authors set forth the good basic chemistry that demonstrates that there could never have been an organic soup, and present some of the evidence out there in the world indicating that there never was. Denton and Overman also cite a number of experts who suggest that there is no evidence for such a primitive soup but rather considerable evidence against it.

Chlorophyll itself,  and many of the intermediates along its pathway of synthesis can form triplet states, which would destroy surrounding lipids by a free radical cascade apart from the context of the enzymes that manufacture them and the apoproteins into which they are inserted at the conclusion of their synthesis. According to Asada  ‘triplet excited pigments are physiologically equivalent to the active oxygens’, and according to Sandmann and Scheer, chlorophyll triplets ‘are already highly toxic by themselves … .’The entire process of chlorophyll synthesis from δ-aminolevulinic acid to protoporphyrin IX is apparently tightly coupled to avoid leakage of intermediates. Almost all of the enzymes of chlorophyll biosynthesis are involved in handling phototoxic material. For many of these enzymes, if they are not there when their substrate is manufactured, the cell will be destroyed by their substrate on the loose in the wrong place at the wrong time. Apel has cited four of the enzymes of chlorophyll biosynthesis for which this has been proven to be the case. This is a significant problem for evolutionists, who need time for these enzymes to evolve successively. Each time a new enzyme evolved it would have produced a new phototoxin until the next enzyme evolved.

Triplet state chlorophyll, generated in the reaction centres when singlet (excited state) chlorophyll cannot get rid of its energy quickly enough, as may be the case when excess photon energy is coming in, lasts long enough to generate very damaging singlet oxygen (1O2), which attacks lipids, proteins, chlorophyll and DNA.Evolutionists maintain that ground-state oxygen (3O2, a triplet state biradical) was not around when photosynthesis evolved. There is, however, considerable evidence that there has never been a time in Earth’s history when there was not significant free oxygen in the atmosphere (see Dimroth and Kimberley, Thaxton, Bradley and Olsen, Overman and Pannenberg,34 Denton). The evolutionists’ own analyses suggest that the last common ancestor for the bacteria and archaea already had sophisticated enzyme systems for using O2 and for disarming its reactive by-products. Since these organisms had already evolved by 3.5 Ga, on the evolutionists’ timescale,37 this also suggests something rather ominous for the absence of oxygen theory.

In the system that presently exists, a sophisticated complex of enzymes and pigments quenches the excess energy and scavenges the dangerous oxygen species generated by excess light. CuZn superoxide dismutase (in most higher plants) converts superoxide (O2-), the primary product of photoreduction of dioxygen in PSI, to H2O2 in the highest-known diffusion-controlled rate among enzymatic reactions. It appears that about one molecule of superoxide dismutase attaches to the surface of the membrane in the vicinity of the PSI complex, along with ascorbate peroxidase (APX). Ascorbate reduces the H2O2 generated, in a reaction catalyzed by APX. The product of this reaction, the monodehydroascorbate radical, is reduced again to ascorbate by photoreduced ferredoxin (Fd) in PSI.The enzymes and other reducing species of this system could not evolve gradually and then microcompartmentalize over time because nothing works unless everything is in place. This means that the first appearance of oxygen would have been lethal to the cell, whether the source of oxygen was biological or non-biological. Enzymes such as superoxide dismutase would not have been able to evolve at all. APX, for example, has only about 31–33% homology with cytochrome c peroxidase, from which it is thought to have evolved.Cells without these enzymes exposed to ground-state oxygen would simply have been destroyed before hundreds of base pair changes generated the enzymes from something else.

Natural selection is not evolution’s friend. In answer to the question, ‘Why would evolution produce a series of enzymes that only generate useless intermediates until all of the enzymes needed for the end product have evolved?’

The question, ‘Why and how would evolution go about trying to produce a protein for binding pigment molecules before pigment molecules existed?’ is another major challenge for proponents of evolution.

If chlorophyll evolved before the antenna proteins that bind it, it would in all likelihood destroy the cell, so the proteins had to evolve first. But natural selection could not favor a ‘newly evolved’ protein which could bind chlorophyll and other pigment molecules before those crucial pigments had themselves come into existence! Each binding site must be engineered to bind chlorophyll an or chlorophyll b only or carotene only. The carotene molecules must be present in just the right places for quenching triplet states in the chlorophylls. Even if the pigment molecules were already around, producing just the right protein would be an extremely difficult task. It would not only have to bind pigment molecules only, but it would need to bind just the right pigments in just the right places in just the right orientation so that energy could be transferred perfectly between them, with a little lower energy at each step. Anything else would do nothing or would transfer energy at random, and the complex would accomplish nothing at best and burn up the cell at worst.

And there is another problem for evolution. The insertion of the pigment molecules changes the conformation of the apoprotein from about 20% to about 60% α-helical content. So evolution would have to produce a protein with a wrong shape that would assume just the right shape by the insertion of pigment molecules in just the right positions and orientations when those pigment molecules had not yet evolved.

The energy transfer timeframe between pigment molecules in the antenna complex is between 10-15 and 10-9seconds. The system that God engineered captures 95–99% of the photon energy for photochemistry, even though there are four other ways the energy can be lost during the slightly less than a billionth of a second the system has for capturing it. Humans certainly cannot begin to design systems with such efficiency, but the evolutionists are determined that chance, what Cairns-Smith calls ‘old fumble fingers’, can.

Our understanding of the assembly of apoproteins with their pigments is very poor, but we do know that the chloroplast encoded chlorophyll a binding proteins of PSI and PSII core complexes are inserted cotranslationally into the thylakoid. Protein intermediates of the D1 protein have been observed due to ribosome pausing. It may be that this ribosome pausing permits cotranslational binding of chlorophyll a to the protein. This kind of controlled insertion, with synthesis of otherwise phototoxic material, is precisely what we would expect from intelligent planning and forethought, but how might ‘old fumble fingers’ hit on such a scheme?

Chlorophyll biosynthesis is a complex pathway with 17 highly specific steps, of which eight last steps are used by specific enzymes uniquely in this pathway.

Even if we find in the sequence space the right steps to make the enzymes required to permit the synthesis of the products of these intermediate steps, so what ? the intermediate products would have no function, and no survival advantage of the organism would be provided. Natural selection could not operate to favor a system with anything less than all seventeen enzymes being present, functioning and processing all intermediate products to get the final product. What evolutionary process could possibly produce complex sophisticated enzymes that generate nothing useful until the whole process is complete? And even if everything were in place correctly, and chlorophyll were synthesized correctly, so what ? Unless chlorophyll AND all other proteins and protein complexes were fully in place, fully evolved and functional, correctly interlocked and working in an interdependent manner, photosynthesis would not happen. But even if photosynthesis would happen, so what? Why would the organism choose such an extremely complex mechanism, if it was surviving just fine previously? Furthermore, you do not just need the right enzymes. For the assembly of a biological system of multiple parts, following steps must be explained: the origin of the genome information to produce all subunits and assembly cofactors. Parts availability, synchronization, manufacturing and assembly coordination through genetic information, and interface compatibility. The individual parts must precisely fit together. All these steps are better explained through a super intelligent and powerful designer, rather than mindless natural processes by chance, or/and evolution since we observe all the time minds capabilities producing machines and factories, producing machines and end products.

everything *has* to be in place at once or else an organism has no survival advantage. The thing is, there’s no driver for any of the pieces to evolve individually because single parts confer no advantage in and of themselves. The necessity for the parts of the system to be in place all at once is simply evidence of creation. Photosynthesis missing one piece (like chlorophylls) is like a car missing just one piece of the drive train (such as a differential); it’s not that it doesn’t function as well – it doesn’t function at all!


[th][/th]





Chlorophylls absorb photons by means of an excitation process analogous to the photoelectric effect. These pigments contain a complex ring structure, called a porphyrin ring, with alternating single and double bonds. At the center of the ring is a magnesium atom. Photons absorbed by the pigment molecule excite electrons in the ring, which are then channeled away through the alternating carbon-bond system. Several small side groups attached to the outside of the ring alter the absorption properties of the molecule in different kinds of chlorophyll . Chlorophyll absorbs in only two narrow bands, but does so with high efficiency. Therefore, plants and most other photosynthetic organisms achieve far higher overall photon capture rates with chlorophyll than with other pigments. 9


When Molecules Absorb or Emit Light,They Change Their Electronic State 10
Chlorophyll appears green to our eyes because it absorbs light mainly in the red and blue parts of the spectrum, so only some of the light enriched in green wavelengths (about 550 nm) is reflected into our eyes (see Figure 7.3).
The absorption of light is represented by Equation 7.3, in which chlorophyll (Chl) in its lowest-energy, or ground, state absorbs a photon (represented by hn) and makes a transition to a higher-energy, or excited, state (Chl*):

Chl + hn → Chl*


The distribution of electrons in the excited molecule is somewhat different from the distribution in the groundstate molecule (Figure 7.5)



The excited molecule, such as chlorophyll (X1 ), transfers the excitation energy by resonance to an adjacent chlorophyll molecule (X2 ) and returns to its ground state.

Light in the visible range is absorbed by the electrons of the molecule, i.e., the photon energy is used to promote the electrons from their ground state to a higher energy level. 6 The photon promotes one electron to a higher energy level, leaving a defect electron (hole) in the lower level. Often, electron and hole are described as a pair of charged particles that attract each other. This bound electron–hole pair is the exciton that stores the photon energy. As the electron and the hole are located on the same molecule, the distance between the two is confined to roughly the diameter of the molecule.  What is transferred is the "excited electron and the hole". We shall call this entity an "exciton". Thus, we can talk about exciton transfer. 8 We shall deal here with energy transfer between different pigments ("heterogeneous" transfer), as well as with transfer between identical molecules ("homogeneous" transfer). The latter can be repeated many times, giving rise to energy migration.

The calculated (and actually observed) "critical distances" over which the transfer probability equals 50%, are of the order of 5 nm. In a chloroplast, the distance between different pigment molecules much less than 5 nm, so that the probability of energy transfer must be quite high. The shorter the distance between pigment molecules involved in the transfer of excitation energy, the greater the probability that it will be transferred.

The crucial question is: How can a Frenkel exciton move in a pigment protein 
complexes ( PPC )? To answer this question, we have to consider the electron-electron interaction between two adjacent dye molecules. Let us call one of these molecules the donor D and the other the acceptor A.


Absorption of blue light excites the chlorophyll to a higher energy state than absorption of red light because the energy of photons is higher when their wavelength is shorter. In the higher excited state, chlorophyll is extremely unstable, very rapidly gives up some of its energy to the surroundings as heat, and enters the lowest excited state, where it can be stable for a maximum of several nanoseconds (10–9 s). Because of this inherent instability of the excited state, any process that captures its energy must be extremely rapid. In the lowest excited state, the excited chlorophyll has four alternative pathways for disposing of its available energy.

1. Excited chlorophyll can re-emit a photon and thereby return to its ground state—a process known as fluorescence. When it does so, the wavelength of fluorescence is slightly longer (and of lower energy) than the wavelength of absorption because a portion of the excitation energy is converted into heat before the fluorescent photon is emitted. Chlorophylls fluoresce in the red region of the spectrum.
2. The excited chlorophyll can return to its ground state by directly converting its excitation energy into heat, with no emission of a photon.
3. Chlorophyll may participate in energy transfer, during which an excited chlorophyll transfers its energy to another molecule.
4. A fourth process is photochemistry, in which the energy of the excited state causes chemical reactions to occur. The photochemical reactions of photosynthesis are among the fastest known chemical reactions. This extreme speed is necessary for photochemistry to compete with the three other possible reactions of the excited state just described.

Photosynthetic Pigments Absorb the Light That Powers Photosynthesis
The energy of sunlight is first absorbed by the pigments of the plant. All pigments active in photosynthesis are found in the chloroplast. Structures and absorption spectra of several photosynthetic pigments are shown in Figures 7.6 and 7.7, respectively.


FIGURE 7.6 Molecular structure of some photosynthetic pigments. 
(A) The chlorophylls have a porphyrin-like ring structure with a magnesium atom (Mg) coordinated in the center and a long hydrophobic hydrocarbon tail that anchors them in the photosynthetic membrane. The porphyrin-like ring is the site of the electron rearrangements that occur when the chlorophyll is excited and of the unpaired electrons when it is either oxidized or reduced. Various chlorophylls differ chiefly in the substituents around the rings and the pattern of double bonds. 
(B) Carotenoids are linear polyenes that serve as both antenna pigments and photoprotective agents. 
(C) Bilin pigments are open-chain tetrapyrroles found in antenna structures known as phycobilisomes that occur in cyanobacteria and red algae.



9


Absorption Spectra and Pigments

How does a molecule “capture” the energy of light? A photon can be envisioned as a very fast-moving packet of energy. When it strikes a molecule, its energy is either lost as heat or absorbed by the electrons of the molecule, boosting those electrons into higher energy levels. Whether or not the photon’s energy is absorbed depends on how much energy it carries (defined by its wavelength) and on the chemical nature of the molecule it hits. Electrons occupy discrete energy levels in their orbits around atomic nuclei. To boost an electron into a different energy level requires just the right amount of energy, just as reaching the next rung on a ladder requires you to raise your foot just the right distance. A specific atom can, therefore, absorb only certain photons of light—namely, those that correspond to the atom’s available electron energy levels. As a result, each molecule has a characteristic absorption spectrum, the range and efficiency of photons it is capable of absorbing. Molecules that are good absorbers of light in the visible range are called pigments. Organisms have  a variety of different pigments, but there are only two general types used in green plant photosynthesis: carotenoids and chlorophylls. Chlorophylls absorb photons within narrow energy ranges. Two kinds of chlorophyll in plants, chlorophylls a and b, preferentially absorb violet-blue and red light (figure 10.5). Neither of these pigments absorbs photons with wavelengths between about 500 and 600 nanometers, and light of these wavelengths is, therefore, reflected by plants. When these photons are subsequently absorbed by the pigment in our eyes, we perceive them as green. Chlorophyll a is the main photosynthetic pigment and is the only pigment that can act directly to convert light energy to chemical energy. However, chlorophyll b, acting as an accessory or secondary light-absorbing pigment, complements and adds to the light absorption of chlorophyll a. Chlorophyll b has an absorption spectrum shifted toward the green wavelengths. Therefore, chlorophyll b can absorb photons chlorophyll a cannot. Chlorophyll b therefore greatly increases the proportion of the photons in sunlight that plants can harvest. An important group of accessory pigments, the carotenoids, assist in photosynthesis by capturing energy from light of wavelengths that are not efficiently absorbed by either chlorophyll.

Chlorophylls and Carotenoids


Chlorophylls absorb photons by means of an excitation process analogous to the photoelectric effect. These pigments contain a complex ring structure, called a porphyrin ring, with alternating single and double bonds. At the center of the ring is a magnesium atom. Photons absorbed by the pigment molecule excite electrons in the ring, which are then channeled away through the alternating carbon-bond system. Several small side groups attached to the outside of the ring alter the absorption properties of the molecule in different kinds of chlorophyll (figure 10.6).



The precise absorption spectrum is also influenced by the local microenvironment created by the association of chlorophyll with specific proteins.  It is reasonable to ask why these photosynthetic organisms do not use a pigment like retinal (the pigment in our eyes), which has a broad absorption spectrum that covers the range of 500 to 600 nanometers. The most likely hypothesis involves photoefficiency. Although retinal absorbs a broad range of wavelengths, it does so with relatively low efficiency. Chlorophyll, in contrast, absorbs in only two narrow bands, but does so with high efficiency. Therefore, plants and most other photosynthetic organisms achieve far higher overall photon capture rates with chlorophyll than with other pigments.



1) https://answersingenesis.org/evidence-against-evolution/shining-light-on-the-evolution-of-photosynthesis/
2) http://www.synarchive.com/syn/24
3. http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.94.171&rep=rep1&type=pdf
4. https://creation.com/shining-light-on-the-evolution-of-photosynthesis
5. https://br.answers.yahoo.com/question/index?qid=20120702140557AAfDaJu
6. The Biophysics of Photosynthesis, page 8
7. http://www.life.illinois.edu/govindjee/biochem494/foerster.htm
8. Chlorophyll Fluorescence Understanding Crop Performance— Basics and Applications, page 8
9. http://www.mhhe.com/biosci/genbio/raven6b/graphics/raven06b/other/raven06b_10.pdf
10. Plant Physiology, 3rd ed by Lincoln Taiz and Eduardo Zeiger, page 11
11. https://uncommondescent.com/intelligent-design/is-photosynthesis-irreducibly-complex/#more-2255



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Light absorption excites the chlorophyll molecule

What happens when a chromophore absorbs a photon? What is a Chromophore?
When a photon with a certain wavelength hits a chromophore molecule that absorbs light of this wavelength, the energy of the photon excites electrons and transfers them to a higher energy level. This occurs as an “all or nothing” process. According to the principle of energy conservation expressed by the first law of thermodynamics, the energy of the chromophore is increased by the energy of the photon, which results in an excited state of the chromophore molecule. The energy is absorbed only in discrete quanta, resulting in discrete excitation states.

A sequence of alternating double and single bonds in rings, which form a system of conjugated bonds, is responsible for light absorption. The phytol chain is not involved in light absorption, but it anchors the chlorophyll molecule in the thylakoid membrane and provides it with the right orientation. Differences in the structure of these pigments result in certain variations in their absorption spectra. All chlorophylls absorb radiation within the wavelength region
of 400– 720 nm and have two main absorption bands: one in the blue range (higher excitation level) and the other in the red range (lower excitation level). In solutions of organic solvents, chlorophyll a shows maximum absorption at the wavelengths of around 420 and 660 nm, while chlorophyll b has absorption peaks at 435 and 642 nm

The energy required to excite a chromophore molecule depends on the chromophore structure. A general property of chromophores is that they contain many conjugated double bonds, 10 in the case of the tetrapyrrole ring of chlorophyll -a. These double bonds are delocalized. Figure 2.5 shows two possible resonance forms. After absorption of energy, an electron of the conjugated system is elevated to a higher orbit. This excitation state is termed singlet. Figure 2.6 shows a scheme of the excitation process. As a rule, the higher the number of double bonds in the conjugated system, the lower the amount of energy required to produce a first singlet state. For the excitation of chlorophyll, dark red light is sufficient, whereas butadiene, with only two conjugated double bonds, requires energy-rich ultraviolet light for excitation. The light absorption of the conjugated system of the tetrapyrrole ring is influenced by the side chains. Thus, the differences in the absorption maxima of chl-a and chl-b mentioned previously can be explained by an electron attracting effect of the carbonyl side chain in ring b of chl-b (Fig. 2.5). maxima in the spectra are relatively broad. At a higher resolution the spectra can be shown to consist of many separate absorption lines. This fine structure of the absorption spectra is due to chlorophyll molecules that are in the ground and in the singlet states as well in rotation and vibration. In the energy scheme the various rotation and vibration energy levels are drawn as fine lines and the corresponding ground states as solid lines (Fig. 2.6).

The spectra of chl-a and chl-b (Fig. 2.3) each have two main absorption maxima, showing that each chlorophyll has two main excitation states. 



The two main excitation states of chlorophyll are known as the first and second singlet (Fig. 2.6). The absorption maxima in the spectra are relatively broad. At a higher resolution the spectra can be shown to consist of many separate absorption lines. This fine structure of the absorption spectra is due to chlorophyll molecules that are in the ground and in the singlet states as well in rotation and vibration. In the energy scheme the various rotation and vibration energy levels are drawn as fine lines and the corresponding ground states as solid lines (Fig. 2.6).The energy levels of the various rotation and vibration states of the ground state overlap with the lowest energy levels of the first singlet.





After absorption of energy, an electron of the conjugated system is elevated to a higher orbit. This excitation state is termed singlet. Figure 2.6 shows a scheme of the excitation process.





Analogously, the energy levels of the first and the second singlet also overlap. If a chlorophyll molecule absorbs light in the region of its absorption maximum (blue light), one of its electrons is elevated to the second singlet state. This second singlet state with a half-life of only 10^12 s is too unstable to use its energy for chemical work. The excited molecules lose energy as heat by rotations and vibrations until the first singlet state is reached. This first singlet state can also be attained by absorption of a photon of red light, which contains less energy. The first singlet state is much more stable than the second one; its half-life time is 4 · 10^9 s. The return of the chlorophyll molecule from the first singlet state to the ground state can proceed in different ways:

1. The most important path for the conversion of the energy released upon the return of the first singlet state to the ground state is its utilization for chemical work. The chlorophyll molecule transfers the excited electron from the first singlet state to an electron acceptor and a positively charged chlorophyll radical chl• + remains. This is possible since the excited electron is bound less strongly to the chromophore molecule than in the ground state. When the chlorophyll molecule returns to the ground state, the free energy derived from this process is conserved for chemical work. As an alternative, the electron deficit in the chl• +  radical may be replenished by another electron donor (e.g., water )

2. The excited chlorophyll can return to the ground state by releasing excitation energy as light; this emitted light is named fluorescence. Due to vibrations and rotations, part of the excitation energy is usually lost as heat, with the result that the fluorescence light has less energy (corresponding to a longer wavelength) than the energy of the excitation light, which was required for attaining the first singlet state.

3. It is also possible that the return from the first singlet to the ground state proceeds in a stepwise fashion via the various levels of vibration and rotation energy, by which the energy difference is completely converted into heat.

4. By releasing part of the excitation energy as heat, the chlorophyll molecule can attain a lower energy excitation state, called the first triplet state. This triplet state cannot be reached directly from the ground state by excitation, since the spin of the excited electrons has been reversed. Since the probability of a reversal spin is low, the triplet state does not occur frequently. In the case of a very high excitation, however, some of the electrons of the chlorophyll molecules can reach this state. By emitting so-called phosphorescent light, the molecule can return from the triplet state to the ground state. Phosphorescent light is lower in energy than the light required to attain the first singlet state. The return from the triplet state to the ground state requires a reversal of the electron spin. As this is rather improbable, the triplet state, in comparison to the first singlet state, has a relatively long half-life time (10-4 to 10-2 s). The triplet state of the chlorophyll has no function in photosynthesis per se. In its triplet state, however, the chlorophyll can excite oxygen to a singlet state, whereby the oxygen becomes very reactive with a damaging effect on cell constituents.

5. The return to the ground state can be coupled with the excitation of a neighboring chromophore molecule. This transfer is important for the function of the antennae and will be described in the following section.

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

We know now that several hundred pigments are associated with each reaction center and that each reaction center must operate four times to produce one molecule of oxygen—hence the value of 2500 chlorophylls per O2.



Light absorbed by chlorophyll excites the electrons in the ring as shown above. Light energy is captured by pigment molecules in the antenna complexes when photons strike electrons in their conjugated double bonds (alternating single and double bonds). 4 

Pigments have an alternating arrangement of single and double bonds in the molecule, these are conjugated bonds that share electrons. Pigments conjugated bonds share electrons in pi orbitals across the whole structure. 
Conjugated Bond length determines wavelength to be absorbed -  The specific wavelength of light that can be absorbed is determined by the number and structure of conjugated bonds in the pigment molecule.  Chlorophyll's conjugated bonds are found in the porphyrin ring, made up of a cyclic tetrapyrrole, that chelates Mg, and in the conjugated side chain that forms a long hydrocarbon tail to the heme ring. Electrons move readily along a conjugated bond series like they do in copper wire. Some photon has a wavelength that fits with the pigment's electrons resonating among its molecular bonds. 
When a photon of just the right amount of energy strikes an electron resonating in the array pigments, the electron can absorb the photon and get promoted to a higher quantum level. The photon must have just the exact amount of energy to boost the electron from its current level to its new level or it cannot be absorbed. If the incoming photon is just right to promote an electron, in that pigment, the newly energized electron resonates along the bonds at the higher energy level where it can pass to the reaction center from the array. 
The pigments are cradled by proteins to make sure they are placed and ranked to function together to collect sunlight with minimal damage. Photosystems have the accessory pigments in the larger outer antenna array and the primary photosynthetic pigment chlorophyll in the reaction center, all supported by proteins. The photosystem array is made up of the core proteins surrounded by the peripheral proteins, which anchor and support the pigments to allow electrons to flow. 
The antenna array has light-harvesting pigment complexes that usually contain three xanthophyll molecules, two luteins and one neoxanthin, and nearly equal amounts of Chlorophyll a and Chlorophyll b. Antenna pigments capture many wavelengths to increase the electron flow passed to the reaction center. 
Core proteins bind or cradle the reaction center pigments, the critical chlorophyll a dimer and carotenoids. 
Plant cells use what we call quantum entanglement between electrons so they have a nearly 100% efficiency in harvesting solar energy from the captured photons. 
Quantum entanglement between a pair of electrons shows that any change to one electron is an instantly synched change in the other, no matter how far apart they might be. Though physically separated, the two particles act as a single entity. 
This entanglements may exist across the plants entire light havesting photoreaction array of pigments the pant uses for light collection. This outer antenna must then pass the energy inwards to the reaction center's paired Chlorophyll A molecules and the photolysis center. 

The chlorophylls and bacteriochlorophylls (pigments found in certain bacteria) are the typical pigments of photosynthetic organisms, but all organisms contain a mixture of more than one kind of pigment, each serving a specific function. A long hydrocarbon tail is almost always attached to the ring structure. The tail anchors the chlorophyll to the hydrophobic portion of its environment. The ring structure contains some loosely bound electrons and is the part of the molecule involved in electron transitions and redox reactions.

Action Spectra Relate Light Absorption to Photosynthetic Activity
The use of action spectra has been central to the development of our current understanding of photosynthesis. An action spectrum depicts the magnitude of a response of a biological system to light, as a function of wavelength. For
example, an action spectrum for photosynthesis can be constructed from measurements of oxygen evolution at different wavelengths (Figure 7.8 )



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

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

We know now that several hundred pigments are associated with each reaction center and that each reaction center must operate four times to produce one molecule of oxygen—hence the value of 2500 chlorophylls per O2.

No chlorophyll pigments, no light is captured,  no photosynthesis, no advanced life. The origin and evolution of photosynthesis is considered to be the key to the origin of life. Cyanobacterias doing photosynthesis appeared very early , according to evolutionary timescale, about 3,5 bio years ago.

Chlorophylls are essential pigments for all photo-trophic organisms.  Chlorophyll biosynthesis is a complex pathway with 17 or more steps (Beale, 1999)  The enzymes in the last eight steps, from Protoporphyrin IX, to Chlorophyllide a, are unique and exclusively used in the Chlorophyll biosynthesis pathway. Unless the pathway goes all the way though, chlorophyll a is not produced, if you stop earlier, no function, no survival advantage..... The later steps include the insertion of magnesium and the elaboration of the ring system and its substituents. The earliest version of the pathway (and that used by most modern anoxygenic photosynthetic organisms) almost certainly was anaerobic, both not requiring and not tolerating the presence of O2. However, all modern oxygenic photosynthetic organisms now require O2 as an oxidant at several steps in the pathway. This has been explained in terms of gene replacement  ( why should evolution simply replace genes to do a different task ?? ) of the genes coding for the enzymes at these steps, with the result that the overall pathway is unchanged but the enzymes at key steps are completely different in different groups of phototrophs (Raymond and Blankenship, 2004)

So fantasious explanations as from Miller will not do it - co-opting parts from other biological systems. That  fairy tale pseudo scientific idea of borrowing, copying, modifying, and combining together preexisting parts operating in other biological systems, and assemble them to a chlorophyll molecule with a new function , perfectly ordered, with perfect fits, and new functions,with the help of saint time , how could that miracle be done ? Impossible.....

Robert Blankenship, molecular mechanics of photosynthesis , page 228
it is not conceivable that highly complex molecules such as chlorophylls were synthesized by prebiotic chemistry, given their very specific functional groups and multiple chiral centers.

but why after all, would chemoautotrophs evolve photosynthesis ? why should there have been a transition from anoxygenic, to oxygenic photosynthesis ? what adds difficulty , is, there are different types of light harvesting energy capturing systems, each one doing the same job, but in a very different way. Furthermore, for oxygenic photosynthesis, two reaction centers and photosystems are required. But 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 subunit.


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?


Chlorophyll biosynthesis
Protein involved in the synthesis of chlorophylls. These photosynthetic pigments are magnesium-porphyrin complexes with a long hydrophobic terpenoid side chain (the alcohol phytol). Angiosperms have only a light-dependent pathway for chlorophyll biosynthesis, other oxygenic organisms seem to have both the light-dependent and the light-independent pathways. Non-oxygenic organisms, which make bacteriochlorophyll, only have a light-independent pathway.

               


tetrapyrroles, (ii) formation of protoporphyrin IX





Chlorophyll a biosynthetic pathway utilizes a variety of enzymes.Genes code for the enzymes on the Mg-tetrapyrroles of both bacteriochlorophyll a and chlorophyll a. It begins with glutamic acid, which is transformed into a 5-aminolevulinic acid (ALA). Two molecules of ALA are then reduced to porphobilinogen (PBG), and four molecules of PBG are then coupled, forming protoporphyrin IX

When forming protoporphyrin, Mg-chelatase acts as a catalyst for the insertion of Mg into the chlorophyll a structure. The pathway then uses either a light-dependent process, driven by the enzyme protochlorophyllide oxidoreductase. Protochlorophyllide is a precursor to the production of a chlorophyll a molecule, or a light-independent process driven by other enzymes, to form a cyclic ring, and the reduction of another ring in the structure. Attachment of the phytol tail completes the process of chlorophyll biosynthesis.

Early Evolution of Photosynthesis1

Evolution of PHOTOSYNTHETIC PIGMENTS

Chlorophylls are essential pigments for all photo-trophic organisms. Chlorophylls are themselves the product of a long evolutionary development, and can possibly be used to help understand the evolution of other aspects of photosynthesis. Chlorophyll biosynthesis is a complex pathway with 17 or more steps (Beale, 1999). The early part of the pathway is identical to heme biosynthesis in almost all steps and has clearly been recruited ( how did it do this , and why should it ? ) from that older pathway. The later steps include the insertion of magnesium and the elaboration of the ring system and its substituents. The earliest version of the pathway (and that used by most modern anoxygenic photosynthetic organisms) almost certainly was anaerobic, both not requiring and not
tolerating the presence of O2. However, all modern oxygenic photosynthetic organisms now require O2 as an oxidant at several steps in the pathway. This has been explained in terms of gene replacement  ( why should evolution simply replace genes to do a different task ?? ) of the genes coding for the enzymes at these steps, with the result that the overall pathway is unchanged but the enzymes at key steps are completely different in different groups of phototrophs (Raymond and Blankenship, 2004)

that seems to me quit a ad hoc explanation, or maybe not a explanation, but a assertion without any evidence , just guesswork......

Shining Light on the Evolution of Photosynthesis

The assembly of chlorophyll takes seventeen enzymes.21 Natural selection could not operate to favour a system with anything less than all seventeen being present and functioning. What evolutionary process could possibly produce complex sophisticated enzymes that generate nothing useful until the whole process is complete? Some evolutionists argue that the assumed primeval organic soup had many of the simpler chemicals, and that only as they were used up did it become necessary to generate the earlier enzymes in the pathway. In The Mystery of Life’s Origin: Reassessing Current Theories, the authors set forth the good basic chemistry that demonstrates that there could never have been an organic soup, and present some of the evidence out there in the world indicating that there never was.22 Denton23 and Overman24 also cite a number of experts who suggest that there is no evidence for such a primitive soup but rather considerable evidence against it.

Chlorophyll itself, and many of the intermediates along its pathway of synthesis can form triplet states, which would destroy surrounding lipids by a free radical cascade apart from the context of the enzymes that manufacture them and the apoproteins into which they are inserted at the conclusion of their synthesis.25 According to Asada26 ‘triplet excited pigments are physiologically equivalent to the active oxygens’, and according to Sandmann and Scheer, chlorophyll triplets ‘are already highly toxic by themselves … .’27 The entire process of chlorophyll synthesis from δ-aminolevulinic acid to protoporphyrin IX is apparently tightly coupled to avoid leakage of intermediates.28 Almost all of the enzymes of chlorophyll biosynthesis are involved in handling phototoxic material.29 For many of these enzymes, if they are not there when their substrate is manufactured, the cell will be destroyed by their substrate on the loose in the wrong place at the wrong time. Apel30 has cited four of the enzymes of chlorophyll biosynthesis for which this has been proven to be the case. This is a significant problem for evolutionists, who need time for these enzymes to evolve successively. Each time a new enzyme evolved it would have produced a new phototoxin until the next enzyme evolved.

Tetrapyrrole biosynthesis

Tetrapyrroles are large macrocyclic compounds derived from a common biosynthetic pathway [PMID: 16564539]. The end-product, uroporphyrinogen III, is used to synthesise a number of important molecules, including vitamin B12, haem, sirohaem, chlorophyll, coenzyme F430 and phytochromobilin [PMID: 17227226].

   The first stage in tetrapyrrole synthesis is the synthesis of 5-aminoaevulinic acid ALA via two possible routes: (1) condensation of succinyl CoA and glycine (C4 pathway) using ALA synthase (EC:2.3.1.37), or (2) decarboxylation of glutamate (C5 pathway) via three different enzymes, glutamyl-tRNA synthetase (EC:6.1.1.17) to charge a tRNA with glutamate, glutamyl-tRNA reductase (EC:1.2.1.70) to reduce glutamyl-tRNA to glutamate-1-semialdehyde (GSA), and GSA aminotransferase (EC:5.4.3. 8 )to catalyse a transamination reaction to produce ALA.

   The second stage is to convert ALA to uroporphyrinogen III, the first macrocyclic tetrapyrrolic structure in the pathway. This is achieved by the action of three enzymes in one common pathway: porphobilinogen (PBG) synthase (or ALA dehydratase, EC:4.2.1.24) to condense two ALA molecules to generate porphobilinogen; hydroxymethylbilane synthase (or PBG deaminase, EC:2.5.1.61) to polymerise four PBG molecules into preuroporphyrinogen (tetrapyrrole structure); and uroporphyrinogen III synthase (EC:4.2.1.75) to link two pyrrole units together (rings A and D) to yield uroporphyrinogen III.

   Uroporphyrinogen III is the first branch point of the pathway. To synthesise cobalamin (vitamin B12), sirohaem, and coenzyme F430, uroporphyrinogen III needs to be converted into precorrin-2 by the action of uroporphyrinogen III methyltransferase (EC:2.1.1.107). To synthesise haem and chlorophyll, uroporphyrinogen III needs to be decarboxylated into coproporphyrinogen III by the action of uroporphyrinogen III decarboxylase (EC:4.1.1.37) [PMID: 11215515].

This entry represents 5-aminoaevulinic acid (ALA) synthase (EC:2.3.1.37), which catalyses the first stage of tetrapyrrole biosynthesis by the C4 pathway, namely the condensation of succinyl CoA and glycine. ALA synthase is a pyridoxal-phosphate-dependent enzyme. During catalysis, glycine initially binds to the enzyme cofactor, and after condensation with succinyl CoA, CoA, carbon dioxide and 5-aminolevulinic acid are produced [PMID: 11215515].


A model for tetrapyrrole synthesis as the primary mechanism for plastid-to-nucleus signaling during chloroplast biogenesis



Tetrapyrrole Metabolism



Porphyrin Biosynthesis (early stages)




Tetrapyrrole biosynthesis, glutamate-1-semialdehyde aminotransferase

The first stage in tetrapyrrole synthesis is the synthesis of 5-aminoaevulinic acid ALA via two possible routes:

1. condensation of succinyl CoA and glycine (C4 pathway) using ALA synthase (EC:2.3.1.37)

2. decarboxylation of glutamate (C5 pathway) via three different enzymes, glutamyl-tRNA synthetase (EC:6.1.1.17) to charge a tRNA with glutamate, glutamyl-tRNA reductase (EC:1.2.1.70) to reduce glutamyl-tRNA to glutamate-1-semialdehyde (GSA), and GSA aminotransferase (EC:5.4.3.8 )to catalyse a transamination reaction to produce ALA.


Porphyrin Biosynthesis (early stages)


Protoporphyrin IX Biosynthetic pathway




The first stage ( C5 Beale pathway ) :

The amino acid L-Glutamate is converted to Aminolevulinic acid (ALA) via three different enzymes:



 =>>     =>>


ALA is synthesized from glutamate (Glu) via the so-called C5 pathway consisting of three enzymatic steps as described below.

It happens in following steps :

Phase 1:

Glutamate—tRNA ligase  (EC:6.1.1.17)   catalyzes  L-Glutamate into  L-Glutamyl-tRNA(Glu)

Following the  chemical reaction:

The 3 substrates of this enzyme are


ATP, L-Glutamate, and L-Glutamyl-tRNA(Glu)

whereas its  3 products are

AMP, Diphosphate, and L-Glutamyl-tRNA(Glu)

_EC 6.1.1.17 Glutamate--tRNA ligase.





Phase 2:

V-shaped structure of glutamyl-tRNA reductase, the first enzyme of tRNA-dependent  tetrapyrrole biosynthesis



Phase 3:




Protoporphyrin IX Biosynthetic pathway



Tetrapyrrole biosynthesis, glutamate-1-semialdehyde aminotransferase

The second stage

5- aminolevulinic acid (ALA)   is converted to Uroporphyrinogen III (UROGEN), the first macrocyclic tetrapyrrolic structure in the pathway.

This is achieved by the action of three enzymes in one common pathway:





Phase 1:





Phase 2:





Phase 3:


EC 4.2.1.75 Uroporphyrinogen-III synthase. to link two pyrrole units together (rings A and D)to yield Uroporphyrinogen III

Following is the reaction :

Hydroxymethylbilane = Uroporphyrinogen III + Water H(2)O.

EC 4.2.1.75 Uroporphyrinogen-III synthase.



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3 Tetrapyrrole biosynthesis the third stage on Sat Mar 01, 2014 3:44 pm

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Porphyrin Biosynthesis (later stages)




The third stage

Uroporphyrinogen III (UROGEN) to Protoporphyrin IX (PROTO)

This is achieved by the action of following enzymes :


Phase 1:

Uroporphyrinogen III (UROGEN) is decarboxilated into Coproporphyrinogen III (COPROGEN) by the action of EC 4.1.1.37 Uroporphyrinogen decarboxylase (UROD)


Uroporphyrinogen III decarboxylase (UROD) is a chemical reaction that removes a carboxyl group and releases carbon dioxide (CO2). Usually, decarboxylation refers to a reaction of carboxylic acids, removing a carbon atom from a carbon chain. The reverse process, which is the first chemical step in photosynthesis, is called carboxylation, the addition of CO2 to a compound. Enzymes that catalyze decarboxylations are called decarboxylases or, the more formal term, carboxy-lyases (EC number 4.1.1).


Following is the reaction :

Uroporphyrinogen III (UROGEN) = Coproporphyrinogen III (COPROGEN) + 4 Water CO(2).

EC 4.1.1.37 Uroporphyrinogen decarboxylase (UROD)




Phase 2:

EC 1.3.3.3 Coproporphyrinogen oxidase (CPO) oxydates Coproporphyrinogen III (COPROGEN) into Protoporphyrinogen IX (PROTOOGEN)


Coproporphyrinogen III oxidase (CPO) is an enzyme involved in the sixth step of porphyrin metabolism it catalyses the oxidative decarboxylation of coproporphyrinogen III to proto-porphyrinogen IX in the haem and chlorophyll biosynthetic pathways.

Following is the reaction :

Coproporphyrinogen III (COPROGEN) + O(2) Oxygen + 2 H(+) hydrogen = Protoporphyrinogen IX (PROTOOGEN) + 2 CO(2) Carbon dioxyde + 2 H(2)O Water.

EC 1.3.3.3 Coproporphyrinogen oxidase (CPO)

Phase 3:

EC 1.3.3.4 Protoporphyrinogen oxidase. (PPO) removes Hydrogen atoms from Protoporphyrinogen IX (the product of the sixth step in the production of heme) to form Protoporphyrin IX .

Following is the reaction :

Protoporphyrinogen IX + 3 O(2) Oxygen = Protoporphyrin IX + 3 Hydrogen peroxide (H 2O 2)

EC 1.3.3.4 Protoporphyrinogen oxidase. (PPO)

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4 the fourth stage on Sat Mar 01, 2014 3:45 pm

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The fourth stage:


EC 6.6.1.1 Magnesium chelatase. (CHLD) is a three-component enzyme that catalyses the insertion of Mg2+ Magnesium into Protoporphyrinogen IX.

This is the first unique step in the synthesis of bacteriochlorophyll. As a result, it is thought that Mg-chelatase has an important role in channeling intermediates into the (bacterio)chlorophyll branch in response to conditions suitable for photosynthetic growth.

Following is the reaction :

ATP + Protoporphyrin IX + Mg2+ Magnesium into + H(2)O Water = adp + Phosphate + Mg-protoporphyrin IX + 2 H(+) Hydrogen

EC 6.6.1.1 Magnesium chelatase. (CHLD)
[/b]






EC 1.14.13.81 Magnesium-protoporphyrin IX monomethyl ester (oxidative) cyclase


Following is the reaction :

Magnesium-protoporphyrin IX 13-monomethyl ester + 3 NADPH + 3 Oxygen O(2) = Divinylprotochlorophyllide + 3 NADP(+) + 5 Water H(2)O (overall reaction)

(1a) magnesium-protoporphyrin IX 13-monomethyl ester + NADPH + H+ + O2 = 131-hydroxy-magnesium-protoporphyrin IX 13-monomethyl ester + NADP+ + H2O

(1b) 131-hydroxy-magnesium-protoporphyrin IX 13-monomethyl ester + NADPH + H+ + O2 = 131-oxo-magnesium-protoporphyrin IX 13-monomethyl ester + NADP+ + 2 H2O

(1c) 131-oxo-magnesium-protoporphyrin IX 13-monomethyl ester + NADPH + H+ + O2 = divinylprotochlorophyllide + NADP+ + 2 H2O



Requires Fe(II) Iron for activity.

EC 1.14.13.81 Magnesium-protoporphyrin Ix monomethyl ester (oxidative) cyclase (CRD1)

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5 the latest stage on Sat Mar 01, 2014 3:46 pm

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EC 1.3.1.33 Protochlorophyllide reductase (PRA) Catalyzes a light-dependent trans-reduction of the D-ring of protochlorophyllide; the product has the (7S,8S)-configuration.

This enzyme converts = Protochlorophyllide to Chlorophyllide a


Following is the reaction :

Chlorophyllide a + NADP(+) = Protochlorophyllide + NADPH.

EC 1.3.1.33 Protochlorophyllide reductase (PRA)



EC 1.3.1.75 Divinyl chlorophyllide a 8-vinyl-reductase catalyzes the conversion of divinyl chlorophyllide to monovinyl chlorophyllide. Reduces the 8-vinyl group of the tetrapyrrole to an ethyl group using NADPH as the reductant.

Following is the reaction :

Chlorophyllide a + NADP(+) = Divinyl chlorophyllide a + Nadph


EC 1.3.1.75 Divinyl chlorophyllide a 8-vinyl-reductase



_EC 2.5.1.62 Chlorophyll synthase ChlG
represents the strictly cyanobacterial and plant-specific chlorophyll synthase ChlG. ChlG is the enzyme (esterase) which attaches the side chain moiety onto chlorophyllide a. Both geranylgeranyl and phytyl pyrophosphates are substrates to varying degrees in enzymes from different sources [PMID: 12828371]. Thus, ChlG may act as the final or penultimate step in chlorophyll biosynthesis (along with the geranylgeranyl reductase, ChlP).

Following is the reaction :

Chlorophyllide a + Phytyl diphosphate = Chlorophyllide a + ADP; Adenosine 5'-diphosphate.


_EC 2.5.1.62 Chlorophyll synthase.

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Chlorophyll Biosynthesis in Bacteria: The Origins of Structural and Functional Diversity

http://www.annualreviews.org/doi/full/10.1146/annurev.micro.61.080706.093242


The use of photochemical reaction centers to convert light energy into chemical energy, chlorophototrophy, occurs in organisms belonging to only five eubacterial phyla: Cyanobacteria, Proteobacteria, Chlorobi, Chloroflexi, and Firmicutes. All chlorophototrophs synthesize two types of pigments: (a) chlorophylls and bacteriochlorophylls, which function in both light harvesting and uniquely in photochemistry; and (b) carotenoids, which function primarily as photoprotective pigments but can also participate in light harvesting. Although hundreds of carotenoids have been identified, only 12 types of chlorophylls (Chl a, b, d; divinyl-Chl a and b; and 81-hydroxy-Chl a) and bacteriochlorophylls (BChl a, b, c, d, e, and g) are currently known to occur in bacteria. This review summarizes recent progress in the identification of genes and enzymes in the biosynthetic pathways leading to Chls and BChls, the essential tetrapyrrole cofactors of photosynthesis, and addresses the mechanisms for generating functional diversity for solar energy capture and conversion in chlorophototrophs.

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http://www.ebi.ac.uk/interpro/entry/IPR004639

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2978374/

Protein complexes in chlorophyll biosynthetic enzymes

Chlorophyll Biosynthesis

In the first phase of chlorophyll biosynthesis, the amino acid glutamic acid is converted to 5-aminolevulinic acid (ALA) (Web Figure 7.11.A). This reaction is unusual in that it involves a covalent intermediate in which the glutamic acid is attached to a transfer RNA molecule. This is one of a very small number of examples in biochemistry in which a tRNA is utilized in a process other than protein synthesis. Two molecules of ALA are then condensed to form porphobilinogen (PBG), which ultimately form the pyrrole rings in chlorophyll. The next phase is the assembly of a porphyrin structure from four molecules of PBG. This phase consists of six distinct enzymatic steps, ending with the product protoporphyrin IX.




The biosynthetic pathway of chlorophyll. The pathway begins with glutamic acid, which is converted to 5-aminolevulinic acid (ALA). Two molecules of ALA are condensed to form porphobilinogen (PBG). Four PBG molecules are linked to form protoporphyrin IX. The magnesium (Mg) is then inserted, and the light-dependent cyclization of ring E, the reduction of ring D, and the attachment of the phytol tail complete the process. Many steps in the process are omitted in this figure.

All the biosynthesis steps up to this point are the same for the synthesis of both chlorophyll and heme (see textbook Figures 7.27 and 7.28). But here the pathway branches, and the fate of the molecule depends on which metal is inserted into the center of the porphyrin. If magnesium is inserted by an enzyme called magnesium chelatase, then the additional steps needed to convert the molecule into chlorophyll take place; if iron is inserted, the species ultimately becomes heme.

The next phase of the chlorophyll biosynthetic pathway is the formation of the fifth ring (ring E) by cyclization of one of the propionic acid side chains to form protochlorophyllide. The pathway involves the reduction of one of the double bonds in ring D, using NADPH. This process is driven by light in angiosperms and is carried out by an enzyme called protochlorophyllide oxidoreductase (POR). Non-oxygen-evolving photosynthetic bacteria carry out this reaction without light, using a completely different set of enzymes. Cyanobacteria, algae, lower plants, and gymnosperms contain both the light-dependent POR pathway and the light-independent pathway. Seedlings of angiosperms grown in complete darkness lack chlorophyll, because the POR enzyme requires light. These etiolated plants very rapidly turn green when exposed to light. The final step in the chlorophyll biosynthetic pathway is the attachment of the phytol tail, which is catalyzed by an enzyme called chlorophyll synthetase (Malkin and Nyogi 2000).

The elucidation of the biosynthetic pathways of chlorophylls and related pigments is a difficult task, in part because many of the enzymes are present in low abundance. Recently, genetic analysis has been used to clarify many aspects of these processes (Suzuki et al. 1997, Armstrong and Apel 1998).[/b]

In the first phase of chlorophyll biosynthesis, the amino acid glutamic acid is converted to 5-aminolevulinic acid (ALA) Web Figure 7.11.A

Proteins are found on the inside, in the membrane, on the surface and on the outside of cells. They form complicated structures and they interact with other molecules and proteins. Protein complexes and protein-protein interactions are challenging to investigate and in the beginning of protein research most studies were done with single proteins, often in water. Although, in vivo proteins rarely function alone.

To study protein complexes, two enzymes in the chlorophyll biosynthetic pathway were selected, Mg-chelatase in Rhodobacter capsulatus (bacteria) and the MPE cyclase complex in Hordeum vulgare (barley) and Arabidopsis thaliana (mouse- ear cress). Chlorophyll is a pigment formed through a complicated reaction path. Chlorophyll biosynthesis takes place in chlorophyll-producing organisms. The first committed step towards chlorophyll biosynthesis is performed by the enzyme complex Mg-chelatase. Mg-chelatase inserts a Mg2+ ion into the porphyrin substrate. The pathway is continued by a methyltransferase and thereafter the MPE cyclase complex which performs a complicated ring-closure in the porphyrin.


Mg-chelatase is composed of three proteins, BchI (40 kDa), BchD (60 kDa) and BchH (130 kDa). A cryo-electron microscopy model of the BchID complex (7.5 Å) revealed a two-tired hexameric ring structure with an arrangement of the subunits as a trimer of dimers. The transient full complex of Mg-chelatase, BchIDH, was chemically cross-linked and BchH was found to interact with the D- side of the BchID complex.

The MPE cyclase complex was more difficult to study and two of the three core components of the complex are still unknown. An interesting enzyme, NADPH- dependent thioredoxin reductase C (NTRC), was found to stimulate the MPE cyclase reaction together with a 2-Cys peroxiredoxin. NTRC was characterised further with regards to function and structure. The enzyme consists of a fusion between a NADPH-dependent thioredoxin reductase polypeptide and a thioredoxin polypeptide in the C-terminal. The three-dimensional structure of NTRC was determined with cryo-electron microscopy (10.0 Å) and revealed a tetramer.

1.3 What interactions hold a protein complex together?

What interactions (forces) hold a protein complex together? This is an important question to be asked. For a complex formation to even occur, it has to be energetically favourable. There are both intramolecular forces, acting within the protein, as well as intermolecular forces, between proteins in a complex. Some forces to be considered are hydrogen bonds, the hydrophobic effect, Coulombic interactions and van der Waals force


A hydrogen bond is an interaction between a hydrogen atom and an electronegative atom (oxygen, nitrogen, chloride or fluoride). The hydrogen atom needs also to be bound to another electronegative atom. Hydrogen bonds help proteins form their well-known organised secondary structure, helices and sheets. Hydrogen bonds are also creating tertiary and quaternary structure in a protein and between subunits in a protein complex. Another force, the hydrophobic effect, is important for protein folding and structure. For soluble proteins and protein complexes, the hydrophobic amino acids (alanine, valine, leucine, isoleucine, methionine, phenylalanine and tryptophan) have their side-chains pointing towards the core of the structure, to avoid the hydrophilic water solution and thereby stabilising the structure (McNaught and Wilkinson 1997).

Another type of interaction is electrostatic interaction between electrically charged particles, called Coulomb´s law. In Coulombic interactions, the acidic (aspartate and glutamate) or basic (lysine, arginine and histidine) amino acid residues are important. The pH of the solution will decide whether the residues will be charged or not and consequently they will interact according to Coulomb´s law. By adding salt to the solution, the high charge-charge interaction energy can be decreased (Baldwin 2007).

In van der Waals force, the attractions between molecules or surfaces are the sum of all attractive or repulsive forces between them, excluding covalent bonds and electrostatic interactions. The force is considered weak, compared to for example covalent bonds and hydrogen bonds but they are still very important for protein- protein interactions (McNaught and Wilkinson 1997).

1.4 Why form a protein complex?


Why do proteins form complexes? One can think of several answers to that question. The first obvious answer would be that more than one protein or subunit of a protein is needed to perform an enzymatic step or reaction. Therefore, to achieve a functional protein, a complex formation or oligomerization of the protein is needed.

Another reason to form a complex can be to facilitate a reaction pathway and a way of channeling a substrate between enzymes in a pathway. This is especially important in cases when the substrate is toxic to the cell or organism, as in the case with porphyrins (Eckhardt, Grimm et al. 2004). The substrate channeling then protects the cell from the toxic substance.

Some (soluble) proteins have a hydrophobic surface and cannot be stable unless in its oligomeric state, e.g. a ring structure forming a channel, so the hydrophobic parts of the protein are turned inwards the ring structure. Other proteins need a partner protein with which to form complex to be stable, that is to stay in its native form, at least in vitro as in the example of BchD of Mg-chelatase (Jensen, Gibson et al. 1999; Axelsson, Lundqvist et al. 2006).

Complex formation can also be due to regulation. As a way to regulate a reaction step or a pathway, proteins form high-molecular well-organized complexes, and therefore have a biological function (Trost, Fermani et al. 2006). Another benefit with forming a complex is achieving stability, for example with a metal ion to stabilize the structure of the complex. One example of such a structure is an iron-sulfur cluster (Meyer 2008). However, the reason why some proteins form high molecular mass complexes is still unknown.

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Post-translational control of tetrapyrrole biosynthesis in plants, algae, and cyanobacteria

Abstract

The tetrapyrrole biosynthetic pathway provides the vital cofactors and pigments for photoautotrophic growth (chlorophyll), several essential redox reactions in electron transport chains (haem), N- and S-assimilation (sirohaem), and photomorphogenic processes (phytochromobilin). While the biochemistry of the pathway is well understood and almost all genes encoding enzymes of tetrapyrrole biosynthesis have been identified in plants, the post-translational control and organization of the pathway remains to be clarified. Post-translational mechanisms controlling metabolic activities are of particular interest since tetrapyrrole biosynthesis needs adaptation to environmental challenges. This review surveys post-translational mechanisms that have been reported to modulate metabolic activities and organization of the tetrapyrrole biosynthesis pathway.

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Shining light on the evolution of photosynthesis

The assembly of chlorophyll takes seventeen enzymes.21 Natural selection could not operate to favour a system with anything less than all seventeen being present and functioning. What evolutionary process could possibly produce complex sophisticated enzymes that generate nothing useful until the whole process is complete? Some evolutionists argue that the assumed primeval organic soup had many of the simpler chemicals, and that only as they were used up did it become necessary to generate the earlier enzymes in the pathway. In The Mystery of Life’s Origin: Reassessing Current Theories, the authors set forth the good basic chemistry that demonstrates that there could never have been an organic soup, and present some of the evidence out there in the world indicating that there never was.22 Denton23 and Overman24 also cite a number of experts who suggest that there is no evidence for such a primitive soup but rather considerable evidence against it.

Chlorophyll itself, and many of the intermediates along its pathway of synthesis can form triplet states, which would destroy surrounding lipids by a free radical cascade apart from the context of the enzymes that manufacture them and the apoproteins into which they are inserted at the conclusion of their synthesis.25 According to Asada26 ‘triplet excited pigments are physiologically equivalent to the active oxygens’, and according to Sandmann and Scheer, chlorophyll triplets ‘are already highly toxic by themselves … .’27 The entire process of chlorophyll synthesis from δ–aminolevulinic acid to protoporphyrin IX is apparently tightly coupled to avoid leakage of intermediates.28 Almost all of the enzymes of chlorophyll biosynthesis are involved in handling phototoxic material.29 For many of these enzymes, if they are not there when their substrate is manufactured, the cell will be destroyed by their substrate on the loose in the wrong place at the wrong time. Apel30 has cited four of the enzymes of chlorophyll biosynthesis for which this has been proven to be the case. This is a significant problem for evolutionists, who need time for these enzymes to evolve successively. Each time a new enzyme evolved it would have produced a new phototoxin until the next enzyme evolved.

Triplet state chlorophyll, generated in the reaction centres when singlet (excited state) chlorophyll cannot get rid of its energy quickly enough, as may be the case when excess photon energy is coming in, lasts long enough to generate very damaging singlet oxygen (1O2), which attacks lipids, proteins, chlorophyll and DNA.31 Evolutionists maintain that ground-state oxygen (3O2, a triplet state biradical) was not around when photosynthesis evolved. There is, however, considerable evidence that there has never been a time in Earth’s history when there was not significant free oxygen in the atmosphere (see Dimroth and Kimberley,32 Thaxton, Bradley and Olsen,33 Overman and Pannenberg,34 Denton35). The evolutionists’ own analyses suggest that the last common ancestor for the bacteria and archaea already had sophisticated enzyme systems for using O2 and for disarming its reactive by-products.36 Since these organisms had already evolved by 3.5 Ga, on the evolutionists’ timescale,37 this also suggests something rather ominous for the absence of oxygen theory.

In the system that presently exists, a sophisticated complex of enzymes and pigments quenches the excess energy and scavenges the dangerous oxygen species generated by excess light. CuZn superoxide dismutase (in most higher plants) converts superoxide (O2–), the primary product of photoreduction of dioxygen in PSI,38 to H2O2 in the highest-known diffusion-controlled rate among enzymatic reactions.39 It appears that about one molecule of superoxide dismutase attaches to the surface of the membrane in the vicinity of the PSI complex, along with ascorbate peroxidase (APX). Ascorbate reduces the H2O2 generated, in a reaction catalyzed by APX. The product of this reaction, the monodehydroascorbate radical, is reduced again to ascorbate by photoreduced ferredoxin (Fd) in PSI.40 The enzymes and other reducing species of this system could not evolve gradually and then microcompartmentalize over time because nothing works unless everything is in place. This means that the first appearance of oxygen would have been lethal to the cell, whether the source of oxygen was biological or non-biological. Enzymes such as superoxide dismutase would not have been able to evolve at all. APX, for example, has only about 31–33% homology with cytochrome c peroxidase, from which it is thought to have evolved.41 Cells without these enzymes exposed to ground-state oxygen would simply have been destroyed before hundreds of base pair changes generated the enzymes from something else.

Natural selection is not evolution’s friend. In answer to the question, ‘Why would evolution produce a series of enzymes that only generate useless intermediates until all of the enzymes needed for the end product have evolved?’ the evolutionist might respond, ‘Why not?’ The ‘why not’ is in the maths.



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10 Early Evolution of Photosynthesis1 on Wed Mar 05, 2014 11:55 am

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Early Evolution of Photosynthesis1

However, all modern oxygenic photosynthetic organisms now require O2 as an oxidant at several steps in the pathway. This has been explained in terms of gene replacement of the genes coding for the enzymes at these steps, with the result that the overall pathway is unchanged but the enzymes at key steps are completely different in different groups of phototrophs (Raymond and Blankenship, 2004).

Gene replacement. Cool. So evolution selects to " replace " the genes and the job gets done. Amazing.....

But, why after all, would evolution produce a series of enzymes that only generate useless intermediates until all of the enzymes needed for the end product have evolved? Not only that: unless the whole photosynthesis apparatus is in place, Chlorophyll has no function. And where did it get the energy from, if the ATP Synthase motor ( another irreducible complex system ) was not in place, fully functioning? And how could it be fed with protons, if the thylakoid membrane was not fully formed? Photosynthesis is after all not only made of irreducibly complex systems, like the Photosystem I and II, Rubisco, etc. but the whole process is interdependent, that means, if one enzyme or protein complex is not in place, the whole process ceased to function. The only solution out of this is, that the whole system is made all together at once, with the full mechanism in place.


By tinkering with the chlorophyll molecule, evolution had managed to contrive a version that soaks up the last bit of sunlight, adapting the bacteria to life in perpetual shade - an astonishing feat, achieved by evolutionary trial and error. 1

1. http://www.science20.com/news_articles/lightharvesting_molecules_absorb_any_color_of_sunlight-154542



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solar pannels actually just absorb the light. the conversion is done by other parts in the process. In order to gain electricity through Solar power, the installantion of a Photovoltaic system is required. Wiki: A solar power system is designed to supply usable solar power by means of photovoltaics.  If any of the mentioned components are not installed , solar energy cannot be gained and stored. Chlorophyll  absorbs photons, which are transmitted to the reaction center in photosystem II. They have the EXACT same function as solar pannels. They capture solar energy.  Do you think it would make sense to construct solar pannel factories, and not all other parts to gain energy ? the solar pannels by their own would have no function. what function would chlorophyll exercise without all other parts in photosynthesis in place and interconnected, to gain atp energy, and glucose, the end product ? There would be no function, in the same manner, as solar pannels by their own would have no function. Chlorophyll biosynthesis  is enormously complex. Its like a factory at work with several machines, a multi step process. 17 irreducible complex processes, each requires a individual molecular machine , taking the product of one enzyme and elaborating it further. The last eight enzymes have NO OTHER use in any other biological process. they have a exclusive use only in that pathway

No solar pannels, no energy caption, no photovolaic system. No chlorophyll, no caption of photons, no photosynthesis, no plant life. Chlorophyll by its own has no function. So there would be no sense to produce it in a complex manufacturing process, without all other parts for photosytnehsis in place. Evolution has no forsight. So lets suppose, hundreds of millions of years would produce chlorophyll, SO WHAT ???! - by their own, there is no function for them, and if they dont have function, evolution would not make a non functional molecule. chlorophyll by its own, without the other proteins used in the photosynthesis pathway, would have no use. Its as if you would make solar pannels, without use.







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I rarely see an atheist concede an argument of ID. But at Portland Skeptics Adam McBale pretty much grasped the concept and acknowledged :

Adam Macbale But even if it is the case that "the step by step mechanism is not a sufficient nor adequate explanation for the complex molecular proceedings observed in living cells and organisms," the argument as posed here in this synopsis does nothing to immediately imply that the only other solution is intelligent design. 

The crux of the argument is that natural selection would have no reason to select for components of a complex system that would be useful only in the completion of the much larger system, which is the main supposition that you're making here. It sounds pretty reasonable though. but is it true that those components are doing literally nothing else, or have no other effect on the organism? And still, nothing there suggests, if those things were true, that it has to have then been designed. 

What the argument suggests, at most, is that the step by step mechanism is inadequate, and then I think it sort of wants us to invoke the "complex systems can't possibly arise out of chaos" idea, an idea about which I think there is a pretty unanimous consensus (they totally can). 

But then, even if we were to take this as evidence of intelligent design, why is this is this the only cogent example we can find (assuming it's the only cogent example we can find). You'd think that if things were being created by some more-powerful being then there would be tons of examples all around. Why did we have to try so hard to find just this one?

Further, the final statement of the argument is a huge leap. We went from discussing a particular thing to making a statement about all things, literally "all living beings." You can't go in that direction. You have to make a statement about all living beings, and then discuss a particular living being. That is, if your intention is to make a logical claim, anyway. 

Granted, I haven't read the much longer, fleshed-out argument in that link. Does it address these points?



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Chlorophyll: Photosynthesis is a Symbiosis of Mineral and Organic Molecules 1

Chlorophyll produced during photosynthesis is an excellent example of symbiosis in Intelligent Design. The complex chemistry of plants requires that Chlorophyll atoms are mysteriously arranged in plants by two complex symbiotic relationships of other organic catalyst molecules and minerals. One catalyst contains a single iron atom in the middle of a complex hydrocarbon. The other contains a single zinc atom in the middle of another complex hydrocarbon. These two complex catalysts are somehow produced during photosynthesis by other complex hydrocarbons in plants. They are not consumed or decomposed in the chemical process, but repeatedly circulate to produce chlorophyll in the complex chlorophyll molecule. Life could not exist if these complex symbiotic relationships between complex organic molecules and minerals did not exist from the first instance of any plant life ranging from the simplest algal cell to the most complex plants on earth. If it took millions of years for each plant to evolve these very complex molecules there would be no life on earth today.

Magnesium is one of many metals found in the dust of the earth. One atom of magnesium is found at the center of the approximate 123-atom chlorophyll hydrocarbon. Chlorophyll has the incredible ability to convert sunlight, water, and carbon dioxide into healthy organic food for plants and animals. If you took all the magnesium out of a huge tree and put it in the palm of your hand, you would have less than a pinhead of magnesium. Yet, without this tiny speck of the micronutrient trace element magnesium used in the process of photosynthesis, there would be no life on earth.

From the first instant of life, plants took up iron, zinc, magnesium, and dozens of other elements and combined them with carbon dioxide and water in extremely complex combinations of organic molecules. There would never have been the first plant life without this highly complex symbiotic process occurring all at once, where two or more chemical compounds work together to make other beneficial compounds not millions of years apart. Most plants and trees rely on the wind to move their seeds.If this took millions of years to accomplish instead of the first year, plants and trees would stunt themselves and die by being inundated and buried with the seeds from the same plants or trees.

Likewise, none of the components of animal life could function perfectly unless all the multitudes of other components were perfectly functioning and fully in operation at the same instant. Each plant and animal was complete at the first instant. The many mechanisms required to produce its seed existed, with the mystery of the growth of a new organism locked inside each seed. To believe that these millions of functions developed one at time over millions of years requires an enormously confused imagination. Chlorophyll resulting from photosynthesis and symbiosis between organic and inorganic chemicals is only one of billions of symbiotic relationships in nature that prove Intelligent Design. Evolution excludes all symbiosis and is not scientific by any stretch of the imagination.

The two currently accepted photosystem units are Photosystem II and Photosystem I, which have their own distinct reaction center chlorophylls, named P680 and P700, respectively.[2] These pigments are named after the wavelength (in nanometers) of their red-peak absorption maximum. The identity, function and spectral properties of the types of chlorophyll in each photosystem are distinct and determined by each other and the protein structure surrounding them. Once extracted from the protein into a solvent (such as acetone or methanol),[3][4][5] these chlorophyll pigments can be separated in a simple paper chromatography experiment, and, based on the number of polar groups between chlorophyll a and chlorophyll b, will chemically separate out on the paper.
The function of the reaction center chlorophyll is to use the energy absorbed by and transferred to it from the other chlorophyll pigments in the photosystems to undergo a charge separation, a specific redox reaction in which the chlorophyll donates an electron into a series of molecular intermediates called an electron transport chain. The charged reaction center chlorophyll (P680+) is then reduced back to its ground state by accepting an electron. In Photosystem II, the electron which reduces P680+ ultimately comes from the oxidation of water into O2 and H+ through several intermediates. This reaction is how photosynthetic organisms like plants produce O2 gas, and is the source for practically all the O2 in Earth's atmosphere. Photosystem I typically works in series with Photosystem II, thus the P700+ of Photosystem I is usually reduced, via many intermediates in the thylakoid membrane, by electrons ultimately from Photosystem II. Electron transfer reactions in the thylakoid membranes are complex, however, and the source of electrons used to reduce P700+ can vary.

The electron flow produced by the reaction center chlorophyll pigments is used to shuttle H+ ions across the thylakoid membrane, setting up a chemiosmotic potential mainly used to produce ATP chemical energy, and those electrons ultimately reduce NADP+ to NADPH a universal reductant used to reduce CO2 into sugars as well as for other biosynthetic reductions.

Reaction center chlorophyll-protein complexes are capable of directly absorbing light and performing charge separation events without other chlorophyll pigments, but the absorption cross section (the likelihood of absorbing a photon under a given light intensity) is small. Thus, the remaining chlorophylls in the photosystem and antenna pigment protein complexes associated with the photosystems all cooperatively absorb and funnel light energy to the reaction center. Besides chlorophyll a, there are other pigments, called accessory pigments, which occur in these pigment-protein antenna complexes.

It's unthinkable to believe that a system as complicated from this arose from chance.




1. http://www.intelligentdesigntheory.info/chlorophyll_symbiosis_minerals_organic_molecules.htm
2. http://tremulous.net/forum/index.php?topic=11878.60

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Understanding chlorophylls: Central magnesium ion and phytyl as structural determinants 1

The central Mg2+ ion and phytyl are very conservative constituents of Chls. This poses a question of the molecular basis for the evolutionary selection of the Mg2+ ion as the occupant of the central cavity in Chls and phytol to become a unit universally associated with the tetrapyrrolic macrocycle. This sparks the further question of how exactly these residues shape pigment properties. A coordinatively unsaturated Mg ion chelated by a tetrapyrrole acts as the coordination center and, being a closed shell element, does not electronically perturb the pigment π-electron system.

A viewpoint: Why chlorophyll a? 2

Chl a appears to be unique and irreplaceable, particularly if global scale oxygenic photosynthesis is considered. Its uniqueness is determined by its physicochemical properties, but there is more. Other contributing factors include specially tailored protein environments, and functional compatibility with neighboring electron transporting cofactors. Thus, the same molecule, Chl a in vivo, is capable of generating a radical cation at ?1 V or higher (in PS II), a radical anion at -1 V or lower (in PS I), or of being completely redox silent (in antenna holochromes). While various Chls function as light-harvesting pigments, only one of them, Chl a, depending on its protein environment, functions either as a light harvester or as a redox participant in electronic excitation trapping (primary charge separation) and electron transporting events in the reaction centers of Photosystems II and I (PS II, PS I) of oxygenic organisms. Only Chl a  is indispensable for oxygenic photosynthesis; it is the only member of the Chl family that is present in all organisms that carry out oxygenic photosynthesis, from primitive cyanobacterial cells to sequoia trees. Depending on their evolutionary ancestry, various taxa of photosynthetic organisms contain different sets of light harvesting Chls. 

1. http://www.sciencedirect.com/science/article/pii/S0005272808006701#bib5
2. https://sci-hub.bz/https://link.springer.com/article/10.1007/s11120-008-9395-x

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