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Theory of Intelligent Design, the best explanation of Origins » Photosynthesis, Protozoans,Plants and Bacterias » Enzymes and protein complexes needed in photosynthesis

Enzymes and protein complexes needed in photosynthesis

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photosynthesis is a interdependent system. Unless following enzymes and protein complexes are present, photosynthesis will not occur

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




Light-dependent reactions

The light-dependent reactions, or photoreduction, is the first stage of photosynthesis, is a process by which plants capture and store energy from sunlight. In this process, light energy is converted into chemical energy, in the form of the energy-carrying molecules ATP and NADPH. In the light-independent reactions, the formed NADPH and ATP drive the reduction of CO2 to more useful organic compounds, such as glucose.


For the light reactions following enzymes and proteins complexes are  needed


Thylakoid membrane

Chlorophyll pigments

Light harvesting complex

Photosystem II

Photosystem II reaction Center

Oxygen evolving complex

other accessory pigments

Pheophytin

Plastoquinone

Cytochrome b6f complex

Plastocyanin

Photosystem I

Photosystem I reaction Center

Iron-sulfur protein

Ferredoxin

ATP synthase enzyme






Light-independent reactions

The Calvin cycle describes the synthesis of glucose from carbon dioxide and water by oxygen-producing photosynthesis. It uses sunlight for energy.
The second step, called the Calvin cycle, the actual fixation of carbon dioxide is carried out. This process consumes ATP and NADPH. The Calvin cycle in plants accounts for the preponderance of carbon fixation on land. In algae and cyanobacteria, it accounts for the preponderance of carbon fixation in the oceans.

Rubisco

Phosphoglycerate kinase

Glyceraldehyde-3-phosphate dehydrogenase (NADP+) (phosphorylating)

Triosephosphate isomerase

Fructose-bisphosphate aldolase

Transketolase

Aldolase

Sedoheptulose-bisphosphatase

Transketolase

Ribose-5-phosphate isomerase

Phosphoribulokinase







Last edited by Admin on Thu May 05, 2016 1:01 pm; edited 18 times in total

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2 the calvin cycle on Sun Mar 30, 2014 8:10 pm

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http://en.wikipedia.org/wiki/Light-independent_reactions

1.The enzyme RuBisCO catalyses the carboxylation of ribulose-1,5-bisphosphate, RuBP, a 5-carbon compound, by carbon dioxide (a total of 6 carbons) in a two-step reaction. The product of the first step is enediol-enzyme complex that can capture CO
2 or O2. Thus, enediol-enzyme complex is the real carboxylase/oxygenase. The CO2 that is captured by enediol in second step produces a six-carbon intermediate initially that immediately splits in half, forming two molecules of 3-phosphoglycerate, or 3-PGA, a 3-carbon compound (also: 3-phosphoglyceric acid, PGA, 3PGA).




2.The enzyme phosphoglycerate kinase catalyses the phosphorylation of 3-PGA by ATP (which was produced in the light-dependent stage). 1,3-Bisphosphoglycerate (1,3BPGA, glycerate-1,3-bisphosphate) and ADP are the products. (However, note that two 3-PGAs are produced for every CO2 that enters the cycle, so this step utilizes two ATP per CO2 fixed.)

3.The enzyme glyceraldehyde 3-phosphate dehydrogenase catalyses the reduction of 1,3BPGA by NADPH (which is another product of the light-dependent stage). Glyceraldehyde 3-phosphate (also called G3P, GP, TP, PGAL, GAP) is produced, and the NADPH itself is oxidized and becomes NADP+. Again, two NADPH are utilized per CO2 fixed.




1. Triose phosphate isomerase converts some G3P reversibly into dihydroxyacetone phosphate (DHAP), also a 3-carbon molecule.
2. Aldolase and fructose-1,6-bisphosphatase convert a G3P and a DHAP into fructose 6-phosphate (6C). A phosphate ion is lost into solution.
3. Then fixation of another CO2 generates two more G3P.
4. F6P has two carbons removed by transketolase, giving erythrose-4-phosphate. The two carbons on transketolase are added to a G3P, giving the ketose xylulose-5-phosphate (Xu5P).
5. E4P and a DHAP (formed from one of the G3P from the second CO2 fixation) are converted into sedoheptulose-1,7-bisphosphate (7C) by aldolase enzyme.
6. Sedoheptulose-1,7-bisphosphatase (one of only three enzymes of the Calvin cycle that are unique to plants) cleaves sedoheptulose-1,7-bisphosphate into sedoheptulose-7-phosphate, releasing an inorganic phosphate ion into solution.
7. Fixation of a third CO2 generates two more G3P. The ketose S7P has two carbons removed by transketolase, giving ribose-5-phosphate (R5P), and the two carbons remaining on transketolase are transferred to one of the G3P, giving another Xu5P. This leaves one G3P as the product of fixation of 3 CO2, with generation of three pentoses which can be converted to Ru5P.
8. R5P is converted into ribulose-5-phosphate (Ru5P, RuP) by phosphopentose isomerase. Xu5P is converted into RuP by phosphopentose epimerase.
9. Finally, phosphoribulokinase (another plant unique enzyme of the pathway) phosphorylates RuP into RuBP, ribulose-1,5-bisphosphate, completing the Calvin cycle. This requires the input of one ATP.



Last edited by Admin on Fri Aug 14, 2015 2:37 pm; edited 1 time in total

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Behe's own definition of IC:

By irreducibly complex I mean a single system composed of several well-matched, interacting parts that contribute to the basic function, wherein the removal of any one of the parts causes the system to effectively cease functioning.

The whole structure of evolution is based on small stepwise changes from random chance that become fixed in the genome by natural selection. The point is that irreducibly complex systems do not fit the evolutionary structure.

http://www.rae.org/pdf/interdep.pdf

The existence of interdependent systems in nature is evidence for design by God.


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



A gasoline engine "comes to life" only when many different independent conditions are met at the same time. Take away the spark plug, and it will not run at all. Leave out the pistons, and it will not run. Without oil or gasoline, it will not run. The list of interdependent conditions goes on and on. Even if all other conditions are met, it must be given an initial crank in order to start. Likewise, living creatures have inter-dependent characteristics which determine their very existence. Photosynthesis does not work without the conversion of energy into enzymatic and dark reaction cicle activity.

Compared to photosynthesis, a gasoline engine is extremely primitive. In order for photosynthesis to arise spontaneously, the sum of the parts of enzymes, genes, proteins , and protein complexes would have to come together intact in order to function, and the chemical reactions which would produce glucose would have to be started all at once. Each of the enzymes and protein complexes need complex biosynthesis pathways to be produced ( with several enzymes and proteins in the pathway working in a stepwise fashion , and if one step is missed , the final product is not produced )
How and why would evolution produce for example  the oxygen evolving complex, if by its own it would not have any function ? The enzymes and protein complexes do have only function, if working like in a car engine, each contributing to the final goal. And most of these parts  would have no other function, than only in photosynthesis.

It was always accepted that each of the biochemical reactions was catalyzed by a specific enzyme and still, it took quite some time before it was realized that the chlorophyll and the other pigments are protein-bound and that they are only active as protein-chlorophyll (and protein-pigment, respectively) complexes. The isolated pigments themselves were useless for photosynthesis. The pigment-protein complex, (most) proteins of the electron transport chain as well as the catalyst of ATP synthesis (ATP synthase) are integral compounds of the photosynthesis membrane(s) (= the thylacoid membranes of algae and higher green plants, cytoplasmatic membranes of photosynthetically active bacteria and blue-green algae). The location within the membrane (at the out- or the inside, for example) and the relative arrangement of the proteins towards each other are important prerequisites of energy transformation.

The requirements for energy transformation are even higher: completely intact membranes that are impermeable for protons and that enclose compartments thus maintaining a stable electrochemical gradient between inside and outside. The production of ATP is based on a directed proton dislocation paralleled by a change of the compartment's pH and of its membrane potential.


Following proteins, enzymes, and protein complexes are involved in photosynthesis. Some of them , like photosystem II , are made of several subunits and co-factors, and metal clusters.


Light reaction :


Thylakoid membrane, Chlorophyll pigments, Light harvesting complex, Photosystem II,  Photosystem II reaction Center, Oxygen evolving complex,Pheophytin, Plastoquinone,  Cytochrome b6f complex,  Plastocyanin,  Photosystem I,  Photosystem I reaction Center,  Iron-sulfur protein,  Ferredoxin,  ATP synthase enzyme

Light independent reactions

Rubisco, Phosphoglycerate kinase, Glyceraldehyde-3-phosphate dehydrogenase (NADP+) (phosphorylating), Triosephosphate isomerase,  Fructose-bisphosphate aldolase, Transketolase, Aldolase, Sedoheptulose-bisphosphatase, Transketolase, Ribose-5-phosphate isomerase, Phosphoribulokinase,

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Thylakoid membrane

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5 Essential parts of oxygenic photosynthesis on Thu May 05, 2016 11:11 am

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A gasoline engine "comes to life" only when many different independent conditions are met at the same time. Take away the spark plug, and it will not run at all. Leave out the pistons, and it will not run. Without oil or gasoline, it will not run. The list of interdependent conditions goes on and on. Even if all other conditions are met, it must be given an initial crank in order to start. Likewise, living creatures have inter-dependent characteristics which determine their very existence. Photosynthesis does not work without the conversion of energy into enzymatic and dark reaction cicle activity.

Compared to photosynthesis, a gasoline engine is extremely primitive. In order for photosynthesis to arise spontaneously, the sum of the parts of enzymes, genes, proteins , and protein complexes would have to come together intact in order to function, and the chemical reactions which would produce glucose would have to be started all at once. Each of the enzymes and protein complexes need complex biosynthesis pathways to be produced ( with several enzymes and proteins in the pathway working in a stepwise fashion , and if one step is missed , the final product is not produced ) 
How and why would evolution produce for example  the oxygen evolving complex, if by its own it would not have any function ? The enzymes and protein complexes do have only function, if working like in a car engine, each contributing to the final goal. And most of these parts  would have no other function, than only in photosynthesis.



Essential parts of oxygenic photosynthesis

The light reactions

1. Lipid bilayer membranes are critical to the early stages of energy storage, such that photosynthesismust be viewed as a process that is at heart membrane-based. 4
2. Chlorophyll is an essential component of photosynthesis, which helps plants get energy from light. 1
3. The light harvesting complexes, also called antenna complexes,  are essential for collecting sunlight and regulating photosynthesis 2
4. Photosystem II (PSII) is a key component of photosynthesis 2
4a.The reaction center is the key component for the primary events in the photochemical conversion of light into chemical energy. 19
5. The oxygen evolving is responsible for catalyzing the oxidation of water to molecular oxygen in plants, algae, and cyanobacteria. 3
6. Of these essential redox components, tyrosine, P680, pheophytin, QA, and Qj have been shown to be bound to two key polypeptides (Dl and D2) 8
7. If the oxidation of plastoquinone takes place in the cytochrome b6 f complex that is located in the stroma, then the plastoquinone must diffuse within the lipid bilayer from the   grana membranes to the stromal membranes. In
    either case, a long-distance diffusion process is necessary to complete the traversal of the electron transport chain.
8  The cytochromeb6 f complex  is an essential player in noncyclic and cyclic electron flow 4
9) Plastocyanin is an essential member of photosynthetic electron transport and functions near PS I.  5
10  PSI is necessary to provide the energy to reduce NADP+ to NADPH  6
10a.The reaction center is the key component for the primary events in the photochemical conversion of light into chemical energy. 19
11) Ferredoxin (Fd) proteins are required for the electron transfer process  from the bound Fe–S centers in the Photosystem I reaction center to NADP+. 4
12) Ferredoxin—NADP(+) reductase same as 9
13) ATP synthase is essential in plants for solar energy conversion and carbon fixation.

The dark or light independent reactions

14) Rubisco  is essential for the photosynthetic process.
15) Phosphoglycerate kinase is required to catalyse the phosphorylation of 3-PGA by ATP 10
16) Glyceraldehyde-3-phosphate dehydrogenase (NADP+) (phosphorylating) is essential to catalyse the reduction of 1,3BPGA by NADPH 10
17) Triosephosphate isomerase is needed to catalyze  the reversible interconversion of the triose phosphate isomers dihydroxyacetone phosphate and D-glyceraldehyde 3-phosphate. 11
18) Fructose-bisphosphate aldolase is a key enzyme to catalyze a reversible reaction that splits the aldol, fructose 1,6-bisphosphate, into the triose phosphates dihydroxyacetone phosphate (DHAP) and glyceraldehyde 3-phosphate (G3P). 12
19) Transketolase catalyzes  the conversion of sedoheptulose-7-P and glyceraldehyde-3-P to pentoses, the aldose D-ribose-5-P and the ketose D-xylulose-5-P. 13
20) Aldolase performs an aldol reaction (creating an aldol) or its reverse (cleaving an aldol). 14
21) Sedoheptulose-bisphosphatase catalyzes the removal of a phosphate group from sedoheptulose 1,7-bisphosphate to produce sedoheptulose 7-phosphate. 15
22) Transketolase catalyzes the reverse reaction, the conversion of sedoheptulose-7-P and glyceraldehyde-3-P to pentoses, the aldose D-ribose-5-P and the ketose D-xylulose-5-P. 16
23) Ribose-5-phosphate isomerase (Rpi) is an enzyme that catalyzes the conversion between ribose-5-phosphate (R5P) and ribulose-5-phosphate (Ru5P). 17
24) Phosphoribulokinase catalyzes the chemical reaction ATP + D-ribulose 5-phosphate \rightleftharpoons ADP + D-ribulose 1,5-bisphosphate

1) http://www.newworldencyclopedia.org/entry/Chlorophyll
2) http://www.nature.com/nature/journal/v421/n6923/full/nature01344.html
3) http://www.sciencedirect.com/science/article/pii/S0010854507001877
4) Blankenship: Molecular mechanisms of photosynthesis
5) http://www.esalq.usp.br/lepse/imgs/conteudo_thumb/24-Katoh.pdf
6) http://www.nature.com/nsmb/journal/v8/n7/full/nsb0701_577.html
7) http://www.atpsynthase.info/Basics.html
8  Concepts in Photobiology: Photosynthesis and Photomorphogenesis page 26
9) Handbook of Plant and Crop Physiology, Third Edition page 394
10) https://en.wikipedia.org/wiki/Phosphoglycerate_kinase
11) https://en.wikipedia.org/wiki/Triosephosphate_isomerase
12) https://en.wikipedia.org/wiki/Fructose-bisphosphate_aldolase
13) https://en.wikipedia.org/wiki/Transketolase
14) https://en.wikipedia.org/wiki/Sedoheptulose-bisphosphatase
15) https://en.wikipedia.org/wiki/Transketolase
15) https://en.wikipedia.org/wiki/Sedoheptulose-bisphosphatase
14) https://en.wikipedia.org/wiki/Aldolase
15) https://en.wikipedia.org/wiki/Sedoheptulose-bisphosphatase
16) https://en.wikipedia.org/wiki/Transketolase
17) https://en.wikipedia.org/wiki/Ribose-5-phosphate_isomerase
18) https://en.wikipedia.org/wiki/Phosphoribulokinase
19) http://www.sciencedirect.com/science/article/pii/S0014579398012459

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