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A11. Fixing CO2 - Biology

A11.  Fixing CO2 - Biology


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Of the five different pathways known to fix CO2, all require ATP except one. That one is present in both methanogen, which produce methane from CO2 and H2 and in the acetogens, which produce acetate (CH3CO2-) in the form of acetylCoA. The simpler reactions of forming acetic acid and methane are shown below:

[mathrm{2CO_2 + 4H_2 ightarrow CH_3CO_2H + 2H_2O}]

[mathrm{CO_2 + 4H_2 ightarrow CH_4 + 2H_2O}]

The DG0 values for these reaction (calculated using DG0f for gas phase H2, CO2 and CH4 and liquid acetic acid and water are -75 and -131 kJ, respectively, at 250C, showing that they are thermodynamically favored. Making AcetylCoA, a "high" energy molecule compared to its hydrolysis products (as is ATP) from acetic acid and CoASH, a would require energy input. A proton gradient is the likely source.

Some bacteria and Achaea cells (primordial or present) use the reductive acetylCoA pathway, also known as the Wood-Ljungdahl pathway, to form, in a noncyclic process, acetyl CoA from CO2 and at the same time makes ATP. This process is paid for by a proton gradient. This has been described by Shock as "a free lunch you get paid to eat". The energetics of the present acetyl CoA pathway based on the overall reaction below show an approximate DG0 value of -59 kJ/mol which can drive ATP synthesis.

[mathrm{2CO_2 + 4H_2 + CoASH ightarrow CH_3COSCoA + 3H_2O}]

The concentration of carbon dioxide in the primordial ocean was 1000 times higher than now. Vents produced large amounts of methane and hydrogen gas. There was little oxygen and hence lots of Fe2+. The enzymes involved in this acetyl-CoA pathway of carbon fixation have FeS clusters. It has also been shown that bubbles (which are really membrane bound spaces) of FeS and NiS can be made in deep sea vents. These could not only encapsulate precursor molecules but also serve as catalysts. Vents also can catalyze the fixation of nitrogen (to ammonia) and laboratory studied show that FeS can catalyze the conversion of formate (found in vents) into pyrimidines and purines. The studies of present methanogens and vent chemistry suggest that the critical ingredients and conditions for development of the first biological cells probably occurred in the vents.

To produce polymers, an energy source and monomers must exists. Concentration gradients found in simulations of vents produce million fold concentrated molecules. The transient heating and cooling of any double-stranded nucleic acids could lead to concentration amplification by a PCR like strand separation followed by reannealing. In addition, these vent regions possess a powerful, reoccurring energy source, a pH gradient, as the alkaline vented material entered the acidic oceans that exists with high CO2 concentrations, creating a gradient across an inorganic membrane. This is startlingly analogous to the pH gradient across membranes (acidic outside, alkaline inside) driven by the membrane complexes in the mitochondria and bacteria. Lane et al argue that the existence of membrane proton gradients as an energy source in all cells (eukaryotes, bacteria, and archaea) and in chloroplasts, mitochondria, corroborate their hypothesis. Bacteria and archaea share homologous ATPases and electron carriers (ferredoxins, quinones, and cytochromes). These similarities contrast to the differences in enzyme structures in fermentative pathways. Arguments that proton pumps evolved to pump proteins (and reduce pH gradients) can't explain their ubiquitous presence even in organisms not subjected to low pH. Hence the ubiquity of proton pumps supports the conjecture that they arose from the first protocells, possible comprised of inorganic walls and ultimately with amphiphilic molecules synthesized from precursors.

Creationists would argue that it would be impossible to evolve a structure with the complexity of membrane ATPase (which serve to collapse a pH gradient as the power the synthesis of molecules with large negative DG0 of hydrolysis). Lane et al propose that the earliest cells evolved ATPase like molecules in alkaline vents where pH gradients analogous to those in cells today arose. They envision cell-like columns lined by FeS membrane like structure with alkaline conditions inside and acid conditions outside. Nonpolar or amphiphilic molecule would line the inside of the cells/columns. A ATPase-like system could then take advantage of the pH gradient which constantly replenishes itself. If structures as complicated as ribosomes evolved from a subsequent RNA world, surely ATPase-like molecules could also. Other chemistry might have evolved earlier to utilize the energy source provided by the pH gradient.

If life originated in the vents, it would need an energy source to leave the vents. Presumably it would have evolved one to utilized pH gradient to replace the one it left in the alkaline vents. The substrate level phosphorylation of glycolysis that requires ATP input to make ATP would not provide the energy source needed. Cells that left would have had to produce their own proton gradient. Perhaps all the was needed initially was concerted conformational changes in proteins that upon exposure of a different pH changed their shape inducing pKa shifts in adjacent proton donors/acceptors leading to vectorial discharge of protons across a membrane. Perhaps the method described above in protocells was sufficient.

Recent analyses by Poehlein et a show that CO2 reduction (fixation) can be coupled to the production of a sodium ion gradient, which could collapse to drive ATP synthesis. Analysis of the genome of a gram positive bacteria, Acetobacterium woodii, an acetogen, shows the it has an ancient pathway for production of acetyl-CoA that can, in an anabolic fashion form biomass or in a catabolic fashion be cleaved to acetate with the production of ATP. It does not require classic electron carriers like ubiquinone or cytochrome C linked to protein gradient formation to drive ATP synthesis. Rather it has only a ferredoxin:NAD+ oxioreductase which couples oxidation to the formation of a sodium ion gradient, which collapses through an sodium ion transporter/ATP synthase to drive ATP synthase. A plausible reaction scheme based on genomic analysis is shown below:

Figure: Acetyl-CoA Synthase and Acetogenesis

Contributors

  • Prof. Henry Jakubowski (College of St. Benedict/St. John's University)

A11. Fixing CO2 - Biology

By the end of this section, you will be able to:

  • Describe the Calvin cycle
  • Define carbon fixation
  • Explain how photosynthesis works in the energy cycle of all living organisms

After the energy from the sun is converted and packaged into ATP and NADPH, the cell has the fuel needed to build food in the form of carbohydrate molecules. The carbohydrate molecules made will have a backbone of carbon atoms. Where does the carbon come from? The carbon atoms used to build carbohydrate molecules comes from carbon dioxide, the gas that animals exhale with each breath. The Calvin cycle is the term used for the reactions of photosynthesis that use the energy stored by the light-dependent reactions to form glucose and other carbohydrate molecules.


Water

For land plants, water availability can function as a limiting factor in photosynthesis and plant growth. Besides the requirement for a small amount of water in the photosynthetic reaction itself, large amounts of water are transpired from the leaves that is, water evaporates from the leaves to the atmosphere via the stomata. Stomata are small openings through the leaf epidermis, or outer skin they permit the entry of carbon dioxide but inevitably also allow the exit of water vapour. The stomata open and close according to the physiological needs of the leaf. In hot and arid climates the stomata may close to conserve water, but this closure limits the entry of carbon dioxide and hence the rate of photosynthesis. The decreased transpiration means there is less cooling of the leaves and hence leaf temperatures rise. The decreased carbon dioxide concentration inside the leaves and the increased leaf temperatures favour the wasteful process of photorespiration. If the level of carbon dioxide in the atmosphere increases, more carbon dioxide could enter through a smaller opening of the stomata, so more photosynthesis could occur with a given supply of water.


Differences in carbon fixation pathways

A comparison of the differences between the various carbon pathways is provided in the table.

Differences in the major carbon-fixation pathways in plants
pathway carbon-assimilation process first stable intermediate product stomate activity photorespiration plant types using this pathway
*Crassulacean acid metabolism.
C3 Calvin-Benson cycle only phosphoglycerate (PGA), a three-carbon acid open during the day, closed at night colder, wetter environments characterized by low-to-medium light intensities
C4 adds CO2 to phosphoenolpyruvate (PEP) to form oxaloacetate first the Calvin-Benson cycle follows oxaloacetate, a four-carbon acid, which is later reduced to malate open during the day, closed at night suppressed plants living in warmer, drier environments characterized by high light intensity
CAM* adds CO2 to phosphoenolpyruvate (PEP) to form oxaloacetate first the Calvin-Benson cycle follows oxaloacetate, a four-carbon acid, which is later reduced to malate and stored in vacuoles closed during the day suppressed succulents (members of Crassulaceae), which occur in warmer, drier environments characterized by high light intensity

Assimilation of Carbon Dioxide in Microorganisms

Although most microorganisms can fix or assimilate carbon dioxide (CO2), only autotrophic ones use CO2 as their sole or principal carbon source.

The reduction or assimilation of CO2 takes place at the expense of much energy. Usually autotrophic microorganisms obtain the required energy by trapping light during photosynthesis (photoautotrophs), but some derive it from the oxidation of reduced inorganic electron donors (chemo- autotrophs).

Microorganisms can fix CO2 or convert this inorganic molecule to organic carbon and assimilate it in certain major ways, which are the Calvin cycle (also called Calvin-Benson cycle, or reductive pentose phosphate pathway), the reductive tricarboxylic acid cycle (also called reductive TCA cycle, or reverse citric acid cycle), the hydroxypropionate cycle or acetyl-CoA pathway.

Carbon dioxide (CO2) is incorporated by almost all microbial autotrophs using Calvin cycle, a special metabolic pathway. Although this cycle in most photosynthetic microorganisms, it is absent in archaea (archaebacteria), some obligately anaerobic bacteria, and some microaerophilic bacteria. These microorganisms usually use rest of the two above mentioned pathways.

The reductive tricaboxylic cycle is used by some archaea (archaebacteria), e.g., Thermoproteus, Sulfolobous and by bacteria such as Chlorobium, a green sulphur bacterium. Chloroflexus, a green non-sulphur photoautotroph uses the unique pathway of hydroxypropinonate.

Calvin Cycle:

Phototropic microorganisms (microalgae, cyanobacteria, purple and green bacteria), like plants, assimilate CO2 to produce carbohydrate principally through Calvin cycle (Fig 25.7). The latter is named for its discover Melvin Calvin and is also popular by the names Calvin-Bensen cycle or reductive pentose phosphate cycle.

The Calvin cycle requires NAD(P)H and ATP and two key enzymes, ribulose-1, 5-biphosphate carboxylase (ribulose bisphosphate carboxylase) and phosphoribulokinase. To understand the Calvin-cycle easily, it can be divided into three phases (carboxylation, reduction, and regeneration).

The Carboxylation Phase:

During this phase of CO2 fixation the enzyme ribulose-1, 5-biphosphate carboxylase or ribulose bisphosphate carboxylase (in short form called RUBISCO) catalyzes the incorporation of CO2 to ribulose-1, 5-biphosphate (RuBP) to generate two molecules of 3-phosphoglyceric acid (PGA).

3-phosphoglyccric acid (PGA) is reduced to glyceraldehyde 3-phosphate with the envolvement of two enzymes. Phosphoglycerate kinase enzyme reduces 3-phosphoglyceric acid into 1, 3-byphosphate glyceric acid which is then reduced to glyceraldehyde 3-phosphate by enzyme glyceraldehyde 3-phosphate dehydrogenase.

The Regeneration Phase:

During this phase the ribulose-1, 5-biphosphate (RuBP) is regenerated and carbohydrates such as fructose and glucose are produced. Glyceraldehyde 3-phosphate is converted to dihydroxyacetone phosphate (DHAP) this conversion is reversible.

Most of these two i.e., glyceraldehyde 3-phosphate and DHAP are used to regenerate ribulose-1, 5-biphosphate via various intermediate steps involv­ing transketolase and transaldolase reactions, the remaining ones are used in the biosynthesis of carbohydrates.

The stoichiometry of the Calvin cycle can be represented in few words as 12 NADPH and 18ATP are required to synthesize 1 hexose molecule (glucose) from 6 molecules of CO2.

The overall equation can be summarized as under:

6CO2 + 18ATP + 12NADPH + 12H + + 12H2O → 1 Hexose + 18ADP+ 18Pi + 12NADP +

Reductive or Reverse Tricarboxilic Acid Cycle (Reduced TCA Cycle):

The reductive tricarboxylic acid cycle (reduced TCA cycle, reduced Kreb’s cycle, or reduced citric acid cycle), also called reverse TCA cycle is used as alternative mechanism of CO2 fixation by phototrophite green sulphur bacteria (e.g., Chlorobium) and by some nonphoto-trophic archaebacteria (Thermoproteus, Sulfolobus and Aquifex).

In this cycle, the CO2 fixation takes place by a reversal of steps in the tricarboxylic acid cycle (a major pathway of respiration by which pyruvate is completely oxidised to CO2). In Chlorobium, there are two ferredoxin-linked enzymes that catalyse the reductive fixation of CO2into intermediates of the tricarboxylic acid cycle.

The two ferredoxin-linked reactions involve the carboxylation of succinyl-CoA to α-ketoglutarate and the carboxylation of acetyl-CoA to pyruvate (Fig. 25.8).

The reductive tricarboxylic acid cycle starts from oxaloacetate and each complete turn of the cycle results in three molecules of CO2 being incorporated and pyruvate as the product.

All reactions of the cycle are catalysed by enzymes of normal tricarboxylic acid cycle, but they work in reverse. One exception is citrate lyase, an ATP-dependent enzyme that cleaves citrate into acetyl-CoA and oxaloacetate in green sulphur bacteria.

Citrate lyase replaces citrate synthetase that produces citrate from oxaloacetate and acetyl-CoA in the normal TCA cycle. However, the acetyl-CoA of reduced TCA cycle produces pyruvate, which is converted to phosphoenolpyruvate that then results in triose-phosphate. The triose-phosphate converts into hexose- phosphate (glucose-phosphate), which is utilized in cell material.

Hydroxypropionate Pathway:

Hydroxypropionate pathway (Fig. 25.9) is also a mechanism of autotrophic CO2 fixation unique to green non-sulphur bacteria (Chloroflexus). Choroflexus, an anoxigenic photoautotroph, uses either H2 or H2S as electron donors.

In hydroxypropionate pathway, two molecules of CO2 are reduced to glyoxylate. Acetyl-CoA is carboxylated to yield methylmanonyl-CoA. This intermediate is rearranged to yield acetyl-CoA and glycoxylate. The latter is converted to cell material.

Hydroxypropionate pathway has so far been confirmed only in Chloroflexus and appears to be of evolutionary significance. Chloroflexus is a “hybrid” photoautotroph in the sense that its photosynthetic mechanism shows features characteristic of both purple sulphur bacteria and green sulphur bacteria. Bacteriochlorophyll a located in the cytoplasmic membrane of cells of Chloroflexus is arranged to form a photosynthetic reaction centre structurally similar to those of purple bacteria.

Chloroflexus, on the other hand, contains bacteriochlorophyll c and chlorosomes (oblong bacteriochlorophyll-rich bodies bound by a thin, non-unit membrane lying attached to the cytoplasmic membrane in the periphery of the cell) like green sulphur bacteria.

It has thus been proposed that modern Choloroflexus may be a vestige of a very early phototrophic ancestor that perhaps first evolved a photosynthetic reaction centre and then received chlorosome-specific genes by lateral transfer.


The Plan to Grab the World's Carbon With Supercharged Plants

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Joanne Chory is tackling climate change as a biologist: by engineering plants to grab even more carbon from the air than they already do. Ryan Lash/TED

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In humanity’s battle against man-made climate change, the Earth itself provides one of the most important weapons, a natural system that breathes in Earth-warming CO2 and exhales oxygen.

Yes, I’m talking about plants, engineered by nature itself over the course of millennia to harness the Earth’s natural conditions to turn sunlight and CO2 into oxygen and organic matter. Plants are the key to many climate-change-fighting tactics. Want to cut down on the methane gas that’s contributing to global warming? Eat more plants (and fewer farting cows). Want to offset some of the carbon emissions from your airline or consumer retail company? Buy a forest of oxygen-emitting trees. Want to create a natural fuel that won’t puff black clouds full of CO2 into the air? Consider vegetable oil (or photosynthesizing algae, which isn’t a plant but has a lot in common with them).

Plant biologist Joanne Chory thinks plants can do more. She has studied the genetics of plants at the Salk Institute in San Diego for more than 30 years, and she and the rest of the five-person Harnessing Plants Initiative team are convinced that photosynthesis itself can be exploited to create a biological solution to carbon capture.

Engineers have tried to do this with massive machines, to limited effect. “As plant biologists, we just looked at the problem a little differently. We didn’t think of an engineering solution. We didn't think about building a big machine that could suck in air and then capture the CO2 on a sponge, or whatever. We said, 'That’s what plants were evolved to do,'” Chory says.

Unlike engineered solutions, biology harnesses evolutionary time, because plants have already evolved for 500 million years to be great at sucking up CO2. In fact, according to the Salk Institute, every year plants and other photosynthetic life capture 746 gigatons of CO2 and then release 727 gigatons of CO2 back. If it weren’t for the 37 gigatons of CO2 humans also release into the atmosphere annually, the global carbon cycle would be healthy. But, as it stands, each year the Earth is left with 18 gigatons of CO2 it cannot naturally handle.

Chory believes the key to fixing that imbalance is to train plants to suck up just a little more CO2 and keep it longer. She is working on engineering the world’s crop plants to have bigger, deeper roots made of a natural waxy substance called suberin—found in cork and cantaloupe rinds—which is an incredible carbon-capturer and is resistant to decomposition. By encouraging plants to have bigger, deeper, more suberin-rich roots, Chory can trick them into fighting climate change as they grow. The roots will store CO2, and when farmers harvest their crops in the fall, those deep-buried roots will stay in the soil and keep their carbon sequestered in the dirt, potentially for hundreds of years.

“Every year plants and other photosynthetic organisms take up an incredible amount of CO2—like twentyfold more than we ever put up when we burn fossil fuels—but then at the end of the growing season most plants just die, and they decompose, and it goes back up as CO2. That's been a real problem,” she told WIRED last week in Vancouver, British Columbia, at the TED 2019 conference, where she received an Audacious Project prize of more than $35 million to scale this project. It was the second-largest donation in the Salk Institute’s history. “We’re going to make them amazing.”

If she and her team can breed these plants and get them into the global agricultural food chain, Chory believes they can contribute a 20 to 46 percent reduction in excess CO2 emissions annually.

The benefits don’t stop there, according to Chory. Those roots will very slowly break down and deposit their carbon little by little in the soil. This could reverse some of the human-caused depletion that has removed carbon and other nutrients from the soil due to agricultural practices that “treat soil like dirt,” to quote UC Merced soil scientist Asmeret Asefaw Berhe, who also spoke at TED 2019. Berhe explained that nutrient soil depletion from agriculture has left it less fertile, with fewer nutrients for the plants to absorb from the soil.

“I think we can get the plants to help us,” Chory said in conversation with Berhe. She’s banking on the hope that the team’s plants will deposit carbon back into the soil in a way that makes it more fertile. That’s how Chory and the team plan to scale up their solution: by convincing farmers that suberin-rich crops will not only help with climate change but also help feed the growing populations of the world.

And they’ll have to, because farmers are not going to sign on to grow weirdly root-huge plants if doing so hurts their yields.

“These plants will be stronger and more sustainable,” Chory says. “The old adage is, feed the soil not the plant,” she explains, and that’s what the team believes these roots will do.

Right now, the Salk team is at the beginning phases of this project. They’ve identified genetic pathways that control for the three traits they want to bring out in plants: increasing suberin, enlarging root systems, and making the roots grow down deeper into the ground. Now they will begin to test combining those three traits in a model plant called arabidopsis in the lab, before moving on to crop plants like corn, soybean, and rice. They hope to have prototypes of souped up versions of major crops within five years and are already in talks with agricultural companies to partner on testing them.

They plan to combine these traits using traditional plant-breeding techniques first, and possibly down the line use gene editing techniques like CRISPR to accelerate trait adoption. The team is trying to move fast in every way.

And time is off the essence. Not just because the next 11 years may be our last best chance to reverse course away from catastrophic climate change, but because Chory herself is facing a looming deadline.

She has Parkinson’s disease and is growing increasingly symptomatic. “My days are going to be numbered in a way that I can see. So that gives me a sense of urgency,” she says. She plans to spend the rest of her scientific career on this single project to use plants to mitigate global climate change.

For Chory, that’s a big departure from her previous work, which, though instrumental to enabling this current project, was never focused on solving a specific urgent problem. Until now, she’d been doing basic research, contributing to overall human knowledge without any sort of mandate that her discoveries cure a specific ill. All of that work allowed her and the team to reach the insight that plants could be harnessed to help with climate change. But applying that science to solve a specific problem feels very, very different and requires her to step far outside her comfort zone.

Applying for the Audacious Project meant going through months of work with TED and consultants hired to help the project finalists refine their pitch to philanthropists. It meant coming to Vancouver and speaking directly about how her work translates to the real world. The day before her talk, Chory was incredibly nervous. A consultant who worked to prepare her, Chris Addy of Bridgespan Group, said that Chory was probably the most nervous of all eight Audacious Project leads. But she got up there and pitched her vision, because of how much it matters to her.

“She gets notes like, ‘Thank you for saving the world!” says her husband, scientist Stephen Worland, who is CEO of therapeutics company Effector and with whom Chory has two grown children.

“That's why I feel like I have the weight of the world on my shoulders. Five people can't save it,” she says. “But we can be a part of it. I feel really strongly that I want to do that now, because I’m getting to the end of my career, really.”

Her newfound mission means that, as she faces Parkinson’s and the looming end of her career, Chory is working probably more hours than ever before. “My daughter said to me, ‘I never remember you working this hard,’” she says. Then she quickly adds, “That felt like a victory, actually, because I was working pretty hard the whole time they were growing up, but she didn't really miss me.”

Now, without kids in the house, Chory is free to work all the time. Trying to save the world, one deep, fat, waxy plant root at a time.


Contents

These reactions are closely coupled to the thylakoid electron transport chain as the energy required to reduce the carbon dioxide is provided by NADPH produced in photosystem I during the light dependent reactions. The process of photorespiration, also known as C2 cycle, is also coupled to the calvin cycle, as it results from an alternative reaction of the RuBisCO enzyme, and its final byproduct is another glyceraldehyde-3-P.

The Calvin cycle, Calvin–Benson–Bassham (CBB) cycle, reductive pentose phosphate cycle (RPP cycle) or C3 cycle is a series of biochemical redox reactions that take place in the stroma of chloroplast in photosynthetic organisms.

Photosynthesis occurs in two stages in a cell. In the first stage, light-dependent reactions capture the energy of light and use it to make the energy-storage and transport molecules ATP and NADPH. The Calvin cycle uses the energy from short-lived electronically excited carriers to convert carbon dioxide and water into organic compounds [4] that can be used by the organism (and by animals that feed on it). This set of reactions is also called carbon fixation. The key enzyme of the cycle is called RuBisCO. In the following biochemical equations, the chemical species (phosphates and carboxylic acids) exist in equilibria among their various ionized states as governed by the pH.

The enzymes in the Calvin cycle are functionally equivalent to most enzymes used in other metabolic pathways such as gluconeogenesis and the pentose phosphate pathway, but they are found in the chloroplast stroma instead of the cell cytosol, separating the reactions. They are activated in the light (which is why the name "dark reaction" is misleading), and also by products of the light-dependent reaction. These regulatory functions prevent the Calvin cycle from being respired to carbon dioxide. Energy (in the form of ATP) would be wasted in carrying out these reactions that have no net productivity.

The sum of reactions in the Calvin cycle is the following:

Hexose (six-carbon) sugars are not a product of the Calvin cycle. Although many texts list a product of photosynthesis as C
6 H
12 O
6 , this is mainly a convenience to counter the equation of respiration, where six-carbon sugars are oxidized in mitochondria. The carbohydrate products of the Calvin cycle are three-carbon sugar phosphate molecules, or "triose phosphates", namely, glyceraldehyde-3-phosphate (G3P).

Steps Edit

In the first stage of the Calvin cycle, a CO
2 molecule is incorporated into one of two three-carbon molecules (glyceraldehyde 3-phosphate or G3P), where it uses up two molecules of ATP and two molecules of NADPH, which had been produced in the light-dependent stage. The three steps involved are:

  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. [5] The product of the first step is enediol-enzyme complex that can capture CO
    2 or O
    2 . Thus, enediol-enzyme complex is the real carboxylase/oxygenase. The CO
    2 that is captured by enediol in second step produces an unstable six-carbon compound called 2-carboxy 3-keto 1,5-biphosphoribotol (CKABP [6] ) (or 3-keto-2-carboxyarabinitol 1,5-bisphosphate) that immediately splits into 2 molecules of 3-phosphoglycerate (also written as 3-phosphoglyceric acid, PGA, 3PGA, or 3-PGA), a 3-carbon compound. [7]
  2. The enzyme phosphoglycerate kinase catalyses the phosphorylation of 3-PGA by ATP (which was produced in the light-dependent stage). 1,3-Bisphosphoglycerate (glycerate-1,3-bisphosphate) and ADP are the products. (However, note that two 3-PGAs are produced for every CO
    2 that enters the cycle, so this step utilizes two ATP per CO
    2 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 CO
    2 fixed.

The next stage in the Calvin cycle is to regenerate RuBP. Five G3P molecules produce three RuBP molecules, using up three molecules of ATP. Since each CO
2 molecule produces two G3P molecules, three CO
2 molecules produce six G3P molecules, of which five are used to regenerate RuBP, leaving a net gain of one G3P molecule per three CO
2 molecules (as would be expected from the number of carbon atoms involved).

The regeneration stage can be broken down into steps.

    converts all of the G3P reversibly into dihydroxyacetone phosphate (DHAP), also a 3-carbon molecule. and fructose-1,6-bisphosphatase convert a G3P and a DHAP into fructose 6-phosphate (6C). A phosphate ion is lost into solution.
  1. Then fixation of another CO
    2 generates two more G3P.
  2. F6P has two carbons removed by transketolase, giving erythrose-4-phosphate (E4P). The two carbons on transketolase are added to a G3P, giving the ketose xylulose-5-phosphate (Xu5P).
  3. E4P and a DHAP (formed from one of the G3P from the second CO
    2 fixation) are converted into sedoheptulose-1,7-bisphosphate (7C) by aldolase enzyme.
  4. 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.
  5. Fixation of a third CO
    2 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 CO
    2 , with generation of three pentoses that can be converted to Ru5P.
  6. R5P is converted into ribulose-5-phosphate (Ru5P, RuP) by phosphopentose isomerase. Xu5P is converted into RuP by phosphopentose epimerase.
  7. 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.

Thus, of six G3P produced, five are used to make three RuBP (5C) molecules (totaling 15 carbons), with only one G3P available for subsequent conversion to hexose. This requires nine ATP molecules and six NADPH molecules per three CO
2 molecules. The equation of the overall Calvin cycle is shown diagrammatically below.

RuBisCO also reacts competitively with O
2 instead of CO
2 in photorespiration. The rate of photorespiration is higher at high temperatures. Photorespiration turns RuBP into 3-PGA and 2-phosphoglycolate, a 2-carbon molecule that can be converted via glycolate and glyoxalate to glycine. Via the glycine cleavage system and tetrahydrofolate, two glycines are converted into serine + CO
2 . Serine can be converted back to 3-phosphoglycerate. Thus, only 3 of 4 carbons from two phosphoglycolates can be converted back to 3-PGA. It can be seen that photorespiration has very negative consequences for the plant, because, rather than fixing CO
2 , this process leads to loss of CO
2 . C4 carbon fixation evolved to circumvent photorespiration, but can occur only in certain plants native to very warm or tropical climates—corn, for example.

Products Edit

The immediate products of one turn of the Calvin cycle are 2 glyceraldehyde-3-phosphate (G3P) molecules, 3 ADP, and 2 NADP + . (ADP and NADP + are not really "products." They are regenerated and later used again in the Light-dependent reactions). Each G3P molecule is composed of 3 carbons. For the Calvin cycle to continue, RuBP (ribulose 1,5-bisphosphate) must be regenerated. So, 5 out of 6 carbons from the 2 G3P molecules are used for this purpose. Therefore, there is only 1 net carbon produced to play with for each turn. To create 1 surplus G3P requires 3 carbons, and therefore 3 turns of the Calvin cycle. To make one glucose molecule (which can be created from 2 G3P molecules) would require 6 turns of the Calvin cycle. Surplus G3P can also be used to form other carbohydrates such as starch, sucrose, and cellulose, depending on what the plant needs. [8]

These reactions do not occur in the dark or at night. There is a light-dependent regulation of the cycle enzymes, as the third step requires reduced NADP.

There are two regulation systems at work when the cycle must be turned on or off: the thioredoxin/ferredoxin activation system, which activates some of the cycle enzymes and the RuBisCo enzyme activation, active in the Calvin cycle, which involves its own activase.

The thioredoxin/ferredoxin system activates the enzymes glyceraldehyde-3-P dehydrogenase, glyceraldehyde-3-P phosphatase, fructose-1,6-bisphosphatase, sedoheptulose-1,7-bisphosphatase, and ribulose-5-phosphatase kinase, which are key points of the process. This happens when light is available, as the ferredoxin protein is reduced in the photosystem I complex of the thylakoid electron chain when electrons are circulating through it. [9] Ferredoxin then binds to and reduces the thioredoxin protein, which activates the cycle enzymes by severing a cystine bond found in all these enzymes. This is a dynamic process as the same bond is formed again by other proteins that deactivate the enzymes. The implications of this process are that the enzymes remain mostly activated by day and are deactivated in the dark when there is no more reduced ferredoxin available.

The enzyme RuBisCo has its own, more complex activation process. It requires that a specific lysine amino acid be carbamylated to activate the enzyme. This lysine binds to RuBP and leads to a non-functional state if left uncarbamylated. A specific activase enzyme, called RuBisCo activase, helps this carbamylation process by removing one proton from the lysine and making the binding of the carbon dioxide molecule possible. Even then the RuBisCo enzyme is not yet functional, as it needs a magnesium ion bound to the lysine to function. This magnesium ion is released from the thylakoid lumen when the inner pH drops due to the active pumping of protons from the electron flow. RuBisCo activase itself is activated by increased concentrations of ATP in the stroma caused by its phosphorylation.


Rubisco proton production can enhance carbon dioxide acquisition

Carboxysome evolution pathways. Credit: Ben Long, The Australian National University

Rubisco is arguably the most abundant—and most important—protein on Earth. This enzyme drives photosynthesis, the process that plants use to convert sunlight into energy to fuel crop growth and yield. Rubisco's role is to capture and fix carbon dioxide (CO2) into sugar that fuels the plant's activities. However, as much as Rubisco benefits plant growth, it also can operate at a notoriously slow pace that creates a hindrance to photosynthetic efficiency.

About 20 percent of the time Rubisco fixes oxygen (O2) molecules instead of CO2, costing the plant energy that could have been utilized to create yield. This time- and energy-consuming process is called photorespiration, where the plant sends its enzymes through three different compartments within the plant cell.

"However, many photosynthetic organisms have evolved mechanisms to overcome some of Rubisco's limitations," said Ben Long who led this recent study published in PNAS for a research project called Realizing Increased Photosynthetic Efficiency (RIPE). RIPE, which is led by Illinois in partnership with the Australian National University (ANU), is engineering crops to be more productive by improving photosynthesis.

"Among these organisms are microalgae and cyanobacteria from aquatic environments, which have efficiently functioning Rubisco enzymes sitting inside liquid protein droplets and protein compartments called pyrenoids and carboxysomes," said lead researcher Long from the ANU Research School of Biology.

How these protein compartments assist in the Rubisco function is not entirely known. The team from ANU aimed to find the answer by using a mathematical model that focused on the chemical reaction Rubisco carries out. As it collects CO2 from the atmosphere, Rubisco also releases positively charged protons.

"Inside Rubisco compartments, these protons can speed up Rubisco by increasing the amount of CO2 available. The protons do this by helping the conversion of bicarbonate into CO2," said Long. "Bicarbonate is the major source of CO2 in aquatic environments and photosynthetic organisms that use bicarbonate can tell us a lot about how to improve crop plants."

The mathematical model gives the ANU team a better idea as to why these special Rubisco compartments might improve the enzyme's function and it also gives them more insight into how they may have evolved. One hypothesis from the study suggests that periods of low CO2 in the earth's ancient atmosphere may have been the trigger for the cyanobacteria and microalgae to evolve these specialized compartments, while they might also be beneficial for organisms that grow in dim light environments.

ANU members of the Realizing Increased Photosynthetic Efficiency (RIPE) project are trying to build these specialized Rubisco compartments in crop plants to assist in increasing yield.

"The outcomes of this study," explained Long, "provide an insight into the correct function of specialized Rubisco compartments and give us a better understanding of how we expect them to perform in plants."


Gas diet

In the latest work, Milo and his team used a mix of genetic engineering and lab evolution to create a strain of E. coli that can get all its carbon from CO2. First, they gave the bacterium genes that encode a pair of enzymes that allow photosynthetic organisms to convert CO2 into organic carbon. Plants and cyanobacteria power this conversion with light, but that wasn’t feasible for E. coli. Instead, Milo’s team inserted a gene that lets the bacterium glean energy from an organic molecule called formate.

Even with these additions, the bacterium refused to swap its sugar meals for CO2. To further tweak the strain, the researchers cultured successive generations of the modified E. coli for a year, giving them only minute quantities of sugar, and CO2 at concentrations about 250 times those in Earth’s atmosphere. They hoped that the bacteria would evolve mutations to adapt to this new diet. After about 200 days, the first cells capable of using CO2 as their only carbon source emerged. And after 300 days, these bacteria grew faster in the lab conditions than did those that could not consume CO2.

The CO2-eating, or autotrophic, E. coli strains can still grow on sugar — and would use that source of fuel over CO2, given the choice, says Milo. Compared with normal E. coli, which can double in number every 20 minutes, the autotrophic E. coli are laggards, dividing every 18 hours when grown in an atmosphere that is 10% CO2. They are not able to subsist without sugar on atmospheric levels of CO2 — currently 0.041%.

Milo and his team hope to make their bacteria grow faster and live on lower levels of CO2. They are also trying to understand how the E. coli evolved to eat CO2: changes in just 11 genes seemed to allow the switch, and they are now working on determining how.

The work is a “milestone” and shows the power of melding engineering and evolution to improve natural processes, says Cheryl Kerfeld, a bioengineer at Michigan State University in East Lansing and the Lawrence Berkeley National Laboratory in California.

Already, E. coli is used to make synthetic versions of useful chemicals such as insulin and human growth hormone. Milo says that his team’s work could expand the products the bacteria can make, to include renewable fuels, food and other substances. But he doesn’t see this happening soon.

“This is a proof-of-concept paper,” agrees Erb. “It will take a couple years until we see this organism applied.”


Watch the video: The Science Behind CO2 Delivery Solutions (July 2022).


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