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==Carbon isotope discrimination==
==Carbon isotope discrimination==
Some [[carboxylase]]s, particularly rubisco, preferentially bind the light carbon stable isotope [[carbon-12]] over the heavier [[carbon-13]]. This is known as carbon isotope discrimination and results in carbon-12 to carbon-13 ratios in the plant that are lower than in the free air. Measurement of this ratio is important in the evaluation of water use efficiency in plants, and also in assessing the possible or likely sources of carbon in global carbon cycle studies.
Some [[carboxylase]]s, particularly rubisco, preferentially bind the lighter carbon stable isotope [[carbon-12]] over the heavier [[carbon-13]]. This is known as carbon isotope discrimination and results in carbon-12 to carbon-13 ratios in the plant that are lower than in the free air. Measurement of this ratio is important in the evaluation of water use efficiency in plants, and also in assessing the possible or likely sources of carbon in global carbon cycle studies.


==Other reduced carbon==
==Other reduced carbon==

Revision as of 19:46, 5 January 2012

For other uses, see Carbon cycle and Carbon sequestration.
Filamentous cyanobacterium
A present-day representative of the cyanobacteria that changed the world.

In biology, carbon fixation is the reduction of carbon dioxide to organic compounds by living organisms. The obvious example is photosynthesis. Carbon fixation requires both a source of energy such as sunlight, and an electron donor such as water. All life depends on fixed carbon. Organisms that grow by fixing carbon are called autotrophs—plants for example. Heterotrophs, like animals, are organisms which grow by using the fixed carbon produced by autotrophs. Some organisms can go either way. Fixed carbon, reduced carbon, and organic carbon all mean organic compounds. Carbon dioxide, in all its guises, is inorganic carbon.

Photosynthesis

Photosynthesis uses energy from sunlight to drive an autotrophic carbon fixation pathway.

Oxygenic photosynthesis

Oxygenic photosynthesis is used by the chief primary producers—plants, algae, and cyanobacteria. They contain the pigment chlorophyll, and use the Calvin cycle to fix carbon autotrophically.

Somewhere between 3.5 and 2.3 billion years ago, cyanobacteria evolved oxygenic photosynthesis.[1][2][3] The process works like this:

2H2O → 4e- + 4H+ + O2
CO2 + 4e- + 4H+ → CH2O + H2O

The essential innovation is the first step, the dissociation of water into electrons, protons, and free oxygen. This allows the use of water, one of the most abundant substances on Earth, as an electron donor—as a source of reducing power. The release of free oxygen is a side-effect of enormous consequence. The first step uses the energy of sunlight to oxidize water to O2, and, ultimately, to produce ATP

ADP + Pi ⇌ ATP + H2O

and the reductant, NADPH

NADP+ + 2e- + 2H+ ⇌ NADPH + H+

The second step, the actual fixation of carbon dioxide, is carried out in the Calvin cycle, which consumes ATP and NADPH. Although redox is thought of as electron transfer, fixing carbon dioxide requires transfer of hydrogen as well. Of course, NADPH can be used to further reduce CH2O. Energy is not stored by fixed carbon alone, but by fixed carbon and free oxygen together.

Anoxygenic photosynthesis

The purple bacteria, green sulfur bacteria, and green nonsulfur bacteria are anoxygenic photosynthetic organisms containing the pigment bacteriochlorophyll. The purple bacteria use the Calvin cycle. The green sulfur bacteria use the reductive citric acid cycle. The green nonsulfur bacteria use the 3-hydroxypropionate bicycle.

Obligately heterotrophic phototrophs

Phototrophs are organisms which convert sunlight to metabolic energy. Phototrophy is known in eukaryotes, across six phyla of bacteria, and in Archaea. However, phototrophy does not necessarily imply autotrophic carbon fixation. In recent decades, a great many phototrophic bacteria and archaea, which lack autotrophic carbon fixation pathways, have been discovered. They are obligately heterotrophic phototrophs, not photoautotrophs. Whether obligately heterotrophic phototrophy should be called photosynthesis is a matter of opinion.

In the early 1970s, the simplest phototrophic mechanism now known, was discovered in some obligately heterotrophic archaea of the Halobacteriales. The cell membrane of these organisms is spanned by molecules of the purple pigment bacteriorhodopsin, a protein that binds retinal. When light activates the retinal, the protein pumps protons across the membrane, and the organism makes ATP using the proton gradient generated.[4][5] Some uncultured marine proteobacteria also have the genes needed to produce retinal and bacteriorhodopsin, and are presumably phototrophic.[6][7] These organisms produce metabolic energy by photophosphorylation, but do not fix carbon autotrophically.

In the 1980s, the heliobacteria, of the Firmicutes, were discovered. They retain bacteriochlorophyll and a rudimentary version of the type I reaction center found in the green sulfur bacteria. The heliobacteria are obligately heterotrophic, and another example of phototrophs that do not fix carbon autotrophically.

Calvin cycle

The reductive pentose phosphate cycle, or the Calvin-Benson-Bassham cycle, or simply the Calvin cycle, was the first autotrophic carbon fixation pathway to be recognized. It was worked-out in the late 1940s and the 1950s by Melvin Calvin, Andrew Benson, James Bassham, and others. Calvin won the 1961 Nobel Prize in Chemistry for his work. 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.

The Calvin cycle makes sugar by reducing carbon dioxide. It makes glyceraldehyde 3-phosphate (GAP) which is a phosphate of the triose, glyceraldehyde ((CH2O)3)

3CO2 + 3(4e- + 4H+) + Pi → GAP + 4H2O

or accounting for NADPH and ATP

3CO2 + 6NADPH + 6H+ + 9ATP + 5H2O → GAP + 6NADP+ + 9ADP + 8Pi

Carbon concentrating mechanisms

Some plants have adapted the anaplerotic pathway

CO2 + H2O → HCO3- + H+
pyruvate + ATP + Pi → PEP + AMP + PPi
HCO3- + H+ + PEP → oxaloacetate + Pi

for use in inorganic carbon concentrating mechanisms. Carbonic anhydrase (CA) catalyzes the hydrolysis of carbon dioxide to bicarbonate; pyruvate, phosphate dikinase (PPDK), the phosphorylation of pyruvate to phosphoenolpyruvate (PEP); and PEP carboxylase (PEPC), the carboxylation of PEP to oxaloacetate. The hydrolysis of ATP to AMP results in the consumption of two ATP. Plants, which have adapted this pathway to concentrate carbon dioxide, reduce the oxaloacetic acid produced to a 4-carbon dicarboxylic acid, either malic acid or aspartic acid. The acid is transported into the stromas of actively photosynthesizing chloroplasts, where it is decarboxylated to a 3-carbon monocarboxylic acid, which can be recycled, releasing carbon dioxide for use in the Calvin cycle.

CAM plants that use Crassulacean acid metabolism as an adaptation for arid conditions. CO2 enters through the stomata during the night and is converted into the 4-carbon compound, malic acid, which releases CO2 for use in the Calvin cycle during the day, when the stomata are closed. The jade plant (Crassula ovata) and cacti are typical of CAM plants. Sixteen thousand species of plants use CAM.[8] These plants have a carbon isotope signature of -20 to -10 ‰.[9]

C4 plants preface the Calvin cycle with reactions that incorporate CO2 into one of the 4-carbon compounds, malic acid or aspartic acid. C4 plants have a distinctive internal leaf anatomy. Tropical grasses, such as sugar cane and maize are C4 plants, but there are many broadleaf plants that are C4. Overall, 7600 species of terrestrial plants use C4 carbon fixation, representing around 3% of all species.[10] These plants have a carbon isotope signature of -16 to -10 ‰.[9]

C3 plants that use the Calvin cycle for the initial steps that incorporate CO2 into organic matter, forming a 3-carbon compound as the first stable. This form of photosynthesis occurs in the majority of terrestrial species of plants. Plants that use this pathway have a carbon isotope signature of -24 to -33‰.[9]

Fossil carbon

Kerogen is a mixture of organic chemical compounds that make up a portion of the organic matter in sedimentary rocks.

Other autotrophic pathways

Six autotrophic carbon fixation pathways are known as of 2011. The Calvin cycle fixes carbon in the chloroplasts of plants and algae, and in the cyanobacteria. It also fixes carbon in the anoxygenic photosynthetic proteobacteria called purple bacteria, and in some non-phototrophic proteobacteria.[11] Of the five other autotrophic pathways, two are known only in bacteria, two only in archaea, and one in both bacteria and archaea.

Reductive citric acid cycle

The reductive citric acid cycle is the oxidative citric acid cycle run in reverse. It has been found in anaerobic and microaerobic bacteria. It was proposed in 1966 by Evans, Buchanan and Arnon who were working with the anoxygenic photosynthetic green sulfur bacterium that they called Chlorobium thiosulfatophilum. The reductive citric acid cycle is sometimes called the Arnon-Buchanan cycle.[12]

Reductive acetyl CoA pathway

The reductive acetyl CoA pathway has been found in strictly anaerobic bacteria and archaea. It was proposed in 1965 by Ljungdahl and Wood. They were working with the gram-positive acetic acid producing bacterium Clostridium thermoaceticum, which is now named Moorella thermoacetica. The reductive acetyl CoA pathway is sometimes called the Wood-Ljungdahl pathway.[13][14]

3-Hydroxypropionate bicycle

The 3-hydroxypropionate bicycle is known only in green nonsulfur bacteria. It was proposed in 2002 for the anoxygenic photosynthetic Chloroflexus aurantiacus. None of the enzymes used by the 3-hydroxypropionate bicycle are especially oxygen sensitive.[15][16]

3-Hydroxypropionate/4-hydroxybutyrate cycle

The 3-hydroxypropionate/4-hydroxybutyrate cycle has been found in aerobic archaea. It was proposed in 2007 for the extreme thermoacidophile archaeon Metallosphaera sedula.[17]

Dicarboxylate/4-hydroxybutyrate cycle

The dicarboxylate/4-hydroxybutyrate cycle has been found in anaerobic archaea. It was proposed in 2008 for the hyperthermophile archeon Ignicoccus hospitalis.[18]

Non-autotrophic pathways

Although almost all heterotrophs cannot synthesize complete organic molecules from carbon dioxide, some carbon dioxide is incorporated in their metabolism.[19] Notably pyruvate carboxylase consumes carbon dioxide (as bicarbonate ions) as part of gluconeogenesis.

Carbon isotope discrimination

Some carboxylases, particularly rubisco, preferentially bind the lighter carbon stable isotope carbon-12 over the heavier carbon-13.  This is known as carbon isotope discrimination and results in carbon-12 to carbon-13 ratios in the plant that are lower than in the free air.  Measurement of this ratio is important in the evaluation of water use efficiency in plants, and also in assessing the possible or likely sources of carbon in global carbon cycle studies.

Other reduced carbon

Non-biological carbon fixation is of interest, according to Graham Cairns-Smith, in the study of the origins of life.

References

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