Carbon fixation
Encyclopedia
In biology
, carbon fixation is the reduction
of carbon dioxide
to organic compound
s by living organism
s. 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 autotroph
s—plant
s for example. Heterotroph
s, like animal
s, 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.
uses energy from sunlight to drive an autotrophic carbon fixation pathway
.
, 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.
The process works like this:
The essential innovation is the first step, the dissociation of water into electron
s, 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
and the reductant, NADPH
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.
. 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.
s are organisms which convert sunlight to metabolic energy. Phototrophy is known in eukaryotes, across six phyla
of bacteria, and in archaea
. Plants and cyanobacteria are generally photoautotrophs. Otherwise photoautotrophic algae may be facultative
heterotrophs that feed on dissolved organic carbon. Otherwise photoautotrophic dinoflagellate
s may feed by engulfing prey, ensnaring prey and digesting them externally, or just sucking the insides out of them. To complicate things, some algae have lost the ability to photosynthesize, and are no longer either phototrophs or autotrophs. Cyanobacteria aside, phototrophic bacteria are generally facultative or even obligate
heterotrophs. Some authors apply the word photosynthesis to obligately heterotrophic photoheterotrophs. Others restrict it to photoautotrophs.
Before the 1970s, the only known phototrophs were the organisms that use photosynthesis to fix carbon autotrophically. Then, 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. Some uncultured marine proteobacteria also have the genes needed to produce retinal and bacteriorhodopsin, and are presumably phototrophic. 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.
, 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. Specifically, it makes glyceraldehyde 3-phosphate
(GAP) which is a phosphate of the triose
, glyceraldehyde ((CH2O)3)
or accounting for NADPH and ATP, but not for water
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 2ATP. 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. These plants have a carbon isotope signature of -20 to -10 ‰.
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. These plants have a carbon isotope signature of -16 to -10 ‰.
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‰.
is a mixture of organic chemical compounds that make up a portion of the organic matter in sedimentary rock
s.
s 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.
Of the five other autotrophic pathways, two are known only in bacteria
, two only in archaea
, and one in both bacteria and archaea.
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.
acetic acid
producing bacterium Clostridium thermoaceticum, which is now named Moorella thermoacetica. The reductive acetyl CoA pathway is sometimes called the Wood-Ljungdahl pathway.
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.
It was proposed in 2007 for the extreme thermoacidophile archaeon Metallosphaera sedula
.
It was proposed in 2008 for the hyperthermophile archeon Ignicoccus hospitalis
.
consumes carbon dioxide (as bicarbonate ions) as part of gluconeogenesis
.
, in the study of the origins of life.
Biology
Biology is a natural science concerned with the study of life and living organisms, including their structure, function, growth, origin, evolution, distribution, and taxonomy. Biology is a vast subject containing many subdivisions, topics, and disciplines...
, carbon fixation is the reduction
Redox
Redox reactions describe all chemical reactions in which atoms have their oxidation state changed....
of carbon dioxide
Carbon dioxide
Carbon dioxide is a naturally occurring chemical compound composed of two oxygen atoms covalently bonded to a single carbon atom...
to organic compound
Organic compound
An organic compound is any member of a large class of gaseous, liquid, or solid chemical compounds whose molecules contain carbon. For historical reasons discussed below, a few types of carbon-containing compounds such as carbides, carbonates, simple oxides of carbon, and cyanides, as well as the...
s by living organism
Organism
In biology, an organism is any contiguous living system . In at least some form, all organisms are capable of response to stimuli, reproduction, growth and development, and maintenance of homoeostasis as a stable whole.An organism may either be unicellular or, as in the case of humans, comprise...
s. The obvious example is photosynthesis
Photosynthesis
Photosynthesis is a chemical process that converts carbon dioxide into organic compounds, especially sugars, using the energy from sunlight. Photosynthesis occurs in plants, algae, and many species of bacteria, but not in archaea. Photosynthetic organisms are called photoautotrophs, since they can...
. Carbon fixation requires both a source of energy such as sunlight, and an electron donor
Electron donor
An electron donor is a chemical entity that donates electrons to another compound. It is a reducing agent that, by virtue of its donating electrons, is itself oxidized in the process....
such as water. All life depends on fixed carbon. Organisms that grow by fixing carbon are called autotroph
Autotroph
An autotroph, or producer, is an organism that produces complex organic compounds from simple inorganic molecules using energy from light or inorganic chemical reactions . They are the producers in a food chain, such as plants on land or algae in water...
s—plant
Plant
Plants are living organisms belonging to the kingdom Plantae. Precise definitions of the kingdom vary, but as the term is used here, plants include familiar organisms such as trees, flowers, herbs, bushes, grasses, vines, ferns, mosses, and green algae. The group is also called green plants or...
s for example. Heterotroph
Heterotroph
A heterotroph is an organism that cannot fix carbon and uses organic carbon for growth. This contrasts with autotrophs, such as plants and algae, which can use energy from sunlight or inorganic compounds to produce organic compounds such as carbohydrates, fats, and proteins from inorganic carbon...
s, like animal
Animal
Animals are a major group of multicellular, eukaryotic organisms of the kingdom Animalia or Metazoa. Their body plan eventually becomes fixed as they develop, although some undergo a process of metamorphosis later on in their life. Most animals are motile, meaning they can move spontaneously and...
s, are organisms which grow by using the fixed carbon produced
Primary production
400px|thumb|Global oceanic and terrestrial photoautotroph abundance, from September [[1997]] to August 2000. As an estimate of autotroph biomass, it is only a rough indicator of primary production potential, and not an actual estimate of it...
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
PhotosynthesisPhotosynthesis
Photosynthesis is a chemical process that converts carbon dioxide into organic compounds, especially sugars, using the energy from sunlight. Photosynthesis occurs in plants, algae, and many species of bacteria, but not in archaea. Photosynthetic organisms are called photoautotrophs, since they can...
uses energy from sunlight to drive an autotrophic carbon fixation pathway
Metabolic pathway
In biochemistry, metabolic pathways are series of chemical reactions occurring within a cell. In each pathway, a principal chemical is modified by a series of chemical reactions. Enzymes catalyze these reactions, and often require dietary minerals, vitamins, and other cofactors in order to function...
.
Oxygenic photosynthesis
Oxygenic photosynthesis is used by the chief primary producers—plants, algaeAlgae
Algae are a large and diverse group of simple, typically autotrophic organisms, ranging from unicellular to multicellular forms, such as the giant kelps that grow to 65 meters in length. They are photosynthetic like plants, and "simple" because their tissues are not organized into the many...
, and cyanobacteria. They contain the pigment chlorophyll
Chlorophyll
Chlorophyll is a green pigment found in almost all plants, algae, and cyanobacteria. Its name is derived from the Greek words χλωρος, chloros and φύλλον, phyllon . Chlorophyll is an extremely important biomolecule, critical in photosynthesis, which allows plants to obtain energy from light...
, and use the Calvin cycle
Calvin cycle
The Calvin cycle or Calvin–Benson-Bassham cycle or reductive pentose phosphate cycle or C3 cycle or CBB cycle is a series of biochemical redox reactions that take place in the stroma of chloroplasts in photosynthetic organisms...
to fix carbon autotrophically.
Somewhere between 3.5 and 2.3 billion years ago, cyanobacteria evolved oxygenic photosynthesis.
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 electron
Electron transfer
Electron transfer is the process by which an electron moves from an atom or a chemical species to another atom or chemical species...
s, protons
Hydronium
In chemistry, a hydronium ion is the cation , a type of oxonium ion produced by protonation of water. This cation is often used to represent the nature of the proton in aqueous solution, where the proton is highly solvated...
, and free oxygen
Oxygen
Oxygen is the element with atomic number 8 and represented by the symbol O. Its name derives from the Greek roots ὀξύς and -γενής , because at the time of naming, it was mistakenly thought that all acids required oxygen in their composition...
. 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
Adenosine triphosphate
Adenosine-5'-triphosphate is a multifunctional nucleoside triphosphate used in cells as a coenzyme. It is often called the "molecular unit of currency" of intracellular energy transfer. ATP transports chemical energy within cells for metabolism...
- ADP3- + Pi3- + 2H+ ATP4- + 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
Electron transfer
Electron transfer is the process by which an electron moves from an atom or a chemical species to another atom or chemical species...
, 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 bacteriochlorophyllBacteriochlorophyll
Bacteriochlorophylls are photosynthetic pigments that occur in various phototrophic bacteria. They were discovered by Von Neil in 1932 . They are related to chlorophylls, which are the primary pigments in plants, algae, and cyanobacteria. Groups that contain bacteriochlorophyll conduct...
. The purple bacteria
Purple bacteria
Purple bacteria or purple photosynthetic bacteria are proteobacteria that are phototrophic, that is capable of producing energy through photosynthesis...
use the Calvin cycle. The green sulfur bacteria
Green sulfur bacteria
The green sulfur bacteria are a family of obligately anaerobic photoautotrophic bacteria. Most closely related to the distant Bacteroidetes, they are accordingly assigned their own phylum....
use the reductive citric acid cycle. The green nonsulfur bacteria use the 3-hydroxypropionate bicycle.
Photoheterotrophy
PhototrophPhototroph
Phototrophs are the organisms that carry out photosynthesis to acquire energy. They use the energy from sunlight to convert carbon dioxide and water into organic material to be utilized in cellular functions such as biosynthesis and respiration.Most phototrophs are autotrophs, also known as...
s are organisms which convert sunlight to metabolic energy. Phototrophy is known in eukaryotes, across six phyla
Phylum
In biology, a phylum The term was coined by Georges Cuvier from Greek φῦλον phylon, "race, stock," related to φυλή phyle, "tribe, clan." is a taxonomic rank below kingdom and above class. "Phylum" is equivalent to the botanical term division....
of bacteria, and in archaea
Archaea
The Archaea are a group of single-celled microorganisms. A single individual or species from this domain is called an archaeon...
. Plants and cyanobacteria are generally photoautotrophs. Otherwise photoautotrophic algae may be facultative
Facultative
Facultative means "optional" or "discretionary" , used mainly in biology in phrases such as:* Facultative anaerobe, an organism that can use oxygen but also has anaerobic methods of energy production...
heterotrophs that feed on dissolved organic carbon. Otherwise photoautotrophic dinoflagellate
Dinoflagellate
The dinoflagellates are a large group of flagellate protists. Most are marine plankton, but they are common in fresh water habitats as well. Their populations are distributed depending on temperature, salinity, or depth...
s may feed by engulfing prey, ensnaring prey and digesting them externally, or just sucking the insides out of them. To complicate things, some algae have lost the ability to photosynthesize, and are no longer either phototrophs or autotrophs. Cyanobacteria aside, phototrophic bacteria are generally facultative or even obligate
Obligate
Obligate means "by necessity" and is used mainly in biology in phrases such as:* Obligate aerobe, an organism that cannot survive without oxygen* Obligate anaerobe, an organism that cannot survive in the presence of oxygen...
heterotrophs. Some authors apply the word photosynthesis to obligately heterotrophic photoheterotrophs. Others restrict it to photoautotrophs.
Before the 1970s, the only known phototrophs were the organisms that use photosynthesis to fix carbon autotrophically. Then, the simplest phototrophic mechanism now known, was discovered in some obligately heterotrophic archaea
Archaea
The Archaea are a group of single-celled microorganisms. A single individual or species from this domain is called an archaeon...
of the Halobacteriales
Halobacteriales
In taxonomy, the Halobacteriales are an order of the Halobacteria, found in water saturated or nearly saturated with salt. They are also called halophiles, though this name is also used for other organisms which live in somewhat less concentrated salt water. They are common in most environments...
. The cell membrane of these organisms is spanned by molecules of the purple pigment bacteriorhodopsin
Bacteriorhodopsin
Bacteriorhodopsin is a protein used by Archaea, the most notable one being Halobacteria. It acts as a proton pump; that is, it captures light energy and uses it to move protons across the membrane out of the cell...
, a protein that binds retinal
Retinal
Retinal, also called retinaldehyde or vitamin A aldehyde, is one of the many forms of vitamin A . Retinal is a polyene chromophore, and bound to proteins called opsins, is the chemical basis of animal vision...
. When light activates the retinal, the protein pumps protons across the membrane, and the organism makes ATP using the proton gradient generated. Some uncultured marine proteobacteria also have the genes needed to produce retinal and bacteriorhodopsin, and are presumably phototrophic. These organisms produce metabolic energy by photophosphorylation, but do not fix carbon autotrophically.
In the 1980s, the heliobacteria
Heliobacteria
The heliobacteria are phototrophic, that is to say, they convert light energy into chemical energy by photosynthesis; they use a PSI type reaction center. The primary pigment involved is bacteriochlorophyll g, which is unique to the group and has a unique absorption spectrum; this gives the...
, of the Firmicutes
Firmicutes
The Firmicutes are a phylum of bacteria, most of which have Gram-positive cell wall structure. A few, however, such as Megasphaera, Pectinatus, Selenomonas and Zymophilus, have a porous pseudo-outer-membrane that causes them to stain Gram-negative...
, 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 CalvinMelvin Calvin
Melvin Ellis Calvin was an American chemist most famed for discovering the Calvin cycle along with Andrew Benson and James Bassham, for which he was awarded the 1961 Nobel Prize in Chemistry. He spent most of his five-decade career at the University of California, Berkeley.- Life :Calvin was born...
, Andrew Benson
Andrew Benson
Andrew Alm Benson is an American biologist and a professor of biology at the University of California, San Diego until his retirement in 1989...
, James Bassham
James Bassham
James Alan Bassham James Alan Bassham James Alan Bassham (born November 26, 1922 in Sacramento, California is an American scientist known for his work on photosynthesis.He received a B.S. degree in chemistry in 1945 from the University of California and his Ph.D. degree in 1949...
, and others. Calvin won the 1961 Nobel Prize in Chemistry
Nobel Prize in Chemistry
The Nobel Prize in Chemistry is awarded annually by the Royal Swedish Academy of Sciences to scientists in the various fields of chemistry. It is one of the five Nobel Prizes established by the will of Alfred Nobel in 1895, awarded for outstanding contributions in chemistry, physics, literature,...
for his work. The Calvin cycle in plants accounts for the preponderance of carbon fixation on land. In algae
Algae
Algae are a large and diverse group of simple, typically autotrophic organisms, ranging from unicellular to multicellular forms, such as the giant kelps that grow to 65 meters in length. They are photosynthetic like plants, and "simple" because their tissues are not organized into the many...
and cyanobacteria, it accounts for the preponderance of carbon fixation in the oceans.
The Calvin cycle makes sugar by reducing carbon dioxide. Specifically, it makes glyceraldehyde 3-phosphate
Glyceraldehyde 3-phosphate
Glyceraldehyde 3-phosphate, also known as triose phosphate or 3-phosphoglyceraldehyde and abbreviated as G3P, GADP, GAP, TP, GALP or PGAL, is a chemical compound that occurs as an intermediate in several central metabolic pathways of all organisms...
(GAP) which is a phosphate of the triose
Triose
A triose is a monosaccharide, or simple sugar, containing three carbon atoms. There are only three possible trioses: L-Glyceraldehyde and D-Glyceraldehyde, both aldotrioses because the carbonyl group is at the end of the chain, and dihydroxyacetone, a ketotriose because the carbonyl group is in...
, glyceraldehyde ((CH2O)3)
- 3CO2 + 3(4e- + 4H+) + Pi3- + H+ → GAP2- + 4H2O
or accounting for NADPH and ATP, but not for water
- 3CO2 + 6NADPH + 9ATP → 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- + PEP → oxaloacetate + Pi
for use in inorganic carbon concentrating mechanisms. Carbonic anhydrase
Carbonic anhydrase
The carbonic anhydrases form a family of enzymes that catalyze the rapid interconversion of carbon dioxide and water to bicarbonate and protons , a reversible reaction that occurs rather slowly in the absence of a catalyst...
(CA) catalyzes the hydrolysis of carbon dioxide to bicarbonate
Bicarbonate
In inorganic chemistry, bicarbonate is an intermediate form in the deprotonation of carbonic acid...
; pyruvate, phosphate dikinase
Pyruvate, phosphate dikinase
In enzymology, a pyruvate, phosphate dikinase is an enzyme that catalyzes the chemical reactionThe 3 substrates of this enzyme are ATP, pyruvate, and phosphate, whereas its 3 products are AMP, phosphoenolpyruvate , and diphosphate...
(PPDK), the phosphorylation of pyruvate to phosphoenolpyruvate
Phosphoenolpyruvate
Phosphoenolpyruvic acid , or phosphoenolpyruvate as the anion, is an important chemical compound in biochemistry. It has the high-energy phosphate bond found in living organisms, and is involved in glycolysis and gluconeogenesis...
(PEP); and PEP carboxylase (PEPC), the carboxylation of PEP to oxaloacetate. The hydrolysis of ATP to AMP
Adenosine monophosphate
Adenosine monophosphate , also known as 5'-adenylic acid, is a nucleotide that is used as a monomer in RNA. It is an ester of phosphoric acid and the nucleoside adenosine. AMP consists of a phosphate group, the sugar ribose, and the nucleobase adenine...
results in the consumption of 2ATP. Plants, which have adapted this pathway to concentrate carbon dioxide, reduce the oxaloacetic acid produced to a 4-carbon dicarboxylic acid, either malic acid
Malic acid
Malic acid is an organic compound with the formula HO2CCH2CHOHCO2H. It is a dicarboxylic acid which is made by all living organisms, contributes to the pleasantly sour taste of fruits, and is used as a food additive. Malic acid has two stereoisomeric forms , though only the L-isomer exists...
or aspartic acid
Aspartic acid
Aspartic acid is an α-amino acid with the chemical formula HOOCCHCH2COOH. The carboxylate anion, salt, or ester of aspartic acid is known as aspartate. The L-isomer of aspartate is one of the 20 proteinogenic amino acids, i.e., the building blocks of proteins...
. 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
Crassula
Crassula is a large genus of succulent plants containing many species, including the popular Jade Plant, Crassula ovata. They are native to many parts of the globe, but cultivated varieties are almost exclusively from the Eastern Cape of South Africa....
) and cacti
Cacti
-See also:* RRDtool The underlying software upon which Cacti is built* MRTG The original Multi Router Traffic Grapher from which RRDtool was "extracted".* Munin -External links:******...
are typical of CAM plants. Sixteen thousand species of plants use CAM. These plants have a carbon isotope signature of -20 to -10 ‰.
C4 plants
C4 carbon fixation
C4 carbon fixation is one of three biochemical mechanisms, along with and CAM photosynthesis, used in carbon fixation. It is named for the 4-carbon molecule present in the first product of carbon fixation in these plants, in contrast to the 3-carbon molecule products in plants. fixation is an...
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
Maize
Maize known in many English-speaking countries as corn or mielie/mealie, is a grain domesticated by indigenous peoples in Mesoamerica in prehistoric times. The leafy stalk produces ears which contain seeds called kernels. Though technically a grain, maize kernels are used in cooking as a vegetable...
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. These plants have a carbon isotope signature of -16 to -10 ‰.
C3 plants
C3 carbon fixation
carbon fixation is a metabolic pathway for carbon fixation in photosynthesis. This process converts carbon dioxide and ribulose bisphosphate into 3-phosphoglycerate through the following reaction:...
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‰.
Fossil carbon
KerogenKerogen
Kerogen is a mixture of organic chemical compounds that make up a portion of the organic matter in sedimentary rocks. It is insoluble in normal organic solvents because of the huge molecular weight of its component compounds. The soluble portion is known as bitumen. When heated to the right...
is a mixture of organic chemical compounds that make up a portion of the organic matter in sedimentary rock
Sedimentary rock
Sedimentary rock are types of rock that are formed by the deposition of material at the Earth's surface and within bodies of water. Sedimentation is the collective name for processes that cause mineral and/or organic particles to settle and accumulate or minerals to precipitate from a solution....
s.
Other autotrophic pathways
Six autotrophic carbon fixation pathways are known as of 2011. The Calvin cycle fixes carbon in the chloroplastChloroplast
Chloroplasts are organelles found in plant cells and other eukaryotic organisms that conduct photosynthesis. Chloroplasts capture light energy to conserve free energy in the form of ATP and reduce NADP to NADPH through a complex set of processes called photosynthesis.Chloroplasts are green...
s of plants and algae, and in the cyanobacteria. It also fixes carbon in the anoxygenic photosynthetic proteobacteria
Proteobacteria
The Proteobacteria are a major group of bacteria. They include a wide variety of pathogens, such as Escherichia, Salmonella, Vibrio, Helicobacter, and many other notable genera....
called purple bacteria
Purple bacteria
Purple bacteria or purple photosynthetic bacteria are proteobacteria that are phototrophic, that is capable of producing energy through photosynthesis...
, and in some non-phototrophic proteobacteria.
Of the five other autotrophic pathways, two are known only in bacteria
Bacteria
Bacteria are a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria have a wide range of shapes, ranging from spheres to rods and spirals...
, two only in archaea
Archaea
The Archaea are a group of single-celled microorganisms. A single individual or species from this domain is called an archaeon...
, and one in both bacteria and archaea.
Reductive citric acid cycle
The reductive citric acid cycleReverse Krebs cycle
The reverse Krebs cycle...
is the oxidative citric acid cycle
Citric acid cycle
The citric acid cycle — also known as the tricarboxylic acid cycle , the Krebs cycle, or the Szent-Györgyi-Krebs cycle — is a series of chemical reactions which is used by all aerobic living organisms to generate energy through the oxidization of acetate derived from carbohydrates, fats and...
run in reverse. It has been found in anaerobic
Anaerobic
Anaerobic is a word which literally means without oxygen, as opposed to aerobic.In wastewater treatment the absence of oxygen is indicated as anoxic; and anaerobic is used to indicate the absence of a common electron acceptor such as nitrate, sulfate or oxygen.Anaerobic may refer to:*Anaerobic...
and microaerobic bacteria. It was proposed in 1966 by Evans, Buchanan and Arnon who were working with the anoxygenic photosynthetic green sulfur bacterium
Green sulfur bacteria
The green sulfur bacteria are a family of obligately anaerobic photoautotrophic bacteria. Most closely related to the distant Bacteroidetes, they are accordingly assigned their own phylum....
that they called Chlorobium thiosulfatophilum. The reductive citric acid cycle is sometimes called the Arnon-Buchanan cycle.
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-positiveGram-positive
Gram-positive bacteria are those that are stained dark blue or violet by Gram staining. This is in contrast to Gram-negative bacteria, which cannot retain the crystal violet stain, instead taking up the counterstain and appearing red or pink...
acetic acid
Acetic acid
Acetic acid is an organic compound with the chemical formula CH3CO2H . It is a colourless liquid that when undiluted is also called glacial acetic acid. Acetic acid is the main component of vinegar , and has a distinctive sour taste and pungent smell...
producing bacterium Clostridium thermoaceticum, which is now named Moorella thermoacetica. The reductive acetyl CoA pathway is sometimes called the Wood-Ljungdahl pathway.
3-Hydroxypropionate bicycle
The 3-hydroxypropionate bicycle3-Hydroxypropionate pathway
3-Hydroxypropionate Pathway is a CO2 assimilatory pathway observed in bacteria. Inorganic CO2 is fixed by acetyl-CoA and propionyl-CoA carboxylases thus forming malyl-CoA and glyoxylate. Malyl-CoA is further split into acetyl-CoA...
is known only in green nonsulfur bacteria. It was proposed in 2002 for the anoxygenic photosynthetic Chloroflexus aurantiacus
Chloroflexus aurantiacus
Chloroflexus aurantiacus is a photosynthetic bacterium isolated from hot springs, belonging to the green non-sulfur bacteria. This organism is thermophilic and can grow at temperatures from 35 °C to 70 °C. Chloroflexus aurantiacus can survive in the dark if oxygen is available. When grown in the...
. None of the enzymes used by the 3-hydroxypropionate bicycle are especially oxygen sensitive.
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
Metallosphaera
In taxonomy, Metallosphaera is a genus of the Sulfolobaceae.-External links:...
.
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
Ignicoccus
Ignicoccus is a genus of Archaea living in marine hydrothermal vents. They were discovered in Kolbeinsey Ridge north of Iceland and in the Pacific Ocean in 2000 .-Systematics:...
.
Non-autotrophic pathways
Although almost all heterotrophs cannot synthesize complete organic molecules from carbon dioxide, some carbon dioxide is incorporated in their metabolism. Notably pyruvate carboxylasePyruvate carboxylase
Pyruvate carboxylase is an enzyme of the ligase class that catalyzes the irreversible carboxylation of pyruvate to form oxaloacetate .It is an important anaplerotic reaction that creates oxaloacetate from pyruvate...
consumes carbon dioxide (as bicarbonate ions) as part of gluconeogenesis
Gluconeogenesis
Gluconeogenesis is a metabolic pathway that results in the generation of glucose from non-carbohydrate carbon substrates such as lactate, glycerol, and glucogenic amino acids....
.
Other reduced carbon
Non-biological carbon fixation is of interest, according to Graham Cairns-SmithGraham Cairns-Smith
Alexander Graham Cairns-Smith is an organic chemist and molecular biologist at the University of Glasgow, most famous for his controversial 1985 book, Seven Clues to the Origin of Life...
, in the study of the origins of life.