Carbon fixation

Cyanobacteria such as these carry out photosynthesis. Their emergence foreshadowed the evolution of many photosynthetic plants,
which oxygenated Earth's atmosphere.

Carbon fixation or сarbon assimilation is the conversion process of inorganic carbon (carbon dioxide) to organic compounds by
living organisms. The most prominent example is photosynthesis, although chemosynthesis is another form of carbon fixation that can
take place in the absence of sunlight. Organisms that grow by fixing carbon are called autotrophs. Autotrophs include
photoautotrophs, which synthesize organic compounds using the energy of sunlight, and lithoautotrophs, which synthesize organic
compounds using the energy of inorganic oxidation. Heterotrophs are organisms that grow using the carbon fixed by autotrophs. The
organic compounds are used by heterotrophs to produce energy and to build body structures. "Fixed carbon", "reduced carbon", and
"organic carbon" are equivalent terms for various organic compounds.

Net vs gross CO2 fixation

Graphic showing net annual amounts of CO2 fixation by land and sea-based organisms.

It is estimated that approximately 258 billion tons of carbon dioxide are converted by photosynthesis annually. The majority of the
fixation occurs in marine environments, especially areas of high nutrients. The gross amount of carbon dioxide fixed is much larger
since approximately 40% is consumed by respiration following photosynthesis.[1] Given the scale of this process, it is understandable
that RuBisCO is the most abundant protein on Earth.

Overview of 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.[2]

Oxygenic photosynthesis

In photosynthesis, energy from sunlight drives the carbon fixation pathway. Oxygenic photosynthesis is used by the primary
producers—plants, algae, and cyanobacteria. They contain the pigment chlorophyll, and use the Calvin cycle to fix carbon
autotrophically. The process works like this:

2H2O → 4e− + 4H+ + O2

CO2 + 4e− + 4H+ → CH2O + H2O

In the first step, water is dissociated 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+

In 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. The Calvin cycle converts carbon dioxide into sugar, as triose phosphate (TP),
which is glyceraldehyde 3-phosphate (GAP) together with dihydroxyacetone phosphate (DHAP):

3 CO2 + 12 e− + 12 H+ + Pi → TP + 4 H2O

An alternative perspective accounts for NADPH (source of e −) and ATP:

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

The formula for inorganic phosphate (P i) is HOPO32− + 2H+. Formulas for triose and TP are C2H3O2-CH2OH and C2H3O2-CH2OPO32−
+ 2H+

Evolutionary considerations

Somewhere between 3.5 and 2.3 billion years ago, the ancestors of cyanobacteria evolved oxygenic photosynthesis, enabling the use
of the abundant yet relatively oxidized molecule H2O as an electron donor to the electron transport chain of light-catalyzed proton-
pumping responsible for efficient ATP synthesis. [3][4] When this evolutionary breakthrough occurred, autotrophy (growth using
inorganic carbon as the sole carbon source) is believed to have already been developed. However, the proliferation of cyanobacteria,
due to their novel ability to exploit water as a source of electrons, radically altered the global environment by oxygenating the
atmosphere and by achieving large fluxes of CO2 consumption.[5]

Carbon concentrating mechanisms

Many photosynthetic organisms have not acquired inorganic carbon concentrating mechanisms (CCM), which increase the
concentration of carbon dioxide available to the initial carboxylase of the Calvin cycle, the enzyme RuBisCO. The benefits of CCM
include increased tolerance to low external concentrations of inorganic carbon, and reduced losses to photorespiration. CCM can make
plants more tolerant of heat and water stress.

Carbon concentrating mechanisms use the enzyme carbonic anhydrase (CA), which catalyze both the dehydration of bicarbonate to
carbon dioxide and the hydration of carbon dioxide to bicarbonate

HCO3− + H+ ⇌ CO2 + H2O

Lipid membranes are much less permeable to bicarbonate than to carbon dioxide. To capture inorganic carbon more effectively, some
plants have adapted the anaplerotic reactions

HCO3− + H+ + PEP → OAA + Pi

catalyzed by PEP carboxylase (PEPC), to carboxylate phosphoenolpyruvate (PEP) to oxaloacetate (OAA) which is a C4 dicarboxylic
acid.

CAM plants

CAM plants that use Crassulacean acid metabolism as an adaptation for arid conditions. CO 2 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 dung jade plant (Crassula ovata) and cacti are typical of CAM plants. Sixteen thousand species of plants
use CAM.[6] These plants have a carbon isotope signature of −20 to −10 ‰. [7]

C4 plants

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. [8]
These plants have a carbon isotope signature of −16 to −10 ‰.[7]

C3 plants

The large majority of plants are C3 plants. They are so-called to distinguish them from the CAM and C4 plants, and because the
carboxylation products of the Calvin cycle are 3-carbon compounds. They lack C4 dicarboxylic acid cycles, and therefore have higher
carbon dioxide compensation points than CAM or C4 plants. C3 plants have a carbon isotope signature of −24 to −33‰.[7]

Other autotrophic pathways

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.[9]

Reductive acetyl CoA pathway

The reductive acetyl CoA pathway operated in strictly anaerobic bacteria (acetogens) and archaea (methanogens). The pathway 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. Hydrogenotrophic methanogenesis, which is only found in certain
archaea and accounts for 80% of global methanogenesis, is also based on the reductive acetyl CoA pathway. The pathway is often
referred to as the Wood–Ljungdahl pathway.[10][11]

3-Hydroxypropionate and two related cycles

The 3-hydroxypropionate cycle is utilized only by green nonsulfur bacteria. It was proposed in 2002 for the anoxygenic photosynthetic
Chloroflexus aurantiacus. None of the enzymes that participate in the 3-hydroxypropionate cycle are especially oxygen
sensitive.[12][13]

A variant of the 3-hydroxypropionate pathway was found to operate in aerobic extreme thermoacidophile archaeon Metallosphaera
sedula. This pathway, called the 3-hydroxypropionate/4-hydroxybutyrate cycle .[14] And yet another variant of the 3-
hydroxypropionate pathway is the dicarboxylate/4-hydroxybutyrate cycle. It was discovered in anaerobic archaea. It was proposed in
2008 for the hyperthermophile archeon Ignicoccus hospitalis.[15]

Chemosynthesis

Chemosynthesis is carbon fixation driven by the oxidation of inorganic substances (e.g., hydrogen gas or hydrogen sulfide). Sulfur-
and hydrogen-oxidizing bacteria often use the Calvin cycle or the reductive citric acid cycle.[16]

Non-autotrophic pathways

Although almost all heterotrophs cannot synthesize complete organic molecules from carbon dioxide, some carbon dioxide is
incorporated in their metabolism.[17] Notably pyruvate carboxylase consumes carbon dioxide (as bicarbonate ions) as part of
gluconeogenesis, and carbon dioxide is consumed in various anaplerotic reactions.

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 higher 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.

Photosynthesis: Pathway of Carbon Fixation

Photosynthesis is the synthesis of organic molecules using the energy of light. For the sugar glucose (one of the most abundant
products of photosynthesis) the equation is:

6CO2 + 12H2O -> C6H12O6 + 6H2O + 6O2

Light provides the energy to:

 transfer electrons from water to nicotinamide adenine dinucleotide phosphate (NADP+) forming NADPH
 generate ATP

The details of these processes are described in Photosynthesis: The Role of Light.

ATP and NADPH provide the energy and electrons to reduce carbon dioxide (CO 2) to organic molecules.

The Steps

 CO2 combines with the phosphorylated 5-carbon sugar ribulose bisphosphate

 This reaction is catalyzed by the enzyme ribulose bisphosphate carboxylase oxygenase (RUBISCO)(an enzyme which can
fairly claim to be the most abundant protein on earth)
 The resulting 6-carbon compound breaks down into two molecules of 3-phosphoglyceric acid (PGA)
 The PGA molecules are further phosphorylated (by ATP) and are reduced (by NADPH) to form phosphoglyceraldehyde
(PGAL)
 Phosphoglyceraldehyde serves as the starting material for the synthesis of glucose and fructose
  Glucose and fructose make the disaccharide sucrose, which travels in solution to other parts of the plant (e.g., fruit, roots)
 Glucose is also the monomer used in the synthesis of the polysaccharides starch and cellulose

The graphic shows the steps in the fixation of carbon dioxide during photosynthesis. These steps were worked out by Melvin Calvin
and his colleagues at the University of California and, for this reason, are named The Calvin Cycle.

Link to graphic showing how they did it.

All the reactions of carbon fixation occur in the stroma of the chloroplast.