energy delivered to the electron acceptors is used to move hydrogen ions across the thylakoid membrane into the lumen. the electron is eventually used to reduce the co-enzyme nadp with a h+ to nadph (which has functions in the light-independent reaction); at that point, the path of that electron ends. the cyclic reaction is similar to that of the non-cyclic but differs in that it generates only atp, and no reduced nadp (nadph) is created. the cyclic reaction takes place only at photosystem i. once the electron is displaced from the photosystem, the electron is passed down the electron acceptor molecules and returns to photosystem i, from where it was emitted, hence the name cyclic reaction. water photolysis linear electron transport through a photosystem will leave the reaction center of that photosystem oxidized. elevating another electron will first require re-reduction of the reaction center. the excited electrons lost from the reaction center (p700) of photosystem i are replaced by transfer from plastocyanin, whose electrons come from electron transport through photosystem ii. photosystem ii, as the first step of the z-scheme, requires an external source of electrons to reduce its oxidized chlorophyll a reaction center. the source of electrons for photosynthesis in green plants and cyanobacteria is water. two water molecules are oxidized by the energy of four successive charge-separation reactions of photosystem ii to yield a molecule of diatomic oxygen and four hydrogen ions. the electrons yielded are transferred to a redox-active tyrosine residue that is oxidized by the energy of p680+. this resets the ability of p680 to absorb another photon and release another photo-dissociated electron. the oxidation of water is catalyzed in photosystem ii by a redox-active structure that contains four manganese ions and a calcium ion; this oxygen-evolving complex binds two water molecules and contains the four oxidizing equivalents that are used to drive the water-oxidizing reaction (kok's s-state diagrams). the hydrogen ions are released in the thylakoid lumen and therefore contribute to the transmembrane chemiosmotic potential that leads to atp synthesis. oxygen is a waste product of light-dependent reactions, but the majority of organisms on earth use oxygen and its energy for cellular respiration, including photosynthetic organisms. light-independent reactions calvin cycle in the light-independent (or "dark") reactions, the enzyme rubisco captures co2 from the atmosphere and, in a process called the calvin cycle, uses the newly formed nadph and releases three-carbon sugars, which are later combined to form sucrose and starch. the overall equation for the light-independent reactions in green plants is: 128 3 co2 + 9 atp + 6 nadph + 6 h+ → c3h6o3-phosphate + 9 adp + 8 pi + 6 nadp+ + 3 h2o overview of the calvin cycle and carbon fixation carbon fixation produces the three-carbon sugar intermediate, which is then converted into the final carbohydrate products. the simple carbon sugars produced by photosynthesis are then used to form other organic compounds, such as the building material cellulose, the precursors for lipid and amino acid biosynthesis, or as a fuel in cellular respiration. the latter occurs not only in plants but also in animals when the carbon and energy from plants is passed through a food chain. the fixation or reduction of carbon dioxide is a process in which carbon dioxide combines with a five-carbon sugar, ribulose 1,5-bisphosphate, to yield two molecules of a three-carbon compound, glycerate 3-phosphate, also known as 3-phosphoglycerate. glycerate 3-phosphate, in the presence of atp and nadph produced during the light-dependent stages, is reduced to glyceraldehyde 3-phosphate. this product is also referred to as 3-phosphoglyceraldehyde (pgal) or, more generically, as triose phosphate. most (5 out of 6 molecules) of the glyceraldehyde 3-phosphate produced are used to regenerate ribulose 1,5-bisphosphate so the process can continue. the triose phosphates not thus "recycled" often condense to form hexose phosphates, which ultimately yield sucrose, starch and cellulose, as well as glucose and fructose. the sugars produced during carbon metabolism yield carbon skeletons that can be used for other metabolic reactions like the production of amino acids and lipids. on land overview of c4 carbon fixation. (this image mistakenly shows lactic acid instead of pyruvate, and all the species ending in "-ate" are shown as unionized acids, such as malic acid and so on.) in hot and dry conditions, plants close their stomata to prevent water loss. under these conditions, co2 will decrease and oxygen gas, produced by the light reactions of photosynthesis, will increase, causing an increase of photorespiration by the oxygenase activity of ribulose-1,5-bisphosphate carboxylase/oxygenase and decrease in carbon fixation. some plants have evolved mechanisms to increase the co2 concentration in the leaves under these conditions. plants that use the c4 carbon fixation process chemically fix carbon dioxide in the cells of the mesophyll by adding it to the three-carbon molecule phosphoenolpyruvate (pep), a reaction catalyzed by an enzyme called pep carboxylase, creating the four-carbon organic acid oxaloacetic acid. oxaloacetic acid or malate synthesized by this process is then translocated to specialized bundle sheath cells where the enzyme rubisco and other calvin cycle enzymes are located, and where co2 released by decarboxylation of the four-carbon acids is then fixed by rubisco activity to the three-carbon 3-phosphoglyceric acids. the physical separation of rubisco from the oxygen-generating light reactions reduces photorespiration and increases co2 fixation and, thus, the photosynthetic capacity of the leaf. c4 plants can produce more sugar than c3 plants in conditions of high light and temperature. many important crop plants are c4 plants, including maize, sorghum, sugarcane, and millet. plants that do not use pep-carboxylase in carbon fixation are called c3 plants because the primary carboxylation reaction, catalyzed by rubisco, produces the three-carbon 3-phosphoglyceric acids directly in the calvin-benson cycle. over 90% of plants use c3 carbon fixation, compared to 3% that use c4 carbon fixation; however, the evolution of c4 in over 60 plant lineages makes it a striking example of convergent evolution. c2 photosynthesis, which involves carbon-concentration by selective breakdown of photorespiratory glycine, is both an evolutionary precursor to c4 and a useful ccm in its own right. xerophytes, such as cacti and most succulents, also use pep carboxylase to capture carbon dioxide in a process called crassulacean acid metabolism (cam). in contrast to c4 metabolism, which spatially separates the co2 fixation to pep from the calvin cycle, cam temporally separates these two processes. cam plants have a different leaf anatomy from c3 plants, and fix the co2 at night, when their stomata are open. cam plants store the co2 mostly in the form of malic acid via carboxylation of phosphoenolpyruvate to oxaloacetate, which is then reduced to malate. decarboxylation of malate during the day releases co2 inside the leaves, thus allowing carbon fixation to 3-phosphoglycerate by rubisco. cam is used by 16,000 species of plants. calcium oxalate accumulating plants, such as amaranthus hybridus and colobanthus quitensis, show a variation of photosynthesis where calcium oxalate crystals function as dynamic carbon pools, supplying carbon dioxide (co2) to photosynthetic cells when stomata are partially or totally closed. this process was named alarm photosynthesis. under stress conditions (e.g. water deficit) oxalate released from calcium oxalate crystals is converted to co2 by an oxalate oxidase enzyme and the produced co2 can support the calvin cycle reactions. reactive hydrogen peroxide (h2o2), the byproduct of oxalate oxidase reaction, can be neutralized by catalase. alarm photosynthesis represents a photosynthetic variant to be added to the well-known c4 and cam pathways. however, alarm photosynthesis, in contrast to these pathways, operates as a biochemical pump that collects carbon from the organ interior (or from the soil) and not from the atmosphere. in water cyanobacteria possess carboxysomes, which increase the concentration of co2 around rubisco to increase the rate of photosynthesis. an enzyme, carbonic anhydrase, located within the carboxysome releases co2 from dissolved hydrocarbonate ions (hco−3). before the co2 diffuses out it is quickly sponged up by rubisco, which is concentrated within the carboxysomes. hco−3 ions are made from co2 outside the cell by another carbonic anhydrase and are actively pumped into the cell by a membrane protein. they cannot cross the membrane as they are charged, and within the cytosol they turn back into co2 very slowly without the help of carbonic anhydrase. this causes the hco−3 ions to accumulate within the cell from where they diffuse into the carboxysomes. pyrenoids in algae and hornworts also act to concentrate co2 around rubisco. order and kinetics the overall process of photosynthesis takes place in four stages: stagedescriptiontime scale 1energy transfer in antenna chlorophyll (thylakoid membranes)femtosecond to picosecond 2transfer of electrons in photochemical reactions (thylakoid membranes)picosecond to nanosecond 3electron transport chain and atp synthesis (thylakoid membranes)microsecond to millisecond 4carbon fixation and export of stable productsmillisecond to second efficiency plants usually convert light into chemical energy with a photosynthetic efficiency of 3–6%. absorbed light that is unconverted is dissipated primarily as heat, with a small fraction (1–2%) re-emitted as chlorophyll fluorescence at longer (redder) wavelengths. this fact allows measurement of the light reaction of photosynthesis by using chlorophyll fluorometers. actual plants' photosynthetic efficiency varies with the frequency of the light being converted, light intensity, temperature and proportion of carbon dioxide in the atmosphere, and can vary from 0.1% to 8%. by comparison, solar panels convert light into electric energy at an efficiency of approximately 6–20% for mass-produced panels, and above 40% in laboratory devices. scientists are studying photosynthesis in hopes of developing plants with increased yield. the efficiency of both light and dark reactions can be measured but the relationship between the two can be complex. for example, the atp and nadph energy molecules, created by the light reaction, can be used for carbon fixation or for photorespiration in c3 plants. electrons may also flow to other electron sinks. for this reason, it is not uncommon for authors to differentiate between work done under non-photorespiratory conditions and under photorespiratory conditions. chlorophyll fluorescence of photosystem ii can measure the light reaction, and infrared gas analyzers can measure the dark reaction. it is also possible to investigate both at the same time using an integrated chlorophyll fluorometer and gas exchange system, or by using two separate systems together. infrared gas analyzers and some moisture sensors are sensitive enough to measure the photosynthetic assimilation of co2, and of δh2o using reliable methods co2 is commonly measured in μmols/(m2/s), parts per million or volume per million and h2o is commonly measured in mmol/(m2/s) or in mbars. by measuring co2 assimilation, δh2o, leaf temperature, barometric pressure, leaf area, and photosynthetically active radiation or par, it becomes possible to estimate, "a" or carbon assimilation, "e" or transpiration, "gs" or stomatal conductance, and ci or intracellular co2. however, it is more common to used chlorophyll fluorescence for plant stress measurement, where appropriate, because the most commonly used parameters fv/fm and y(ii) or f/fm' can be measured in a few seconds, allowing the investigation of larger plant populations. gas exchange systems that offer control of co2 levels, above and below ambient, allow the common practice of measurement of a/ci curves, at different co2 levels, to characterize a plant's photosynthetic response. integrated chlorophyll fluorometer – gas exchange systems allow a more precise measure of photosynthetic response and mechanisms. while standard gas exchange photosynthesis systems can measure ci, or substomatal co2 levels, the addition of integrated chlorophyll fluorescence measurements allows a more precise measurement of cc to replace ci. the estimation of co2 at the site of carboxylation in the chloroplast, or cc, becomes possible with the measurement of mesophyll conductance or gm using an integrated system. photosynthesis measurement systems are not designed to directly measure the amount of light absorbed by the leaf. but analysis of chlorophyll-fluorescence, p700- and p515-absorbance and gas exchange measurements reveal detailed information about e.g. the photosystems, quantum efficiency and the co2 assimilation rates. with some instruments, even wavelength-dependency of the photosynthetic efficiency can be analyzed. a phenomenon known as quantum walk increases the efficiency of the energy transport of light significantly. in the photosynthetic cell of an alga, bacterium, or plant, there are light-sensitive molecules called chromophores arranged in an antenna-shaped structure named a photocomplex. when a photon is absorbed by a chromophore, it is converted into a quasiparticle referred to as an exciton, which jumps from chromophore to chromophore towards the reaction center of the photocomplex, a collection of molecules that traps its energy in a chemical form accessible to