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Certain species adapted to conditions of strong sunlight and aridity, such as many Euphorbia and cactus species, have their main photosynthetic organs in their stems.

The cells in the interior tissues of a leaf, called the mesophyll, can contain between 450,000 and 800,000 chloroplasts for every square millimeter of leaf.

The general equation for photosynthesis as first proposed by Cornelius van Niel is therefore: This equation emphasizes that water is both a reactant in the light-dependent reaction and a product of the light-independent reaction, but canceling n water molecules from each side gives the net equation: Photosynthesis occurs in two stages. Embedded within the stroma are stacks of thylakoids (grana), which are the site of photosynthesis. The thylakoid itself is enclosed by the thylakoid membrane, and within the enclosed volume is a lumen or thylakoid space.

The hydrogen freed by the splitting of water is used in the creation of two further compounds that act as an immediate energy storage means: reduced nicotinamide adenine dinucleotide phosphate (NADPH) and adenosine triphosphate (ATP), the "energy currency" of cells.In plants, algae and cyanobacteria, long-term energy storage in the form of sugars is produced by a subsequent sequence of reactions called the Calvin cycle; some bacteria use different mechanisms, such as the reverse Krebs cycle, to achieve the same end.The bacteriorhodopsin changes its configuration in response to sunlight, acting as a proton pump. These pigments are embedded in plants and algae in complexes called antenna proteins.This produces a proton gradient more directly, which is then converted to chemical energy. In such proteins, the pigments are arranged to work together.Some organisms employ even more radical variants of photosynthesis. Besides chlorophyll, plants also use pigments such as carotenes and xanthophylls.

Some archea use a simpler method that employs a pigment similar to those used for vision in animals. Algae also use chlorophyll, but various other pigments are present, such as phycocyanin, carotenes, and xanthophylls in green algae, phycoerythrin in red algae (rhodophytes) and fucoxanthin in brown algae and diatoms resulting in a wide variety of colors.The surface of the leaf is coated with a water-resistant waxy cuticle that protects the leaf from excessive evaporation of water and decreases the absorption of ultraviolet or blue light to reduce heating.The transparent epidermis layer allows light to pass through to the palisade mesophyll cells where most of the photosynthesis takes place.During the second stage, the light-independent reactions use these products to capture and reduce carbon dioxide. Plants absorb light primarily using the pigment chlorophyll.Most organisms that utilize oxygenic photosynthesis use visible light for the light-dependent reactions, although at least three use shortwave infrared or, more specifically, far-red radiation. The green part of the light spectrum is not absorbed but is reflected which is the reason that most plants have a green color.Composite image showing the global distribution of photosynthesis, including both oceanic phytoplankton and terrestrial vegetation.