The primary function of chloroplasts is photosynthesis, the light-driven fixation of carbon dioxide into organic compounds. The products of the photochemical reactions that occur within thylakoid membranes provide the material with which the plant cells grow and on which all forms of life on the surface of Earth depend.

Photosynthesis begins when light is absorbed by the green pigment chlorophyll, which occurs only in photosynthetic thylakoid membranes. The absorbed light energy is transferred to a reaction center called Photosystem II (PSII), where electrons are removed from water to release molecular oxygen. The electrons are carried through an electron transport chain in thylakoid membranes to Photosystem I (PSI) to eventually produce reduced compounds (for example, NADPH) that drive carbon fixation reactions. The flow of electrons through this linked set of carriers also transfers protons (H+) from the stroma to the thylakoid lumen, which generates a concentration gradient. These protons can only flow back to the stroma through protein channels within the thylakoid membrane. At the stromal end of the membrane channels is adenosine triphosphate (ATP) synthase, which uses the flow of H+ to drive the synthesis of H+ ATP. ATP is used as the primary energy source for biosynthetic reactions within the cell. The ATP and NADPH created are then used to produce sugars from carbon dioxide.

The most abundant enzyme in the biosphere, ribulose 1,5-bisphosphate carboxylase/oxygenase (rubisco, for short), catalyzes the reaction of carbon dioxide with ribulose 1,5-bisphosphate, a 5-carbon compound, to make glyceraldehyde 3-phosphate and 3-phosphoglycerate. These two 3-carbon compounds enter the reductive pentose-phosphate cycle (also called the Calvin-Benson cycle) and eventually are converted to a 6-carbon sugar, glucose 6-phosphate, the ultimate product. Glucose 6-phosphate is the precursor of many of the storage products in the plant cell, such as starch, sucrose, and lipids, and is also the starting point for biosynthesis of most of the cellular material. All fatty acids and most amino acids used by the cell are also synthesized in the chloroplast.

Rubisco is a large enzyme—containing eight large (molecular weight 52,000) and eight small (molecular weight 14,000) subunits—that is also very sluggish, catalyzing a reaction only three times per second even when saturated with carbon dioxide. The usual concentration of carbon dioxide in the watery cell interior is sufficient for only one-half this rate. Perhaps these are the reasons why plants developed mechanisms to achieve a high concentration of the enzyme in the stroma to catalyze this reaction that is essential to maintenance of life. Approximately two million molecules of rubisco are present in each chloroplast.
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