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Chloroplasts are one of the cellular organelles, and the site of photosynthesis, a basic metabolism in plants. the structure of chloroplasts is shown in image above. Chloroplasts posses an inner system of membranes, called thylakoids, which are surrounded by fluid compartments called stroma. Thylakoids contain chlorophyll where the light reaction occurs. In stroma, carbon reduction is carried out through the dark reaction. In the light reaction, ATP, chemical energy, and NADPH, reduction power, are synthesized using light energy. The ATP and NADPH generated by the light reaction system are transported to the dark reaction system, where carbon dioxide is fixed and carbohydrates are synthesized by the Calvin cycle. Some plants concentrate carbon dioxide into organic acids before the Calvin cycle.

In chloroplast there are independent genes. These are some of the extranuclear genes. Some chloroplasts proteins are synthesized in chloroplasts. The complete chloroplast genomes of several plants have been sequenced. Chloroplasts reproduce by division rather than synthesis and are divided between the two daughter-cells during cell division. However, at the time of sexual reproduction, chloroplast genes are transferred only through the maternal gamete in most cases. For this reason characters based on differences in chloroplast genes do not follow the Mendelian pattern of inheritance. Chloroplast DNA also contains introns, i. e. base sequences that do not code for protein. When proteins are synthesized, the mRNA is processed to remove the introns at first, and then the base sequences that code for protein are connected. This process is called splicing.