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Chloroplast DNA

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plural: chloroplast DNAs

DNA in the chloroplast that carries the code for proteins and RNAs essential to the various functions of the chloroplast, such as photosynthesis



Chloroplast DNA (cpDNA) is the DNA present in the organelle chloroplast. It is sometimes called the plastosome to refer to the genome of the chloroplasts as well as other plastids. It is one of the extranuclear DNA in eukaryotes. Other DNAs that occur outside the nucleus is the mitochondrial DNA (mtDNA), which is the DNA in the mitochondrion. Similar to the nuclear DNA, the extranuclear DNA is an organic compound made up of linear chains of monomeric nucleotides. Each nucleotide component, in turn, is made up of phosphoric acid, deoxyribose sugar, and nitrogenous base. DNAs are involved in the preservation, replication, and expression of hereditary information.

History and terminology

The presence of DNA in chloroplasts was first suggested during the early 1950s [1]. Subsequent studies supported the existence of extranuclear DNA in the chloroplasts of other plant species came about in the late 1950s and early 1960s. In 1963, Masahiro R. Ishida, together with Ruth Sager, was acknowledged for being the first to extract the chloroplast DNA. They were able to isolate chloroplasts from the alga, Chlamydomonas, and found an enriched satellite DNA that has a buoyant density of 1,702 gm/cm3 and GC content of 39.3%.[2] Soon, more DNA molecules were obtained from the chloroplasts of higher plant species by other independent research teams.

Structure and Characteristics

cpDNA is typically circular, and consists of base pairs ranging from 120,000 to 170,000 long. It has about 120 genes. Several copies of cpDNA molecules are present in each chloroplast. A chloroplast is one of the plastids, the others are chromoplasts and leucoplasts. The chloroplasts are the photosynthetic type of plastid containing high amounts of chlorophyll (the green pigment). The chloroplast has at least three membrane systems: outer membrane, inner membrane, and thylakoid system (the site of photosynthesis). The stroma, which is the matrix of the chloroplast, in between the grana contains cpDNA, enzymes, molecules, and ions. It is where the dark reactions of photosynthesis occur. Most cpDNAs contain inverted repeats of about 4,000 to 25,000 base pairs long, with the exceptions of pea plants and certain red algae that do not have inverted repeats in their cpDNAs.

Chloroplast DNA vs. Mitochondrial DNA vs. Nuclear DNA

Both cpDNA and mtDNA are extranuclear DNA. They are semi-autonomous, self-reproducing cytoplasmic structure, with their own genetic system. Both of them are believed to be maternally-inherited and have endosymbiotic origins. In most multicellular cells, both cpDNA and mtDNA are organized as a circular DNA, similar to the prokaryotic DNA, thus, supporting the theory of endosymbiosis. cpDNA, though, are larger and more complex than mtDNA.[3] cpDNA has about 120 genes whereas mtDNA has about 37 genes. Both of them encodes for proteins and RNAs vital to their functions. For instance, mtDNA encodes for proteins of electron transport chain involved in aerobic respiration (ATP synthesis). cpDNA, in turn, encodes for proteins essential to photosynthesis.

Contrary to the nuclear DNA, both cpDNA and mtDNA occur in multiple copies since there are several chloroplasts and mitochondria occurring inside a cell. A cell often contains thousands of copies of mtDNA and cpDNA. Nuclear DNAs are compacted into chromatin structures through histones. During mitosis and meiosis, mitochondria and chloroplasts randomly segregate. Thus, their genetic material segregates randomly as well into new daughter cells. [4]

Chloroplast DNA Inheritance

The pattern of inheritance involving cpDNA does not follow the Mendelian pattern of inheritance. Rather, certain traits are inconsistent with the Mendelian laws. For instance, German botanist Karl Erich Correns observed such inconsistencies in four-o'clock plants (Mirabilis jalapa). In 1909, he noticed that the same plant had a mixture of leaf colors, i.e. some were green, others were white, and still others, variegated. Pollinating the flower of one leaf color (e.g. white) with the pollen of another leaf color (e.g. green), the seeds would develop into plants with leaves resembling that of the maternal origin (i.e. in this case, white).[5]

Common biological reactions


DNA replication is a process whereby the original (parent) strands of DNA in the double helix are separated and each one is copied to produce a new (daughter) strand. cpDNA replication is hypothesized to occur by a double displacement loop (D-loop) mechanism.


DNA carries the genetic information that codes for a particular protein. Thus, during protein translation, the genetic code for a protein is first copied into the RNA (specifically, mRNA). This process of creating a copy of DNA into mRNA through the help of the enzyme RNA polymerase is called transcription. cpDNAs of land plants encode for rRNAs, tRNAs, ribosomal proteins, and RNA polymerase subunits, which are all essential for protein synthesis. Another RNA polymerase encoded by the nuclear DNA is also involved.

Biological function

cpDNA encodes for proteins and RNAs essential to proper metabolism. In particular, it encodes for the following:[3] rRNAs (23S, 16S, 5S, 4.5S), tRNAs (about 30-31), ribosomal proteins (about 21), four RNA polymerase subunits, photosystem I, photosystem II, cytochrome bf complex, ATP synthase, and the large subunit of ribulose bisphosphate carboxylase (rubisco). Rubisco is the major protein component of the chloroplast stroma. It is the enzyme that catalyzes the addition of CO2 to ribulose-1,5-bisphosphate during the Calvin cycle. Apart from protein synthesis machinery and photosynthesis, cpDNA has also a role in the synthesis of 11 subunits of a protein complex that mediate redox reactions to recycle electrons.[6]

Endosymbiotic gene transfer

It is presumed that in due course some parts of the chloroplast genome were transferred to the nuclear genome. The process is called endosymbiotic gene transfers. Because of this transfer, the chloroplast genome is greatly reduced compared with that of cyanobacteria, which are conjectured as the ancestral origin of chloroplasts.



  • chloroplast deoxyribonucleic acid


  • cpDNA

Further reading

See also


  1. Chiba, .Y (1951). Cytochemical studies on chloroplasts. I. Cytologic demonstration of nucleic acids in chloroplasts. Cytologia (Tokyo), 16: 259–264. [Link]
  2. Sugiura, M. (2005). History of chloroplast genomics. In: Govindjee, Beatty J.T., Gest H., Allen J.F. (eds) Discoveries in Photosynthesis. Advances in Photosynthesis and Respiration, vol 20. Springer, Dordrecht.
  3. Cooper, G. M. (2015). Chloroplasts and Other Plastids. Retrieved from [Link]
  4. Inheritance of mitochondrial and chloroplast DNA. (2019). Retrieved from [Link]
  5. Chloroplast DNA. (2011). Retrieved from [Link]
  6. Krause, K. (2008). "From chloroplasts to "cryptic" plastids: Evolution of plastid genomes in parasitic plants". Current Genetics, 54 (3): 111–21. doi:10.1007/s00294-008-0208-8

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