Okazaki fragment: Difference between revisions
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The term [[Okazaki_fragment|Okazaki fragment]] relates to short [[Oligonucleotide|oligonucleotide]] sequences that are synthesised during [[DNA|DNA]] replication as part of the lagging strand of DNA running in the 5' 3' direction. They were named after [[Reiji Okazaki|Reiji Okazaki]] who, using [[Radioactive label|radioactive labels]] in bacterial [[DNA|DNA]], observed an increase of short [[Oligonucleotide|oligonucleotides]] directly after the replication process had begun, but a greater amount of larger polynucleotides after a longer time period had elapsed. This helped explain the mechanisms involved in the replication of the 5' 3' strand of parental [[DNA|DNA]] by [[DNA polymerase|DNA polymerase]] <ref>Becker W, Kleinsmith L, Hardin J and Bertoni G (2009) The World of the Cell, 7th edition,San Francisco: Pearson Benjamin Cummings, p. 560</ref>. | |||
The term [[Okazaki_fragment|Okazaki fragment]] relates to short [[Oligonucleotide|oligonucleotide]] sequences that are synthesised during DNA replication as part of the lagging strand of DNA running in the 5'3' direction. They were named after Reiji Okazaki who, using radioactive labels in bacterial DNA, observed an increase of short oligonucleotides directly after the replication process had begun, but a greater amount of larger polynucleotides after a longer time period had elapsed. This helped explain the mechanisms involved in the replication of the 5'3' strand of parental DNA by DNA polymerase<ref>Becker W, Kleinsmith L, Hardin J and Bertoni G (2009) The World of the Cell, 7th edition,San Francisco: Pearson Benjamin Cummings, p. 560</ref>. | |||
== Synthesis of Okazaki fragments == | == Synthesis of Okazaki fragments == | ||
Due to [[DNA polymerase|DNA polymerase]] only being able to replicate DNA in the 5'3' direction, only the 3'5' strand of DNA can be replicated continuously. The antiparallel strand is termed the "lagging strand", as its replication is discontinuous. DNA polymerase III replicates short sections of the DNA strand, each around 1000 [[Nucleotide|nucleotides]] long<ref>Becker W, Kleinsmith L, Hardin J and Bertoni G (2009) The World of the Cell, 7th edition,San Francisco: Pearson Benjamin Cummings, p. 560</ref>, by polymerising [[Deoxynucleoside triphosphate|deoxynucleoside triphosphates]] (dATP, dGTP, dCTP or dTTP)<ref name="null">Berg J, Tymoczko J, Stryer L (2007) Biochemistry, 6th edition, New York: W.H. Freeman, p. 793</ref>. In order for DNA polymerase III to bind, a short RNA [[Primer|primer]] is synthesised by the enzyme [[DNA primase|DNA primase]] at regular intervals along the lagging strand as the [[Replication fork|replication fork]] moves along the DNA molecule. The lagging strand forms a loop in order for the DNA polymerase III [[Holoenzyme|holoenzyme]] to synthesise each fragment in the 5'3' direction. This is also referred to as the "[[Trombone Model|Trombone Model]]"<ref>Berg J, Tymoczko J, Stryer L (2007) Biochemistry, 6th edition, New York: W.H. Freeman, p. 800</ref>. | Due to [[DNA polymerase|DNA polymerase]] only being able to replicate DNA in the 5' 3' direction, only the 3' 5' strand of [[DNA|DNA]] can be replicated continuously. The antiparallel strand is termed the "lagging strand", as its replication is discontinuous. [[DNA polymerase III|DNA polymerase III]] replicates short sections of the [[DNA|DNA]] strand, each around 1000 [[Nucleotide|nucleotides]] long<ref>Becker W, Kleinsmith L, Hardin J and Bertoni G (2009) The World of the Cell, 7th edition,San Francisco: Pearson Benjamin Cummings, p. 560</ref>, by polymerising [[Deoxynucleoside triphosphate|deoxynucleoside triphosphates]] ([[DATP|dATP]], [[DGTP|dGTP]], [[DCTP|dCTP]] or [[DTTP|dTTP]]) <ref name="null">Berg J, Tymoczko J, Stryer L (2007) Biochemistry, 6th edition, New York: W.H. Freeman, p. 793</ref>. In order for [[DNA polymerase III|DNA polymerase III]] to bind, a short [[RNA|RNA]] [[Primer|primer]] is synthesised by the enzyme [[DNA primase|DNA primase]] at regular intervals along the lagging strand as the [[Replication fork|replication fork]] moves along the [[DNA|DNA]] molecule. The lagging strand forms a loop in order for the [[DNA polymerase III|DNA polymerase III]] [[Holoenzyme|holoenzyme]] to synthesise each fragment in the 5' 3' direction. This is also referred to as the "[[Trombone Model|Trombone Model]]" <ref>Berg J, Tymoczko J, Stryer L (2007) Biochemistry, 6th edition, New York: W.H. Freeman, p. 800</ref>. | ||
== Joining of Okazaki fragments == | == Joining of Okazaki fragments == | ||
The DNA polymerase III holoenzyme leaves gaps in the base sequence between individual Okazaki fragments where the RNA primer is still bound. DNA polymerase I now removes the RNA primer and closes the gap between the two fragments by synthesising the complementary strand in the 5'3' direction. The remaining nick in the deoxyribose-phosphate backbone is sealed by the action of [[DNA ligase|DNA ligase]], which joins the 5' [[Phosphate|phosphate]] on the growing lagging strand to the 3' [[Hydroxyl|hydroxyl]]-group on the newly synthesised Okazaki fragment<ref>Alberts B, Johnson A, Lewis J, Raff M, Roberts K and Walter P (2008) Molecular Biology of the Cell, 5th edition, New York: Garland Science, p. 272</ref>. | The [[DNA polymerase III|DNA polymerase III]] [[Holoenzyme|holoenzyme]] leaves gaps in the base sequence between individual Okazaki fragments where the [[RNA primer|RNA primer]] is still bound. [[DNA polymerase I|DNA polymerase I]] now removes the [[RNA primer|RNA primer]] and closes the gap between the two fragments by synthesising the complementary strand in the 5' 3' direction. The remaining nick in the deoxyribose-phosphate backbone is sealed by the action of [[DNA ligase|DNA ligase]], which joins the 5' [[Phosphate|phosphate]] on the growing lagging strand to the 3' [[Hydroxyl|hydroxyl]]-group on the newly synthesised Okazaki fragment<ref>Alberts B, Johnson A, Lewis J, Raff M, Roberts K and Walter P (2008) Molecular Biology of the Cell, 5th edition, New York: Garland Science, p. 272</ref>. | ||
== References == | == References == | ||
<references /> | <references /> | ||
Latest revision as of 13:50, 21 October 2016
The term Okazaki fragment relates to short oligonucleotide sequences that are synthesised during DNA replication as part of the lagging strand of DNA running in the 5' 3' direction. They were named after Reiji Okazaki who, using radioactive labels in bacterial DNA, observed an increase of short oligonucleotides directly after the replication process had begun, but a greater amount of larger polynucleotides after a longer time period had elapsed. This helped explain the mechanisms involved in the replication of the 5' 3' strand of parental DNA by DNA polymerase [1].
Synthesis of Okazaki fragments
Due to DNA polymerase only being able to replicate DNA in the 5' 3' direction, only the 3' 5' strand of DNA can be replicated continuously. The antiparallel strand is termed the "lagging strand", as its replication is discontinuous. DNA polymerase III replicates short sections of the DNA strand, each around 1000 nucleotides long[2], by polymerising deoxynucleoside triphosphates (dATP, dGTP, dCTP or dTTP) [3]. In order for DNA polymerase III to bind, a short RNA primer is synthesised by the enzyme DNA primase at regular intervals along the lagging strand as the replication fork moves along the DNA molecule. The lagging strand forms a loop in order for the DNA polymerase III holoenzyme to synthesise each fragment in the 5' 3' direction. This is also referred to as the "Trombone Model" [4].
Joining of Okazaki fragments
The DNA polymerase III holoenzyme leaves gaps in the base sequence between individual Okazaki fragments where the RNA primer is still bound. DNA polymerase I now removes the RNA primer and closes the gap between the two fragments by synthesising the complementary strand in the 5' 3' direction. The remaining nick in the deoxyribose-phosphate backbone is sealed by the action of DNA ligase, which joins the 5' phosphate on the growing lagging strand to the 3' hydroxyl-group on the newly synthesised Okazaki fragment[5].
References
- ↑ Becker W, Kleinsmith L, Hardin J and Bertoni G (2009) The World of the Cell, 7th edition,San Francisco: Pearson Benjamin Cummings, p. 560
- ↑ Becker W, Kleinsmith L, Hardin J and Bertoni G (2009) The World of the Cell, 7th edition,San Francisco: Pearson Benjamin Cummings, p. 560
- ↑ Berg J, Tymoczko J, Stryer L (2007) Biochemistry, 6th edition, New York: W.H. Freeman, p. 793
- ↑ Berg J, Tymoczko J, Stryer L (2007) Biochemistry, 6th edition, New York: W.H. Freeman, p. 800
- ↑ Alberts B, Johnson A, Lewis J, Raff M, Roberts K and Walter P (2008) Molecular Biology of the Cell, 5th edition, New York: Garland Science, p. 272