DNA replication

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[[DNA|DNA]] replication is a duplication process where exact copies of [[DNA]] within [[Cells|cells]] are replicated, with very low error rate. They typically occur at a rate of 1 in 10<sup>9</sup><sup></sup><sup></sup> bases per replication. In [[Mitosis]], DNA replication occurs during the [[S phase|S phase]]. DNA must be duplicated before the division takes place to main the chromosomal number of the two daughter cells. At the end of the division, two genetically identical daughter cells are formed. DNA replication is called [[Semi-conservative replication|Semi-conservative replication]].  
 
[[DNA|DNA]] replication is a duplication process where exact copies of [[DNA]] within [[Cells|cells]] are replicated, with very low error rate. They typically occur at a rate of 1 in 10<sup>9</sup><sup></sup><sup></sup> bases per replication. In [[Mitosis]], DNA replication occurs during the [[S phase|S phase]]. DNA must be duplicated before the division takes place to main the chromosomal number of the two daughter cells. At the end of the division, two genetically identical daughter cells are formed. DNA replication is called [[Semi-conservative replication|Semi-conservative replication]].  
  
Within DNA replication the two strands are replicated in slightly different ways. The leading strand, the strand that runs 5' to 3', is replicated continuously. This is because it is known that the DNA polymerase is only able to synthesize in the 5' to 3' direction so the leading strand is in the correct orientation for the DNA polymerase so it can be replicated continuously. On the other hand, the lagging strand runs from 3' to 5' prime which means that it cannot be replicated continuously because the DNA polymerase can't replicate in that direction. This means that the lagging strand is replicated in fragments, which are given the name Okazaki fragments. The DNA is able to form loops so that the DNA polymerase can synthesize the new strand of DNA in the 5' to 3' direction. Other enzymes are then used to join up the gaps that are created through the replication in fragments<ref>Burg J M, Tymoczko J L, Gatto, Jr G J, Stryer L. Biochemistry Eighth Edition. 2015. W.H. Freeman and Company. New York. Pg 831</ref>.
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Within DNA replication the two strands are replicated in slightly different ways. The leading strand, the strand that runs 5' to 3', is replicated continuously. This is because it is known that the DNA polymerase is only able to synthesize in the 5' to 3' direction so the leading strand is in the correct orientation for the DNA polymerase so it can be replicated continuously. On the other hand, the lagging strand runs from 3' to 5' prime which means that it cannot be replicated continuously because the DNA polymerase can't replicate in that direction. This means that the lagging strand is replicated in fragments, which are given the name Okazaki fragments. The DNA is able to form loops so that the DNA polymerase can synthesize the new strand of DNA in the 5' to 3' direction. Other enzymes are then used to join up the gaps that are created through the replication in fragments<ref>Burg J M, Tymoczko J L, Gatto, Jr G J, Stryer L. Biochemistry Eighth Edition. 2015. W.H. Freeman and Company. New York. Pg 831</ref>.  
  
 
=== Bacterial enzymes  ===
 
=== Bacterial enzymes  ===
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*[[Type I topoisomerase]] - Catalyses a reversible formation of a nick on 1 antiparallel DNA strand. This breakage is at a single point on DNA [[Phosphate backbone]], allowing the dsDNA to unravel<ref name="Topoisomerase">Cooper, G. M. (2000). The Cell: Molecular Approach. 2nd Edition. Washington, D.C: ASM Press.</ref>.  
 
*[[Type I topoisomerase]] - Catalyses a reversible formation of a nick on 1 antiparallel DNA strand. This breakage is at a single point on DNA [[Phosphate backbone]], allowing the dsDNA to unravel<ref name="Topoisomerase">Cooper, G. M. (2000). The Cell: Molecular Approach. 2nd Edition. Washington, D.C: ASM Press.</ref>.  
*[[Dna A]] - Initiates DNA replication by [[OriC]] recognition on bacterial DNA. Hexamer binds to sequences in the DNA, putting strain on the backbone of the molecule, resulting in the unravelling of a neighbouring tandem array of 13-mer sequences, which are AT rich. In addition, it instigates [[DNA helicase double strand unzipping|DNA helicase double strand unzipping]]<ref name="Dna A">Messer, W., Blaesing, F., Majka, J., Nardmann, J., Schaper, S., Schmidt, A., Seitz, H., Speck, C., Tüngler, D., Wegrzyn, G., Weigel, C., Welzeck, M., Zakrzewska-Czerwinska, J.,(1999). Functional domains of DnaA proteins. Available at: http://www.sciencedirect.com/science/article/pii/S0300908499002151 (last assessed on 29/11/12).</ref>.  
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*[[Dna A]] - Initiates DNA replication by [[OriC]] recognition on bacterial DNA. Hexamer binds to sequences in the DNA, putting strain on the backbone of the molecule, resulting in the unravelling of a neighbouring tandem array of 13-mer sequences, which are AT-rich. In addition, it instigates [[DNA helicase double strand unzipping|DNA helicase double strand unzipping]]<ref name="Dna A">Messer, W., Blaesing, F., Majka, J., Nardmann, J., Schaper, S., Schmidt, A., Seitz, H., Speck, C., Tüngler, D., Wegrzyn, G., Weigel, C., Welzeck, M., Zakrzewska-Czerwinska, J.,(1999). Functional domains of DnaA proteins. Available at: http://www.sciencedirect.com/science/article/pii/S0300908499002151 (last assessed on 29/11/12).</ref>.  
 
*[[DNA helicase|DNA Helicase]] - Unzips double-stranded DNA by breaking [[Hydrogen bonds|hydrogen bonds]] between base pairs, to allow other enzymes to access bases. It is a ring-like structure with a hole in the centre of the enzyme large enough for only ssDNA to pass through. This separates the two strands from each other, translocating along the lagging strand in a 5' to 3' direction, which is ATP dependent (requires energy). Also known as DnaB.<ref name="Topoisomerase" />.  
 
*[[DNA helicase|DNA Helicase]] - Unzips double-stranded DNA by breaking [[Hydrogen bonds|hydrogen bonds]] between base pairs, to allow other enzymes to access bases. It is a ring-like structure with a hole in the centre of the enzyme large enough for only ssDNA to pass through. This separates the two strands from each other, translocating along the lagging strand in a 5' to 3' direction, which is ATP dependent (requires energy). Also known as DnaB.<ref name="Topoisomerase" />.  
*[[SSB protein]] - the protein that stops unravelled DNA from reforming into a double strand<ref name="SSB protein">Benkovic, S. J, Valentine, A. M., and Salinas, F. (2001). Replisome-mediated DNA replication. </ref>  
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*[[SSB protein]] - the protein that stops unravelled DNA from reforming into a double strand<ref name="SSB protein">Benkovic, S. J, Valentine, A. M., and Salinas, F. (2001). Replisome-mediated DNA replication. </ref>.
 
*[[DNA Primase|Primase]] - Catalyses the polymerisation of short [[RNA|RNA]] strands (primers) which promote [[DNA polymerase III|DNA polymerase III]] to bind and initiate the replication. Note, this enzyme is functionally an [[RNA polymerase]]<ref name="Topoisomerase" />.  
 
*[[DNA Primase|Primase]] - Catalyses the polymerisation of short [[RNA|RNA]] strands (primers) which promote [[DNA polymerase III|DNA polymerase III]] to bind and initiate the replication. Note, this enzyme is functionally an [[RNA polymerase]]<ref name="Topoisomerase" />.  
*[[DNA Polymerase|DNA Polymerase III]] - Catalyses the addition of nucleotides ([[DNTPs]]) onto both DNA strands (i.e. leader and lagging). The addition is strictly in 5 '- 3' direction. Two of these enzyme cores join together, recruited by DnaB, and form a holoenzyme that synthesises a new strand for both the leading and lagging strands simultaneously.
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*[[DNA Polymerase|DNA Polymerase III]] - Catalyses the addition of nucleotides ([[DNTPs]]) onto both DNA strands (i.e. leader and lagging). The addition is strictly in 5 '- 3' direction. Two of these enzyme cores join together, recruited by DnaB, and form a holoenzyme that synthesises a new strand for both the leading and lagging strands simultaneously.  
 
*[[RNase H]] - Catalyses degradation of RNA primers (DNA and RNA hybrids<ref name="Topoisomerase" />)  
 
*[[RNase H]] - Catalyses degradation of RNA primers (DNA and RNA hybrids<ref name="Topoisomerase" />)  
 
*[[DNA polymerase I|DNA Polymerase I]] - Catalyses the addition of short DNA fragments (Okazaki fragments) in place of now degraded [[RNA primer|RNA primers]]; also got a proofreading via [[3' to 5' exonuclease]] activity (reduces the error rate<ref name="Topoisomerase" />)
 
*[[DNA polymerase I|DNA Polymerase I]] - Catalyses the addition of short DNA fragments (Okazaki fragments) in place of now degraded [[RNA primer|RNA primers]]; also got a proofreading via [[3' to 5' exonuclease]] activity (reduces the error rate<ref name="Topoisomerase" />)
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*[[Dna ligase|DNA Ligase]] - Joins [[Phosphate backbone]] at the lagging strand ([[Okazaki fragments|Okazaki fragments]]<ref name="Topoisomerase" />)  
 
*[[Dna ligase|DNA Ligase]] - Joins [[Phosphate backbone]] at the lagging strand ([[Okazaki fragments|Okazaki fragments]]<ref name="Topoisomerase" />)  
 
*[[Type II topoisomerase]] - Catalyses a reversible formation of a nick on 2 antiparallel DNA strands (at the same position on each). This allows produced circular DNA to escape from parental (segregation). Once again, nicks form at [[Phosphate backbones]]<ref name="Topoisomerase" />.  
 
*[[Type II topoisomerase]] - Catalyses a reversible formation of a nick on 2 antiparallel DNA strands (at the same position on each). This allows produced circular DNA to escape from parental (segregation). Once again, nicks form at [[Phosphate backbones]]<ref name="Topoisomerase" />.  
*[[DNA Polymerase II]] - Involved in DNA repair (e.g. during dimerisation of thymine bases via mutagens of radiation<ref>Berg, M. J., Tymoczko, J. L., and Stryer, L. (2002). Biochemistry. 2nd Edition. New York: Freeman and Co.</ref>)
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*[[DNA Polymerase II]] - Involved in DNA repair (e.g. during dimerisation of thymine bases via mutagens of radiation<ref>Berg, M. J., Tymoczko, J. L., and Stryer, L. (2002). Biochemistry. 2nd Edition. New York: Freeman and Co.</ref>.)
  
 
Here are two YouTube Video's which depict what occurs in DNA replication in bacteria. It highlights some of the enzymes listed above and there function in DNA replication. The first one shows an animation of DNA replication and the other shows replication fork coupling which displays DNA ability to form loops.  
 
Here are two YouTube Video's which depict what occurs in DNA replication in bacteria. It highlights some of the enzymes listed above and there function in DNA replication. The first one shows an animation of DNA replication and the other shows replication fork coupling which displays DNA ability to form loops.  

Latest revision as of 20:26, 6 December 2018

DNA replication is a duplication process where exact copies of DNA within cells are replicated, with very low error rate. They typically occur at a rate of 1 in 109 bases per replication. In Mitosis, DNA replication occurs during the S phase. DNA must be duplicated before the division takes place to main the chromosomal number of the two daughter cells. At the end of the division, two genetically identical daughter cells are formed. DNA replication is called Semi-conservative replication.

Within DNA replication the two strands are replicated in slightly different ways. The leading strand, the strand that runs 5' to 3', is replicated continuously. This is because it is known that the DNA polymerase is only able to synthesize in the 5' to 3' direction so the leading strand is in the correct orientation for the DNA polymerase so it can be replicated continuously. On the other hand, the lagging strand runs from 3' to 5' prime which means that it cannot be replicated continuously because the DNA polymerase can't replicate in that direction. This means that the lagging strand is replicated in fragments, which are given the name Okazaki fragments. The DNA is able to form loops so that the DNA polymerase can synthesize the new strand of DNA in the 5' to 3' direction. Other enzymes are then used to join up the gaps that are created through the replication in fragments[1].

Bacterial enzymes

Unlike DNA replication in Eukaryotes (e.g. animals), Bacteria have a limited set of key enzymes associated with this process. These are enumerated below, according to their supposed chronological order during replication in E. coli.

Here are two YouTube Video's which depict what occurs in DNA replication in bacteria. It highlights some of the enzymes listed above and there function in DNA replication. The first one shows an animation of DNA replication and the other shows replication fork coupling which displays DNA ability to form loops.

  1. https://www.youtube.com/watch?v=0Ha9nppnwOc
  2. https://www.youtube.com/watch?v=QMX7IpME7X8

References

  1. Burg J M, Tymoczko J L, Gatto, Jr G J, Stryer L. Biochemistry Eighth Edition. 2015. W.H. Freeman and Company. New York. Pg 831
  2. 2.0 2.1 2.2 2.3 2.4 2.5 2.6 Cooper, G. M. (2000). The Cell: Molecular Approach. 2nd Edition. Washington, D.C: ASM Press.
  3. Messer, W., Blaesing, F., Majka, J., Nardmann, J., Schaper, S., Schmidt, A., Seitz, H., Speck, C., Tüngler, D., Wegrzyn, G., Weigel, C., Welzeck, M., Zakrzewska-Czerwinska, J.,(1999). Functional domains of DnaA proteins. Available at: http://www.sciencedirect.com/science/article/pii/S0300908499002151 (last assessed on 29/11/12).
  4. Benkovic, S. J, Valentine, A. M., and Salinas, F. (2001). Replisome-mediated DNA replication.
  5. Berg, M. J., Tymoczko, J. L., and Stryer, L. (2002). Biochemistry. 2nd Edition. New York: Freeman and Co.
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