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Click Here! For A Review of the Entire Process of DNA Replication!

Click Here! For A Review of the Entire Process of DNA Replication!. http://www.wiley.com/college/pratt/0471393878/student/animations/dna_replication/index.html. Proteins of DNA Replication.

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Click Here! For A Review of the Entire Process of DNA Replication!

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  1. Click Here! For A Review of the Entire Process of DNA Replication!

  2. http://www.wiley.com/college/pratt/0471393878/student/animations/dna_replication/index.htmlhttp://www.wiley.com/college/pratt/0471393878/student/animations/dna_replication/index.html

  3. Proteins of DNA Replication • DNA Helicases - These proteins bind to the double stranded DNA and stimulate the separation of the two strands. • DNA single-stranded binding proteins - These proteins bind to the DNA as a tetramer and stabilize the single-stranded structure that is generated by the action of the helicases. Replication is 100 times faster when these proteins are attached to the single-stranded DNA. • DNA Gyrase - This enzyme catalyzes the formation of negative supercoils that is thought to aid with the unwinding process. • In addition to these proteins, several other enzymes are involved in bacterial DNA replication. • DNA Polymerase - DNA Polymerase I (Pol I) was the first enzyme discovered with polymerase activity, and it is the best characterized enzyme. Although this was the first enzyme to be discovered that had the required polymerase activities, it is not the primary enzyme involved with bacterial DNA replication. That enzyme is DNA Polymerase III (Pol III). Three activities are associated with DNA polymerase I; • 5' to 3' elongation (polymerase activity) • 3' to 5' exonuclease (proof-reading activity) • 5' to 3' exonuclease (repair activity) • The second two activities of DNA Pol I are important for replication, but DNA Polymerase III (Pol III) is the enzyme that performs the 5'-3' polymerase function. • Primase - The requirement for a free 3' hydroxyl group is fulfilled by the RNA primers that are synthesized at the initiation sites by these enzymes. • DNA Ligase - Nicks occur in the developing molecule because the RNA primer is removed and synthesis proceeds in a discontinuous manner on the lagging strand. The final replication product does not have any nicks because DNA ligase forms a covalent phosphodiester linkage between 3'-hydroxyl and 5'-phosphate groups.

  4. A General Model for DNA Replication • The DNA molecule is unwound and prepared for synthesis by the action of DNA gyrase, DNA helicase and the single-stranded DNA binding proteins. • A free 3'OH group is required for replication, but when the two chains separate no group of that nature exists. RNA primers are synthesized, and the free 3'OH of the primer is used to begin replication. • The replication fork moves in one direction, but DNA replication only goes in the 5' to 3' direction. This paradox is resolved by the use of Okazaki fragments. These are short, discontinuous replication products that are produced off the lagging strand. This is in comparison to the continuous strand that is made off the leading strand. • The final product does not have RNA stretches in it. These are removed by the 5' to 3' exonuclease action of Polymerase I. • 5. The final product does not have any gaps in the DNA that result from the removal of the RNA primer. These are filled in by the action of DNA Polymerase I. • 6. DNA polymerase does not have the ability to form the final bond. This is done by the enzyme DNA ligase. To get an idea of the rate of DNA Replication: http://www.youtube.com/watch?v=4jtmOZaIvS0

  5. Enzymes of DNA Replication Helicase: Unwounds a portion of the DNA Double HelixRNA Primase: Attaches RNA primers to the replicating strands.DNA Polymerase delta (ä): Binds to the 5' - 3' strand in order to bring nucleotides and create the daughter leading strand.DNA Polymerase epsilon (å): Binds to the 3' - 5' strand in order to create discontinuous segments starting from different RNA primers.Exonuclease (DNA Polymerase I): Finds and removes the RNA Primers DNA Ligase: Adds phosphate in the remaining gaps of the phosphate - sugar backboneNucleases: Remove wrong nucleotides from the daughter strand.

  6. DNA Replication Bubbles

  7. A large number of enzymes and other proteins are involved in the synthesis of new DNA at a replication fork

  8. Step-by-StepDNA Replication

  9. Steps of DNA Replication in Eukaryotes Step 1: The first major step for the DNA Replication to take place is the breaking of hydrogen bonds between bases of the two antiparallel strands. The unwounding of the two strands is the starting point. The splitting happens in places of the chains which are rich in A-T. That is because there are only two bonds between Adenine and Thymine (there are three hydrogen bonds between Cytosine and Guanine). Helicase is the enzyme that splits the two strands. The initiation point where the splitting starts is called "origin of replication".The structure that is created is known as "Replication Fork".

  10. Step 2: One of the most important steps of DNA Replication is the binding of RNA Primase in the the initiation point of the 3'-5' parent chain. RNA Primase can attract RNA nucleotides which bind to the DNA nucleotides of the 3'-5' strand due to the hydrogen bonds between the bases. RNA nucleotides are the primers (starters) for the binding of DNA nucleotides.

  11. Step 3A: The elongation process is different for the 5'-3' and 3'-5' template. a)5'-3' Template: The 3'-5' proceeding daughter strand -that uses a 5'-3' template- is called leading strand because DNA Polymerase ä can "read" the template and continuously adds nucleotides (complementary to the nucleotides of the template, for example Adenine opposite to Thymine etc).

  12. Step 3B: 3'-5'Template: The 3'-5' template cannot be "read" by DNA Polymerase ä. The replication of this template is complicated and the new strand is called lagging strand. In the lagging strand the RNA Primase adds more RNA Primers. DNA polymerase å reads the template and lengthens the bursts. The gap between two RNA primers is called "Okazaki Fragments". The RNA Primers are necessary for DNA Polymerase å to bind Nucleotides to the 3' end of them. The daughter strand is elongated with the binding of more DNA nucleotides. Need some more help? http://207.207.4.198/pub/flash/24/menu.swf

  13. Step 4: In the lagging strand the DNA Pol I -exonuclease- reads the fragments and removes the RNA Primers. The gaps are closed with the action of DNA Polymerase (adds complementary nucleotides to the gaps) and DNA Ligase (adds phosphate in the remaining gaps of the phosphate - sugar backbone). Each new double helix is consisted of one old and one new chain. This is what we call semiconservative replication. (Proposed by Watson & Crick and tested by Meselson & Stahl) Meselson & Stahl Experiment

  14. http://www.contexo.info/DNA_Basics/DNA%20Replication.htm

  15. When DNA Duplication is over: The usual replication machinery provides no way to complete the 5’ ends of daughter DNA strands. Fig. 16.18

  16. After Replication: The DNA Replication is not completed before a mechanism of repair fixes possible errors caused during the replication. Enzymes like nucleases remove the wrong nucleotides and the DNA Polymerase fills the gaps.

  17. In mismatch repair, special enzymes fix incorrectly paired nucleotides. • A hereditary defect in one of these enzymesis associated with a form of colon cancer. • In nucleotide excision repair, a nuclease cuts out a segment of a damaged strand. • The gap is filled in by DNA polymerase and ligase. Fig. 16.17

  18. Animations for DNA semi conservative replication http://www.johnkyrk.com/DNAreplication.html Process http://dangerousintersection.org/2008/05/11/computer-animation-of-dna-at-work-at-the-molecular-level/ http://www.people.virginia.edu/~rjh9u/dnarep01anim.html http://www.people.virginia.edu/~rjh9u/repforks.html http://www.fed.cuhk.edu.hk/~johnson/teaching/genetics/animations/dna_replication.htmhttp://www.wwnorton.com/college/biology/mbio/animations/dna_replication.asp http://brodylab.eng.uci.edu/animations/files/9-973824225.swf http://www.wiley.com/college/pratt/0471393878/student/animations/dna_replication/index.html DNA Repair http://www.nature.com/nrc/journal/v1/n1/animation/nrc1001-022a_swf_MEDIA1.html

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