1 / 29

Figure 30-28 The replication of E. coli DNA.

Topoisomerase: relieves supercoiling—nicks and reaneals one strand of DNA. DNA B: a helicase that separates ds DNA into ss DNA via ATP hydrolysis. Figure 30-28 The replication of E. coli DNA. Functional domains in the Klenow Fragment (left) and DNA Polymerase I (PDB).

medea
Télécharger la présentation

Figure 30-28 The replication of E. coli DNA.

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. Topoisomerase: relieves supercoiling—nicks and reaneals one strand of DNA. DNA B: a helicase that separates ds DNA into ss DNA via ATP hydrolysis Figure 30-28 The replication of E. coli DNA.

  2. Functional domains in the Klenow Fragment (left) and DNA Polymerase I (PDB). Produced from subtilisin or trypsin cleavage Retains polymerase and 3’-5’ exo activity

  3. Figure 30-8b X-Ray structure of E. coli DNA polymerase I Klenow fragment (KF) in complex with a dsDNA (a tube-and-arrow representation of the complex in the same orientation as Part a). Page 1141

  4. The structure of the Klenow fragment of DNAP I from E. coli Fingers Palm

  5. Mismatch repair during DNA replicaiton

  6. Replacing RNA primers

  7. Nick Translation • Requires 5’-3’ activity of DNA pol I • Steps • At a nick (free 3’ OH) in the DNA the DNA pol I binds and digests nucleotides in a 5’-3’ direction • The DNA polymerase activity synthesizes a new DNA strand • A nick remains as the DNA pol I dissociates from the ds DNA. • The nick is closed via DNA ligase Source: Lehninger pg. 940

  8. Figure 30-20 The reactions catalyzed by E. coli DNA ligase. Page 1150

  9. Figure 30-21 X-Ray structure of DNA ligase from Thermus filiformis. Page 1151

  10. DNA Pol III holoenzyme.

  11. Figure 30-13b The  subunit of E. coli Pol III holoenzyme. Space-filling model of sliding clamp in hypothetical complex with B-DNA. Page 1146

  12. Sliding clamp http://www.callutheran.edu/Academic_Programs/Departments/BioDev/omm/poliiib_2/poliiib.htm

  13. Here’s a computer modelof DNA replicationhttp://www.youtube.com/watch?v=4jtmOZaIvS0 This is a pretty good outline: http://www.youtube.com/watch?v=teV62zrm2P0&NR=1 Another one with review questions (perhaps oversimplified) http://www.wiley.com/college/pratt/0471393878/student/animations/dna_replication/index.html

  14. FIDELITY OF REPLICATION • Expect 1/103-4, get 1/108-10. • Factors • 3’5’ exonuclease activity in DNA pols • Use of “tagged” primers to initiate synthesis • Battery of repair enzymes • Cells maintain balanced levels of dNTPs

  15. This article is a simple overview of repair processes • http://www.nature.com/nature/journal/v421/n6921/full/nature01408.html

  16. DNA repair Ilkka Koskela Katri Vilkman

  17. Foreword DNA • variation is an essential factor to evolution (1000-10^6 lesions per day) • stability is important for the individual (less than 1/1000 mutations are permanent) • A relatively large amount of genes are devoted to coding DNA repair functions.

  18. Sources of damage: heat metabolic accidents (free radicals) radiation (UV, X-Ray) exposure to substances (especially aromatic compounds) Types of damage: deamination of nucleotides depurination of nucleotides oxidation of bases breaks in DNA strands

  19. Diseases • colon cancer • cellular ultraviolet sensitivity • Werner syndrome (premature aging, retarded growth) • Bloom syndrome (sunlight hypersensitivity)

  20. Damage of the double helix • Single strand damage • information is still backed up in the other strand • Double strand damage • no backup • can cause the chromosome to break up

  21. Single strand repair • Base excision repair • A base-specific DNA glycosylase detects an altered base and removes it • AP endonuclease and phosphodiesterase remove sugar phosphate • DNA Polymerase fills and DNA ligase seals the nick

  22. Single strand repair • Nucleotide excision repair • a large multienzyme compound scans the DNA strand for anomalities • upon detection a nuclease cuts the strand on both sides of the damage • DNA helicase removes the oligonucleotide • the gap is repaired by DNA polymerase and DNA ligase enzymes

  23. Double strand repair • Nonhomologous end-joining • only in emergency situations • two broken ends of DNA are joined together • a couple of nucleotides are cut from both of the strands • ligase joins the strands together

  24. Double strand repair • Homologous end-joining • damaged site is copied from the other chromosome by special recombination proteins

  25. DNA repair enzymes • a lot of DNA damage -> elevated levels of repair enzymes • extreme change in cell's environment (heat, UV, radiation) activates genes that code DNA repair enzymes • For an example, heat-shock proteins are produced in heat-shock response when being subjected to high temperatures.

  26. Cell Cycle and DNA repair • Cell cycle is delayed if there is a lot of DNA damage. • Repairing DNA as well as signals sent by damaged DNA delays progression of cell cycle. ->ensures that DNA damages are repaired before the cell divides

  27. References • Pictures • http://www.2modern.com/index.asp?PageAction=VIEWPROD&ProdID=985 • http://www.senescence.info/WS.jpg • http://en.wikipedia.org/wiki/Dna • http://www.funpecrp.com.br/gmr/year2003/vol1-2/imagens/sim0001fig1.jpg • http://www.science.siu.edu/microbiology/micr460/PageMill%20Images/image32.gif • http://www.bio.brandeis.edu/haberlab/jehsite/images/nhejd.gif • http://www.biochemsoctrans.org/bst/029/0655/bst0290655f02.gif • http://www.antigenics.com/products/tech/hsp/images/animation.jpg • http://bioinformatics.psb.ugent.be/images/illust_cell_cycle_large.jpg

More Related