Discwk3 fig

Discwk3 fig - DnaA Make sure you review this mechanism as...

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Unformatted text preview: DnaA Make sure you review this mechanism as well as Replication initiation for both Euks and Proks. Note that DnaA uses ATP binding to get onto the DNA, and then uses ATP hydrolysis to get off the DNA. This is analogous to the Clamp loader, which needs ATP to bind the clamp and get on the DNA, and which uses ATP hydrolysis to release the clamp and get off the DNA. This is also similar to the DnaC protein which helps load DnaB. It needs to bind ATP to be able to help load DnaB, and then it releases gets by hydrolyzing ATP. Try to look for common mechanisms like this when you’re studying. a | ATP–DnaA forms a right-handed helical filament. Side and axial views of four symmetry-related DnaA tetramers (RCSB Protein Data Bank (PDB) ID 2HCB) are shown35. The domains of each protomer are coloured as in Figure 2.The initial monomer of the filament is coloured grey to distinguish a single subunit of the filament. b | The same view of the helical filament as in panel a, but highlighting the helical insert (green) of DnaA. This conserved structural feature of the initiator clade lines the axial channel of the filament. Alternating subunits are coloured grey and yellow. c | A proposed mechanism for the ATP–DnaA filament during origin remodelling. The formation of a positive, toroidal DNA wrap by the ATP– DnaA filament might destabilize the origin by introducing strain into the DNAunwinding element (DUE) through compensatory negative supercoiling (top M. Mott and J. Berger. Nature Reviews Microbiology 5, 343-354 (May 2007) panel), which would facilitate DNA melting (bottom-left panel). Coincident with or after opening, the interior of oligomerized ATP–DnaA might directly engage the unwound DUE (bottom-right panel). Wednesday, February 9, 2011 Figure 30.16 The probable course of events during initiation of E. coli replication at oriC. Tetramers of DnaA protein bind at each of the four 9-bp repeats in oriC; then additional DnaA protein binds to give a nucleosomelike structure with DNA on the outside. The three 13-bp A:Trich regions are then “melted” to yield an open complex, and the DnaB protein delivered from the DnaB:DnaC protein complex enters. The helicase activity of DnaB unwinds the duplex, displacing DnaA protein. SSB protein binds to single-stranded DNA as it is generated, preventing its re-annealing. Wednesday, February 9, 2011 by University of California - Berkeley on 09/15/10. For personal use only. V277-BI75-19 ARI 11 May 2006 15:36 Telomerase uses its own RNA template to extend the 3’ ends of chromosomes a DNA substrate binding to the RNP anchor site(s) and RNA template 5' -GGTTAGGGTTAGGGTTAGGGTTAGGGTTAG 3' -CCAAT AAUCCCAAUC 5' 3' b Elongation of the 3' end of the DNA substrate by nucleotide addition and 5' template boundary recognition 5' -GGTTAGGGTTAGGGTTAGGGTTAGGGTTAG GGTTAG AAUCCCAAUC 3' -CCAAT 5' 3' d 5' -GGTTAGGGTTAGGGTTAGGGTTAGGGTTAG GGTTAG GGT AAUCCCAAUC 3' -CCAAT 5' 3' Initiation of a second round of nucleotide addition resulting in processive repeat addition c DNA substrate and enzyme translocation 5' -GGTTAGGGTTAGGGTTAGGGTTAGGGTTAG GGTTAG 3' -CCAAT AAUCCCAAUC 3' 5' http://www.mun.ca/biochem/courses/3107/images/telomerase_model.gif Figure 1. Model for processive elongation by telomerase. Processive extension of DNA by telomerase requires a number of steps, as illustrated here for the human enzyme. (a) First, the telomeric DNA is recognized by the telomerase ribonucleoprotein (RNP), consisting of at least the TERT protein, including the anchor site(s) (shades of gray) and the RNA subunit (depicted in blue and as unstructured here for simplicity). The 3 end of the DNA forms a hybrid with the RNA template (boxed in blue), whereas the more 5 region of the DNA is postulated to interact with the “template-proximal” and “template-distal” anchor site(s). (b) Next, template-directed addition of nucleotides to the 3 end of the DNA occurs sequentially until the 5 end of the template is reached (nucleotide addition processivity). Added nucleotides (red) are displayed. (c) Telomerase undergoes the translocation reaction and repositions the 3 end of the DNA in concert with recognition of the 3 template boundary. (d ) Another round of nucleotide addition is initiated. Added nucleotides (purple) are displayed. Reiterative translocation and nucleotide addition result in the addition of multiple repeats. Repeat addition is regulated by RNA-DNA, TERT-DNA, TERT-RNA, and TERT-TERT interactions and possibly by an intrinsic nuclease activity as well as telomerase-associated proteins. This model is based on numerous studies performed with Tetrahymena, human, and yeast telomerases (60, 89–92, 97–99, 182). See text for more details. Wednesday, February 9, 2011 C. Autexier and N. Lue. Annu. Rev. Biochem. 2006. Telomerase and telomere length in tumorigenesis Changes in telomere length over time during tumour progression, compared with changes in normal tissue. Tumours generally have shorter telomeres than the surrounding normal tissue, owing to the fact that they have had a longer proliferative history in the absence of telomerase activity. This telomere shortening could eventually lead to increased cell death and loss of cell viability within the tumour. However, telomerase is reactivated in more than 90% of all types of human tumour, thereby rescuing short telomeres and perpetuating cells with short telomeres and high chromosomal instability. Similarly, most metastases also contain telomerase-positive cells, which indicates that telomerase is required to sustain their growth. The fact that cancer cells have shorter telomeres than normal cells, together with the fact that cancer growth seems to depend on telomerase reactivation, indicates that therapeutic strategies that are aimed at inhibiting telomerase will preferentially kill tumour cells and have no toxicity on normal cells. The presence or absence of telomerase activity is indicated by the plus symbol and minus symbol respectively. b | The composition of cells in a tumour over the same time-frame. Maria A. Blasco, “Telomeres and human disease: aging, cancer and beyond”. Nature Review Genetics, 2005 Wednesday, February 9, 2011 BER and NER in E. coli Just different diagrams of the same things covered in class Modi%ied from Robert Weaver. Molecular Biology. Wednesday, February 9, 2011 NHEJ often causes loss of sequence information Non-homologous end joining often results in loss of sequence information since unlike HR, it does not seek long stretches of homology with another sister chromosome. This diagram illustrates one way in which this kind of repair can result in loss of sequence. There are other re-joining schemes that can also lead to loss of info such as breakage that causes sticky ends which become degraded before rejoining to another free DNA end. In NHEJ, broken chromosomes are paired with whatever other free end is nearby. This could result in rejoining of the same broken chromosome or it could result in pairing of unrelated sequence segments. Robert Weaver. Molecular Biology. Wednesday, February 9, 2011 ...
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Discwk3 fig - DnaA Make sure you review this mechanism as...

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