1. There are three scholarships for pre-medical students that are available for the 2010- 2011 academic year. These are: Whatcom County Medical Society Scholarship: one $500 award Dr. Ralph & Mrs. Eleanor Rinne Pre-Medical Scholarship: two $1500 awards If you would like to apply, please visit http://www.careers.wwu.edu/prehealth_financialaid.shtml for a statement of eligibility and for application details. Or, you may stop by Old Main 380 or Old Main 280 to pick up an application. Completed applications are due in Old Main 380 (Academic Advising Center) by Monday, May 3, 2010.

2. http://www.nature.com/nature/journal/v421/n6921/full/na ture01408.html Cute animations http://www.sciencemag.org/cgi/reprint/266/5193/1926.pdf Nucleotide Excision Repair

4. DNA damage (black triangle) results in either repair or tolerance. a, During damage tolerance, damaged sites are recognized by the replication machinery before they can be repaired, resulting in an arrest that can be relieved by replicative bypass (translesion DNA synthesis). b, DNA repair involves the excision of bases and DNA synthesis (red wavy lines), which requires double-stranded DNA. Mispaired bases, usually generated by mistakes during DNA replication, are excised as single nucleotides during mismatch repair. A damaged base is excised as a single free base (base excision repair) or as an oligonucleotide fragment (nucleotide excision repair). Such fragments are generated by incisions flanking either side of the damaged base. Nucleotide excision repair can also transpire in some organisms by a distinct biochemical mechanism involving only a single incision next to a site of damage (unimodal incision). c, The cell has a network of complex signalling pathways that arrest the cell cycle and may ultimately lead to programmed cell death.

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

6. 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

7. Figure 30-51Types and sites of chemical damage to which DNA is normally susceptible in vivo. Red, oxidation; blue, hydrolysis; green, methylation. Page 1173

8. O 6 -alkylguanine has a different pattern of H-bond donor and acceptor atoms than the parent guanine base. As a result, it basepairs with T instead of C, giving rise to G  A transition after the second round of replication: Endogenous and exogenous alkylating agents (tobacco smoke, some anticancer drugs):

9. O6-alkylguanine DNA alkyltransferase (AGT) Directly repaires alkylation damage (O 6 -alkylguanines) by transferring the O 6 -alkyl group from damaged guanine in DNA to a Cys residue in the AGT active site in a stoichiometric reaction. The protein is inactivated via alkylation and undergoes proteolytic degradation.  AGT protein is highly conserved:  helix-turn-helix DNA binding motif  the alkylated base is “flipped” out of the helix to enter the hydrophobic alkyl-binding pocket of the protein  high metabolic cost for the cell is outweighed by the need to maintain genetic integrity

10. Figure 30-52The cyclobutylthymine dimer that forms on UV irradiation of two adjacent thymine residues on a DNA strand. Photolyase: repairs cyclobutane pyrimidine dimers. Uses the energy of light to catalyze the reversal of the cyclobutane bonds, producing intact DNA. Not very important in mammals.

11. Figure 30-55The mechanism of nucleotide excision repair (NER) of pyrimidine photodimers. Page 1176

12. 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

13. Figure 30-56Action of DNA glycosylases. These enzymes hydrolyze the glycosidic bond of their corresponding altered base (red) to yield an AP site. Page 1177

14. Figure 30-57X-Ray structure of human uracil– DNA glycosylase (UDG) in complex with a 10-bp DNA containing a U·G base pair. Page 1178

15. Base Excision Repair Used for repair of small damaged bases in DNA (AP sites, oxidized, deaminated, and methylated bases) Several steps are involved: a) modified base is excised by N-glycosylase to give an abasic site b) the abasic site is cleaved c) the resulting single-nucleotide gap is filled by DNA Polymerase d) DNA Ligase seals the nicks Example: uracil DNA glycosylase

16. Figure 30-58 The mechanism of mismatch repair in E. coli. Page 1179

17. Figure 30-59Regulation of the SOS response in E. coli. Page 1180

18. 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

19. Mismatch Repair Mismatch Repair deals with correcting mismatches of normal bases. Steps in MMR: Recognition of a mismatch Identification of newly synthesized strand Removal of mismatchGap repair by DNA Pol

20. 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

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

22. 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.

23. 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

24. 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/i mage32.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