(Genotype)

1. (Genotype) Replication (Chemistry, Phenotype) Replication (Chemistry, Phenotype)

7. DNA Replication Action of DNA polymerase. DNA polymerases assemble incoming deoxynucleoside triphosphates on single-stranded DNA templates such that the growing strand is elongated in its 5’ to 3’ direction.

9. Priming of DNA synthesis by short RNA segments.

10. DNA Polymerase DNA polymerase activity 3’-5’ exonuclease 5’-3’ exonuclease 3’-5’ exonuclease cleaves misincorporated nucleotides 5’-3’ exonuclease Cleaves RNA primers from growing strands

11. Helicase: separate DNA strands • DNA primase: RNA polymerase that lays down the primer • DNA polymerase replicates DNA • b clamp increases processivity • DNA gyrase/topoisomerase: prevents supercoiling

12. Helicase and gyrase/topoisomerase E. coli DNA replicated at 1000 nucleotides/s 1300 µM DNA would flail around at 100 revolutions/s Since it is circular it instead supercoils Accumulates +100 supercoils/s these need to be alleviated DNA is naturally negatively supercoiled and this promotes unwinding However, GyrA, type II topoisomerase further helps by introducing negative supercoiling

18. Proofreading E. coli polymerase makes mistakes every 109 -1010 nucleotides added Given that the genome is 4.6x106 bp this means 1 error per 1000 to 10000 replications

19. Proofreading requires Proper base pairing

24. Even a properly inserted nucleotide is removed a significant amount of the time just to be sure….

26. Many types of DNA polymerase in E. coli Pol I: DNA repair, excision of RNA primers Pol II: DNA repair Pol III: main DNA replicase Pol IV and V?

31. Eukaryotic DNA polymerases Pol : a primase Pol : main polymerase Pol : mitochondrion Pols : DNA repair

32. The reactions catalyzed by reverse transcriptase.

33. NMR structure of the telomeric oligonucleotide d(GGGGTTTTGGGG).

35. Errors do occur Point mutations Insertions Deletions Rearrangements Spontaneous mutation rate = 10-10 to 10-12/cell division in bacteria 1 nucleotide change/per 1000 takes 200,000 yrs. in humans

36. Types and sites of chemical damage to which DNA is normally susceptible in vivo. Red, oxidation; blue, hydrolysis; green, methylation.

37. Mispairing of A with C or G with T: Tautomerization

38. Hydrolysis

39. Need to get rid of uracil in DNA

40. Hydrolysis Depurination occurs 6000 times per day in a mammalian cell

42. Methylation

44. Oxidation Guanosine Hydroxoguanosine

45. Oxidation Strand Breaks

46. Deletions due to strand breaks

49. Insertions and deletions Caused by repetitive sequences and intercalators abasic sites single strand breaks

50. Triplet repeat expansion/contraction CAG or CGG repeats (polyGln)