1. Fig. 10-CO, Biosynthesis of Nucleic acid: DNA Replication Fidelity— Proofreading Self-correcting

2. Fig. 10-1, Mechanism for transfer of information in the cell Flow of genetic information Central Dogma of Molecular biology template amplifyworkhouse Retrovirus (HIV) Reverse transcriptase genes cDNA

3. Prokaryotic Replication Challenges in duplication of circular double- stranded DNA –achievement of continuous unwinding and separation of the two DNA strands –protection of unwound portions from attack by nucleases that attack single-stranded DNA –synthesis of the DNA template from 5’ -> 3’ on both antiparallel strand –efficient protection from errors in replication

4. Fig. 10-2, Semiconservative replication Double strand- Protected from nuclease Template N 15 N 14 N 14

5. Fig. 10-3, N 15 N 14 Experiment

6. Fig. 10-4, Bidirectional replication Origin of replication 2 Replication forks replicators

7. Fig. 10-5, p. 266 Polymerization Net chain growth DNA polymerase RNA primer Phosphodiester bond pyrophosphate

8. Fig. 10-6, Semidiscontinuous model- DNA polymerase reaction 5’ to 3’Nascent chain-new strand 1000-2000 nts

9. AIDS: acquired immune deficiency syndrome Stop polymerization

10. Turnover number: speed Processivity: nts join before enzyme dissociates PolII-repair enzyme, Pol VI and V-SOS response Exonuclease 5’-3’—repair, remove RNA primer (several nts), 3’-5’—proofreading (once a nt)

11. Table 10-2, p.242 major polymerase complex--clamp

12. Fig. 10-8 Need energy Supercoiling and replication unwinding

13. Fig. 10-9 Replication fork Helicase: open helix SSB: single-strand binding (protect from nuclease) Primase (primosome: primer and proteins): RNA (de novo) 2 molecules of Pol III (synthesis)+ primosome= replisome Pol I-remove primer and add new DNA nts DNA ligase

14. Table 10-3,

15. Fig. 10-10 Proofreading- 10 9 to 10 10 Mispairing- 10 4 to 10 5

16. Why is T but not U

17. Fig. 10-11 Remove RNA primer & mistakes (mutagen)

18. Fig. 10-11 Label DNA for probe Nick translation by DNA polymerase-cut and patch

19. Fig. 10-12 UV pyrimidine dimer Interfere replication and transcription Thymine dimer (base pairing mistake)

20. Fig. 10-13 Free oxygen radicals-destroy sugar ring

21. Fig. 10-14 Mismatch repair in E. coli Parental strand- Methylated Eu: Adenine Pro: Cytosine

22. Fig. 10-15 Base excision repair Remove sugar and phosphate Pol I

23. Fig. 10-16 Nucleotide excision repair (UV dimer) Xeroderma pigmentosum- Skin cancer

24. Fig. 10-17 DNA recombining DNA recombination homologous recombination Homologous sequences gametes meiosis

25. Light blueDark blue homologous recombination Immune cell: immunoglobulin Hot spots (requires PRDM9- Histone methyltransferase) Meiosis—aneuploidy, 10-25% inaccurate Holiday model Chromosome pairing RecBCD: initial RecA: SS binding RuvA, B, C: branch migration

26. Fig. 10-19 The eukaryotic cell cycle Less than 24 hours to hundreds of days Mitosis and Cell division G0—quiescent Not growing and dividing : neuron Eukaryotic DNA replication Multiple origins Time control (cell cycle) Lots proteins and enzymes

27. Fig. 10-20 Initiation of the DNA replication cycle in eukaryotic Replicator, Replicons (500-50,000 bps) ORC: Origin recognition complex RAP-replication activator protein RLFs: replication licensing factors (cytosolic-nuclear membrane break down) Pre-RC-pre-replication complex CDKs-cyclin-dependent protein kinases Phosphorylation of the RAP, RLF, ORC-trigger replication and prevent new pre-RC

28.  - Pol III-lagging strand, primase  repair Main Pol Repair, remove primer

29. Fig. 10-21

31. Fig. 10-22 Eukaryotic replication fork PCNA: proliferating cell nuclear antigen= Sliding clamp RFC: replication factor C-attaching PCNA to Pol FEN-1, RNaseH1: degrade the RNA primers Polymerase  -primer and 20 nts

32. Problems at the end of DNA molecule- get shorter

33. Telomere replication 5’TTAGGG3’-1000 times Telomerase-ribonuclear protein RNA complement of the telomere -CCCUAA

35. Reverse transcriptase Telomerase-ribonuclear protein RNA complement of the telomere -CCCUAA Not active in most adult tissues Reactive in cancer cells Mice lacking telomerase: stop Shortening-other protective ways