1. Chapter 12 Outline 12.1 Genetic Information Must Be Accurately Copied Every Time a Cell Divides, 316 12.2 All DNA Replication Takes Place in a Semiconservative Manner, 316 12.3 The Replication of DNA Requires a Large Number of Enzymes and Proteins, 324 12.4 Recombination Takes Place Through the Breakage, Alignment, and Repair of DNA Strands, 335

2. 12.1 Genetic Information Must Be Accurately Copied Every Time a Cell Divides Replication has to be extremely accurate: 1 error/million bp leads to 6400 mistakes every time a cell divides, which would be catastrophic. Replication also takes place at high speed: E. coli replicates its DNA at a rate of 1000 nucleotides/second.

3. 12.2 All DNA Replication Takes Place in a Semiconservative Manner

4. Conservative replication model Dispersive replication model Semiconservative replication Proposed DNA Replication Models

6. Two isotopes of nitrogen: 14 N common form; 15 N rare heavy form E. coli were grown in a 15 N media first, then transferred to 14 N media. Cultured E. coli were subjected to equilibrium density gradient centrifugation. Meselson and Stahl’s Experiment

8. Replicons: units of replication Replication origin Theta replication: circular DNA, E. coli; single origin of replication forming a replication fork, usually a bidirectional replication Rolling-circle replication: virus, F factor of E. coli; single origin of replication Modes of Replication

9. Eukaryotic cells; thousands of origins; a typical replicon: 200,000 ~ 300,000 bp in length Linear Eukaryotic Replication

14. Requirements of replication: A template strand Raw material: nucleotides Enzymes and other proteins Linear Eukaryotic Replication

15. Direction of replication: DNA polymerase add nucleotides only to the 3′ end of a growing strand. The replication can only go 5′  3′. Linear Eukaryotic Replication

18. Direction of replication: Leading strand: undergoes continuous replication Lagging strand: undergoes discontinuous replication Okazaki fragment: the discontinuously synthesized short DNA fragments forming the lagging strand Linear Eukaryotic Replication

19. 12.3 The Replication of DNA Requires a Large Number of Enzymes and Proteins

20. Bacterial DNA Replication Initiation: 245 bp in the oriC (single origin replicon); an initiation protein Unwinding of DNA is performed by Helicase. Gyrase removes supercoiling ahead of the replication fork. Single stranded DNA is prevented from annealing by single stranded binding proteins. Primers: an existing group of RNA nucleotides with a 3′- OH group to which a new nucleotide can be added; usually 10 ~ 12 nucleotides long Primase: RNA polymerase

21. Bacterial DNA Replication Elongation: carried out by DNA polymerase III Removing RNA primer: DNA polymerase I DNA ligase: connecting nicks after RNA primers are removed Termination: when a replication fork meets or by termination protein

22. Bacterial DNA Replication The fidelity of DNA replication Proofreading: DNA polymerase I: 3′  5′ exonuclease activity removes the incorrectly paired nucleotide. Mismatch repair: correcting errors after replication is complete

26. Eukaryotic DNA Replication Eukaryotic DNA polymerase DNA polymerase  acts like Primase to initiate DNA polymerase  - replicates lagging strand DNA polymerase  - replicates leading strand

27. Eukaryotic DNA Replication Replication at the ends of chromosomes: Telomeres and telomerase