1. Chromatin Structure and Replication1 Chromosome Structure and Replication From chapters 5 & 6 Chapter 5 While we will not cover DNA structure in class formally, but you should review materials in the chapter on the fundamental structures of DNA. We will discuss in class chromatin structure covered on pages pp 184-192. In Chapter 6, you will not be responsible for the details of homologous recombination. Questions in this chapter you should be able to answer: Chapter 5- #s 1, 3, 4, 5A& B, 7, 11-14, 16 Chapter 6- #s 1 - 8, 12 -16 DNA Helicase

2. Chromatin Structure and Replication2 From Chapter 5 Eukaryotic DNA exists as chromatin Chromatin = DNA + histones Nucleosome core Histone octet H1 Nucleosome

3. Chromatin Structure and Replication3 Nucleosomes allow for DNA condensation and “remodeling” Histone modifications Hetero- & Euchromatin DNA supercoiling “Inheritable” Supercoiling

4. Chromatin Structure and Replication4 From Chapter 6 Why is DNA replication said to be ‘semiconservatve’? Read How We know about Meselson and Stahl experiment

5. Chromatin Structure and Replication5 In what direction does DNA replication occur? Where does energy for addition of nucleotide come from? What happens if a base mismatch occurs? DNA Orietation

6. Chromatin Structure and Replication6 Why does DNA replication only occur in the 5’ to 3’ direction? (Picture not in 4 th edition)

7. Chromatin Structure and Replication7 1)How many nM / mM? 2) How many nM between 4 - 5? 3) How many bases between 4 – 5? 4) How long to replicate this region? Answer Question 6-1A How long until forks 4 and 5 meet? Distance between bases is 0.34 nm Replication rate is 100 bases / sec Where does DNA replication begin on a chromosome?

8. Chromatin Structure and Replication8 How is DNA synthesized on 3’ end ‘behind’ advancing replication fork? Okasaki fragments

9. Chromatin Structure and Replication9 Why does DNA synthesis begin with an RNA primer? How are Okasaki fragments synthesized and connected?

10. Chromatin Structure and Replication10 How do other proteins contribute to DNA replication? Helicase Topoisomerase ssDNA binding proteins Sliding clamp DNA Polymerases Ligase DNA Replication Replication Fork

11. Chromatin Structure and Replication11 What is the telomere replication problem? The telomere replication problem On the 3’ ends Telomeres and aging and cancer

12. Chromatin Structure and Replication12 How does telomerase solve the problem?? RNA template Telomerase and cancer treatment Telomere Replication

13. Chromatin Structure and Replication13 How is damaged DNA repaired? Surveillance & repair proteins 1) Mismatch repair during S-phase -- how does the cell know which base to replace? 2) Excision repair (mismatch) -- post S-phase -- 3 steps -- 50% chance of error

14. Chromatin Structure and Replication14 How is damaged DNA repaired? 3) End-joining of DS breaks -- Nonhomologous end joining -- short deletion 4) Homologous recombination -- usually S-phase -- sequence on homolog is used

15. Gene & Genome Evolution15 Mutations accumulate over time Numerous single-nucleotide polymorphisms (SNP) distinguish individual genomes Consequence of “point mutations” 10 7 + documented in humans Can influence: Our individual physical traits Disease susceptibility Risk factors for disorders e.g., Macular Degeneration SNP in Complement factor H His  Tyr 5 – 7x >risk