L312/Spring 2007 Lecture 18 Drummond March 27

1. L312/Spring 2007 Lecture 18 Drummond March 27 For today: Focus on Ch. 18 Cell cycle regulation (611 - 625) Last time: DNA is highly compacted wrapped around histone octamer (eight histone proteins) DNA + histones = nucleosome histones form ‘beads on a string structure’ beads on a string folds into a 30 nm width fiber further compacted into chromatin How does the cell ‘remember’ where specific genes are? How are genes marked for expression at a specific time? The histone code: Histone tails (N-termini of protein) are modified specific sites are modified; focus on lysine (K) and serine (S) the ‘code’ corresponds to DNA compaction or availability heterochromatin=poorly accessible/compacted DNA euchromatin=accessible/actively transcribed regions Organization of the nucleus and DNA in the nucleus Today: Specific views of cell cycle control and checkpoint arrest focus on why arrest or progression might be appropriate focus on the mechanism of arrest or progression

2. Levels of chromosomal organization

3. Identification of the histone and nucleosome core components Distinguish Histones from nucleosomes

4. An introduction to the ‘histone code’ What are these amino acids?

5. Chromosome structure and compaction changes with the cell cycle What happens to the nuclear lamina? Minimal transcription and translation Expression to maintain Cellular function Analogy revisited

6. Specific progression points where events are triggered

7. Examples of “checkpoints” How do GPRs and RTKs fit in? What are examples of rapidly or Slowly dividing cells?

8. Sites where the cell cycle is halted based on failed ‘tests’ of readiness Broader question: how might these conditions be sensed by the cell? what regulates progression through the cell cycle?

9. Cell cycle progression at the broadest level: the role of cyclins and cdks Cyclin dependent kinase is active when cyclin is bound (hence cdks) M-cyclin + cdk = M-cdk Why kinases? Cyclin expression varies with the cell cycle Cyclins regulate specific kinases (cdks) Kinases switch on or off specific pathways (e.g., regulate cell cycle progression) (remember cascades and integrated responses)

10. M-cyclin regulates initiation of mitosis How is the very rapid decay Of the M-cyclin activity achieved? Many cyclins available; Usually specific to process

11. Ubiquitin mediates M-cyclin degradation Proteasome (large protein degrading machinery within the cell) mediates breakdown (but what triggered modification?) Roles of APC

12. Architecture of the 20S proteasome Degradation occurs here by Threonine- proteases

13. Identification of M-cdk (M-cyclin plus cdk) 1 mm (huge!); mostly S/M phases Readily monitored Cell cycle can be controlled with drugs

14. It couldn’t be that simple: phosphorylation status is crucial to M-cdk The key is that phosphorylation at specific sites is crucial for function. Multiple required inputs exponentially increases the level of complexity for regulation.

15. Cyclins and cdks regulate the cell cycle Not the same Cyclin or cdk! How might this setup avoid re-replication of DNA?

16. Examples of cell cycle regulated genes in Yeast What is the experiment? What do the colors represent? What is the magnitude of change? Are all genes cell cycle regulated?

17. How is replication Triggered in S-phase? Modulating phosphorylation status is the single most important ‘switch’ in the cell (by kinases and phosphatases)