1. How is the chromosome organized?

2. What role does horizontal gen transfer play in the organization of the genome.

3. Which class of genes is rarely transferred horizontally? Why?

4. List the major mechanisms by which horizontal gene transfer occurs in prokaryotes?

5. What does it mean to classify based on frequency of recombination?

6. What are ecotypes and how could they be used for classification?

7. Do Shigella and E. coli really represent a difference in genus?

8. How are replication, PCR and sequencing the same or different?

9. What are the defining characteristics of third and fourth generation sequencing?

10. Know the new form of sequencing from the videos and be able to answer basic questions about these technologies.

11. What is accomplished during genome assembly?

12. How can protein homology assist in genome annotation?

13. What is a chromosomal island and how can one be identified as being of foreign origin?

14. What is a pathogenicity island and how does one move between bacterial species?

15. What lifestyle is typical of prokaryotes that have genomes smaller than those of certain viruses?

16. Which is likely to have more genes, a prokaryote with 8Mbp of DNA or a eukaryote with 10Mbp?

17. What do microarrays tell you that studying gene expression by assaying individual enzymes cannot?

18. What do we learn from proteomics?

19. What is the interactome?

20. What techniques are used to monitor the metabolome?

21. What is the principle of Maldi-TOF?

22. What is a homologous gene, gene family?

23. Contrast gene paralogs with gene orthologs

24. How might transposons be especially important in the evolution of pathogenic bacteria?

25. What is the difference between core and pan genome?