DQ7.1: How would you characterize the relationship between Bacteria or Archaea and the "accessory elements" known as plasmids? Is this a mutualism? Are the microbes being parasitized?

DQ7.2: How are plasmids important in lateral gene transfer (LGT)?

DQ7.3: Compare and contrast bacterial/archaeal genomes with eukaryotic genomes. What are the most important differences, and why?

DQ7.4: What is the evidence, if any, that so-called "junk DNA" in eukaryotes might not be merely accumulated "junk"?

DQ7.5: How might the lack of introns in microbial genomes influence the transcription and translation of proteins?

DQ7.6: What evidence suggests that gene content is in constant flux in Bacteria and Archaea? How does one read a dotplot comparing two genomes? What consequences does this flux have?

DQ7.7: What important constraints are there on changes in microbial gene order?

DQ7.8: What do transformation, conjugation, and transduction have to do with lateral DNA transfer?

DQ7.9: Explain the natural role of restriction enzymes.

DQ7.10: Explain "amelioration in coding regions" (Fig. 7.22) and why codon position matters.

DQ7.11: Can you interpret a tree diagram that provides evidence for LGT, such as the one in Fig. 7.25?

DQ7.12: In what sense is there a balance between vertical evolution, gene loss, and LGT?