How did comparisons of different rRNA sequences lead to thediscovery of Archaea? Why did Woese use rRNA genes to constructmolecular phylogenies? Which groups are most similar (bacteria,archaea, and eukaryotes) with respect to the following structuresor processes: cellular membrane biochemistry, DNA replication, RNAtranscription, mechanism of protein translation, initiation ofprotein translation. Explain the argument that the most fundamentaldivide in the Tree of Life is between Bacteria and Archaea. Why ismembrane composition cited as the basis of the ‘eukaryote paradox’?Know the arguments for discontinuing use of the term “prokaryote”and be able to explain why you think (or don’t think) thatprokaryote is a useful and/or accurate term. How do Lateral GeneTransfers (LGT), aka horizontal gene transfer, confoundreconstruction of phylogenetic trees? Name three processes ofbacteria and archaea that result in LGT. How can we overcome thisdifficulty in understanding the (vertical) evolutionary history ofmicrobes? What kinds of genes seem resistant to LGT? Explain thestatement “we are embedded in a microbial world” – be sure toinclude the production of oxygen on Earth in your answer. Rememberthat thermodynamics tells us that energy flows out of all systems,but matter cycles. Much of the nutrient (matter) cycling that weall depend on requires microbial activity. Name the nutrient cyclesthat we described in lecture that require microbial activity. Whendid the plant- nitrogen-fixing-bacterial symbiosis emerge inearth’s history? Chlorophylls are an innovation of which group oforganisms? Why is nitrogen limiting in most ecosystems?