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MCB 229 Spring 2000 Study Guide 13 Prof. Terry
Covers Lecture for March 28

This study guide is intended for you to use while you are doing the assigned text reading. Quiz questions will be made with reference to topics in this study guide. Quiz #13, based on questions from this study guide, must be completed by midnight before the class on Tuesday, March 28. You will need to create your "myWebCT" account and visit the MCB 229 WebCT page in order to access this quiz.

Chapter 19. Microbial Evolution & Taxonomy. Also skim Chs. 20-24.
  1. This chapter has lots of information, and I don't expect you to adsorb all of it. Use these questions as an indicator of where to spend some time.
  2. Do the terms "systematics", "taxonomy", and "classification" mean the same thing? Page 394 is a very readable introduction to these topics.
  3. What is a stromatolite? What organisms create(d) them? Where would you find them today?
  4. What are the 3 domains? Take a good look at Fig. 19.3, the "universal phylogenetic tree". Are the lengths of lines between different organisms drawn arbitrarily, or do they mean something? If so, what?
  5. The speculations about when fundamental divisions between the 3 domains occurred in evolutionary time (p. 396) are interesting but still only speculations. Don't bother memorizing these details.
  6. What is the plural of "genus"? What is the sequence of taxonomic ranks, starting with kingdom and ending with species?
  7. How are bacterial "species" different from eukaryotic species? What do the terms "strain", "biovar", "serovar", "morphovar" mean? What is a "type strain"?
  8. What is the difference between a “phenetic” and a “phylogenetic” classification system? Suppose you were asked to develop a classification of automobiles. How would you go about making a phenetic classification? A phylogenetic classification?
  9. What is an association coefficient? What does an association coefficient of .95 mean? of .05?
  10. What is a dendogram? Compare the data shown in the matrix in Fig. 19.5a with the dendogram in Fig. 19.5c. Which is easier to read?
  11. What kinds of "classical characteristics" are used in microbial taxonomy? What kinds of molecular characteristics are used?
  12. Explain how 16S RNA functions as a "yardstick" for microbial evolution. How is 16S RNA homology determined experimentally? Why is this molecule (and to a lesser degree 5S RNA), rather than some other measure, used to establish relatedness in bacteria?
  13. What is meant by a "molecular chronometer"? What assumption(s) underlie this idea?
  14. In phylogenetic analysis, what is meant by an "unrooted" tree? A "rooted" tree?
  15. Fig. 19.9 contrasts the small ribosomal subunit RNA for each of the 3 domains, illustrating how many regions of this RNA form base pairs with other parts of the molecule. How do such RNAs from these 3 domains differ?
  16. Not all biologists agree with the notion of "3 domains". One variant hypothesis includes a fourth domain, the "Eocytes". What are eocytes?
  17. Skim the discussion of Kingdoms (pp. 409-410); I don't hold you responsible for this.
  18. What is Bergey's manual? Is the first edition a phenetic or phylogenetic system? How about the forthcoming second edition? Briefly skim pp. 413-418 and Chapters 20-24 of your text, which is a highly abridged version of Bergey’s Manual. To practice using this section, find answers to the following questions from Chs. 20-24 (use the index):
    (a) In what taxonomic group would you assign purple and green bacteria?
    (b) What is unusual about the genus Prochloron?
    (c) What genus (or genera) of bacteria contain stalks?
    (d) How do bdellovibrios obtain energy?
    (e) Where would you go to find large populations of Sphaerotilus?
    (f) How are Chlamydias and Ricketssias different?
    (g) What is the relationship between actinomycetes and Streptomyces?
    (h) What are the proteobacteria? Are they a homogeneous or heterogenenous group?
    (i) Mycoplasmas have no wall, so they can't easily be classified as gram- or gram+. To which group are they assigned based on ribosomal RNA data?
  19. Contrast the gram-positive and the gram-negative bacteria in terms of phylogeny. Which of these groups shows greater evolutionary similarity? How could you explain this?