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300-09%20Tax%20FINAL

300-09%20Tax%20FINAL - BISC300L Wed Mar 4 2009 Taxonomy of...

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TAXONOMY 3/4/09 1 1 BISC300L Wed., Mar. 4, 2009 Taxonomy of Bacteria and Archaea Chap. 17 FINAL VERSION. Print time 3/4/09 3:45 PM There is a nice, very concise summary of the phyla of Archaea and Bacteria on p. 505- 508. TAXONOMY 3/4/09 2 2 Scientific names On a future exam, I’ll ask you to give the name of the organism that causes tuberculosis: Mycobacterium tuberculosis Genus species The first letter of the genus name is uppercase (capitalized). All other letters, including the first letter of the species name, are lowercase (not capitalized). When written by hand, the entire name is underlined (the editor’s mark to indicate that the font should be italic when typed). In published writing: Once you give the complete scientific name, you can use the first letter of the genus (uppercase, italic, with a period) as an abbreviation for the genus. Don’t abbreviate the species name. For example, after you first mention Mycobacterium tuberculosis , you may call it M. tuberculosis thereafter. TAXONOMY 3/4/09 3 3 Table 17.1 Taxa n n Dons Play Chess On Fine Grain sand taxon ( sing .), taxa ( pl .); phylum ( sing .), phyla ( pl .); genus ( sing .), genera ( pl .); species ( sing .), species ( pl .). In Prof. Caron’s talk about eukaryotic microorganisms, he might have kingdoms in his classification scheme. TAXONOMY 3/4/09 4 4 Numerical taxonomy .
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TAXONOMY 3/4/09 5 5 The similarity coefficient, S AB If A and B are two strains: S AB = where: a is the number of shared traits, b is the number of traits positive for A but not B, c is the number of traits positive for B but not A. See big example in Box 17.2. a+b+c a Note that we don’t count traits for which A and B are both negative. If A and B are bacteria of the same species, we expect S AB to be >0.7. If they are of the same genus, we expect S AB to be >0.5. TAXONOMY 3/4/09 6 6 Exam question on S AB + - 10 + + 9 + + 8 + - 7 - + 6 + + 5 + + 4 + + 3 - + 2 + + 1 STRAIN B STRAIN A TRAIT a) What is the S AB for these two strains? b) What is the S AB for these two strains if Traits 4 and 8 were both negative for both Strain A and Strain B? Give a decimal number. TAXONOMY 3/4/09 7 7 Classification based on DNA sequence n TAXONOMY 3/4/09 8 8 E. coli H. sapiens (YOU) Fig. 17.2 Similarities in 5S rRNAs The small subunit ( SSU ) of the bacterial ribosome contains 16S rRNA , which corresponds to 18S rRNA of eukaryotes. The large subunit ( LSU ) of the bacterial ribosome contains 5S rRNA and 23S rRNA. Comparisons
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