Midterm exam #1 - Fall 1997


1. What are the 3 primary evolutionary branches of life? (5 points)

Bacteria, Eukarya, and Archaea

2. Give one example of how all living things are alike. (5 points)

For example: All cells encode information in the form of DNA, in exactly the same chemical and stereochemical structures, using the same genetic code.

3. Give an example of a generally-accepted fundamental difference between prokaryotes and eukaryotes, and why it's not such a fundamental difference after all. (5 points)

For example: prokaryotes are small and eukaryotes are large.

But - many eukaryotes are quite small (e.g. eukaryotic nanoplancton <2um) and many prokaryotes are large (e.g. Epulopiscium >500um).

4. Why did microbiologists in the past not concern themselves with evoluionary relationships, whereas botanists and zoologists did? (5 points)

Because they didn't have any way to determine evolutionary relationship, whereas plants & animals have complex morphology that can be used to decipher phylogeny.

5. What is the difference between phylogeny and taxonomy? (5 points)

Taxonomies are artificial classification schemes

Phylogenies are natural, evolutionary relationships

6. Whar are the most important differences between the 3-Domain molecular phylogenetic tree and the 5-Kingdom 'classical' tree? (5 points)

The 3-Domain tree is objective and quantitative, whereas the 3-Kingdon tree is subjective and qualitative.

7. It's long been thought likely that the chloroplasts of plants & algae might have originated from cyanobacteria that lived symbiotically in the ancestors of plants. How was this hypothesis proven? (5 points)

These organelles have their own DNA, including ssu-rRNA genes, which were analyzed by molecular phylogenetic analysis.

8. What are the steps of a molecular phylogenetic analysis? (5 points)

9. What are the properties that are important for a macromolecule (such as ssu-rRNA) to be good for molecular phylogenetic analysis? (10 points)

10. Briefly describe one method other than ssu-rRNA molecular phylogenetic analysis that is commonly used to identify organisms. (5 points)

For example: Lipid analysis

Lipids are extracted from a carefully grown culture and separated by gas chromatography. The resulting lipid 'profile' is diagnostic of particular organisms.

11. Align the following sequences: (5 points)


Sequence A : - G A A U U C G G G C C C
Sequence B : A G A A U C C G G G C C C
Sequence C : - G A A U - U G G G C C -

12. Align the following RNAs: (5 points)

  RNA A            RNA B             RNA C


13. What kind of monkey is the Yeti according to this signature table of A1-site RNA? (10 points)

     Position Old-world monkeys New-world monkeys  Yeti
       7            U X                C +           C
      10            Y X                R +           A
      19            C X                R +           G
      26            U X                A +           A
      30            G X                U +           U
                    0/5               5/5

            The Yeti seems to new-world monkey

14. Complete the similarity table with these aligned sequences (5 points)

                                       A   B   C   D
Sequence A : G G G U U C G C C C    A XXX XXX XXX XXX
Sequence B : G A C U U C G G U C    B 0.6 XXX XXX XXX
Sequence C : G A C U U U G G U C    C 0.5 0.9 XXX XXX
Sequence D : C C G G U G A C G G    D 0.3 0.1 0.1 XXX

15. Why is the observed dissimilarity between two sequences an underestimate of the evolutionary distance between those sequences? (5 points)

Because more than one change at a position is counted as only a single difference (or even no difference, if it is a reversion or convergent change).

16. Answer the following questions about this tree. Sequence F is an outgroup sequence: (2 points each for 10 points)

Which 2 sequences are most closely related? D and E

Which sequence is most closely related to sequence A? B

Circle the last common ancestor of sequences A, B, and C.

Of sequences A-E, which is the least primative? A (or C)

17. This tree was constructed using sequences of methionyl-tRNAs (tRNAMet). Given E. coli, Salmonella, Shigella, and Serratia are all very closely related enterobacteria, and Bacillus subtilis is a Gram-positive bacterium originally included in the analysis as an outgroup, how could you explain this unusual tree? (5 points)

There are 2 different methionyl tRNAs - the initiator and elongator tRNA(Met). The Salmonella sequence must be one version and the other sequences are the other version, i.e. the Salmonella is the elongator tRNA(Met) and the others are the initiator tRNA(Met), or visa versa.