MB 409 - Microbial Diversity - Midterm Exam #1

1. What are the three main evolutionary groups of living things? (5 points)

Archaea (archaebacteria)
Bacteria (eubacteria)
Eukarya (eukaryotes)

2. Give two examples of supposed differences between prokaryotes and eukaryotes and describe how they are mistaken. One of the examples must be a molecular/biochemical difference. (5 points each for 10 points)

For example:

Histones - Bacteria also have histone-like proteins
Archaea even package their DNA with histones into nucleosomes!

Polyadenylated mRNA - Bacteria also polyadenylate their mRNAs, only with shorter poly(A) tails

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

Taxonomies are artificial classification schemes

Phylogenies are natural (evolutionary) schemes

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

1. Decide what sequence to analyse
2. Determine that sequence experimentally
3. Identify homologous residues (align the sequences)
4. Perform the phylogenetic analysis

5. How do the 'Evolutionary ladder' theory and Haeckel's evolutionary tree differ? (5 points)

In the ladder theory, species were thought to evolve progressively, from inferior to superior, whereas in evolutionary trees, species are shown to evolve by diversification.

6. What are the important properties of small subunit ribosomal RNA (ssu-rRNA) that make it such a good molecule for molecular phylogenetic analyis? (10 points)

Clock-like behavior - because it is large and made of many independent units (evolving at different rates) and is conserved in function

Phylogenetic range - it is present in all organisms

Large database available for comparison

7. Read the sequence from this DNA sequencing gel (10 points):

8. Align the following sequences (5 points):

Sequence A - AAAUUCGUUUAG      - A A A U U C G U U U A G -
Sequence B - AAAUCCGUUUAG      - A A A U C C G U U U A G -
Sequence C - AAAUACGUUUAG      - A A A U A C G U U U A G -

9. Align the following RNAs (10 points):

10. Which group of Archaea does 'Isolate X' most likely belong to based on its R2 RNA? (10 points)

Position number    Crenarchaea     Euryarchaea     Korarchea
     4             Y (C or U)          C               U
     5                 U               U               A
     8                 A               G               C
    11                 C               G               G
    15             R (A or G)          C               U
    18                 U               U               C
    19                 A               G           Y (C or U)
    20                 A               A               U
    21                 A               A           Y (C or U)
    22                 G               G               A
                      5/10           9/10            2/10

So it must be a Euyrachaea!

11. Please complete the similarity table with these aligned sequences (1 point each for 10 points).

                                   A     B   C    D    E
Sequence A  - AAAUUCGUUU        A   --  0.9 0.7  0.6  0.4
Sequence B  - AAAUUUGUUU        B   --  --  0.7  0.6  0.4
Sequence C  - AGACUAGUUU        C   --  --   --  0.9  0.4
Sequence D  - AGACUAGUCU        D   --  --   --   --  0.3
Sequence E  - GAAGAAAUUC        E   --  --   --   --   --

12. Answer the following questions about this tree (2 points each for 10 points)

Which sequence (A - F) is the outgroup? F
Which 2 sequences are most closely related? B and C
Which sequence is most similar to E? D
Which sequence (other than perhaps the outgroup) is the most primative? D

13. The following tree was constructed based on a set of ssu-rRNA sequences:

Given that maple, pine, and oak are all vascular plants (trees, in fact), and that Bacillus subtilis is a Gram-positive bacterium originally included in the analysis as an outgroup, how could you explain this unusual tree? (5 points)

The maple sequence is probably either the mitochondrial or chloroplast gene rather than the nuclear gene!