MB 495 C/D - Microbial Diversity - Spring 1995

Midterm Exam #1


1. Briefly describe the implication of the observation that all living things are mostly alike. (5 points)

2. Give one biochemical/molecular instance in which the classical division between eukaryotes and prokaryotes is incorrect, and describe why it is incorrect. (5 points)

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

4. What are the three main evolutionary groups (Domains, or Kingdoms) of life? Which of these groups are prokaryotic and which eukaryotic? (5 points)

5. What is the endosymbiont theory for the origin of mitochondria and chloroplasts? (5 points)

6. What is the main property a sequence must have in order to change in a clock-like manner? (5 points)

7. Align the following sequences: (10 points)

 Seq 1 AUGCGCUUCGGCGC   Seq 1  __ __ __ __ __ __ __ __ __ __ __ __ __ __ __ __
 Seq 2 AGCGCUCCGGCGC    Seq 2  __ __ __ __ __ __ __ __ __ __ __ __ __ __ __ __
 Seq 3 ACGCGCGAAAGCGCA  Seq 3  __ __ __ __ __ __ __ __ __ __ __ __ __ __ __ __
 Seq 4 AGCGCGCAAGCGCG   Seq 4  __ __ __ __ __ __ __ __ __ __ __ __ __ __ __ __

8. Align the sequences of the following RNAs: (10 points)

      U C          A G           C A
    U     G      G     A       G     A	Seq 1  __ __ __ __ __ __ __ __ __ __ __ __ __ __ __ __
     C - G        G - C         G - C	Seq 2  __ __ __ __ __ __ __ __ __ __ __ __ __ __ __ __	
     A - U        A - U         A - U	Seq 3  __ __ __ __ __ __ __ __ __ __ __ __ __ __ __ __
     G - C        G - C         G - U
     U - A G C    C - G G A    C
                                U - A G

9. Given the RNA secondary structure below and the table of signature nucleotides, what kind of purple bacterium does the RNA come from (alpha, beta, gamma, delta, or epsilon)? _____________ (10 points)

                           groups of purple Bacteria
                --------------------------------------------------
   Position     alpha      beta      gamma      delta      epsilon
      2           G         G          G          A           G
      8           C         U          U          C           C
     10           G         G          G          G           A
     13           C         U          C          C           U
     26           C         U          C         U/C          C
     30           U         U          C          C           C
     42           A         A          G          G           G
     49           U         C          C          A           G
     72           C         C          U          U           C
     74           A         G          A         G/A         G/A

10. Fill out the blank spaces in the similarity matrix below based on the sequence alignment: (10 points)

                             A     B     C     D     E
  Seq A AUCGUCCGGA     A     X     X     X     X     X
  Seq B AUCGUCCGGA     B    1.0    X     X     X     X
  Seq C AUGGUCCGGA     C    ___   ___    X     X     X
  Seq D AUGGUCCGGA     D    ___   ___   ___    X     X
  Seq E AUAGUCUGGA     E    ___   ___   ___   ___    X

11. Describe briefly the difference between % similarity and evolutionary distance. (10 points)

12. Answer the following questions given the tree below: (10 points)

Which sequence (A - F) is the 'outgroup'? _____

Which of the two sequence are most closely related? _____ and _____

Which sequence is most similar to sequence E? _____

Which sequence is least similar to sequence E? _____

Circle the 'root' of the sub-tree of sequence A-E.

13. The timescale for the evolution of life (below) is based on the geologic record and the 5-Kingdom tree. In light of the 3-Kingdom molecular-phylogenetic tree, in what way is this timescale clearly incorrect, and what does the geologic record suggest about the ancestral phenotype of eukaryotes? (10 points)