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)
