Midterm exam #1 - Spring 1999

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

Bacteria, Archaea, and Eukarya

2. Give an example of how all known living things are fundamentally the same. (5 points)

e.g., all living things encode information in the form of DNA (the exact same chemical and sterochemical structure) using the same genetic code.

3. Give another example of how all living things are the same. (5 points)

e.g. all living things are cells - an internal cytoplasm bound on all sides, and separated from the environment by, a semi-permiable lipid membrane.

4. Describe one method other than molecular phylogenetics used to determine relationships between microbial organisms. (10 points)

e.g. DNA:DNA hybridization.

The extent that the genomic DNAs of 2 species will hybridize is a general measure of how much sequence similarity there is between the genomes, and therefore how closely related they are. This method is widely used to define bacterial species - in general, two organisms are considered to be the same species if the DNA:DNA hybridization is 70% or greater, or different species of the same genus if they have measurable hybridization less than 70%.

5. Read this sequence, from 5´ to 3´. (10 points)


7. Align these P3 RNA sequences (you do not need to fill all of the spaces provided). (10 points)

B. duece    GGAGUUUGCUCC     - G G A G U U U G C U C C -
C. treise   UGGCGUUCGCGCC    U G G C G U U C G C G C C -

8. Align the sequences of these two RNAs on the basis of their secondary structures. (10 points)

A.unum A5 RNA  B.duece A5 RNA

A.unum A5 RNA  : - A G A G A G G A A A C U G - C U U U
B.duece A5 RNA : A G A G A G A U U C G U U G A U U U A

9. Dr. Heavens T. Mergatroid recently compiled a signature nucleotide table for distinguishing phylogenetic groups of the Gram-positive Bacteria based on A5 RNA (see the structures in the previous question), using the A. unum RNA as the numbering standard. Is B. duece a member of the High or Low G+C Gram-positive Bacteria (show your work)? (10 points)

B. duece is a low G+C Gram-positive bacterium:

                              High G+C         Low G+C
     Position   B.duece    Gram-positives   Gram-positives
         1         G            A X              G +
         3         G            A X              G +
         7         U            R X              U +
        17         A            Y X              R +
(Y = U or C; R = G or A)  0/4 - No!      4/4 - Yes!

10. Fill in the similarity matrix for this sequence alignment. (10 points)

                                    A    B    C    D
      Sequence A   AAAAUUAAAA       X    X    X    X 
      Sequence B   AAAAGGAAAA      0.8   X    X    X 
      Sequence C   ACAACCAACA      0.6  0.6   X    X 
      Sequence D   ACAAAAAACA      0.6  0.6  0.8   X

11. Why does sequence similarity (e.g. in a similarity matrix) underestimate evolutionary distance? (5 points)

Counting differences between two sequences, as in a similarity matrix, underestimates the number of changes that occured between them because more than one evolutionary change at a single position (e.g. A -> G -> U) counts as only one difference between two sequences, and in the case of reversion counts as no change at all (e.g. A -> G -> A).

12. Redraw this phenogram as a dendrogram... (5 points)

... and complete this distance matrix from the tree. (5 points)

                    E. coli     C. vinosum   A. ruber    B. brevis
       E. coli         X             X          X           X   
       C. vinosum     0.2            X          X           X   
       A. ruber       0.4           0.4         X           X   
       B. brevis      0.6           0.6        0.6          X

13. The Mars Transport, in the year 2004, brings back a sample of icy 'soil' dug from 2 meters below the surface of the Mars North pole. Attempts to cultivate anything from the sample fail, but scientists successfully use small-subunit ribosomal RNA-targeted primers and PCR to obtain 4 reasonable-looking ribosomal RNA sequences (called Mars1, Mars2, Mars3, and Mars4) from the sample. Below is a tree of these sequences relative to some earthly sequences. What can you tell me about how life on Mars and Earth are related, assuming that the sequences are not contamination from Earth or some other artifact? (10 points)

1) Life on Mars is alot like life on Earth - at least with RNA and protein (making protein is the function of the ribosome and therefore ribosomal RNA), even to the point that their are ribosomal RNAs that are enough like those of Earth life to be amplified using PCR primers based on the earthly sequences. This implies that life on Mars and life on Earth share a common ancestry - they did not arise independently.

2) Life on Mars is more diverse (phylogenetically) than it is on Earth - these 4 sequences span far more evolutionary distance than do all three earthly Kingdoms. It is likely that Mars life is even more diverse, since these are only 4 fairly arbitrarily-chosen sequences. What other sequences might be there that our primers didn't pick up? What might be in other samples/environments?

3) All of life on Earth is specifically related to one of the Mars sequences - Mars1.

4) All of this suggests the possibility that Earth was originally colonized by some Mars organism related to Mars1.

Last updated February 1, 1999 by JWBrown
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