Midterm exam #1 - MB 409 - Spring 2003 Name __________Key____________

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

Bacteria, Archaea and Eukarya

2. __C__ The difference betwen a photoautotroph and a photoheterotroph is... (3 points)

A. Photoautotrophs get both their carbon and energy from light, photoheterotrophs use organic compounds for carbon.
B. Photoautotrophs get their energy from light, photoheterotrophs get their energy from organic compounds.
C. Photoautotrophs get their carbon from CO2, photoheterotrophs get their carbon from organic compounds.
D. Photoautotrophs self-fertilize when exposed to light, photoheterotrophs reproduce by conjugation in the presence of light with a member of the opposite mating type.
E. Photoautotrophs and photoheterotrophs are two different names for the same thing

3. __E__ An example of how all living things are much alike would be... (3 points)

A. All organisms use the same sugar in their RNA (D-ribose)
B. Each organism use the same code for amino acids in translation
C. All organisms have ribosomal RNA
D. All organisms have the same standard 20 amino acids in their proteins
E. All of the above.

4. __A__ The fact that all living things are much alike biochemically means, for one thing, that... (3 points)

A. All living things share a common ancestry
B. Life may have originated on Mars and traveled here early in the Earth’s history
C. The last common ancestor existed before any of this biochemistry had evolved
D. Eukaryotes evolved from Bacteria.
E. The Central Dogma needs to be redefined to put RNA at the beginning of the information flow.

5. __D__ Charles Darwin, in The Origin of Species, described evolution proceeding by... (3 points)

A. Progression
B. Improvement
C. Punctuated equilibrium
D. Diversification
E. Dischronization

6. __E__ Which if the following is not an important factor for a molecule to be good for molecular phylogenetic analysis: (3 points)

A. No horizontal transfer
B. Clock-like behaavior
C. Large existing data set
D. Wide phylogenetic range
E. Present in gene families

7. __A__ Unlike previous trees based on phenotypic data, a molecular phylogenetic tree is... (3 points)

A. Objective
B. Subjective
C. Correct
D. Progressive
E. Unsynchronized

8. __B__ Why is raw sequence dis-similarity an underestimate of evolutionary distance? (3 points)

A. Because sequences are under selective pressure
B. Because multiple sequence changes at one site are undercounted
C. Because sequences that have changed cannot be aligned properly
D. Because sequence change is unrelated to evolutionary distance
E. Because sequences diverge by evolutionary drift in a pseudo-random walk

9. __C__ Long branch attraction is caused by .... (3 points)

A. all organisms in the tree evolving at the same rate
B. the organisms in the tree evolving at different rates
C. the underestimation of evolutionary distances
D. the overestimation of evolutionary distances
E. evolutionary pressure toward G+C or A+T richness

10. __E__ Which of the following is not an algorithm for generating an phylogenetic tree? (3 points)

A. Fitch-Margoliash
B. Neighbor-joining
C. Maximum parsimony
D. Maximum likelihood
E. Bootstrapping

11. __A__ A fumarole is a .... (3 points)

A. hot spring that produced only steam
B. hydrothermal vent that emits noxious gases
C. hydrothermally heated soil
D. deep-sea hydrothermal vent
E. controlled environment for storing cigars

12. List the basic steps in a molecular phylogenetic analysis are (5 points):

1. Decide on a dataset - the genes you're going to use and the organisms you need in your analysis
2. Obtain these sequences, from databases and eexperimeentaally
3. Identify homologous residies, i.e. align the sequences
4. Perform the phylogenetic analysis, i.e. signature analysis & treee construction

13. Briefly describe how microarrays or large-format hybridization arrays can be used to identify organisms. (5 points)

An array, in either large format or a microarray, can contain probes complementary to the conserved and variable regions of the ssu rRNA from a diverse range of organisms. These can be probed with rRNA PCR products, and the spots that light up in the array will specify the organism, or, in the case that a population of organisms is being used, tell you what the composition of the population is.

14. Answer the questions using this tree based on the genes encoding the nuclear RNase P RNA from several vertibrates. (2 point each for a total of 10 points)

A. Which organism(s) is/are most closely related to Bufo bufo ?

Discoglossus jeanneae and Alytes obstetricans

B. Which organim(s) is/are the outgroup?

Danio rerio & Onchorhynchus sp.

C. What is the approximate evolutionary distance between tarsiers and mice? _____0.45____

D. Draw a circle around the node that represents the last common ancestor of mammals.

E. Based on your knowledge of zoology, what problem do you see with this tree?

Mammals seem to have emerged from amphibians rather than reptiles.

15. Attached to this test is the secondary structure of the E. coli ssu-rRNA and an unknown ssu-rRNA. Below is a short signature table designed to discriminate between bacterial, archaeal, and eukaryotic ssu-rRNAs. The nucleotide numbering on the signature table is based on the E. coli ssu-rRNA (i.e. the E. coli RNA is the reference sequence). Perform a signature analysis, and identify which kind of organism the unknown is. Show your work - no credit will be awarded without it! (10 points)

     Position Bacteria Archaea Eukarya Unknown 

        952      U-       CX      CX      U
        962      C-       GX      UX      C
        966      G-       UX      UX      G
        973      G-       CX      G-      G
        975      A-       GX      GX      A
       1045      C-       GX      A/GX    C
       1060      UX       C-      C-      C
       1086      U-       CX      C/U-    U
       1087      G-       CX      UX      G
       1109      C-       AX      AX      C
       1110      A-       GX      GX      A
                10/11    1/11    3/11

The unknown is a bacterium

16. Align the following sequences. (10 points)





17. Fill in the similarity matrix for the following alignment. (10 points)

                           A   B   C   D   E
Sequence A : GGGGGGGGGG A  -   -   -   -   -
Sequence B : GGGGGGGGGG B 1.0  -   -   -   -
Sequence C : GCGGGGGAGG C 0.8 0.8  -   -   -
Sequence D : GAGGGGGAGG D 0.8 0.8 0.8  -   -
Sequence E : GUAAGGGCGG E 0.6 0.6 0.6 0.6  -

8. Convert the dendrogram below into a phenogram. (10 points)

19. Given the distance matrix below, use the neighbor-joining method to draw a tree. (10 points)

                   A   B   C   D   E
A = B.alba      A  -   -   -   -   -
B = B.gracile   B 0.6  -   -   -   -
C = B.marinus   C 0.2 0.6  -   -   -
D = B.minimus   D 0.6 0.4 0.6  -   -
E = T.alba      E 0.7 0.7 0.7 0.7  -

For 5 points extra-credit, label the lengths of the branches in this tree.


NCSU Honor Pledge:

I have neither given nor received unauthorized aid on this test.

Sign _____Key__________________________________ Date __2/16/04____