Take home quiz #4

Correct answers are indicated in red.

  1. A group of organisms that is defined be a shared primitive character is
    A) monophyletic
    B) paraphyletic
    C) polyphyletic (this is less accurate, but also gives you the point)
     
  2. An autapomorphy of group of organisms is useful to establish the relation between this group and other groups. correct / incorrect
     
  3. According to Hennig a natural taxonomy should be based on (circle all that apply, more than one might be correct)
    clades,
    monophyletic groups,
    paraphyletic groups,
    shared derived characters,
    autapomorphies,
    a Hennigian comb
      
  4. A shared derived character characterizes a
    A) monophyletic
    B) paraphyletic
    C) polyphyletic
      
  5. If you have an unrooted tree (i.e. you don't know where inside the tree the ancestor is located), can you define clades using this tree? NO
      
  6. Which of the following statements is correct:
    A) All homologous sequences show significant similarity in a pairwise sequence comparison.
    B) All complex sequences that show significant similarity in a pairwise sequence comparison are homologous.
    C) Both of these statements are correct.
       
  7. You compare two circular genomes from closely related organisms using a Genome Dot Plot. How would you detect an inversion that occurred symmetrically around the origin of replication.

    The rearrangement is sketched on the right, the resulting figure in GenePlot is on the left. Arrows and numbers along the axes correspond to the ones added to the circle.
     
  8. How would the plot change, if for one of the genomes the origin of replication were not coinciding with the origin of the coordinate system?

    Same as above, but the ORI is moved to the ORI* for the genome on the X-axis (could be that the Ori is still at the old place, but the plot start at the place labeled ORI*. As a result arrow one is roken into two pieces Ia and Ib. Ia is at the far end of the x axis.

       
  9. How could you assess, if an alignment between two sequences is reliable?
    Compare structures to determine if residues in same spatial position are aligned to one another.
    Determine if residues involved in the catalytic site are aligned (e.g., residues that bind an inhibitor).
      
  10. What might be the reason that a multiple global sequence alignment is more reliable than a pairwise alignment.
    In case of divergent sequences, less divergent sequences help to distinguish conserved from less conserved residues. The alignment between divergent sequences should focus on the conserved residues.
       
  11. In an in vitro selection system, how could you couple the selection for a protein function to the encoding poly nucleic acid?
    Enclose RNA and encoded protein in a vesicle.
    Link encoded protein to encoding RNA (via puromycin)
         
  12. Why does recombination accelerate evolution? (hint: check out Muller's ratchet)
    Recombination can bring to advantagous mutations that arose in different organisms togetjer in a single gene. (It also helps to remove slightly deleterious mutations.)
        
  13. In defining protein space JALVIEW uses
    A) the presence or absence of a conserved sequence motif to define protein space
    B) each alignment column as a dimension to define protein space
    C) a tree based on percent identity to define a groups that have to close to each other in sequence space
       
  14. In comparing two genomes using the gene plot program at the NCBI,
    A) All blast hits better than a cutoff value are displayed
    B) Only best reciprocal blast hits are displayed
    C) Only genes located on the main chromosome are included in the analyses
      
  15. Molecular phylogenies are usually calculated and unrooted trees. Correct/incorrect
      
  16. Most of the ORFs identified with the ORF finder program at the NCBI are real, i.e., these are actually transcribed and translated. Correct/incorrect
      
  17. Programs like Glimmer
    A) identify most "real" ORFs
    B) frequently identify ORFs that are not real
    C) both A and B are correct
     
  18. Extra credit for undergraduate students:
    Which molecule(s) was/were first used to determine the root of the tree of life?
    ATP synthases, followed by elongation factors, dehydogenases, followed by amino acyl tRNA synthetases, followed by GTP binding domain in the signal recognition particle
      
  19. Extra Credit: The name(s) of the person re-discovering the endosymbiont hypothesis is
    Carl Woese and George Fox
    Lynn Margulis
    Günter Wächtershäuser