Take home quiz #4

(Please return a hardcopy of your answers by Friday, October 17th)

Correct answers will be posted on Friday during the late afternoon.

  
  1. 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.
       
  2. What might be the reason that a multiple global sequence alignment is more reliable than a pairwise alignment.
         
  3. 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

  4. Natural selection directs sequence evolution so strongly that for a given function (e.g., ATP binding) that is selected for, one always obtains a similar sequence.  Correct/incorrect?

  5. Without selection for function there would be no detectable significant similarity in the pairwise comparison of homologous protein from an archaeon and a eukaryote. Correct/incorrect?

  6. Intein sequences frequently are under less purifying selection as compared to their host proteins.

  7. "Mitochondrial Eve" lived around 200000 years ago. Which genes in modern human trace their ancestry to this person?

  8. Were other humans alive at the same time as "Mitochondrial Eve"? Yes /No

  9. What is the chance that one of your beta hemoglobin gene descended in a direct line from "Mitochondrial Eve"?
    A) about 50% or 1/2,
    B) about 25% or 1/4,
    C) about 2/10000

  10. What were the names of the scientists involved in the discovery of the Archaea?
    A) Carl Woese, George Fox, Otto Kandler
    B) Stanley Miller, Harold Urey
    C) Sidney Altman, Thomas Cech
    (for graduate students: what did the others do?)

  11. Does clustalx2 provide for the possibility to treat gaps inserted at the beginning and end of a sequence differently from gaps inserted into the middle of a sequence? Yes /No

  12. Does clustalx2 allow for different gap opening and extension penalties?

  13. How often did primary plastids evolve?

  14. Do diatoms have secondary or primary plastids? Yes /No

  15. Do cyanobacteria (also sometimes called blue green algae) have plastids? Yes /No

  16. What is a GI number?
    A) A unique number that is given to every submitted sequence. If the sequence is changed, it receives a new GI number.
    B) The Genomic Isoform number is given to every type of enzyme. This number provides easy access to enzymes from different organisms that have the same or similar function.
    C) A unique number that is given to every submitted sequence. If the sequence is changed, it retains this number. This makes it easy to track changes that occurred to a sequence.
    D) A unique number that is given to every submitted sequence. If the sequence is changed, a suffix is added to the number. This makes it easy to track changes that occurred to a sequence.

  17. In a BLAST search, what does the filter for low-complexity do ?
    A) It replaces regions of low complexity in the databank with the symbol for any residue.
    B) It replaces regions of low complexity in the query sequence with the symbol for any residue.
    C) It allows retrieving of "Warning Sequences" that are part of the databank and alert you to the fact that your query is of low complexity.

  18. In the interleaved multiple sequence file format used in phylip
    A) the sequence length is limited to 1000 residues
    B) the sequence names are limited to 10 characters
    C) the number of sequences is limited to 100

  19. In a multiple sequence fasta file sequences always are unaligned. Correct /Incorrect

  20. In a multiple sequence fasta file the
    A) end of a sequence is indicated by a *
    B) a new sequence always begins after an annotation line, which is a line beginning with a ">" character
    C) Sequence names are not allowed to contain a space
    D) conserved residues are indicated by a *, conservative substitutions are indicated by a : or a .

  21. A disadvantage of the clustal programs is that they only read and write multiple sequence files in clustal's "aln" format. Correct /Incorrect
        
  22. Extra credit for undergraduate students:
    Which molecule(s) was/were first used to determine the root of the tree of life?
      
  23. Extra Credit: The name(s) of the person re-discovering the endosymbiont hypothesis is
    Carl Woese and George Fox
    Lynn Margulis
    Günter Wächtershäuser