Take-Home-Quiz #2

Due Date: Monday, October 1st, 10.59am

You can study in groups, but you should be alone when you answer these questions, and you should not copy someone else's answers.
If you cut and past from the web, please indicate the webpage you used as a source.
Please hand in a hardcopy.

  1. Proteins with the same or similar function always show significant similarity in their primary sequence. True or false?
    Explain your answer in less than 30 words.

  2. If two linear amino acid sequences of moderate complexity show significant similarity, they usually have evolved from a common ancestor. True or false?

  3. All sequences that have shared ancestry are known to be significantly similar in their primary sequence. True or false?

  4. A pairwise sequence alignment of sequences X and Y resulted in an E-Value of 12. This means,
    1. X and Y do not have a significant sequence similarity
    2. X and Y definitely are not homologous
    3. X and Y are products of a divergent evolution
    4. They are completely unrelated and thus have no evolutionary relationship

  5. How would you recognize an internal duplication in a dot plot? (a sketch is one possible way to answer this question)

  6. How does a region of low complexity look in Dotlet?  (a sketch is one possible way to answer this question)

  7. You do BLAST searches of the Swiss Protein and the non-redundant databank using the same sequence query, and you use the same programs. You get the same top hits, however, the E-values for the top hit are different. Why does this happen?

  8. How old is planet Earth?

  9. How old are the oldest sedimentary rocks?

  10. What is a Snowball Earth event?

  11. How old (approximately) is the Universe according to the Big Bang Scenario?

  12. When did the rise in atmospheric oxygen occur? Why do you think that happened?

  13. What are two of the most commonly used matrices for aligning protein sequences?
    a) PubMed and Blosum
    b) PAM and Blosum
    c) Gonnet and JTT
    d) none of the above, explain:______________

  14. You do a BLAST search using a new unidentified protein sequence as query. Which search program(s) could you use?
          A) blastn, B) blastp, C) blastx, or D) tblastx

  15. You sequenced a cDNA (i.e., a DNA that was made by copying an mRNA into a DNA). Which blast programs could/should you use in your quest to determine the function of the encoded protein.

  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?

  18. The non redundant databank for protein sequences maintained by the NCBI (single most correct answer)
         A) Does not contain any redundant sequences
         B) Is less redundant than the additive combination of all available data banks
         C) Is less redundant than the Swiss Protein databank

  19. Retrieving related articles to a Pubmed entry (the parent article) will only retrieve articles that were published before the parent entry. Correct / incorrect

  20. What are the names of the three domains of life? 

  21. How many prokaryotic kingdoms does the “five kingdoms” scheme include? 

  22. In a blast search, the E-value of a match gives the significance of a match. Is this a measure of the probability to identify a sequences as homologous that is in reality not homologous, or does this measure the probability to miss a homologous sequence present in the databank

  23. You align two sequences that are about 20% identical. Which scoring matrix would be most appropriate:
    (A) PAM 1
    (B) PAM 20
    (C) PAM 80
    (D) PAM 200

  24. You align two sequences that are about 20% identical. Which scoring matrix would be most appropriate:
    (A) Blosum 20
    (B) Blosum 35
    (C) Blosum 65
    (D) Blosum 80

  25. What is not needed for evolution to occur?

A) Offspring not identical to parents
B) More offspring than necessary to replace parent population
C) Recombination between parents
D) Competition for resources and mates

Extra point questions:

  1. How would you recognize an inversion in the Dotlet? (a sketch is one possible way to answer this question – what are you comparing protein or DNA? One strand or two?)

  2. Is the F-ATPase catalytic subunit homologous to rho termination factor that unwinds the newly synthesized RNA from the DNA? Explain your answer.

  3. What explanation recently emerged to question the identity of the allegedly earliest microfossils, which are believed to resemble Cyanobacteria and date back to 3.5 Ga?

For graduate students (extra point for undergraduates)

  1. Given to sequences ATTAGAC and AGTAAC draw and fill in the matrix that an alignment algorithm using dynamic programming would use. Assume a gap penalty of zero and a positive score of 1 for identity. What is the optimal score? Which alignment(s) correspond(s) to this score.