Take home quiz #3

Please return a hardcopy of your answers by Friday, October 5th

 

Questions for graduate students are bonus questions for others.

  1. Two sequences A and B show significant similarity in a BLAST search .  It is known that sequence B is homologous to sequence C.  Which additional information would you require to conclude that sequence A is homologous to sequence C.  (The P-value for the pairwise comparison of A with C is 0.12). 
  2. If the size of the database increases how will the E value of a match be effected?
  3. Currently, what are the two major heuristic algorithms for performing database searches: ------------------- and ---------------------
  4. Assume that you are trying to characterize a protein with a length of 1200 amino acids.  What findings might alert you to the possibility that this protein has been invaded by an intein? 
  5. What are inteins?
  6. What are introns?
  7. What are exons?

8-12: questions deleted - same as in quiz 2

  1. You use a protein-encoding genomic sequence to search a nucleotide database.  Assume that there are proteins encoded in the database that are homologous to the encoded protein.  How might you infer that an intron is present in the genomic sequence? 
  2. A pairwise sequence alignment calculated with the Needleman-Wunch algorithm is the best possible alignment given the parameters (scoring matrix, gap penalty).
    A) this alignment is always better in aligning homologous structures than a multiple sequence alignment
    B) The Needleman-Wunch algorithm provides the single best alignment.
    C) The alignment is optimal (as measured by the alignment score), but there might be many equally optimal pathways/traces through the scoring table.
  3. What are the three steps clustal performs to align sequences?
  4. What are some of the advantages and uses of multiple sequence alignment compared to pairwise sequence alignment?
  5. Which biomolecule was first used to place microorganisms onto the tree of life?
  6. 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?)
  7. Offspring that is similar to its parants and the creation of variation is necessary for evolution by natural selection to occur. One way for the variation to occur is through random point mutation. What other processes do or could occur?
  8. Are any of the processes that you listed in question 13 a violation of the Darwinian theory of natural selection? Give a one sentence explanation of your reasoning.
  9. How can the ATPases help to find the root in the tree of life?
  10. What are the names of the three domains of life? Which od these are more related to one another?
  11. Why is the RNA world assumed often assumed to be precursor of the two biopolymer world?
  12. What process is called transcription, and what enzymes perform it?
  13. What process is called translation, and what enzymes perform it?
  14. What process is called replication, and what enzymes perform it?
  15. When performing sequence alignments a protein sequence is more informative
    for evolutionary analysis then DNA sequences. So many times programs
    dealing with sequence alignments covert the DNA sequences to amino acid
    sequences before continuing with the alignment. Convert the two DNA
    sequences to amino acid sequences so such programs like RevTrans and
    PROTA2DNA don't have to.

    Sequence #1: AGACAAUGGCCG / Sequence #2: CUGCAGCGUCCC

    Choices:

    a) Ser Gln Arg Pro / Arg Pro Gln Leu
    b) Arg Gln Trp Pro / Leu Gln Arg Pro
    c) Ile Met Thr Gln / Leu Gln Pro Trp
    d) Gly Pro Trp Lys / Ala Met Trp Lys

  16. For Graduate students: What are Okazaki fragments?
  17. For Graduate students: Does natural selection depend to the presence of a biopolymer that can be replicated? Explain your answer.