Take home Quiz #6 -- Due Friday, November 19th

1. What kind of analyses can you perform using clustalx?
   
   
2. Which program options and parameters should you adjust in clustalx to obtain a more accurate phylogenetic reconstruction.
   
   
3. Assume you have calculated a molecular phylogeny (=tree). Describe at least three approaches that would allow you to assess if a single branch in this tree is significantly supported by the alignment from which this tree was calculated. (Use less than 20 words per approach.)
   
   
4. If one wants to root the universal tree of life, what could one use as an outgroup?
   
   
5. Give at least three types of methods that are frequently used to calculated trees from aligned sequences.
   
   
6. What were the names of the scientists who began to use small subunit ribosomal RNA as a taxonomic tool for bacterial systematics?
   
   
7. In analyzing a bacterial genome (e.g., Bacillus subtilis), you try to identify genes that were transferred from the archaea. Which reference genomes could you choose in TAX PLOT?
   
   
8. Are there any advantages of a command line interface over a Graphics User Interface?
   
   
9. If you were hired by a pharmaceutical company to study genome rearrangements in four related Staphylococcus aureus strains, whose genomes were sequenced in house (and which are considered as proprietary information that is not available on the NCBI or related servers), what type of program(s) could you use to approach this problem (i.e. to study genome rearrangements).
   
   
10. Which structural elements make up the secondary structure of proteins?
    
    
11. What can you do using the Swiss Protein data bank viewer?
    
    
12. Which structural elements are often represented as only slightly curved yellow arrows?
    
    
13. In the binding of the NAG inhibitor to the catalytic site of lysozyme, do hydrophobic, non-polar interaction contribute to substrate binding?
    
    
14. How many histones form the core of the nucleosome?
    Are all of these identical? Are all of these homologous?
    How would you expect the ancestral nucleosome to have looked like?
    
    
15. In less than 6 sentences, discuss the relationship between the F-ATPsynthase catalytic subunits, the F-ATPsynthase non-catalytic subunits, the homologous flagellar assembly ATPase (flii) and the hexameric helicase that has a Rossman-type ATP binding site. What about other enzymes that have the same type of nucleotide binding fold?
    
    
16. Are all nucleotide binding sites homologous? (E.g. consider the one in F-ATPases and the one in the carbamoyl phosphate synthetase?)
    
    
    
    
17. 
    
    
    
    Assume that the tree depicted above was calculated for homologs of enolase. In case an organism's genome encoded more than one homolog these are labeled a and b or 1 and 2 (this is a purely fictional example!).
    
    a) What part of the tree (if any) can be used as an outgroup? (specify what the addressed question would be for the outgroup selected)
    
    b) When did the gene duplication happen that gave rise to homologs a and b in fungi.
    
    c) Would we expect to find homologs of a and b in other eukaryotes? If yes, in which groups?
    
    d) What are possible explanation(s) for Plasmodium having paralogs 1 and 2?
    
    
    
18. a) Given the following tree, which type of protein appears to be the one labeled as extein? (bet: beta subunit of the F-ATPase, fl: flagellar assembly ATPase, ttf: transcription termination factor.
    
    b) Assuming that the extein sequence was obtained from Burkholderia brasilensis, does this tree give you any reason to suspect that the extein might encode a paralog to the transcription termination factor?
    
    c) Does your assessment of potential paralogy change, in case the extein sequence was obtained from Enterobacter cloacae? (assuming that the branching order in the tree below is reliable.)
        Would this change the likely function you assume for this protein?
        Based on this scenario (the one described in c) would you expect to find more than one ttf in Escherichia.coli?
        In members of the genus Neisseria?
        In Bacillus subtilis?
    
    (If you are an undergraduate student, b and c are bonus questions).