• March 20th, 2016

Protein families (bioinformatics)

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Assignment : Protein families

  1. List and briefly explain three structural or functional features that are associated with amino acid conservation in multiple sequence alignments? (6 marks).
  2. Explain the statement ‘within a protein family, structure is conserved but function can evolve’. (15 marks)
  3. Suggest and briefly explain an evolutionary mechanism by which a protein family can develop a novel function with no detrimental effect to the evolving species. (4 marks)
  4. Describe briefly how phylogenetic trees can be generated from protein sequences (details of specific algorithms are not required). What information can be deduced from such a tree, and how might a tree be used by evolutionary biologists? What features of a protein family would be useful for investigating (a) very distant and (b) very close evolutionary relationships? (8marks)
  5. With reference to the ‘pp’ protein of practical 4, explain why it is appropriate to view the protein domain family as the appropriate unit of protein evolution. (4 marks)
  6. For multi-domain proteins, explain the reach and limitations of protein function prediction using protein domain family information. (10 marks).
  7. Explain how PSI-BLAST detects more distant homologs than a plain BLAST search. (3 marks).

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