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Self Assessment Questions

These questions can be answered in less than 100 words. Please Email you group tutor with you answers before Monday 16th March.

  1. Define the term "hydrophobicity" (when used in relation to amino acids and proteins)
  2. Why is the amino acid proline often referred to as a "helix breaker"?
  3. What are the principles underlying amino acid residue side chain conformations in proteins?
  4. What information, other than the amino acid sequence itself, is available in a SwissProt entry?
  5. Which databases on the Internet would you use to find protein sequence patterns associated with specific functions?
  6. Describe a program or technique which can be used to represent a protein structure within a page of HTML.
  7. Discuss briefly the four building blocks that form DNA and the way these are assembled to form a double helix.
  8. Indicate the different roles within the cell of rRNA, tRNA and mRNA.
  9. What is the structure of the lac operon and indicate how it is regulated.
  10. What are Signal Recognition Particles?
  11. How do the four bases in mRNA code for twenty amino acids and control initiation/termination during translation?
  12. Why are glycine residues often conserved in homologous protein sequences?
  13. Give the phi/psi torsion angle limits for right-handed alpha-helices, beta-strands and left-handed helices.
  14. Why are cations often bound to the C-terminal of alpha-helices?
  15. Give three reasons why the substitution of an Asp(D) by a Trp(W) in a protein sequence is unlikely.
  16. Which type of interaction, H-bonding, hydrophobic interactions or ionic interactions, is likely to be the most important in energy terms in causing protein molecules in dilute aqueous solution to associate with each other? Why?
  17. Why is the pKa of the epsilon-amino group higher than that of the alpha-amino group of Lys?
  18. Which of the following amino acids are likely to be found in the interior of a protein and which on the exterior: Val, Pro, Phe, Asp, Lys, His, Gly.
  19. Histones have high percentages of basic (Arg and Lys) amino acids. Will it be easy to determine their sequences by peptide mapping? Why or why not?
  20. Two of the twenty amino acid residues which occur in proteins have side groups which contain asymmetric carbons. Which are they and what is the R/S classification of each asymmetric centre?