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Self-Assessment Short Answer Questions # 2

Please send the answers to these questions, by email, to your group tutor before 5 May 2000.
Model answers will be posted by 12 May and your marked answers will be returned shortly after that.
Important. Please note that all the questions can be answered in, at most, 150 Words. Some will require only a few words. Please don't write essays - if you do they probably won't be marked. To give you an idea please look at last year's Questions and Answers.
  1. Why is it never correct to describe two protein sequences as "50% homologous"?
  2. What is the main difference between the programs BLAST and PSI-BLAST?
  3. What is the Dayhoff Matrix, and what is it used for?
  4. Which of the twenty naturally occurring amino acids occurs most often in proteins? Which occurs least often?
  5. What other physicochemical properties of proteins, besides hydropathy, can be analysed and plotted against amino acid position using a similar technique?
  6. How do you print the greater-than sign in HTML?
  7. What is the difference between server side and client side image maps?
  8. What disadvantages can there be to web pages that rely on external resources such as database entries?
  9. Write a fragment of HTML code to link to the Medline entry for a paper describing a structure of HIV protease.
  10. Give one example of a helper application other than Rasmol, and one example of a plugin other than Chime.
  11. Name one hydrophobicity scale in common use. What are hydrophobicity scales most often used for?
  12. Describe the origin (at atomic level) of the two forces that make up van der Waals interactions.
  13. Define the first solvation shell of a protein.
  14. What is a force field?
  15. Your colleague would like to start modelling proteins but only has a PC and a limited budget. What program or programs would you recommend?
  16. What types of helix other than the standard alpha helix have been found in proteins?
  17. What restrictions are there on the amino acid sequence of a type I beta turn?
  18. Give two examples of common features of protein structure that are classed as "super-secondary structure".
  19. Describe very briefly how CD spectroscopy can be used to determine secondary structure composition.
  20. Why do Asp and Glu show a statistically significant preference for the alpha-helical conformation?