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Answers to Self-Assessment Short Answer Questions # 2

Here are the answers to the Self-Assessment Short Answer Questions # 2.

  1. Why is it never correct to describe two protein sequences as "50% homologous"?
    The word "homologous" is a technical term for DNA or protein sequences that are evolutionarily related: i.e. they share a common ancestor. Sequences are either homologous, or they are not. It can be correct to describe sequences as distant homologues.

  2. What is the main difference between the programs BLAST and PSI-BLAST?
    BLAST is a simple program for finding homologues to a single sequence in a database. PSI-BLAST (Position Specific Iterative BLAST) starts with a simple run of BLAST. It then aligns all the matching sequences to the original sequence and re-runs the search with the consensus sequence from that multiple sequence alignment. This procedure is repeated until no new matches are found. PSI-BLAST is much more sensitive than BLAST.

  3. What is the Dayhoff Matrix, and what is it used for?
    It is a table, compiled from multiple sequence alignments, that describes the likelihood of each amino acid being mutated into each other one. It was compiled by Margaret Dayhoff in the late 70s from alignments constructed by hand. This matrix and similar ones constructed since are used in database searching programs (like BLAST and PSI-BLAST) and in sequence alignment.

  4. Which of the twenty naturally occurring amino acids occurs most often in proteins? Which occurs least often?
    See http://www.expasy.ch/tools/pscale/A.A.composition.html

  5. What other physicochemical properties of proteins, besides hydropathy, can be analysed and plotted against amino acid position using a similar technique?
    Size; flexibility; likelihood of being in helix, strand or coil; accessibility See http://www.expasy.ch/cgi-bin/protscale.pl

  6. How do you print the greater-than sign in HTML?
    Like this: >

  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?
    Web resources are often moved, or even removed by their maintainers without warning. Even a simple change of the name of a server will result in broken links. If the maintainers of a large database change the way it is structured links to individual entries may be broken.

  9. Write a fragment of HTML code to link to the Medline entry for a paper describing a structure of HIV protease.
    One example would be:
    "The structure of HIV protease was solved by <a href="http://www.ncbi.nlm.nih.gov/cgi-bin/Entrez/referer?/htbin-post/Entrez/query%3fdb=m&form=6&uid=2682266&Dopt=r">Tom Blundell and colleagues</a>at Birkbeck College, London."
    This is reproduced as "The structure of HIV protease was solved by Tom Blundell and colleagues at Birkbeck College, London."

  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?
    The Eisenberg and Kyte & Doolittle hydrophobicity scales are commonly used (although there are very many others). They are used in programs that plot the way that the hydrophobicity of a protein sequence changes along its length. These programs are often used to identify hydrophobic regions that may cross cell or organelle membranes.

  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.
    The layer of water molecules closest to the protein surface. These waters tend to be more highly ordered that water molecules further from the protein, to form networks of hydrogen bonds with each other and with the protein, and to cluster around polar and charged amino acids.

  14. What is a force field?
    A force field is the force exerted on an atom due to all the other atoms, expressed as a function of the positions of the other atoms. The force field function also contains parameters, derived from experimental evidence, that form a mechanical (i.e. not quantum mechanical) model of how the atoms in one or more molecules interact together. The main force field equation will contain terms to model bond strength, torsion angle twist, van der Waals and electrostatic interactions, hydrogen bonds, among others.

  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?
    Simple programs for visualisation: Rasmol, Chime (both free)
    SwissModel: free program for protein visualisation and homology modelling
    Hyperchem: the cheapest "integrated package" for molecular modelling and the only one that runs on Windows.
    It might also be possible to use the PC as a terminal to a Unix machine and run a molecular simulation like Amber there. Some versions of this program are free.

  16. What types of helix other than the standard alpha helix have been found in proteins?
    3.10 helices and pi helices. Pi helices are very rare.

  17. What restrictions are there on the amino acid sequence of a type I beta turn?
    Proline is often found in position i+1.

  18. Give two examples of common features of protein structure that are classed as "super-secondary structure".
    Helix-turn-helix; beta hairpin; beta-alpha-beta unit.

  19. Describe very briefly how CD spectroscopy can be used to determine secondary structure composition.
    CD spectroscopy measures the difference between the absorbance of right- and left- circularly polarised light by a substance. There are marked differences between CD absorbancies between ~260 and 180 nm of proteins where different secondary structures predominate.

  20. Why do Asp and Glu show a statistically significant preference for the alpha-helical conformation?
    Charged amino acids are often found in alpha helices as these often lie on the outer (solvent accessible) side of a protein. Also, the negatively charged residues Asp and Glu will be attracted to the positive (N-terminal) end of a helix dipole. The effect is more marked with Glu.