Answers to Self-Assessment Short Answer Questions # 2
Here are the answers to the Self-Assessment Short Answer Questions # 2.
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.
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.
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.
Which of the twenty naturally occurring amino acids occurs most often
in proteins? Which occurs least often?
Most often: Leucine (about 9.0%). Alanine comes a close second.
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
How do you print the greater-than sign in HTML?
Like this: >
What is the difference between server side and client side image maps?
Server side image maps: the coordinates of the point that is "clicked"
are sent to the server, and any image processing is done there
Client side image maps: all processing is done on the client machine
(by the browser software). It is therefore browser dependent.
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.
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."
Give one example of a helper application other than Rasmol, and one
example of a plugin other than Chime
Helper application: Mage (used to view kinemages)
Plugin: Flash (used to view animations created by Macromedia Director)
or QuickTime (used to view movies)
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.
Describe the origin (at atomic level) of the two forces that make up
van der Waals interactions.
Attractive force at larger distances: London dispersion forces.
Electrons in motion - transient dipoles that attract each other will be
induced in neighbouring atoms.
Repulsive forces at smaller distances: steric hindrance caused by
repulsion between negatively charged electrons once the electron shells
start to overlap.
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.
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.
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.
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.
What restrictions are there on the amino acid sequence of a type I
beta turn?
Proline is often found in position i+1.
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.
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.
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.