FCH 532 Homework 5
1. What are the differences and similarities between FASTA, CLUSTAL, and
BLAST algorithms?
2. Why is it preferred to use polypeptide sequence rather than nucleic acid sequence
to determine relationships between genes?
3. Outline the differences and similarities between B-DNA, A-DNA, and Z-DNA.
(i.e. handedness, pitch, etc.)
4. What are the differences of hydrogen bonding, hydrophobic forces, and
electrostatic interactions with regards to nucleic acid structures?
5. A-T base pairs in DNA exhibit greater variability in their propeller twisting than
do G-C base pairs. Suggest the structural basis for this phenomenon.
6. Calculate the Tm of a double stranded DNA molecule with 0.5 mol% G+C content
in a 0.1M NaCl solution.
7. At Na+ concentrations >5M, the Tm of DNA decreases with increasing [Na+].
Explain this behavior. (Hint: consider the solvation requirements of Na+)
8. When the helix axis of a closed circular duplex DNA of 2340 bp is constrained to
lie in a plane, thte DNA has a twist (T) of 212. When released, the DNA takes up
its normal twist of 10.4 bp per turn. Indicate the values of the linking number (L),
writhing number (W), and twist for both the constrained and unconstrained
conformational states of this DNA circle. What is the super helix density, , of
both the constrained and unconstrained DNA circles?
9. A closed circular duplex DNA has a 100-bp segment of alternating C and G
residues. On transfer to a solution containing a high salt concentration, this
segment undergoes a transition from the B conformation to the Z conformation.
What is the accompanying change in its linking number, writing number, and
twist?
10. Type IA and type II topoisomerases exhibit no significant sequence similarity,
but have been suggested that they are related based on their enzymatic
mechanisms. What are the similarities in the mechanisms?