Question
1. (a) What is the structural difference between all deoxyribonucleotides and all ribonucleotides and why does this make DNA more appropriate to act as the genetic material than RNA. (4 points)
(b) Why is uracil replaced by thymine in DNA? (4 points)
(c) Can ribonucleotides base-pair with a deoxyriboncleotides and if so when does this happen? (4 points)
(d) The two strands in DNA are antiparallel. What does this mean? (4 points)
(e) Why are they antiparallel? (4 points)
2. A single stranded DNA molecule has the following sequence: 5′-GGTTAGGTTAGGTTAGGTTA-3′
(a) To fully replicate this molecule, what is the sequence of the primer that must be synthesized by the primase enzyme (assume a primer length of 5 bp). (Here and below write how you would conventionally write a single stranded DNA sequence, i.e. without the template.) (4 points)
(b) When fully replicated, what is the sequence of the newly synthesized DNA strand? (4 points)
(c) What is the sequence of the molecule synthesized in the absence of DNA pol I? (4 points)
(d) What is the sequence of what would be synthesized in the absence of DNA ligase? (4 points)
(e) What is the total number of H-bonds that are formed during the synthesis of the DNA strand (from the very beginning)? (4 points)
3. Different temperature sensitive mutants of E. coli in genes encoding proteins involved in replication were grown at the permissive temperature for several generations and while still actively growing the temperature was raised to the restrictive temperature. After raising temperature, the synthesis of new DNA was assessed using radioactively labeled nucleotides. Assume the mutations completely inactivate the proteins at the restrictive temperature and that function of the mutant protein was abolished instantly temperature was raised. Would any new DNA be detected in the following mutants after raising the temperature?
(4 points each) (a) DnaA
(b) DNA helicase
(c) DNA primase
(d) DNA pol I
(e) DNA pol III
