Problem Set 8: RNA Metabolism
1) Write the sequence of the messenger RNA molecule synthesized from a DNA template
strand having the sequence:
(5')ATCGTACCGTTA(3')
Ans: (3')UAGCAUGGCAAU(5'). Also acceptable is (5')UAACGGUACGAU(3').
2) The specific sequences that E. coli RNA polymerase usually binds to in E. coli DNA
before initiating transcription generally contain more A=T base pairs than GC base pairs. In
no more than a few sentences, speculate on why this might be the case.
Ans: Because A=T base pairs are stabilized by only two hydrogen bonds (compared with
three for GC pairs), double-stranded regions rich in A=T pairs are easier for RNA
polymerase to bind and unwind in preparation for the transcription of one of the DNA
strands.
3) Compare and contrast -dependent and -independent termination of transcription in
prokaryotes.
Ans: In both, the transcription complex pauses at specific sequences in the DNA template. In
-independent termination, the formation of hairpin structures causes pausing which leads to
dissociation of the product RNA and the polymerase from the template DNA and hence to
termination. In -dependent termination, the features that cause pausing are unclear, and
dissociation requires the presence of the  protein.
4) Describe in words (not using structures) the important features of the structures present on
the 5' and 3' ends of mature (processed) eukaryotic mRNAs.
Ans: At the 5' end there is a cap consisting of a guanosine joined to the 5'-terminal nucleotide
through a 5' to 5' triphosphate group. This guanine nucleotide is methylated on N-7. The
next two nucleotides in the chain are also sometimes methylated on their 2'-OH groups. At
the 3' end is the poly(A) tail consisting of a run of 80–250 adenylate residues.