Problem 2
DNA polymerases are capable of editing and error correction, whereas the capacity for error correction in RNA polymerases seems to be limited. Given that a single base error in either replication or transcription can lead to an error in protein synthesis, suggest a possible biological explanation for this difference.
Problem 3
Predict the likely effects of a mutation in the sequence \(\left(5^{\prime}\right)\) AAUAAA in a eukaryotic mRNA transcript.
Problem 4
The RNA genome of phage \(Q \beta\) is the nontemplate strand, or coding strand, and when introduced into the cell, it functions as an mRNA. Suppose the RNA replicase of phage \(\mathrm{Q} \beta\) synthesized primarily template-strand RNA and uniquely incorporated this, rather than nontemplate strands, into the viral particles. What would be the fate of the template strands when they entered a new cell? What enzyme would have to be included in the viral particles for successful invasion of a host cell?
Problem 5
The gene encoding the \(E\). coli enzyme enolase begins with the sequence ATGTCCAAAATCGTA. What is the sequence of the RNA transcript specified by this part of the gene?
Problem 6
Describe three properties common to the reactions catalyzed by DNA polymerase, RNA polymerase, reverse transcriptase, and RNA replicase. How is the enzyme polynucleotide phosphorylase similar to and different from these four enzymes?
Problem 7
While studying human transcription in the 1960s, James Darnell carried out an experiment that has become a classic in biochemistry, but at the time, it was incredibly perplexing. Darnell and coworkers used radioactive isotopes, such as \({ }^{32} \mathrm{P}\) ]-labeled phosphate, to isolate and quantify RNAs from a cultured line of human cancer cells (HeLa). With this approach, they were able to identify those RNAs present in the nucleus and those present in the cytoplasm. The results were puzzling, because it was obvious that a large amount of transcription was occurring in the nucleus, but comparatively little radioactive mRNA was isolated from the cytoplasm. Moreover, the nuclear- isolated RNAs were much longer than those isolated from the cytoplasm. What can account for these observations?
Problem 9
What is the minimum number of transesterification reactions needed to splice an intron from a pre-mRNA transcript? Explain.
Problem 12
In eukaryotes, premRNA splicing by the spliceosome occurs only in the nucleus and translation of mRNAs occurs only in the cytosol. Why might the separation of these two activities into different cellular compartments be important?
Problem 14
RNA viruses have relatively small genomes. For example, the single-stranded RNAs of retroviruses have about 10,000 nucleotides, and the \(Q \beta\) RNA is only 4,220 nucleotides long. How might the properties of reverse transcriptase and RNA replicase have contributed to the small size of these viral genomes?
Problem 15
The practical limit for the number of different RNA sequences that can be screened in a SELEX experiment is \(10^{15}\). a. Suppose you are working with oligonucleotides that are 36 nucleotides long. How many sequences exist in a randomized pool containing every sequence possible? b. What percentage of these can a SELEX experiment screen? c. Suppose you wish to select an RNA molecule that catalyzes the hydrolysis of a particular ester. From what you know about catalysis, propose a SELEX strategy that might allow you to select the appropriate catalyst.
