Chapter 11

Proflavin is a compound that inserts itself into DNA and causes frameshift mutations (page 473 ). How would the effect on the amino acid sequence of a proflavin-induced mutation differ between an overlapping and a nonoverlapping code?

You have just isolated a new drug that has only one effect on cell metabolism; it totally inhibits the breakdown of pre-rRNA to ribosomal RNA. After treating a culture of mammalian cells with this drug, you give the cells \(\left[^{3} \mathrm{H}\right]\) uridine for 2 minutes, and then grow the cells in the presence of the drug in unlabeled medium for 4 hours before extracting the \(\mathrm{RNA}\) and centrifuging it through a sucrose gradient. Draw the curves you would obtain by plotting both absorbance at \(260 \mathrm{nm}\) and radioactivity against the fraction number of the gradient. Label the abscissa \((X\) -axis) using S values of RNA.

Suppose that you found an enzyme that incorporated nucleotides randomly into a polymer without the requirement for a template. How many different codons would you be able to find in synthetic RNAs made using two different nucleotide precursors (e.g., CTP and ATP)? (An enzyme called polynucleotide phosphorylase catalyzes this type of reaction and was used in studies that identified codons.)

Do you think it would be theoretically possible to have a genetic code with only two letters, A and T? If so, what would be the minimum number of nucleotides required to make a codon?

On page 454 , experiments are reported that lead to the synthesis of ribozymes with unique catalytic properties. In 2001 , an artificial ribozyme was isolated that was capable of incorporating up to 14 ribonucleotides onto the end of an existing RNA using an RNA strand as a template. The ribozyme could use any RNA sequence as a template and would incorporate complementary nucleotides into the newly synthesized RNA strand with an accuracy of 98.5 percent. If you were a proponent of an ancient RNA world, how would you use this finding to argue your case? Would this prove the existence of an ancient RNA world? If not, what do you think would provide the strongest evidence for such a world?

How is it possible that mRNA synthesis occurs at a greater rate in bacterial cells than any other class, yet very little mRNA is present within the cell?

If a codon for serine is \(5^{\prime}-\mathrm{AGC}-3^{\prime},\) the anticodon for this triplet would be \(5^{\prime}----3^{\prime} .\) How would the wobble phenomenon affect this codon-anticodon interaction?

One of the main arguments that proteins evolved before DNA (i.e., that the RNA world evolved into an RNA-protein world rather than an RNA-DNA world) is based on the fact that the translational machinery involves a large variety of RNAs (e.g., tRNAs, rRNAs), whereas the transcriptional machinery shows no evidence of RNA involvement. Can you explain how such an argument about the stages of early evolution might be based on these observations?

Frameshift mutations and nonsense mutations were described on page \(474 .\) It was noted that nonsense mutations often lead to the destruction by NMD of an mRNA containing a premature termination codon. Would you expect mRNAs containing frameshift mutations to be subject to NMD?

Genes are usually discovered by finding an abnormal phenotype resulting from a genetic mutation. Alternatively, they can often be identified by examining the DNA sequence of a genome. Why do you suppose that the genes encoding miRNAs were not discovered until very recently?

It was suggested on page 464 that synonymous codon changes do not generally alter an organism's phenotype. Can you think of an occasion where this might not be true? What does this say about the coding requirements of the genetic material?