What would be the likely cellular effects of a large deletion in the gene encoding the polymerase responsible for adding 3′ poly(A) tails to eukaryotic mRNAs?

What is the minimum number of transesterification reactions required to splice an intron from a precursor transcript?

Compare and contrast splicing mechanisms used by spliceosomes, group I introns, and group II introns, with respect to the nucleophiles, proteins, or nucleic acids involved and how the specificity of splice sites is achieved.

Self-splicing introns do not require an energy source, such as ATP or GTP, to catalyze splicing. How does self-splicing proceed with a reasonable yield of products?

Given what you have learned about the catalytic mechanism of group I self-splicing introns, propose an experiment to identify new group I introns in the total RNA isolated from an individual organism. Include a unique feature of the group I splicing reaction mechanism in your answer.

Strains of bacteria lacking the enzymes required for rRNA modification have been engineered in the laboratory and seem to grow normally, despite the absence of modified rRNA. What would happen to these bacterial strains if they were forced to compete with wild-type bacteria? Explain.

Is it correct to call an RNA molecule that catalyzes a reaction on itself an enzyme? Explain your answer.

What accounts for the directionality of mRNA transport out of the nucleus?

What would happen to the lifetime of a human mRNA if a nonhydrolyzable phosphodiester analog were introduced near its 5′ end?

Some RNA editing involves the deletion and/or addition of nucleotides to an mRNA. Other RNA editing reactions involve the alteration of bases in an mRNA, without the addition or deletion of nucleotides. Which bases may be altered in RNA editing? What reactions occur to alter them, and what bases are they converted to? What changes in coding occur as a result of the base alterations?

What do the editing reactions catalyzed by APOBEC and ADAR enzymes have in common?

All living systems share key properties (see Chapter 1). Why did the discovery of RNA catalysis trigger the development of an RNA world hypothesis as a stage in the evolution of life?

Two different sequences in a primary mRNA transcript are critical to its cleavage in preparation for the addition of a poly(A) tail to the 3′ end. What are those sequences, and which of them, if either, is (are) retained in the mature and modified mRNA?

Following the first step in the splicing of a group II intron, an internal A residue in the intron is linked to other nucleotides by three phosphodiester bonds. What groups on the adenosine are involved in the phosphodiester bonds, and to what is each bond linked?

The double-stranded RNA endonuclease called Dicer is found in the cytoplasm of many eukaryotic cells. What type of RNA does it cleave?

If the tRNA nucleotidyltransferase or the enzyme that converts some U residues to pseudouridine in tRNA were inactivated in a eukaryotic cell, which inactivation would most likely be lethal?

RNA enzymes (ribozymes) have been discovered in cells ranging from bacteria to humans. What kinds of reactions are catalyzed by these naturally occurring ribozymes?