In Figure 8-3, why are the arrows for genes 1 and 2 pointing in opposite directions?

In Figure 8-5, draw the “one gene” at much higher resolution with the following components: DNA, RNA polymerase(s), RNA(s).

In Figure 8-6, describe where the gene promoter is located.

In Figure 8-9b, write a sequence that could form the hairpin loop structure.

How do you know that the events in Figure 8-13 are occurring in the nucleus?

In Figure 8-15, what do you think would be the effect of a G to A mutation in the first G residue of the intron?

By comparing Figures 8-16 and 8-17, evaluate what is/are the function(s) of proteins U1–U6.

By comparing Figures 8-16 and 8-17 with Figure 8-18, speculate what features of RNA permit self-splicing (that is, in the absence of proteins).

In Figure 8-20, three very different situations are shown that all result in gene silencing. What do these situations have in common to make this is possible?

In Figure 8-22, show how the double-stranded RNA is able to silence the transgene. What would have to happen for the transgene to also silence the flanking cellular gene (in yellow)?

In prokaryotes and eukaryotes, describe what else is happening to the RNA while RNA polymerase is synthesizing a transcript from the DNA template.

List three examples of proteins that act on nucleic acids during transcription.

What is the primary function of the sigma factor? Is there a protein in eukaryotes analogous to the sigma factor?

You have identified a mutation in yeast, a unicellular eukaryote, that prevents the capping of the 5′ end of the RNA transcript. However, much to your surprise, all the enzymes required for capping are normal. You determine that the mutation is, instead, in one of the subunits of RNA polymerase II. Which subunit is mutant, and how does this mutation result in failure to add a cap to yeast RNA?

Why is RNA produced only from the template DNA strand and not from both strands?

A linear plasmid contains only two genes, which are transcribed in opposite directions, each one from the end, toward the center of the plasmid. Draw diagrams of

Are there similarities between the DNA replication bubbles and the transcription bubbles found in eukaryotes? Explain.

Which of the following statements are true about eukaryotic mRNA?

A researcher was mutating prokaryotic cells by inserting segments of DNA. In this way, she made the following mutation:

You will learn more about genetic engineering in Chapter 10, but for now, put on your genetic engineer’s cap and try to solve this problem. E. coli is widely used in laboratories to produce proteins from other organisms.

Draw a prokaryotic gene and its RNA product. Be sure to include the promoter, transcription start site, transcription termination site, untranslated regions, and labeled 5′ and 3′ ends.

Draw a two-intron eukaryotic gene and its pre-mRNA and mRNA products. Be sure to include all the features of the prokaryotic gene included in your answer to Problem 19, plus the processing events required to produce the mRNA.

A certain Drosophila protein-encoding gene has one intron. If a large sample of null alleles of this gene is examined, will any of the mutant sites be expected

What are self-splicing introns, and why does their existence support the theory that RNA evolved before protein?

Antibiotics are drugs that selectively kill bacteria without harming animals. Many antibiotics act by selectively binding to certain proteins that are critical for bacterial function. Explain why some of the most successful antibiotics target bacterial RNA polymerase.

Describe four types of RNA that perform distinct functions.

The following data represent the base compositions of double-stranded DNA from two different bacterial species and their RNA products obtained in experiments conducted in vitro:

A human gene was initially identified as having three exons and two introns. The exons are 456, 224, and 524 bp, whereas the introns are 2.3 kb and 4.6 kb.

While working in your laboratory, you isolate an mRNA from C. elegans that you suspect is essential for embryos to develop successfully. With the assumption that you are able to turn mRNA into double-stranded RNA, design an experiment to test your hypothesis.

Glyphosate is an herbicide used to kill weeds. It is the main component of a product made by the Monsanto Company called Roundup. Glyphosate kills plants by inhibiting an enzyme in the shikimate pathway called EPSPS. This herbicide is considered safe because animals do not have the shikimate pathway. To sell even more of their herbicide, Monsanto commissioned its plant geneticists to engineer several crop plants, including corn, to be resistant to glyphosate. To do so, the scientists had to introduce an EPSPS enzyme that was resistant to inhibition by glyphosate into crop plants and then test the transformed plants for resistance to the herbicide.

Imagine that you are one of these scientists and that you have managed to successfully introduce the resistant EPSPS gene into the corn chromosomes. You find that some of the transgenic plants are resistant to the herbicide, whereas others are not. Your supervisor is very upset and demands an explanation of why some of the plants are not resistant even though they have the transgene in their chromosomes. Draw a picture to help him understand.

Many human cancers result when a normal gene mutates and leads to uncontrolled growth (a tumor). Genes that cause cancer when they mutate are called oncogenes. Chemotherapy is effective against many tumors because it targets rapidly dividing cells and kills them. Unfortunately, chemotherapy has many side effects, such as hair loss or nausea, because it also kills many of our normal cells that are rapidly dividing, such as those in the hair follicles or stomach lining.

Many scientists and large pharmaceutical companies are excited about the prospects of exploiting the RNAi pathway to selectively inhibit oncogenes in lifethreatening tumors. Explain in very general terms how gene-silencing therapy might work to treat cancer and why this type of therapy would have fewer side effects than chemotherapy.

Would you expect self-splicing introns to be on average longer or shorter than introns spliced by spliceosomes? Justify your answer.

A scientist who inserted a plant gene into human chromosomes was not able to detect any transcription from the plant gene. Propose an explanation based on what you have learned about transcription. Now devise an experiment to test your hypothesis.