In the chapter-opening photograph of kernels on an ear of corn, what is the genetic basis of the following (Hint: Refer to Figure 15-4 for some clues):

In Figure 15-3a, what would the kernel phenotype be if the strain were homozygous for all dominant markers on chromosome 9?

For Figure 15-7, draw out a series of steps that could explain the origin of this large plasmid containing many transposable elements.

Draw a figure for the mode of transposition not shown in Figure 15-8, retrotransposition.

In Figure 15-10, show where the transposase would have to cut to generate a 6-bp target-site duplication. Also show the location of the cut to generate a 4-bp target-site duplication.

If the transposable element in Figure 15-14 were a DNA transposon that had an intron in its transposase gene, would the intron be removed during transposition? Justify your answer.

For Figure 15-22, draw the pre-mRNA that is transcribed from this gene and then draw its mRNA.

Describe the generation of multiple-drug-resistant plasmids.

Briefly describe the experiment that demonstrates that the transposition of the Ty1 element in yeast takes place through an RNA intermediate.

Explain how the properties of P elements in Drosophila make gene-transfer experiments possible in this organism.

Although DNA transposons are abundant in the genomes of multicellular eukaryotes, class 1 elements usually make up the largest fraction of very large genomes such as those from humans (~2500 Mb), maize (~2500 Mb), and barley (~5000 Mb). Given what you know about class 1 and class 2 elements, what is it about their distinct mechanisms of transposition that would account for this consistent difference in abundance?

As you saw in Figure 15-22, the genes of multicellular eukaryotes often contain many transposable elements. Why do most of these elements not affect the expression of the gene?

What are safe havens? Are there any places in the much more compact bacterial genomes that might be a safe haven for insertion elements?

Nobel prizes are usually awarded many years after the actual discovery. For example, James Watson, Francis Crick, and Maurice Wilkens were awarded the Nobel Prize in Medicine or Physiology in 1962, almost a decade after their discovery of the double-helical structure of DNA. However, Barbara McClintock was awarded the Nobel Prize in 1983, almost four decades after her discovery of transposable elements in maize. Why do you think it took this long for the significance of her discovery to be recognized in this manner?

Transposase protein can

Which of the following are safe havens for transposable element insertions?

Why can’t retrotransposons move from one cell to another like retroviruses?

Unlike retrotransposons, DNA transposons

The major difference between retrotransposons and retroviruses is

Which of the following is true of reverse transcriptase?

Which transposable element is used to introduce foreign DNA into the fruit fly Drosophila melanogaster?

What is the major reason why the maize genome is much larger than the rice genome?

Why are transposable elements found much more often in introns than in exons?

Approximately what percentage of the human genome is derived from transposable elements?

Why do plants and animals thrive with so many transposable elements in their genomes?

The insertion of transposable elements into genes can alter the normal pattern of expression. In the following situations, describe the possible consequences on gene expression.

Before the integration of a transposon, its transposase makes a staggered cut in the host target DNA. If the staggered cut is at the sites of the arrows below, draw what the sequence of the host DNA will be after the transposon has been inserted. Represent the transposon as a rectangle.

In Drosophila, M. Green found a singed allele (sn) with some unusual characteristics. Females homozygous for this X-linked allele have singed bristles, but they have numerous patches of sn⁺ (wild-type) bristles on their heads, thoraxes, and abdomens. When these flies are mated with sn males, some females give only singed progeny, but others give both singed and wild-type progeny in variable proportions. Explain these results.

Consider two maize plants:

What phenotypes would be produced and in what proportions when (1) each plant is crossed with a base-pair-substitution mutant c/c and (2) the plant in part a is crossed with the plant in part b? Assume that Ac and c are unlinked, that the chromosome-breakage frequency is negligible, and that mutant c/C is Ac⁺.

You meet your friend, a scientist, at the gym and she begins telling you about a mouse gene that she is studying in the lab. The product of this gene is an enzyme required to make the fur brown. The gene is called FB, and the enzyme is called FB enzyme. When FB is mutant and cannot produce the FB enzyme, the fur is white. The scientist tells you that she has isolated the gene from two mice with brown fur and that, surprisingly, she found that the two genes differ by the presence of a 250-bp SINE (like the human Alu element) in the FB gene of one mouse but not in the gene of the other. She does not understand how this difference is possible, especially given that she determined that both mice make the FB enzyme. Can you help her formulate a hypothesis that explains why the mouse can still produce FB enzyme with a transposable element in its FB gene?

The yeast genome has class 1 elements (Ty1, Ty2, and so forth) but no class 2 elements. What is a possible reason why DNA elements have not been successful in the yeast genome?

In addition to Tc1, the C. elegans genome contains other families of DNA transposons such as Tc2, Tc3, Tc4, and Tc5. Like Tc1, their transposition is repressed in the germ line but not in somatic cells. Predict the behavior of these elements in the mutant strains where Tc1 is no longer repressed due to mutations in the RNAi pathway. Justify your answer.

Based on the mechanism of gene silencing, what features of transposable elements does the RNAi pathway exploit to ensure that the host’s own genes are not also silenced?

What are the similarities and differences between retroviruses and retrotransposons? It has been hypothesized that retroviruses evolved from retrotransposons. Do you agree with this model? Justify your answer.

You have isolated a transposable element from the human genome and have determined its DNA sequence. How would you use this sequence to determine the copy number of the element in the human genome if you just had a computer with an Internet connection? (Hint: see Chapter 14.)

Following up on the previous question, how would you determine whether other primates had a similar element in their genomes?

Of all the genes in the human genome, the ones with the most characterized Alu insertions are those that cause hemophilia, including several insertions in the factor VIII and factor IX genes. Based on this fact, your colleague hypothesizes that the Alu element prefers to insert into these genes. Do you agree? What other reason can you provide that also explains these data?

If all members of a transposable element family can be silenced by dsRNA synthesized from a single family member, how is it possible for one element family (like Tc1) to have 32 copies in the C. elegans genome while another family (Tc2) has fewer than 5 copies?

How can the CRISPR and pi-cluster loci change over time?