PROBLEMS

WORKING WITH THE FIGURES

Question 15.1

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):

  1. the fully pigmented kernel?

  2. the unpigmented kernels? Note that they can arise in two different ways.

Question 15.2

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

Question 15.3

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

Question 15.4

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

Question 15.5

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.

Question 15.6

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.

Question 15.7

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

BASIC PROBLEMS

Question 15.8

Describe the generation of multiple-drug-resistant plasmids.

Question 15.9

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

Question 15.10

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

Question 15.11

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?

Question 15.12

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?

Question 15.13

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

Question 15.14

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?

Question 15.15

Transposase protein can

  1. bind to DNA.

  2. catalyze the excision of a transposable element from a donor site.

  3. catalyze the insertion of a transposable element into a target site.

  4. All of the above

Question 15.16

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

  1. Introns

  2. Exons

  3. Other transposable elements

  4. a and c are both correct.

Question 15.17

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

  1. Because they do not encode the Env protein

  2. Because they are nonautonomous elements

  3. Because they require reverse transcriptase

  4. a and b are both true.

Question 15.18

Unlike retrotransposons, DNA transposons

  1. have terminal inverted repeats.

  2. generate a target-site duplication upon insertion.

  3. ranspose via an RNA intermediate.

  4. are not found in prokaryotes.

Question 15.19

The major difference between retrotransposons and retroviruses is

  1. retrotransposons encode reverse transcriptase.

  2. retroviruses move from one site in the genome to another.

  3. retroviruses encode the env gene, which allows them to move from one cell to another.

  4. None of the above are correct.

579

Question 15.20

Which of the following is true of reverse transcriptase?

  1. It is required for the movement of DNA transposons.

  2. It catalyzes the synthesis of DNA from RNA.

  3. It is required for the transposition of retrotransposons.

  4. b and c are correct.

Question 15.21

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

  1. Ac element

  2. P element

  3. Alu element

  4. Composite transposons

Question 15.22

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

  1. Maize has more genes than rice.

  2. Rice has more genes than maize.

  3. Maize has more DNA transposons than rice.

  4. Maize has more retrotransposons than rice.

Question 15.23

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

  1. Because transposable elements prefer to insert into introns

  2. Because transposable elements prefer to insert into exons

  3. Because transposable elements insert into both exons and introns but selection removes exon insertions

  4. None of the above are true.

Question 15.24

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

  1. 10%

  2. 25%

  3. 50%

  4. 75%

Question 15.25

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

  1. Most of the transposable elements are inactive due to mutation.

  2. Active transposable elements are silenced by the host.

  3. Most transposable elements are inserted in safe havens.

  4. All of the above are true.

CHALLENGING PROBLEMS

Question 15.26

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.

  1. A LINE inserts into an enhancer of a human gene.

  2. A transposable element contains a binding site for a transcriptional repressor and inserts adjacent to a promoter.

  3. An Alu element inserts into the 3′ splice (AG) site of an intron in a human gene.

  4. A Ds element that was inserted into the exon of a maize gene excises imperfectly and leaves three base pairs behind in the exon.

  5. Another excision by that same Ds element leaves two base pairs behind in the exon.

  6. A Ds element that was inserted into the middle of an intron excises imperfectly and leaves five base pairs behind in the intron.

Question 15.27

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.

Question 15.28

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.

Question 15.29

Consider two maize plants:

  1. Genotype C/cm; Ac/Ac+, where cm is an unstable allele caused by a Ds insertion

  2. Genotype C/cm, where cm is an unstable allele caused by Ac insertion

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+.

Question 15.30

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?

580

Question 15.31

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?

Question 15.32

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.

Question 15.33

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?

Question 15.34

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.

Question 15.35

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.)

Question 15.36

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

Question 15.37

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?

Question 15.38

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?

Question 15.39

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