Question: Outline how you would use the technique

> How does gene cloning produce many copies of a gene?

> Describe the important features of cloning vectors. Explain the purpose of selectable markers in cloning experiments.

> Table 21.3 describes the cleavage sites of five different restriction enzymes. After these restriction enzymes have cleaved the DNA, four of them produce sticky ends that can hydrogen bond with complementary sticky ends, as shown in Figure 21.1. The effi

> What is the advantage of genetic recombination, which is depicted in part (b)? From Figure 20.1: DO DO A da Two with Meiosis is parental genotype A crossover occurs between homologous chromatids. completed to yield 4 haploid cells. A B b Two with re

> DNA sequencing can help us to identify mutations within genes. The following data are derived from an experiment in which a normal gene and a mutant gene have been sequenced: Locate and describe the mutation G= Yellow A- Green T- Red C-

> What phase of PCR (exponential, linear, or stationary) is analyzed to quantitate the amount of DNA or RNA in a sample? Explain why this phase is chosen.

> What type of probe is used for real-time PCR? Explain how the level of fluorescence correlates with the level of PCR product.

> Starting with a sample of RNA that contains the mRNA for the β-globin gene, explain how you could create many copies of the β-globin cDNA using reverse transcriptase PCR.

> What is the functional significance of sticky ends in a cloning experiment? What type of bonding makes the ends sticky?

> A bacterium is exposed to a drug that inhibits the N protein. What would you expect to happen if the bacterium was later infected by phage λ? Would phage λ follow the lytic cycle, the lysogenic cycle, or neither? Explain your answer.

> Experimentally, when an E. coli bacterium already has a λ prophage integrated into its chromosome, another λ phage cannot usually infect the cell and establish the lysogenic or lytic cycle. Based on your understanding of the genetic regulation of the pha

> A researcher identified a mutation in PR of phage λ that causes its transcription rate to be increased 10-fold. Do you think this mutation would favor the lytic or lysogenic cycle? Explain your answer.

> Richard Boyce and Paul Howard-Flanders conducted an experiment that provided biochemical evidence that thymine dimers are removed from DNA by a DNA repair system. In their studies, bacterial DNA was radiolabeled so the amount of radioactivity reflected t

> Gerald Rubin and Allan Spradling devised a method of introducing a transposon into Drosophila. This approach has been important for the transposon tagging of many Drosophila genes. The researchers began with a P element that had been cloned on a plasmid.

> What is a reactive oxygen species?

> Tumor-suppressor genes are normal human genes that prevent uncontrollable cell growth. Starting with a normal laboratory human cell line, describe how you could use transposon tagging to identify tumor-suppressor genes. (Note: When a TE hops into a tumor

> Compare and contrast anti-miRNA oligonucleotides, locked nucleic acids (LNAs), and antagomirs, which may eventually be used to treat certain forms of cancer. 

> As described in Chapter 21, the CRISPR-Cas system has been modified so it can be used as a gene mutagenesis tool (look ahead to Figure 21.13). Describe how the gene mutagenesis tool works, and explain how the natural CRISPR-Cas system is altered to produ

> Explain how the data of Fire and Mello suggested that doublestranded RNA is responsible for the silencing of mex-3 mRNA.

> In Experiment 17A, were Fire and Mello injecting pre-miRNA or pre-siRNA? Explain.

> In your own words, explain the term transposon tagging.

> As described in experimental question E2 and also in Chapter 21, the technique of Northern blotting can be used to detect the level of transcription of a specific RNA. Draw the results you would expect from a Northern blot if bacteria were grown in media

> A protein called trypsin, which plays a role in digestion, is made by pancreatic cells and secreted from those cells. Starting with a sample of pancreatic cells, a researcher modified the gene that encodes trypsin by mutating the ER signal sequence so it

> Look back at Figure 16.7. If you crossed an F2 offspring to a homozygous B-I B-I plant, what phenotypic results would you expect for the F3 offspring? From Figure 16.7: Strain A: B' B' (This strain is homozygous for the weak allele. The ' symbol ind

> Let’s suppose you were interested in developing drugs to prevent epigenetic changes that may contribute to cancer. What cellular proteins would be the target of your drugs? What possible side effects might your drugs cause?

> Which of these two changes is more difficult for DNA repair enzymes to fix correctly? Explain why

> A research study indicated that an agent in cigarette smoke caused the silencing of a tumor-suppressor gene called p53. However, using sequencing, no mutation was found in the DNA sequence for this gene. Give two possible explanations for these results.

> 5-Azocytidine is an inhibitor of DNA methyltransferase. If this drug were fed to female mice during pregnancy, explain how you think it would affect the coat color of offspring carrying the Avy allele.

> In the experiments described in Figure 16.8, explain the relationship between coat color and DNA methylation. How is coat color related to the diet of the mother? From Figure 16.8: Promoter within Transposable element transposable Normal promoter el

> A gene, which we will call gene C, can be epigenetically modified in such a way that its expression in some cells is permanently silenced. Describe how you could conduct cell-fusion experiments to determine if a cis- or a trans-epigenetic mechanism is re

> Chapter 21 describes a blotting method known as Northern blotting, in which a short segment of cloned DNA is used as a probe to detect RNA that is transcribed from a particular gene. The DNA probe, which is labeled, is complementary to the RNA that the r

> As described in Chapter 21, an electrophoretic mobility shift assay (EMSA) can be used to determine if a protein binds to a segment of DNA. When a segment of DNA is bound by a protein, its mobility will be retarded, and the DNA band will appear higher in

> The work of McClintock showed that the presence of a transposon can create a mutable site or locus that is subject to frequent chromosome breakage. Why do you think a transposon creates a mutable site? If chromosome breakage occurs, do you think the tran

> You will need to understand question 3 in More Genetic TIPS before answering this question. A gene that is normally expressed in pancreatic cells was cloned and then subjected to promoter bashing. As shown here, four regions, labeled A–

> You will need to understand question 3 in More Genetic TIPS before answering this question. A muscle-specific gene was cloned and then subjected to promoter bashing. As shown here, six regions, labeled A–F, were deleted, and then the DN

> Restriction enzymes, described in Chapter 21, are enzymes that recognize a particular DNA sequence and cleave the DNA (along the DNA backbone) at that site. The restriction enzyme known as NotI recognizes the sequence 5′â€&#

> When DNA replication occurs over an apurinic site, what is the probability that a mutation will occur?

> Researchers can isolate a sample of cells, such as skin fibroblasts, and grow them in the laboratory. This procedure is called a cell culture. A cell culture can be exposed to a sample of DNA. If the cells are treated with agents that make their membrane

> Briefly describe the method of chromatin immunoprecipitation sequencing (ChIP-Seq). How is it used to determine nucleosome positions within a genome?

> Let’s suppose you have isolated a mutant strain of E. coli in which the lac operon is constitutively expressed. To understand the nature of this defect, you create a merozygote in which the mutant strain contains an F′

> A mutant strain has a defective lac operator site that results in the constitutive expression of the lac operon. Outline an experiment you would carry out to demonstrate that the operator site must be physically adjacent to the genes that it influences.

> Explain how the data shown in Figure 14.9 indicate that two operator sites are necessary for repression of the lac operon. What would the results have been if all three operator sites were required for the binding of lac repressor? From Figure 14.9:

> An absentminded researcher follows the protocol described in Figure 14.7 and (at the end of the experiment) does not observe any yellow color in any of the tubes. Yikes! Which of the following mistakes could account for this observation? A. Forgot to so

> This question combines your knowledge of bacterial conjugation (described in Chapter 7) and the genetic regulation that directs the phage λ reproductive cycles. When researchers mix donor Hfr strains with recipient F– bacteria that are lysogenic for phag

> Briefly explain how McClintock determined that Ds was occasionally moving from one chromosomal location to another. Discuss the type of data she examined to arrive at this conclusion.

> During an Ames test, bacteria were exposed to a potential mutagen. Also, as a control, another sample of bacteria was not exposed to the mutagen. In both cases, 10 million bacteria were plated and the following results were obtained: No mutagen: 17 colo

> How would you modify the Ames test to evaluate physical mutagens? Would it be necessary to add the rat liver extract? Explain why or why not.

> Can this trait be passed to offspring?

> From an experimental point of view, is it better to use haploid or diploid organisms for mutagen testing? Consider the Ames test when preparing your answer.

> Explain how the technique of replica plating supports the random mutation theory but conflicts with the physiological adaptation hypothesis.

> Some drugs that inhibit HIV proliferation are inhibitors of HIV protease. Explain how these drugs would help to stop the spread of HIV.

> Certain drugs to combat human viral diseases affect spike glycoproteins in the viral envelope. Discuss how you think such drugs may prevent viral infection.

> Following the infection of healthy tobacco leaves by reconstituted viruses, what two characteristics did Fraenkel-Conrat and Singer analyze? Explain how their results were consistent with the idea that the RNA of TMV is responsible for the traits of the

> What is a reconstituted virus?

> What is heterosis? Discuss whether it is caused by a single gene or several genes. Discuss the two major hypotheses proposed to explain heterosis. Which do you think is more likely to be correct?

> From a biological viewpoint, speculate as to why many traits seem to fit a normal distribution. Students with a strong background in math and statistics may want to explain how a normal distribution is generated, and what it means. Can you think of biolo

> Discuss why heritability is an important phenomenon in agriculture.

> Has the DNA sequence of the eye color gene been changed in part (b) compared with part (a)? How do we explain the phenotypic difference? From Figure 19.3: (a) Normal eye (b) Variegated eye

> Most new mutations are detrimental, yet rare beneficial mutations can be adaptive. With regard to the fate of new mutations, discuss whether you think it is more important for natural selection to select against detrimental alleles or to select in favor

> Discuss the role of mutation in the origin of genetic polymorphisms. Suppose that a genetic polymorphism involves two alleles at frequencies of 0.45 and 0.55. Describe three different scenarios to explain these observed allele frequencies. You can propos

> Discuss examples of positive and negative assortative mating in natural populations, human populations, and agriculturally important species.

> At the molecular level, how do you think a gain-of-function mutation in a developmental gene might cause it to be expressed in the wrong place or at the wrong time? Explain what type of DNA sequence would be altered.

> It seems that developmental genetics boils down to a complex network of gene regulation. Try to draw a structure of this network for Drosophila. How many genes do you think are necessary to complete the developmental network for the fruit fly? How many g

> Compare and contrast the experimental advantages and disadvantages of Drosophila, C. elegans, mammals, and Arabidopsis.

> Make a list of the types of traits you would like to see altered in transgenic plants and animals. Suggest techniques to accomplish these alterations.

> If you have access to the necessary computer software, make a sequence file and analyze it in the following ways: What is the translated sequence in all three reading frames? What is the longest open reading frame? Is the sequence homologous to any known

> Let’s suppose you are in charge of organizing and publicizing a database for the mouse genome. Make a list of innovative strategies you would initiate to make the mouse genome database useful and effective.

> Make a list of the benefits that may arise from genetic testing as well as possible negative consequences. Discuss the items on your list.

> Explain what the term position effect means.

> What is the principle of parsimony?

> Which goals of the Human Genome Project do you think are the most important? Why? Discuss the types of ethical problems that might arise as a result of identifying all of our genes.

> What is a molecular marker? Give two examples. Discuss why it is generally easier to locate and map molecular markers rather than functional genes.

> A commercially available strain of P. syringae marketed as Frostban B is used to combat frost damage. This is a naturally occurring strain that carries a loss-of-function mutation in a gene that encodes a protein that is expressed on the surface of the b

> Discuss the advantages and disadvantages of gene therapy. A limited amount of funding is available for gene therapy research. Make a priority list of the three top diseases for which you would fund research. Discuss your choices.

> Based on your current knowledge of genetics, discuss whether or not you think the selfish DNA hypothesis is correct.

> Make a list of possible research questions that could be answered using site-directed mutagenesis or CRISPR-Cas technology.

> Discuss and make a list of some of the reasons why determining the amount of a particular gene product would be useful to a geneticist. Use specific examples of known genes (e.g., β-globin gene and other genes) when making your list.

> If homologous and site-specific recombination could not occur, what would be the harmful and the beneficial consequences?

> Make a list of the similarities and differences among homologous recombination, site-specific recombination, and transposition.

> A large amount of research is aimed at studying mutation. However, there is not an infinite amount of research money. Where would you put your money for mutation research? A. Testing of potential mutagens B. Investigating molecular effects of mutagens

> What is the function of PRM?

> Discuss the times in a person’s life when it is most important to avoid mutagens. Which parts of a person’s body should be the most highly protected from mutagens?

> In E. coli, a variety of mutator strains have been identified in which the spontaneous rate of mutation is much higher than in normal strains. Make a list of the types of abnormalities that could cause a strain of bacteria to become a mutator strain. Whi

> Browse the Internet to determine the drugs that are used to treat people with AIDS. Which proteins do these drugs affect? Discuss how an understanding of the HIV reproductive cycle has been helpful in developing treatments for AIDS.

> Certain environmental conditions such as exposure to UV light are known to activate lysogenic λ prophages and cause them to progress into the lytic cycle. UV light initially causes the repressor protein to be proteolytically degraded. Make a flow diagram

> Discuss the properties of emerging viruses. What are the challenges associated with combating them?

> Discuss the advantages and disadvantages of genetic regulation at the different points identified in Figure 14.1. From Figure 14.1: REGULATION OF GENE EXPRESSION Gene Transcription Genetic regulatory proteins bind to the DNA and control the rate of

> Go to the PubMed website and do a search using the words noncoding RNA and disease. Scan through the journal articles you retrieve and make a list of the roles that ncRNAs may play in human diseases.

> Review the concept of an RNA world described in Section 17.1. Discuss which ncRNAs described in Table 17.1 may have arisen during the RNA world, and which probably arose after the modern DNA/RNA/protein world came into being. From Table 17.1: Exampl

> Discuss the similarities and differences of phenotypic variations that are caused by epigenetic gene regulation versus variation in gene sequences (epigenetics versus genetics).

> Go to the PubMed website and search using the words epigenetic and cancer. Scan through the journal articles you retrieve, and make a list of environmental agents that may cause epigenetic changes that contribute to cancer.

> Which form of HIV RNA, fully spliced, incompletely spiced, or unspliced, is needed during the early stage of the synthesis of HIV components?

> Enhancers can occur almost anywhere in DNA and affect the transcription of a gene. Let’s suppose you have a gene cloned on a piece of DNA, and the DNA fragment is 50,000 bp in length. Using cloning methods described in Chapter 21, you can cut out short s

> Explain how DNA methylation could be used to regulate gene expression in a tissue-specific way. When and where would de novo methylation occur, and when would demethylation occur? What would occur in the cells that give rise to eggs and sperm?

> Looking at Figure 14.10, discuss possible “molecular ways” that the cAMP-CAP complex and lac repressor may influence RNA polymerase function. In other words, try to explain how the bending and looping in DNA may affect

> Do you think that Darwin would object to the neutral theory of evolution?

> Compare the forms of speciation that are slow to those that occur more rapidly. Make a list of the slow and fast forms. With regard to mechanisms of genetic change, what features do slow and rapid speciation have in common? What features are different?

> The raw material for evolution is random mutation. Discuss whether or not you view evolution as a random process.

> What technique must be used to visualize a virus?

> Discuss how researchers determined that TMV is a virus that causes damage to plants.