Question: What is a restriction enzyme? What structure

> As described in Chapter 15 (Figures 15.7 and 15.8), certain regulatory transcription factors bind to DNA and activate RNA polymerase II. When glucocorticoid binds to the glucocorticoid receptor (a regulatory transcription factor), this changes the confor

> An electrophoretic mobility shift assay can be used to study the binding of proteins to a segment of DNA. In the experiment shown here, an EMSA was used to examine the requirements for the binding of RNA polymerase II (from eukaryotic cells) to the promo

> Certain hormones, such as epinephrine, can increase the levels of cAMP within cells. Let’s suppose you pretreat cells with or without epinephrine and then prepare a cell extract that contains the CREB protein (see Chapter 15 for a description of the CREB

> Describe the rationale behind the electrophoretic mobility shift assay.

> A cloned gene fragment contains a regulatory element that is recognized by a regulatory transcription factor. Previous experiments have shown that the presence of a hormone results in transcriptional activation by this transcription factor. To study this

> Explain the basis for using an antibody as a probe in a Western blotting experiment.

> What environmental conditions favor a switch to the lytic cycle?

> Let’s suppose a researcher was interested in the effects of mutations on the expression of a protein-encoding gene that encodes a polypeptide that is 472 amino acids in length. This polypeptide is expressed in leaf cells of Arabidopsis thaliana. Because

> If you wanted to know if a protein was made during a particular stage of development, what technique would you choose?

> Outline the general strategy used in metagenomics.

> What is meant by sequencing by synthesis?

> Discuss the advantages of next-generation sequencing technologies

> A bacterium has a genome size of 4.4 Mb. If a researcher carries out shotgun DNA sequencing and sequences a total of 19 Mb, what is the probability that a base will be left unsequenced? What percentage of the total genome will be left unsequenced?

> Describe how you would clone a gene by positional cloning. Explain how a (previously made) contig would make this task much easier.

> A human gene, which we will call gene X, is located on chromosome 11 and is found as a normal allele and a recessive disease causing allele. The location of gene X has been approximated on the map shown here, which contains four STSs, labeled STS-1, STS-

> Four cosmid clones, which we will call cosmids A, B, C, and D, were hybridized to each other in pairwise combinations. The insert size of each cosmid was also analyzed. The following results were obtained: Draw a map that shows the order of the inserts

> Take a look at question 3 in More Genetic TIPS and the codon table in Chapter 13. Assuming that a mutation causing a single base change is more likely than one causing a double base change, propose how the Asn-141, Ile-141, and Thr-141 codons arose. In y

> Let’s suppose a drug inhibits the function of the N protein. Would such a drug favor the lysogenic cycle, favor the lytic cycle, or prevent both cycles from occurring?

> What would you expect to be the minimum percentage of matching peaks in an automated DNA fingerprint for the following pairs of individuals? A. Mother and son B. Sister and brother C. Uncle and niece D. Grandfather and grandson

> As discussed in this chapter and Chapter 27, genes are sometimes transferred between different species via horizontal gene transfer. Discuss how horizontal gene transfer might lead to misleading results when constructing a phylogenetic tree. How could yo

> A homologous DNA region, which was 20,000 bp in length, was sequenced from four different species. The following numbers of nucleotide differences were obtained: Construct a phylogenetic tree that describes the evolutionary relationships among these fou

> Discuss how the principle of parsimony can be used in a cladistics approach to constructing a phylogenetic tree.

> A team of researchers has obtained a dinosaur bone (Tyrannosaurus rex) and has attempted to extract ancient DNA from it. Using primers for the 12S rRNA mitochondrial gene, they carried out PCR and obtained a DNA segment that had a sequence homologous to

> In Chapter 23, a technique called fluorescence in situ hybridization (FISH) is described. In this method, a labeled piece of DNA is hybridized to a set of chromosomes. Let’s suppose that you cloned a piece of DNA from G. pubescens (see

> From the results of the experiment of Figure 29.13, explain how we know that the kiwis are more closely related to the emu and cassowary than to the moas. Cite particular regions in the sequences that support your answer. From Figure 29.13: Experime

> Prehistoric specimens often contain minute amounts of ancient DNA. What technique can be used to increase the amount of DNA in an older sample? Explain how this technique is performed and how it increases the amount of a specific region of DNA.

> Explain why molecular techniques were needed to provide evidence for the neutral theory of evolution.

> A species of antelope has 20 chromosomes per set. The species is divided by a mountain range into two separate populations, which we will call the eastern and western population. In a comparison of the karyotypes of these two populations, it was discover

> What is meant by the term emerging virus?

> F1 hybrids between two species of cotton, Gossypium barbadense and Gossypium hirsutum, are very vigorous plants. However, F1 crosses produce many seeds that do not germinate and a high percentage of very weak F2 offspring. Suggest two reasons for these o

> A researcher sequenced a portion of a bacterial gene and obtained the following sequence, beginning with the start codon, which is underlined: ATG CCG GAT TAC CCG GTC CCA AAC AAA ATG ATC GGC CGC CGA ATC TAT CCC The bacterial strain that contained this g

> Two diploid species of closely related frogs, which we will call species A and species B, were analyzed with regard to the genes that encode an enzyme called hexokinase. Species A has two distinct copies of this gene: A1 and A2. In other words, this dipl

> Sympatric speciation by allotetraploidy has been proposed as a common mechanism for speciation. Let’s suppose you were interested in the origin of certain grass species in southern California. Experimentally, how would you go about determining if some of

> Two populations of snakes are separated by a river. The snakes cross the river only on rare occasions. The snakes in the two populations look very similar to each other, except that the members of the population on the eastern bank of the river have a ye

> What is a biological control agent? Briefly describe two examples.

> Which of the following statements about molecular markers are true? A. All molecular markers are segments of DNA that carry specific genes. B. A molecular marker is a segment of DNA that is found at a specific location in a genome. C. We can follow th

> For each of the following, decide if it could be appropriately described as a genome: A. The E. coli chromosome B. Human chromosome 11 C. A complete set of 10 chromosomes in corn D. A copy of the single-stranded RNA packaged into human immunodeficien

> A person with a rare genetic disease has a sample of her chromosomes subjected to in situ hybridization using a probe that is known to recognize band p11 on chromosome 7. Even though her chromosomes look cytologically normal, the probe does not bind to t

> What is bioremediation? What is the difference between biotransformation and biodegradation?

> Which cycle produces new phage particles?

> A conjugation-deficient strain of A. radiobacter is used to combat crown gall disease. Explain how this bacterium prevents the disease, and describe the advantage of using a conjugation-deficient strain.

> What is a recombinant microorganism? Discuss examples.

> Make a list of the differences between the Holliday model and the double-strand break model.

> What is gene conversion?

> In the Holliday model for homologous recombination, the resolution steps can produce recombinant or nonrecombinant chromosomes. Explain how this can occur.

> What are recombinant chromosomes? How do they differ from the original parental chromosomes from which they are derived?

> Draw the structural feature of a dideoxyribonucleotide that causes chain termination. Explain how it does this.

> What is cDNA? In eukaryotes, how does cDNA differ from genomic DNA?

> Write a double-stranded DNA sequence that is 20 base pairs in length and is palindromic.

> During which step of the reproductive cycle can a virus remain latent?

> According to the double-strand break model, does gene conversion necessarily involve DNA mismatch repair? Explain.

> What events does the RecA protein facilitate?

> In recombinant chromosomes, where is gene conversion likely to take place: near the breakpoint or far away from the breakpoint? Explain.

> Discuss three important advances that have resulted from gene cloning

> Is homologous recombination an example of mutation? Explain.

> What two molecular mechanisms can result in gene conversion? Do both occur in the double-strand break model?

> Which steps in the double-strand break model for recombination would be inhibited if the following proteins were missing? Explain the function of each protein required for the step that is inhibited. A. RecBCD B. RecA C. RecG D. RuvABC

> The molecular mechanism of SCE is similar to homologous recombination between homologs except that the two segments of DNA are sister chromatids instead of homologous chromatids. If branch migration occurs during SCE, will a heteroduplex be formed? Expla

> Describe the similarities and differences between homologous recombination involving sister chromatid exchange (SCE) and that involving homologs. Would you expect the same types of proteins to be involved in both processes? Explain.

> In Chapters 12 through 16, we discussed many sequences that are outside a coding sequence but are important for gene expression. Look up two of these sequences and write them out. Explain how a mutation could change these sequences, thereby altering gene

> If a mutation prevented IRP from binding to the IRE in the ferritin mRNA, how would the mutation affect the regulation of ferritin synthesis? Do you think there would be too much or too little ferritin?

> A point mutation occurs in the middle of the coding sequence for a gene. Which types of mutations—silent, missense, nonsense, and frameshift—would be most likely to disrupt protein function and which would be least likely?

> Is each of the following mutations a silent, missense, nonsense, or frameshift mutation? The original DNA strand is 5′–ATGGGACTAGATACC–3′. (Note: Only the coding strand is shown; the first codon is methionine.) A. 5′–ATGGGTCTAGATACC–3′ B. 5′–ATGCGACTAG

> Lactose permease is encoded by the lacY gene of the lac operon. Suppose a mutation occurred at codon 64 that changed the normal glycine codon into a valine codon. The mutant lactose permease is unable to function. However, a second mutation, which change

> X-rays strike a chromosome in a living cell and ultimately cause the cell to die. Did the X-rays produce a mutation? Explain why or why not.

> How would each of the following types of mutations affect protein function or the amount of functional protein that is expressed from a gene? A. Nonsense mutation B. Missense mutation C. Up promoter mutation D. Mutation that affects splicing

> What does a suppressor mutation suppress? What is the difference between an intragenic and an intergenic suppressor?

> Achondroplasia is a rare form of dwarfism. It is caused by an autosomal dominant mutation within a single gene. Among 1,422,000 live births, the number of babies born with achondroplasia was 31. Among those 31 babies, 18 of them had one parent with achon

> What is the difference between the mutation rate and the mutation frequency?

> With regard to TNRE, what is meant by the term anticipation?

> Trinucleotide repeat expansions (TNREs) are associated with several different human inherited diseases. Certain types of TNREs produce a long stretch of the amino acid glutamine within the encoded protein. When a TNRE exerts its detrimental effect by pro

> Why are insulators important for gene regulation in eukaryotes?

> What is the difference between an ancestral character and a shared derived character?

> If a mutagen causes bases to be removed from nucleotides within DNA, what repair system would fix this damage?

> Give an example of a mutagen that can change cytosine to uracil. Which DNA repair system(s) would be able to repair this defect?

> Are mutations random events? Explain your answer.

> A gene mutation changes an AT base pair to GC. This change causes a gene to encode a truncated protein that is nonfunctional. An organism that carries this mutation cannot survive at high temperatures. Make a list of all the genetic terms that could be u

> Distinguish between spontaneous and induced mutations. Which are more harmful? Which are avoidable?

> Explain what happens to the sequence of DNA during trinucleotide repeat expansion (TNRE). If someone was mildly affected with a TNRE disorder, what issues would be important when considering possible effects in future offspring?

> What type of mutation (transition, transversion, or frameshift) would you expect each of the following mutagens to cause? A. Nitrous acid B. 5-Bromouracil C. Proflavin

> Explain how a mutagen can interfere with DNA replication to cause a mutation. Give two examples.

> Make a drawing that shows how alkylating agents alter the structure of DNA, and explain the process.

> Discuss the consequences of a germ-line versus a somatic mutation.

> What is the difference between de novo methylation and maintenance methylation?

> As discussed in Chapter 25, most forms of cancer are caused by environmental agents that produce mutations in somatic cells. Is an individual with cancer considered a genetic mosaic? Explain why or why not.

> Which of the following mutations could be appropriately described as a position effect? A. A point mutation at the –10 position in the promoter region prevents transcription. B. A translocation places the coding sequence for a muscle-specific gene next

> Is a random mutation more likely to be beneficial or harmful? Explain your answer.

> Explain two ways that a chromosomal rearrangement can cause a position effect.

> Is each of the following mutations a transition, transversion, addition, or deletion? The original DNA strand is 5′–GGACTAGATAC–3′ (Note: Only the coding DNA strand is shown.) A. 5′–GAACTAGATAC–3′ B. 5′–GGACTAGAGAC–3′ C. 5′–GGACTAGTAC–3′ D. 5′–GGAG

> Describe how lytic bacteriophages are released from their host cells.

> What is the role of reverse transcriptase in the reproductive cycle of HIV and other retroviruses?

> Compare and contrast the entry step of the viral reproductive cycle of phage λ and HIV.

> Describe why the attachment step in a viral reproductive cycle is usually specific for one or just a few cell types.

> What do the terms host cell and host range mean?

> Explain why the events shown in part (a) inhibit transcription. From Figure 15.15a: Enhancer CpG island Core promoter Coding sequence Activator - protein Methylation CH, CH, CH, CH, CH, CH, Methyl groups block the binding of an activator protein to

> What is a viral envelope? Describe how it is made.

> In general, why is it important to regulate genes? Discuss examples of situations in which it would be advantageous for a bacterial cell to regulate genes.

> What is antisense RNA? How does it affect the translation of a complementary mRNA?

> Translational control is usually aimed at preventing the initiation of translation. With regard to cellular efficiency, why do you think this is the case?

> Mutations in tRNA genes can create tRNAs that recognize stop codons. Because stop codons are sometimes called nonsense codons, these types of mutations that affect tRNAs are called nonsense suppressors. For example, a normal tRNAGly has an anticodon sequ