Base Distortions

Identify the normal functions of the following genes whose mutations are associated with the development of cancer.

APC (familial adenomatous polyposis)

253

Identify the normal functions of the following genes whose mutations are associated with the development of cancer.

Which of these genes would you classify as a proto-oncogene and which as a tumor suppressor gene? Explain your categorization for each gene.

275

Identify the normal functions of the following genes whose mutations are associated with the development of cancer.

p53 (Li–Fraumeni syndrome)

247

Identify the normal functions of the following genes whose mutations are associated with the development of cancer.

RB1 (retinoblastoma)

263

In this chapter, we focused on how gene mutations arise and how cells repair DNA damage. At the same time, we found opportunities to consider the methods and reasoning by which much of this information was acquired. From the explanations given in the chapter,

How do we know that mutations occur randomly?

440

Go online to the Online Mendelian Inheritance of Man (OMIM) website. Look up the following genetic conditions and answer the questions posed about them.

Go to the 'Molecular Genetics' section and describe the most common mutation of the CF gene.

238

Go online to the Online Mendelian Inheritance of Man (OMIM) website. Look up the following genetic conditions and answer the questions posed about them.

Look up cystic fibrosis (CF), OMIM 602421, and give the gene name and abbreviation and the chromosome location of the gene.

358

Go online to the Online Mendelian Inheritance of Man (OMIM) website. Look up the following genetic conditions and answer the questions posed about them.

Go to the 'Population Genetics' section discussing the TSD gene. In a few sentences, summarize the human population in which TSD is most frequently found and give the approximate frequency of heterozygous carriers for the TSD mutation in North American Jews.

296

Go online to the Online Mendelian Inheritance of Man (OMIM) website. Look up the following genetic conditions and answer the questions posed about them.

Look up Tay–Sachs disease (TSD), OMIM number 272800, and give the name and abbreviation of the affected gene and the chromosome location of the gene.

270

For the retinal cancer retinoblastoma, the inheritance of one mutated copy of RB1 from one of the parents is often referred to as a mutation that produces a 'dominant predisposition to cancer.' This means that the first mutation does not produce cancer but makes it very likely that cancer will develop.

Explain why cancer is almost certain to develop with the inheritance of one mutated copy of RB1.

239

When working on barley plants, two researchers independently identify a short-plant mutation and develop homozygous recessive lines of short plants. Careful measurements of the height of mutant short plants versus normal tall plants indicate that the two mutant lines have the same height. How would you determine if these two mutant lines carry mutation of the same gene or of different genes?

304

What is the difference between a transition mutation and a transversion mutation?

459

Price et al. [(1999). J. Bacteriol. 181:2358–2362] conducted a genetic study of the toxin transport protein (PA) of Bacillus anthracis, the bacterium that causes anthrax in humans. Within the 2294-nucleotide gene in 26 strains they identified five point mutations—two missense and three synonyms—among different isolates. Necropsy samples from an anthrax outbreak in 1979 revealed a novel missense mutation and five unique nucleotide changes among ten victims. The authors concluded that these data indicate little or no horizontal transfer between different B. anthracis strains.

On what basis did the authors conclude that evidence of horizontal transfer is absent from their data?

243

Price et al. [(1999). J. Bacteriol. 181:2358–2362] conducted a genetic study of the toxin transport protein (PA) of Bacillus anthracis, the bacterium that causes anthrax in humans. Within the 2294-nucleotide gene in 26 strains they identified five point mutations—two missense and three synonyms—among different isolates. Necropsy samples from an anthrax outbreak in 1979 revealed a novel missense mutation and five unique nucleotide changes among ten victims. The authors concluded that these data indicate little or no horizontal transfer between different B. anthracis strains.

Which types of nucleotide changes (missense or synonyms) cause amino acid changes?

277

Explain the following processes involving chromosome mutations and cancer development. How the chromosome mutation producing Burkitt lymphoma generates the disease.

260

Explain the following processes involving chromosome mutations and cancer development.

How the chromosome mutation producing the Philadelphia chromosome leads to CML.

266

What are the differences between a synonymous mutation, a missense mutation, and a nonsense mutation?

459

Why would a mutation in a somatic cell of a multicellular organism not necessarily result in a detectable phenotype?

409

Most mutations are thought to be deleterious. Why, then, is it reasonable to state that mutations are essential to the evolutionary process?

405

Why is a random mutation more likely to be deleterious than beneficial?

386

Most mutations in a diploid organism are recessive. Why?

451

The effect of base-pair substitution mutations on protein function varies widely from no detectable effect to the complete loss of protein function (null allele). Why do the functional consequences of base-pair substitution vary so widely?

259

When the amino acid sequences of insulin isolated from different organisms were determined, differences were noted. For example, alanine was substituted for threonine, serine for glycine, and valine for isoleucine at corresponding positions in the protein. List the single-base changes that could occur in codons of the genetic code to produce these amino acid changes.

What is the difference between a silent mutation and a neutral mutation?

485

Describe the purpose of the Ames test. How are his⁻ bacteria used in the Ames test? What mutational event is identified using his⁻ bacteria?

247

In studies of the amino acid sequence of wild-type and mutant forms of tryptophan synthetase in E. coli, the following changes have been observed: Determine a set of triplet codes in which only a single-nucleotide change produces each amino acid change.

460

In numerous population studies of spontaneous mutation, two observations are made consistently: (1) Most mutations are recessive, and (2) forward mutation is more frequent than reversion. What do you think are the likely explanations for these two observations?

258

Two different mutations are identified in a haploid strain of yeast. The first prevents the synthesis of adenine by a nonsense mutation of the ade-1 gene. In this mutation, a base-pair substitution changes a tryptophan codon (UGG) to a stop codon (UGA). The second affects one of several duplicate tRNA genes. This base-pair substitution mutation changes the anticodon sequence of a tRNAᵀʳᵖ from

3′−ACC−5′ to 3′−ACU−5′

Do you consider the first mutation to be a forward mutation or a reversion? Why?

263

Two different mutations are identified in a haploid strain of yeast. The first prevents the synthesis of adenine by a nonsense mutation of the ade-1 gene. In this mutation, a base-pair substitution changes a tryptophan codon (UGG) to a stop codon (UGA). The second affects one of several duplicate tRNA genes. This base-pair substitution mutation changes the anticodon sequence of a tRNAᵀʳᵖ from

3′−ACC−5′ to 3′−ACU−5′

Assuming there are no other mutations in the genome, will this double-mutant yeast strain be able to grow on minimal medium? If growth will occur, characterize the nature of growth relative to wild type.

277

Two different mutations are identified in a haploid strain of yeast. The first prevents the synthesis of adenine by a nonsense mutation of the ade-1 gene. In this mutation, a base-pair substitution changes a tryptophan codon (UGG) to a stop codon (UGA). The second affects one of several duplicate tRNA genes. This base-pair substitution mutation changes the anticodon sequence of a tRNAᵀʳᵖ from

3′−ACC−5′ to 3′−ACU−5′

Do you consider the second mutation to be a forward mutation or a reversion? Why?

310

Why are frameshift mutations likely to be more detrimental than point mutations, in which a single pyrimidine or purine has been substituted?

277

What is the phenotypic effect of inserting a Ds element into the maize C gene? How do Ds and Ac produce maize kernels that are mostly yellow with purple spots?

213

If you were to look up Gaucher disease on the OMIM website, you would see that there are three major types, designated Type I (OMIM 230800), Type II (OMIM 230900), and Type III (OMIM 231000). All three types are mutations of the gene for acid-β-glucosidase, encoded on chromosome 1. Different mutations of this gene produce the three types of Gaucher disease that differ somewhat in their symptoms and disease severity.

Thinking about the production or function of the acid-β-glucosidase enzyme, why do you suppose different mutations of this gene produce differences in symptoms and disease severity?

268

If you were to look up Gaucher disease on the OMIM website, you would see that there are three major types, designated Type I (OMIM 230800), Type II (OMIM 230900), and Type III (OMIM 231000). All three types are mutations of the gene for acid-β-glucosidase, encoded on chromosome 1. Different mutations of this gene produce the three types of Gaucher disease that differ somewhat in their symptoms and disease severity.

For each mutation, speculate about whether the acid-β-glucosidase enzyme is merely reduced in function or whether its production is eliminated, and explain why.

231

Why are X rays more potent mutagens than UV radiation?

351

Total cholesterol in blood is reported as the number of milligrams (mg) of cholesterol per 100 milliliters (mL) of blood. The normal range is 180–220 mg/100 mL. A gene mutation altering the function of cell-surface cholesterol receptors restricts the ability of cells to collect cholesterol from blood and draw it into cells. This defect results in elevated blood cholesterol levels. Individuals who are heterozygous for a mutant allele and a wild-type allele have levels of 300–600 mg/100 mL, and those who are homozygous for the mutation have levels of 800–1000 mg/100 mL. Identify the genetic term that best describes the inheritance of this form of elevated cholesterol level, and justify your choice.

441

Look over the 10 diseases approved for genetic health risk assessment listed in Application Chapter B. Select one disease other than the three discussed in Application Chapter B or in this chapter (alpha-1 antitrypsin deficiency, late-onset Alzheimer disease, and celiac disease) or another of the diseases of your choice. Do a brief Internet search to find and download (1) one article for a nonscientific audience identifying the gene or genes whose alleles are associated with occurrence of the disease and (2) one scientific paper that provides data supporting the association of specific alleles of the gene or genes with the disease. Write a short summary combining the information contained in the two papers.

Several types of mutation are identified and described in the chapter. These include (1) promoter mutation, (2) splice site mutation, (3) missense mutation, (4) frameshift mutation, and 5) nonsense mutation. Match the following mutation descriptions with the type(s) of mutations listed above. More than one mutation type might match a description.

A null mutation that does not produce any functional protein product.

Several types of mutation are identified and described in the chapter. These include (1) promoter mutation, (2) splice site mutation, (3) missense mutation, (4) frameshift mutation, and 5) nonsense mutation. Match the following mutation descriptions with the type(s) of mutations listed above. More than one mutation type might match a description.

A mutation that produces a protein that is shorter than the wild-type protein but does not have any amino acid changes in the portion produced.

353

Several types of mutation are identified and described in the chapter. These include (1) promoter mutation, (2) splice site mutation, (3) missense mutation, (4) frameshift mutation, and 5) nonsense mutation. Match the following mutation descriptions with the type(s) of mutations listed above. More than one mutation type might match a description.

A mutation that produces a mutant protein that differs from the wild-type protein at one amino acid position.

461

Several types of mutation are identified and described in the chapter. These include (1) promoter mutation, (2) splice site mutation, (3) missense mutation, (4) frameshift mutation, and 5) nonsense mutation. Match the following mutation descriptions with the type(s) of mutations listed above. More than one mutation type might match a description.

A mutation that produces about 5% of the wild-type amount of an mRNA.

315

Several types of mutation are identified and described in the chapter. These include (1) promoter mutation, (2) splice site mutation, (3) missense mutation, (4) frameshift mutation, and 5) nonsense mutation. Match the following mutation descriptions with the type(s) of mutations listed above. More than one mutation type might match a description.

A mutation that changes several amino acids in a protein and results in a protein that is shorter than the wild-type product.

474

A glycine residue is in position 210 of the tryptophan synthetase enzyme of wild-type E. coli. If the codon specifying glycine is GGA, how many single-base substitutions will result in an amino acid substitution at position 210? What are they? How many will result if the wild-type codon is GGU?

316

Refer to Figure 13.7 to respond to the following:

A base-substitution mutation that altered the sequence shown in part (a) eliminated the synthesis of all but one polypeptide. The altered sequence is shown here:

5'-AUGCAUACCUAUGUGACCCUUGGA-3'

Determine why.

394

Dominant mutations can be categorized according to whether they increase or decrease the overall activity of a gene or gene product. Although a loss-of-function mutation (a mutation that inactivates the gene product) is usually recessive, for some genes, one dose of the normal gene product, encoded by the normal allele, is not sufficient to produce a normal phenotype. In this case, a loss-of-function mutation in the gene will be dominant, and the gene is said to be haploinsufficient. A second category of dominant mutation is the gain-of-function mutation, which results in a new activity or increased activity or expression of a gene or gene product. The gene therapy technique currently being used in clinical trials involves the 'addition' to somatic cells of a normal copy of a gene. In other words, a normal copy of the gene is inserted into the genome of the mutant somatic cell, but the mutated copy of the gene is not removed or replaced. Will this strategy work for either of the two aforementioned types of dominant mutations?

420

A significant number of mutations in the HBB gene that cause human β-thalassemia occur within introns or in upstream noncoding sequences. Explain why mutations in these regions often lead to severe disease, although they may not directly alter the coding regions of the gene.

393

Using the adenine–thymine base pair in this DNA sequence ...GCTC... ...CGAG... Give the sequence after a transversion mutation.

301

Using the adenine–thymine base pair in this DNA sequence ...GCTC... ...CGAG... Give the sequence after a transition mutation.

266

The partial amino acid sequence of a wild-type protein is … Arg-Met-Tyr-Thr-Leu-Cys-Ser … The same portion of the protein from a mutant has the sequence … Arg-Met-Leu-Tyr-Ala-Leu-Phe … Give the sequence of the wild-type DNA template strand. Use A/G if the nucleotide could be either purine, T/C if it could be either pyrimidine, N if any nucleotide could occur at a site, or the alternative nucleotides if a purine and a pyrimidine are possible.

338

The partial amino acid sequence of a wild-type protein is … Arg-Met-Tyr-Thr-Leu-Cys-Ser … The same portion of the protein from a mutant has the sequence … Arg-Met-Leu-Tyr-Ala-Leu-Phe … Identify the type of mutation.

459

Speculate on how improved living conditions and medical care in the developed nations might affect human mutation rates, both neutral and deleterious.

343

The two DNA and polypeptide sequences shown are for alleles at a hypothetical locus that produce different polypeptides, both five amino acids long. In each case, the lower DNA strand is the template strand: allele A₁ 5′. . . ATGCATGTAAGTGCATGA. . . 3′ 3′. . . TACGTACATTCACGTACT. . . 5′ A₁ polypeptide N–Met–His–Val–Ser–Ala–C allele A₂ 5′. . . ATGCAAGTAAGTGCATGA . . . 3′ 3′. . . TACGTTCATTCACGTACT . . . 5′ A₂ polypeptide. N–Met–Gln–Val–Ser–Ala–C Based on DNA and polypeptide sequences alone, is there any way to determine which allele is dominant and which is recessive? Why or why not?

339

Many human genes are known to have homologs in the mouse genome. One approach to investigating human hereditary disease is to produce mutations of the mouse homologs of human genes by methods that can precisely target specific nucleotides for mutation. Despite the homologies that exist between human and mouse genes, some attempts to study human hereditary disease processes by inducing mutations in mouse genes indicate there is little to be learned about human disease in this way. In general terms, describe how and why the study of mouse gene mutations might fail to produce useful information about human disease processes.

315

Many human genes are known to have homologs in the mouse genome. One approach to investigating human hereditary disease is to produce mutations of the mouse homologs of human genes by methods that can precisely target specific nucleotides for mutation. Numerous studies of mutations of the mouse homologs of human genes have yielded valuable information about how gene mutations influence the human disease process. In general terms, describe how and why creating mutations of the mouse homologs can give information about human hereditary disease processes.

375

The human β-globin wild-type allele and a certain mutant allele are identical in sequence except for a single base-pair substitution that changes one nucleotide at the end of intron 2. The wild-type and mutant sequences of the affected portion of pre-mRNA are

Intron 2 Exon 3 _
wild type 5′-CCUCCCACAG CUCCUG-3′
mutant. 5′-CCUCCCACUG CUCCUG-3′

This is one example of how DNA sequence change occurring somewhere other than in an exon can produce mutation. List other kinds of DNA sequence changes occurring outside exons that can produce mutation. In each case, characterize the kind of change you would expect to see in mutant mRNA or mutant protein.

289

The human β-globin wild-type allele and a certain mutant allele are identical in sequence except for a single base-pair substitution that changes one nucleotide at the end of intron 2. The wild-type and mutant sequences of the affected portion of pre-mRNA are

Intron 2 Exon 3 _
wild type 5′-CCUCCCACAG CUCCUG-3′
mutant. 5′-CCUCCCACUG CUCCUG-3′

Speculate about the way in which this base substitution causes mutation of β-globin protein.

265

The fluctuation test performed by Luria and Delbrück is consistent with the random mutation hypothesis. Briefly describe their experiment and identify how the results match the prediction of the random mutation hypothesis. What would have to be different about the experimental results for them to agree with the prediction of the adaptive mutation hypothesis?

614

Mutations in the CFTR gene result in cystic fibrosis in humans, a condition in which abnormal secretions are present in the lungs, pancreas, and sweat glands. The gene was mapped to a 500-kb region on chromosome 7 containing three candidate genes.

How would you prove that your chosen candidate is the CFTR gene?

452

Mutations in the CFTR gene result in cystic fibrosis in humans, a condition in which abnormal secretions are present in the lungs, pancreas, and sweat glands. The gene was mapped to a 500-kb region on chromosome 7 containing three candidate genes.

Using your knowledge of the disease symptoms, how would you distinguish between the candidate genes to decide which is most likely to encode the CFTR gene?

351

In a bacterial culture in which all cells are unable to synthesize leucine (leu⁻), a potent mutagen is added, and the cells are allowed to undergo one round of replication. At that point, samples are taken, a series of dilutions are made, and the cells are plated on either minimal medium or minimal medium containing leucine. The first culture condition (minimal medium) allows the growth of only leu⁺ cells, while the second culture condition (minimal medium with leucine added) allows growth of all cells. The results of the experiment are as follows: Culture Condition Dilution Colonies Minimal medium 10⁻¹ 18 Minimal medium + leucine 10⁻⁷ 9 What is the rate of mutation at the locus associated with leucine biosynthesis?

356

In this chapter, three features of genes or of DNA sequence that contribute to the occurrence of mutational hotspots were described. Identify those three features and briefly describe why they are associated with mutational hotspots.

427

Briefly compare the production of DNA double-strand breaks in bacteria versus the double-strand breaks that precede homologous recombination.

313

Imagine yourself as one of the team of geneticists who launches a study of the genetic effects of high-energy radiation on the surviving Japanese population immediately following the atom bomb attacks at Hiroshima and Nagasaki in 1945. Demonstrate your insights into both chromosomal and gene mutation by outlining a short-term and long-term study that addresses these radiation effects. Be sure to include strategies for considering the effects on both somatic and germ-line tissues.

385

During mismatch repair, why is it necessary to distinguish between the template strand and the newly made daughter strand? Describe how this is accomplished.

342

With the knowledge that radiation causes mutations, many assume that human-made forms of radiation are the major contributors to the mutational load in humans. What evidence suggests otherwise?

320

Marfan syndrome is an autosomal dominant disorder in humans. It results from mutation of a gene on chromosome 15 that produces the connective tissue protein fibrillin. In its wild-type form, fibrillin gives connective tissues, such as cartilage, elasticity. When mutated, however, fibrillin is rigid and produces a range of phenotypic complications, including excessive growth of the long bones of the leg and arm, sunken chest, dislocation of the lens of the eye, and susceptibility to aortic aneurysm, which can lead to sudden death in some cases. Different sets of symptoms are seen among various family members, as shown in the pedigree below. Each quadrant of the circles and squares represents a different symptom, as the key indicates. All cases of Marfan syndrome are caused by mutation of the fibrillin gene, and all family members with Marfan syndrome carry the same mutant allele. What do the differences shown in the phenotypes of family members say about the expression of the mutant allele?

404

Yeast are single-celled eukaryotic organisms that grow in culture as either haploids or diploids. Diploid yeast are generated when two haploid strains fuse together. Seven haploid mutant strains of yeast exhibit similar normal growth habit at 25°C, but at 37°C, they show different growth capabilities. The table below displays the growth pattern Researchers induce fusion in pairs of haploid yeast strains (all possible combinations), and the resulting diploids are tested for their ability to grow at 37°C. The results of the growth experiment are shown below. How many different genes are mutated among these seven yeast strains? Identify the strains that represent each gene mutation.

472

Yeast are single-celled eukaryotic organisms that grow in culture as either haploids or diploids. Diploid yeast are generated when two haploid strains fuse together. Seven haploid mutant strains of yeast exhibit similar normal growth habit at 25°C, but at 37°C, they show different growth capabilities. The table below displays the growth pattern Hypothesize about the nature of the mutation affecting each of these mutant yeast strains, including why strains B and G display different growth habit at C37°C than the other strains.

258

Most organisms display a circadian rhythm, a cycling of biological processes that is roughly synchronized with day length (e.g., jet lag occurs in humans when rapid movement between time zones causes established circadian rhythms to be out of synch with daylight hours). In Drosophila, pupae eclose (emerge as adults after metamorphosis) at dawn.

In most plants, such as Arabidopsis, genes whose encoded products have roles related to photosynthesis have expression patterns that vary in a circadian manner. Using this knowledge, how would you screen for Arabidopsis mutants that have an impaired circadian rhythm?

276

Most organisms display a circadian rhythm, a cycling of biological processes that is roughly synchronized with day length (e.g., jet lag occurs in humans when rapid movement between time zones causes established circadian rhythms to be out of synch with daylight hours). In Drosophila, pupae eclose (emerge as adults after metamorphosis) at dawn.

Using this knowledge, how would you screen for Drosophila mutants that have an impaired circadian rhythm?

244

Assume that a mutation affects the gene for each of the following eukaryotic RNA polymerases. Match each mutation with the possible effects from the list provided. More than one effect is possible for each mutation.

RNA Polymerase Mutation Effect(s)
RNA pol I _______________
RNA pol II _______________
RNA pol III _______________
snRNA _______________

Ribosomal RNA is not processed.

238

Assume that a mutation affects the gene for each of the following eukaryotic RNA polymerases. Match each mutation with the possible effects from the list provided. More than one effect is possible for each mutation.

RNA Polymerase Mutation Effect(s)
RNA pol I _______________
RNA pol II _______________
RNA pol III _______________
snRNA _______________

Some tRNA is not synthesized.

300

Assume that a mutation affects the gene for each of the following eukaryotic RNA polymerases. Match each mutation with the possible effects from the list provided. More than one effect is possible for each mutation.

RNA Polymerase Mutation Effect(s)
RNA pol I _______________
RNA pol II _______________
RNA pol III _______________
snRNA _______________

Some rRNA is not synthesized.

278

Assume that a mutation affects the gene for each of the following eukaryotic RNA polymerases. Match each mutation with the possible effects from the list provided. More than one effect is possible for each mutation.

RNA Polymerase Mutation Effect(s)
RNA pol I _______________
RNA pol II _______________
RNA pol III _______________
snRNA _______________

Pre-mRNA does not have introns removed.

214

Among Betazoids in the world of Star Trek®, the ability to read minds is under the control of a gene called mindreader (abbreviated mr). Most Betazoids can read minds, but rare recessive mutations in the mr gene result in two alternative phenotypes: delayed-receivers and insensitives. Delayed-receivers have some mind-reading ability but perform the task much more slowly than normal Betazoids. Insensitives cannot read minds at all. Betazoid genes do not have introns, so the gene only contains coding DNA. It is 3332 nucleotides in length, and Betazoids use a four-letter genetic code. The following table shows some data from five unrelated mr mutations. Mutation Description of Mutation Phenotype _ mr-1 Nonsense mutation in codon 829 Delayed-receiver mr-2 Missense mutation in codon 52 Delayed-receiver mr-3 Deletion of nucleotides 83–150 Delayed-receiver mr-4 Missense mutation in codon 192 Insensitive mr-5 Deletion of nucleotides 83–93 Insensitive For each mutation, provide a plausible explanation for why it gives rise to its associated phenotype and not to the other phenotype. For example, hypothesize why the mr-1 nonsense mutation in codon 829 gives rise to the milder delayed-receiver phenotype rather than the more severe insensitive phenotype. Then repeat this type of analysis for the other mutations. (More than one explanation is possible, so be creative within plausible bounds!)

327

Assume that a mutation affects the gene for each of the following eukaryotic RNA polymerases. Match each mutation with the possible effects from the list provided. More than one effect is possible for each mutation.

RNA Polymerase Mutation Effect(s)
RNA pol I _______________
RNA pol II _______________
RNA pol III _______________
snRNA _______________

Some pre-mRNA is not synthesized.

248

Most organisms display a circadian rhythm, a cycling of biological processes that is roughly synchronized with day length (e.g., jet lag occurs in humans when rapid movement between time zones causes established circadian rhythms to be out of synch with daylight hours). In Drosophila, pupae eclose (emerge as adults after metamorphosis) at dawn. In each case, how would you clone the genes you identified by mutation?

227

Shown here are the amino acid sequences of the wild-type and three mutant forms of a short protein.
___________________________________________________
Wild-type: Met-Trp-Tyr-Arg-Gly-Ser-Pro-Thr
Mutant 1: Met-Trp
Mutant 2: Met-Trp-His-Arg-Gly-Ser-Pro-Thr
Mutant 3: Met-Cys-Ile-Val-Val-Val-Gln-His _

Use this information to answer the following questions:

Using the genetic coding dictionary, predict the type of mutation that led to each altered protein.

702

Shown below are two homologous lengths of the alpha and beta chains of human hemoglobin. Consult a genetic code dictionary (Figure 13.7), and determine how many amino acid substitutions may have occurred as a result of a single nucleotide substitution. For any that cannot occur as a result of a single change, determine the minimal mutational distance.

Alpha: ala val ala his val asp asp met pro
Beta: gly leu ala his leu asp asn leu lys

299

Mutations in the IL2RG gene cause approximately 30 percent of severe combined immunodeficiency disorder (SCID) cases in humans. These mutations result in alterations to a protein component of cytokine receptors that are essential for proper development of the immune system. The IL2RG gene is composed of eight exons and contains upstream and downstream sequences that are necessary for proper transcription and translation. Below are some of the mutations observed. For each, explain its likely influence on the IL2RG gene product (assume its length to be 375 amino acids).

Large deletion covering Exons 2 and 3

349

Mutations in the IL2RG gene cause approximately 30 percent of severe combined immunodeficiency disorder (SCID) cases in humans. These mutations result in alterations to a protein component of cytokine receptors that are essential for proper development of the immune system. The IL2RG gene is composed of eight exons and contains upstream and downstream sequences that are necessary for proper transcription and translation. Below are some of the mutations observed. For each, explain its likely influence on the IL2RG gene product (assume its length to be 375 amino acids).

Deletion in Exon 2, in frame

292

Mutations in the IL2RG gene cause approximately 30 percent of severe combined immunodeficiency disorder (SCID) cases in humans. These mutations result in alterations to a protein component of cytokine receptors that are essential for proper development of the immune system. The IL2RG gene is composed of eight exons and contains upstream and downstream sequences that are necessary for proper transcription and translation. Below are some of the mutations observed. For each, explain its likely influence on the IL2RG gene product (assume its length to be 375 amino acids).

Deletion in Exon 2, causing frameshift

311

Mutations in the IL2RG gene cause approximately 30 percent of severe combined immunodeficiency disorder (SCID) cases in humans. These mutations result in alterations to a protein component of cytokine receptors that are essential for proper development of the immune system. The IL2RG gene is composed of eight exons and contains upstream and downstream sequences that are necessary for proper transcription and translation. Below are some of the mutations observed. For each, explain its likely influence on the IL2RG gene product (assume its length to be 375 amino acids).

Missense mutation

329

Mutations in the IL2RG gene cause approximately 30 percent of severe combined immunodeficiency disorder (SCID) cases in humans. These mutations result in alterations to a protein component of cytokine receptors that are essential for proper development of the immune system. The IL2RG gene is composed of eight exons and contains upstream and downstream sequences that are necessary for proper transcription and translation. Below are some of the mutations observed. For each, explain its likely influence on the IL2RG gene product (assume its length to be 375 amino acids).

Insertion in Exon 7, causing frameshift

Mutations in the IL2RG gene cause approximately 30 percent of severe combined immunodeficiency disorder (SCID) cases in humans. These mutations result in alterations to a protein component of cytokine receptors that are essential for proper development of the immune system. The IL2RG gene is composed of eight exons and contains upstream and downstream sequences that are necessary for proper transcription and translation. Below are some of the mutations observed. For each, explain its likely influence on the IL2RG gene product (assume its length to be 375 amino acids).

Insertion in Exon 1, causing frameshift

272

Mutations in the IL2RG gene cause approximately 30 percent of severe combined immunodeficiency disorder (SCID) cases in humans. These mutations result in alterations to a protein component of cytokine receptors that are essential for proper development of the immune system. The IL2RG gene is composed of eight exons and contains upstream and downstream sequences that are necessary for proper transcription and translation. Below are some of the mutations observed. For each, explain its likely influence on the IL2RG gene product (assume its length to be 375 amino acids).

Nonsense mutation in a coding region

355

Alkaptonuria is a human autosomal recessive disorder caused by mutation of the HAO gene that encodes the enzyme homogentisic acid oxidase. A map of the HAO gene region reveals four BamHI restriction sites (B1 to B4) in the wild-type allele and three BamHI restriction sites in the mutant allele. BamHI utilizes the restriction sequence 5′-GGATCC-3′. The BamHI restriction sequence identified as B3 is altered to 5′-GGAACC-3′ in the mutant allele. The mutation results in a Ser-to-Thr missense mutation. Restriction maps of the two alleles are shown below, and the binding sites of two molecular probes (probe A and probe B) are identified. DNA samples taken from a mother (M), father (F), and two children (C1 and C2) are analyzed by Southern blotting of BamHI-digested DNA. The gel electrophoresis results are illustrated. Explain how the DNA sequence change results in a Ser-to-Thr missense mutation.

329

In an experiment employing the methods of the Ames test, two strains of Salmonella are used. Strain A contains a base-substitution mutation, and Strain B contains a frameshift mutation. Four plates are prepared to test the mutagenicity of the compound ethyl methanesulfonate (EMS). Plate 1 is a control plate with Strain A and S9 extract but no EMS. Plate 2 is also a control plate and contains Strain B and S9 extract but no EMS. Plate 3 contains Strain A along with S9 extract and EMS, and Plate 4 contains Strain B, S9 extract, and EMS. Characterize the expected distribution of colony growth on the four plates. Defend your growth prediction for each plate.

258

In an experiment employing the methods of the Ames test, two strains of Salmonella are used. Strain A contains a base-substitution mutation, and Strain B contains a frameshift mutation. Four plates are prepared to test the mutagenicity of the compound ethyl methanesulfonate (EMS). Plate 1 is a control plate with Strain A and S9 extract but no EMS. Plate 2 is also a control plate and contains Strain B and S9 extract but no EMS. Plate 3 contains Strain A along with S9 extract and EMS, and Plate 4 contains Strain B, S9 extract, and EMS. What event is being detected by growth of a colony on any of the four plates?

302

In an experiment employing the methods of the Ames test, two strains of Salmonella are used. Strain A contains a base-substitution mutation, and Strain B contains a frameshift mutation. Four plates are prepared to test the mutagenicity of the compound ethyl methanesulfonate (EMS). Plate 1 is a control plate with Strain A and S9 extract but no EMS. Plate 2 is also a control plate and contains Strain B and S9 extract but no EMS. Plate 3 contains Strain A along with S9 extract and EMS, and Plate 4 contains Strain B, S9 extract, and EMS. Why is the S9 extract added to each of the plates?

291

In an experiment employing the methods of the Ames test, two strains of Salmonella are used. Strain A contains a base-substitution mutation, and Strain B contains a frameshift mutation. Four plates are prepared to test the mutagenicity of the compound ethyl methanesulfonate (EMS). Plate 1 is a control plate with Strain A and S9 extract but no EMS. Plate 2 is also a control plate and contains Strain B and S9 extract but no EMS. Plate 3 contains Strain A along with S9 extract and EMS, and Plate 4 contains Strain B, S9 extract, and EMS. Suppose the compound being tested was proflavin instead of EMS. Would this change the Ames test results? Explain why or why not.

352

Infantile cardiomyopathy is a devastating disorder that is fatal during the first year of life due to defects in the function of heart muscles resulting from mitochondrial dysfunction. A study, performed by Götz et al. [(2011). Am. J. Hum. Genet. 88:635–642), identified two different causative mutations in the gene for mitochondrial alanyl-tRNA synthetase (mtAlaRS). One mutation changes a leucine residue at amino acid position 155 to arginine (p.Leu155Arg). The other mutation changes arginine at position 592 to tryptophan (p.Arg592Trp). The mtAlaRS enzyme has an N-terminal domain (amino acids 36–481) that catalyzes tRNA aminoacylation and an internal editing domain (amino acids 484–782) that catalyzes deacylation in the case that the tRNA is charged with the wrong amino acid. Consider the position of the disease causing missense mutations in the mtAlaRS gene in the context of the known protein domains of this enzyme. What predictions can you make about how these mutations impair protein synthesis within mitochondria in different ways?

245

Infantile cardiomyopathy is a devastating disorder that is fatal during the first year of life due to defects in the function of heart muscles resulting from mitochondrial dysfunction. A study, performed by Götz et al. [(2011). Am. J. Hum. Genet. 88:635–642), identified two different causative mutations in the gene for mitochondrial alanyl-tRNA synthetase (mtAlaRS). One mutation changes a leucine residue at amino acid position 155 to arginine (p.Leu155Arg). The other mutation changes arginine at position 592 to tryptophan (p.Arg592Trp). The mtAlaRS enzyme has an N-terminal domain (amino acids 36–481) that catalyzes tRNA aminoacylation and an internal editing domain (amino acids 484–782) that catalyzes deacylation in the case that the tRNA is charged with the wrong amino acid.

Which mutation would you predict has a more severe impairment of translation in mitochondria, and why?

310

Base-substitution mutations often change the amino acid specified by a codon. For each of the amino acid changes listed, determine which ones can result from a one–base-pair substitution. For those that can result from a one–base-pair substitution, give the possible wild-type and mutant codons, listing multiple possibilities if there is more than one option. (Use either Figure 9.13 or the genetic code in Table A to help solve this problem).

Wild-type Mutant
a. Ser Ala
b. Cys Ser
c. Pro Glu
d. Lys Stop
e. Met His
f. Met Ile

581

The two gels illustrated contain dideoxynucleotide DNA-sequencing information for a wild-type segment and mutant segment of DNA corresponding to the N-terminal end of a protein. The start codon and the next five codons are sequenced.

What is the cause of the mutation?

234

Multiple Choice

A mutation occurred that changed the sequence 5' AAGCTTGC 3' to 5' AAGCTTTGC 3'. What is the name for this type of mutation?

Which of the following mutations changes one codon to a chemically different amino acid?

532