Genetics Ch. 19

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

A. Nitrous acid causes A→G and C→T mutations, which are transition mutations. B. 5-bromouracil causes G→A mutations, which are transitions. C. Proflavin causes small additions or deletions, which may result in frameshift mutations.

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

Nucleotide excision repair or homologous recombination repair could fix this damage.

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

Random mutations are more likely to be harmful than beneficial. The genes within each species have evolved to work properly. They have functional promoters, coding sequences, terminators, and so on, that allow the genes to be expressed. Mutations are more likely to disrupt these sequences. For example, mutations within the coding sequence may produce early stop codons, frameshift mutations, and missense mutations that result in a nonfunctional polypeptide. On rare occasions, however, mutations are beneficial; they may produce a gene that is expressed better than the original gene or produce a polypeptide that functions better.

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

Anticipation means that the TNRE expands even further in future generations. Anticipation may depend on the sex of the parent with the TNRE.

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?

Nonsense and frameshift mutations would be most likely to disrupt protein function. A nonsense mutation would cause the protein to be much shorter and a frameshift mutation would alter the amino acid sequence downstream from the mutation. A missense mutation only affects a single amino acid, so it is less likely to disrupt protein function, but it could alter a protein's function if it occurred in an important region of the protein. A silent mutation would not alter protein function.

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

One possibility is that a translocation may move a gene next to a heterochromatic region of another chromosome and thereby diminish its expression or the gene might be moved next to a euchromatic region and increase its expression. Another possibility is that the translocation breakpoint may move the gene next to a different promoter or regulatory sequences that may then influence the gene's expression.

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.

The X rays did not produce a mutation, because a mutation is a heritable change in the genetic material. In this case, the X rays have killed the cell, so changes in DNA structure cannot be passed from cell to cell or from parent to offspring.

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

A suppressor mutation suppresses the phenotypic effects of some other mutation. Intragenic suppressors are within the same gene as the first mutation. Intergenic suppressors are in another gene.

A segment of DNA has the following sequence: TTGGATGCTG AACCTACGAC What would the sequence be immediately after reaction with nitrous acid? Let the letters H represent hypoxanthine and U represent uracil. Let's suppose this DNA was reacted with nitrous acid. The nitrous acid was then removed, and the DNA was replicated for two generations. What would be the sequences of the DNA products after the DNA had replicated two times? (Note: Hypoxanthine pairs with cytosine.) Your answer should contain the sequences of four double helices.

A. TTGGHTGUTGG HHUUTHUGHUU First round of replication TTGGHTGUTGG CCAAACACCAA AACCCACAACC HHUUTHUGHUU Second round of replication B. TTGGHTGUTGG TTGGGTGTTGG AACCCACAACC AACCCACAACC CCAAACACCAA CCAAACACCAA GGTTTGTGGTT HHUUTHUGHUU

Which of the following mutations could be appropriately described as a position effect? A point mutation at the -10 position in the promoter region prevents transcription. A translocation places the coding sequence for a muscle-specific gene next to an enhancer that is turned on in nerve cells. An inversion flips a gene from the long arm of chromosome 17 (which is euchromatic) to the short arm (which is heterochromatic).

A. No, the position (i.e., chromosomal location) of a gene has not been altered. B. Yes, the expression of a gene has been altered because it has been moved to a new chromosomal location. C. Yes, the expression of a gene has been altered because it has been moved to a new chromosomal location.

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 changes codon 50 from an alanine codon to a threonine codon, is able to restore function. Is each of the following terms appropriate or inappropriate to describe this second mutation? Reversion Intragenic suppressor Intergenic suppressor Missense mutation

A. Not appropriate, because the second mutation is at a different codon. B. Appropriate. C. Not appropriate, because the second mutation is in the same gene as the first mutation. D. Appropriate.

Are mutations random events? Explain your answer.

According to random mutation theory, spontaneous mutations can occur in any gene and do not involve exposure of the organism to a particular environment that selects for specific types of mutation. However, the structure of chromatin may cause certain regions of the DNA to be more susceptible to random mutations. For example, DNA in an open conformation may be more accessible to mutagens and more likely to incur mutations. Similarly, hot spots—certain regions of a gene that are more likely to mutate than other regions—can occur within a single gene. Also, another reason that some genes mutate at a higher rate is that some genes are larger than others, which provides a greater chance of mutation.

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?

During TNRE, a trinucleotide repeat sequence gets longer. If someone was mildly affected with a TNRE disorder, he or she might be concerned that an expansion of the repeat might occur during gamete formation, yielding offspring more severely affected with the disorder, a phenomenon called anticipation. This phenomenon may depend on the sex of the parent with the TNRE.

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 used to describe this type of mutation.

It is a gene mutation, a point mutation, a base substitution, a transition mutation, a deleterious mutation, a mutant allele, a nonsense mutation, a conditional mutation, and a temperature-sensitive lethal mutation.

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

Nitrous acid can change a cytosine to uracil. Excision repair systems could remove the defect and replace it with the correct base.

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

The mutation rate is the number of new mutations per gene per generation. The mutation frequency is the number of copies of a mutant gene within a population, divided by the total number of copies (mutant and nonmutant) of that gene. The mutation frequency may be much higher than the mutation rate if new mutations accumulate within a population over the course of many generations.

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

When cells from a master plate were replica plated onto two plates containing selective media with the T1 phage, T1-resistant colonies were observed at the same locations on both plates. These results indicate that the mutations occurred randomly while on the master plate (in the absence of T1) rather than occurring as a result of exposure to T1. In other words, mutations are random events and selective conditions may promote the survival of mutant strains that occur randomly.

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.

Yes, a person with cancer is a genetic mosaic. The cancerous tissue contains gene mutations that are not found in noncancerous cells of the body.

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

A. A nonsense mutation would probably inhibit protein function, particularly if it was not near the end of the coding sequence. B. A missense mutation may or may not affect protein function, depending on the nature of the amino acid substitution and whether the substitution is in a critical region of the protein. C. An up promoter mutation would increase the amount of functional protein. D. This mutation may affect protein function if the alteration in splicing changes an exon in the mRNA that results in a protein with a perturbed structure.

Which of the following examples is likely to be caused by a somatic mutation? A purple flower has a small patch of white tissue. One child, in a family of seven, is an albino. One apple tree, in a very large orchard, produces its apples 2 weeks earlier than any of the other trees. A 60-year-old smoker develops lung cancer.

A. Yes B. No, the albino trait affects the entire individual. C. No, the early apple-producing trait affects the entire tree. D. Yes

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.) 5′-GAACTAGATAC-3′ 5′-GGACTAGAGAC-3′ 5′-GGACTAGTAC-3′ 5′-GGAGTAGATAC-3′

A. G→A, which is a transition. B. T→G, which is a transversion. C. A single-nucleotide deletion. D. C→G, which is a transversion.

How would nucleotide excision repair be affected if one of the following proteins was missing? Describe the condition of the DNA if the repair was attempted in the absence of the protein. UvrA UvrC UvrD DNA polymerase

A. If UvrA was missing, the repair system would not be able to identify a damaged DNA segment. B. If UvrC was missing, the repair system could identify the damaged segment, but it would be unable to make cuts in the damaged DNA strand. C. If UvrD was missing, the repair system could identify the damaged segment and make cuts in the damaged strand, but it could not unwind the damaged and undamaged strands and thereby remove the damaged segment. D. If DNA polymerase was missing, the repair system could identify the damaged segment, make cuts in the damaged strand, and unwind the damaged and undamaged strands to remove the damaged segment, but it could not synthesize a complementary DNA strand using the undamaged strands as a template.

Three common ways to repair changes in DNA structure are nucleotide excision repair, mismatch repair, and homologous Page 490 recombination repair. Which of these three mechanisms would be used to fix the following types of DNA changes? A change in the structure of a base caused by a mutagen in a nondividing eukaryotic cell A change in DNA sequence caused by a mistake made by DNA polymerase A thymine dimer in the DNA of an actively dividing bacterial cell

A. Nucleotide excision repair B. Mismatch repair C. Recombinational repair and nucleotide excision repair

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.

Haploid cells are more sensitive to mutation because they have only a single copy of each gene. Therefore, recessive mutations that inhibit cell growth are easily detected. In diploid cells, it would take a mutation in both copies of the same gene to detect its phenotypic effects.

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

If a mutation within the germ line is passed to an offspring, all of the cells of the offspring's body will carry the mutation. A somatic mutation affects only the somatic cell in which it originated and all of the daughter cells that the somatic cell produces. If a somatic mutation occurs early during embryonic development, it may affect a fairly large region of the organism. Because germ-line mutations affect the entire organism, they are potentially more harmful (or beneficial), but this is not always the case. Somatic mutations can cause quite harmful effects such as cancer.

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

Mismatch repair is aimed at eliminating mismatches that may have occurred during DNA replication. In such a case, the wrong base is in the newly made strand. The binding of MutH, which occurs on a hemimethylated sequence, provides a sensing mechanism to distinguish between the unmethylated and methylated strands. In other words, MutH binds to the hemimethylated DNA in a way that allows the mismatch repair system to distinguish which strand is methylated and which is not.

When DNA N-glycosylase recognizes a thymine dimer, it detects only the thymine located on the 5′ side of the dimer as being abnormal. Make a drawing and explain the steps whereby a thymine dimer is repaired by the consecutive actions of DNA N-glycosylase, AP endonuclease, and DNA polymerase.

The DNA N-glycosylase would first make a cut between the base and the sugar. This would release the thymine base from the nucleotide to which it was directly attached, but the thymine would still be connected to the adjacent (3') thymine. AP endonuclease would then make a nick in this DNA strand, and DNA polymerase would remove the abnormal region and at the same time replace it with normal nucleotides (a process called nick translation). Finally, the strand would be sealed by DNA ligase.

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

A spontaneous mutation originates within a living cell. It may be due to spontaneous changes in nucleotide structure, errors in DNA replication, or products of normal metabolism that may alter the structure of DNA. The causes of induced mutations originate from outside the cell. They may be physical agents, such as UV light or X rays, or chemicals that act as mutagens. Both spontaneous and induced mutations may cause a harmful phenotype such as a cancer. In many cases, induced mutations are avoidable if the individual can prevent exposure to the environmental agent that acts as a mutagen.

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

A thymine dimer can interfere with DNA replication because DNA polymerase cannot slide past the dimer and add bases to the newly growing strand. Alkylating mutagens such as nitrous acid will cause mistakes in the base pairing during DNA replication. For example, an alkylated cytosine will base pair with adenine, thereby creating a mutation in the newly made strand. A third example of a mutagen that can interfere with DNA replication is 5-bromouracil, which is a thymine analogue. It may base pair with guanine instead of adenine during DNA replication.

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.) 5′-ATGGGTCTAGATACC-3′ 5′-ATGCGACTAGATACC-3′ 5′-ATGGGACTAGTTACC-3′ 5′-ATGGGACTAAGATACC-3′

A. Silent, because the same amino acid (glycine) is encoded by GGA and GGT. B. Missense, because a different amino acid is encoded by CGA compared to GGA. C. Missense, because a different amino acid is encoded by GTT compared to GAT. D. Frameshift, because an extra base is inserted into the sequence.

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 producing a glutamine stretch, are the following statements true or false? The TNRE is within the coding sequence of the gene. The TNRE prevents RNA polymerase from transcribing the gene properly. The trinucleotide sequence is CAG. The trinucleotide sequence is CCG.

A. True B. False; the TNRE is not within the promoter, it is within the coding sequence. C. True; CAG is a codon for glutamine. D. False; CCG is a codon for proline.

With regard to the repair of double-strand breaks, what are the advantages and disadvantages of homologous recombination repair versus nonhomologous end joining?

Because sister chromatids are genetically identical, an advantage of homologous recombination is that it can be an error-free mechanism to repair a double-stranded break. A disadvantage, however, is that HRR occurs only during the S and G2 phases of the cell cycle in eukaryotes or following DNA replication in bacteria. An advantage of nonhomologous end joining is that it doesn't involve the participation of a sister chromatid, so it can occur at any stage of the cell cycle. However, a disadvantage is that NHEJ can result in small deletions in the region that has been repaired. Overall, NHEJ is a quick but error-prone repair mechanism, while HRR is a more accurate method of repair that is limited to certain stages of the cell cycle.

Discuss the similarities and differences between nucleotide excision repair and the mismatch repair system.

Both types of repair systems recognize an abnormality in the DNA and excise the abnormal strand. The normal strand is then used as a template to synthesize a complementary strand of DNA. The systems differ in the types of abnormalities they detect. The mismatch repair system detects base pair mismatches, while the excision repair system recognizes thymine dimers, chemically modified bases, missing bases, and certain types of crosslinks. The mismatch repair system operates immediately after DNA replication, allowing it to distinguish between the daughter strand (which contains the wrong base) and the parental strand. The excision repair system can operate at any time in the cell cycle.

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 expression.

Here are two possible examples: The consensus sequences for many bacterial promoters are -35: 5'-TTGACA-3' and -10: 5'-TATAAT-3'. Most mutations that alter the consensus sequences would be expected to decrease the rate of transcription. For example, a mutation that changed the -35 region to 5'-GAGACA-3' would decrease transcription. The sequence 5'-TGACGTCA-3' is recognized by the CREB transcription factor. If this sequence was changed to 5'-TGAGGTCA-3' the CREB protein would not recognize it very well and the adjacent gene would not be regulated properly in the presence of cAMP.

An individual carries a somatic mutation that changes a lysine codon into a glutamic acid codon. Prior to acquiring this mutation, the individual had been exposed to UV light, proflavin, and 5-bromouracil. Which of these three agents would be the most likely to have caused this somatic mutation? Explain your answer.

The answer is 5-bromouracil. If this chemical is incorporated into DNA, it can change an AT base pair into a CG base pair. A lysine codon, AAG, could be changed into a glutamic acid codon, CAG, with this chemical. By comparison, UV light is expected to produce thymine dimers, which would not lead to a mutation creating a glutamic acid codon, and proflavin is expected to cause a frameshift mutation.

In the treatment of cancer, the basis for many types of chemotherapy and radiation therapy is that mutagens are more effective at killing dividing cells than nondividing cells. Explain why. What are possible harmful side effects of chemotherapy and radiation therapy?

The effects of mutations are cumulative. If one mutation occurs in a cell, this mutation will be passed to the daughter cells. If a mutation then occurs in a daughter cell, there will be two mutations. These two mutations will be passed to the next generation of daughter cells, and so forth. The accumulation of many mutations eventually kills the cells. That is why mutagens are more effective at killing dividing cells compared to nondividing cells. It is because the number of mutations accumulates to a lethal level. There are two main side effects to this type of treatment. First, some normal (noncancerous) cells of the body, particularly skin cells and intestinal cells, are actively dividing. These cells are also killed by chemotherapy and radiation therapy. Secondly, it is possible that the therapy may produce mutations that will cause noncancerous cells to become cancerous. For these reasons, there is a maximal dose of chemotherapy or radiation therapy that is recommended.

In E. coli, a methyltransferase enzyme encoded by the dam gene recognizes the sequence 5′-GATC-3′ and attaches a methyl group to the nitrogen at position 6 of adenine. E. coli strains that have the dam gene deleted are known to have a higher spontaneous mutation rate than normal strains. Explain why.

The mismatch repair system, which detects mistakes made by DNA polymerase, would not function properly. As described in Figure 19.20, the MutH protein recognizes the sequence GATC when it is hemimethylated. If an E. coli strain was missing the dam methylase, this sequence would not be methylated, and MutH could not bind there. Therefore, mistakes, involving base pair mismatches caused by DNA polymerase, would not be repaired. This would increase the spontaneous mutation rate in this strain.

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 achondroplasia. The remaining babies had two unaffected parents. What is the mutation frequency for this disorder among these 1,422,000 babies? What is the mutation rate for achondroplasia?

The mutation frequency is the total number of mutant alleles divided by the total number of alleles in the population. In this case, if there are 1,422,000 babies, there are 2,844,000 copies of this gene (because each baby has 2 copies). The mutation frequency is 31/2,844,000, which equals 1.09 × 10-5. The mutation rate is the number of new mutations per generation. There are 13 babies who did not have a parent with achondroplasia; thus, thirteen is the number of new mutations. Because the mutation rate is calculated as the number of new mutations in a given gene per generation, you divide 13 by 2,844,000. In this case, the mutation rate is 4.6 × 10-6.

What are the two main mechanisms by which cells repair double-strand breaks? Briefly describe each one.

The two main mechanisms by which cells can repair DSBs are homologous recombination (HR) and nonhomologous end joining (NHEJ). In homologous recombination a segment of an undamaged sister chromatid is used as a template to repair a DSB in the damaged sister chromatid. The steps in this repair mechanism are shown in Figure 19.21. During nonhomologous end joining, the two broken ends of DNA are simply pieced back together (see Figure 19.22).

What is the underlying genetic defect that causes xeroderma pigmentosum? How can the symptoms of this disease be explained by the genetic defect?

The underlying genetic defect that causes xeroderma pigmentosum is a defect in one of the genes that encode a polypeptide involved with nucleotide excision repair. Individuals with XP thus have a deficiency in repairing DNA abnormalities, such as thymine dimers and abnormal bases. Therefore, they are very sensitive to environmental agents such as UV light, which is more likely to cause mutations in these people compared to unaffected individuals. For this reason, people with XP develop pigmentation abnormalities and premalignant lesions, and have a high predisposition to skin cancer.

Outline how you would use the technique of replica plating to show that antibiotic resistance is due to random mutations.

To show that antibiotic resistance is due to random mutation, you could follow the same basic strategy shown in Figure 19.6 except the secondary plates would contain the antibiotic instead of T1 phage. If the antibiotic resistance arose as a result of random mutation on the master plate, you would expect the antibiotic-resistant colonies to appear at the same locations on two different secondary plates.