HOW GENES AND GENOMES EVOLVE

Generating Genetic Variation

9-1 Which of the following statements is false?

(a) A mutation that arises in a mother’s somatic cell often causes a disease in her daughter.

(b) All mutations in an asexually reproducing single-celled organism are passed on to progeny.

(c) In an evolutionary sense, somatic cells exist only to help propagate germ-line cells.

(d) A mutation is passed on to offspring only if it is present in the germ line.

9-2 Your friend works in a lab that is studying why a particular mutant strain of Drosophila grows an eye on its wing. Your friend discovers that this mutant strain of Drosophila is expressing a transcription factor incorrectly. In the mutant Drosophila, this transcription factor, which is normally expressed in the primordial eye tissue, is now misexpressed in the wing primordial wing tissue, thus turning on transcription of the set of genes required to produce an eye in the wing primordial tissue. If this hypothesis is true, which of the following types of genetic change would most likely lead to this situation?

(a) a mutation within the transcription factor gene that leads to a premature stop codon after the third amino acid

(b) a mutation within the transcription factor gene that leads to a substitution of a positively charged amino acid for a negatively charged amino acid

(c) a mutation within an upstream enhancer of the gene

(d) a mutation in the TATA box of the gene

9-3 Match the type of phenotypic change below with the type of genetic change most likely to cause it. Each type of genetic change may be used more than once, or may not be used at all.

Phenotypic changes:

1. A protein normally localized in the nucleus is now localized in the cytoplasm. _________

2. A protein acquires a DNA binding domain. _________

3. Tandem copies of a gene are found in the genome. _________

4. A copy of a bacterial gene is now found integrated on a human chromosome. _________

5. A protein becomes much more unstable. _________

6. A protein normally expressed only in the liver is now expressed in blood cells. _________

Types of genetic change:

A. mutation within a gene

B. gene duplication

C. mutation in a regulatory region

D. exon shuffling

E. horizontal gene transfer

9-4 For each of the following sentences, fill in the blanks with the best word or phrase in the list below. Not all words or phrases will be used; use each word or phrase only once.

Sexual reproduction in a multicellular organism involves specialized reproductive cells, called __________________s, which come together to form a __________________ that will divide to produce both reproductive and __________________ cells. A point mutation in the DNA is considered a __________________ mutation if it changes a nucleotide that leads to no phenotypic consequence; a point mutation is considered __________________ if it changes a nucleotide within a gene and causes the protein to be non-functional.

common somatic

gamete neutral

homologous intron

deleterious cellulose

unequal zygote

9-5 Transposable elements litter the genomes of primates, and a few of them are still capable of moving to new regions of the genome. If a transposable element jumped into an important gene in one of your cells when you were a baby and caused a disease, is it likely that your child would also have the disease? Explain.

9-6 What is the most likely explanation of why the overall mutation rates in bacteria and in humans are roughly similar?

(a) Cell division needs to be fast.

(b) Most mutations are silent.

(c) There is a narrow range of mutation rates that offers an optimal balance between keeping the genome stable and generating sufficient diversity in a population.

(d) It benefits a multicellular organism to have some variability among its cells.

9-7 For each statement below, indicate whether it is true or false and explain why.

A. To meet a challenge or develop a new function, evolution essentially builds from first principles, designing from scratch, to find the best possible solution.

B. Nearly every instance of DNA duplication leads to a new functional gene.

C. A pseudogene is very similar to a functional gene but cannot be expressed because of mutations.

D. Most genes in vertebrates are unique, and only a few genes are members of multigene families.

E. Horizontal transfer is very rare and thus has had little influence on the genomes of bacteria.

9-8 Two individuals are represented in each choice in Figure Q9-8; individual 1 is one of the parents of individual 2. The asterisk seen in each choice indicates the occurrence of a single mutation during the cell division. Which of the choices in Figure Q9-8 will lead to a mutation in every cell of the individual in which the original mutation occurred?

Figure Q9-8

9-9 Two individuals are represented in Figure Q9-9; individual 1 is one of the parents of individual 2. The asterisk indicates the occurrence of a single mutation.

Figure Q9-9

What is the chance that individual 2 will inherit the mutation in individual 1?

(a) 100%

(b) 50%

(c) 1 in 100,000

(d) none

9-10 Consider a gene with a particular function. Mutation X and mutation Y each cause defects in the function of the encoded protein, yet a gene containing both mutations X and Y encodes a protein that works even better than the original protein. The odds are exceedingly small that a single mutational event will generate both mutations X and Y. Explain a simple way that an organism with a mutant gene containing both mutations X and Y could arise during evolution.

9-11 For each of the following sentences, fill in the blanks with the best word or phrase in the list below. Not all words or phrases will be used; use each word or phrase only once.

Most variation between individual humans is in the form of __________________. __________________ may arise by recombination within introns and can create proteins with novel combinations of domains. Scientists and government regulators must be very careful when introducing herbicide-resistant transgenic corn plants into the environment, because if resistant weeds arise from __________________ then the herbicides could become useless. Families of related genes can arise from a single ancestral copy by __________________ and subsequent __________________.

divergence purifying selection

exon shuffling single-nucleotide polymorphisms

gene duplication synteny

horizontal gene transfer unequal crossing-over

9-12 Figure Q9-12 shows an experiment used to determine the spontaneous mutation rate in E. coli. If the spontaneous mutation rate in E. coli is 1 mistake in every 10⁹ nucleotides copied, about how many colonies would you expect to see on the plates lacking histidine if you were to assay 10¹¹cells from the culture for their ability to form colonies?

Figure Q9-12

(a) 1

(b) 2

(c) 10

(d) 100

9-13 The spontaneous mutation rate in E. coli was determined by performing assays to test for the frequency of an AT to GC change. These assays were performed using E. coli that started out unable to produce histidine (His^–) because of an inserted UGA stop codon that disrupted the region coding for an enzyme required to produce histidine. When a spontaneous mutation arose that enabled the UGA stop codon to code for tryptophan, the E. coli cells were then able to produce the enzyme required for histidine production. Would you expect a change in the spontaneous mutation rate of 1 mistake every 10⁹ nucleotides copied if reversion of the stop codon to cysteine (instead of tryptophan) could cause the bacteria to produce histidine? Explain. (The codon table is shown in Figure Q9-13 to help you answer this question.)

Figure Q9-13

9-14 Which of the following changes is least likely to arise from a point mutation in a regulatory region of a gene?

(a) a mutation that changes the time in an organism’s life during which a protein is expressed

(b) a mutation that eliminates the production of a protein in a specific cell type

(c) a mutation that changes the subcellular localization of a protein

(d) a mutation that increases the level of protein production in a cell

9-15 Which of the following statements about gene families is false?

(a) Because gene duplication can occur when crossover events occur, genes are always duplicated onto homologous chromosomes.

(b) Not all duplicated genes will become functional members of gene families.

(c) Whole genome duplication can contribute to the formation of gene families.

(d) Duplicated genes can diverge in both their regulatory regions and their coding regions.

9-16 Figure Q9-16 shows the evolutionary history of the globin gene family members.

Figure Q9-16

Given this information, which of the following statements is true?

(a) The ancestral globin gene arose 500 million years ago.

(b) The ?-globin gene is more closely related to the ?-globin gene than to the?-globin gene.

(c) The nucleotide sequences of the two ?-globins will be most similar because they are the closest together on the chromosome.

(d) The fetal ?-globins arose from a gene duplication that occurred 200 million years ago, which gave rise to a ?-globin expressed in the fetus and a ?-globin expressed in the adult.

9-17 Panels (A) and (B) of Figure Q9-17 show substrates of exon shuffling and the outcome of exon shuffling after recombination. Horizontal lines and small filled circles represent chromosomes and centromeres, respectively. Exons are labeled A, B, C, and D. Homologous recombination or shuffling may take place at short, repeated homologous DNA sequences in introns; because DNA sequences have a polarity, the repeated sequences can be considered to have a head and a tail and thus are drawn as arrows. A large X represents a recombinational crossover. Panel (A) shows that recombination between two direct repeats located on opposite sides of the centromere yields one circular product that contains a centromere and a second product that lacks a centromere and will therefore be lost when the cell divides. Panel (B) shows that recombination between inverted repeats flanking the centromere will keep the rearranged chromosome intact. Draw the products of recombination when the repeated sequences are located on different chromosomes, as shown in panels (C) and (D). Will these products be faithfully transmitted during cell division?

Figure Q9-17

9-18 Which of the following would contribute most to successful exon shuffling?

(a) shorter introns

(b) a haploid genome

(c) exons that code for more than one protein domain

(d) introns that contain regions of similarity to one another

Reconstructing Life’s Family Tree

9-19 Which of the following statements is true?

(a) The intron structure of most genes is conserved among vertebrates.

(b) The more nucleotides there are in an organism’s genome, the more genes there will be in its genome.

(c) Because the fly Drosophila melanogaster and humans diverged from a common ancestor so long ago, a gene in the fly will show more similarity to another gene from the same species than it will to a human gene.

(d) An organism from the same Order will be more likely to have genomes of the same size than will a more evolutionarily diverged animal.

9-20 Given the evolutionary relationship between higher primates shown in Figure Q9-20, which of the following statements is false?

Figure Q9-20

(a) The last common ancestor of humans, chimpanzees, gorillas, and orangutans lived about 14 million years ago.

(b) Chimpanzees are more closely related to gorillas than to humans.

(c) Humans and chimpanzees diverged about 6 million years ago.

(d) Orangutans are the most divergent of the four species shown in Fig. Q9-20.

9-21 In humans and in chimpanzees, 99% of the Alu retrotransposons are in corresponding positions. Which of the following statements below is the most likely explanation for this similarity?

(a) The Alu retrotransposon is not capable of transposition in humans.

(b) Most of the Alu sequences in the chimpanzee genome underwent duplication and divergence before humans and chimpanzees diverged.

(c) The Alu retrotransposons are in the most beneficial position in the genome for primates.

(d) The Alu retrotransposons must also be in the same position in flies.

9-22 You are interested in finding out how the budding yeast Saccharomyces cerevisiae is so good at making bread and have collected five new related species from the wild. You sequence the genomes of all of these new species and also consult with a fungal biologist to help you construct the phylogenetic tree shown in Figure Q9-22. You find that species V, W, and X make pretty good bread whereas species Y and Z do not, suggesting that the last common ancestor of species X and S. cerevisiae may have the genes necessary for making good bread. You compare the gene sequences of species X and S. cerevisiae and find many identical coding sequences, but you also identify nucleotides that differ between the two species. Which species would be the best to examine to determine what the sequence was in the last common ancestor of species X and S. cerevisiae?

Figure Q9-22

(a) species V

(b) species W

(c) species Y

(d) species Z

9-23 Which of the following statements is false?

(a) The human genome is more similar to the orangutan genome than it is to the mouse genome.

(b) A comparison of genomes shows that 90% of the human genome shares regions of conserved synteny with the mouse genome.

(c) Primates, dogs, mice, and chickens all have about the same number of genes.

(d) Genes that code for ribosomal RNA share significant similarity in all eucaryotes but are much more difficult to recognize in archaea.

9-24 The puffer fish, Fugu rubripes, has a genome that is one-tenth the size of mammalian genomes. Which of the following statements is not a possible reason for this size difference?

(a) Intron sequences in Fugu are shorter than those in mammals.

(b) Fugu lacks the repetitive DNA found in mammals.

(c) The Fugu genome seems to have lost sequences faster than it has gained sequences over evolutionary time.

(d) Fugu has lost many genes that are part of gene families.

9-25 Which of the following regions of the genome is the least likely to be conserved over evolutionary time?

(a) the upstream regulatory region of a gene that encodes the region conferring tissue specificity

(b) the upstream regulatory region of a gene that binds to RNA polymerase

(c) the portion of the genome that codes for proteins

(d) the portion of the genome that codes for RNAs that are not translated into protein

9-26 The evolutionary relationships between seven different species, G, H, J, K, L, M, and N are diagrammed in Figure Q9-26.

Figure Q9-26

Given this information, which of the following statements is false?

(a) These are all highly related species, because the sequence divergence between the most divergent species is 3%.

(b) Species M is just as related to species G as it is to species J.

(c) Species N is more closely related to the last common ancestor of all of these species than to any of the other species shown in the diagram.

(d) Species G and H are as closely related to each other as species J and K are to each other.

9-27 You are working in a human genetics laboratory that studies causes and treatments for eye cataracts in newborns. This disease is thought to be caused by a deficiency in the enzyme galactokinase, but the human gene that encodes this enzyme has not yet been identified. At a talk by a visiting scientist, you learn about a strain of baker’s yeast that contains a mutation called gal1^– in its galactokinase gene. Because this gene is needed to metabolize galactose, the mutant strain cannot grow in galactose medium. Knowing that all living things evolved from a common ancestor and that distantly related organisms often have homologous genes that perform similar functions, you wonder whether the human galactokinase gene can function in yeast. Because you have an optimistic temperament, you decide to pursue this line of experimentation. You isolate mRNA gene transcripts from human cells, use reverse transcriptase to make complementary DNA (cDNA) copies of the mRNA molecules, and ligate the cDNAs into circular plasmid DNA molecules that can be stably propagated in yeast cells. You then transform the pool of plasmids into gal1^– yeast cells so that each cell receives a single plasmid. What will happen when you spread the plasmid-containing cells on Petri dishes that contain galactose as a carbon source? How can this approach help you find the human gene encoding galactokinase?

9-28 A. When a mutation arises, it can have three possible consequences: beneficial to the individual, selectively neutral, or detrimental. Order these from most likely to least likely.

B. The spread of a mutation in subsequent generations will, of course, depend on its consequences to individuals that inherit it. Order the three possibilities in part A to indicate which is most likely to spread and become over-represented in subsequent generations, and which is most likely to become under-represented or disappear from the population.

9-29 Some types of gene are more highly conserved than others. For each of the following pairs of gene functions, choose the one that is more likely to be highly conserved.

A. genes involved in sexual reproduction / genes involved in sugar metabolism

B. DNA replication / developmental pathways

C. hormone production / lipid synthesis

9-30 Figure Q9-30 shows a hypothetical phylogenetic tree. Use this tree to answer the following questions.

Figure Q9-30

A. How many years ago did species M and N diverge from their last common ancestor?

B. How much nucleotide divergence is there on average between species M and N?

C. Are species M and N more or less closely related to each other than species P and S are?

D. In looking for functionally important nucleotide sequences, is it more informative to compare the genome sequences of species M and N or those of species M and Q?

9-31 For each statement below, indicate whether it is true or false and explain why.

A. All highly conserved stretches of DNA in the genome are transcribed into RNA.

B. To find functionally important regions of the genome, it is more useful to compare species whose last common ancestor lived 100 million years ago rather than 5 million years ago.

C. Most mutations and genome alterations have neutral consequences.

D. Proteins required for growth, metabolism, and cell division are more highly conserved than those involved in development and in response to the environment.

E. Introns and transposons tend to slow the evolution of new genes.

9-32 Your friend has sequenced the genome of her favorite experimental organism, a kind of yeast. She wants to identify the locations of all the genes in this genome. To aid her search, she collaborates with another researcher, one who has sequenced the genome of a distantly related yeast species. Luckily, the absence of introns simplifies the effort. She and her collaborator use a computer program to align similar stretches of DNA sequence from the two genomes. The program yields the graphical output shown in Figure Q9-32, where the horizontal lines represent a portion of the two genomic sequences and vertical lines indicate where the sequences differ. (No vertical line means that the sequence is identical in the two yeasts.) Label both the functionally conserved regions and the divergent (nonconserved) sequences. Are all of the functionally conserved regions likely to be transcribed into RNA? If not, what might be the function of the nontranscribed conserved regions?

Figure Q9-32

9-33 The genomes of some vertebrates are much smaller than those of others. For example, the genome of the puffer fish Fugu is much smaller than the human genome, and even much smaller than those of other fish, primarily because of the small size of its introns.

A. Describe a mechanism that might drive evolution toward small introns or loss of introns and could therefore account for the evolutionary loss of introns according to the “introns early” hypothesis.

B. Describe a mechanism that might drive evolution toward more or larger introns and could thereby account for the evolutionary appearance of introns according to the “introns late” hypothesis.

9-34 It is thought that all eucaryotes all have about 300 genes in common. Would you predict that these genes would be used at different times during the life cycle of multicellular animals? Explain your answer.

9-35 Which of the following functions do you not expect to find in the set of genes found in all organisms on Earth?

(a) DNA replication

(b) DNA repair

(c) protein production

(d) RNA splicing

9-36 Which of the following generalities about genomes is true?

(a) All vertebrate genomes contain roughly the same number of genes.

(b) All unicellular organisms contain roughly the same number of genes.

(c) The larger an organism, the more genes it has.

(d) The more types of cell an organism has, the more genes it has.

Examining The Human Genome

9-37 The human genome has 3.2 × 10⁹ nucleotide pairs. At its peak, the Human Genome Project was generating raw nucleotide sequences at a rate of 1000 nucleotides per second. At the rate of 1000 nucleotides per second, how long would it take to generate 3.2 × 10⁹ nucleotides of sequence?

9-38 The average size of a protein in a human cell is about 430 amino acids, yet the average gene in the human genome is 27,000 nucleotide pairs long. Explain.

9-39 Which of the following statement about pseudogenes is false?

(a) Pseudogenes code for microRNAs.

(b) Pseudogenes share significant nucleotide similarity with functional genes.

(c) Pseudogenes are no longer expressed in the cell.

(d) There are estimated to be approximately 20,000 pseudogenes in the human genome.

9-40 Which of the following statements about the human genome is false?

(a) More than 40% of the human genome is made up of mobile genetic elements.

(b) More of the human genome codes for intron sequences than for exon sequences.

(c) About 1.5% of the human genome codes for exons.

(d) The exons are mainly what is conserved between the genomes of humans and other mammals.

9-41 The nucleotide sequences between individuals differ by 0.1%, yet the human genome is made up of about 3 × 10⁹ nucleotide pairs. Which of the following statements is false?

(a) In most human cells, the homologous autosomes differ from each other by 0.1%.

(b) All changes between human individuals are single-nucleotide polymorphisms.

(c) Any two individuals (other than identical twins) will generally have more than 3 million genetic differences in their genomes.

(d) Much of the variation between human individuals was present 100,000 years ago, when the human population was small.

9-42 Propose a reason to explain why highly repetitive regions of the genome are particularly susceptible to expansions and contractions in number.

9-43 Which of the following processes is not thought to contribute to diversity in the genome of human individuals?

(a) exon shuffling

(b) single-nucleotide polymorphisms

(c) CA repeats

(d) duplication and deletion of large blocks of sequence

9-44 For each statement below, indicate whether it is true or false and explain why.

A. The increased complexity of humans compared with flies and worms is largely due to the vastly larger number of genes in humans.

B. Repeats of the CA dinucleotide are useful for crime investigations and other forensic applications.

C. Most single-nucleotide polymorphisms cause no observable functional differences between individual humans.

D. There is little conserved synteny between human and mouse genes.

E. The differences between multicellular organisms are largely explained by the different kinds of genes carried on their chromosomes.

9-45 The number of distinct protein species found in humans and other organisms can vastly exceed the number of genes. This is largely due to ______________.

(a) protein degradation

(b) alternative splicing

(c) homologous genes

(d) mutation

9-46 You are studying a gene that has four exons and can undergo alternative splicing. Exon 1 has two alternatives, exon 2 has five alternatives, exon 3 has three alternatives, and exon 4 has four alternatives. If all possible splicing combinations were used, how many different splice isoforms could be produced for this gene?

(a) 22

(b) 30

(c) 60

(d) 120

9-47 Alternative exons can arise through the duplication and divergence of existing exons. What type of mutation below would be least tolerated during the evolution of a new exon?

(a) a nucleotide change of A to G

(b) a deletion of three consecutive bases.

(c) mutation of the first nucleotide in the intron

(d) a nucleotide change that alters a TT dinucleotide to AA

How We Know: Counting Genes

9-48 Explain how ESTs are identified and how they aid in finding the genes within an organism’s genome.

9-49 Your friend discovered a new multicellular organism living under the polar ice caps, and brought it back to the laboratory, where it seems to be growing well. Your friend is particularly interested in the proteins that allow this organism to survive in extreme cold. Because he is interested in proteins and because he has learned that most of the human genome does not code for exons, he is considering sequencing expressed sequence tags from this organism. What do you think the pitfalls of this approach might be? Explain.

9-50 The yeast genome was sequencedmore than 10 years ago, yet the total number of genes continues to be refined. The sequencing of closely related yeast species was important for validating the identity of short (less than 100 nucleotides long) open reading frames (ORFs) that were otherwise difficult to predict. What is the main reason that these short ORFs are hard to find?

(a) The human genome does not have short ORFs.

(b) The short ORFs code for RNAs.

(c) Many short stretches of DNA may, by random chance, not have a stop codon, making it difficult to distinguish those that code for proteins from those that do not.

(d) Short ORFs occur mainly in gene-rich regions, making them difficult to identify by computer programs