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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 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 nonfunctional.

cellulose intron

common neutral

deleterious somatic

gamete unequal

homologous zygote

9-5 You discover that the underlying cause of a disease is a protein that is now less stable than the non-

disease-causing version of the protein. This change is most likely to be due to ________.

(a) a mutation within a gene.

(b) a mutation within the regulatory DNA of a gene.

(c) gene duplication.

(d) horizontal gene transfer.

9-6 You isolate a pathogenic strain of E. coli from a patient and discover that this E. coli strain is resistant

to an antibiotic. Common laboratory strains of E. coli are not resistant to this antibiotic, nor are any

other previously isolated pathogenic E. coli strains. However, such resistance has been observed in other

bacteria in the hospital in which the patient was treated. This newly discovered antibiotic resistance in E.

coli is most likely due to _______.

(a) a mutation within a gene.

(b) a mutation within the regulatory DNA of a gene.

(c) gene duplication.

(d) horizontal gene transfer.

9-7 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.

9-8 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.

9-9 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 gene transfer is very rare and thus has had little influence on the genomes of bacteria.

9-10 Two individuals are represented in each choice in Figure Q9-10; 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 Q9-10 will lead to a mutation in every cell of the individual in

which the original mutation occurred?

Figure Q9-10

9-11 Two individuals are represented in Figure Q9-11; individual 1 is one of the parents of individual 2.

The asterisk indicates the occurrence of a single mutation.

Figure Q9-11

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

9-12 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.

9-13 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?

9-14 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 overrepresented in subsequent generations, and which is most likely to become

underrepresented or disappear from the population.

9-15 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

9-16 Figure Q9-16 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 1011 cells from the

culture for their ability to form colonies?

Figure Q9-16

(a) 1

(b) 2

(c) 10

(d) 100

9-17 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 Q9-17 to help you answer

this question.)

Figure Q9-17

9-18 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

9-19 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.

9-20 Which of the following statements about the globin gene family is true?

(a) The globin protein, which can carry oxygen molecules throughout an organism’s body, was first seen

in ancient vertebrate species about 500 million years ago.

(b) The gene duplication that led to the expansion of the globin gene family led to the separation and

distribution of globin on many chromosomes in mammals, such that no chromosome has more than a

single functional member of the globin gene family.

(c) As globin gene family members diverged over the course of evolution, all the DNA sequence

variations that have accumulated between family members are within the regulatory DNA sequences

that affect when and how strongly each globin gene is expressed.

(d) Some of the duplicated globin genes that arose during vertebrate evolution acquired inactivating

mutations and became pseudogenes in modern vertebrates.

9-21 Which of the following statements 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.

9-22 Figure Q9-22 shows the evolutionary history of the globin gene family members.

Figure Q9-22

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

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

(b) The α-globin gene is more closely related to the ε-globin gene than to the δ-globin gene.

(c) The nucleotide sequences of the two γ-globins will be most similar because they are the closest

together on the chromosome.

(d) The fetal β-globins arose from a gene duplication that occurred 200 million years ago, which gave

rise to a β-globin expressed in the fetus and a β-globin expressed in the adult.

9-23 Panels (A) and (B) of Figure Q9-23 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 Q9-23

9-24 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

9-25 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 as another will be more likely to have a genome of the same size

than will a more evolutionarily diverged animal.

9-26 Which of the following statements about homologous genes is true?

(a) For protein-coding genes, homologous genes will show more similarity in their amino acid sequences

than in their nucleotide sequences.

(b) Fewer than 1% of human genes have homologs in the nematode and the fruit fly.

(c) Most homologous genes arose by gene duplication.

(d) A gene in humans that has homologs in plants and prokaryotes will show the same level of similarity

in nucleotide sequence when the human and prokaryotic sequences are compared as when the human

and chimpanzee sequences are compared.

9-27 Figure Q9-27 shows the nucleotide sequence from a protein-coding region of a gene in humans,

chimpanzees, and gorillas and the protein sequence produced from this gene. The seventeen amino

acids encoded by this DNA are numbered below. The two codons that are not conserved in all three

species have been boxed. These two codons code for amino acids 3 and 15.

Figure Q9-27

Which of these statements is consistent with these sequence-comparison data?

(a) The gorilla sequence is more similar to the chimp sequence than to the human sequence.

(b) Since these sequences are so similar, this protein must also be found in invertebrates.

(c) The chimp DNA sequence has likely diverged at the DNA coding for amino acid 15 from the sequence

found in the last common ancestor of humans and chimps.

(d) The last common ancestor of chimps and gorillas most likely used AAA to code for amino acid

number 3.

9-28 Given the evolutionary relationship between higher primates shown in Figure Q9-28, which of the

following statements is false?

Figure Q9-28

(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 Figure Q9-28.

9-29 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 Q9-29. 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 Q9-29

(a) species V

(b) species W

(c) species Y

(d) species Z

9-30 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 eukaryotes but are much more

difficult to recognize in archaea.

9-31 The pufferfish, 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.

9-32 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

9-33 The evolutionary relationships between seven different species—G, H, J, K, L, M, and N—are

diagrammed in Figure Q9-33.

Figure Q9-33

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.

9-34 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

9-35 Figure Q9-35 shows a hypothetical phylogenetic tree. Use this tree to answer the following

questions.

Figure Q9-35

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?

9-36 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.

9-37 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 Q9-37, 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 Q9-37

9-38 The genomes of some vertebrates are much smaller than those of others. For example, the

genome of the pufferfish Fugu is much smaller than the human genome, and even much smaller than

genomes 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.

9-39 It is thought that all eukaryotes 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.

9-40 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

9-41 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.

Transposons and Viruses

9-42 Which of the following statements about mobile genetic elements is true?

(a) Mobile genetic elements can sometimes rearrange the DNA sequences of the genome in which they

are embedded by accidentally excising neighboring chromosomal regions and reinserting these

sequences into different places within the genome.

(b) DNA-only transposons do not code for proteins but instead rely on transposases found in cells that

are infected by viruses.

(c) The two major families of transposable sequences found in the human genome are DNA-only

transposons that move by replicative transposition.

(d) During cut-and-paste transposition, the donor DNA will no longer have the mobile genetic element

embedded in its sequence when transposition is complete.

9-43 Mobile genetic elements are sometimes called “jumping genes,” because they move from place to

place throughout the genome. The exact mechanism by which they achieve this mobility depends on the

genes contained within the mobile element. Which of the following mobile genetic elements carries

both a transposase gene and a reverse transcriptase gene?

(a) L1

(b) B1

(c) Alu

(d) Tn3

9-44 Which of the following is true of a retrovirus but not of the Alu retrotransposon?

(a) It requires cellular enzymes to make copies.

(b) It can be inserted into the genome.

(c) It can be excised and moved to a new location in the genome.

(d) It encodes its own reverse transcriptase.

9-45 Which of the following DNA sequences is not commonly carried on a DNA-only transposon?

(a) transposase gene

(b) reverse transcriptase gene

(c) recognition site for transposase

(d) antibiotic-resistance gene

9-46 HIV is a human retrovirus that integrates into the host cell’s genome and will eventually replicate,

produce viral proteins, and ultimately escape from the host cell. Which of the following proteins is not

encoded in the HIV genome?

(a) reverse transcriptase

(b) envelope protein

(c) RNA polymerase

(d) capsid protein

9-47 Some retrotransposons and retroviruses integrate preferentially into regions of the chromosome

that are packaged in euchromatin and are also located outside the coding regions of genes that contain

information for making a protein. Why might these mobile genetic elements have evolved this strategy?

9-48 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.

9-49 Viral genomes _________.

(a) can be made of DNA.

(b) can be made of RNA.

(c) can be either double-stranded or single-stranded.

(d) All answers above are true.

9-50 Which of the following statements about retroviruses is false?

(a) Retroviruses are packaged with a few molecules of reverse transcriptase in each virus particle.

(b) Retroviruses use the host-genome integrase enzyme to create the provirus.

(c) The production of viral RNAs can occur long after the initial infection of the host cell by the

retrovirus.

(d) Viral RNAs are translated by host-cell ribosomes to produce the proteins required for the production

of viral particles.

Examining the Human Genome

9-51 A finished draft of the human genome was published in ______.

(a) 1965.

(b) 1984.

(c) 2004.

(d) 2012.

9-52 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?

9-53 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.

9-54 Which of the following statements about the human genome is false?

(a) About 50% of the human genome is made up of mobile genetic elements.

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

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

(d) Only the exons are conserved between the genomes of humans and other mammals.

9-55 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.

9-56 Propose a reason to explain why highly repetitive regions of the genome are particularly

susceptible to expansions and contractions in number.

9-57 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

9-58 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.

9-59 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.

9-60 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

9-61 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

9-62 Which of the following statements about what we have learned by comparing the modern-day

human genome to other genomes is true?

(a) Modern humans whose ancestors come from Europe or Asia share up to 4 percent of their genome

with Neanderthals.

(b) Accelerated changes, which were found when comparing the human genome to other mammalian

genomes, were not found when comparing the modern-day human genome to the Neanderthal

genome.

(c) The human genome is far more gene-dense than the yeast genome.

(d) In syntenic regions of the human and mouse genomes, both gene order and the placements of more

than 95% of the mobile genetic elements are conserved.

How We Know: Counting Genes

9-63 Explain how ESTs are identified and how they aid in finding the genes within an organism’s

genome.

9-64 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.

9-65 The yeast genome was sequenced more than 15 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 without the genomes

of other yeast for comparison?

(a) Short ORFs are found only in yeast.

(b) The short ORFs code for RNAs.

(c) Many short stretches of DNA may lack a stop codon simply by chance, making it difficult to

distinguish those DNA sequences 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.

ANSWERS

9-1 Choice (a) is false. Mutations are carried in the genetic material, and the only genetic material

passed along to the offspring of a sexually reproducing organism comes from a germ-line cell (not a

somatic cell).

9-2 (c) A mutation within an upstream enhancer of the gene will affect the regulation of gene

expression. Mutations within the coding sequence [choices (a) and (b)] will lead to a mutated protein

being produced in the proper tissues at the proper time. A mutation in the TATA box of the gene will

probably lead to no expression at all [choice (d)].

9-3 1—A; 2—D; 3—B; 4—E; 5—A; 6—C

9-4 Sexual reproduction in a multicellular organism involves specialized reproductive cells, called

gametes, which come together to form a zygote that will divide to produce both reproductive and

somatic cells. A point mutation in the DNA is considered a neutral mutation if it changes a nucleotide

that leads to no phenotypic consequence; a point mutation is considered deleterious if it changes a

nucleotide within a gene and causes the protein to be nonfunctional.

9-5 (a)

9-6 (d) Horizontal gene transfer of antibiotic-resistance genes occurs commonly among bacterial strains,

and human beings are hosts to a plethora of bacteria. Although it is possible that there is a gene in the

normal E. coli genome that can lead to antibiotic resistance when mutated or duplicated [choices (a),

(b), or (c)], this is less likely, especially given that this type of antibiotic resistance has never been

observed.

9-7 It is not likely that your child would have the disease, because it is unlikely that the mutation is

carried in the germ line. Probably the mutation occurred in a cell that gave rise to somatic cells and not

germ cells. Only mutations in germ cells are passed on to progeny.

9-8 Choice (c) is the correct answer. Choice (b) is true but cannot explain the similar mutation rate.

9-9 A. False. Evolution can work only by tinkering with the tools and materials on hand, not by starting

from scratch to make completely new genes or pathways. New functions arise from the ancestral

functions by a process of gradual mutational change, and thus may not represent the best possible

solution to a problem.

B. False. Many duplications are subsequently lost or become pseudogenes, and only a few evolve into

new genes.

C. True. Pseudogenes look very similar to normal genes but cannot produce a full-length protein, as a

result of one or more disabling mutations.

D. False. A large proportion of the genes in vertebrates (and many other species) are members of

multigene families.

E. False. By some estimates, 20% of the genomic DNA in some bacterial species arose by horizontal gene

transfer.

9-10 (c)

9-11 (b) Although the mutation in individual 1 arose before the differentiation of germ cells, these

organisms are diploid and thus only half of individual 1’s germ cells will contain the mutation.

9-12 The simplest way to evolve the new gene is by duplication and divergence. If the gene is duplicated,

then the cell or lineage can maintain one functional, intact old copy of the original gene and can thus

tolerate the disabling mutations in the other copy. The other copy can first be modified by the X or Y

mutation that impairs its function; second, at some later time, the gene with the single mutation can

acquire the additional mutation to yield the doubly mutant X + Y gene with the new or improved

function.

9-13 On galactose medium, the original gal1– yeast cells cannot grow, nor can cells that received

plasmids containing most human cDNA sequences. However, yeast cells that received a plasmid with the

human galactokinase gene will probably be able to grow on galactose medium and produce many

progeny. This kind of “selection” procedure is very powerful, because even if only 1 in 100,000 cells has

the ability to grow under particular conditions, it will be easy to find it. The other 99,999 cells will die in

the Petri dish and will therefore be invisible to the investigator. Indeed, scientists have found that the

human galactokinase gene can function perfectly well in yeast and thus can “rescue” the defect of the

gal1– mutant. It was initially astonishing that genes from humans can function properly in yeast, but this

phenomenon has now been observed for many genes.

9-14 A. The order is selectively neutral, detrimental, beneficial. Most nucleotide changes in the genome,

or mutations, will have little or no effect on the fitness of the individual because many changes are not

located in regions that encode a protein or regulate the expression of a gene. Even changes within a

coding region may not change the amino acid encoded or may cause a conservative amino acid

change—for example, from one small nonpolar amino acid to another. Most changes that have a

functional consequence will interfere with the regulation of a gene or the behavior of the encoded

protein, usually rendering it useless and occasionally making it harmful or yielding a new function. Only

very rarely will a mutation improve the performance of the gene or its encoded protein.

B. The order is beneficial, selectively neutral, detrimental. Individuals bearing beneficial mutations will

be more likely to have more offspring than others in the population, and thus the beneficial mutations

will become overrepresented in the population in subsequent generations. Individuals bearing

detrimental mutations will be likely to have fewer children and grandchildren, and thus these mutations

will be culled from the population, although perhaps not eliminated.

9-15 Most variation between individual humans is in the form of single-nucleotide polymorphisms. Exon

shuffling 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 horizontal

gene transfer then the herbicides could become useless. Families of related genes can arise from a

single ancestral copy by gene duplication and subsequent divergence.

9-16 (d)

9-17 There would be a twofold increase. Two different mutations could arise to change the stop codon

to a codon coding for cysteine. This mutation would lead to a doubling of the observed spontaneous

mutation rate, from 1 in 109 to 2 in 109, in comparison with a single mutation that can change the stop

codon to a codon coding for tryptophan. Because spontaneous mutations are rare, this would not be a

particularly significant change.

9-18 (c) Information for the subcellular localization of a protein is usually encoded within the translated

portion of the gene.

9-19 (a) Regions of homology between nonhomologous chromosomes will cause gene duplications onto

a different chromosome (as well as chromosome rearrangements).

9-20 Choice (d) is correct. Globin proteins have been found in insects, primitive fish, and marine worms

in addition to vertebrates [making choice (a) incorrect]. Gene duplication does not necessarily mean

distribution among chromosomes, and in humans, the β-globin genes are located in a cluster on

Chromosome 11 while the α-globin genes are on Chromosome 16 [choice (b)]. Mutations have occurred

in both the regulatory DNA sequences and within the protein-coding regions of the globin genes [choice

(c)].

9-21 (a)

9-22 Choice (d) is correct. The α-globin and β-globin genes arose 500 million years ago, not the ancestral

globin gene [choice (a)]. The α-globin gene is as related to the ε-globin gene as it is to the δ-globin gene

[choice (b)]. The distance between the γ-globins on the chromosome cannot be used to predict

sequence similarity [choice (c)].

9-23 See Figure A9-23. The products of panel (C) will be segregated to progeny cells reliably. In contrast,

one product in panel (D) will have two centromeres and the other will lack a centromere. The

chromosome without a centromere will be rapidly lost as cells divide. The chromosome containing two

centromeres will probably be broken during mitosis and will subsequently be lost or severely damaged.

Figure A9-23

9-24 Choice (d) is the correct answer. Exon shuffling is facilitated by long introns [thus choice (a) is

incorrect] and by short exons that each code for one protein domain [thus choice (c) is incorrect].

Because exon shuffling can occur by recombination between introns, introns with regions of similarity to

one another will facilitate shuffling. A haploid genome will probably be less prone to exon shuffling than

a diploid genome [thus choice (b) is incorrect], because having two copies of each gene allows an

organism to keep one copy of the gene as a backup while it shuffles the other copy.

9-25 Choice (a) is correct. There is no necessary correlation between genome size and gene number

[choice (b)]. There are some fly genes, particularly those with a conserved function, that show much

greater similarity to human genes than to another fly gene [choice (c)]. Genome size does not

necessarily correlate with evolutionary relatedness [choice (d)].

9-26 (a) Because of the degeneracy of the genetic code, nucleotide sequences can diverge but still code

for identical amino acids.

9-27 (c)

9-28 (b)

9-29 (c)

9-30 (d) The gene that codes for the ribosomal RNA of the small ribosomal subunit is conserved in all

living species.

9-31 (d)

9-32 (a)

9-33 (c) Species N has also diverged from the last common ancestor (just like all the other species in the

diagram).

9-34 A. sugar metabolism

B. DNA replication

C. lipid synthesis

These pathways or phenomena are fundamental to the growth and proliferation of all cells, including

bacteria, and thus are likely to be highly conserved from species to species.

9-35 A. M and N diverged 10 million years ago.

B. There is an average of 2.0% nucleotide substitution in species M compared with species N (follow the

path connecting the two species, which is twice the distance between each one and their common

ancestor).

C. Neither more nor less. They show roughly the same degree of relatedness. The sequence divergence

between species M and N is about 2.0%, the same as that between species P and S. Both pairs of species

diverged 10 million years ago.

D. It is more informative to compare species that are separated by a greater evolutionary distance; thus,

comparing species M and Q, which diverged 20 million years ago, will be better able to identify

sequences that are likely to be important for function. Closely related species share many sequences by

chance, because there has been insufficient time for neutral mutations to accumulate.

9-36 A. False. Many highly conserved stretches of DNA are not transcribed but instead contain

information critical for regulating where and when genes are expressed.

B. True. Species that diverged recently have many identical stretches of DNA sequence by chance,

whereas sequence similarity between species that diverged long ago is probably due to functional

constraints. The sequences that are necessary to preserve the function of the gene will not be able to

undergo changes and thus are more likely to be similar between species that diverged long ago.

C. True. Most genomic changes do not alter the amino acid sequence of proteins or the regulatory

properties of genes. Even some mutations that cause minor alterations have little effect on protein

function.

D. True. All organisms need to perform a similar basic set of fundamental functions, such as those for

metabolism, protein synthesis, and DNA replication. Proteins involved in these functions are shared by

descent, and their evolution is constrained. Different species and cells are likely to require different

developmental paths and to encounter different environmental challenges, so the proteins involved in

these processes will tend to be more variable. For example, bacteria do not undergo elaborate

developmental programs and so lack many of the regulators of development found in eukaryotes.

E. False. Introns and transposons can act as sites where recombinational crossovers occur. Transposons

can also catalyze genetic rearrangements. Rearrangements occurring within these sequences are less

likely to be detrimental than those occurring elsewhere in the genome. In general, only the short intron

sequences required for splicing are important to intron function; alterations in sequences outside the

splicing sites may have no consequences for intron function and thus will not be subject to purifying

selection.

9-37 See Figure A9-37. Not all of the functionally conserved regions will be transcribed into RNA. Some

of the functionally conserved regions are likely to encode RNA and others are likely to be critical for

regulating when the gene is transcribed and when it is turned off. These nontranscribed regulatory

regions may be conserved nearly as much as the coding regions.

Figure A9-37

9-38 A. Spontaneous deletions or selection pressure to decrease the time or cost of DNA replication may

cause a loss of introns.

B. Acquisition of intron sequences provides a selective advantage for those organisms that experience

transposon insertions. According to this idea, introns became sinks for transposon and virus insertion to

protect the rest of the genome. Alternatively, introns may provide another advantage to the host

genome: by providing ample sites for crossing-over, larger introns could facilitate exon shuffling and

thus the generation of new genes with novel functions.

9-39 No, these genes are likely to be involved in basic cellular functions such as DNA replication and

protein production, and in the basic functions of eukaryotic cells such as the functioning of the nucleus

and the movement of items between cellular compartments. Genes involved in basic cellular functions

are likely to be used all the time in an organism’s life and are not likely to be activated at a specific stage

of life. The genes found in all eukaryotes probably existed in the primordial eukaryotic cells.

9-40 (d) Not all organisms have introns and therefore not all organisms will have genes involved in RNA

splicing.

9-41 (a)

9-42 (d)

9-43 (a)

9-44 (d)

9-45 (b) The reverse transcriptase gene is found on retrotransposons that move via an RNA

intermediate. Choices (a), (c), and (d) are all sequences that can be found in mobile genetic elements.

9-46 (c)

9-47 The most evolutionarily successful mobile genetic elements are those that are best at reproducing

themselves. To increase the number of copies of a particular element, the element must meet two

criteria: (1) it must not kill its host, and (2) it must maximize its ability to continue reproducing. If an

element inserts into the coding region of a gene, it might disable the gene and thereby confer a selective

disadvantage in the reproduction or survival of its host. Thus, elements that devised a way to avoid

insertion into coding regions were probably better able to increase their copy number throughout the

human population. If an element inserts into a heterochromatic region of a chromosome, its genes may

not be expressed and therefore it may become immobile. Elements that devised a way to direct

insertion into euchromatin would be more likely to maintain mobility and thereby increase their copy

number over time.

9-48 (b)

9-49 (d)

9-50 (b) Integrase is typically encoded by the viral genome.

9-51 (c)

9-52 It would take approximately 37 days; 60 seconds/minute means 86400 seconds in a day. At peak

rate, you can obtain 86,400,000 nucleotides per day.

9-53 In the human genome, the exons are relatively short, whereas the introns can be quite large. A

protein 430 amino acid residues long will need fewer than 1300 nucleotides to code for it. Furthermore,

many genes in the human genome undergo alternative splicing, so some of those 27,000 nucleotides

may be coding for alternative exons that are not used every time the gene is transcribed.

9-54 (d) About 5% of the human genome is highly conserved with other mammalian genomes, yet only

about 1.5% of the human genome codes for exons.

9-55 (b)

9-56 Highly repetitive regions of the genome are particularly susceptible to unequal genetic exchange

during homologous recombination.

9-57 (a)

9-58 A. False. The number of genes differs only by about a factor of two. It is thought that the increased

complexity of humans is due largely to differences in when and where the genes are expressed.

Differences in the timing of splicing may also be a major contributor to the relative complexity of

humans.

B. True. There are CA repeats in many locations throughout the genome. Because the number of repeats

at a given location varies greatly between individuals and families, it can be used as an identifying

characteristic to match two samples (such as blood samples) from the same or related individuals.

C. True. Nearly all single-nucleotide polymorphisms have no effect on the appearance or behavior of the

individual, but a few cause important differences.

D. False. Human and mouse chromosomes show extensive synteny, with blocks of chromosomal DNA

exhibiting homologous genes arranged in the same order between the two species.

E. False. Multicellular organisms are built from essentially the same toolbox of gene building blocks, but

the parts are put together differently because of regulatory differences that dictate when and where

and how much of each protein is made. Alternative splicing can also have an important role, as it can

generate several proteins from a single gene in some species, yet the homologous gene in other species

may produce only one protein.

9-59 (b) Alternative splicing can produce several different mRNA transcripts from a single gene, and

these transcripts can be translated into several different but related proteins. Choices (c) and (d) do not

yield more protein species than genes. Protein degradation [choice (a)] can produce several proteins

from a single gene, but this mechanism is used sparingly.

9-60 (d) 2 × 5 × 3 × 4 = 120.

9-61 (c) The first two nucleotides in the intron are critical for signaling the exon–intron boundary;

changing them would make the exon unable to be properly spliced.

9-62 (a)

9-63 To identify expressed sequence tags, or ESTs, mRNA must first be isolated from cells. This mRNA is

converted into complementary DNA (cDNA) with the use of specialized nucleic acid polymerases. The

nucleotide sequence of a short region of each cDNA is then determined. Each short sequence (or EST)

corresponds to a portion of a gene that was expressed in the cells from which the mRNA was isolated;

each sequence can be used as a tag to identify or manipulate the gene from which it came. A collection

of ESTs can be input into a computer to search for matches to the total genome sequence and can

thereby identify the sequences and chromosomal locations of many genes.

9-64 Although expressed sequence tags (ESTs) can be very useful in identifying genes, the use of ESTs in

this case may not work for several reasons. Two of these are:

1. ESTs are made from mRNAs, and thus represent actively transcribed genes. Your friend is studying the

proteins that permit survival in extreme cold. Since the organism is no longer living in the extreme cold,

the genes required for survival may no longer be expressed.

2. Because ESTs are made from mRNAs and because genes can be expressed at different levels, you will

sequence the ESTs from genes that are abundantly transcribed more often than those that may be

transcribed rarely.

9-65 (c)