Chapter 9 How Genes and Genomes Evolve

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

C

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

D

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.

D

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.

B

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

B

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

B

A finished draft of the human genome was published in ______. (a) 1965. (b) 1984. (c) 2004. (d) 2012.

C

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.

B

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

A

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.

A

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

A

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

A

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

A

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.

A

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.

A

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.

A

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.

A

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.

A

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

A

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.

B

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.

B

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.

B

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.

C

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

C

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.

C

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.

C

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.

C

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

C

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

C

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

C

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

D

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

D

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.

D

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.

D

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.

D

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.

D

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.

D

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.

D

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

D

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

D

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

D

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

Genes involved in sugar metabolism, developmental pathways, lip synthesis