ch 9

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

(d) RNA splicing

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.

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

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.

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

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.

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

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.

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

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

(a) L1

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.

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

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.

(a) Pseudogenes code for microRNAs.

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.

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

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.

(a) a mutation within a gene.

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

(a) exon shuffling

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

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

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.

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

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.

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

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.

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

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.

(b) alternative splicing.

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

(b) reverse transcriptase gene

9-51 A finished draft of the human genome was published in ______. (a) 1965. (b) 1984. (c) 2004. (d) 2012.

(c) 2004.

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.

(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.

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

(c) RNA polymerase

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

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

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

(c) mutation of the first nucleotide in the intron

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

(d) 120

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.

(d) All answers above are true.

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.

(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.

9-31 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.

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

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.

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

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.

(d) It encodes its own reverse transcriptase.

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.

(d) Some of the duplicated globin genes that arose during vertebrate evolution acquired inactivating mutations and became pseudogenes in modern vertebrates.

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.

(d) horizontal gene transfer.

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

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

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.

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.

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.

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