Campbell Biology, 11e (Urry)

Chapter 21 Genomes and Their Evolution

21.1 Multiple-Choice Questions

1) What is metagenomics?
A) genomics as applied to a species that most typifies the average phenotype of its genus
B) the sequencing of one or two representative genes from several species
C) the sequencing of only the most highly conserved genes in a lineage
D) sequencing DNA from a group of species from the same ecosystem

2) Which of the following processes is an early step in the whole-genome shotgun approach to
sequencing?
A) break genomic DNA at random sites
B) map the position of cloned DNA fragments
C) randomly select DNA primers and hybridize these to random positions of chromosomes in
preparation for sequencing

3) Using modern techniques of sequencing by synthesis and the shotgun approach, sequences are
assembled into chromosomes by ________.
A) placing them on previously generated genetic maps
B) cloning them into plasmid vectors
C) computer analysis looking for sequence overlaps
D) cloning them into plasmid vectors, placing them on previously generated genetic maps,
followed by computer analysis looking for sequence overlaps

4) Which of the following statements defines proteomics?

A) It is the linkage of each gene to a particular protein.
B) It is the study of the full protein set and its properties.
C) It is the totality of the functional possibilities of a single protein.
D) It is the study of how amino acids are ordered in a protein.

5) Bioinformatics can be used to scan for short sequences that specify known mRNAs, called
________.
A) expressed sequence tags
B) multigene families
C) proteomes
D) short tandem repeats

6) Which of the following processes correctly describes gene annotation in bioinformatics?

A) finding transcriptional start and stop sites, RNA splice sites, and ESTs in DNA sequences
B) assigning names to newly discovered genes
C) describing the functions of noncoding regions of the genome
D) matching the corresponding phenotypes of different species

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7) Bioinformatics includes ________.
I. using computer programs to align DNA sequences
II. creating recombinant DNA from separate species
III. developing computer-based tools for genome analysis
IV. using mathematical tools to make sense of biological systems
A) I and II
B) II and III
C) II and IV
D) I, III, and IV

8) After finding a new medicinal plant, a pharmaceutical company decides to determine if the
plant has genes similar to those of other known medicinal plants. What would annotation of the
genome of this plant allow the company to determine?
A) what proteins are produced by the plant
B) what mRNA transcripts are produced by the plant
C) identify genes and determine their functions
D) identify the location of mRNA within the plant cells

9) If the sequence of a cDNA has matches with DNA sequences in the genome, then this
genomic DNA could be described by which of the following statements?
A) The sequence codes for a protein.
B) The sequence codes for an rRNA.
C) The sequence is part of an intron.
D) The sequence is a regulatory sequence.

10) Which of the following techniques would be most appropriate to test the hypothesis that
humans and chimps differ in the expression of a large set of shared genes?
A) DNA microarray analysis
B) polymerase chain reaction (PCR)
C) DNA sequencing
D) protein-protein interaction assays

11) What can proteomics reveal that genomics cannot?

A) the number of genes characteristic of a species
B) the patterns of alternative splicing
C) the set of proteins present within a cell or tissue type
D) the movement of transposable elements within the genome

12) A sequence database such as GenBank could be used to carry out which of the following
processes?
A) Determine the expression pattern for specific human genes.
B) Construct a tree to determine the evolutionary relationships between various bird species.
C) Search for genes that have not yet been identified in eukaryotic genomes.
D) Compare patterns of gene expression in cancerous and non-cancerous cells.

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13) Current analysis indicates that less than 2% of the human genome codes for proteins. Based
on the systems approach employed by the ENCODE project, what percentage of the genome is
estimated to be transcribed at some point in at least one cell type?
A) less than 2%
B) about 50%
C) about 75%
D) 100%

14) Which of the following statements is a correct representation of gene density?

A) Humans have 1,000 Mb per genome.
B) C. elegans has ~20,000 genes.
C) Humans have ~20,000 protein-encoding genes in a 3,000 Mb.
D) Saccharomyces has a genome 40 times the size of a human genome.

15) Why might the cricket genome have eleven times as many base pairs as that of Drosophila
melanogaster?
A) Crickets have higher gene density.
B) Drosophila are more complex organisms.
C) Crickets must have more noncoding DNA.
D) Crickets must make many more proteins.

16) Which of the following conclusions has led to the comparison between the number of human
genes and those of other animal species?
A) The density of the human genome is far higher than in most other animals.
B) The number of proteins expressed by the human genome is far greater than the number of its
genes.
C) Most human DNA consists of genes for protein, tRNA, rRNA, and miRNA.
D) The genomes of most other organisms are significantly smaller than the human genome.

17) Why is it more difficult to identify eukaryotic genes than prokaryotic genes using genomic
techniques?
A) The proteins are larger in eukaryotes than in prokaryotes.
B) The coding portions of genes in eukaryotes are shorter than in prokaryotes.
C) There are no start codons in eukaryotic genes.
D) There are introns in eukaryotic genes.

18) Which of the following statements correctly describes one of the characteristics of alternative
splicing in vertebrate genomes?
A) Vertebrate genomes can produce more than one polypeptide from a single gene.
B) Vertebrate genomes can produce only one polypeptide from a single gene.
C) Vertebrate genomes are always smaller than other organisms.
D) Alternative splicing leaves introns in vertebrate genes after they are transcribed.

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19) Which of the following statements correctly describes one characteristic of a multigene
family?
A) A multigene family includes multiple genes whose products must be coordinately expressed.
B) A multigene family includes genes whose sequences are very similar and that probably arose
by duplication.
C) A multigene family includes a gene whose exons can be spliced in a number of different
ways.
D) A multigene family includes a highly conserved gene found in a number of different species.

20) Which of the following statements correctly describes one characteristic of retrotransposons?
A) They use an RNA molecule as an intermediate in transposition.
B) They are found only in animal cells.
C) They generally move by a cut-and-paste mechanism.
D) They contribute a significant portion of the genetic variability seen within a population of
gametes.

21) In humans, the embryonic and fetal forms of hemoglobin have a higher affinity for oxygen
than that of adults. Why is this the case?
A) Nonidentical genes produce different versions of globins during development.
B) Pseudogenes interfere with gene expression in adults.
C) The attachment of methyl groups to cytosine following birth changes the type of hemoglobin
produced.
D) Histone proteins change shape during embryonic development.

22) Why is sequencing of eukaryotic genomes more difficult than sequencing genomes of
bacteria or archaea?
A) It is due to the large size of eukaryotic proteins.
B) Eukaryotic genomes contain sequences for hard-to-find proteins.
C) There is a high proportion of G-C base pairs in eukaryotic DNA, which makes sequencing
difficult to complete.
D) The large size of eukaryotic genomes and the large amount of eukaryotic repetitive DNA
make sequencing difficult.

23) How do transposons and retrotransposons differ in how they move around in a genome?
A) Transposons move by viruses and retrotransposons move by plasmids.
B) Transposons move by means of a DNA intermediate and retrotransposons move by means of
an RNA intermediate.
C) Transposons move by means of a RNA intermediate and retrotransposons move by means of
an DNA intermediate.
D) Transposons move by viruses and retrotransposons move by bacteria.

24) How do transposable elements and short tandem repeats (STRs) differ?
A) STRs occur within exons; transposable elements occur within introns.
B) STRs occur within introns; transposable elements occur within exons.
C) STRs make up only a small percentage of a given genome while transposable elements often
make up larger parts of a given genome.
D) The repeated unit in STRs is much larger than the repeated unit of transposable elements.
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25) Which of the following can be duplicated in a genome?
A) only DNA sequences
B) only entire sets of chromosomes
C) only entire chromosomes
D) DNA sequences, chromosomes, or sets of chromosomes

26) Unequal crossing over during prophase I can result in one sister chromosome with a deletion
and another with a duplication. A mutated form of hemoglobin, so-called hemoglobin Lepore,
exists in the human population. Hemoglobin Lepore has a deleted series of amino acids. If this
mutated form was caused by unequal crossing over, what would be an expected consequence?
A) There should also be persons whose hemoglobin contains two copies of the series of amino
acids that is deleted in hemoglobin Lepore.
B) Each of the genes in the hemoglobin gene family must show the same deletion.
C) The deleted gene must have undergone exon shuffling.
D) The deleted region must be located in a different area of the individual's genome.

27) Use the following information to answer the question.

The figure shows a diagram of blocks of genes on human chromosome 16 and the locations of
blocks of similar genes on four chromosomes of the mouse.

Which of the following statements describes the result of the movement of these blocks?
A) During evolutionary time, these sequences have separated and have returned to their original
positions.
B) DNA sequences within these blocks have become increasingly divergent.
C) Sequences represented have duplicated at least three times.
D) Chromosomal translocations have moved blocks of sequences to other chromosomes.

28) Humans have 23 pairs of chromosomes, and chimps have 24 pairs of chromosomes. What is
the most likely explanation for these differences in human and chimp genomes?
A) The common ancestor of humans and chimps had 24 pairs of chromosomes. During human
evolution, two human chromosomes fused end to end.
B) In the evolution of chimps, new adaptations resulted from additional chromosomal material.
C) At some point in evolution, human and chimp ancestors reproduced with each other.
D) Errors in mitosis resulted in an additional pair of chromosomes in chimps.

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29) During which of the following processes does exon shuffling occur?
A) splicing of DNA
B) DNA replication
C) meiotic recombination
D) translation

30) When gene duplication occurs to its ultimate extent by doubling all genes in a genome,
which of the following results has occurred?
A) pseudogene creation
B) creation of a gene cluster
C) creation of a polyploid
D) creation of a diploid

31) Which of the following types of genes or gene families may be created by mutations that
occur in one member of a gene pair that arose from gene duplication?
A) only a pseudogene
B) only a gene with a new function
C) only a gene family with two distinct but related members
D) a pseudogene, a gene with a new function, and a gene family with two distinct but related
members

32) Based on the data in the Amino Acid Sequence Identity Table, which two members of the
human globin gene family are the most divergent?
A) α1 and ß
B) Αγ and ß
C) α1 and a2
D) α1 and G?

33) Fragments of DNA have been extracted from the remnants of extinct woolly mammoths,
amplified, and sequenced. How can these fragments of DNA now be used?
A) to introduce certain mammoth traits into relatives, such as elephants
B) to clone live woolly mammoths
C) to understand the reasons why mammoths went extinct
D) to better understand the evolutionary relationships among members of related taxa

34) Homeotic genes contain a homeobox sequence that is highly conserved among very diverse
species. The homeobox is the code for the domain of a protein that binds to DNA in a regulatory
developmental process. Which of the following statements is therefore correct regarding
homeotic genes?
A) Homeotic genes are selectively expressed as an organism develops.
B) Homeoboxes cannot be expressed in nonhomeotic genes.
C) Homeotic genes in apes and humans are very different.
D) All organisms must have homeotic genes.

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35) A recent study compared the Homo sapiens genome with that of Neanderthals. The results of
the study indicated that there was a mixing of the two genomes at some period in evolutionary
history. Which of the following potential discoveries of additional data might be consistent with
this hypothesis?
A) some Neanderthal sequences not found in living humans
B) a few modern H. sapiens with some Neanderthal sequences
C) duplications of several Neanderthal genes on a Neanderthal chromosome
D) some Neanderthal chromosomes that are shorter than their counterparts in living humans

36) Several of the different globin genes are expressed in humans, but at different times in
development. Which of the listed mechanisms could allow for this?
A) exon shuffling
B) pseudogene activation
C) differential translation of mRNAs
D) differential gene regulation over time

37) Biologists now routinely test for homology between genes in different species. If genes are
determined to be homologous, how are they related to each other?
A) by descent from a common ancestor
B) because of convergent evolution
C) by chance mutations
D) in function but not structure

38) A current view of how the human and chimpanzee can share most of their nucleotide
sequences yet exhibit significant phenotypic differences is that many of the most important
sequence differences alter ________.
A) structural genes
B) the number of repeated sequences
C) regulatory sequences
D) environmental factors

39) Studies in knockout mice have demonstrated an important role of the FOXP2 transcription
factor in the development of vocalizations. Recent sequence comparisons of the FOXP2 gene in
Neanderthals and modern humans show that while the DNA sequence may be different, the
protein sequence it codes for is identical. Which of the following conclusions might logically be
inferred from this information?
A) There was a problem with the experiment because different DNA sequences cannot result in
the same protein sequence.
B) The differences in DNA sequence support the hypothesis that Neanderthals were primitive
beings that could only grunt.
C) Human and Neanderthal vocalizations may have been more similar than previously thought.
D) The experiments in mice demonstrating the function of the FOXP2 gene are not relevant to
humans and Neanderthals because they are not primates.

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40) Comparisons of DNA sequences within the human species have revealed many variations.
Which of the following variations involves duplication of relatively long stretches of DNA?
A) CNVs
B) SNPs
C) STRs
D) Transposable elements

41) A microarray is a tool used in genetic research to determine the mRNAs being produced in a
particular tissue, and their relative level of expression. Known genes can therefore be assayed for
their expression in different situations. One use of the technology is in cancer diagnosis and
treatment. If a known gene functions as a tumor suppressor, predict which of the following
pieces of evidence would be most useful in diagnosis of a cancer due to a mutation in this tumor-
suppressor gene.
A) The tissue sample shows a high level of gene expression relative to a control (noncancerous)
sample.
B) The tissue sample responds to treatment with a mitosis-promoting compound.
C) The mRNAs for the targeted tumor suppressor sequence are not being produced.
D) The mRNAs for cyclins and kinases show unusually high levels of expression.

1) Bioinformatics includes all of the following except

A) using computer programs to align DNA sequences.
B) using DNA technology to combine DNA from two different sources in a test tube.
C) developing computer-based tools for genome analysis.
D) using mathematical tools to make sense of biological systems.

2) Homeotic genes
A) encode transcription factors that control the expression of genes responsible for specific
anatomical structures.
B) are found only in Drosophila and other arthropods.
C) are the only genes that contain the homeobox domain.
D) encode proteins that form anatomical structures in the fly.

3) Two eukaryotic proteins have one domain in common but are otherwise very different. Which
of the following processes is most likely to have contributed to this similarity?
A) gene duplication
B) alternative splicing
C) exon shuffling
D) random point mutations

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