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

Answer: D

2) An early step in shotgun sequencing is to _____.
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

Answer: A

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.

Answer: C

4) Proteomics is defined as the _____.
A) linkage of each gene to a particular protein
B) study of the full protein set encoded by a genome
C) totality of the functional possibilities of a single protein

D) study of how amino acids are ordered in a protein

Answer: B

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

Answer: A

6) What is 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

Answer: A

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

Answer: D

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. To do this, the company annotates the genome of the new plant to _____.
A) determine what proteins are produced

B) determine what mRNA transcripts are produced
C) identify genes and determine their functions
D) identify the location of mRNA within the plant cells

Answer: C

9) If the sequence of a cDNA has matches with DNA sequences in the genome, then this genomic DNA is likely to _____.
A) code for a protein
B) code for an rRNA

C) be part of an intron
D) be a regulatory sequence

Answer: A

10) In what sense are studies by nineteenth-century naturalists and those by early twenty-first- century genomic biologists similar?
A) Both focused on cellular evolution.
B) Both worked to understand how genes evolved.

C) Both took a reductionist approach by studying only one small part of a complex system.

D) Both focused on observing and describing what exists in their realms of investigation.

Answer: D

11) 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 reactin (PCR)

C) DNA sequencing
D) protein-protein interaction assays

Answer: A

12) A DNA microarray is a tool that owes its existence to earlier genomics investigations. What essential contribution of genomics makes microarrays possible?
A) recently improved RNA sequencing technologies
B) continuously improving methods of gene cloning

C) more efficient techniques for cDNA synthesis
D) knowledge of which DNA sequences to synthesize for the array

Answer: D

13) 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

Answer: C

14) A sequence database such as GenBank could be used to do all of the following EXCEPT A) Compare cow and human insulin protein sequences.
B) Construct a tree to determine the evolutionary relationships between various bird species.

C) Search for genes in a fruit fly that are similar to a human gene.

D) Compare patterns of gene expression in cancerous and non-cancerous cells.

Answer: D

15) 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 contain functional elements (includes functional RNAs and regulatory sequences)?

A) Less than 2%

B) About 50%
C) At least 80%
D) 100%

Answer: C

16) Which of the following is a representation of gene density?

A) Humans have 2900 Mb per genome.
B) C. elegans has ~20,000 genes.
C) Humans have ~20,000 protein-encoding genes in 2900 Mb.

D) Fritillaria has a genome 40 times the size of a human.

Answer: C

17) 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.

Answer: C

18) The comparison between the number of human genes and those of other animal species has led to many conclusions, including that _____.
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 more 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

Answer: B

19) It is more difficult to identify eukaryotic genes than prokaryotic genes because in eukaryotes _____.
A) the proteins are larger than in prokaryotes
B) the coding portions of genes are shorter than in prokaryotes

C) there are no start codons
D) there are introns

Answer: D

20) If alternative splicing did NOT occur then _____.
A) the human genome would likely contain many more genes
B) the E. coli genome would contain many fewer genes
C) there would be little correlation between the complexity of organisms and genome size

D) there would be many fewer genes devoted to metabolism in Arabidopsis and yeast

Answer: A

21) A multigene family is composed of _____.
A) multiple genes whose products must be coordinately expressed
B) genes whose sequences are very similar and that probably arose by duplication

C) a gene whose exons can be spliced in a number of different ways
D) a highly conserved gene found in a number of different species

Answer: B

22) Retrotransposons _____.
A) use an RNA molecule as an intermediate in transposition
B) are found only in animal cells
C) generally move by a cut-and-paste mechanism
D) contribute a significant portion of the genetic variability seen within a population of gametes

Answer: A

23) In humans, the embryonic and fetal forms of hemoglobin have a higher affinity for oxygen than that of adults. This is due to _____.
A) nonidentical genes that produce different versions of globins during development.
B) pseudogenes, which interfere with gene expression in adults.

C) the attachment of methyl groups to cytosine following birth, which changes the type of hemoglobin produced.
D) histone proteins changing shape during embryonic development.

Answer: A

24) Sequencing eukaryotic genomes is more difficult than sequencing genomes of bacteria or archaea because of the _____.
A) large size of eukaryotic proteins
B) hard-to-find proteins

C) high proportion of G-C base pairs in eukaryotic DNA
D) large size of eukaryotic genomes and the large amount of eukaryotic repetitive DNA

Answer: D

25) Because they both produce a reverse transcriptase, long interspersed nuclear elements (LINEs) as transposable elements may be related to _____.
A) plasmids
B) retroviruses

C) poliovirus
D) parasitic bacteria

Answer: B

26) Although transposable elements and short tandem repeats (STRs) are repetitive DNAs, they differ in that _____.
A) STRs occur within exons; transposable elements occur within introns
B) STRs occur within introns; transposable elements occur within exons

C) the repeated unit in STRs is clustered one after another; transposable element repeats are scattered throughout the genome
D) the repeated unit in STRs is much larger than the repeated unit of transposable elements

Answer: C

27) 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

Answer: D

28) 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.

Answer: A

The figure above 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.

29) The movement of these blocks suggests that _____.
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

Answer: D

30) Humans have twenty-three pairs of chromosomes and chimps have twenty-four 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 twenty-four pairs of chromosomes. After the two groups evolved, 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.

Answer: A

31) Exon shuffling occurs during _____.

A) splicing of DNA
B) DNA replication
C) meiotic recombination

D) translation

Answer: C

32) When gene duplication occurs to its ultimate extent by doubling all genes in a genome, what has occurred?
A) pseudogene creation
B) creation of a gene cluster

C) creation of a polyploid
D) creation of a diploid

Answer: C

33) Mutations that occur in one member of a gene pair that arose from gene duplication may create _____.
A) a pseudogene
B) a gene with a new function

C) 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

Answer: D

34) Based on the data in the Amino Acid Identity Table, which two members of the human globin gene family are the most divergent?
A) a1 and ß
B) ? and ß

C) a1 and a2
D) a1 and G?

Answer: B

35) Fragments of DNA have been extracted from the remnants of extinct woolly mammoths, amplified, and sequenced. These can now be used to _____.
A) introduce certain mammoth traits into relatives, such as elephants
B) clone live woolly mammoths

C) appreciate the reasons why mammoths went extinct
D) better understand the evolutionary relationships among members of related taxa

Answer: D

36) Homeotic genes contain a homeobox sequence that is highly conserved among very diverse species. The homeobox is the code for that domain of a protein that binds to DNA in a regulatory developmental process. Therefore, you would expect that _____.
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

Answer: A

37) 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. Additional data consistent with this hypothesis could be the discovery of _____.
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

Answer: B

38) Several of the different globin genes are expressed in humans, but at different times in development. What mechanism could allow for this?
A) exon shuffling
B) pseudogene activation

C) differential translation of mRNAs
D) differential gene regulation over time

Answer: D

39) Biologists now routinely test for homology between genes in different species. If genes are determined to be homologous, it means that they are related _____.
A) by descent from a common ancestor
B) because of convergent evolution

C) by chance mutations
D) in function but not structure

Answer: A

40) A current view of how the human and chimpanzee can share most of their nucleotide sequence 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

Answer: C

41) 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. What 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.

Answer: C

42) Comparisons of DNA sequences within the human species have revealed many variations. Which of the following variations involves duplication of relatively long stretches of chromosomes, often including the duplication of protein-coding genes?
A) CNVs

B) SNPs
C) STRs
D) Transposable elements

Answer: A

43) 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.

Answer: C