Deck 20: Genomics

Question 1

In comparing DNA sequences from two different eukaryotic organisms,which do you expect to vary the most?

A)sequences that code for exons
B)sequences that code for introns
C)sequences that code for a polypeptide
D)sequences that regulate transcription
E)sequences that code for micro-RNAs

Answer 1

B

Question 2

Even though bacteria are more simple than eukaryotes,genomic data on bacteria was surprising because _____.

A)very few species contain plasmids
B)there is only one copy of each gene present within a bacterial genome
C)there are many genes of unknown function
D)bacterial genomes are always contained on a single circular chromosome
E)there is almost no difference between the genomes of diverse bacteria

Answer 2

C

Question 3

The mechanism for the spread of LINES involves some unusual features,including _____.

A)translation in the cytoplasm of an mRNA that was synthesized in the nucleus
B)the nuclear localization of RNA polymerase
C)the transport of mRNA from the cytoplasm to the nucleus
D)the use of an enzyme that cuts DNA
E)the use of RNA polymerase to transcribe an mRNA

Answer 3

C

Question 4

The bulk of the sequence data in whole genome sequencing comes from _____.

A)relatively large (~ 160 kb)sequences cloned into BACs
B)relatively small (~ 1000 base-pair)sequences cloned into plasmids
C)whole chromosomes obtained without cloning
D)whole chromosomes cloned into plasmids

Question 5

Sequencing eukaryotic genomes is more difficult than sequencing genomes of bacteria or archaea because of _____.

A)the large size of eukaryotic proteins
B)the hard to find proteins
C)the high proportion of G-C base pairs in eukaryotic DNA
D)the large size of eukaryotic genomes and the large amount of eukaryotic repetitive DNA
E)the large size of eukaryotic genomes,the large amount of eukaryotic repetitive DNA,and the high proportion of G-C base pairs in eukaryotic DNA

Question 6

Although transposable elements and simple tandem repeats (STRs)are both 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
E)variation in STR repeat number comes from STR movement in the genome;variation in transposable element repeat number comes from errors in DNA replication

Question 7

Imagine that your goal is to isolate mouse mutants that stabilize microsatellite repeat sequences (i.e. ,lower the frequency at which their repeat number changes).Which of the following mutations would you predict to have this stabilizing effect?

A)a mutation that reduces the rate of transcription
B)a mutation that reduces the rate of translation
C)a mutation that increases the rate of DNA synthesis
D)a mutation that reduces the occurrence of homologous recombination
E)a mutation that inactivates reverse transcriptase and/or integrase

Question 8

After finding a new medicinal plant,a pharmaceutical company decides to determine if the plant has any genes that are the same or similar to those of other known medicinal plants.To do this,the company annotates the genome which will _____.

A)determine what protein could be synthesized in a medicine
B)determine what mRNA transcripts are available
C)identify genes and their positions within the genome
D)learn how gene products interact to produce phenotypes

Question 9

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

Question 10

In what sense are studies by 19th-century naturalists and those by early 21st-century genomic biologists similar?

A)Both focus narrowly on the underlying mechanisms of biology.
B)Both use evolutionary theory to guide their work.
C)Both take a reductionist approach by studying only one small part of a complex system.
D)Both focus on observing and describing what exists in their realms of investigation.
E)Both constantly strive to create theoretical frameworks in which to understand their findings.

Question 11

In establishing paternity by DNA fingerprinting,what proportion of microsatellite repeat alleles in a child come from the father?

A)only ones on the X chromosome
B)1/4
C)1/2
D)3/4

Question 12

Which of the following makes it difficult to identify eukaryotic genes?

A)the proteins are larger in eukaryotes than prokaryotes
B)the coding portions of genes are longer in eukaryotes than prokaryotes
C)the lack of analogy between eukaryotic genes
D)the presence of many introns

Question 13

Why are transposable elements considered to be selfish genes?

A)They have multiple promoters.
B)They require multiple RNA polymerases for transcription.
C)They replicate using the host's resources without direct benefit to the host.
D)They do not produce mRNA.

Question 14

If the sequence of a cDNA matches a DNA sequence in the genome,then this genomic DNA is likely to _____.

A)code for a protein
B)code for a ribozyme
C)code for an rRNA
D)be part of an intron
E)be a regulatory sequence

Question 15

Biologists now routinely test for homology among potentially related species using DNA sequences.These tests reveal if the sequences from each species _____.

A)are related by descent from a common ancestor
B)are related because of convergent evolution
C)are related by chance mutations
D)code for identical proteins
E)code for identical RNAs

Question 16

A scientist needs to find a collaborating scientist to help her with organizing a large amount of sequence data from the genome of a previously unsequenced and rare plant.This scientist should find a collaborator who specializes in _____,

A)proteomics
B)functional genomics
C)evolutionary genomics
D)bioinformatics

Question 17

Imagine that you've sequenced the genome of a human pathogenic bacterium.In the early stages of analysis,you discover a stretch of DNA that has a significantly different GC content (the proportion of bases that are G and

A)convergent evolution
B)both sequences are introns
C)a high rate of mutation
D)a low rate of mutation
E)lateral gene transfer

Question 18

When comparing the genomes of a bacterial parasite versus a free-living,nonparasitic bacterium,one expects to find _____.

A)the proportion of G-C base pairs will be significantly higher in the parasite
B)no homology between the free-living and parasitic bacteria
C)there will be a higher proportion of genes of unknown function in the parasite
D)the parasite will have acquired a smaller proportion of its genes through lateral gene transfer
E)the parasite will have a smaller genome

Question 19

LINES transposable elements are closely related to _____.

A)plasmids
B)retroviruses
C)poliovirus
D)restriction enzymes
E)DNA polymerase

Question 20

Forensic DNA fingerprinting often involves recovery of minute quantities of DNA from a crime scene.What is a concern in analyzing this DNA?

A)There is seldom enough DNA to allow PCR amplification.
B)Even with these tiny amounts of DNA,there may be too much DNA for efficient PCR.
C)Restriction enzymes may not work efficiently on the PCR-amplified DNA.
D)It is critical to avoid the introduction of contaminating human DNA unrelated to the crime.

Question 21

The following table from the Venter et al.paper presents the numbers of different types of genes discovered in this study.

As with many new endeavors,concerns have been raised by some that genomics will fundamentally change the way biological research is practiced.Examine the full reference for the Venter et al.paper and consider the way this work was done.Now think of some seminal works in the history of biology,for example,Darwin's On the Origin of Species and Watson and Crick's publication on DNA structure.What do you think the concern might be that has been voiced about genomics?

A)Genomics will offer deep insights too rapidly for the biological community to comprehend.
B)Genomics is so based in technology that it cannot possibly reveal important knowledge of biology.
C)Genomics makes biology a "big-team science" that will squeeze out innovative individuals or small groups of scientists who traditionally have provided our greatest insights.
D)Genomics is really computer science,not biology,and therefore offers little for understanding life.

Question 22

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)both a gene with a new function and a pseudogene
E)a pseudogene,a gene with a new function,and a gene family with two distinct but related members

Question 23

Which of the following questions is asked in functional genomics research?

A)What is the number of Drosophila genes?
B)How does the GC content of human DNA vary across the genome?
C)What is the pattern of gene expression during mouse development?
D)How many introns exist in the human CFTR gene?
E)How closely related are the visual pigment genes of mouse and human?

Question 24

The following table from the Venter et al.paper presents the numbers of different types of genes discovered in this study.

Refer to the paragraph on the Venter et al.paper and Table 20.1 Because DNAs for sequencing were chosen at random with no way of knowing which organism they came from,how could genes be identified?

A)by searching for ORFs,especially those with translation start and stop sites
B)by searching for similarity between predicted ORFs and those in existing databases
C)by searching for exons bounded by consensus donor and acceptor splice sites (those that mark exon/intron boundaries)
D)by searching for ORFs,particularly those with translation start and stop sites,as well as for similarity between predicted ORFs and those in existing databases
E)by searching for ORFs,particularly those with translation start and stop sites;for similarity between predicted ORFs and those in existing databases;and for exons bounded by consensus donor and acceptor splice sites (those that mark exon/intron boundaries)

Question 25

In the microarray shown in the figure above,if you were searching for genes whose expression was inhibited by hormone treatment,you would search for sequences spotted on the array that showed _____ fluorescence.

A)no
B)high levels of
C)green
D)red
E)yellow

Question 26

Refer to the paragraph on the Venter et al.paper.Why was it necessary to modify the standard sequence assembly algorithms when analyzing DNAs from many different pooled species?

A)Sequencing techniques had improved sufficiently that obtaining accurate repetitive sequences was no longer a technical challenge.
B)Sequence-read lengths of repetitive DNA had increased sufficiently by the time of the Venter et al.work that they were almost as long as the sequences from nonrepetitive DNA were.
C)DNAs from abundant organisms would occur frequently in the sample,making them look like repetitive DNAs.
D)DNAs from the largest organisms would occur infrequently in the sample,making them look like repetitive DNAs.

Question 27

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 levels of mRNAs present in a particular cell type
E)the movement of transposable elements within the genome

Question 28

Like DNA microarrays,Northern blots analyze the levels of mRNA.However,Northern blots are almost always prepared with a probe tagged with one label,whereas DNA microarrays almost always use two groups of probes,each one tagged with a different fluorescent label.What advantage is conferred by using two labels for the microarray probes?

A)The two labels increase the sensitivity of the microarray.
B)The two labels allow the analysis of the expression of more genes.
C)The two labels allow simultaneous assay of levels of DNA and RNA.
D)The two labels allow comparison of gene expression between two samples.
E)Probing the array with two labels is equivalent to doing two experiments at once.

Question 29

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 and proteins
D)environmental factors
E)adults but not immature phenotypes

Question 30

If one wished to test the hypothesis that humans and chimps differ due to differences in the expression of a large set of shared genes,the technique to use would be _____.

A)Southern blotting
B)PCR
C)DNA sequencing
D)protein-protein interaction assays
E)DNA microarray analysis

Question 31

The figure above compares the proportion of genes devoted to various functions in a set of model organisms.Based on this figure,which one of the following statements is false?

A)The function of roughly half of eukaryotic genes is unknown.
B)Humans have the highest proportion of genes devoted to defense and immunity.
C)The mustard plant and yeast have a small fraction of genes devoted to cell communication.
D)A relatively small but similar proportion of genes are devoted to transcription and translation in all these organisms.
E)Drosophila is unusual in having so few genes devoted to protein folding and degradation.

Question 32

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
E)the concept that hybridization between single-stranded nucleic acids can be used as a means of identifying any DNA sequence

Question 33

Refer to the paragraph on the Venter et al.paper.Why would any sequence assembly program be written so as to ignore repeated sequences?

A)These sequences are too unreliable to consider.
B)These sequences are too hard to obtain to justify the effort.
C)These sequences are too short to be useful for assembly.
D)These sequences are difficult to place within an assembly.

Question 34

The following table from the Venter et al.paper presents the numbers of different types of genes discovered in this study.

Refer to the paragraph on the Venter et al.paper and Table 20.1 If practical applications arise from this or similar metagenomic studies,what might these be?

A)New genes with useful properties may be identified and ultimately put to use.
B)New microbial species could be isolated from seawater.
C)An increased knowledge of the diversity of marine ecosystems could lead to increased appreciation of diversity in all ecosystems.
D)Species discovered in the Sargasso Sea may also be found to inhabit less-remote waters.

Question 35

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 an aneuploid
E)creation of a diploid

Question 36

The following table from the Venter et al.paper presents the numbers of different types of genes discovered in this study.

Refer to the paragraph on the Venter et al.paper and Table 20.1 How do you think putative genes were placed into the categories shown in the preceding table?

A)by searching for ORFs,especially those with translation start and stop sites
B)by searching for matches,especially of the predicted gene products,with previously identified gene products of known function
C)by expressing the cloned genes in E.coli and then running biochemical analyses of the products
D)all of the above

Question 37

If alternative splicing did not occur,a prediction would be that _____.

A)the human genome would contain many more genes
B)the yeast 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
E)there would be many fewer genes devoted to DNA replication and modification in humans

Question 38

In eukaryotes,the major mechanism of introducing new genes into the genome is _____.

A)duplication and divergence
B)lateral gene transfer
C)pseudogene creation
D)pseudogene restoration
E)unequal crossing over at microsatellite repeats