Deck 21: Genomes and Their Evolution

Question 1

If genome size varies,with humans at 2900 Mb,a specific member of the lily family at 120 000 Mb,and a yeast at 13 Mb,what does this tell us?

A)Size matters less than gene density.
B)Size does not compare to gene density.
C)Size is not correlated with the organism's phenotype.
D)Size is mostly due to "junk" DNA.
E)Size is comparable only within phyla.

Answer 1

C

Question 2

Why is it unwise to try to relate an organism's complexity with its size or number of cells?

A)A very large organism may be composed of very few cells or very few cell types.
B)A single-celled organism, such as a bacterium or a protist, still has to conduct all the complex life functions of a large multicellular organism.
C)A single-celled organism that is also eukaryotic, such as a yeast, still reproduces mitotically.
D)A simple organism can have a much larger genome.
E)A complex organism can have a very small and simple genome.

Answer 2

B

Question 3

Which procedure is not required when the shotgun approach to sequencing is modified as sequencing by synthesis,in which many small fragments are sequenced simultaneously?

A)use of restriction enzymes
B)sequencing each fragment
C)cloning each fragment into a plasmid
D)ordering the sequences
E)PCR amplification

Answer 3

C

Question 4

Alu elements account for about 10% of the human genome.What are Alu elements?

A)noncoding regions
B)viral remnants
C)transposable elements
D)short sequences that code for RNA
E)transposons that code for RNA

Question 5

The comparison between the number of human genes and those of other animal species has led to many conclusions,including

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 other organisms are most significantly smaller than the human genome.

Question 6

Why might the cricket genome have 11 times as many base pairs as that of Drosophila melanogaster?

A)The two insect species evolved at very different geologic eras.
B)Crickets have higher gene density.
C)Drosophila are more complex organisms.
D)Crickets must have more noncoding DNA.
E)Crickets must make many more proteins.

Question 7

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 genes in 2900 Mb.
D)Humans have 27 000 bp in introns.
E)Fritillaria has a genome 40 times the size of a human.

Question 8

A microarray known as a GeneChip,with most now-known human protein coding sequences,has been developed to aid in the study of human cancer by first comparing two to three subsets of cancer subtypes.What kind of information might be gleaned from this GeneChip to aid in cancer prevention?

A)information about whether or not a patient has this type of cancer prior to treatment
B)evidence that might suggest how best to treat a person's cancer
C)data that could alert patients to what kind of cancer they were likely to acquire
D)information about which parent might have provided a patient with cancer-causing genes
E)information on cancer epidemiology in the United States or elsewhere

Question 9

Which of the following most correctly describes a shotgun technique for sequencing a genome?

A)genetic mapping followed immediately by sequencing
B)physical mapping followed immediately by sequencing
C)cloning large genome fragments into very large vectors, followed by sequencing
D)cloning several sizes of fragments into various size vectors, sequencing the clone and then ordering them
E)cloning the whole genome directly, from one end to the other

Question 10

What is bioinformatics?

A)a technique using 3-D images of genes in order to predict how and when they will be expressed
B)a method that uses very large national and international databases to access and work with sequence information
C)a software program available from NIH to design genes
D)a series of search programs that allow a student to identify who in the world is trying to sequence a given species
E)a procedure that uses software to order DNA sequences in a variety of comparable ways

Question 11

The biggest problem with the shotgun technique is its tendency to underestimate the size of the genome.Which of the following might best account for this?

A)skipping some of the clones to be sequenced
B)missing some of the overlapping regions of the clones
C)counting some of the overlapping regions of the clones twice
D)having some of the clones die during the experiment and therefore not be represented
E)short repetitive sequences hinder reassembly

Question 12

What is proteomics?

A)the linkage of each gene to a particular protein
B)the study of the full protein set encoded by a genome
C)the totality of the functional possibilities of a single protein
D)the study of how amino acids are ordered in a protein
E)the study of how a single gene activates many proteins

Question 13

Barbara McClintock,who achieved fame for discovering that genes could move within genomes,had her meticulous work ignored for nearly four decades,but eventually won the Nobel Prize.Why was her work so distrusted?

A)The work of women scientists was still not allowed to be published.
B)Geneticists did not want to lose their cherished notions of DNA stability.
C)There were too many alternative explanations for transposition.
D)She allowed no one else to duplicate her work.
E)She worked only with maize, which was considered "merely" a plant.

Question 14

What characteristic of short tandem repeat DNA makes it useful for studying evolution?

A)The number of repeats varies widely from person to person or animal to animal.
B)The sequence of DNA that is repeated varies significantly from individual to individual.
C)The sequence variation is acted upon differently by natural selection in different environments.
D)Every racial and ethnic group has inherited different short tandem repeats.
E)Each short tandem repeat can be correlated with a specific disease.

Question 15

Bioinformatics can be used to scan sequences for probable genes looking for start and stop sites for transcription and for translation,for probable splice sites,and for sequences that specify known mRNAs.Such sequences containing these elements are called

A)expressed sequence tags.
B)cDNA.
C)multigene families.
D)proteomes.
E)short tandem repeats.

Question 16

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)the many tandem repeats such as those found in centromeres and telomeres.
D)a gene whose exons can be spliced in a number of different ways.
E)a highly conserved gene found in a number of different species.

Question 17

What is gene annotation in bioinformatics?

A)identifying protein coding regions within a sequence
B)describing the functions of protein-coding genes
C)describing the functions of noncoding regions of the genome
D)matching the corresponding phenotypes of different species
E)comparing the protein sequences within a single phylum

Question 18

What is the most probable explanation for the presence of pseudogenes in a genome such as our own?

A)They are genes that had a function at one time, but that have lost their function because they have been translocated to a new location.
B)They are genes that have accumulated mutations to such a degree that they would code for different functional products if activated.
C)They are duplicates or near duplicates of functional genes but cannot function because they would provide inappropriate dosage of protein products.
D)They are genes with significant inverted sequences.
E)They are genes that have acquired mutations and are not expressed, even though they have nearly identical sequences to expressed genes.

Question 19

Fragments of DNA have been extracted from the remnants of extinct woolly mammoths,amplified,and sequenced.These can now be used to

A)introduce into relatives, such as elephants, certain mammoth traits.
B)clone live woolly mammoths.
C)study the relationships among woolly mammoths and other wool-producers.
D)understand the evolutionary relationships among members of related taxa.
E)appreciate the reasons why mammoths went extinct.

Question 20

What is metagenomics?

A)genomics as applied to a species that most typifies the average phenotype of its genus
B)the sequence 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
E)genomics as applied to an entire phylum

Question 21

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)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)STRs are found in eukaryotes; transposable elements are found in prokaryotes.

Question 22

The large common repository for genetic sequences hosted by NCBI is called

A)GenBank.
B)BLAST.
C)GenesRus.
D)Prodata.
E)TreeNoMix.

Question 23

What is the benefit of metagenomics?

A)A community assemblage can be determined through mass sequencing and each specific species does not have to be isolated and cultured.
B)High throughput sequencing allows for faster identification of the genome.
C)It allows for a systems approach to genomics, relating parts of the organism to other parts.
D)It combines bioinformatics with genomics to get a clearer picture.
E)Many labs can work on the same problem and place the information into a shared database.

Question 24

In comparing the genomes of humans and those of other higher primates,it is seen that humans have a large metacentric pair we call chromosome 2 among our 46 chromosomes,whereas the other primates of this group have 48 chromosomes and any pair like the human chromosome 2 pair is not present; instead,the primate groups each have two pairs of midsize acrocentric chromosomes.What is the most likely explanation?

A)The ancestral organism had 48 chromosomes and at some point a centric fusion event occurred and provided some selective advantage.
B)The ancestral organism had 46 chromosomes, but primates evolved when one of the pairs broke in half.
C)At some point in evolution, human ancestors and primate ancestors were able to mate and produce fertile offspring, making a new species.
D)Chromosome breakage results in additional centromeres being made in order for meiosis to proceed successfully.
E)Transposable elements transferred significantly large segments of the chromosomes to new locations.

Question 25

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
E)a very large transposition

Question 26

Gene sequences that remain very similar over many species are said to be

A)the same.
B)noncoding regions.
C)highly conserved.
D)of the same family.
E)resistant to mutation.

Question 27

Which of the following can be duplicated in a genome?

A)DNA sequences above a minimum size only
B)DNA sequences below a minimum size only
C)entire chromosomes only
D)entire sets of chromosomes only
E)sequences, chromosomes, or sets of chromosomes

Question 28

Which of the following studies would not likely be characterized as evo-devo?

A)the study of a particular species to see whether or not it has developmental regulation
B)a study of the assortment of homeotic genes in the zebra
C)a comparison of the functions of a particular homeotic gene among four species of reptiles
D)a study of the environmental pressures on developmental stages such as the tadpole
E)a fossil comparison of organisms from the Devonian era

Question 29

It took 13 years and multiple labs to complete the first sequencing of the human genome (from 1990-2003).In 2007,a lab could complete the task in four months.This dramatic change in time to completion is a result of

A)more importance being placed on it and thus more money being put into it.
B)the development of high throughput methods and equipment.
C)more scientists becoming interested in the subject.
D)there being an initial learning curve; now we are proficient at it.
E)repetition: once the first one was done, it was easier to repeat it.

Question 30

A project initiated at the University of Guelph is attempting to catalogue the differences of a short sequence within the mitochondrial DNA in all animal species.This ________ should allow the quick identification of a species.

A)shotgun approach
B)DNA barcoding
C)microarray
D)genechip
E)STR DNA

Question 31

In order to determine the probable function of a particular sequence of DNA in humans,what might be the most reasonable approach?

A)Prepare a knockout mouse without a copy of this sequence and examine the mouse phenotype.
B)Genetically engineer a mouse with a copy of this sequence and examine its phenotype.
C)Look for a reasonably identical sequence in another species, prepare a knockout of this sequence in that species, and look for the consequences.
D)Prepare a genetically engineered bacterial culture with the sequence inserted and assess which new protein is synthesized.
E)Mate two individuals heterozygous for the normal and mutated sequences.

Question 32

A consortium of 25 Canadian scientists,led by Dr.Rudnicki at the University of Ottawa,is looking at gene expression in both ________ cells.This is important in understanding regenerative medicine.

A)embryonic and adult stem
B)muscle and nervous tissue
C)RNA and DNA in
D)differentiation and post-fertilized
E)transposable elements and heterochromatin

Question 33

A recent report has indicated several conclusions about comparisons of our genome with that of Neanderthals.This report concludes,in part,that,at some period in evolutionary history,there was a mixture of the two genomes.This is evidenced by

A)some Neanderthal sequences not found in humans.
B)a small number of modern H. sapiens with Neanderthal sequences.
C)Neanderthal Y chromosomes preserved in the modern population of males.
D)mitochondrial sequences common to both groups.
E)lack of FOXP2 in humans

Question 34

The α-globin and β-globin gene families are found on different chromosomes in humans.What is the suspected reason for this?

A)They evolved at different times.
B)There was a gene duplication event.
C)The α-globin originally coded for a different protein family.
D)Our ancestors didn't use the α-globin genes.
E)They were originally on the same chromosome but one set was moved via transposable elements.

Question 35

Researchers at the University of British Columbia are working on a way to analyze gene expression within a single cell as it differentiates.This is significant because

A)cDNA libraries could be made.
B)tissue identification would be easier.
C)RNA is needed to understand expression and probing a cell as it undergoes differentiation is impossible at this point.
D)DNA within a single cell is difficult to extract.
E)generation of totipotent adult stem cells would be possible.

Question 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.Which of the following would you then expect?

A)that homeotic genes are selectively expressed over developmental time
B)that a homeobox-containing gene has to be a developmental regulator
C)that homeoboxes cannot be expressed in nonhomeotic genes
D)that all organisms must have homeotic genes
E)that all organisms must have homeobox-containing genes

Question 37

What are genomic "hot spots"?

A)the locations that correspond to most genetic diseases
B)the areas of a genome that most often mutate due to environmental effects
C)the locations that most often correspond with chromosomal breakpoints
D)the locations that correspond to most genetic diseases and the locations that most often correspond with chromosomal breakpoints
E)the locations that correspond to most genetic diseases, the areas of a genome that most often mutate due to environmental effects, and the locations that most often correspond with chromosomal breakpoints

Question 38

Why is it more difficult to identify eukaryotic genes than prokaryotic genes?

A)because in eukaryotes the proteins are larger than in prokaryotes
B)because in eukaryotes the coding portions of genes are shorter than in prokaryotes
C)because in eukaryotes there are no start codons
D)because in eukaryotes there are introns
E)because in eukaryotes there are more short tandem repeats

Question 39

Approximately how many bacterial genomes are in the process of being sequenced?

A)10
B)100
C)2 000
D)5 000
E)15 000

Question 40

When does exon shuffling occur?

A)during splicing of DNA
B)during mitotic recombination
C)as an alternative splicing pattern in post-transcriptional processing
D)as an alternative cleavage or modification post-translationally
E)as the result of faulty DNA repair

Question 41

Use the following information to answer the questions below.
You have isolated a gene sequence from the mustard plant Arabidopsis and have BLAST searched the NCBI database.Your sequence hit several EST sequences that were identified as transcription factors.These sequences were found in E.coli,Chlamydomonas (a green algae),yeast,mice,and humans and only had a few base pair differences.
What can be said about this sequence?

A)It appears to be highly conserved.
B)It has had many duplication events.
C)It is an ancient gene.
D)This sequence has been transposed to other species.
E)It must be junk DNA.

Question 42

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
E)bioinformatics

Question 43

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.
E)are responsible for patterning during plant development.

Question 44

Use the following figure to answer the next few questions.

This 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.
Why is sequencing of eukaryotic genomes more difficult than sequencing genomes of bacteria or archaea?

A)because of the large size of eukaryotic proteins
B)because of hard-to-find proteins
C)because of the high proportion of G-C base pairs in eukaryotic DNA
D)because of the large size of eukaryotic genomes and the large amount of eukaryotic repetitive DNA
E)because a different technique must be used to sequence eukaryotic DNA

Question 45

Use the following information to answer the questions below.
You have isolated a gene sequence from the mustard plant Arabidopsis and have BLAST searched the NCBI database.Your sequence hit several EST sequences that were identified as transcription factors.These sequences were found in E.coli,Chlamydomonas (a green algae),yeast,mice,and humans and only had a few base pair differences.
What can be surmised about your transcription factor?

A)It is likely involved in a universal metabolic function.
B)There is not enough information to conclude anything.
C)It is unique to Arabidopsis.
D)It is part of a large gene family.
E)It is a transgene.

Question 46

Using modern techniques of sequencing by synthesis and the shotgun approach,how are sequences assembled into chromosomes?

A)by placing sequences on previously generated genetic maps
B)by cloning sequences into plasmid vectors
C)by computer analysis looking for sequence overlaps
D)by cloning sequences into plasmid vectors, placing them on previously generated genetic maps, followed by computer analysis looking for sequence overlaps
E)by ligating sequence fragments together

Question 47

Use the following information to answer the questions below.
You have isolated a gene sequence from the mustard plant Arabidopsis and have BLAST searched the NCBI database.Your sequence hit several EST sequences that were identified as transcription factors.These sequences were found in E.coli,Chlamydomonas (a green algae),yeast,mice,and humans and only had a few base pair differences.
When you compared your sequence to the database,what were you practising?

A)good science
B)proteomics
C)bioinformatics
D)computer skills
E)shotgun research

Question 48

What is an early step in shotgun 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
D)sequence fragments

Question 49

Use the following figure to answer the next few questions.

This 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.
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.
E)higher mammals have more convergence of gene sequences related in function.

Question 50

What does it mean if genomic DNA matches the sequence of a cDNA?

A)The genomic DNA likely codes for a protein.
B)The genomic DNA likely codes for an rRNA.
C)The genomic DNA is likely part of an intron.
D)The genomic DNA is likely to be a regulatory sequence.
E)The genomic DNA is likely to be repetitive DNA.

Question 51

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 by annotating the genome of the new plant.Why does the company do this?

A)to determine what proteins are produced
B)to determine what mRNA transcripts are produced
C)to identify genes and determine their functions
D)to identify the location of mRNA within the plant cells
E)to determine the location of the plants introns

Question 52

Use the following figure to answer the next few questions.

This 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.
In humans,hemoglobin in the embryo has a higher affinity for oxygen than in adults.What is this 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 change shape during embryonic development
E)different promotors

Question 53

Bioinformatics includes all of the following except

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

Question 54

Use the following figure to answer the next few questions.

This 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.
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)intron activation
C)pseudogene activation
D)differential translation of mRNAs
E)differential gene regulation over time

Question 55

Use the following figure to answer the next few questions.

This 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.
How might identical and obviously duplicated gene sequences have gotten from one chromosome to another?

A)by normal meiotic recombination
B)by normal mitotic recombination between sister chromatids
C)by transcription followed by recombination
D)by chromosomal translocation
E)by deletion followed by insertion

Question 56

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)list of most common repetitive DNA sequences

Question 57

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
E)the number of short tandem repeats

Question 58

Based on the systems approach employed by the ENCODE project,what percentage of the genome is estimated to contain functional elements (including functional RNAs and regulatory sequences)?

A)less than 2%
B)about 25%
C)about 50%
D)at least 80%
E)100%

Question 59

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)RNA splicing
C)exon shuffling
D)histone modification
E)random point mutations

Question 60

One of the characteristics of retrotransposons is that

A)they code for an enzyme that synthesizes DNA using an RNA template.
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.
E)their amplification is dependent on a retrovirus.

Question 61

Human and chimpanzee share most of their nucleotide sequence yet exhibit significant phenotypic differences.What is likely to be the most important sequence differences between these two species?

A)structural genes
B)the number of repeated sequences
C)regulatory sequences
D)environmental factors
E)introns

Question 62

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 be logically 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 mice are not primates.
E)Vocalizations were not important for Neanderthals.

Question 63

Which of the following variations in human DNA sequences involves duplication of relatively long stretches of chromosomes,often including the duplication of protein-coding genes?

A)copy number variants
B)single nucleotide polymorphisms
C)short tandem repeats
D)transposable elements
E)exon shuffling

Question 64

What is most likely if genes from different species are determined to be homologous?

A)The genes descended from a common ancestor.
B)Homology is observed because of convergent evolution.
C)The homology is a result of chance mutations.
D)Homology is found in gene structure but the function of the gene products will be different.
E)The species being compared will also have a similar genome size and structure.