Deck 17: Genomes

Question 1

The human genome

A) contains very few repeated sequences.
B) has 3.3 billion base pairs.
C) was sequenced by hierarchical sequencing only.
D) has genes evenly distributed along chromosomes.
E) has few genes with introns.

Answer 1

B

Question 2

Which of the following statements about the Human Genome Project (HGP) is false?

A) The sequencing of smaller genomes helped in the development of methods that benefited the HGP.
B) Only privately funded groups were involved in the sequencing effort.
C) The HGP was in part spurred on by a desire to determine the specific DNA damage caused by radiation from the atomic blasts on Japan during World War II.
D) One objective of the HGP was to identify genetic changes associated with disease.
E) All of the above are true; none is false.

Answer 2

B

Question 3

In what way does a ddNTP differ from its dNTP counterparts?

A) The ddNTP has an extra - COOH group.
B) The ddNTP has an extra - OH group.
C) The ddNTP is missing an - OH group.
D) The ddNTP is a doublet of the dNTP.
E) The ddNTP is not attached to the base.

Answer 3

The ddNTP is missing an - OH group.

Question 4

Eukaryotic protein-coding genes differ from their prokaryotic counterparts in that eukaryotic genes

A) are double-stranded.
B) are present in only a single copy.
C) contain introns.
D) have promoters.
E) are transcribed into mRNA.

Question 5

In the situation described above, which sequence does enzyme A recognize as a site at which to cut? (Note that the enzyme cuts in the middle of its recognition sequence.)

A) GTTA
B) ACGT
C) TGGA
D) CGCG
E) GTCG

Question 6

Suppose a long sequence of DNA is cut with four different restriction enzymes. Which restriction enzyme should produce the fewest number of fragments?

A) One that cuts at the sequence GACT
B) One that cuts at the sequence GCCTCT
C) One that cuts at the sequence AGTTCTAT
D) One that cuts at the sequence CAGTTCTATG
E) Each of these enzymes should produce roughly the same number of fragments.

Question 7

The genomes of the fruit fly and the nematode are similar to that of yeast, except that the former organisms have many genes for

A) intercellular signaling.
B) synthesis of polysaccharides.
C) cell cycle regulation.
D) intracellular protein targeting.
E) transposable elements.

Question 8

The minimum genome of Mycoplasma genitalium

A) has 100 genes.
B) has been used to create new species.
C) has an RNA genome.
D) is larger than the genome of E. coli.
E) was derived by transposon mutagenesis.

Question 9

The DNA sequences that code for eukaryotic rRNA

A) are transcribed only at the ribosome.
B) are repeated hundreds of times.
C) contain all the genes clustered directly beside one another.
D) are on only one human chromosome.
E) are identical to the sequences that code for miRNA.

Question 10

Which of the following about genome sequencing is true?

A) In hierarchical sequencing, but not high-throughput sequencing, DNA is amplified in BAC vectors.
B) In hierarchical sequencing, a genetic map is made after the DNA is sequenced.
C) Shotgun sequencing is considerably slower than hierarchical sequencing.
D) The human genome was first sequenced by high-throughput methods.
E) DNA sequence determination by chain termination is the basis of shotgun sequencing only.

Question 11

A comparison of the genomes of yeast and bacteria shows that only yeast has many genes for

A) energy metabolism.
B) cell wall synthesis.
C) intracellular protein targeting.
D) DNA-binding proteins.
E) RNA polymerase.

Question 12

The gene most responsible for differences in size among different breeds of dogs is the _______ gene.

A) myostatin
B) phosphofructokinase
C) insulin-like growth factor
D) tyrosine growth factor
E) giant

Question 13

What is the major disadvantage of hierarchical sequencing as compared to shotgun sequencing?

A) Hierarchical sequencing requires more sophisticated computer algorithms.
B) Hierarchical sequencing requires special restriction enzymes, whereas shotgun sequencing does not.
C) Hierarchical sequencing requires more steps than shotgun sequencing, and hence is slower.
D) Both a and b are disadvantages.
E) None of the above is a disadvantage.

Question 14

In hierarchical sequencing, what role do bacterial artificial chromosomes play?

A) They are used to amplify and maintain copies of a given sequence.
B) They are used to determine the chromosomal location of a given sequence fragment.
C) They are used to break DNA into fragments.
D) Each one contains a genomic library.
E) None of the above; bacterial artificial chromosomes are not used in hierarchical sequencing.

Question 15

Which of the following is a disadvantage of shotgun sequencing as compared to hierarchical sequencing?

A) Shotgun sequencing requires a more detailed genetic map.
B) Shotgun sequencing requires the use of bacterial artificial chromosomes.
C) Shotgun sequencing is more expensive.
D) Shotgun sequencing relies more on careful aligning of DNA fragments.
E) None of the above

Question 16

The maximum length of DNA that can be sequenced at one time by means of the standard technology is about _______ bases.

A) 700
B) 3,000
C) 7,000
D) 30,000
E) 70,000

Question 17

Which is not true of metagenomics?

A) It has been done with bacteria.
B) It is done on rRNA sequences.
C) It has revealed many new metabolic capacities.
D) It involves extracting DNA from the environment.
E) It cannot be done on seawater.

Question 18

Transposons

A) always use RNA for replication.
B) are approximately 50 bp long.
C) are made up of either DNA or RNA.
D) do not contain genes coding for proteins.
E) make up about 40 percent of the human genome.

Question 19

Increasing the activity of myostatin in a dog will most likely lead to

A) increased muscle development.
B) decreased muscle development.
C) increased size.
D) decreased size.
E) a change in coat color.

Question 20

Vertebrate gene families

A) have mostly inactive genes.
B) include the globins.
C) are not produced by gene duplications.
D) increase the number of unique genes in the genome.
E) are not transcribed.

Question 21

During the process of gene expression, RNA polymerase would most likely be found

A) in a highly repetitive sequence.
B) in a noncoding sequence.
C) in an open reading frame.
D) at a metagenomic site.
E) in a pseudogene.

Question 22

_______ are the host of the bacterium Haemophilus influenzae.

A) Dogs
B) Humans
C) Birds
D) Both a and b
E) None of the above

Question 23

The causative agent of SARS is

A) a Gram-positive bacterium.
B) a Gram-negative bacterium.
C) a virus.
D) a fungus.
E) unknown.

Question 24

By necessity, which of the following will be included in an open reading frame?

A) A transposable element
B) A start codon
C) A chromatin sequence
D) Regulatory sequences
E) All of the above

Question 25

The first free-living organism to have its complete genome sequenced was

A) the bacterium Haemophilus influenzae.
B) the bacterium Mycoplasma genitaliu.
C) the fruitfly Drosophila melanogaster.
D) the typhus-causing bacterium Rickettsia prowazekii.
E) E. coli strain 0157:H7.

Question 26

Which of the following statements about chromosome structure and function is false?

A) Telomere sequences are found at the ends of chromosomes.
B) Remodeling of chromatin structure can alter gene expression.
C) A chromosome has a single DNA molecule.
D) Short tandem repeats are an example of noncoding DNA.
E) All of the above are true; none is false.

Question 27

The bacterium responsible for the most common sexually transmitted disease in the United States is

A) Streptomyces coelicolor.
B) Rickettsia prowazekii.
C) Chlamydia trachomatis.
D) Treponema pallidum.
E) Neisseria gonorrhoeae.

Question 28

The florescent dye attached to ddNTPs in DNA sequencing

A) aids in visualization of the DNA strand when the ddNTP is incorporated.
B) acts as a catalyst for the reaction.
C) terminates the reaction.
D) aids in electrophoresis.
E) None of the above

Question 29

The bacterium that is the source for most of the naturally occurring antibiotics in current clinical use is

A) Streptomyces coelicolor.
B) Rickettsia prowazekii.
C) Chlamydia trachomatis.
D) E. coli 0157:H7.
E) Haemophilus influenzae.

Question 30

The major difference between noninfective strains of Haemophilus influenzae and highly infective strains is that

A) the infective strains have genes for glycolysis that the noninfective strains lack.
B) the noninfective strains lack the enzymes needed to synthesize amino acids.
C) the infective strains have surface proteins that attach the bacterium to respiratory tracts.
D) the noninfective strains lacks open reading frames.
E) the infective and noninfective strains have different regulatory sequences.

Question 31

A promoter is an example of a(n)

A) open reading frame.
B) transposable element.
C) chromatin sequence.
D) rRNA gene.
E) regulatory sequence.

Question 32

Massively parallel sequencing can sequence about _______ base pairs of DNA within seven hours.

A) 5,000
B) 50,000
C) 5,000,000
D) 50,000,000
E) 5,000,000,000

Question 33

Which of the following would not be required for the purpose of determining the sequence of a 400-base-pair DNA fragment by the standard ddNTP sequencing method?

A) The four dNTPs (dATP, dCTP, dGTP, dTTP)
B) DNA polymerase
C) A short, artificially synthesized primer
D) A bacterial artificial chromosome
E) All of the above would be required.

Question 34

Which of the following statements about transposable elements is true?

A) Their insertion into genes can disrupt gene function.
B) Their position can vary in different strains of bacteria.
C) All are transposons.
D) Both a and b
E) Both b and c

Question 35

In DNA sequencing, ddNTPs are added at much lower concentrations than are dNTPs. If ddNTPs were added at higher concentrations, what would be the most likely result?

A) The ddNTPs would bind to one another.
B) All of the reactions would terminate early and long strands would not be produced.
C) The reactions would terminate early or late.
D) The ddNTPs would bind to DNA polymerase.
E) The ddNTPs would not bind to the dye.

Question 36

Which of the following is used in massively parallel DNA sequencing but not in conventional sequencing?

A) ddNTPs
B) The polymerase chain reaction
C) Microbeads
D) Both a and b
E) Both b and c

Question 37

Studies find that a bacterium of the genus Buchnera has been living as a parasite of aphids for many millions of years. This bacterium lacks certain genes that are involved in the production of the cell wall found in other related bacteria. The field of biology in which such studies were carried out is called

A) metagenomics.
B) eukaryotic genomics.
C) proteomics.
D) comparative genomics.
E) haplotype mapping.

Question 38

A lab sequencing the DNA of various species of pathogenic bacteria with the goal of determining their evolutionary relationships would be practicing _______ genomics.

A) functional
B) operational
C) meta-
D) comparative
E) eukaryotic

Question 39

Which of the following statements about the pathogenic strain 0157:H7 of E. coli is true?

A) It differs from the harmless laboratory strains of E. coli by only a few genes.
B) It shares several genes with other pathogenic bacteria, suggesting extensive genetic exchange among these species.
C) It is the primary cause of tuberculosis in the United States.
D) Both a and b
E) Both a and c

Question 40

Craig Venter, a leader of one of the teams that sequenced the human genome, has now turned his attention to cataloging the microbial life of the oceans. His studies, which involve PCR amplification of microbial DNA and a sequencing of the PCR products, are part of a field of biology called

A) functional genomics.
B) transposon-tagging.
C) proteomics.
D) phenomics.
E) metagenomics.

Question 41

Which of the following is most likely to be required for the evolution of a pseudogene?

A) Natural selection
B) A highly repetitive sequence
C) A transposable element
D) A gene family
E) Heterochromatin

Question 42

In what way is the genome of Arabidopsis most unlike that of the typical plant?

A) It has very few plant defense genes.
B) It has very few photosynthesis genes.
C) It has much more repetitive DNA.
D) It is much smaller.
E) It does not have duplicate genes.

Question 43

Selective inactivation studies show that the minimal genome of a C. elegans worm consists of about _______ genes.

A) 400
B) 2,000
C) 10,000
D) 20,000
E) 100,000

Question 44

Which of the following statements about the nematode C. elegans is false?

A) It has a transparent body.
B) Despite having a small number of cells, it has a nervous system.
C) Despite having a small number of cells, it can reproduce sexually.
D) It normally lives in soil.
E) All of the above are true; none is false.

Question 45

Which of the following is least likely to be associated with metagenomics?

A) Bacterial culture techniques
B) Shotgun sequencing
C) Comparative genomics
D) PCR
E) Sampling from the field

Question 46

Which of the following is likely to be found in a eukaryotic genome but not in a prokaryotic one?

A) Regulatory sequences
B) Coding sequences
C) Open reading frames
D) RNA genes
E) Telomeric sequences

Question 47

The minimal genome for a free-living bacterium that can survive in the laboratory is likely to consist of _______ genes.

A) 50 or fewer
B) about 50 to 100
C) about 100 to 500
D) about 500 to 2,000
E) more than 2,000

Question 48

In some species of moths, the genes that make chorion for the eggshell are found in multiple copies in order to maximize the production of chorion at specific times. In this regard, these chorion genes are most like

A) pseudogenes.
B) highly repetitive DNA.
C) rRNA genes.
D) transposons.
E) introns.

Question 49

Which of the following techniques or tools is most suited to determining the minimal genome of a free-living bacterium?

A) Metagenomics
B) Haplotype mapping
C) Hierarchical sequencing
D) Bacterial artificial chromosomes
E) Selective inactivation of genes

Question 50

Which of the following statements about pseudogenes is true?

A) There often is little selective pressure to get rid of pseudogenes.
B) The sequences of a pseudogene and its functional counterpart must be very different.
C) In some gene families, pseudogenes outnumber functional genes.
D) Both a and b
E) Both a and c

Question 51

Which of the following statements comparing the worm C. elegans and the fly D. melanogaster is true?

A) The fly has a larger genome.
B) The fly has more genes.
C) The fly undergoes a more complicated developmental transformation.
D) Both a and b
E) Both a and c

Question 52

The most striking difference between the genomes of E. coli and S. cerevisae is that the yeast genome contains many more genes devoted to

A) metabolism.
B) membrane transport.
C) DNA replication, repair, and recombination.
D) targeting proteins to organelles.
E) energy production and storage.

Question 53

Which of the following is required for the formation of gene families?

A) Repetitive DNA
B) Pseudogenes
C) Transposable elements
D) Regulatory sequences
E) Gene duplication

Question 54

Which of the following statements about genomes is true?

A) Most genes found in the genomes of complex multicellular organisms are not required for survival.
B) As complexity increases from bacteria to yeast to invertebrate to vertebrate, gene number increases more than does the size of the genome.
C) As complexity increases from bacteria to yeast to invertebrate to vertebrate, the proportion of the genome consisting of coding sequence increases.
D) Both a and b
E) Both b and c

Question 55

Which of the following statements about the globin genes in humans is false?

A) They are all expressed at the same time.
B) They all arose from a single common ancestor gene a long time ago.
C) They are an example of a gene family.
D) Some of the different genes carry out different functions.
E) All of the above are true; none is false.

Question 56

Think about what you know about the comparative genomics of plants (such as Arabidopsis) and animals (such as the nematode C. elegans) and imagine the following scenario. If a plant were to acquire mobility, such that it could more easily escape adverse conditions and enemies, genes involved in which of the following functions would most likely be lost over evolutionary time?

A) Photosynthesis
B) Cell signaling
C) Plant defense
D) Cell growth
E) Metabolism

Question 57

Which of the following statements about eukaryotic genomes is false?

A) They tend to be larger than prokaryotic genomes.
B) They tend to have more regulatory sequences than prokaryotic genomes.
C) The percentage of the genome devoted to coding sequence is higher than in prokaryotic genomes.
D) They usually have more repetitive DNA than prokaryotic genomes.
E) All of the above are true; none is false.

Question 58

Humans have roughly _______ the number of genes as D. melanogaster and about _______ the number of genes as S. cerevisae.

A) twice; twice
B) twice; six times
C) six times; six times
D) six times; 100 times
E) 100 times; 1000 times

Question 59

Techniques associated with which of the following are most likely to generate ethical concerns?

A) Metagenomics
B) Creation of a minimal genome
C) Shotgun sequencing
D) Hierarchical sequencing
E) Comparative genomics

Question 60

You are told that a genome is about 10 Mb long, has 5,000 genes, and that 65% of its sequence is coding sequence. This genome most likely belongs to a(n)

A) virus.
B) bacterium.
C) yeast.
D) plant.
E) animal.

Question 61

Which of the following is a major difference between LINEs and SINEs?

A) Proteins are translated from LINEs but not from SINEs.
B) SINEs make RNA copies of themselves, whereas LINEs do not.
C) LINEs make RNA copies of themselves, whereas SINEs do not.
D) SINEs are larger than LINEs.
E) SINEs can move from place to place in the genome, whereas LINEs cannot.

Question 62

Which of the following statements would be considered an expression of genetic determinism?

A) The proteome is more complex than the genome.
B) The phenotype is a reflection of the genotype.
C) Studying genes provides a limited understanding of what is going on in the cell.
D) The metabolome exerts considerable influence on the likelihood of a person's developing diabetes.
E) High levels of glucose may be an indicator of coronary heart disease.

Question 63

The usefulness of genomic scans for determining the likelihood that a person will eventually develop diabetes is limited because

A) multiple genes contribute to the development of the disease.
B) environmental factors influence the likelihood of contracting the disease.
C) epigenetic factors play a role in whether one will acquire the disease.
D) All of the above
E) None of the above

Question 64

Two-dimensional gel electrophoresis separates proteins based on _______ and _______.

A) size; concentration
B) size; shape
C) size; charge
D) concentration; shape
E) shape; charge

Question 65

Which of the following fields or approaches is most likely to lead directly to a reduction in the negative side effects associated with a drug used to treat diabetes?

A) Comparative genomics
B) Metagenomics
C) Metabolomics
D) Pharmacogenomics
E) Selective inactivation

Question 66

Which of the following techniques, tools, or activities would be most directly connected to identifying the genetic variants associated with a complex human disease like schizophrenia?

A) Determining the metabolome
B) Selective inactivation
C) Metagenomics
D) Haplotype mapping
E) Performing a pseudogene screen

Question 67

Which of the following is an example of a secondary metabolite?

A) Tannins produced by oak trees to ward against herbivores
B) The enzyme phosophofructokinase used in glycolysis
C) Hemoglobin used to carry oxygen in the blood
D) Both a and b
E) Both b and c

Question 68

Which of the following human chromosomes has the fewest genes?

A) Chromosome 1
B) Chromosome 19
C) Chromosome 21
D) The X chromosome
E) The Y chromosome

Question 69

A piece of DNA that is 3 kb in length is found in many locations throughout the genome. How would you decide whether this was a LINE or a DNA transposon?

A) Count the number of copies in the genome. If it has more than 10,000 copies, it is a LINE; if not, it is a DNA transposon.
B) Count the number of copies in the genome. If it has more than 10,000 copies, it is a DNA transposon; if not, it is a LINE.
C) If it contains the sequence GCTCGATC it is a LINE; if not, it is a DNA transposon.
D) If it uses an RNA intermediate, it is a LINE; if not, it is a DNA transposon.
E) If it uses a copy and paste mechanism of copying, it is a DNA transposon; if not, it is a LINE.

Question 70

Which of the following statements about the human proteome is false?

A) It is the sum total of all proteins produced by an organism.
B) It is more complex than the genome.
C) It includes the small molecules found in a cell.
D) Its study often involves two-dimensional gel electrophoresis.
E) All of the above are true; none is false.

Question 71

What percentage of the human genome is DNA that codes for proteins?

A) Less than 5%
B) Between 5 and 15%
C) Between 15 and 25%
D) Between 25 and 40%
E) Over 40%

Question 72

Which of the following statements comparing the human genome to that of invertebrates like C. elegans and D. melanogaster is true?

A) A larger fraction of DNA in the human genome is for coding proteins.
B) The human genome is more than ten times larger.
C) The average human gene codes for more proteins than the average invertebrate gene.
D) Both a and b
E) Both b and c

Question 73

The Human Genome Project could not have proceeded without the new field of _______, which uses complex mathematics and computer programs to analyze DNA sequences.

Question 74

Genomic information can be stored in a _______, which is a collection of many different cloned fragments of the genome.

Question 75

The Alu element, which accounts for over 10% of the human genome, is an example of a

A) LINE.
B) SINE.
C) halotype.
D) globin gene.
E) DNA transposon.

Question 76

What is the most likely explanation for the abundance of transposons in eukaryotic genomes?

A) They are needed to provide mutations.
B) They are needed to increase genetic recombination.
C) They are genomic parasites.
D) They assist in the process of DNA repair.
E) They provide reverse transcriptase.

Question 77

A study comparing the proteins that are produced in sperm cells to those of skin cells would be an example of

A) comparative genomics.
B) functional genomics.
C) pharmacogenomics.
D) metabolomics.
E) proteomics.

Question 78

In the context of metabolomics, glucose would be considered a

A) haplotype.
B) primary metabolite.
C) secondary metabolite.
D) tertiary metabolite.
E) None of the above

Question 79

Which of the following diseases is most unlike the others with respect to its genetic basis?

A) Coronary heart disease
B) Sickle cell anemia
C) Alzheimer's disease
D) Type I diabetes
E) Rheumatoid arthritis

Question 80

Which of the following is not a main type of transposon in the human genome?

A) SINEs
B) LINEs
C) DNA transposons
D) Retrotransposons
E) Each of the above is a main type of human transposon.