Deck 18: Genomics

Question 1

Recombination frequency between genes can be used to generate a

A)genetic map.
B)physical map.
C)restriction map.
D)haplotype map.

Answer 1

A

Question 2

Sequences of DNA assembled by identifying overlaps among smaller DNA segments are known as

A)single strand polymorphisms.
B)synteny.
C)draft sequences.
D)the proteome.
E)a contig.

Answer 2

E

Question 3

A defining characteristic of draft sequences is that they have

A)many gaps in regions of highly repetitive DNA.
B)less than 1 error in 10,000 nucleotides.
C)been found in various proteomes across the eukaryote life forms.
D)been produced by alternative splicing.
E)several problems,the main one being their contiguous DNA fragments.

Answer 3

A

Question 4

Both dideoxy terminator and next-generation sequencing methods require a genomic library to be constructed prior to sequencing the DNA of interest.

Question 5

Humans are diploid organisms,containing two sets of chromosomes.How many sets of chromosomes does wheat,Triticum aestivum,have?

A)1
B)2
C)4
D)6
E)8

Question 6

To avoid confusion and facilitate ease of data interpretation,researchers working on cloned DNA from the same species use

A)restriction fragment length polymorphisms.
B)shotgun sequencing.
C)sequenced-tagged sites.
D)clone by clone sequencing.
E)consensus sequencing.

Question 7

The majority of DNA in a human can be described as

A)composed of short interspersed elements.
B)noncoding.
C)simple sequence repeats.
D)segmental duplications.
E)structural.

Question 8

The sequencing method that cuts the DNA of an entire chromosome into small fragments and then clones these fragments is called

A)shotgun sequencing.
B)clone-by-clone sequencing.
C)RFLP sequencing.
D)consensus sequencing.

Question 9

The sequencing method that cuts DNA segments into fragments,arranges those fragments based on overlapping nucleotide sequences,and then clones these fragments is called

A)shotgun sequencing.
B)clone-by-clone sequencing.
C)RFLP sequencing.
D)consensus sequencing.

Question 10

When comparing the genomes of prokaryotes verse eukaryotes,it can be accurately stated that

A)eukaryotic genomes are larger than prokaryotic genomes.
B)eukaryotic genomes are smaller than prokaryotic genomes.
C)the size of the organism determines the size of the genome.
D)larger and more complex organisms have more genes than smaller,less complex organisms.

Question 11

A large portion (45%)of the human genome is composed of

A)introns.
B)exons.
C)templates.
D)transposons.
E)pseudogenes.

Question 12

Distances on a genetic map are measured in ________ units.

A)centromere
B)DNA
C)dalton
D)centimorgan

Question 13

Match each of the following characteristics with the appropriate sequencing method. • Next-generation sequencing
• Dideoxy terminator sequencing
• Both dideoxy terminator and next-generation sequencing

Question 14

The relative location of genes on a chromosome as determined by recombination frequencies is illustrated in a ________ map.

A)DNA
B)genetic
C)chromosomal
D)physical

Question 15

You have been asked to construct a physical map of the baboon genome.What would be helpful in this task?

A)Chromosome maps and STSs
B)BLAST and ENCODE data
C)Gene linkage data
D)Microarrays and SAGE

Question 16

Which of the following were challenges that had to be overcome to sequence the genome of wheat,Triticum aestivum? (Select all that apply)

A)Lack of advanced sequencing technology
B)Large genome size (~5 times as large as human genome)
C)High mutation rate of wheat genes
D)Lack of interest/support in sequencing the genome
E)An abundance of repetitive DNA

Question 17

Given a sequencing reaction length of approximately 500 successive nucleotides,what is the absolute minimum number of sequencing reactions needed to determine the complete human genome,excluding overlap and redundancy?

A)3)1 billion
B)6200
C)12.4 million
D)6)2 million

Question 18

Using actual landmarks within DNA sequences,scientists can generate a ________ map.

A)genetic
B)DNA
C)physical
D)chromosomal

Question 19

The organism with the largest relative genome size is

A)rice.
B)human.
C)fruit fly.
D)yeast.

Question 20

When comparing the actual number of genes,the organism with the highest number is

A)rice.
B)human.
C)fruit fly.
D)yeast.

Question 21

A human gene is composed of numerous fragments of protein-encoding information known as ________.

A)DNA
B)mRNA
C)exons
D)introns

Question 22

The current estimates of the ENCODE project for percent functionality of the human genome based on the ENCODE definition of functionality is ________ the estimate of functionality based on the selected-effect functionality definition.

A)greater than
B)less than
C)equal to

Question 23

The reason segmental duplications pose a logistical challenge in the proper alignment of DNA sequences is that they

A)are inherently repetitive.
B)contain large numbers of LINEs,which interfere with sequence annotation.
C)interfere with BLAST analysis.
D)are often found in areas of constitutive heterochromatin.

Question 24

You are studying a novel protein.To learn more about it,you performed a screen in yeast to identify proteins that could interact with it.From the screen you got a clone for a second gene.You had the clone sequenced,and you translated the gene sequence on your computer.What is the next logical step to learn more about the function of these two proteins?

A)Run a BLAST search.
B)Identify the intron/exon organization.
C)Localize the gene to a specific chromosomal region.
D)Search the human genome sequence for your clone.

Question 25

Non-coding DNA regions within a gene are referred to as

A)introns.
B)exons.
C)templates.
D)transposons.
E)pseudogenes.

Question 26

Groups of related,but distinctly different genes that appear to have arisen from a single ancestral gene are referred to as

A)segmental duplications.
B)pseudogenes.
C)tandem clusters.
D)multigene families.
E)expressed sequences.

Question 27

The important advances stemming from comparative genomics include the ability to (Select all that apply)

A)draw particular conclusions about species.
B)draw general conclusions about evolution.
C)infer function about an unsequenced genome using synteny.
D)develop a haplotype map.
E)distinguish how proteins bind to receptors.

Question 28

An accurate and comprehensive description of pseudogenes must include the statement that (Select all that apply)

A)pseudogenes may have some gene-like features such as a promoter and splice sites.
B)pseudogenes encode proteins,but the translated proteins are non-functional.
C)pseudogenes can provide insight into the evolutionary history of the related functional gene.
D)every pseudogene has a similar DNA sequence to some functional gene.
E)all pseudogene pretend to transcribe other genes when they only transcribe one type of genetic information.

Question 29

Long interspersed elements (LINEs)are a type of

A)pseudogene.
B)proteome.
C)exon.
D)intron.
E)transposon.

Question 30

The primary significance of the 1000 Genomes Project is to

A)take into account the variation in human genomes across populations.
B)account for the inherent error rate of sequencing by including a greater sample size.
C)identify the 1000 most important genes to human health.
D)trace human ancestors back 1000 years.

Question 31

The ENCODE project seeks to

A)sequence the genomes of all animals.
B)sequence the DNA of all organisms.
C)identify the coding sequences of human DNA.
D)identify the functional elements of the human genome.
E)identify the proteins encoded by the human genome.

Question 32

Every cell within one organism has the same genome.In what way(s)can these cells differ from each other? (Select all that apply)

A)Number of chromosomes
B)Ratio of organelles
C)Proteins produced
D)Number of genes in the DNA
E)Surface area of cell membrane

Question 33

The inclusive term that describes all of the DNA in the nucleus of a cell is its

A)genome.
B)chromosome.
C)gene.
D)proteome.

Question 34

Identical copies of genes that can be transcribed simultaneously are called

A)segmental duplications.
B)pseudogenes.
C)tandem clusters.
D)multigene families.
E)expressed sequences.

Question 35

The ends of chromosomes are called ________.

A)telomeres
B)centromeres
C)caps
D)DNA termini

Question 36

In your research,you are comparing the transcriptome and the proteome for two related species.One gene in species B has a similar transcript but a much smaller protein than in species A,and the protein seems to be nonfunctional.What do you predict about this gene? (Select all that apply)

A)It is a pseudogene.
B)It will have an increased number of persistent mutations in species B.
C)It probably has a STOP codon early in the coding region.
D)It probably has a defect in the enhancer region.
E)It probably is not methylated correctly.

Question 37

Silent copies of genes that have been inactivated by mutations are called

A)pseudogenes.
B)clones.
C)exons.
D)introns.

Question 38

Mobile bits of DNA that can jump from one location on a chromosome to another location are called

A)simple sequence repeats.
B)transposons.
C)exons.
D)introns.
E)pseudogenes.

Question 39

Some regions of chromosomes remain highly condensed,tightly coiled,and untranscribed throughout the cell cycle.These regions are referred to as

A)transposable elements.
B)single sequence repeats.
C)noncoding DNA.
D)short interspersed elements.
E)constitutive heterchromatin.

Question 40

Your research group has recently determined the complete genomic sequence of the organism Examus biologisium.You instruct your group to begin sequence annotation,which involves

A)shotgun cloning.
B)the alignment of contigs.
C)the identification of open reading frames.
D)the construction of a genetic map.

Question 41

Your research team has been asked to quantify levels of cellular RNAs in rats before and after exercise.The primary focus of your work will be to analyze the

A)proteome.
B)spliceosome.
C)nucleosome.
D)different RNA motifs.
E)transcriptome.

Question 42

The most ethical decisions for usage of genomic data and technology,like sequencing human genomes for customized treatments and constructing deadly pathogens for study,are based on (Select all that apply)

A)consensus in the scientific community.
B)oversight from governmental agencies.
C)the directives of large financial donors.
D)what can safely be achieved in the laboratory.
E)subjectivity.

Question 43

A pharmaceutical company is developing a new drug to treat a rare disease.They need to determine which of the cell's proteins can bind the drug.What tool can help them survey the proteome for drug interactions?

A)Protein microarray
B)DNA microarray
C)SAGE
D)ENCODE
E)Using a monoclonal antibody

Question 44

The best technique for detecting chromosomal abnormalities is

A)EST
B)FISH
C)STS
D)SNP

Question 45

In the United States it is currently legal for a company to patent genes.

Question 46

In vertebrates,the family of myogenic regulatory factors (MRFs)plays a major role in muscle development.This family consists of four related genes which have distinct but overlapping functions.This gene family is represented by only a single gene in Drosophila,called nautilus.You want to know whether nautilus plays a role like all of the MRFs put together,or more like one in particular.What is a quick and easy way to begin to address this question?

A)Compare the DNA and protein sequences of all the genes to determine if nautilus is more similar to one MRF than another.
B)Use a DNA microarray to compare gene activation patterns between nautilus and the MRFs.
C)Compare the proteome of a cell expressing nautilus to the those of cells expressing each of the MRFs in turn.
D)Generate four transgenic Drosophila strains that express the MRFs in a mutant nautilus background.

Question 47

As a scientist working for an anti-bioterrorism task force,you are asked to evaluate some biological samples for the presence of Yersinia pestis,the organism that causes the plague.After confirming that the samples do contain Y.pestis,you instruct your team to begin sequencing the strain.Since the genome sequence of Y.pestis is already known,why would sequencing this strain be useful?

A)To provide better data for the genome database
B)To establish the course of infection,and determine whether the strain is altered by causing infection
C)To help determine the source of the strain,and learn whether it has been genetically engineered
D)To create a vaccine for this particular strain

Question 48

Conserved arrangements of segments of DNA in related genomes are referred to as

A)synteny.
B)homology.
C)analogous DNA.
D)a contig.
E)a comparative genome.

Question 49

Rice and its grain relatives,maize,barley,and wheat,diverged from a common ancestor 50 million years ago.However,the chromosomes of these plants demonstrate extensive conserved arrangements of segments.This phenomenon is called

A)linkage disequilibrium.
B)single nucleotide polymorphisms.
C)contig.
D)synteny.
E)expressed sequence equilibrium.

Question 50

Microarrays are created by robotically placing DNA on to a microscope slide and probing with

A)RNA from the tissue of interest.
B)another DNA from the tissue of interest.
C)SNPs from the tissue of interest.
D)STSs from the tissue of interest.
E)clone-by-clone sequencing.

Question 51

How did the rice genome project influence other genome projects?

A)It was the first genome sequenced,so it proved it could be done.
B)It sped up the genome analysis of other cereal crops,due to synteny.
C)It sped up the analysis of the human genome,since rice has even more genes.
D)It helped analysis of all genomes,since it was the basis of the ENCODE algorithms.

Question 52

As the director of a new nonprofit functional genomics research center,it is your job to oversee the set up of each laboratory necessary for achieving the center's research goals.Therefore,you plan to include a(n)(Select all that apply)

A)DNA microarray facility.
B)proteomics lab.
C)lab to improve sequencing speed and cost.
D)mutagenesis facility.
E)ancient DNA laboratory.