Deck 9: Functional and Comparative Genomics

Question 1

The drug ________ is added to mouse cell cultures to select against transformants that do not have the desired gene knockout.

A)ampicillin
B)kanamycin
C)neomycin
D)G418
E)ganciclovir

Answer 1

E

Question 2

A transgene is a

A)hybrid gene.
B)gene that contains no introns.
C)bacterial gene that is found in mammalian cells.
D)human gene of viral origin.
E)gene introduced into an organism by artificial means.

Answer 2

E

Question 3

The ________ gene is responsible for removing many of the drugs introduced into the human body.

A)HAR-1
B)CYP2D6
C)ASPM
D)FOXP2
E)BRCA1

Answer 3

B

Question 4

Metagenomic analysis involves

A)culturing microbes isolated from the environment.
B)extracting DNA from cultured microbes.
C)analyzing DNA from environmental samples.
D)sequencing cloned DNA individually.
E)determining culture conditions for different microbes.

Question 5

The representational oligonucleotide microarray analysis (ROMA)represents

A)a functional genomics approach.
B)a structural genomics approach.
C)a comparative genomics approach.
D)a metagenomics approach.
E)a pharmacogenomics approach.

Question 6

Linkage disequilibrium refers to a condition in which

A)a set of SNPs recombine often.
B)a set of haplotypes recombine often.
C)a set of specific alleles of two or more genes tend to appear together.
D)a set of specific alleles of two or more genes only rarely appear together.
E)a haplotype block rearranges every generation.

Question 7

If you are setting up a PCR reaction,how much extension time per cycle should you allocate for the Taq DNA polymerase to amplify a 5-kb DNA fragment from a 10-kb template?

A)1 minute
B)2.5 minutes
C)5 minutes
D)10 minutes
E)20 minutes

Question 8

Which of the following statements correctly describes reverse genetics?

A)A mutated phenotype in an organism leads to the associated gene.
B)A mutated gene is introduced into an organism to determine the phenotype.
C)A gene is studied to understand the protein it encodes.
D)A transcript is used to make a protein encoded by a gene.
E)A gene is identified by bioinformatics.

Question 9

The subfield of genomics that deals with gene expression and interaction is

A)comparative genomics.
B)functional genomics.
C)structural genomics.
D)hypothetical genomics.
E)expression genomics.

Question 10

Which of the following is not used in PCR amplification of DNA?

A)Double-stranded DNA template
B)Oligonucleotide primers
C)DNA polymerase
D)Buffer
E)ddNTPs

Question 11

Which of the following is an archaean that has been identified in the human gut?

A)Escherichia coli
B)Enterobacter aerogenes
C)Bifidobacterium longum
D)Methanobrevibacter smithii
E)Caenorhabditis elegans

Question 12

Which of the following does not occur during PCR?

A)Denaturation at high temperatures
B)Synthesis of oligonucleotide primers
C)Annealing of oligonucleotide primers
D)Extension of primers by DNA polymerase
E)Changes in the reaction temperature by a thermocycler

Question 13

The Alu family is an example of

A)short interspersed repeat elements.
B)intermediate repeat elements.
C)long interspersed repeat elements.
D)terminal sequences.
E)gene-flanking sequences.

Question 14

A genomic region can rapidly become very common in a population due to

A)positive selection.
B)negative selection.
C)specific selection.
D)linkage equilibrium.
E)homologous recombination.

Question 15

The human-accelerated region 1 (HAR-1)gene

A)was identified by functional genomics.
B)is identical to the chimpanzee HAR-1.
C)encodes for the human accelerated region-1 protein.
D)is a small,noncoding RNA expressed in the brain.
E)is a small,regulatory RNA that regulates gene expression.

Question 16

RNA interference functions by

A)degrading the protein encoded by a specific mRNA.
B)degrading the RNA strand that is encoded by the Slicer gene.
C)transcribing double-stranded RNA into protein.
D)disrupting the chromosomal copy of the gene.
E)degrading the RNA complementary to the short,double-stranded RNA.

Question 17

The polymerase chain reaction has revolutionized genetics because

A)it is capable of making virtually unlimited copies of DNA for study.
B)it is capable of making copies of DNA with very little starting material.
C)it is capable of making large numbers of DNA copies very quickly.
D)All of these
E)A and B only

Question 18

Which of the following triggers the RNAi pathway?

A)mRNA
B)rRNA
C)tRNA
D)shRNA
E)snRNA

Question 19

Pharmacogenomics is the study of how

A)the genome affects responses to drugs.
B)the genome leads to new drug discoveries.
C)the genome affects microbial communities in the body.
D)the genome is affected by drug use.
E)medicines influence the genome of cancer cells.

Question 20

Sequence similarity between genes plays an important role in assigning gene function.

Question 21

Why is the Taq DNA polymerase well-suited for PCR?

Question 22

What are the different methods by which we can assign function to particular genes?

Question 23

Calculate the number of copies that would be produced from a single starting molecule after 10 rounds of PCR.

Question 24

Imagine that you are using random PCR primers to amplify fragments of DNA.Would you expect to get more amplification products if you set the PCR machine at a higher or lower annealing temperature and why?

Question 25

The transcriptome is the complete set of polypeptides produced by an organism.

Question 26

List the steps involved in constructing a knockout mutant in yeast.

Question 27

The genome of cancer cells tends to become unstable.

Question 28

The 16S rRNA gene from human gut microflora was amplified and sequenced to understand how the gut microbes are related.

Question 29

Both strands of the short,double-stranded regulatory RNA molecules are required by the Slicer protein in order to target the complementary RNA for degradation.

Question 30

Why are BLAST comparisons based on protein sequences often easier to interpret than those based on DNA sequences?

Question 31

BLAST is a software that searches for similarities between DNA sequences only.

Question 32

The FOXP2 protein appears to play a critical role in brain size regulation.

Question 33

Cy3 and Cy5 are radioactive tags used in microarrays.

Question 34

Bioinformatics is a relatively new field that combines elements of genomics with computer science and mathematics.

Question 35

"Knockout" mutants have had the activities of certain genes eliminated,which can aid the researchers in determining the effects of those genes on physiology,development,and other functions.

Question 36

What is the difference between a "knockout" and a "knockdown" of a gene?

Question 37

A microbiome consists of

A)all the microorganisms on Earth.
B)the community of microorganisms in a particular environment.
C)the transcriptome from a particular microorganism under different environments.
D)the proteome from a particular microorganism under different environments.
E)the proteome from different microorganisms in a particular environment.

Question 38

Why are the number of proteins in the eukaryotic proteome so much greater than the number of eukaryotic genes?

Question 39

After how many PCR cycles,starting from a single starting molecule,will fragments consisting of only the target DNA (the DNA between the primers)be generated?

Question 40

How do we know that some of the microbes in our gut are beneficial to us?

Question 41

How can we explain the fact that the human genome contains far fewer genes than was predicted would be necessary for our survival?

Question 42

What does a large haplotype block suggest about a genomic region?

Question 43

What is one advantage that an RNAi screen may have over a screen for gene knockouts?

Question 44

Why are two selectable markers present in the target vector used for making mouse gene knockouts?

Question 45

Why does the transcriptome differ within an organism's cell types?