BIOL 241 Exam 3 Multiple Choice

While analyzing the function of an unknown eukaryotic gene, you noticed that it contains leucine zippers. Based on this information, this gene is likely to:

a. Code for a microRNA.

b. Regulate alternative splicing.

c. Code for a protein that forms dimers.

d. Code for a protein that binds to translational regulatory elements.

e. Code for a protein that repairs DNA.

c. Code for a protein that forms dimers.

Functional transformer (tra) proteins are made in Drosophila females, but not in males. This is accomplished by:

a. The binding of male-specific or female-specific Dsx (double sex) transcription factor to Tra promoter.

b. The binding of Dsx microRNA to Tra mRNA.

c. The binding of Sxl mcroRNA to Tra mRNA.

d. The Sxl-mediated alternative splicing.

e. The sex-specific methylation Tra promoter by Sxl.

d. The Sxl-mediated alternative splicing.d. The Sxl-mediated alternative splicing.

Regarding siRNA, which of the following statements is correct?

a. The RISC complex cleaves injected-dsRNA into short 21 base pairs of dsRNA.

b. siRNA usually binds to target mRNA at specific sites in the 3' UTR.

c. siRNA usually binds to target mRNA at specific sites in the coding sequence.

d. siRNA mediates gene silencing by predominantly inhibiting translation.

e. siRNA mediates gene silencing by degrading target mRNA.

e. siRNA mediates gene silencing by degrading target mRNA.

The Ames test demonstrates that:

a. Spontaneous mutations are random.

b. Certain chemicals, after processed by liver enzymes, are mutagenic.

c. Transcription factors bind to DNA at specific sequences.

d. Nucleosomes in eukaryotic chromosomes can be remodeled.

e. Certain proteins are capable of interacting with each other in vivo.

b. Certain chemicals, after processed by liver enzymes, are mutagenic.

The human disease xeroderma pigmentosum is caused by disruption of:

a. Base excision repair pathway.

b. SOS response.

c. Homologous recombination repair pathway.

d. Mismatch repair pathway.

e. Nucleotide excision repair pathway.

e. Nucleotide excision repair pathway.

Which of the following events is most likely to cause frameshift mutations?

a. Tautomeric shifts.

b. Deamination of cytosines.

c. Depurinations.

d. Treating cells with base analogs.

e. Treating cells with intercalating agents.

e. Treating cells with intercalating agents.

A microarray (gene-chip) experiment is useful for:

a. Detecting RFLP between two homologous chromosomes.

b. Detecting homologous genes between two species.

c. Detecting phosphorylation targets of a particular kinase.

d. Determining the possible alternative sliced isoforms from a particular gene.

e. Comparing the level of mRNA of different genes between cells at two different states.

e. Comparing the level of mRNA of different genes between cells at two different states.

hich of the following statements best describes the generation of expressed sequence tags (ESTs)?

a. Sequencing of transcription factor-bound DNA.

b. Sequencing ends of genomic DNA clones.

c. Sequencing of gaps between contigs.

d. Sequencing ends of cDNA clones.

e. Sequencing of genomic DNA clones from euchromatic regions.

d. Sequencing ends of cDNA clones.

In Drosophila, mutants generated by engineered P-elements allow the technique of plasmid rescue. The goal of this technique is to:

a. Position the gene functions along a pathway.

b. Determine whether the mutations are loss-of-function or gain-of-function.

c. Recover the genomic DNA flanking the inserted P-element.

d. Mobilize the P-elements to insert transposons into new locations.

e. Purify the mRNA from rRNA and tRNA.

c. Recover the genomic DNA flanking the inserted P-element.

Comparing genomes from various prokaryotic species, which of the following statements is correct?

a. Prokaryotic organisms contain mostly linear chromosomes.

b. Different prokaryotic organisms contain similar amount of genomic DNA.

c. Genes in prokaryotic organisms are always expressed as single-gene mRNAs.

d. Genes in prokaryotic organisms contain introns.

e. Prokaryotic genomes contain few repetitive sequences.

e. Prokaryotic genomes contain few repetitive sequences.

The genome size of Staphylococcus aureus, a gram-positive bacterium, is 2.88mb (106 bases). Based on the comparison of prokaryotic genomes, the number of genes in Staphylococcus aureus is expected to be:

a. 28000.

b. 14000.

c. 4000.

d. 2800.

e. 1400.

d. 2800.

Horizontal gene transfer is likely facilitated by:

a. Transposon-mediated DNA movement from one chromosome to a non-homologous chromosome.

b. The transfer of DNA from agarose gel onto nitrocellulose membrane.

c. The transformation by DNA from closely related species.

d. The detection of clones containing specific DNA on nitrocellulose membrane with radioactively labeled probes.

e. The mating between F+ and F- bacterial strains.

c. The transformation by DNA from closely related species.

hich of the following statements is an example of synteny?

a. α and β globin genes show similarities in their amino acid sequences.

b. α and β globin genes show similarities in the intron positions.

c. α and β globin genes exhibit different temporal regulations of their respective expressions.

d. E. coli and B. subtilis exhibit similar gene density.

e. Rice and sorghum show similarities in the order of genes along the chromosomes.

e. Rice and sorghum show similarities in the order of genes along the chromosomes.

Comparing gene density, which of the following statements is correct?

a. Genomes of different prokaryotic species have similar gene densities.

b. Eukaryotic genomes on average have higher gene density (number of genes/kb) than the prokaryotic genomes

c. Genomes of different eukaryotic species have similar gene densities.

d. Gene density is uniform along different human chromosomes.

e. Gene density is uniform along each human chromosome.

a. Genomes of different prokaryotic species have similar gene densities.

Comparing human and C. elegans genomes, which of the following features is similar?

a. The amount of DNA.

b. The number of genes.

c. The number of introns per gene.

d. The average size of introns.

e. The number of identified protein domains.

e. The number of identified protein domains.

When using 2D gels to separate the cellular proteins, the proteins are first separated by:

a. Their molecular weights.

b. Their ability to bind to DNA.

c. Their mass-to-charge ratios.

d. Their electric charges.

e. Their ability to form disulfide bonds.

d. Their electric charges.

When a haploid petite mutant mates with haploid normal yeast, the resulting diploid zygote exhibits the normal phenotype. After sporulation (meiosis), all haploid progeny are normal. This pattern of inheritance describes:

a. Segregational petite.

b. Neutral petite.

c. Suppressive petite.

d. Haploinsufficient.

e. Dominant negative.

b. Neutral petite.

A different yeast petite mutant is isolated. To determine the type of mutation causing this phenotype, the haploid petite and wild type strains are crossed. The diploid zygotes are petite, and all the haploid ascospores after sporulation are petite. The explanation for this mutation is that:

a. It disrupts a nuclear gene that participates in mitochondrial function.

b. The inheritance of mitochondrial genome in yeast is strictly maternal.

c. The inheritance of mitochondrial genome in yeast is strictly paternal.

d. It affects mitochondrial genes, which disrupt mitochondrial function, but gives normal mitochondria proliferation advantage.

e. It affects mitochondrial genes, which disrupt mitochondrial function, but gives defective mitochondria proliferation advantage.

e. It affects mitochondrial genes, which disrupt mitochondrial function, but gives defective mitochondria proliferation advantage.

Regarding mitochondrial genomes, which of the following statements is incorrect?

a. The mitochondrial genome is a circular DNA.

b. Human mitochondrial genome contains ~17kb of DNA.

c. Most of the mitochondrial proteins are encoded by the mitochondrial genome.

d. The inheritance of mitochondrial genome in human is maternal.

e. The mitochondrial genome encodes genes that are critical for energy metablism.

c. Most of the mitochondrial proteins are encoded by the mitochondrial genome.

The ChIP (chromatin immunoprecipitation) assays will identify:

a. The differences in mRNA abundances of different genes between cells at two different states.

b. The differences in restriction sites between two homologous chromosomes.

c. The protein-protein interactions.

d. The sequences of transcription enhancer elements.

e. The sequences of intron/exon boundaries of different genes.

d. The sequences of transcription enhancer elements.

Which of the following techniques will be useful for identifying proteins that physically bind to protein-of-interest?

a. Yeast 2-hybrid screen.

b. Luria and Delbruck fluctuation test.

c. 2-dimentional gel.

d. Microarray analysis.

e. Epitasis test.

a. Yeast 2-hybrid screen.

To generate mouse mutants by homologous recombination, researchers often make a targeting construct, which contains a flanking thymidine kinase gene. The purpose of this thymidine kinase gene is to:

a. Mediate the transposition of the targeting construct when it is integrated into the ES cell genome.

b. Serve as a marker to selecting ES cells with constructs integrated by homologous recombination.

c. Increase the efficacy of construct integration into the embryonic stem (ES) cell genome.

d. Increase the likelihood that transfected ES cells become germ cells when injected into blastocyst.

e. Serve as a selectable marker for the presence of the targeting construct in the ES cell genome.

b. Serve as a marker to selecting ES cells with constructs integrated by homologous recombination.

n using the CRISPR/Cas system for genomic editing, the specificity of Cas9 is controlled by?

a. Palindromic restriction sites.

b. MicroRNA.

c. Flanking direct repeats.

d. Flanking inverted repeats.

e. Guide RNA.

e. Guide RNA.

In eukaryotic gene regulation, which of the following events is likely to be associated with an increase in gene transcription?

a. Methylation of cytosines in CG islands near a transcription unit.

b. Deacetylation of lysines in histone tails near a transcription unit.

c. Acetylation of lysines histone tails near a transcription unit.

d. The expression of microRNAs with sequences complementary to the promoter regions.

e. The binding the transcription factors to silencer elements.

c. Acetylation of lysines histone tails near a transcription unit.

Regarding the helix-turn-helix motif, which of the following statements is correct?

a. This motif allows proteins to repair specific DNA damages.

b. This motif allows microRNAs to bind to their targets.

c. This motif allows RNA-binding proteins to regulate alternative splicing.

d. This motif allows proteins to be imported into the nucleus.

e. This motif allows proteins to bind to specific regulatory DNA sequences.

e. This motif allows proteins to bind to specific regulatory DNA sequences.

After analyzing the sequence of a gene, you have found that it contains leucine zippers. Based on this, which of the following statements is correct?

a. This gene encodes a microRNA.

b. This gene encodes a protein that forms dimers.

c. The gene encodes a protein that binds to RNA.

d. This domain allows the protein to bind to specific DNA sequences.

e. This domain allows the protein to cleave dsRNA into smaller pieces.

b. This gene encodes a protein that forms dimers.

The Drosophila DSCAM locus is capable of expressing multiple isoforms. This is accomplished by:

a. Duplication of the DSCAM gene onto different chromosomes.

b. Transcription initiation from alternative promoters.

c. Translation inhibition by small non-coding RNA.

d. The usage of alternative transcription termination sites.

e. Alternative splicing.

e. Alternative splicing.

Regarding siRNA, which of the following statements is incorrect?

a. Dicer cleaves injected-dsRNA into short 21 base pairs of dsRNA.

b. siRNA usually binds to target mRNA at specific sites in the 3' UTR.

c. siRNA is typically perfectly complementary to target mRNA.

d. siRNA typically negatively regulates gene expression.

e. siRNA mediates gene silencing by degrading target mRNA.

b. siRNA usually binds to target mRNA at specific sites in the 3' UTR.

The Luria-Delbrück fluctuation test demonstrated that:

a. Spontaneous mutations are random.

b. Certain chemicals, after processed by liver enzymes, are mutagenic.

c. Transcription factors bind to DNA at specific sequences.

d. Nucleosomes in eukaryotic chromosomes can be remodeled.

e. Certain proteins are capable of interacting with each other in vivo.

a. Spontaneous mutations are random.

Regarding xeroderma pigmentosum (XP), which of the following statements is incorrect?

a. XP is caused by mutations in the components of nucleotide excision repair pathway.

b. XP mutations are typically autosomal recessive.

c. Individuals with XP are sensitive to UV light.

d. Individuals with XP are often freckled and have high disposition for skin cancers.

e. XP is caused by mutation in the components of mismatch repair pathway.

e. XP is caused by mutation in the components of mismatch repair pathway.

Which of the following events is most likely to cause translocations?

a. Tautomeric shifts.

b. Treating cells with X rays.

c. Depurinations.

d. Treating cells with base analogs.

e. Treating cells with intercalating agents.

b. Treating cells with X rays.

Sequencing the ends of clones from cDNA library is known as?

a. Sanger sequencing.

b. Maxam-Gilbert sequencing.

c. Map-based sequencing.

d. Expressed sequence tag sequencing.

e. Shotgun sequencing.

d. Expressed sequence tag sequencing

Bisulfite sequencing is typically used to determine:

a. The methylation state of histone proteins in eukaryotic chromosomes.

b. The DNA sequence of whole eukaryotic genomes.

c. The acetylation state of histone proteins in c eukaryotic chromosomes.

d. The methylation state of DNA in eukaryotic chromosomes.

e. This DNA sequence of actively transcribed genes in eukaryotic genomes.

d. The methylation state of DNA in eukaryotic chromosomes.

Which of the following techniques can detect the difference between two homologous chromosomes?

a. Chromatin immunoprecipitation.

b. Screening cDNA libraries.

c. Chromosome walking.

d. Restriction fragment length polymorphism.

e. Screening genomic libraries.

d. Restriction fragment length polymorphism.

The ChIP (chromatin immunoprecipitation) assays will identify:

a. The differences in mRNA abundances of different genes between cells at two different states.

b. The differences in restriction sites between two homologous chromosomes.

c. The protein-protein interactions.

d. The sequences of transcription enhancer elements.

e. The sequences of intron/exon boundaries of different genes

d. The sequences of transcription enhancer elements.

The dideoxynucleotides (ddNTP) differ from dNTP in:

a. The absence of nitrogen base at the 1' position.

b. The absence of triphosphate at the 5' position.

c. The presence of diphosphate at the 5' position.

d. The absence of hydroxyl group at the 2' position.

e. The absence of hydroxyl group at the 3' position.

e. The absence of hydroxyl group at the 3' position.

Which of the following statements accurately describes the advantage of using RNAi in a genetic screen?

a. RNAi completely inhibits the expression of targeted genes.

b. The identification of genes affected by RNAi is instantaneous.

c. RNAi can only be used in haploid cells.

d. RNAi does not cause off-target effects.

e. RNAi can only be used in diploid cells.

b. The identification of genes affected by RNAi is instantaneous.

Which of the following approaches can be used to introduce specific changes in Drosophila genome?

a. Feeding male flies with EMS.

b. Irradiating male flies with X rays.

c. Mobilizing P element transposons by expressing functional transposase.

d. Injecting embryos with specific gRNA and Cas9 nuclease.

e. Injecting embryos with dsRNA.

d. Injecting embryos with specific gRNA and Cas9 nuclease.

To generate mouse mutants by homologous recombination, researchers often make a targeting construct, which contains a flanking thymidine kinase gene. The purpose of this thymidine kinase gene is to:

a. Serve as a marker to selecting ES cells with constructs integrated by homologous recombination.

b. Increase the efficacy of construct integration into the embryonic stem (ES) cell genome.

c. Increase the likelihood that transfected ES cells become germ cells when injected into blastocyst.

d. Serve as a selectable marker for the presence of the targeting construct in the ES cell genome.

e. Mediate the transposition of the targeting construct when it is integrated into the ES cell genome.

a. Serve as a marker to selecting ES cells with constructs integrated by homologous recombination.

1) If the CpG sequences near the promoter of a eukaryotic gene are under-methylated, this suggests that:

a. This gene is being actively transcribed.

b. This gene encodes a microRNA.

c. This gene has multiple alternatively spliced variants.

d. This gene is not being actively transcribed.

e. This gene is located in heterochromatin.

a. This gene is being actively transcribed.

Regarding eukaryotic transcription enhancers, which of the following statements is correct?

a. They enhance transcription initiation only when they are within 1kb of the core promoter sequence.

b. They enhance transcription initiation only when they are located upstream of the core promoter sequence.

c. They enhance transcription initiation only when they are located downstream of the core promoter sequence.

d. They can enhance transcription initiation from a great distance.

e. They enhance transcription initiation only when other enhancer elements are present.

d. They can enhance transcription initiation from a great distance.

While analyzing the function of an unknown eukaryotic gene, you notice that it contains a helix-turn-helix motif. Based on this information, this gene is likely to:

a. Code for a DNA-binding protein.

b. Regulate transcription.

c. Code for a protein localized in the nucleus.

d. All of the above.

e. None of the above.

d. All of the above.

As mentioned in class, the Drosophila DSCAM gene is required for axonal repulsion. The DSCAM locus is capable of expressing multiple isoforms. This is accomplished by:

a. Binding of microRNA to the promoter sequence.

b. Binding of microRNA to the 3'UTR of mRNA.

c. Alternative usage of different exons during splicing.

d. Incorporation of the DSCAM mRNA into the RISC complex.

e. The usage of alternative transcription initiation sites.

c. Alternative usage of different exons during splicing.

The Ames test demonstrates that:

a. Spontaneous mutations are random.

b. Certain chemicals, after processed by liver enzymes, are mutagenic.

c. Transcription factors bind to DNA at specific sequences.

d. Nucleosomes in eukaryotic chromosomes can be remodeled.

e. Certain proteins are capable of interacting with each other in vivo.

b. Certain chemicals, after processed by liver enzymes, are mutagenic.

A new restriction enzyme has been discovered. Digestion of DNA with this enzyme produces restriction fragments that average 4000 bps in length. Based on this, what is likely the number of base pairs in the recognition sequence of this enzyme?

a. 4 bps.

b. 6 bps.

c. 8 bps.

d. 1 kb.

e. 4 kb.

b. 6 bps.

Which of the following vectors have the largest insert capacity?

a. Plasmid.

b. λ phage.

c. Cosmid.

d. Bacterial artificial chromosome.

e. PCR.

d. Bacterial artificial chromosome.

Which of the following enzymes will recognize the bases generated by deamination of cytosines in the DNA?

a. AP endonuclease.

b. Uracil DNA glycosylase.

c. 3'-5' exonuclease of DNA polymerase 1.

d. Photolyase.

e. DNA ligase.

b. Uracil DNA glycosylase.

The E. coli mismatch repair system distinguishes the newly synthesized strand from the old template by:

a. The presence of thymine dimers in the newly synthesized DNA.

b. The presence of methylated cytosines in the newly synthesized DNA.

c. The lack of methylation of adenines at the GATC sequences in the newly synthesized DNA.

d. The presence of bulky bases in the newly synthesized DNA.

e. The lack of methylated cytosines in the newly synthesized DNA.

c. The lack of methylation of adenines at the GATC sequences in the newly synthesized DNA.

To generate mouse mutants by homologous recombination, the targeting construct often contains a flanking thymidine kinase gene. The purpose of this thymidine kinase gene is to:

a. Increase the efficacy of construct integration into the embryonic stem (ES) cell genome.

b. Increase the likelihood that transfected ES cells become germ cells when injected into blastocyst.

c. Serve as a selectable marker for the presence of the targeting construct in the ES cell genome.

d. Serve as a marker to selecting ES cells with constructs integrated by homologous recombination.

e. Mediate the transposition of the targeting construct when it is integrated into the ES cell genome.

d. Serve as a marker to selecting ES cells with constructs integrated by homologous recombination.

Which of the following enzymes is involved in cleaving injected-dsRNA into short 21 base pairs of dsRNA?

a. 3' to 5' exonuclease.

b. Photolyase.

c. Dicer.

d. RISC complex.

e. dam methylase.

c. Dicer.

Which of the following mutagens is most likely to cause one base insertion and deletion?

a. Ethylmethane sulfonate.

b. 5-bromouracil.

c. Acridine orange.

d. UV light.

e. Ionizing irradiation.

c. Acridine orange.

Which of the following techniques will be useful for detecting physical interaction between different proteins?

a. Yeast 2-hybrid screen.

b. Luria and Delbruck fluctuation test.

c. Gel mobility shift assay.

d. Microarray (gene chip) analysis.

e. Epitasis test.

a. Yeast 2-hybrid screen.

Comparing genomes from various prokaryotic species, which of the following statements is correct?

a. Prokaryotic organisms contain mostly linear chromosomes.

b. Different prokaryotic organisms contain similar amount of genomic DNA.

c. Genes in prokaryotic organisms are frequently expressed as poly-cistronic mRNA.

d. Genes in prokaryotic organisms contain small introns.

e. Most prokaryotic genomes contain two circular chromosomes.

c. Genes in prokaryotic organisms are frequently expressed as poly-cistronic mRNA.

Comparing gene density, which of the following statements is correct?

a. Human genome on average has higher gene density (number of genes/kb) than Drosophila genome.

b. Genomes of different eukaryotic species have the same gene density.

c. The gene density of E. coli genome is vastly different from other prokaryotic species.

d. The gene density of eukaryotic genomes is usually higher than those of prokaryotic genomes.

e. None of the above.

e. None of the above.

The ChIP (Chromatin Immuno-precipitation) assay is useful for:

a. Detecting RFLP between two homologous chromosomes.

b. Detecting a direct interaction between two proteins.

c. Identify the binding sites for a sequence-specific transcription activator.

d. Determining the alternative spliced isoforms from a particular gene.

e. Comparing the level of mRNA of different genes between cells at two different states.

c. Identify the binding sites for a sequence-specific transcription activator.

In Sanger's sequencing method, the chain terminators differ from dNTP in:

a. The absence of triphosphate at the 5' position.

b. The absence of hydroxyl group at the 2' position.

c. The absence of hydroxyl group at the 3' position.

d. The presence of methylation in the cytosines.

e. The presence of methylation at the 3' hydroxyl group.

c. The absence of hydroxyl group at the 3' position.

Spontaneous mutations caused by depurination are likely to be?

a. Insertions.

b. Deletions.

c. Base substitutions.

d. Nonsense mutations.

e. Inversions.

c. Base substitutions.

Which of the following characteristics is the main reason that annotation of eukaryotic genomes is challenging?

a. Different eukaryotic genomes have different codon biases.

b. Eukaryotic genes often contain large introns.

c. Eukaryotic genomes contain significant levels of repetitive DNA.

d. In general, eukaryotic mRNAs are longer than those from prokaryotes.

e. Eukaryotic genomes contain more DNA.

b. Eukaryotic genes often contain large introns.

Overexpression of dam methylase in E. coli is likely to?

a. Reduce the mutation rate.

b. Increase the mutation rate.

c. Have no effect on the mutation rate.

d. Increase the expression of mismatch repair genes.

e. Decrease the expression of mismatch repair genes.

b. Increase the mutation rate.

Which of the following events is an example of a direct repair:

a. Repair of TT dimers by photolyase.

b. Repair of TT dimers by UvrA, UvrB, and UvrC enzymes.

c. Repair of uracils in the DNA by BER.

d. Repair of mismatches by the E. coli MutS, MutH, and MutL.

e. Repair of double-stranded breaks by homologous recombination.

a. Repair of TT dimers by photolyase

The human disorder xeroderma pigmentosum is caused by mutations in:

a. Base excision repair.

b. Photoreactivation repair.

c. Nucleotide excision repair.

d. Homologous recombination repair.

e. DNA polymerase proofreading.

c. Nucleotide excision repair.

Regarding 5-bromouracil, which of the following statements is correct?

a. It effectively induces insertion and deletion mutations.

b. It is an example of alkylating agent.

c. It undergoes tautomeric shift at high frequency.

d. It causes the formation of thymine dimers at high frequency.

e. It has the unusual property of base-pairing with thymines.

c. It undergoes tautomeric shift at high frequency.

Horizontal gene transfer refers to:

a. The methodology of transferring DNA from agarose gel onto nitrocellulose membrane.

b. The movement of a gene from one chromosome to a non-homologous chromosome.

c. The exchange of genetic information between different species.

d. The methodology of detecting specific DNA on nitrocellulose membrane with radioactively labeled probes.

e. The exchange of genetic information between F+ and F- bacterial strains.

c. The exchange of genetic information between different species.

In E. coli, the SOS response is mutagenic because:

a. It triggers apoptosis by inducing DNA fragmentation.

b. It causes the excision of transposable elements.

c. It increases deamination of cytosines.

d. It joins double stranded breaks by non-homologous joining.

e. It induces the expression of error-prone DNA polymerase.

e. It induces the expression of error-prone DNA polymerase.

Which of the following experiments is an example of a selection:

a. Identifying mutants defective in cell death regulation in C. elegans.

b. Isolating antibiotic-resistant bacteria mutants on antibiotic containing-plates.

c. Identifying Drosophila mutants that have no wings.

d. Isolating suppressor mutations of Drosophila mutants that have no wings.

e. Using blue-white color to identify those colonies containing DNA inserts.

b. Isolating antibiotic-resistant bacteria mutants on antibiotic containing-plates.

1) If the cytosines in CpG sequences near the promoter of a eukaryotic gene are highly methylated, this suggests that:

a. This gene is expressed at a high level.

b. This gene encodes a non-coding RNA.

c. This gene has multiple alternatively spliced variants.

d. The expression of this gene is repressed.

e. This gene is located in euchromatin.

d. The expression of this gene is repressed.

Bisulfite sequencing is typically used to determine:

a. The methylation state of histone proteins in eukaryotic chromosomes.

b. The DNA sequence of whole eukaryotic genomes.

c. The acetylation state of histone proteins in c eukaryotic chromosomes.

d. The methylation state of DNA in eukaryotic chromosomes.

e. This DNA sequence of actively transcribed genes in eukaryotic genomes.

d. The methylation state of DNA in eukaryotic chromosomes.

While analyzing the function of an unknown eukaryotic gene, you noticed that it contains a zinc finger motif. Based on this information, this gene is likely to:

a. Code for a microRNA.

b. Regulate alternative splicing.

c. Code for a protein that forms dimers.

d. Code for a protein that binds to transcriptional regulatory elements.

e. Code for a protein that repairs DNA.

d. Code for a protein that binds to transcriptional regulatory elements.

The Drosophila DSCAM locus is capable of expressing multiple isoforms. This is accomplished by:

a. Transcription initiation from alternative promoters.

b. Translation inhibition by small non-coding RNA.

c. Alternative splicing.

d. Duplication of the DSCAM gene onto different chromosomes.

e. The usage of alternative transcription termination sites.

c. Alternative splicing.

The Luria-Delbruck fluctuation test demonstrated that:

a. Spontaneous mutations are random.

b. Certain chemicals, after processed by liver enzymes, are mutagenic.

c. Transcription factors bind to DNA at specific sequences.

d. Nucleosomes in eukaryotic chromosomes can be remodeled.

e. Certain proteins are capable of interacting with each other in vivo.

a. Spontaneous mutations are random.

Regarding siRNA, which of the following statements is correct?

a. Injecting single-stranded antisense RNA into cells can efficiently degrade target mRNA.

b. siRNA mediates gene silencing by predominantly inhibiting translation.

c. The RISC complex cleaves injected-dsRNA into short 21 base pairs of dsRNA.

d. siRNA usually binds to target mRNA at specific sites in the 3' UTR.

e. siRNA mediates gene silencing by degrading target mRNA.

e. siRNA mediates gene silencing by degrading target mRNA.

The most common spontaneous mutations are caused by:

a. DNA polymerase inserting nucleotides mistakenly.

b. Template slippages during DNA replication.

c. Tautomeric shifts, which alter base-pairing properties of affected nucleotides.

d. Depurinations.

e. Double-stranded breaks.

d. Depurinations.

Spontaneous mutations caused by slippage during DNA replication are likely to be?

a. Insertions or deletions.

b. Translocations.

c. Base substitutions.

d. Missense mutations.

e. Inversions.

a. Insertions or deletions.

Which of the following enzymes will recognize and directly repair the lesions generated by UV light in E. coli?

a. AP endonuclease.

b. Uracil DNA glycosylase.

c. 3'-5' exonuclease of DNA polymerase 1.

d. Photolyase.

e. Alkyltransferase.

d. Photolyase.

Which of the following enzymes allows the E. coli mismatch repair system to distinguish the newly synthesized strand from the old template?

a. Restriction endonuclease.

b. AP endonuclease.

c. dam methylase.

d. Alkyltransferase.

e. Cytosine methyltransferase.

c. dam methylase.

Which of the following mutagens is most likely to cause large chromosomal aberrations?

a. Ethylmethane sulfonate.

b. 5-bromouracil.

c. Acridine orange.

d. UV light.

e. Ionizing irradiation.

e. Ionizing irradiation.

Which of the following repair mechanisms can fix T^T dimers:

a. Photo-reactivation repair.

b. Base excision repair.

c. Nucleotide excision repair.

d. A and B only.

e. A and C only.

e. A and C only.

Regarding acridine orange, which of the following statements is correct?

a. It effectively induces insertion and deletion mutations.

b. It is an example of alkylating agent.

c. It undergoes tautomeric shift at high frequency.

d. It causes the formation of thymine dimers at high frequency.

e. It has the unusual property of base-pairing with thymines.

a. It effectively induces insertion and deletion mutations.

Expressed sequence tags (ESTs) are generated from:

a. Sequencing of the ends of cDNA clones.

b. Sequencing of genomic DNA clones from shotgun libraries.

c. Sequencing of RFLP between homologous chromosomes.

d. Sequencing of gaps between contigs.

e. Sequencing of genomic DNA clones from chromosome-specific (map-based) libraries.

a. Sequencing of the ends of cDNA clones.

The Chromatin immunoprecipitation assay can be useful for:

a. Detecting the difference in mRNA level of different genes between cells at two different states.

b. Detecting the difference in restriction sites between two homologous chromosomes.

c. Detecting protein-protein interactions.

d. Identify the enhancer elements recognized by a sequence-specific transcription activator.

e. Determining the isoforms generated from alternative splicing from a particular gene.

d. Identify the enhancer elements recognized by a sequence-specific transcription activator.

Comparing genomes from various prokaryotic species, which of the following statements is incorrect?

a. Prokaryotic organisms contain mostly circular chromosomes.

b. Different prokaryotic organisms contain similar amount of genomic DNA.

c. Genes in prokaryotic organisms are frequently expressed as poly-cistronic mRNA.

d. Genes in prokaryotic organisms do not contain introns.

e. The functions of about 40% of the prokaryotic genes are not known.

b. Different prokaryotic organisms contain similar amount of genomic DNA.

The genome size of Bacillus subtilis, a gram-positive bacterium, is 4.2mb (106 bases). Based on the comparison of prokaryotic genomes, the number of genes in Bacillus subtilis is expected to be:

a. 25,000.

b. 8,400.

c. 4,200.

d. 840.

e. 420.

c. 4,200.

Comparing different eukaryotic genomes, which of the following organisms has the highest gene density?

a. Human.

b. Corn (Maize).

c. Drosophila.

d. Yeast.

e. C. elegans.

d. Yeast.

Horizontal gene transfer refers to:

a. The transposition of a DNA fragment from one chromosome to a non-homologous chromosome.

b. The transfer of DNA from agarose gel onto nitrocellulose membrane.

c. The transfer of genetic information between closely related species.

d. The detection of clones containing specific DNA on nitrocellulose membrane with radioactively labeled probes.

e. The mating between F+ and F- bacterial strains.

c. The transfer of genetic information between closely related species.

Conservation in the order of genes along the chromosomes from different species is known as:

a. Orthologs.

b. Synteny.

c. Homologs.

d. Paralogs.

e. Contigs.

b. Synteny.

The condition that a cell has mitochondria of different genotypes is known as:

a. Hemizygous.

b. Homozygous.

c. Heterozygous.

d. Heteroplasmy.

e. Homoplasmy.

d. Heteroplasmy.

Comparing human and Drosophila genomes, which of the following statements is correct?

a. The number of genes is similar.

b. The number of introns per gene is similar.

c. The average size of introns is similar.

d. The number of identified protein domains is similar.

e. The amount of DNA is similar.

d. The number of identified protein domains is similar.

When a haploid petite mutant mates with haploid normal yeast, the resulting diploid zygote exhibits the normal phenotype. After sporulation (meiosis), 50% of the haploid progeny are normal and the other 50% are petite. This pattern of inheritance describes:

a. Segregational petite.

b. Neutral petite.

c. Suppressive petite.

d. Codominance.

e. Incomplete dominance.

a. Segregational petite.

The explanation for the petite mutation in 23) is that:

a. A mutation disrupting a nuclear gene that participates in mitochondrial function.

b. A gain-of-function mutation in a maternal-effect gene that participates mitochondrial function.

c. A loss-of-function mutation in a mitochondrial gene, which disrupts mitochondrial function.

d. A deletion in mitochondrial genome, which gives defective mitochondria proliferation advantage.

e. None of above.

a. A mutation disrupting a nuclear gene that participates in mitochondrial function.

A different yeast petite mutant is isolated. To determine the type of mutation causing this phenotype, the haploid petite and wild type strains are crossed. The diploid zygotes are petite, and all the haploid ascospores after sporulation are petite. This petite mutation is:

a. Recessive.

b. Segregational.

c. Neutral.

d. Suppressive.

e. Dominant.

d. Suppressive.

Which of the following reagents is useful for genomic editing?

a. Double-stranded RNA.

b. Cas9 endonuclease and guide RNA.

c. MicroRNA.

d. AP endonuclease.

e. 3'-5' exonuclease activity of DNA polymerases.

b. Cas9 endonuclease and guide RNA.

Which of the following techniques will be useful for comparing the gene expression at the mRNA levels between cells at two different states?

a. Yeast 2-hybrid screen.

b. Luria and Delbruck fluctuation test.

c. 2-dimentional gel.

d. Microarray analysis.

e. Epitasis test.

d. Microarray analysis.

The dideoxynucleotides (ddNTP) differ from dNTP in:

a. The absence of nitrogen base at the 1' position.

b. The absence of hydroxyl group at the 2' position.

c. The absence of hydroxyl group at the 3' position.

d. The absence of triphosphate at the 5' position.

e. The presence of diphosphate at the 5' position.

c. The absence of hydroxyl group at the 3' position.

If a male with MERRF (Myoclonic Epilepsy with Ragged Red Fibers, a mitochondria disorder) syndrome marries a normal female, what will be the phenotypic ratio of the progeny?

a. All progeny will be normal.

b. All progeny will have MERRF.

c. The sons will have MERRF, but the daughters will be normal.

d. The daughters will have MERRF, but the sons will be normal.

e. 50% of the progeny will be normal and the other 50% will have MERRF.

a. All progeny will be normal.

If a female with MERRF syndrome marries a normal male, what will be the phenotypic ratio of the progeny?

a. All progeny will be normal.

b. All progeny will have MERRF.

c. The sons will have MERRF, but the daughters will be normal.

d. The daughters will have MERRF, but the sons will be normal.

e. 50% of the progeny will be normal and the other 50% will have MERRF.

b. All progeny will have MERRF.

Regarding human genome, which of the following statements is correct?

a. The gene densities of different autosomes are similar.

b. The number of genes in the genome is estimated to be around 25,000 to 30,000.

c. Most of the human DNA contains protein-coding sequences.

d. Human genes are frequently expressed as poly-cistronic operons.

e. The number of introns is fairly constant among human genes.

b. The number of genes in the genome is estimated to be around 25,000 to 30,000.