Deck 21: Molecular Biology Techniques for Cell Biology

Question 1

Which of the following can be used as a cloning vector in molecular biology?

A)a plasmid
B)DNA of a bacteriophage
C)an artificial chromosome
D)a Y chromosome
E)a plasmid,DNA of a bacteriophage,or an artificial chromosome

Answer 1

E

Question 2

A cDNA library

A)is generated by copying genomic DNA with the polymerase chain reaction and cloning the resulting complementary DNA (cDNA).
B)is generated by copying messenger RNA (mRNA)with the enzyme reverse transcriptase and cloning the resulting complementary DNA (cDNA).
C)corresponds to the protein complement of a cell.
D)doesn't contain introns.
E)doesn't contain introns because it is generated by copying messenger RNA (mRNA)with the enzyme reverse transcriptase and cloning the resulting complementary DNA (cDNA).

Answer 2

E

Question 3

You wish to use mRNA profiles to examine gene expression in cells during times of stress.You are investigating the cell's

A)spliceosome.
B)genome.
C)proteome.
D)transcriptome.
E)BLAST (Basic Local Alignment Search Tool).

Answer 3

D

Question 4

Which of the following choices most likely lists the sizes of the four DNA fragments in lane 6 (from top to bottom)of this agarose gel stained with ethidium bromide? (Note: The well that the DNA was loaded into is at the top of the gel image.)

A)600 bp,450 bp,300 bp,100 bp
B)100 bp,300 bp,450 bp,600 bp
C)400 bp,300 bp,600 bp,100 bp
D)300 bp,400 bp,100 bp,600 bp
E)DNA fragment size can't be estimated using an agarose gel.

Question 5

Genome size in eukaryotic organisms

A)varies by many orders of magnitude.
B)is directly related to the total number of genes in an organism.
C)is dependent on the complexity of the organism.
D)varies two- to threefold,depending on whether the organism is unicellular or multicellular.
E)is generally 10 times greater than prokaryotic organisms.

Question 6

The societal challenges created by next-generation sequencing are related to

A)ethical questions of confidentiality and estimation of disease risk for individuals.
B)the high cost of sequencing.
C)the creation of genetically engineered babies.
D)reliable data storage and analysis.
E)ethical questions of confidentiality,estimation of disease risk for individuals,and reliable data storage and analysis.

Question 7

In molecular biology,the term DNA cloning refers to the process of

A)engineering and editing DNA for specific purposes.
B)generating many identical cells for the purpose of research.
C)generating many copies of specific DNA fragments.
D)genetically modifying and making many copies of an entire organism.
E)generating many copies of specific DNA sequences using the polymerase chain reaction.

Question 8

Bacterial and yeast artificial chromosomes are useful tools in molecular biology because

A)they can be used to directly infect human cells and thus treat genetic diseases.
B)they are easy to genetically modify and insert into many different organisms.
C)they can replace the natural chromosomes found in bacteria and yeast.
D)they can carry large DNA fragments (>30,000 bp)such as large eukaryotic genes.
E)they are easy to genetically modify and insert into many different organisms,including the direct infection of human cells for the treatment of genetic diseases.

Question 9

You have constructed a genomic library of Felis catus (domestic cat)in E.coli.You extract the plasmid DNA from the clones,digest the plasmid with restriction enzymes,separate the resulting fragments by gel electrophoresis,and transfer the fragments to a nylon membrane by the Southern blot procedure.You then use a fluorescently labeled probe that is complementary to a gene of interest that may be involved in feline lymphoma.The DNA corresponding to one clone yields a single fluorescent DNA band after probing the Southern blot.Based on this information

A)all of the clones tested,except the one described,have the gene of interest.
B)only the one clone described has the gene of interest.
C)the gene of interest is located entirely on the fluorescent DNA band.
D)the part of the gene complementary to the probe is located on the fluorescent DNA band.
E)only the one clone described contains the part of the gene complementary to the probe on the fluorescent DNA band.

Question 10

Which of the following terms is used to indicate the entire set of proteins that can be made by a cell?

A)transcriptome
B)genome
C)proteome
D)metabolome
E)exome

Question 11

You isolate a new bacterium from soil with a revolutionary new culture technique.You are interested in sequencing the genome of this organism using the whole-genome,or shotgun,sequencing approach.Of the following choices,what would be the best way to prepare the genomic DNA for sequencing?

A)digestion with HpaI (CCGG)
B)digestion with BamHI (GGATCC)
C)digestion with EcoRI (GAATTC)
D)digestion with NotI (GCGGCCGC)
E)digestion with EcoRI,BamHI,and HpaI

Question 12

Analyzing the expression of thousands of genes simultaneously can be accomplished using which of the following techniques?

A)siRNAs
B)Northern blotting
C)DNA microarrays
D)RNAseq
E)DNA microarrays and RNAseq

Question 13

Two-dimensional gel electrophoresis separates

A)DNA fragments based on nucleotide sequence and fragment length.
B)proteins based on affinity for the gel matrix and size of each protein.
C)genomes based on size and structure (linear or circular)of each genome.
D)RNA based on the charge and size of each RNA molecule.
E)proteins based on the charge and size of each protein.

Question 14

Next-generation sequencing methods are revolutionizing biology research and human medicine because they

A)can generate large amounts of sequence data on many samples in parallel.
B)are reducing the cost of sequencing.
C)are increasing the length and reliability of each sequence read.
D)can generate sequence data from very small amounts of DNA.
E)can generate large amounts of sequence data on many samples in parallel,generate sequence data from very small amounts of DNA,and are reducing the cost of sequencing.

Question 15

The normal gene for hemoglobin was isolated,cloned in E.coli,and subjected to restriction enzyme digestion with BamHI.Following gel electrophoresis,three bands are routinely obtained.However,following the same procedure with the hemoglobin gene from an individual with sickle cell anemia,four bands are routinely obtained.These data suggest that

A)the mutation associated with sickle cell anemia results in DNA that breaks easily.
B)the mutation associated with sickle cell anemia results in the loss of a BamHI cut site.
C)the mutation associated with sickle cell anemia results in several new enzyme cut sites for a variety of restriction enzymes.
D)the mutation associated with sickle cell anemia results in the gain of a BamHI cut site.
E)the assay was not performed correctly.

Question 16

Whole genome or shotgun sequencing requires

A)the creation of a cDNA library.
B)the creation of overlapping DNA fragments whose sequences can be aligned into large contiguous fragments (contigs)using computer algorithms.
C)large contiguous fragments (contigs)cloned into yeast artificial chromosomes (YACs)in an ordered fashion.
D)very large amounts of DNA from the organism whose genome is being sequenced.
E)the use of a gene gun to propel DNA-coated particles at high velocities into cells.

Question 17

Antibiotic resistance genes are often included on plasmid vectors because

A)antibiotic resistance is used to select for bacteria cells containing the vector.
B)antibiotic resistance can be used to control the growth of the genetically modified organism.
C)antibiotics are often present in humans being treated for disease.
D)only bacteria are affected by antibiotics.
E)antibiotic resistance genes can be used as transcriptional reporters.

Question 18

Gel electrophoresis separates DNA molecules based on variability in their

A)nucleotide sequence.
B)affinity for agarose.
C)charge.
D)size.
E)charge and size.

Question 19

DNA extracted from hair,blood,or other bodily fluids and tissues from a crime scene can be used as evidence in a criminal case.What features of human DNA are typically used to "match" DNA found at a crime scene with the DNA of an individual?

A)restriction fragment length polymorphisms created by digestion with one restriction endonuclease
B)variability in the number of short tandem repeats at 13 sites within the human genome
C)the complete sequence of the human genome
D)single nucleotide polymorphisms
E)single nucleotide polymorphisms that cause restriction fragment length polymorphisms

Question 20

In the Sanger,or chain termination,method of DNA sequencing,incorporation of the nucleotides stops because

A)the dideoxynucleotide analogs have no 3ʹ-OH group to continue DNA synthesis.
B)the dideoxynucleotide analogs have no 5ʹ-OH group to continue DNA synthesis.
C)the dideoxynucleotide analogs have no 2ʹ-OH group to continue DNA synthesis.
D)the mixture is heated to 92°C to stop DNA synthesis at specific time intervals.
E)the dideoxynucleotide analogs are in greater concentration than the actual nucleotides.

Question 21

Which of the following techniques separates proteins based only on their size?

A)SDS-PAGE (SDS-polyacrylamide gel electrophoresis)
B)mass spectrometry
C)ion-exchange chromatography
D)two-dimensional gel electrophoresis
E)SDS-PAGE and mass spectrometry

Question 22

What new field combines computer science and biology to understand sequence data?

A)transcriptomics
B)genome editing
C)bioinformatics
D)recombinant DNA technology
E)genetic engineering

Question 23

You have discovered a gene that appears to be crucial to the development of the nervous system in C.elegans.However,you have been unsuccessful in creating embryos in which this gene is knocked out.How might you study the function of this gene in C.elegans without creating a "knockout" mutant?

A)CRISPR/Cas targeted gene disruption
B)RNAi gene knockdown
C)transcriptional activator-like effector nucleases (TALENs)targeted gene disruption
D)next-generation sequencing.
E)restriction endonuclease mapping.

Question 24

You wish to investigate proteins from human cells that bind to a specific short sequence of nucleotide bases.Which of the following techniques would allow you to separate proteins from whole cells or complex mixtures based on their ability to bind to a short nucleotide sequence?

A)affinity chromatography
B)Western blot analysis
C)Southern blot analysis
D)immunoprecipitation
E)tandem mass spectrometry

Question 25

The use of recombinant DNA technology to treat genetic diseases ("gene therapy")has been held back by difficulty

A)delivering cloned genes into target cells and getting the genes to function properly.
B)in obtaining the appropriate sequence information from individual people.
C)cloning human genes.
D)in identifying human genes that cause disease.
E)cloning and identifying human genes that cause disease.

Question 26

Point mutations in the human genome that result in addition or deletion of a recognition site for a restriction endonuclease can most easily be detected by

A)RNAseq analysis.
B)Northern blot analysis.
C)Southern blot analysis.
D)restriction fragment length polymorphism analysis.
E)restriction fragment length polymorphism and Southern blot analysis.

Question 27

Retroviruses and bacteria such as Agrobacterium tumefaciens are commonly used to produce

A)genetically identical clones of an organism.
B)yeast hybrid systems.
C)polyclonal and monoclonal antibodies.
D)transgenic organisms.
E)monoclonal antibodies.

Question 28

One of the societal benefits of genetic engineering today is

A)the production of human proteins by bacteria and yeast for the treatment of human diseases.
B)genetically modified humans.
C)gene therapy for many human genetic diseases.
D)human cloning.
E)human cloning and genetically modified humans.

Question 29

The online Basic Local Alignment Search Tool (BLAST)allows users to

A)predict the proteome of a cell under different conditions.
B)align their genome with that of others to explore differences among humans.
C)search molecular biology databases for nucleotide or protein sequences similar to a query sequence.
D)search their own genome for single nucleotide polymorphisms associated with disease.
E)search a database to identify individuals based on their DNA fingerprint.

Question 30

You have determined the base sequence for a gene from Felis catus (domestic cat)that you believe may be involved in feline leukemia.A blastn search returns nucleotide sequences from viruses,not mammals,although the similarity is very low.What other techniques or bioinformatic tools could you use to investigate the function of this gene?

A)RNAseq
B)tblastx search
C)Northern blot analysis
D)protein blast
E)RNAseq and Northern blot analysis

Question 31

What new technique or technology may revolutionize the way in which cell biologists alter the genomes of cells and organisms?

A)genome editing
B)homologous recombination
C)RNA-mediated interference
D)recombinant DNA technology
E)next-generation sequencing

Question 32

In combination with homologous recombination,the CRISPR/Cas system can be used to accomplish

A)gene fusions.
B)gene deletion.
C)point mutations.
D)DNA cloning.
E)gene fusions,gene deletions,or point mutations.

Question 33

Transgenic organisms can be created by

A)electroporation.
B)direct injection.
C)infection with a vector.
D)cloning.
E)electroporation,direct injection,or infection with a vector.

Question 34

You have discovered a gene that appears to be crucial to the development of the nervous system in C.elegans.Which of the following techniques would allow you to investigate the transcriptional regulation and expression of this gene in vivo?

A)DNA cloning
B)restriction endonuclease mapping
C)replacing one copy of the gene with a reporter gene,such as GFP or lacZ
D)transcriptional activator-like effector nucleases (TALENs)targeted gene disruption
E)RNAi gene knockdown

Question 35

The Ti plasmid is crucial to genetic engineering in plants.The key feature of the Ti plasmid is that it

A)uses the CRISPR/Cas system to edit the plant genome.
B)only replicates in bacterial cells.
C)uses zinc finger nucleases (TALENs)to edit the plant genome.
D)leads to insertion of a part of the plasmid DNA into the plant cell chromosomal DNA.
E)acts as an artificial chromosome within plant cells.

Question 36

You have determined the nucleotide and amino acid sequences of a protein involved in feline leukemia.You now want to test the function of this protein in your feline lymphoma cell line.What technique might you use to test the function of the protein?

A)affinity chromatography
B)targeted gene disruption
C)translational fusion
D)two-dimensional gel electrophoresis
E)co-immunoprecipitation

Question 37

You are interested in studying the expression of a gene associated with human cancer during fetal development.Which of the following might be useful to study the expression of this gene over time?

A)DNA microarrays
B)genome-wide association studies
C)Southern blot analysis
D)in situ hybridization
E)DNA microarrays and in situ hybridization

Question 38

The area of study that is involved with comparing genome characteristics and entire genome sequences is called ________.

Question 39

You have determined the base sequence for a gene from Felis catus (domestic cat)that you believe may be involved in feline leukemia.The nucleotide and probable amino acid sequences are similar to retroviral proteins that become embedded in the host cell membrane.You separate the membrane fraction of feline leukemia cell lysate from the cytoplasmic fraction.What technique could you use to determine if your protein of interest is present in the membrane fraction?

A)affinity chromatography
B)liquid chromatography followed by mass spectrometry
C)Southern blot analysis
D)two-dimensional gel electrophoresis
E)liquid chromatography followed by mass spectrometry or two-dimensional gel electrophoresis

Question 40

Comparing the sequence of ________ in the genomes of many organisms has allowed evolutionary biologists to create a comprehensive "tree" of life showing that every organism falls into one of three domains: Bacteria,Archaea,and Eukarya.

Question 41

________ is the sequencing and assembly of random,overlapping cloned DNA fragments into long,contiguous sequences.

Question 42

A genetic element which can replicate autonomously when introduced into a cell grown in culture is a ________.

Question 43

You are given the task of restriction-mapping a portion of a 10 kb linear genome fragment from a virus.You digest the fragment with BamHI and,upon gel electrophoresis,observe bands corresponding to 4 kb,5 kb and 1 kb.When you digest the fragment with the enzyme HindII,you observe bands corresponding to 4 kb and 3 kb.When you digest the 10 kb fragment with both enzymes,you observe bands corresponding to 3 kb,2 kb,and 1 kb,although the 2 kb band is much brighter than the other two bands.Based on this information,draw the restriction map of the 10 kb fragment.

Question 44

The ENCODE project (Encyclopedia of DNA elements)is unique because it seeks to not only identify ________ but also to try to identify genes that produce noncoding RNAs; DNA that regulates gene expression,including enhancers,silencers,and promoters; and epigenetic changes in the genome.

Question 45

________ separates proteins based on their attraction to a specific molecule attached to the surface of the matrix (or beads)of a chromatography column.

Question 46

You wish to investigate proteins from human liver cells that bind to a specific short sequence of nucleotide bases you believe to be an enhancer element.Design an experiment that would allow you to isolate and characterize human proteins that bind to the nucleotide sequence you are interested in.(Include at least two separate techniques in your answer.)

Question 47

Introducing a foreign piece of DNA into an organism in such a way that it can be passed along through the germ line (eggs and sperm)and hence to subsequent generations creates a ________ organism.

Question 48

A genomic library is a collection of ________ that contains DNA fragments representing most,if not all,of the genome of an organism.

Question 49

________ is the application of recombinant DNA technology to practical problems in areas such as medicine,energy production,waste reclamation,and agriculture.

Question 50

What is gene therapy and why hasn't it been successfully developed for the treatment or cure of human genetic diseases to date? What new technique may help advance gene therapy in the future?

Question 51

________ is the combination of computer science and biology to study genomes,transcriptomes,and proteomes.

Question 52

BLAST (basic local alignment search tool)is a bioinformatics tool that allows users to find proteins and nucleotides based on searching for ________.

Question 53

________ involve sequencing thousands of individual people in order to correlate specific genetic mutations in multiple genetic loci to the risk of specific diseases.

Question 54

You have determined the base sequence for a gene from Felis catus (domestic cat)that you believe may be involved in feline leukemia.A BLASTn search results in nucleotide sequence matches from viruses,not mammals,although the similarity is low.What other bioinformatic tools or techniques could you use to investigate the function of this gene? Why would these tools or techniques be more convincing than a BLASTn search? Hypothesize why you think this result might be correct or incorrect.

Question 55

________ is the use of sequences to target molecular complexes to specific genomic sites,where the genomic DNA is directly altered.

Question 56

________ is the process of generating many copies of a specific DNA fragment.