ADL 07 – Flashcards

Which of the following DNA sequences is one strand of a restriction enzyme recognition sequence? 5' GGGTTT 3' 5' GGGGGG 3' 5' GGATCC 3' 5' AAACCC 3'

X-Gal is included in the growth medium on which cells transformed with bacterial plasmids are grown. The reason X-Gal is included is to _______. eliminate bacteria that do not contain plasmid DNA minimize the chances that a vector will re-circularize without incorporating a fragment of foreign DNA identify bacteria that contain a recombinant plasmid eliminate bacteria that do not contain recombinant plasmid

Within a six-base DNA recognition sequence, an enzyme that cuts between the 3rd and 4th bases from the 5' end will generate blunt ends. True False

Which of the following may represent the sequence of one strand of a DNA palindrome recognized by a restriction enzyme? 5' ATGGAT 3' 5' ATGATG 3' 5' ATGGTA 3' 5' ATGCAT 3'

Assuming the DNA of an organism contains equal amounts of A, T, C, and G (25% each), how often would the restriction site GATC be expected in the genome? Once every 256 base pairs Once every 16 base pairs Once every 64 base pairs Once every 4096 base pairs

Which of the following is an example of a selectable marker used in plasmid cloning vectors? A Shine-Dalgarno sequence An origin of replication A multiple cloning site An antibiotic resistance gene

Which type of bacterial vector is best suited for cloning 40-45-kb DNA fragments? Cosmid vectors Lambda vectors Plasmid vectors Bacterial artificial chromosomes

In selecting recombinant bacteria, cells are chosen that are resistant to a specific antibiotic. How are the bacteria made resistant? They are pre-selected for the experiment on this basis. The antibiotic resistance gene is encoded on the donor insert. Resistance is activated by the recombination event. The antibiotic resistance is encoded in the vector. Resistance is activated when the cells are provided with the antibiotic

Which approach for sequencing large DNA molecules uses fragmentation that produces random but overlapping pieces?

The products of restriction digestion can be visualized by gel electrophoresis, which separates fragments based on their size. True False

A 1.5?kb fragment of DNA is cloned into a plasmid vector that is 5.5 kb long at the EcoRI site, and the plasmid vector is then used to transform bacteria. If the plasmid DNA is then extracted from a single bacterial colony and digested with EcoRI, what digestion products will be produced if the plasmid contains the fragment? One 1.5?kb fragment One 7?kb fragment One 5.5?kb fragment One 1.5?kb fragment and one 5.5?kb fragment

Digestion of a 1.1?kb fragment of DNA with BamHI produces two fragments of 700 bp and 400 bp. Digestion of the same 1.1?kb fragment with XhoI produces two fragments of 300 bp and 800 bp. Digestion with both enzymes produces three fragments of 100 bp, 300 bp, and 700 bp. Which of the following statements is true about the DNA fragment? The XhoI site is located within the BamHI 400?bp fragment. The BamHI site is located within the XhoI 300?bp fragment. The BamHI site is located within the XhoI 100?bp fragment. The XhoI site is located within the BamHI 700?bp fragment

Which of the following are the primary constituents of cDNA libraries? Centromere and telomere sequences Both exon and intron sequences Intergenic sequences Exon sequences

What purpose do the ?-lactamase gene serve in the plasmid vector pUC18? The product of this gene provides resistance to tetracycline. The product of this gene provides susceptibility to tetracycline. The product of this gene catalyzes the reaction that converts colourless X-gal into a blue pigment. The product of this gene provides resistance to ampicillin.

What purpose do the lacZ gene serve in the plasmid vector pUC18? The product of this gene provides resistance to ampicillin. The product of this gene catalyzes the reaction that converts colourless X-gal into a blue pigment. The product of this gene provides resistance to tetracycline. The product of this gene provides susceptibility to ampicillin.

What would be the consequence of treating the vector, before ligation, with calf intestinal phosphatase? It would prevent the ends of the plasmids from being ligated. It would reverse the polarity of plasmids' DNA It would prevent the plasmid's DNA from reversing polarity during ligation. It would ligate the ends of the plasmids.

You have constructed four different libraries: a genomic library made from DNA isolated from human brain tissue, a genomic library made from DNA isolated from human muscle tissue, a human brain cDNA library, and a human muscle cDNA library. Which of these would have the greatest diversity of sequences? muscle cDNA library either a brain genomic library or a muscle genomic library either a brain genomic library or a brain cDNA library muscle genomic library either a brain cDNA library or a muscle cDNA library brain genomic library brain cDNA library either a muscle genomic library or a muscle cDNA library

You have constructed four different libraries: a genomic library made from DNA isolated from human brain tissue, a genomic library made from DNA isolated from human muscle tissue, a human brain cDNA library, and a human muscle cDNA library.Sequences contained in which libraries would be expected to overlap completely? brain cDNA library and muscle cDNA library brain genomic library and brain cDNA library brain genomic library and muscle genomic library muscle genomic library and muscle cDNA library

You have constructed four different libraries: a genomic library made from DNA isolated from human brain tissue, a genomic library made from DNA isolated from human muscle tissue, a human brain cDNA library, and a human muscle cDNA library. Sequences contained in which libraries would be expected not to overlap at all? Check all that apply. brain cDNA library and muscle cDNA library muscle genomic library and muscle cDNA library brain genomic library and brain cDNA library brain genomic library and muscle cDNA library muscle genomic library and brain cDNA library brain genomic library and muscle genomic library all sequences would be expected to overlap at least partially.

The human genome is 3×109 bp in length. Calculate how many fragments would result from the complete digestion of the human genome with specific enzymes. Sau3A (?GATC) BamHI (G?GATCC) EcoRI (G?AATTC) NotI (GC?GGCCGC) Sau3A (?GATC) 1.17×10^7 9.72×10^5 4.58×10^4 4.32×10^5 7.32×10^5

The human genome is 3×109 bp in length. Calculate how many fragments would result from the complete digestion of the human genome with specific enzymes. Sau3A (?GATC) BamHI (G?GATCC) EcoRI (G?AATTC) NotI (GC?GGCCGC) BamHI (G?GATCC) 1.17×10^7 9.72×10^5 4.58×10^4 4.32×10^5 7.32×10^5

The human genome is 3×109 bp in length. Calculate how many fragments would result from the complete digestion of the human genome with specific enzymes. Sau3A (?GATC) BamHI (G?GATCC) EcoRI (G?AATTC) NotI (GC?GGCCGC) EcoRI (G?AATTC) 1.17×10^7 9.72×10^5 4.58×10^4 4.32×10^5 7.32×10^5

The human genome is 3×109 bp in length. Calculate how many fragments would result from the complete digestion of the human genome with specific enzymes. Sau3A (?GATC) BamHI (G?GATCC) EcoRI (G?AATTC) NotI (GC?GGCCGC) How would your initial answer for Sau3A change if you knew that the average GC content of the human genome was 45%? 5.81×105 1.97×104 7.32×105 8.69×105 1.15×107

The human genome is 3×109 bp in length. Calculate how many fragments would result from the complete digestion of the human genome with specific enzymes. Sau3A (?GATC) BamHI (G?GATCC) EcoRI (G?AATTC) NotI (GC?GGCCGC) How would your initial answer for BamHI change if you knew that the average GC content of the human genome was 45%? 7.32×105 1.15×107 5.81×105 8.69×105 1.97×104

The human genome is 3×109 bp in length. Calculate how many fragments would result from the complete digestion of the human genome with specific enzymes. Sau3A (?GATC) BamHI (G?GATCC) EcoRI (G?AATTC) NotI (GC?GGCCGC) How would your initial answer for EcoRI change if you knew that the average GC content of the human genome was 45%? 5.81×105 8.69×105 1.97×104 7.32×105 1.15×107

The human genome is 3×109 bp in length. Calculate how many fragments would result from the complete digestion of the human genome with specific enzymes. Sau3A (?GATC) BamHI (G?GATCC) EcoRI (G?AATTC) NotI (GC?GGCCGC) How would your initial answer for NotI change if you knew that the average GC content of the human genome was 45%? 1.15×107 1.97×104 7.32×105 5.81×105 8.69×105

The human genome is 3×10^9 bp. You wish to design a primer to amplify a specific gene in the genome. In general, what length of oligonucleotide would be sufficient to amplify a single unique sequence? To simplify your calculation, assume that all bases occur with an equal frequency. Hint: The frequency of occurrence of a PCR primer in genomic DNA is given by this equation: genomic DNA length × sequence frequency The sequency frequency is (1/4) N , where N corresponds to the number of nucleotides in the site. Express your answer as an integer.

What are the steps in the shotgun approach to whole-genome sequencing?

In the last step of shotgun sequencing, a computer analyzes a large number of fragment sequences to determine the DNA sequence of a whole chromosome. Given the following fragment sequences, what is the overall DNA sequence? Sequences of DNA fragments GATGAC CGATGCG GGCGTCAG GACATGGC TCAGTCGA

Which of the following lists has the steps involved in the whole genome shotgun approach to Sequencing in the correct order? 1. Transformation of E. coli with cloning vector 2. Isolation and shearing of genomic DNA 3. Insertion of genomic fragments into cloning vector 4. Sequencing of cloned fragment ends 5. Sequence assembly 1. Isolation and shearing of genomic DNA 2. Insertion of genomic fragments into cloning vector 3. Transformation of E. coli with cloning vector 4. Sequencing of cloned fragment ends 5. Sequence assembly 1. S1 nuclease digest of single-stranded tails 2. Isolation and shearing of genomic DNA 3. Insertion of genomic fragments into cloning vector 4. Sequencing of cloned fragment ends 5. Sequence assembly 1. Sequence assembly 2. Insertion of genomic fragments into cloning vector 3. Transformation of E. coli with cloning vector 4. Sequencing of cloned fragment ends 5. Isolation and shearing of genomic DNA

The feature of DNA fragment preparation that ensures fragment end overlap is _______. removal of single-stranded tails using S1 nuclease random breakage of genomic DNA by physical shearing the duration of the genomic DNA shearing treatment electrophoretic separation

Which of the following components of the strategy ensures that sequence reads are obtained from the ends of cloned fragments? The use of fluorescently labeled primers The use of primers that anneal to vector sequences near vector/cloned fragment boundaries The use of primers that anneal to cloned fragment sequences near vector/cloned fragment boundaries Use of a restriction enzyme such as SmaI that generates blunt ends

Which of the following organisms would have the lowest predicted gene density (no. genes/megabase of DNA) in genomic DNA? Escherichia coli Homo sapiens (human) Drosophila melanogaster (fruit fly) Neurospora crassa (bread mold)

What are expressed sequence tags (ESTs) used in genomic analyses. Whole genomic DNA sequences Partial cDNA sequences Splice-site consensus sequences Promoter clones

Often, in the absence of experimental data, computerized algorithms are used to predict gene structures from large sequences. What is this approach known as?

A researcher has produced groups of contigs that are linked via paired end sequences, although these include some sequence gaps. What are these groups called?