EXAM 4: QUIZ METHODS: GENES Flashcards
True or false: Restriction nucleases recognize specific sequences on single-stranded DNA.
f
A nuclease hydrolyzes the 22 bonds in a nucleic acid.
phosphodiester
True or false: The sizes of the fragments left after a restriction digest do not depend on the total size of the genome; they depend on the sequence of the genome and the frequency with which the restriction enzyme recognition site is found in the genome.
t
You have an oligonucleotide probe that hybridizes to part of gene A from a eucaryotic cell. Indicate whether a cDNA library (a) or a genomic DNA library (b) will be more appropriate for use in the following applications. You discover that gene A is alternatively spliced and you want to see which predicted alternative splice products the cell actually produces.
cDNA
Which of the following limits the use of PCR to detect and isolate genes?
The sequence at the beginning and end of the DNA to be amplified must be known.
The technique of 56 hybridization can be used to detect a specific RNA expression in a particular region of the brain.
in situ
True or false: During Southern blotting, double-stranded DNA is loaded onto the agarose gel. The DNA becomes denatured (and thus single stranded) as it gets transferred by the alkali solution from the gel to the nitrocellulose or nylon sheet.
t
True or false: A labeled DNA probe binds to the DNA by hybridization.
t
A piece of DNA used to detect a specific sequence in a nucleic acid by hybridization is known as a(n) __.
probe
In situ hybridization can be used to determine the _________________.
distribution of a given type of mRNA in different tissues
Millions of copies of a DNA sequence can be made entirely in vitro by the 26 technique.
Gel electrophoresis
Northern blotting detects a specific sequence in 57.
RNA
True or false: Some restriction nucleases cut in a staggered fashion, leaving short single-stranded regions of DNA at the ends of the cut molecule.
t
True or false: A reproducible set of DNA fragments will be produced every time a restriction nuclease digests a known piece of DNA.
t
You have an oligonucleotide probe that hybridizes to part of gene A from a eucaryotic cell.Indicate whether a cDNA library (a) or a genomic DNA library (b) will be more appropriate for use in the following applications. Gene A encodes a tRNA and you wish to isolate a piece of DNA containing the full-length sequence of the tRNA
Genomic DNA
true or false: PCR is particularly powerful because after each cycle of replication, there is a linear increase in the amount of DNA available.
f
During gel electrophoresis, DNA fragments _______________________.
travel through a matrix containing a microscopic network of pores
A DNA library has been constructed by purifying chromosomal DNA from mice, cutting the DNA with the restriction enzyme NotI, and inserting the fragments into the NotI site of a plasmid vector. What information cannot be retrieved from this library?
sequences of the telomeres
You have an oligonucleotide probe that hybridizes to part of gene A from a eucaryotic cell.Indicate whether a cDNA library (a) or a genomic DNA library (b) will be more appropriate for use in the following applications. You want to study the promoter of a gene A.
Genomic DNA
true or false You want to design a DNA probe used for hybridization to isolate a clone from a cDNA library.: The shorter the DNA probe used to probe the library, the greater the number of colonies to which the probe will hybridize.
t
True or false: A RE that has a 4-base-pair recognition sequence cuts on average once every 44 or 256 base pairs; one that has a 6-base-pair recognition sequence cuts once every 46 or 4096 base pairs; one that has an 8-base-pair recognition sequence cuts once every 48 or 65,536 base pairs; one that has a 12- base-pair recognition sequence cuts once every 412 or 16 million base pairs. To obtain fragments of about 70 kb in size, you would cut with a nuclease that recognizes an 8-base-pair site.
false
Southern blotting detects a specific sequence in 58.
DNA
Why are dideoxyribonucleoside triphosphates used during DNA sequencing?
incorporation of a didoxyribonucleoside triphosphate leads to the termination of replication for that strand.
You have a piece of circular DNA that can be cut by the restriction nucleases XhoI and SmaI, only one time each. If you were to cut this circular piece of DNA with both XhoI and SmaI, how many fragments of DNA would you end up with?
2
You have an oligonucleotide probe that hybridizes to part of gene A from a eucaryotic cell. Indicate whether a cDNA library (a) or a genomic DNA library (b) will be more appropriate for use in the following applications. You want to find both gene A and the genes located near gene A on the chromosome.
Genomic DNA
Nucleases that cut DNA only at Specific short sequences are known as 23.
restriction nucleases
You are interested in a single-stranded DNA molecule that contains the following sequence: 5?- GATTGCAT -3? Which molecule can be used as a probe that will hybridize to your sequence of interest?
5?-ATGCAATC-3?
You have been hired to create a cat that will not cause allergic reactions in cat-lovers. Your co-workers have cloned the gene encoding a protein found in cat saliva, expressed the protein in bacteria, and shown that it causes violent allergic reactions in people. But you soon realize that even if you succeed in making a knockout cat lacking this gene, anyone who buys one will easily be able to make more hypoallergenic cats just by breeding them. Which of the following will ensure that people will always have to buy their hypoallergenic cats from you?
surgically remove the sexual organs of all the knockouts before you sell them.Neutering all the knockout animals that you sell is the only option of the four listed that will prevent happy pet owners from becoming happy pet breeders. The situation described in choice
Restriction enzymes that cut DNA straight across the double helix produce fragments of DNA with 28.
blunt ends
You have purified DNA from your recently deceased goldfish. Which of the following restriction nucleases would you use if you wanted to end up with DNA fragments with an average size of 70 kilobase pairs (kb) after complete digestion of the DNA? The recognition sequence for each enzyme is indicated.
NotI-GCGGCCGC
A double-stranded DNA molecule can be separated into single strands by heating it to 90°C because _______________________.
heat disrupts hydrogen bonding between complementary nucleotides
True or false: if a fragment the size of an entire genome were inserted into a bacterial vector, you would have to screen only one colony to find a clone that hybridized to your probe, but it would be very difficult to find out where on the insert your gene of interest lay.
t
A fragment of DNA is inserted into a 29 in order to be cloned in bacteria.
vector
A short, single-stranded DNA is a(n) __.
oligonucleotide
A 30 library contains a collection of DNA clones derived from mRNAs.
cDNA
Which of the following describes a feature found in bacterial expression vectors but not in cloning vectors?
promoter DNA sequences
You have an oligonucleotide probe that hybridizes to part of gene A from a eucaryotic cell. Indicate whether a cDNA library (a) or a genomic DNA library (b) will be more appropriate for use in the following applications. You want to express gene A in bacteria to produce lots of protein A.
cDNA
True or false: The DNA that is separated on a gel is not labeled.
t
True or false: In this technique, single-stranded DNA is separated by electrophoresis.
f
True or false: The smaller the gene you are seeking, the more likely it is that the gene will be found on a single clone.
t
Two fragments of DNA can be joined together by 27.
DNA ligase
Match the features of a cloning vector in bacteria must contain with the right reason: a bacterial replication origin.
to allow the plasmid to be replicated
A 31 library contains a collection of DNA clones derived from chromosomal DNA.
genomic
DNA can be introduced into bacteria by a mechanism called ____________.
transformation
Why is a heat-stable DNA polymerase from a thermophilic bacterium (the Taq polymerase) used in the polymerase chain reaction PCR rather than a DNA polymerase from E. coli or humans? PCR involves heating the reaction at the beginning of each cycle to separate the newly synthesized ds DNA into single strands so that they can act as templates for the next round.
Using Taq avoids having to add it afresh for each round of DNA replication.
True or false: The larger the genome of the organism from which a library is derived, the larger the fragments inserted into the vector will tend to be.
f
__ can be used to separate DNA fragments of different sizes.
Gel electrophoresis
True or false: This technique involves the transfer of DNA molecules from gel onto nitrocellulose paper or nylon paper.
t
Match the features of a cloning vector in bacteria must contain with the right reason: an antibiotic-resistance gene.
selectable marker gene to allow selection for bacteria that have taken up the recombinant plasmids
True or false: The larger the size of the fragments used to make the library, the fewer colonies you will have to examine to find a clone that hybridizes to your probe.
t
True or false: The larger the size of the fragments used to make the library, the more difficult it will be to find your gene of interest once you have identified a clone that hybridizes to your probe.
t
True or false: the larger the gene you are cloning, the more likely it is that there will be a restriction fragment in the gene, and hence the less likely it is that the entire gene will be found in a clone.
t
Match the features of a cloning vector in bacteria must contain with the right reason: at least one unique restriction site.
to allow easy insertion of foreign DNA
DNA composed of sequences from different sources is known as 24.
recombinant DNA
True or false: Some bacteria use restriction nucleases as protection from foreign DNA.
t
