Question 1

Which technique can be used to estimate the relative copy numbers of particular DNA sequences in a sample?
A) reverse transcriptase PCR
B) quantitative PCR
C) some gel based analysis such as with the Bioanalyzer and Fragment Analyzer gel band density are used in calculating concentration in a lot of labs.
D) normal PCR
E) in vitro transcription

Accepted Answer

Quantitative PCR (qPCR) is a well-established technique for estimating the relative copy numbers of particular DNA sequences in a sample. It allows for the detection and quantification of DNA in real-time, providing a dynamic range of detection and accurate quantification of target DNA. Other techniques such as gel-based analysis can be used to estimate DNA concentration, but they are less accurate and have a lower dynamic range compared to qPCR. Reverse transcriptase PCR (RT-PCR) and in vitro transcription are techniques used for measuring RNA expression levels rather than DNA copy numbers. Normal PCR is not quantitative and does not provide accurate quantification of copy numbers.

Question 2

What is a polylinker?
A) a type of cloning vector
B) a DNA fragment with multiple recognition sequences for restriction endonucleases
C) a type of expression vector
D) an enzyme that joins DNA molecules together
E) a method of getting DNA into a cell

Accepted Answer

A polylinker, also known as a multiple cloning site, is a DNA sequence that contains multiple recognition sites for restriction endonucleases. It is commonly used as part of a cloning vector to allow for the insertion of DNA fragments into the vector at a specific location. Thus, option B is the correct answer.

Question 3

Current estimates indicate that _____% of the human genome is translated into protein.
A) less than 0.5
B) roughly 1.5
C) roughly 10
D) roughly 25
E) more than 50

Accepted Answer

Roughly 1.5% of the human genome is translated into protein. The vast majority of the genome is involved in regulatory functions, structural components, or is non-coding DNA with functions that are not fully understood.

Question 4

Common problems with expression of eukaryotic proteins in bacteria may include proteins:
A) aggregating into inclusion bodies.
B) not folding correctly due to absence of chaperones.
C) not undergoing posttranslational modification.
D) All of the answers are correct.
E) None of the answers is correct.

Accepted Answer

All of the answers are correct. Expression of eukaryotic proteins in bacteria can result in aggregation into inclusion bodies, incorrect folding due to absence of necessary chaperones, and lack of posttranslational modifications necessary for proper protein function.

Question 5

Which statement regarding Type I and Type II restriction endonucleases is NOT accurate?
A) Type I endonucleases cleave DNA at random sites.
B) Type II endonucleases recognize small (4-6 bp) palindromic sequences.
C) Type II endonucleases always make staggered cuts in DNA strands.
D) Type I endonucleases require ATP.
E) Type I endonucleases are generally large, multisubunit complexes.

Accepted Answer

Type II endonucleases may make either blunt-end or staggered cuts, depending on the specific enzyme and the position of the recognition sequence. Therefore, statement C is not always accurate.

Question 6

Which DNA sequence is a palindrome?
A) AATGCC
B) GGATCC
C) GATATG
D) CCCGCG
E) AGTAGT

Accepted Answer

A palindromic DNA sequence reads the same forwards and backwards on complementary strands. GGATCC is a palindrome because its complementary strand is CCTAGG, which reads the same in reverse.

Question 7

A good expression vector for protein expression in E. coli should have which feature(s)?
A) an origin of replication
B) a selectable marker
C) a promoter, operator, and ribosome-binding site
D) All of the answers are correct.
E) None of the answers is correct.

Accepted Answer

A good expression vector for protein expression in E. coli should have all of the features mentioned in options A, B, and C. An origin of replication is necessary to ensure the plasmid is stably maintained in E. coli, a selectable marker allows for the selection of bacteria that have taken up the plasmid, and a promoter, operator, and ribosome-binding site are essential for the efficient expression of the protein of interest. Therefore, all the given answers are correct.

Question 8

Which amino acid when repeated six to ten times at the N- or C-terminal ends of a protein allows that protein to bind to Ni²⁺ ions? A) Glu B) His C) Ala D) Tyr E) Asp

Accepted Answer

The amino acid that is known to bind to Ni²⁺ ions is histidine (His) due to the presence of its imidazole group, which can coordinate with metal ions. When repeated six to ten times, it can form a chelating site that can bind to the metal ions with high affinity. Ala, Glu, Tyr, and Asp do not have the necessary functional groups to bind to metal ions.

Question 9

Which method is NOT used in linkage analysis?
A) comparing densely spaced polymorphisms
B) collecting DNA from a family affected by the disease of interest
C) sequencing selected parts of the genome
D) introducing retroviruses at the mutated locus
E) looking for SNP variants

Accepted Answer

Introducing retroviruses at the mutated locus is not a method used in linkage analysis. The other choices (A, B, C, and E) are commonly used techniques in linkage analysis.

Question 10

Which restriction endonuclease cuts DNA in a way that leaves blunt ends?
A) EcoRI
B) HindIII
C) BamHI
D) EcoRV
E) PstI

Accepted Answer

EcoRV is the only restriction endonuclease listed that cuts DNA in a way that leaves blunt ends.

Question 11

If you wanted to create specific DNA sequence changes to a plasmid in the coding sequence for a protein you are researching, but there are no suitably located restriction sites nearby, which technique would you use?
A) error-prone PCR
B) site-directed mutagenesis
C) oligonucleotide-directed mutagenesis
D) exposing the plasmid DNA to UV light
E) exposing the cells containing the plasmid DNA to chemical mutagens

Accepted Answer

Oligonucleotide-directed mutagenesis allows for specific changes to be made at any location in the DNA sequence without depending on the presence of restriction sites. It involves the synthesis of short, single-stranded DNA molecules called oligonucleotides that are complementary to the target DNA sequence but contain the desired mutation. These oligonucleotides are then introduced to the plasmid-containing cells and used as a template for DNA polymerase-mediated incorporation of the mutations into the plasmid DNA.

Question 12

If you wanted to clone a large fragment of DNA into a unicellular eukaryotic host, what would you use?
A) a bacmid
B) a plasmid
C) a bacterial artificial chromosome
D) a yeast artificial chromosome
E) a virus

Accepted Answer

A large fragment of DNA would likely require a vector that can accommodate a larger insert size. Yeast artificial chromosomes (YACs) can accommodate inserts up to 1 million base pairs, making them a suitable choice for cloning large fragments of DNA.

Question 13

Which list ranks the organisms in order from smallest genome (number of base pairs of DNA) to largest genome?
A) Human, fruit fly, E. coli bacterium
B) E. coli bacterium, human, fruit fly
C) E. coli bacterium, fruit fly, human
D) fruit fly, E. coli bacterium, human
E) fruit fly, human, E. coli bacterium

Accepted Answer

The genome size is smallest in E. coli bacterium, followed by the fruit fly and then the human. Choice C lists the organisms in this order.

Question 14

A good cloning vector should NOT have:
A) an origin of replication.
B) an antibiotic resistance gene.
C) several unique restriction sites.
D) a small size.
E) genes allowing its insertion into the host chromosome.

Accepted Answer

A good cloning vector should be easily maintained in a host, which typically requires an origin of replication, an antibiotic resistance gene for selection, several unique restriction sites for the insertion of foreign DNA, and a small size to facilitate entry into host cells. Genes that allow for the insertion of the vector into the host chromosome are not necessary and can complicate the cloning process.

Question 15

If you want to clone a gene by using E. coli and then transfer that cloned gene into yeast to express the protein the gene encodes, what type of self-replicating DNA should you use for your cloning process?
A) a bacmid
B) a plasmid
C) a yeast artificial chromosome
D) a shuttle vector
E) a bacterial artificial chromosome

Accepted Answer

Shuttle vectors are ideal for transferring genetic material between different organisms, since they contain the necessary elements for replication in both bacterial and eukaryotic cells. In this case, the gene would be cloned into a shuttle vector that can replicate in E. coli and then be transferred into yeast for expression. Bacmids and bacterial artificial chromosomes (BACs) are specifically designed for cloning in bacteria, while yeast artificial chromosomes (YACs) are designed for cloning in yeast, and may not be compatible with both organisms. Plasmids, while commonly used for cloning, would need to be modified with additional regulatory elements to allow for expression in yeast.

Question 16

A restriction endonuclease that has a recognition sequence of 8 bp in length would be expected to cut dsDNA on average once in how many base pairs?
A) 256
B) 1024
C) 4096
D) 65536
E) 1048576

Accepted Answer

A restriction endonuclease with an 8 bp recognition sequence would cut DNA on average once every 4^8 (65536) base pairs, assuming a random distribution of bases.

Question 17

When cloning a gene into a plasmid, which enzyme would you use to covalently attach the gene to the plasmid DNA?
A) DNA polymerase
B) exonuclease III
C) DNA Ligase
D) alkaline phosphatase
E) a restriction endonuclease

Accepted Answer

DNA Ligase is the enzyme that can covalently attach the gene to the plasmid DNA by catalyzing the formation of a phosphodiester bond between the 3'-hydroxyl end of one DNA molecule and the 5'-phosphate end of the other. This process is known as ligation and is an essential step for creating recombinant DNA molecules. DNA polymerase, exonuclease III, alkaline phosphatase, and restriction endonucleases play different roles in genetic engineering but are not used for attaching a gene into a plasmid.

Question 18

Which type of DNA sequence is NOT found in the human genome?
A) long repetitive repeats
B) introns
C) retro-palindromes
D) simple sequence repeats
E) transposons

Accepted Answer

Retro-palindromes are not found in the human genome. While long repetitive repeats, introns, simple sequence repeats, and transposons are all present in the human genome.

Question 19

Current estimates indicate that humans have about _____ genes.
A) 3,000
B) 10,000
C) 30,000
D) 100,000
E) 300,000

Accepted Answer

Current estimates suggest that humans have around 30,000 genes, although this number may vary slightly depending on the method of gene identification used. This is significantly fewer than early estimates of 100,000-140,000 genes.

Question 20

Which way is NOT a means of inserting DNA into a cell?
A) transformation
B) transfection
C) transduction
D) electroporation
E) ligation

Accepted Answer

Ligation is a process of joining two DNA fragments together and is not a means of inserting DNA into a cell. Transformation, transfection, transduction, and electroporation are all methods of introducing DNA into a cell.

Quiz 9: DNA-Based Information Technologies

Which technique can be used to estimate the relative copy numbers of particular DNA sequences in a sample?

What is a polylinker?

Current estimates indicate that _____% of the human genome is translated into protein.

Common problems with expression of eukaryotic proteins in bacteria may include proteins:

Which statement regarding Type I and Type II restriction endonucleases is NOT accurate?

Which DNA sequence is a palindrome?

A good expression vector for protein expression in E. coli should have which feature(s) ?

Which amino acid when repeated six to ten times at the N- or C-terminal ends of a protein allows that protein to bind to Ni²⁺ ions?

Which method is NOT used in linkage analysis?

Which restriction endonuclease cuts DNA in a way that leaves blunt ends?

If you wanted to create specific DNA sequence changes to a plasmid in the coding sequence for a protein you are researching, but there are no suitably located restriction sites nearby, which technique would you use?

If you wanted to clone a large fragment of DNA into a unicellular eukaryotic host, what would you use?

Which list ranks the organisms in order from smallest genome (number of base pairs of DNA) to largest genome?

A good cloning vector should NOT have:

If you want to clone a gene by using E. coli and then transfer that cloned gene into yeast to express the protein the gene encodes, what type of self-replicating DNA should you use for your cloning process?

A restriction endonuclease that has a recognition sequence of 8 bp in length would be expected to cut dsDNA on average once in how many base pairs?

When cloning a gene into a plasmid, which enzyme would you use to covalently attach the gene to the plasmid DNA?

Which type of DNA sequence is NOT found in the human genome?

Current estimates indicate that humans have about _____ genes.

Which way is NOT a means of inserting DNA into a cell?