Deck 16: Genomics

Question 1

Which restriction enzyme leaves blunt ends?

A) EcoR1
B) BamHI
C) HaeII
D) SmaI
E) All of the above

Answer 1

D

Question 2

Vectors capable of entering both prokaryotic and eukaryotic cells are

A) omnivectors.
B) parity vectors.
C) shuttle vectors.
D) universal vectors.
E) dual vectors.

Answer 2

C

Question 3

When DNA is cut with a restriction enzyme, the resulting fragments have

A) a 5' phosphate.
B) a 5' hydroxyl.
C) a 3' hydroxyl.
D) both A and C.
E) both B and C.

Answer 3

D

Question 4

Polymerase chain reaction has revolutionized genetics because

A) it is capable of making large numbers of DNA copies very quickly.
B) it is capable of making virtually unlimited copies of DNA for study.
C) it is capable of making copies of DNA with very little starting material.
D) All of the above
E) A and B only

Question 5

A DNA copy of an mRNA molecule is called

A) mDNA.
B) rDNA.
C) dDNA.
D) rnaDNA.
E) cDNA.

Question 6

Which type of cloning vector occurs in nature?

A) Plasmids and BACs
B) Bacteriophages and cosmids
C) YACs and BACs
D) Plamids and bacteriophages
E) Plamids and cosmids

Question 7

A restriction enzyme cuts DNA and leaves the following end: GGCTA C Which of the following could be the sequence of the corresponding end of the other fragment generated by the enzyme?

A) T
CGATA
B) GGCTA
C
C) CCGAT
G
D) C
GGCTA
E) None of the above

Question 8

Bacteria protect their own DNA from restriction enzyme damage by adding ________ groups to certain nucleotides.

A) methyl
B) hydroxyl
C) carboxyl
D) amino
E) phosphate

Question 9

A polylinker region in a cloning plasmid is characterized by

A) multiple reporter genes.
B) multiple methyl groups.
C) multiple expression vectors.
D) multiple restriction cut sites.
E) multiple cloning targets.

Question 10

A serious problem encountered with artificial chromosomes like YACs is

A) recombination within the host cell.
B) the difficulty of introducing them into cells.
C) the large size of the molecules, making them difficult to construct.
D) A and B
E) none of the above.

Question 11

Many bacteria are naturally capable of taking up endogenous fragments of DNA in their environment, a phenomenon termed

A) conversion.
B) transformation.
C) conjugation.
D) transfection.
E) hybridization.

Question 12

Successful insertion of a DNA fragment into the polylinker region of pUC19 is detected by

A) autoradiography.
B) production of the enzyme β-galactosidase.
C) absence of the enzyme β-galactosidase.
D) the increased size of the plasmid.
E) none of the above.

Question 13

A(n) ________ is basically a photograph using X-ray film, used in such genetics applications as identifying the position of radiolabeled molecules on a gel.

A) northern blot
B) southern blot
C) X-rayogram
D) radiogram
E) autoradiogram

Question 14

The chemical "label" that permits visualization of DNA fragments in sequencing machines is

A) fluorescent dyes.
B) 35S.
C) 32P.
D) tritium.
E) none of the above.

Question 15

In gel electrophoresis, which of the following DNA fragments would travel the farthest distance from the sample well?

A) ATCCCGAT
B) ATCC
C) ATCCCG
D) AT
E) ATCCCGATTGCACGTT

Question 16

In addition to restriction enzymes, which enzyme is required to insert a fragment of DNA into a cloning vector?

A) Topoisomerase
B) DNA ligase
C) RNA polymerase
D) DNA polymerase
E) Reverse transcriptase

Question 17

In DNA electrophoresis, fragment separation is based on

A) fragment size.
B) fragment sequence.
C) fragment charge.
D) fragment nucleotide content.
E) all of the above.

Question 18

________ blots are used to study DNA fragments, while ________ blots are used to study RNA fragments.

A) Western, southern
B) Western, northern
C) Eastern, northern
D) Southern, western
E) Southern, northern

Question 19

The recognition sequences for many restriction enzymes are

A) palindromic.
B) dual repeats.
C) tandem repeats.
D) inverted repeats.
E) terminal repeats.

Question 20

A plasmid used as a cloning vector in E. coli must have

A) unique restriction sites.
B) a selectable marker.
C) an ori sequence.
D) all of the above.
E) B and C only

Question 21

A DNA copy of a messenger RNA molecule is called complementary DNA or cDNA.

Question 22

A linear strand of DNA with two restriction enzyme cut sites will yield three fragments upon digestion.

Question 23

PCR has revolutionized the criminal justice system through DNA fingerprinting. For a given fragment of DNA, showing that a suspect's fingerprint differs from that found at a crime scene immediately excludes him or her from suspicion, yet finding a match does not mean that guilt can be automatically concluded. Why?

Question 24

Polymerase chain reaction, or PCR, is performed with thermostable DNA polymerase enzymes isolated from thermophilic bacteria like Thermus aquaticus. Speculate on why these enzymes do not denature at higher temperatures, as would polymerases isolated from nonthermophiles like humans.

Question 25

The first available drug manufactured with recombinant DNA technology was insulin, marked under the name Humulin.

Question 26

PCR is a genetic technique developed in the 1950s.

Question 27

Briefly describe three mechanisms by which genetic material is transferred between bacterial cells.

Question 28

Exactly why, in Sanger DNA sequencing, do dideoxynucleotides halt the replication process?

Question 29

After how many PCR cycles, starting from a single starting molecule, will fragments consisting of only the target DNA (the DNA between the primers) be generated?

Question 30

A potentially serious problem with Taq polymerase in PCR is its lack of proofreading ability. Briefly explain why this can be a problem and when in the PCR process this can be the most and the least problematic.

Question 31

Cloning vectors are used to introduce novel DNA into cells.

Question 32

Say you were using random PCR primers to amplify fragments of DNA. Would you expect to get more or less amplification products if you set the PCR machine at a relatively higher or lower annealing temperature, respectively, and why?

Question 33

A circular DNA molecule with two restriction enzyme cut sites will yield three fragments upon digestion.

Question 34

The restriction enzyme SmaI cuts DNA at the 6-base recognition sequence 5'-CCCGGG-3'. Calculate the frequency of occurrence of this sequence.

Question 35

Calculate the number of copies produced from a single starting molecule after 10 rounds of PCR.

Question 36

A pUC19 cloning vector is used to introduce a gene of interest into a bacterial strain. The vector is lacking ampR, however. What problem does this result in?

Question 37

In partial restriction digestion, all available cut sites will be cut.

Question 38

Cloning vectors generally possess unique restriction sites and dominant selectable markers.

Question 39

DNA molecules, regardless of size, have a net positive charge.

Question 40

Can you think of an alternative means of identifying successful bacterial transformants in the experiment discussed in question 40?

Question 41

PCR has opened the door to analysis of ancient DNA-DNA taken from long-dead organisms. The most useful DNA fragments in such cases typically come from mitochondrial DNA. Why do you think that is so?

Question 42

Given the DNA oligonucleotide 5'-AGTCTAGGCT-3', reconstruct a sequencing gel based on Sanger sequencing, showing the relative position of each DNA fragment (band) on the gel.

Question 43

It is sometimes not easy to locate or identify genes based on cDNA. How do cDNA and DNA with respect to a given gene differ to create this problem?