Deck 8: Genomics: The Mapping and Sequencing of Genomes

Question 1

The chemical "label" that permits visualization of DNA fragments in an automated sequencing machine is

A)³²P.
B)³⁵S.
C)fluorescent dyes.
D)tritium.
E)None of these

Answer 1

C

Question 2

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

A)an ori sequence.
B)a selectable marker.
C)unique restriction sites.
D)B and C
E)All of these

Answer 2

E

Question 3

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

A)G CTGCA
B)C GTGCA
C)CCGAT G
D)GGCTA C
E)None of these

Answer 3

A

Question 4

The recognition sequences for many restriction enzymes are

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

Question 5

A polylinker region in a cloning plasmid is characterized by

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

Question 6

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

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

Question 7

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

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

Question 8

In a physical map,distances are measured in

A)recombination frequencies.
B)number of SNPs.
C)base pairs.
D)probabilities.
E)microns.

Question 9

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

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

Question 10

The ________ method was used by the Celera Genomics Corporation to sequence the human genome.

A)FISH
B)whole-genome shotgun
C)clone contig
D)radiation hybrid
E)pedigree analysis

Question 11

An SNP always occurs due to

A)a one base-pair change.
B)a three base-pair change.
C)a single restriction site change.
D)a single amino acid change.
E)None of these

Question 12

A DNA copy of an mRNA molecule is called

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

Question 13

Which restriction enzyme leaves blunt ends?

A)XbaI
B)SmaI
C)EcoR1
D)BamHI
E)All of these

Question 14

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

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

Question 15

The first complete nonviral genome sequenced was that of

A)Escherichia coli.
B)Methanococcus.
C)Saccharomyces cerevisiae.
D)the human mitochondrion.
E)Mus musculus.

Question 16

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

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

Question 17

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

A)5' carboxyls.
B)5' hydroxyls.
C)3' hydroxyls.
D)3' phosphates.
E)3' carboxyls.

Question 18

In DNA electrophoresis,fragment separation is based on

A)fragment size.
B)fragment nucleotide content.
C)fragment sequence.
D)fragment charge.
E)All of these

Question 19

Candidate open reading frames of a genome are identified by searching for

A)a start codon "in frame" with a stop codon.
B)a start codon.
C)introns and exons.
D)a promoter.
E)All of these

Question 20

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

Question 21

Which types of cloning vector occur in nature?

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

Question 22

Cloning vectors are used to introduce novel DNA into cells.

Question 23

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

Question 24

The restriction enzyme SmaI cuts DNA at the 6-base recognition sequence 5'-CCCGGG-3'.Calculate the frequency of occurrence of this sequence.(Assume a 50% GC content.)

Question 25

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

Question 26

What is a hapmap?

Question 27

The quality of an assembled sequence does not depend on the sequence coverage.

Question 28

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

Question 29

The human genome consists mostly of noncoding DNA.

Question 30

Describe a DNA microarray setup for assaying mutations associated with a hypothetical genetic disease.

Question 31

Describe the basic approach to shotgun genome sequencing.

Question 32

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

Question 33

What problem does this result in?

Question 34

Can you think of an alternative means of identifying successful bacterial transformants in this experiment?

Question 35

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

Question 36

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

Question 37

How can the recircularization of a restriction-digested vector during a ligation reaction be minimized?

Question 38

Briefly contrast the dideoxy DNA sequencing developed by Fred Sanger with pyrosequencing methods.

Question 39

Archaea are typically found in much the same habitats as bacteria.

Question 40

It is not always easy to locate or identify genes based on cDNA.How is this problem created by the differences between cDNA and DNA with respect to a given gene?

Question 41

What advantage do cDNA libraries have over genomic libraries?

Question 42

Based on DNA sequences of single genes,genomic analysis has confirmed that prokaryotes are divided into two great lineages: the Bacteria and the Archaea.The latter may be more closely related to the Eukarya.Recount the lines of evidence that support these findings.

Question 43

Sequencing the dog genome is currently a high priority for genomics researchers.What insights do you think can be gained about the evolutionary process by analyzing the genome of dogs?

Question 44

Discuss the relative roles of descriptive and hypothesis-driven science in genomics.