Deck 3: Nucleic Acid Structure and Function

Question 1

Increasing the ion concentration increases the T_m because the ions

A) bind to the phosphate groups of the DNA backbone and increase stability.
B) bind to the nucleic acids and disrupt the base pairs, decreasing stability.
C) increase the base length of the DNA, increasing stability.
D) associate with the ribose sugars, decreasing stability.

Answer 1

bind to the phosphate groups of the DNA backbone and increase stability.

Question 2

Which form(s) of DNA exhibit(s) a zigzag arrangement?

A) A-DNA
B) B-DNA
C) Z-DNA
D) A-DNA and B-DNA

Answer 2

Z-DNA

Question 3

The K⁺ ion concentration in a DNA sample is increased from 50 mM to 100 mM. The T_m will

A) remain the same.
B) decrease.
C) increase.
D) vary unpredictably.

Answer 3

increase.

Question 4

The DNA of a bacteria was isolated and it was determined that 15% of the DNA is composed of cytosine. What percentage of the DNA is guanine?

A) 15%
B) 30%
C) 35%
D) 70%

Question 5

DNA strands are considered to be antiparallel. This means the

A) phosphodiester bonds run in the same direction.
B) phosphodiester bonds run in different directions.
C) base pairs form hydrogen bonds.
D) phosphate backbone is on the outside of the helix.

Question 6

When DNA is transcribed into RNA, the strand has the same base sequences as the RNA transcript.

A) antiparallel
B) parallel
C) coding
D) template

Question 7

Which form(s) of DNA exhibit(s) a right-handed helical structure?

A) A-DNA
B) B-DNA
C) Z-DNA
D) A-DNA and B-DNA

Question 8

When DNA is transcribed into RNA, the strand has the complementary sequence to the transcribed RNA.

A) antiparallel
B) parallel
C) coding
D) template

Question 9

The ability to monitor the denaturation of DNA using absorbance is referred to as

A) annealing.
B) supercoiling.
C) melting temperature.
D) hyperchromic effect.

Question 10

As DNA unwinds and denatures, absorbance is predicted to

A) remain the same.
B) decrease.
C) increase.
D) vary unpredictably.

Question 11

The figure below shows part of the primary structure of DNA. Identify the nucleotide.

A) A
B) B
C) C
D) D

Question 12

The basic structure of DNA is a right-handed helix formed by two strands of DNA.

A) antiparallel
B) parallel
C) coding
D) template

Question 13

Predict the complementary strand of the following DNA sequence: 5 ^' -ATCTGAATCT-3 ^'

A) 5 ^' -TCTAAGTCTA-3 ^'
B) 5 ^' -TAGACTTAGA-3 ^'
C) 5 ^' -ATCTGAATCT-3 ^'
D) 5 ^' -AGATTCAGAT-3 ^'

Question 14

The figure below shows part of the primary structure of DNA. Identify the nucleoside.

A) A
B) B
C) C
D) D

Question 15

Chargaff's rule is that the amount of

A) A = G and the amount of C = T.
B) A = C = G = T.
C) A = T and the amount of C = G.
D) A = C and the amount of G = T.

Question 16

How many base pairs per turn does B-DNA contain?

A) 10.0
B) 10.5
C) 11.0
D) 12.0

Question 17

The DNA double helix is considered to be a structure.

A) primary
B) secondary
C) tertiary
D) quaternary

Question 18

The DNA of a bacteria was isolated and it was determined that 15% of the DNA is composed of cytosine. What percentage of the DNA is adenine?

A) 15%
B) 30%
C) 35%
D) 70%

Question 19

What is the melting temperature from the DNA absorbance shown in the figure below?

A) 80 $\degree$ C
B) 85 $\degree$ C
C) 90 $\degree$ C
D) 95 $\degree$ C

Question 20

The interior stacking of the DNA bases in the double helix provides stability through

A) hydrophobic and van der Waals interactions.
B) hydrophilic and van der Waals interactions.
C) hydrophilic and ion-dipole interactions.
D) hydrophobic and ion-dipole interactions.

Question 21

Predict how type II topoisomerases change the supercoil region.

A) Lk = 2
B) Lk = 1
C) Lk = -1
D) Lk = -2

Question 22

Type I topoisomerase activity results in a region of DNA.

A) semiconservative
B) spliced
C) relaxed
D) unrepaired

Question 23

Which of the following binds to DNA using a specific sequence?

A) histones
B) Lac repressor protein
C) double-stranded binding proteins
D) single-stranded binding proteins

Question 24

Which of the following expresses the relationship among the linking number, twist, and writhe?

A) Tw = Lk + Wr
B) Lk = Tw - Wr
C) Lk = Wr - Tw
D) Lk = Tw + Wr

Question 25

Several histones can bind to one DNA molecule, forming a repeating unit called a

A) ribozyme.
B) nucleosome.
C) topoisomerase.
D) nucleoside.

Question 26

What mediates the binding of histone proteins to DNA?

A) ionic attractions
B) London dispersion forces
C) hydrophilic interactions
D) hydrophobic interactions

Question 27

The linking number of a relaxed DNA strand whose axis is not coiling is 30. Predict the twist and writhe of the DNA stand.

A) Wr = 0, Tw = 30
B) Wr = 30, Tw = 0
C) Wr = 15, Tw = 15
D) Wr = 30, Tw = -30

Question 28

Less condensed, gene-rich chromatin is referred to as

A) nucleosomes.
B) histones.
C) heterochromatin.
D) euchromatin.

Question 29

Type II topoisomerase enzymes are important in replication and transcription because they

A) prevent autocleavage.
B) prevent DNA cleavage.
C) relieve the positive supercoiling.
D) stabilize the cleaved complex.

Question 30

Calculate the linking number for a B-DNA strand that contains 735 total base pairs.

A) 50
B) 61
C) 67
D) 70

Question 31

DNA strands containing 20 base pairs, 40 base pairs, and 60 base pairs were denatured and the results were graphed below. Identify the curve from the 60 base pair DNA strand.

A) A
B) B
C) C
D) Not enough information is included to determine the curve.

Question 32

A double helix that crosses itself in a right-handed twist is referred to as a

A) positive supercoil.
B) negative supercoil.
C) topoisomer.
D) linking number.

Question 33

Chromatin that consists of more condensed regions of mostly noncoding DNA are referred to as

A) nucleosomes.
B) histones.
C) heterochromatin.
D) euchromatin.

Question 34

The proteins that bind to DNA in a sequence-independent manner are

A) histones.
B) single-stranded binding proteins.
C) Lac repressor proteins.
D) histones and single-stranded binding proteins.

Question 35

During eukaryotic DNA condensation, nucleosomes are packed together to form

A) histones.
B) chromatin.
C) chromosomes.
D) genes.

Question 36

A double helix that crosses itself in a left-handed twist is referred to as a

A) positive supercoil.
B) negative supercoil.
C) topoisomer.
D) linking number.

Question 37

The process of condensation reduced the size of DNA by

A) 100-fold.
B) 1,000-fold.
C) 10,000-fold.
D) 100,000-fold.

Question 38

The A-T content for several DNA strands is reported below. Which strand would have the highest T_m?

A) 40% A-T
B) 50% A-T
C) 60% A-T
D) 70% A-T

Question 39

Predict how type I topoisomerases change the supercoil region.

A) Lk = 2
B) Lk = 1
C) Lk = -1
D) Lk = -2

Question 40

RNA only contains which of the following bases?

A) thymine
B) adenine
C) uracil
D) guanine

Question 41

The mixing and matching of novel genes in eukaryotic cells occurs through

A) operons.
B) exon shuffling.
C) promoter regions.
D) untranslated regions.

Question 42

Identify the kinetochore in the following figure.

A) A
B) B
C) C
D) D

Question 43

In the eukaryotic cell, the NONcoding sequences on a gene are referred to as

A) exons.
B) operons.
C) introns.
D) promoter.

Question 44

Genes found in prokaryotes that only contain a single coding sequence are referred to as

A) exons.
B) introns.
C) polycistronic.
D) monocistronic.

Question 45

In plasmid transformation, DNA is transferred when

A) bacteriophages infect bacteria.
B) foreign DNA fragments are inserted into the plasmid using multiple cloning sites.
C) there is a horizontal gene transfer during the bacteria mating process.
D) a dead bacterium releases DNA into the environment and it is obtained by another bacterium.

Question 46

In plasmid conjugation, DNA is transferred when

A) bacteriophages infect bacteria.
B) foreign DNA fragments are inserted into the plasmid using multiple cloning sites.
C) there is a horizontal gene transfer during the bacteria mating process.
D) a dead bacterium releases DNA into the environment and it is obtained by another bacterium.

Question 47

Individual nucleotide changes to the genome cause a polymorphism called

A) short tandem repeats.
B) variable number tandem repeats.
C) long tandem repeats.
D) single nucleotide polymorphism.

Question 48

Foreign DNA fragments can be inserted into plasmids using

A) promoters.
B) cloning vectors.
C) cloning sites.
D) recombinant DNA.

Question 49

Not all single nucleotide polymorphisms cause a phenotypic change because sometimes the changes occur in the

A) coding region.
B) noncoding region.
C) promoter sequence.
D) telomeres.

Question 50

Polycistronic genes that contain a coding sequence for proteins that are only involved in one biochemical process are called

A) exons.
B) operons.
C) introns.
D) promoters.

Question 51

__________ maintain the length of the chromosome after replication.

A) Telomeres
B) Centromeres
C) Kinetochores
D) Sister chromatids

Question 52

The exons of a single gene often encode for different functional domains of a protein, which can result in

A) genetic recombination.
B) gene regulation.
C) untranslated regions.
D) termination of transcription.

Question 53

In viral transduction, DNA is transferred when

A) bacteriophages infect bacteria.
B) foreign DNA fragments are inserted into the plasmid using multiple cloning sites.
C) there is a horizontal gene transfer during the bacteria mating process.
D) a dead bacterium releases DNA into the environment and it is obtained by another bacterium.

Question 54

When DNA molecules from multiple sources have been connected in the laboratory, the result is referred to as

A) promoters.
B) cloning vectors.
C) cloning sites.
D) recombinant DNA.

Question 55

Deletions or insertions into the genome cause a polymorphism called

A) short tandem repeats.
B) variable number tandem repeats.
C) long tandem repeats.
D) single nucleotide polymorphism.

Question 56

A common database tool used to determine homologous genomic sequences is called

A) the National Center for Biotechnology Information.
B) the National Human Genome Research Institute.
C) Computational Analysis.
D) Basic Local Alignment Search Tool.

Question 57

Which protein is responsible for the proper separation of the chromosomes during cell division?

A) telomeres
B) centromeres
C) kinetochores
D) sister chromatids

Question 58

Two identical copies of replicated DNA that remain attached until cell division are referred to as

A) telomeres.
B) centromeres.
C) kinetochores.
D) sister chromatids.

Question 59

In the eukaryotic cell, the coding sequences on a gene are referred to as

A) exons.
B) operons.
C) introns.
D) promoter.

Question 60

In a single RNA transcript, polycistronic prokaryotic genes encode protein(s).

A) one
B) two
C) three
D) multiple

Question 61

Which enzyme is used to cleave DNA at specific sequences during the production of recombinant DNA?

A) DNA methylase
B) restriction endonucleases
C) reverse transcriptase
D) DNA ligase

Question 62

The most common purpose for cloning a gene sequence using mRNA is to

A) disrupt antibiotic resistance.
B) determine homologous genomic sequences.
C) generate a library of actively transcribed genes.
D) disrupt the lacZ gene, resulting in blue-white screening.

Question 63

In the production of recombinant DNA, which enzyme links matching cohesive ends using covalent interactions?

A) DNA methylase
B) restriction endonucleases
C) reverse transcriptase
D) DNA ligase

Question 64

In the second temperature phase of PCR, why does the temperature vary from 55 $\degree$ C to 65 $\degree$ C?

A) different ionic strengths
B) different primer concentrations
C) G-C content
D) different amount of hydrogen bonds

Question 65

Identify the phase of PCR amplification where DNA synthesis occurs.

A) A
B) B
C) C
D) D

Question 66

Compare and contrast the arrangements of A-DNA, B-DNA, and Z-DNA.

Question 67

When a gene sequence is cloned using mRNA, the mRNA is isolated from the cell and converted into a double-stranded sequence using which enzyme?

A) DNA methylase
B) restriction endonucleases
C) reverse transcriptase
D) DNA ligase

Question 68

Identify the phase of PCR amplification where DNA is denatured and the strands are separated.

A) A
B) B
C) C
D) D

Question 69

The $\beta$ -galactosidase gene that is inserted into plasmid cloning vectors is used to

A) cleave the DNA in a sequence-specific fashion.
B) disrupt the antibiotic-resistance gene, making it nonfunctional.
C) determine if the cloning has been successful.
D) protect the bacteria from bacteriophage infection.

Question 70

Below are the steps involved in cloning gene sequences using mRNA. Arrange the steps in the appropriate order. 1. The double-stranded cDNA is treated with a restriction endonuclease to generate compatible ends for annealing and ligation.
2) mRNA is isolated from the cell and converted back into double-stranded sequences using reverse transcriptase to generate complementary DNA.
3) The RNA-DNA hybrid is treated with a nuclease to cleave the RNA strand, producing RNA fragments.
4) Reverse transcriptase completes the single-stranded cDNA when it reaches the 5 ^' end of the mRNA transcript.
5) RNA fragments serve as primers for DNA synthesis of the second strand of cDNA using DNA polymerase.

A) 4, 2, 1, 5, 3
B) 2, 4, 3, 5, 1
C) 2, 3, 5, 4, 1
D) 3, 2, 5, 4, 1

Question 71

Explain the difference between the coding strand and the template strand of DNA as it relates to RNA transcription.

Question 72

Compare the primary and secondary structures of DNA.

Question 73

This method of analyzing RNA transcripts relies on a predetermined collection of complementary DNA sequences.

A) plasmid cloning
B) viral transduction
C) RNA-seq
D) gene-expression microarrays

Question 74

When a gene sequence is cloned using mRNA, which enzyme is used to seal the single-strand gaps left behind in the second strand of DNA?

A) DNA methylase
B) restriction endonucleases
C) reverse transcriptase
D) DNA ligase

Question 75

Identify the phase of PCR amplification where the primer is annealed.

A) A
B) B
C) C
D) D

Question 76

DNA regions rich in A-T are more easily denatured than regions with a higher G-C content. Why is this biologically significant?

Question 77

Identify the products when Sm al cleaves the following DNA sequence.

A)a
B)b
C)c
D)d

Question 78

When DNA is sequenced, which analytical technique is used to separate the chain-terminated DNA fragments?

A) gel electrophoresis
B) blue-white screening
C) antibiotic resistance
D) fluorescent labeling

Question 79

Which method of analyzing RNA transcripts is considered to be an unbiased approach because it does not use a predetermined collection of complementary DNA sequence?

A) plasmid cloning
B) viral transduction
C) RNA-seq
D) gene-expression microarrays

Question 80

A sequence of B-DNA contains 78,000 base pairs. Analysis shows that 42% are C-G base pairs. Answer the following questions and show your mathematical work.
a. How many pyrimidine bases are in this sequence?
b. How many nucleotides are cytosines?
c. How many nucleotides are thymines?
d. How many hydrogen bonds does this sequence contain?
e. How many turns of the double helix occur in this sequence?