Deck 24: Nucleic Acid Structure

Question 1

The sequence-specific binding of BamHI to DNA depends primarily on

A)hydrogen bonding and allows binding to less specific sequences as well.
B)hydrogen bonding and precludes binding to any other sequence.
C)stacking interactions and could be mimicked using an intercalation molecule.
D)hydrogen bonding and could be mimicked using an intercalation molecule.
E)none of the above

Answer 1

hydrogen bonding and precludes binding to any other sequence.

Question 2

Matching
Choose the correct answer from the list. Not all the answers will be used.
RNA catalysts are called ______.

A)type I
B)ribocatalyzers
C)C2'-endo
D)repressors
E)ethidium
F)type II
G)C3'-endo
H)hybridized
I)interchanged
J)supercoiled
K)cooperative
L)non-cooperative
M)underwound
N)ribozymes
O)deuterium
P)zinc finger
Q)leucine zipper

Answer 2

ribozymes

Question 3

Matching
Choose the correct answer from the list. Not all the answers will be used.
Naturally occurring circular DNA is typically _______.

A)type I
B)ribocatalyzers
C)C2'-endo
D)repressors
E)ethidium
F)type II
G)C3'-endo
H)hybridized
I)interchanged
J)supercoiled
K)cooperative
L)non-cooperative
M)underwound
N)ribozymes
O)deuterium
P)zinc finger
Q)leucine zipper

Answer 3

underwound

Question 4

Matching
Choose the correct answer from the list. Not all the answers will be used.
Single-strand breaks in DNA are transiently created by ______ topoisomerases.

A)type I
B)ribocatalyzers
C)C2'-endo
D)repressors
E)ethidium
F)type II
G)C3'-endo
H)hybridized
I)interchanged
J)supercoiled
K)cooperative
L)non-cooperative
M)underwound
N)ribozymes
O)deuterium
P)zinc finger
Q)leucine zipper

Question 5

Matching
Choose the correct answer from the list. Not all the answers will be used.
Heptad repeats are found in the ______ region of DNA binding proteins.

A)type I
B)ribocatalyzers
C)C2'-endo
D)repressors
E)ethidium
F)type II
G)C3'-endo
H)hybridized
I)interchanged
J)supercoiled
K)cooperative
L)non-cooperative
M)underwound
N)ribozymes
O)deuterium
P)zinc finger
Q)leucine zipper

Question 6

Matching
Choose the correct answer from the list. Not all the answers will be used.
Complementary DNA and RNA strands can be ______.

A)type I
B)ribocatalyzers
C)C2'-endo
D)repressors
E)ethidium
F)type II
G)C3'-endo
H)hybridized
I)interchanged
J)supercoiled
K)cooperative
L)non-cooperative
M)underwound
N)ribozymes
O)deuterium
P)zinc finger
Q)leucine zipper

Question 7

What evidence suggests that a biological function exists for Z-DNA?

A)Z-DNA is unique because it is made up of alternating pyrimidine and purine residues in the anti and syn conformation.
B)The left-handed nature of Z-DNA allows phosphate separation which is stabilizing..
C)X-ray structure of the protein Z binding Z-DNA has been identified.
D)A and B
E)A, B, and C

Question 8

Histone H1 binds to ____ which allows attachment to _____.

A)the nucleosome core particle; nucleases
B)linker DNA; the next nucleosome
C)the nucleosome core particle; the next nucleosome
D)linker DNA; nucleases
E)none of the above

Question 9

Heat-denatured DNA exhibits ______ UV absorbance, which is called the ______.

A)increased; hyperchromic effect
B)decreased; hyperchromic effect
C)increased; hypochromic effect
D)decreased; hypochromic effect
E)identical; renaturation effect

Question 10

The chromosomes of some viruses and bacteria are ______ and often ______.

A)linear; single stranded
B)linear; supercoiled
C)circular; single stranded
D)circular; supercoiled
E)none of the above

Question 11

Which of the following prokaryotic enzymes can introduce negative supercoils?

A)topoismerase IA
B)topoismerase III
C)DNA gyrase
D)all of the above
E)none of the above

Question 12

Matching
Choose the correct answer from the list. Not all the answers will be used.
In prokaryotes, many of the _____ that bind to DNA contain a HTH motif.

A)type I
B)ribocatalyzers
C)C2'-endo
D)repressors
E)ethidium
F)type II
G)C3'-endo
H)hybridized
I)interchanged
J)supercoiled
K)cooperative
L)non-cooperative
M)underwound
N)ribozymes
O)deuterium
P)zinc finger
Q)leucine zipper

Question 13

Matching
Choose the correct answer from the list. Not all the answers will be used.
_________ topoisomerases that make double-strand breaks in DNA in a controlled fashion.

A)type I
B)ribocatalyzers
C)C2'-endo
D)repressors
E)ethidium
F)type II
G)C3'-endo
H)hybridized
I)interchanged
J)supercoiled
K)cooperative
L)non-cooperative
M)underwound
N)ribozymes
O)deuterium
P)zinc finger
Q)leucine zipper

Question 14

Matching
Choose the correct answer from the list. Not all the answers will be used.
The denaturation of DNA is a ______ cooperative process.

A)type I
B)ribocatalyzers
C)C2'-endo
D)repressors
E)ethidium
F)type II
G)C3'-endo
H)hybridized
I)interchanged
J)supercoiled
K)cooperative
L)non-cooperative
M)underwound
N)ribozymes
O)deuterium
P)zinc finger
Q)leucine zipper

Question 15

Matching
Choose the correct answer from the list. Not all the answers will be used.
The 2-deoxyribose groups assume the ____ conformation in B-DNA.

A)type I
B)ribocatalyzers
C)C2'-endo
D)repressors
E)ethidium
F)type II
G)C3'-endo
H)hybridized
I)interchanged
J)supercoiled
K)cooperative
L)non-cooperative
M)underwound
N)ribozymes
O)deuterium
P)zinc finger
Q)leucine zipper

Question 16

Which of the following scientists is now accredited with generating the X-ray diffraction photograph that played a pivotal role in the discovery of the structure of B-DNA?

A)James Watson
B)Francis Crick
C)Maurice Wilkins
D)Rosalind Franklin
E)all of the above

Question 17

Which of the following would NOT result in the relaxation of supercoiled DNA?

A)heating the DNA to induce denaturation
B)nicking one strand
C)treatment with pancreatic DNaseI
D)treatment with type II topoisomerase
E)treatment with type I topoisomerase

Question 18

Matching
Choose the correct answer from the list. Not all the answers will be used.
________, an ion that intercalates into double-stranded DNA, is often used for staining gels.

A)type I
B)ribocatalyzers
C)C2'-endo
D)repressors
E)ethidium
F)type II
G)C3'-endo
H)hybridized
I)interchanged
J)supercoiled
K)cooperative
L)non-cooperative
M)underwound
N)ribozymes
O)deuterium
P)zinc finger
Q)leucine zipper

Question 19

Which of the following materials would be useful for a researcher seeking to purify chromosomal DNA of lysed E.coli cells from cellular proteins and RNA?

A)ethidium bromide
B)hydroxyapatite
C)acridine orange
D)proflavin
E)DNA gyrase

Question 20

tRNA molecules are
I.extensively base-paired.
II.stabilized by hydrogen bonds.
III.stabilized by stacking interactions.
IV.stabilized by covalent cross links.

A)I, II
B)II, III
C)I, II, III
D)I, III
E)I, II, IV

Question 21

Two circular DNAs are isolated, both with 1000 bp, are electrophoresed side-by-side: #1: twist (T)= +100, writhing number (W)= −5
#2: twist (T)= +1000, writhing number (W)= +5

A)DNA #1 should migrate further.
B)DNA #2 should migrate further.
C)They should migrate the same distance.
D)More information is required to determine.
E)This cannot be determined regardless of additional information.

Question 22

Which of the following topoisomerases require(s)ATP hydrolysis for energy?
I.type IA
II.type IB
III.type II

A)I only
B)II only
C)III only
D)I, II
E)I, II, III

Question 23

An effective antibiotic is ___, which inhibits ______.

A)ciprofloxacin, DNA gyrase
B)doxorubicin, Type IA topoisomerase
C)novobiocin, ATPase
D)camptothecin, Type II topoisomerase
E)none of the above

Question 24

Southern blots identify _____, Northern blots identify ____, and Western blots identify ______.

A)DNA, proteins, RNA
B)DNA, RNA, proteins
C)RNA, proteins, DNA
D)RNA, DNA, proteins
E)proteins, DNA, RNA

Question 25

Which of the following statements about the structure and conformation of DNA is FALSE?

A)DNA binding proteins distort DNA structure
B)Changes in ionic strength can alter DNA structure
C)Specific sequences can cause deviations in conformation.
D)Changes in DNA conformation result from energy minimizations and do not relate to in vivo conditions.
E)All of the above are true.

Question 26

In A-DNA

A)the glycosidic bond is in the syn conformation with a C3'-endo sugar pucker.
B)the glycosidic bond is in the syn conformation with a C2'-endo sugar pucker.
C)the glycosidic bond is in the anti conformation with a C3'-endo sugar pucker.
D)the glycosidic bond is in the anti conformation with a C2'-endo sugar pucker.
E)the glycosidic bond conformation and sugar pucker is dependent on the base.

Question 27

Which atoms, or groups attached to them, face into the minor groove of B-DNA?

A)purine 1 & 2; pyrimidine 2 & 3
B)purine 2 & 3; pyrimidine 2
C)purine 8 & 9; pyrimidine 1 & 6
D)purine 6 & 7; pyrimidine 4 & 5
E)purine 6 & 7; pyrimidine 2

Question 28

Which of the following best describes the structure of RNA-DNA hybrids?
I.They are most similar to A-DNA.
II.They are most similar to B-DNA.
III.They are most similar to Z-DNA.
IV.They are most similar to RNA.

A)I only
B)II only
C)I, II
D)III only
E)IV only

Question 29

Western blots, or ____, identify ______ using ______.

A)Northern blots; RNA; antibodies
B)immunoblots; proteins; antibodies
C)Southern blots; proteins; radioactivity
D)immunoblots; DNA; antibodies
E)Northern blots; DNA; antibodies

Question 30

Indirect readout refers to
I.a protein's ability to form hydrogen bonds through a network of water molecules.
II.the 5 to 3 sequence on the opposite strand of a DNA helix.
III.a protein's ability to recognize a specific DNA sequence by its backbone conformation and flexibility.
IV.the protein's ability to make hydrogen bonds with nonesterified phosphate oxygens

A)I, III, IV
B)II, IV
C)III, IV
D)I, III
E)I, IV

Question 31

Which of the following statements about zinc fingers is FALSE?

A)Zinc fingers contain Cys and His residues.
B)Zinc is tetrahedrally coordinated as part of a small compact protein domain.
C)More than one finger can be found in a protein; as many as 60 have been observed.
D)Zinc fingers are the predominant DNA-binding motif of restriction enzymes.
E)A zinc finger recognizes specific sequences of DNA via its N-terminal helices.

Question 32

During which of the following processes are RNA−DNA hybrids observed?

A)transcription, both eukaryotic and prokaryotic
B)translation, both eukaryotic and prokaryotic
C)replication, both eukaryotic and prokaryotic
D)transcription, prokaryotic only
E)replication, prokaryotic only

Question 33

Which the following sequences of DNA is most likely to form Z-DNA in vitro?

A)5'-ATATATATATATATATATAT-3' 3'-TATATATATATATATATATA-5'
B)5'-AAAAAAAAAAAAAAAAAAAA-3' 3'-TTTTTTTTTTTTTTTTTTTT-5'
C)5'-GCGCGCGCGCGCCGCGCGCG-3' 3'-CGCGCGCGCGCGCGCGCGCG-5'
D)5'-GGGGGGGGGGGGGGGGGGGG-3' 3'-CCCCCCCCCCCCCCCCCCCC-5'
E)5'-GATCGATCGATCGATCGATC-3' 3'-CTAGCTAGCTAGCTAGCTAG-5'

Question 34

The DNA helix is stabilized by
I.hydrogen bonds between phosphate groups.
II.stacking interactions.
III.an entropically favored interaction between hydrophobic groups.
IV.favorable electrostatic interactions.

A)I, II, III, IV
B)I, II, IV
C)II, IV
D)III, IV
E)II, III

Question 35

Which of the following best describes the structure of a nucleosome?

A)approximately 150 bp of DNA wrapped around a set of two H2A/H2B and two H3/H4 dimers with H1 on the outside
B)approximately 15 bp of DNA wrapped around an octamer of H1 with H2A,B, H3 and H4 on the outside
C)approximately 150 bp of DNA wrapped around a tetramer of either H2A/H2B or H3/H4 with H1 on the outside
D)approximately 1500 bp of DNA wrapped around a tetramer of either H2A/H2B or H3/H4 with H1 on the outside
E)approximately 200 bp of DNA wrapped around a tetramer of H2A,H2B,H3, and H4 with H1 on the outside

Question 36

A circular 25000 base pair DNA molecule with no supercoils will have _____ helical twists if it is B-DNA.

A)about 2.5
B)about 25
C)about 250
D)about 2500
E)about 25000.

Question 37

If a circular DNA containing no supercoils is incubated with ethidium bromide

A)the number of twists will increase, positive supercoils will develop, and the linking number will remain the same.
B)the number of twists will decrease, positive supercoils will develop, and the linking number will remain the same.
C)the number of twists will increase, negative supercoils will develop, and the linking number will remain the same.
D)the number of twists will decrease, negative supercoils will develop, and the linking number will remain the same.
E)the linking number will be altered, and both the writhing number and twist will adjust accordingly.

Question 38

The sugar pucker is___ in the ___form.

A)C2'-endo; A-DNA
B)C3'-endo; B-DNA
C)C2'-endo for pyrimidines and C3'-endo for purines: Z-DNA
D)C2'-endo for purines and C3'-endo for pyrimidines: B-DNA
E)C2'-endo for purines and C3'-endo for pyrimidines: A-DNA

Question 39

Which of the following can be determined from a Northern blot?

A)the size of a gene transcript
B)the abundance of a gene transcript
C)the tissue specificity of gene transcript
D)the stage-specificity of a gene transcript
E)all of the above

Question 40

Which atoms, or groups attached to them, face into the major groove of B- DNA?

A)purine 1 & 2; pyrimidine 2 & 3
B)purine 2 & 3; pyrimidine 2
C)purine 8 & 9; pyrimidine 1 & 6
D)purine 6 & 7; pyrimidine 4 & 5
E)purine 6 & 7; pyrimidine 2

Question 41

Which of the following is used to allow effective gel electrophoresis of DNAs > 100,000 base pairs?

A)hydroxyapatite treatment prior to gel loading
B)Northern blots
C)pulsed-field gel electrophoresis
D)Southern Blot
E)Western Blot

Question 42

Which of the following is TRUE regarding the rotation of the bonds in DNA?

A)The vertex angles of the ribose rind are 108^°.
B)The ribose ring always puckers at C3'.
C)Noncovalent interactions between the ribose ring and the phosphate group constrain rotation.
D)A and B
E)B and C

Question 43

Which of the following is FALSE regarding DNA binding to proteins?

A)Most eukaryotic transcription factors contain a conserved DNA-binding basic region.
B)The basic regions typically bind in the major groove of its target DNA.
C)Eukaryotic transcription factors either contain an HTH motif or resemble the met repressor.
D)all of the above
E)none of the above

Question 44

In B-DNA

A)the width of the base pair varies depending on the bases involved.
B)the base planes are rotated approximately 90^° from the axis of the helix.
C)the sugar pucker must be variable depending on the base attached.
D)the helix twist is approximately 10^° per base pair.
E)all of the above

Question 45

Which of the following is NOT a requirement of genetic material?

A)The lifetime of the material must be such that it can undergo repeated decoding.
B)The material must be accessible for replication, transcription, and translation.
C)The material must be capable of duplication.
D)The material must perform a read only function to minimize damaging changes in structure.
E)none of the above

Question 46

E.coli topoisomerase III
I.contains a hole capable of holding duplex DNA that is lined with negatively charged residues.
II.binds the sugar-phosphate backbone such that base recognition is possible.
III.functions by nucleophilic attack on the binding phosphate group.

A)I, II
B)II, III
C)I, III
D)I only
E)II only

Question 47

Nucleosomes
I.reduce the contour length of DNA 7-fold.
II.are bound together by linker histones.
III.come together to form a zigzag double helix.
IV.contain a histone octamer.

A)I, II, III, IV
B)II, III
C)III, IV
D)I, IV
E)II, IV

Question 48

Hammerhead ribozyme

A)contains a catalytic core with a Fe²⁺ at its center.
B)utilizes hydrogen bonding to position itself favorably for nucleophilic attack.
C)enhances the rate of cleavage of itself by a factor of five.
D)A and C
E)B and C

Question 49

Which of the following is FALSE about RNA?

A)It may be double stranded in viral genomes.
B)It may form double stranded stems by binding its complementary bases within the same strand.
C)It always forms a single strand that resembles the structure of B-DNA.
D)It is only synthesized as a single strand.
E)It may be involved in the control of gene expression.

Question 50

Based on the information in this chapter, which of the following sequences would likely bind a repressor if double stranded?

A)5' TGAGCA3'
B)5' TGATCA3'
C)5' TACGTCA3'
D)All of the above would bind the repressor with equal efficiency
E)None of the above would bind would the repressor.