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Biochem 2 > Exam 2- DNA replication > Flashcards

Exam 2- DNA replication Flashcards

1
Q

(T/F) Synthesis of the leading and lagging strands requires a primer only at the start of replication

A

false

true for leading strand but the lagging strand requires a new primer for every Okazaki fragment that is synthesized

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2
Q

(T/F) Base-paired primers consist of RNA that are synthesized by an enzyme

A

true

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3
Q

_______ the enzyme that synthsizes base-paired primers

A

DNA primase

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4
Q

____ used by DNA primase to synthesize short RNA primers

A

ribonucleoside triphosphates (ATP,CTP,GTP, UTP)

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5
Q

which of the ff does not apply to primers?

a. about 10 nucleotides long in eukaryotes
b. are made every 100-200 nucleotides along the lagging strand
c. has a free 3’OH group at its end used to initiate DNA synthesis
d. removed by RNAse H

A

none of the above, all applies :)

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6
Q

(T/F) In prokaryotes, Pol I removes the RNA primer and replaces it with dNTP’s

A

true

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7
Q

_____ enzyme that seals adjacent lagging strand fragments

A

DNA ligase

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8
Q

(T/F) cells use RNA primers to mark these initial (error) sequences as potentially inaccurate regions of new strands that must be replaced with correct complementary sequences

A

true

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9
Q

(T/F) enzymes capable of initiating synthesis of new DNA strands can correct their own base-pairing errors

A

false

would not be efficient at correcting their own base-pairing errors

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10
Q

______ are the proteins involved in the separation of the parental complementary strands

A

DNA helicases and Single-strand DNA binding proteins (SSB proteins)

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11
Q

____ the enzyme that functions to to pry apart double helix

A

DNA helicase

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12
Q

(T/F) DNA helicase does not require the use of energy to carry out its function

A

false

uses energy derived by hydrolysis of ATP to change its shape and migrate along a DNA single strand

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13
Q

(T/F) type of helicase that runs along the lagging strand seems to play the major role in separating the DNA strands

A

true

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14
Q

____ the structure of helicase

A

hexameric (6 subunits)

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15
Q

(T/F) do not unwind duplex but rather assist helicase by stabilizing unwound single stranded DNA

A

true

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16
Q

(T/F) aside from stabilizing the unwound DNA, helix-destabilizing proteins also function to straighten single stranded DNA of the leading strand template to prevent the formation of hairpin loops (DNA folding back on itself)

A

false

it does this to the LAGGING strand

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17
Q

____ are formed when DNA folds back on itself to self-hybridize block the movement of DNA polymerase during DNA synthesis

A

hairpin loops

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18
Q

which of the ff does not apply to single stranded binding proteins?

a. blocks hairpin formations
b. covers the bases when bound to DNA
c. prefer to bind next to previously bound molecules along a DNA strand
d. does not unwind the DNA strands

A

B

exposure of bases needed for base-pairing is not blocked by protein binding

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19
Q

_____ keeps Pol III attached to DNA during polymerization

A

Accessory (sliding) Clamp-Like Protein

Beta subunit of pol III in bacteria

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20
Q

which of the ff does not apply to sliding clamp proteins?

a. assembly requires GTP
b. its assembly is mediated by the clamp loader complex
c. Ring slides freely over single stranded DNA
d. released from DNA when it runs into DNA double strands

A

A

requires ATP

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21
Q

____ human version of E. coli clamp protein

A

proliferating cell nuclear antigen (PCNA)

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22
Q

*(T/F) in both the lagging and leading strands, Pol remains associated with clamp protein for long distance

A

false

this applies only to leading strand

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23
Q

*(T/F) on lagging strand, Pol and its associated clamp protein are released each time they reach the 5’ end of an adjacent Okazaki fragment then cycle back to the next RNA primer to synthesize another Okazaki fragment

A

true

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24
Q

____ a complex formed in prokaryotes when the helicase is directly linked to the primase on the lagging strand

A

primosome

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25
Q

(T/F) The primase is driven by the helicase along the lagging strand, producing the RNA primers needed for each successive Okazaki fragment

A

true

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26
Q

_____ the size of the major replicating protein complex

A

greater that 10^6 daltons in MW

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27
Q

(T/F) lagging strand loops back in such a way that both the leading and lagging strands can be synthesized by the same replication protein complex

A

true

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28
Q

(T/F) the pol of the of the lagging strand is associated with the large protein complex, and cannot be reused to synthesize each successive Okazaki fragment

A

false

it can be reused!

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29
Q

_____ are enzymes that regulate the supercoiling of DNA and prevent its tangling during replication (controls topology, or geometric configuration of DNA)

A

DNA topoisomerases

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30
Q

(T/F) DNA must be unwound ahead of replication fork by topoisomerases to permit movement of DNA polymerase

A

true

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31
Q

____ the speed at which the DNA helix ahead of the replication fork rotates

A

50 revolutions/sec

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32
Q

_____ the speed which the a replication fork moves

A

at 500 nucleotides/sec

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33
Q

______ the topoiomerase that produces transient single-strand breaks in the DNA along the phosphodiester backbone

A

type I topoisomerase

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34
Q

_______ the topoisomerase that generates transient double stranded breaks in DNA that can permit one DNA duplex to pass through another duplex

A

type II topoisomerase

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35
Q

(T/F) type II topoisomerase permits one strand of DNA to swivel relative to the other and thus relieve tension in the DNA during replication

A

false

this is type I

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36
Q

(T/F) DNA gyrase is situated ahead of the replication fork to unwind DNA and permit passage of DNA polymerase

A

true

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37
Q

which of the ff topoisomerases breaks the DNA strand by forming a covalent bond between a tyrosine in its active site and a DNA phosphate?

a. Type I topoisomerase
b. Type II topoisomerase

A

A

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38
Q

which of the ff topoisomerases functions to detangle chromosomes?

a. Type I topoisomerase
b. Type II topoisomerase

A

B

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39
Q

(T/F) type II topoisomerase uses energy from the hydrolysis of ATP to break permanently both strands of one DNA helix and then pass a second helix through the break

A

false

break transiently

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40
Q

(T/F) type II topoisomerase reseals the double stranded break before dissociating from the DNA

A

true

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41
Q

(T/F) DNA gyrase in bacteria are targeted as anti-tumor agents

A

false

as ANTIBIOTICS, does not affect eukaryotes

42
Q

(T/F) humans are affected by antibiotic drugs that target DNA gyrase

A

false

eukaryotic cells dont produce this enzyme

43
Q

(T/F) humans are affected by antibiotic drugs that target DNA gyrase

A

false

eukaryotic cells dont produce this enzyme

44
Q

______ the species used in studies of replication in eukaryotes

A

yeast (S. cerevisiae)

45
Q

(T/F) based on studies done on yeast, it was concluded that DNA replication in eukaryotes is very similar to that of bacteria

A

true

46
Q

which of the ff APPLIES to prokaryotic replication?

a. SSB protein consists of one protein
b. require two or more DNA Pols
c. SSB protein is composed of three
d. Primase is a component of a multisubunit complex containing DNA polymerase alpha

A

A

everything else applies to eukaryotes

47
Q

(T/F) On lagging strand DNA Pol alpha synthesizes an RNA primer followed by short stretch of DNA

A

true

48
Q

(T/F) the short RNA primer synthesized by DNA pol alpha is extended into an okazaki fragment by DNA pol delta and a clamp protein

A

true

49
Q

___ is the principal polymerase in eukaryotes

A

DNA pol delta

50
Q

(T/F) Eukaryotes uses two DNA pols

A

true

alpha and delta

51
Q

(T/F) in prokaryotes, , primase is associated with the DNA pol alpha

A

false

this is for eukaryotes!

52
Q

(T/F) in bacteria, primase is associated with DNA helicase in the primosome

A

true

53
Q

(T/F) Eukaryotic DNA is packaged in nucleosomes unlike that of bacteria

A

true

bacteria DNA exists as a circular DNA

54
Q

(T/F) in prokaryotes, the replication fork passes through nucleosomes without dislodging them from the DNA by an unknown mechanism

A

false

this is in eukaryotes,
bacteria doesn’t have chromosomes

55
Q

nucleosomes occur in about every ____ base pairs in eukaryotes

A

200

fragments are about the same size

56
Q

____ the length of okazaki fragments in bacteria

A

1000-2000 nucleotides

57
Q

(T/F) eukaryotic replication forks move 10 times slower than those of bacteria

A

true

Presence of nucleosomes may hinder movement of DNA Pol thats why they are slow

58
Q

____ the site along a DNA molecule at which DNA replication begins

A

origin of replication

59
Q

_____ the figure in which both parental strands are separated and are in the process of being replicated

A

replication bubble

60
Q

which of the ff is not true about the origin of replication?

a. G-C rich
b. contains several hundred pairs long in bacteria and yeas
c. attracts initiator proteins
d. initiation mechanism is similar in bacteria and eukaryotes

A

A

is A-T rich coz its easier to separate

61
Q

(T/F) Genome of E. coli consists of a single circular DNA molecule with several origin of replication

A

false

contains only one origin

62
Q

(T/F) DNA replication in bacteria only only occurs in presence of sufficient nutrients to support completion of replication

A

true

63
Q

which of the ff is the right order of proteins in the replication initiation in E. coli?

a. initiator proteins, DNA primase, primosome, DNA helicase, additional proteins
b. initiator proteins, DNA helicase, DNA primase, primosome, additional proteins
c. DNA primase, primosome, initiator proteins, DNA helicase, additional proteins
d. initiator proteins, DNA helicase, additional proteins, DNA primase, primosome, initiator proteins

A

B

64
Q

____ the experiment performed which indicated eukaryotic chromosomes have multiple origins of DNA replication by exposing DNA in photographic emulsion

A

autoradiography

65
Q

_____ used to radioactively label newly synthesized DNA

A

3H-thymidine (tritium labeled)

66
Q

(T/F) DNA has bidirectional growth from a central origin of replication occurs at multiple sites along chromosomes

A

true

67
Q

which of the ff is false about the eukaryotic origins of replication?

a. occurs in clusters
b. origins are separated by thousands of base pairs within a replication unit
c. replication forks terminate when they reach the end of the chromosomes
d. origins are in replication units

A

none of the above

68
Q

(T/F) the RNA primers needed to produce the last Okazaki fragment cannot be removed and replaced by DNA using the normal mechanism at the 5’ end of the parental strand

A

false

this is the the 3’ end!

leading strand goes to the 5’ end

69
Q

_____ are the ends of linear eukaryotic chromosomes

A

telomeres

70
Q

(T/F) the lagging strand copies the telomeres to prevent shortening of DNA with each round of DNA replication

A

true

71
Q

(T/F) At the end of a linear chromosome there is no more upstream template strand to which a primer can hybridize and initiate DNA synthesis of the 5’ end of the lagging strand

A

true

72
Q

_____ a protein-RNA complex that recognizes and binds repeats of the 3’ end of the parental strand

A

telomerase

73
Q

(T/F ) telomerase is a type of reverse transcriptase since it uses an RNA template to synthesize DNA

A

true

74
Q

(T/F) the telomeres contain tandem repeats that functions to attract telomerase and are not highly conserved among all eukaryotes

A

false

first part is true

telomeres are highly conserved!

75
Q

(T/F) Telomerase binds at the 3’ end of lagging strand and uses reverse transcriptase activity and its own RNA as a template to synthesize a DNA extension of the 5’ end of the lagging strand template with the help of RNA primer

A

false

binds to the 5’ of lagging strand, extends the 3’ end

76
Q

(T/F) at the completion of telomere extension, the 3’ end is longer than the 5’ end with which it is paired

A

true

77
Q

_____ is formed when telomerase-extended 3’ protruding end at each telomere becomes associated with specialized proteins

A

t-loop

78
Q

which of the following is false about telomeres?

a. reduced telomerase activity is associated with cellular senescence
b. telomeres mechanism to regulate a cell’s lifespan
c. adult cells like cancer cells express telomerase activity
d. are expressed in highly proliferative cells

A

C

Most adult cells do not express telomerase

79
Q

which of the ff cells do not have telomerase activity?

a. hematopoietic stem cells
b. intestinal epithelial cells
c. cells of hair follicles
d. most adult stem cells

A

D

80
Q

_____ were used to demonstrate the involvement of telomerase in maintaining telomeres and its involvement in aging

A

transgenic mice

81
Q

(T/F) mice telomeres are longer and needs 3 generations of breeding before its length is similar to that of humans

A

true

82
Q

which of the ff is not seen in telomerase KO mice?

a. Defects in highly proliferative tissues
b. premature aging
c. Increased tendency to develop tumors
d. chromosomal iinstability

A

none of the above!

all are exhibited in KO mice

83
Q

____ a disorder where humans carry one functional and one nonfunctional copy of telomerase RNA gene. symptoms include skin, lung and liver abnormalities and usually die of bone marrow failure

A

dyskeratosis congenita

84
Q

_____ when cells withdraw from the cell cycle and cease dividing

A

cellular senescence

85
Q

(T/F) Pol I uses its 3’ —> 5’ exonuclease activity to remove the incorrect nucleotide and then its 5’ —> 3’ polymerase activity to add the correct nucleotide

A

true

86
Q

(T/F) sustained DNA damage, like nicks or mismatched bp can be removed by pol 1’s 5’ —> 3’ exonuclease activity similar to the mechanism of removing RNA primer

A

true

this works on SHORT STRETCHES/ PATCHES of DNA

87
Q

(T/F) Exonuclease activity begins at a nick in the phosophodiester backbone

A

true

88
Q

____ the mechanism by which bacteria repair base-pair mismatches that were not fixed by proofreading activities of Pol I or Pol III

A

mismatch repair

89
Q

(T/F) in mismatch repair, any of the strands can be corrected to fix the bp mismatch

A

false

parental (correct strand) must be recognized by the presence of methylated bases to distinguish it from newly synthesized strand

90
Q

(T/F) in E. coli, all G residues in the GATC sequence are methylated and are recognized

A

false

A residues are methylated

91
Q

(T/F) the mismatch repair system contains MutH, MutS, and MutL that recognizes the mismatch and methylated parental strand and is the same in E.coli and in humans

A

false

E. coli has all three
humans lack MutH and recognizes nicks in the new strand (not methylated A)

92
Q

(T/F) in E. coli, mismatch repair mechanism must operate after replication but before the new DNA strand has been methylated

A

true

93
Q

(T/F) – People with mutations in genes that encode proteins of the mismatch repair system have a predisposition for certain types of cancers

A

true

94
Q

*(T/F) pol I removes RNA primer and replaces nucleotides of the lagging strand at the 3’-5’ end

A

false

both occur 5’ to 3’ end of lagging strand

95
Q

*(T/F) during DNA repair, pol I removes the incorrect nucleotide of the growing chain using its 3’ to 5’ exonuclease activity

A

true

96
Q

_______ removes RNA primers in eukaryotes/ recognizes RNA/DNA hybrids

A

RNAse H

97
Q

(T/F) Helicase uses energy derived by hydrolysis of ATP to change its shape and migrate along a DNA single strand; migrates in opposite polarities along the two DNA strands

A

true

98
Q

_______ another name for single-strand DNA binding proteins

A

helix-destabilizing proteins

99
Q

(T/F) base pairing is blocked by helix destabilizing proteins

A

false

100
Q

_____ clusters of origin of replications

A

replication units

Biochem 2 (13 decks)

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