Exam 2- DNA replication

Question 1

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

Answer 1

false

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

Question 2

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

Answer 2

true

Question 3

_______ the enzyme that synthsizes base-paired primers

Answer 3

DNA primase

Question 4

____ used by DNA primase to synthesize short RNA primers

Answer 4

ribonucleoside triphosphates (ATP,CTP,GTP, UTP)

Question 5

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

Answer 5

none of the above, all applies :)

Question 6

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

Answer 6

true

Question 7

_____ enzyme that seals adjacent lagging strand fragments

Answer 7

DNA ligase

Question 8

(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

Answer 8

true

Question 9

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

Answer 9

false

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

Question 10

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

Answer 10

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

Question 11

____ the enzyme that functions to to pry apart double helix

Answer 11

DNA helicase

Question 12

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

Answer 12

false

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

Question 13

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

Answer 13

true

Question 14

____ the structure of helicase

Answer 14

hexameric (6 subunits)

Question 15

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

Answer 15

true

Question 16

(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)

Answer 16

false

it does this to the LAGGING strand

Question 17

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

Answer 17

hairpin loops

Question 18

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

Answer 18

B

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

Question 19

_____ keeps Pol III attached to DNA during polymerization

Answer 19

Accessory (sliding) Clamp-Like Protein

Beta subunit of pol III in bacteria

Question 20

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

Answer 20

A

requires ATP

Question 21

____ human version of E. coli clamp protein

Answer 21

proliferating cell nuclear antigen (PCNA)

Question 22

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

Answer 22

false

this applies only to leading strand

Question 23

*(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

Answer 23

true

Question 24

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

Answer 24

primosome

Question 25

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

Answer 25

true

Question 26

_____ the size of the major replicating protein complex

Answer 26

greater that 10^6 daltons in MW

Question 27

(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

Answer 27

true

Question 28

(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

Answer 28

false it can be reused!

Question 29

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

Answer 29

DNA topoisomerases

Question 30

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

Answer 30

true

Question 31

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

Answer 31

50 revolutions/sec

Question 32

_____ the speed which the a replication fork moves

Answer 32

at 500 nucleotides/sec

Question 33

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

Answer 33

type I topoisomerase

Question 34

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

Answer 34

type II topoisomerase

Question 35

(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

Answer 35

false this is type I

Question 36

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

Answer 36

true

Question 37

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

Answer 37

A

Question 38

which of the ff topoisomerases functions to detangle chromosomes? a. Type I topoisomerase b. Type II topoisomerase

Answer 38

B

Question 39

(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

Answer 39

false break transiently

Question 40

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

Answer 40

true

Question 41

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

Answer 41

false as ANTIBIOTICS, does not affect eukaryotes

Question 42

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

Answer 42

false eukaryotic cells dont produce this enzyme

Question 43

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

Answer 43

false eukaryotic cells dont produce this enzyme

Question 44

______ the species used in studies of replication in eukaryotes

Answer 44

yeast (S. cerevisiae)

Question 45

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

Answer 45

true

Question 46

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

Answer 46

A everything else applies to eukaryotes

Question 47

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

Answer 47

true

Question 48

(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

Answer 48

true

Question 49

___ is the principal polymerase in eukaryotes

Answer 49

DNA pol delta

Question 50

(T/F) Eukaryotes uses two DNA pols

Answer 50

true alpha and delta

Question 51

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

Answer 51

false this is for eukaryotes!

Question 52

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

Answer 52

true

Question 53

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

Answer 53

true bacteria DNA exists as a circular DNA

Question 54

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

Answer 54

false this is in eukaryotes, bacteria doesn't have chromosomes

Question 55

nucleosomes occur in about every ____ base pairs in eukaryotes

Answer 55

200 fragments are about the same size

Question 56

____ the length of okazaki fragments in bacteria

Answer 56

1000-2000 nucleotides

Question 57

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

Answer 57

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

Question 58

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

Answer 58

origin of replication

Question 59

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

Answer 59

replication bubble

Question 60

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

Answer 60

A is A-T rich coz its easier to separate

Question 61

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

Answer 61

false contains only one origin

Question 62

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

Answer 62

true

Question 63

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

Answer 63

B

Question 64

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

Answer 64

autoradiography

Question 65

_____ used to radioactively label newly synthesized DNA

Answer 65

3H-thymidine (tritium labeled)

Question 66

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

Answer 66

true

Question 67

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

Answer 67

none of the above

Question 68

(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

Answer 68

false this is the the 3' end! leading strand goes to the 5' end

Question 69

_____ are the ends of linear eukaryotic chromosomes

Answer 69

telomeres

Question 70

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

Answer 70

true

Question 71

(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

Answer 71

true

Question 72

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

Answer 72

telomerase

Question 73

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

Answer 73

true

Question 74

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

Answer 74

false first part is true telomeres are highly conserved!

Question 75

(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

Answer 75

false binds to the 5' of lagging strand, extends the 3' end

Question 76

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

Answer 76

true

Question 77

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

Answer 77

t-loop

Question 78

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

Answer 78

C Most adult cells do not express telomerase

Question 79

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

Answer 79

D

Question 80

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

Answer 80

transgenic mice

Question 81

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

Answer 81

true

Question 82

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

Answer 82

none of the above! all are exhibited in KO mice

Question 83

____ 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

Answer 83

dyskeratosis congenita

Question 84

_____ when cells withdraw from the cell cycle and cease dividing

Answer 84

cellular senescence

Question 85

(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

Answer 85

true

Question 86

(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

Answer 86

true this works on SHORT STRETCHES/ PATCHES of DNA

Question 87

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

Answer 87

true

Question 88

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

Answer 88

mismatch repair

Question 89

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

Answer 89

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

Question 90

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

Answer 90

false A residues are methylated

Question 91

(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

Answer 91

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

Question 92

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

Answer 92

true

Question 93

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

Answer 93

true

Question 94

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

Answer 94

false both occur 5' to 3' end of lagging strand

Question 95

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

Answer 95

true

Question 96

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

Answer 96

RNAse H

Question 97

(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

Answer 97

true

Question 98

_______ another name for single-strand DNA binding proteins

Answer 98

helix-destabilizing proteins

Question 99

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

Answer 99

false

Question 100

_____ clusters of origin of replications

Answer 100

replication units