DNA replication

Question 1

T/F During DNA synthesis, the template is always read in the 3’ to 5’ direction

Answer 1

True

Question 2

When using a P32 labeled nucleotide in a DNA synthesis reaction, it is critical to make sure that the label is on the gamma phosphate

Answer 2

False, should be on alpha phosphate

Question 3

DNA synthesis reaction has a strong negative net free energy and is essentially irreversible because a high energy bond is transferred from the incoming nucleotide to the growing DNA chain

Answer 3

False.

Question 4

The processivity of a DNA polymerase is the average number of nucleotides added to a DNA chain each time it binds to a primer:template junction

Answer 4

True

Question 5

When positioned in the active site of DNA polymerase, the template strand is kinked 90 degrees between the last paired base and the first unpaired base.

Answer 5

False

Question 6

Proof-reading DNA polymerase contains a 3’ to 5’ exonuclease activity

Answer 6

True

Question 7

No known DNA polymerase can initiate synthesis of a DNA strand de novo (without a primer)

Answer 7

True

Question 8

DNA primase is actually a specialized RNA polymerase

Answer 8

False

Question 9

Function of RNase H in DNA replication is to cleave ribonucleotides that have been mistakenly added to the end of an elongating DNA chain by DNA polymerase.

Answer 9

False

Question 10

DNA helicases involved in replication are ring-shaped enzymes that surround both DNA strands while unwinding them.

Answer 10

False

Question 11

Sliding clamps are enzymes that encircle newly synthesized DNA duplexes during DNA synthesis and clamp the two DNA strands together so they do not dissociate.

Answer 11

False, they keep the polymerase from dissociating from the template.

Question 12

Origins of replication are defined DNA sequences in E. Coli but not in any eukaryotes that have been tested thus far.

Answer 12

False

Question 13

Replication origins usually contain one or more stretches of AT-rich, easily unwound DNA

Answer 13

True

Question 14

Replication origins serve as binding sites for initiator proteins and the replicative DNA helicases.

Answer 14

False, the initiator proteins recruit the DNA helicases to the origins.

Question 15

In the 2-D gel technique for mapping replication origins, the presence of a bubble arc on the gel indicates that the restriction fragment being analyzed contains a replication origin

Answer 15

True

Question 16

In mammals, replication origins can be identified on the basis of binding of the ORC complex

Answer 16

True

Question 17

At chromosome ends there is a division of labor: telomerase extends the 3’ ends while the regular DNA polymerase extends the 5’ ends.

Answer 17

True

Question 18

in telomere t-loops, the ss 3’ ends of chromosomes are base-paired with internal telomere repeats

Answer 18

True

Question 19

In E.coli, the clamp loader must hydrolyze its bound ATP in order to bind and open a sliding clamp.

Answer 19

False

Question 20

The inherent processivity of most DNA polymerases is less than 100 bases

Answer 20

True

Question 21

Telomerase exhibits higher activity on long telomeres than on short telomeres.

Answer 21

False, when telomeres are long, there are inhibitory binding proteins that bind and prevent telomeric activity.

Question 22

The eukaryotic initiator protein is a six subunit protein called ORC

Answer 22

True

Question 23

In E.Coli, if the helicase becomes separated from the DNA pol III holoenzyme, the activity of the helicase is decreased.

Answer 23

True

Question 24

If a DNA helicase that binds ssDNA and translocates along the DNA in the 3’ to 5’ direction was mixed with a standard primer-template complex in the presence of ATP, it would dissociate the primer from the template.

Answer 24

False, this is the job of RNase H.

Question 25

The eukaryotic version of SSB protein is RFC

Answer 25

False, it is RPA. RFC is the eukaryotic sliding clamp loader.

Question 26

In E.coli, there can be as many as 3 DNA pol III enzymes actively engaged in synthesizing DNA at a single replication fork at the same time.

Answer 26

True

Question 27

In eukaryotes, the primer is synthesized by :

Answer 27

complex of DNA primase and DNA pol alpha

Question 28

In E. coli, DNA replication the sliding clamp interacts with :

Answer 28

DNA helicase, and the clamp loader (gamma complex)

Question 29

What happens to the lagging strand DNA pol III when it encounters 5’ end of previous okazaki fragment?

Answer 29

it stops synthesizing DNA, spontaneously dissociates from the DNA and the sliding clamp, but does not diffuse away from replication fork because it remains attached to the t protein.

Question 30

What order do the replication proteins bind to newly unwound stretch of template DNA?

Answer 30

SSB, primase, sliding clamp, pol III, pol I

Question 31

In eukaryotes, the MCM-27 complex is recruited to replication origins when :

Answer 31

CDK activity is low, and cdc6 and cdt1 are present

Question 32

in yeast, telomerase is activated by ____ proteins bound to ds telomere sequences.

Answer 32

cdc13

Question 33

DNA synthesis reaction is initiated by nucleophilic attack of ___ on ____

Answer 33

The terminal 3’ O of primer strand, the alpha phosphorous of the incoming nucleotide.

Question 34

Okazaki fragments are synthesized on the ___ in the ____ direction.

Answer 34

lagging strand, 5’-3’

Question 35

What happens when the wrong nucleotides is accidentally incorporated into a growing DNA chain by DNA polymerase?

Answer 35

DNA synthesis slows drastically, the last 3-4 nucleotides of the primer strand become single-stranded and the end of the primer strand is relocated into the editing site of the enzyme where the incorrect nucleotide is cleaved off.

Question 36

If an incoming dCTP underwent tautomeric shift, it would preferentially bp with a ____ in the template strand.

Answer 36

A

Question 37

What triggers closing of the “fingers” of the DNA polymerase via rotation of the O helix?

Answer 37

successful base pairing of the incoming nucleotide with the template strand.

Question 38

what are the enzymatic activities of E.coli DNA Pol I?

Answer 38

DNA synthesis, 5’ to 3’ exonuclease, and 3’ to 5’ exonuclease

Question 39

In prokaryotes, the leading strand is synthesized by DNA pol ____ and the lagging strand is synthesized by DNA pol ____

Answer 39

iii, iii

Question 40

to activate the eukaryotic replication origin :

Answer 40

phosphorylation of MCM2-7 complex and binding of the GINS and cdc45 proteins to MCM2-7 complex

Question 41

What complex encircles both DNA strands before origin activation but only one DNA strand after origin activation?

Answer 41

MCM-2-7 complex