chapter 34

Question 1

what is a template

Answer 1

a sequence of DNA that directs the synthesis of a complementary sequence

Question 2

what is a primer

Answer 2

the initial segment of a polymer that is to be extended on which elongation depends

Question 3

what is a substrate

Answer 3

deoxyribonucleoside triphosphates: dATP, dTTP, dCTP, dGTP

Question 4

what is the main enzyme used in dna replication

Answer 4

DNA polymerases

Question 5

what do the thumb and finger position of the DNA polymerases do

Answer 5

wrap around DNA and position it at the active site

Question 6

DNA polymerase I from E. coli possesses what type of enzyme for proofreading activity

Answer 6

3’ to 5’ exonuclease

Question 7

DNA polymerase requires what type of molecule for activity

Answer 7

divalent cations usually Mg 2+

Question 8

what do the two Mg 2+ cations do in the polymerase reaction

Answer 8

one assists in orienting the incoming nucleotide with the primer

the other stabilizes the negative charges of the pyrophosphate product

Question 9

the specificity of replication is determined by what TWO things

Answer 9

1. correct hydrogen bonding between the incoming dNTP and the DNA template
2. the overall shape of the incoming base

Question 10

what does primase do in replication

Answer 10

synthesizes a short RNA strand (~5 nucleotides) complementary to a DNA strand that then serves as a primer for DNA synthesis

Question 11

DNA polymerases synthesize only in what direction

Answer 11

5’ to 3’

Question 12

which strand is synthesized continuously

Answer 12

the leading strand

Question 13

which strand is synthesized discontinuously

Answer 13

the lagging strand is synthesized in pieces called Okazaki fragments

Question 14

what is DNA ligase’s role in replication

Answer 14

catalyzes the joining of one DNA fragment with a free 3′-hydroxyl
group to another with a free 5′-phosphoryl group, in a reaction that requires an
energy source, usually ATP. bacteria use NAD+ as an energy source.

Question 15

what is the role of helicase

Answer 15

powered by ATP hydrolysis, separate the strands of the
double helix to make the DNA available for DNA polymerase.
The helicase, which consists of a ring-like structure composed of
six subunits, acts as a wedge to pry the helix apart.

Question 16

what do topoisomerases do

Answer 16

are enzymes that induce or eliminate supercoils.

Type I topoisomerases relax supercoils, a thermodynamically favorable reaction,
while type II topoisomerases, such as DNA gyrase in E. coli, introduce supercoiling at the expense of ATP.

Question 17

The enzyme responsible for the majority of DNA synthesis in E. coli is

Answer 17

DNA polymerase III

Question 18

what does processivity mean

Answer 18

the ability of an enzyme to catalyze many consecutive reactions without releasing its substrate

Question 19

the source of the processivity is what

Answer 19

the sliding clamp, a dimer that encircles the helix

Question 20

how does the sliding clamp work

Answer 20

The sliding clamp is loaded onto the DNA by a protein called the clamp loader, which uses the energy of ATP hydrolysis to open and close the clamp.

Question 21

how are okazaki fragments fixed

Answer 21

DNA polymerase I
removes the RNA primer
and replaces the
sequence with DNA.

DNA ligase joins the
fragments to yield an
intact strand.

Question 22

where does replication begin in e. coli

Answer 22

Replication begins in E. coli at a unique 245 base-pair site called
the origin of replication, oriC locus

Question 23

what is the first step in e. coli replication

Answer 23

Step 1: DnaA proteins bind at distinct sites in the locus.

Question 24

what is the second step in e. coli replication

Answer 24

Step 2. DnaA recruits DnaB,
a helicase that uses ATP
hydrolysis to unwind the
locus. Single-stranded-DNA
binding proteins (SSB) bind
to the AT-rich region of the
oriC locus.

Question 25

what is the third step in e. coli replication

Answer 25

Step 3. The DNA
polymerase III holoenzyme
assembles on the complex.

Question 26

what are the two biochemical difficulties in the free ends of linear DNA

Answer 26

1. They are susceptible to damage by nucleases.
2. Due to the nature of DNA synthesis, the lagging strand will
   shorten upon each round of DNA synthesis.

Question 27

what is the role of telomerase

Answer 27

the G-rich section leading strand of the telomere (the end of a chromosome) is maintained by telomerase

Question 28

high telomerase activity is a characteristic of

Answer 28

cancer cells

Question 29

what does telomerase do to the telomere

Answer 29

elongates the G-rich section of the the leading strand of the telomeres