chapter 34 Flashcards
what is a template
a sequence of DNA that directs the synthesis of a complementary sequence
what is a primer
the initial segment of a polymer that is to be extended on which elongation depends
what is a substrate
deoxyribonucleoside triphosphates: dATP, dTTP, dCTP, dGTP
what is the main enzyme used in dna replication
DNA polymerases
what do the thumb and finger position of the DNA polymerases do
wrap around DNA and position it at the active site
DNA polymerase I from E. coli possesses what type of enzyme for proofreading activity
3’ to 5’ exonuclease
DNA polymerase requires what type of molecule for activity
divalent cations usually Mg 2+
what do the two Mg 2+ cations do in the polymerase reaction
one assists in orienting the incoming nucleotide with the primer
the other stabilizes the negative charges of the pyrophosphate product
the specificity of replication is determined by what TWO things
- correct hydrogen bonding between the incoming dNTP and the DNA template
- the overall shape of the incoming base
what does primase do in replication
synthesizes a short RNA strand (~5 nucleotides) complementary to a DNA strand that then serves as a primer for DNA synthesis
DNA polymerases synthesize only in what direction
5’ to 3’
which strand is synthesized continuously
the leading strand
which strand is synthesized discontinuously
the lagging strand is synthesized in pieces called Okazaki fragments
what is DNA ligase’s role in replication
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.
what is the role of helicase
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.
what do topoisomerases do
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.
The enzyme responsible for the majority of DNA synthesis in E. coli is
DNA polymerase III
what does processivity mean
the ability of an enzyme to catalyze many consecutive reactions without releasing its substrate
the source of the processivity is what
the sliding clamp, a dimer that encircles the helix
how does the sliding clamp work
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.
how are okazaki fragments fixed
DNA polymerase I
removes the RNA primer
and replaces the
sequence with DNA.
DNA ligase joins the
fragments to yield an
intact strand.
where does replication begin in e. coli
Replication begins in E. coli at a unique 245 base-pair site called
the origin of replication, oriC locus
what is the first step in e. coli replication
Step 1: DnaA proteins bind at distinct sites in the locus.
what is the second step in e. coli replication
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.
what is the third step in e. coli replication
Step 3. The DNA
polymerase III holoenzyme
assembles on the complex.
what are the two biochemical difficulties in the free ends of linear DNA
- They are susceptible to damage by nucleases.
- Due to the nature of DNA synthesis, the lagging strand will
shorten upon each round of DNA synthesis.
what is the role of telomerase
the G-rich section leading strand of the telomere (the end of a chromosome) is maintained by telomerase
high telomerase activity is a characteristic of
cancer cells
what does telomerase do to the telomere
elongates the G-rich section of the the leading strand of the telomeres
