05a: DNA Replication Flashcards
T/F: DNA replication is the most accurate biological process.
True
DNA replication uses (non-activated/activated) substrates, (X).
Activated;
X = dNTPs
4 steps for DNA replication. In what order do they occur?
- Initiation
- Priming
- Synthesis
- Termination
All occur simultaneously
Bacterial DNA has (X) shape and how many start sites for replication?
X = circular
One start site (oriC)
OriC is recognized by:
DnaA (initiator protein)
Prok:
Initiator protein, (X), combines with (Y) and interacts with DNA in what way?
X = DnaA
Y = Histone-like proteins (and ATP)
Tight association with DNA, so bends it
Why does replication bubble form?
DnaA bends DNA and AT-rich repeats near OriC open to form bubble
Prok:
DnaB is called (X) and forms complex with (Y), which helps it bind the DNA.
X = helicase
Y = DnaC
Prok:
When does DnaA displace from DNA?
Once helicase binds
Prok:
(X) bind(s) DNA, preventing its coiling, once primase, aka (Y), binds.
X = SSBs
Y = DnaG
T/F: in bacteria, binding of each DNA replication protein to DNA requires ATP.
True
Which DNA polymerase initiates strand synthesis in bacteria?
None! No DNA pol can initiate new strand synthesis
RNA primer is created in which direction? About how long is it?
5’ to 3’ direction;
5-10 NT
There are (X) number of prokaryotic DNA polymerases. Which ones are critically mainly for panicked cell?
X = 5
DNA polymerase 2, 4, 5
DNA polymerase I is known for:
Primer excision (and some repair) in prokaryotes
DNA polymerase 3 is known for:
Replication chain elongation (and some repair) in prokaryotes
List activities of DNA pol 1.
(Prokaryotes)
- Polymerase
- 3’ exonuclease (repair)
- 5’ exonuclease (primer excision)
What does a polymerase’s processivity signify?
Number of NT it can add before dissociating from DNA
Which prokaryotic DNA polymerase has the greatest processivity?
DNA pol 3
Replication bubble has how many DNA polymerase 3?
2 (one at each end of fork)
Which subunit on DNA pol 3 is responsible for proof reading? What’s its specific function?
Epsilon (3’ exonuclease)
Which subunit on DNA pol 3 is responsible for primer excision? What’s its specific function?
DNA pol 3 doesn’t remove primer - DNA pol 1 does that (5’ exonuclease)
How many different subunits does DNA pol 3 have?
10
Which subunit on DNA pol 3 is responsible for replicating strands?
Polymerase (alpha subunits)
T/F: in DNA pol 3, the clamp loader is separate from the core enzyme.
True
Which subunit on DNA pol 3 is the sliding clamp?
Beta subunit
Which subunit on DNA pol 3 is the clamp loader?
Gamma complex
DNA pol 3 replicates (leading/lagging) strand first.
Neither - replicates both strands simultaneously
The sliding clamp for DNA pol 3 has inner diameter of (X) and mainly (negative/positive/neutral) AA on inside.
X = 3.5 nm
Negative
How can DNA pol 3 detect mismatched bases and correct itself?
Defects change in DNA structure
In bacteria, where is the termination site, wrt OriC?
180 degrees from it
Nick translation, carried out by (X), removes how many (Y) at a time?
X = DNA pol 1
Y = RNA primer
1 at a time
T/F: Nick translation requires ATP.
False - DNA pol 1 uses water (hydrolysis) for 5’ exonuclease
The nick after primer removal is sealed by:
DNA ligase
What’s the final step in bacterial termination of DNA synthesis?
Type 2 topoisomerase separates the two interlinking strands of replicated circles and refolds DNA into supercoils
DNA pol gamma is responsible for:
Eukaryotic DNA replication in mitochondrion
Eukaryotic equivalent to beta subunit on prokaryotic DNA pol (X).
X = 3
Beta subunit is clamp; PCNA in euk
DNA pol epsilon is responsible for:
Eukaryotic DNA synthesis of leading strand
DNA pol delta is responsible for:
Eukaryotic DNA synthesis of lagging strand
Primer removal in eukaryotes is carried out by:
Rnase H and Fen1
Helicase in eukaryotes is called:
MCM
Origin of replication in euk is called:
ARC (autonomous replicating sequences)
T/F: Topoisomerase II requires ATP for its function.
True
What makes DNA Pol (X) better suited for primer excision than DNA Pol (Y)?
X = 1 Y = 3
Low processivity
T/F: Type II Topoisomerase only adds negative supercoils.
False
