Ch 20 DNA Replication Flashcards
What is the mechanism of DNA replication?
Semi-conservative replication
Each daughter double helix contains one template strand and one newly synthesized strand.
What is the role of DNA polymerase in DNA replication?
Involved in replicating double-stranded DNA
DNA polymerase synthesizes new DNA strands complementary to the template strands.
What was the nitrogen source used in the E. coli experiment?
15NH4Cl
This was used to label all newly formed nitrogen compounds with 15N.
What method was used to analyze DNA replication in the E. coli experiment?
Density-gradient centrifugation
This method helps separate DNA based on density.
What is a challenge in DNA replication regarding the synthesis of daughter strands?
Synthesis goes in opposite directions
The DNA template has one 5’->3’ strand and one 3’->5’ strand.
What is one challenge in unwinding DNA for replication?
How to unwind and separate the two parental DNA strands
This introduces more supercoils that interfere with the process.
What is the role of helicase in DNA replication?
Separates the two strands of DNA
Most helicases are hexameric proteins shaped like a donut that circles one DNA strand.
How does negative supercoiling affect DNA replication?
Makes the DNA underwound
This underwinding makes it easier for the individual strands to be separated.
What type of protein is a helicase generally classified as?
Hexameric protein
It encircles one DNA strand to facilitate unwinding.
What energy source do replicative helicases use to separate DNA strands?
ATP
ATP powers the helicase’s motion along the DNA strand.
What is the function of single-stranded DNA binding domains (SSBs)?
Defend single-stranded DNA
In eukaryotes, the SSB is known as replication protein A (RPA).
Fill in the blank: The chromosome in bacterial DNA replication is _______.
a circle
True or False: DNA helicases can pull apart the two strands in a DNA double helix.
True
They are enzymes specifically designed for this task.
What is the origin of replication?
The specific point where the DNA double helix begins unwinding
How many replication forks are there at each origin of replication?
Two
What is the replication direction at the origin of replication?
Bidirectional
How many origins of replication do prokaryotes have?
One
How many origins of replication do eukaryotes have?
Many
What are replication foci?
Sites of active DNA synthesis in eukaryotic chromosomes
What model describes the stationary protein machinery in DNA replication?
Factory model of replication
What is the nature of DNA synthesis according to the semidiscontinuous model?
DNA is synthesized in opposite directions
What is the leading strand?
Synthesized continuously from its 5′ end to its 3′ end
What is the lagging strand?
Synthesized semidiscontinuously in small fragments called Okazaki fragments
Where is the 5′ end of each Okazaki fragment located?
Closer to the replication fork than the 3′ end
What enzyme links Okazaki fragments together?
DNA ligase
What is the structure of E. coli DNA polymerase I compared to?
Shaped like a hand
What is the first polymerase to have been characterized?
E. coli DNA polymerase I
What is the purpose of the open and closed conformations of a DNA polymerase?
Not specified in the text
What does the sliding clamp associated with polymerase confer?
Processivity
What is the role of the β-subunit of DNA pol III?
Forms a dimer that encircles DNA to hold on
What is PCNA in humans?
A sliding clamp that functions similarly to the β-subunit of DNA pol III
Fill in the blank: The lagging strand is synthesized in _______ fragments.
Okazaki
True or False: Eukaryotic cells have a single origin of replication.
False
What is the direction of polynucleotide chain synthesis?
5ʹ → 3ʹ direction
What group at the 3ʹ end of a growing polynucleotide chain acts as a nucleophile?
3ʹ OH group
What is eliminated during the formation of a new phosphodiester bond?
PPi
What unwinds the two strands of parental DNA in E. coli replication?
Helicase
What function does topoisomerase serve in DNA replication?
Relieves the overwinding ahead of the replication fork
What protein coats the exposed single strands during replication?
SSB (single-stranded binding protein)
Which DNA polymerase extends the primer to build the leading strand?
DNA polymerase III
What increases the processivity of DNA polymerase III?
Sliding clamp
What does the lagging-strand template do to allow primase to synthesize a new RNA primer?
Loops out
What completes an Okazaki fragment on the lagging strand?
A second DNA polymerase III
Which polymerase replaces DNA polymerase III to remove the RNA primer of the older Okazaki fragment?
DNA polymerase I
What seals the remaining nick between Okazaki fragments?
DNA ligase
What is the role of DNA-Pol I?
Repair and patching of DNA
What is the main enzyme for synthesizing new DNA strands?
DNA-Pol III
What is the function of DNA-Pol II?
Proofreading and repair enzyme
What does DNA gyrase do?
Relieves positive supercoils and relieves torsional stress
What is the role of helicase in DNA replication?
Unwinds DNA helix and causes strand separation
What stabilizes single-stranded regions of DNA?
SSB (single-stranded binding protein)
What synthesizes the RNA primer?
Primase
What is the role of DNA Pol I (or RNase H)?
Removes the RNA primer
What type of topoisomerase is DNA gyrase?
Type II topoisomerase
What is the effect of ciprofloxacin on DNA gyrase?
Results in a large number of DNA breaks
What does the primase reaction produce?
RNA primer sequence
What does DNA polymerase III synthesize?
New DNA strands
What are Okazaki fragments formed due to?
Requirement for DNA synthesis in the 5’ → 3’ direction
What removes the RNA primer as the replication fork moves away?
DNA polymerase I
What makes the final covalent bond between Okazaki fragments?
DNA ligase
What is the direction of DNA synthesis?
5’ -> 3’
How is the leading strand formed during DNA replication?
Continuously
How is the lagging strand formed during DNA replication?
As a series of Okazaki fragments which are later joined
Which polymerase is primarily responsible for new DNA synthesis in prokaryotes?
Pol III
What is the role of Pol I in DNA replication?
Involved in synthesis and repair
What is the function of DNA gyrase in DNA replication?
Introduces a swivel point to prevent supercoiling
What does a helicase do at the replication fork?
Promotes unwinding of DNA
What is the role of single-stranded binding (SSB) protein?
Protects exposed regions of single-stranded DNA
What is synthesized by primase during DNA replication?
RNA primer
What enzyme removes the RNA primer during DNA synthesis?
Pol I
What enzyme seals remaining nicks in the DNA after synthesis?
DNA ligase
During which phase of the eukaryotic cell cycle does DNA replication occur?
S phase
What is a diploid cell?
A cell with two sets of chromosomes
What can cause mutations during DNA replication?
Errors in replication
What is the frequency of errors in replication before proofreading?
Once in 10^6 base pairs
What is the frequency of errors in replication after proofreading?
Once in 10^10 base pairs
What proofreading function does DNA polymerase have?
3’-5’-exonuclease activity
What are mutagens?
Agents that bring about a mutation
What type of damage does ultraviolet light cause in DNA?
Creates pyrimidine dimers
What is a common result of ionizing radiation on DNA?
Break in the phosphodiester backbone
What is base excision repair?
Removal and replacement of modified bases that cannot be directly repaired
How does nucleotide excision repair differ from base excision repair?
Nucleotide excision repair removes a larger segment of DNA
