| What is topoisomerase? | An enzyme that changes the number of times the two strands in a closed DNA molecule cross each other. |
| How does topoisomerase change the number of times the two strands in a closed DNA molecule cross each other? | It does this by cutting the DNA, passing DNA through the break, and resealing the DNA. |
| What is a replisome? | The multiprotein structure that assembles at the bacterial replication fork to undertake synthesis of DNA. |
| What does the replisome contain? | It contains DNA polymerase and other enzymes. |
| How is replication initiated? | Replication initiates when a protein complex binds to the origin and melts the DNA there. |
| What is a conditional lethal mutation? | A mutation that is lethal under one set of conditions, but is not lethal under a second set of conditions, such as temperature. |
| What are dna mutants? | Temperature-sensitive replication mutants in E. coli that identify a set of loci called the dna genes. |
| What is a quick stop mutant? | Temperature-sensitive replication mutants that are defective in replication elongation during synthesis of DNA. |
| What is a slow stop mutant? | Temperature-sensitive replication mutants that are defective in initiation of replication. |
| Define in vitro complementation? | A functional assay used to identify components of a process.
The reaction is reconstructed using extracts from a mutant cell.
Fractions from wild-type cells are then tested for restoration of activity. |
| What is the enzyme that makes DNA? | DNA Polymerases Are the Enzymes That Make DNA |
| In what manners and reaction is the DNA synthesized? | DNA is synthesized in both semiconservative replication and DNA repair reactions. |
| How does the repair synthesis work? | Repair synthesis replaces a short stretch of one strand of DNA containing a damaged base. |
| DNA is synthesized Adding nucleotides to which end? | DNA is synthesized by adding nucleotides to the 3 –OH end of the growing chain. |
| Does all eukaryotic cells and bactrium has the same DNA polymerase? | A bacterium or eukaryotic cell has several different DNA polymerase enzymes. |
| What are the roles of bacterial DNA polymerase? | One bacterial DNA polymerase (a DNA replicase) undertakes semiconservative replication; the others are involved in repair reactions. |
| What are the other activities of DNA polymerase I | DNA polymerase I has a unique 5′–3′ exonuclease activity that can be combined with DNA synthesis to perform nick translation. |
| What does Nick translation do? | Nick translation replaces part of a preexisting strand of duplex DNA with newly synthesized material. |
| What does the High-fidelity DNA polymerases have? | High-fidelity DNA polymerases involved in replication have a precisely constrained active site that favors binding of Watson–Crick base pairs. |
| What is processivity? | The ability of an enzyme to perform multiple catalytic cycles with a single template instead of dissociating after each cycle. |
| What is the use of the DNA polymerases exonuclease activity? | DNA polymerases often have a 3′–5′ exonuclease activity that is used to excise incorrectly paired bases. |
| How is The fidelity of replication is improved? | The fidelity of replication is improved by proofreading by a factor of ~100. |
| What is the structure of DNA polymerases? | Many DNA polymerases have a large cleft composed of three domains that resemble a hand. |
| Where does the DNA lies in DNA polymerase? | DNA lies across the “palm” in a groove created by the “fingers” and “thumb.” |
| How is the leading strand and the lagging strand synthesized? | The DNA polymerase advances continuously when it synthesizes the leading strand (5′–3′), but synthesizes the lagging strand by making short fragments (Okazaki fragments) that are subsequently joined together. |
| What is semidiscontinuous replication? | The mode of replication in which one new strand is synthesized continuously while the other is synthesized discontinuously. |
| Why does the replication need helicase? | Replication requires a helicase to separate the strands of DNA using energy provided by hydrolysis of ATP. |
| What is needed to maintain separated strands? | A single-stranded DNA binding protein is required to maintain the separated strands. |
| What does DNA polymerases need to initiate DNA synthesis? | All DNA polymerases require a 3′–OH priming end to initiate DNA synthesis. |
| The priming end is provide by what? | provided by an RNA primer, a nick in DNA, or a priming protein. |
| What provides a priming end For DNA replication? | a special RNA polymerase called a primase synthesizes an RNA chain that provides the priming end. |
| Where does E.coli’s two priming reactions happen? | the bacterial origin (oriC) and the φX174 origin |
| 4- What does priming on double stranded DNA require? | -always requires a replicase, SSB, and primase.
-DnaB is the helicase that unwinds DNA for replication in E. coli. |
| 5- How does coordination of synthesis of lagging and leading strands happen in different organisms? | Different enzyme units are required to synthesize the leading and lagging strands.
-In E. coli, both these units contain the same catalytic subunit (DnaE).
-In other organisms, different catalytic subunits may be required for each strand. |
| 6- What does The E. coli DNA polymerase III catalytic core and The DNA Pol III holoenzyme contain? | -E. coli DNA polymerase III contains three subunits including a catalytic subunit and a proofreading subunit
-the at DNA Pol III holoenzyme contains least two catalytic cores, a processivity clamp, and a dimerization clamp-loader complex. |
| 7- What's a clamp loader? | -places the processivity subunits on DNA, where they form a circular clamp around the nucleic acid.
-At least one catalytic core is associated with each template strand. |
| 8- What is the The E. coli replisome composed of? | of the holoenzyme complex and the additional enzymes required for chromosome replication. |
| 9- How does the clamp control association of core enzymes with DNA? | The core on the leading strand is processive because its clamp keeps it on the DNA.
The clamp associated with the core on the lagging strand dissociates at the end of each Okazaki fragment and reassembles for the next fragment. |
| 10- What is responsible for interacting with the primase DnaG? And what does it initiate? | The helicase DnaB is responsible for interacting with the primase DnaG to initiate each Okazaki fragment. |
| 11- how are Okazaki fragment formed ?what are they linked by? | -Each Okazaki fragment starts with a primer and stops before the next fragment.
-DNA polymerase I removes the primer and replaces it with DNA. |
| 12- What is DNA ligase? | -makes the bond that connects the 3′ end of one Okazaki fragment to the 5′ beginning of the next fragment. |
| 13- How do Separate Eukaryotic DNA Polymerases Undertake Initiation and Elongation? | -A replication fork has one complex of DNA polymerase α/primase, one complex of DNA polymerase δ, and one complex of DNA polymerase ε.
-The DNA polymerase α/primase complex initiates the synthesis of both DNA strands.
-DNA polymerase ε elongates the leading strand and a second DNA polymerase δ elongates the lagging strand. |
| 14- How does the replication fork act when it reaches a damaged DNA? how does replication complex replace? | It stalls when it arrives , replaced by a specialized DNA polymerase for lesion bypass. |
| 15- What happens after damage has been repaired? | the primosome is required to reinitiate replication by reinserting the replication complex. |
| 16- How does termination of replication happen? | The two replication forks usually meet halfway around the circle, but there are ter sites that cause termination if the replication forks go too far. |
