DNA Replication Block
What are the processivities of DNA polymerases I and III?
DNA polymerase I has a low processivity (20 bases before it disassociates) DNA polymerase III has a high processivity (5 million bases before it disassociates)
What three observations have been made of all DNA polymerases?
1. Incoming base paring is selected by complementary base pairing with a template strand. 2. Chain growth is in the 5' to 3' direction 3. All DNA polymerases require a primer strand to add bases to.
What is the name of the model used to describe DNA replication in mitochondria?
D-Loop Replication
What is the function of DNA polymerase I? What is the Klenow fragment?
DNA polymerase I is an enzyme involved in prokaryotic DNA elongation and repair. It has 3 activities: 5'-3' polymerase activity (synthesis), 5'-3' exonuclease activity (repair and removal) and 3'-5' exonuclease activity (proofreading). The Klenow fragment is a subunit of DNA polymerase I that contains the 5'-3' synthetic and 3'-5' proofreading activities.
What is the function of DNA polymerase III?
DNA polymerase III is also a prokaryotic DNA elongation and repair enzyme. It has a complex structure, made of 10 subunits, which form a "sliding clamp" that works along the strand. It has a higher processivity than DNA polymerase I.
What are some contrasts between features of prokaryotic and eukaryotic DNA replication?
Eukarotic DNA is much longer, the synthesis is much slower and occurs in accordance with the cell cycle. Eukaryotic cells use a large number of DNA polymerase molecules and begin replication at multiple sites.
Where is E-coli DNA initiated and where is it terminated?
It is initiated at the OriC, and terminated at the ter site.
Which DNA polymerase is believed to be responsible for leaDing strand synthesis and which for lAgging strand synthesis in eukaryotes?
Leading strand synthesis: DNA polymerase delta Lagging strand synthesis: DNA polymerase alpha
Where is DNA found in eukaryotes? How is DNA packaged?
Most of the DNA is in the nucleus. A small amount is found in mitochondria.
What proteins are in nucleosomes, and why do they bind to DNA?
Nucleosomes contain positively charged histone molecules. They bind because of their positive charge that attracts the negatively charged phosphate groups of DNA.
What is PCNA, and what role does it play?
Proliferating cell Nuclear Antigen (PCNA) is a cyclin that forms a clamp around the template DNA strand to dramatically increase the processivity of DNA polymerase delta.
How is RNA used in DNA replication as discussed above? What are Okazaki fragments?
RNA acts as the primer for the discontinuous replication of DNA on the 3'-5' (lagging) strand. Okazaki fragments are the pieces of DNA that are replicated on the 3'-5' (lagging) strand that will eventually be joined by ligases to make a complete DNA replicate strand.
In replication, which strand is the leading strand and which is the lagging strand? Which is synthesized continuously, and which is not?
The 5' - 3' strand is the leading strand, the 3' - 5' strand is the lagging strand. The 5'-3' strand (leading) is synthesized continuously. The 3'-5' (lagging) strand is not.
What is the arrangement of nucleosomes after DNA replication? How might nucleosomes affect eukaryotic DNA replication?
The nucleosomes are cooperatively distributed. During replication, there is simultaneous synthesis of new histones with DNA. One daughter strand has the new histones, the other daughter strand has the original ones. The presence of these histones (specifically the original ones, that remain associated with one strand of the replication fork) may be why DNA polymerization is so much slower in eukaryotes)
What does semiconservative replication mean?
The two daughter strands of DNA each contain one strand of the parent DNA.
What is the function of a topiosmerase? A helicase?
Topoisomerase is an enzyme that changes the topography of DNA molecules by cutting strands, allowing the supercoiling to be adjusted and then religating the strands. A helicase is an enzyme that catalyzes the unwinding of ds DNA by disrupting the base-pair hydrogen bonding.
