HRR: DNA synthesis Flashcards
what is semiconservative replication
each DNA molecule has a parent strand and a daughter strand
bonds formed with DNA polymerase are formed ___’ to ___’
3 to 5
DNA synthesis occurs ___’ to ___’
5 to 3
complementary base pairing is required ___ forming 3’ to 5’ bonds
before
what does DNA need in order for the polymerase to work?
a free 3’ hydroxyl end
prokaryotic DNA polymerase I: function
removes the primer and helps fill in the gaps on the lagging strand. Single protein folded into a tertiary structure with three functional domains: 5 to 3 exonuclease, 3 to 5 exonuclease, and 5 to 3 polymerases
prokaryotic DNA polymerase II
involved in repair; not required for replication. has 5 to 3 elongation and 3 to 5 exonuclease
prokaryotic DNA polymerase III
main one; synthesizes leading and lagging strands. has 5 to 3 elongation and 3 to 5 exonuclease
describe the functions of 5 to 3 exonuclease, 3 to 5 exonuclease, and 5 to 3 polymerase
- 5’ to 3’ exonuclease: removes primer
- 3’ to 5’ exonuclease proofreads
- 5’ to 3’ polymerase forms phosphodiester bonds at 10 per second
Define the functions of the a, b and e subunits of DNA polymerase III in DNA replication of prokaryotes.
A: 5 to 3 polymerase activity of 1000 nucleotides per second
B: form dimers around the strand called a sliding clamp. This helps the enzyme go quickly.
E: 3 to 5 exonuclease activity for proofreading. If the polymerase messes up, this will stall it and correct the mistake
what is in the central component of DNA Pol III
the clamp loader and helicase
Specify the 3 main mechanisms that contribute to the high fidelity of DNA replication.
-Complementary base pairing by DNA polymerase
- Proofreading: performed by 3 to 5 exonucleases. The polymerase will be stalled, the 3 to 5 bond will be hydrolyzed and the base will be removed, and DNA polymerase will place the correct base in its spot.
- DNA repair
Describe initiation of DNA synthesis in prokaryotes
- Initiator protein binds to the origin of replication. This recruits the polymerase
- The helicase in the polymerase starts to unwind the DNA. Single stranded binding proteins help protect the DNA
- The RNA primers are synthesized
- The DNA replication bubble is formed. The bubble has two replication forks.
briefly describe a replication fork
The replication fork has a leading strand and a lagging strand. The leading is 5 to 3, and lagging is 3 to 5
differentiate between a replication bubble, a replication fork, and an origin of replication
The replication bubble has two forks moving in opposite directions. the leading/lagging strands will be on opposite sides of the two forks. The origin of replication is where the initiator binds to recruit the polymerase and form the replication bubble
describe the difference between the leading and lagging strands
- the leading strand is primed once, while the lagging strand is primed multiple times
- the leading strand is synthesized continuously, while the lagging strand is synthesized in smaller pieces called okazaki fragments.
- the leading strands runs 5’ to 3’, while the lagging runs 3’ to 5’
describe the function of primase
Primase: enters with helicase/polymerase. It is complementary to the template and allows the DNA polymerase to begin synthesis via a free 3’ hydroxyl group
describe the function of helicase
Helicase helps unwind the DNA
describe the function of topoisomerase
Topoisomerase in prokaryotes can either relax positive/negative supercoils or crease negative supercoils to prevent issues with the DNA winding
Which strand “loops” during synthesis? What is the function of this?
The lagging strand: it allows the pol III to synthesize both stands at the same time. The clamp on the loop with dissociate and reassociate to release the slack on the loop while forming Okazaki fragments
Explain the role of DNA ligase in the synthesis of the lagging strand.
It catalyzes the formation of the phosphodiester bond between Okazaki fragments
What are the main DNA polymerases in eukaryotes
Alpha, delta, epsilon
describe the alpha subunit of DNA polymerase in eukaryotes
generates RNA-DNA primers to initiate lagging strand synthesis
describe the delta subunit of DNA polymerase in eukaryotes
main enzyme for synthesizing the lagging strand and helps fill the gaps between Okazaki fragments
