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
Specify the domains of DNA polymerase I and describe their corresponding functions in DNA replication in prokaryotes
- I: 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
- II: involved in repair; not required for replication
- III: main one; synthesizes leading and lagging strands
describe the subunits of DNA pol I
- 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 and a replication fork
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