L01-7
Explain semi-conservative mechanism of DNA replication
Both strands of DNA serve as a template for synthesizing a new strand. The OG strands are called template/parental. New strands are called newly synthesized/daughter. DNA replication produces 2 new DNA molecules, each with a new strand and an old strand (one daughter one parent)
How many errors per nucleotide added does an accurate DNA polymerase make?
BONUS: this type of repair in our DNA allows the accuracy to go up
about 1 error for every 10,000,000 nucleotides incorporated
BONUS: strand-directed mismatch repair (1 error in 1 billion nucleotides added)
What enzyme seals the nick in the lagging strand of DNA?
DNA ligase
What is the unique activity of DNA polymerase I
3'-5' exonuclease activity
What are the drugs coumarins and quinolones used for treatment of
cancer; coumarins inhibit bacterial type 2 topoisomerase from binding ATP, quinolones inhibit last step of topoisomerase where resealing DNA strand breaks should occur
What are the main 4 things needed for DNA replication?
1. template
2. primer
3. precursors (dNTPs)
4. other proteins (DNA polymerase, sliding clamps, helices, primase, single stranded DNA binding proteins, nucleases, ligases)
Why does Acyclovir inhibit DNA polymerase activity in the treatment of cold sores?
When it is added into the cell, acylclovir is incorporated into the DNA chain instead of GTP. Acyclovir lacks a 3' hydroxyl group, so the chain cannot grow any more
What is the role of topoisomerase?
BONUS: how is topoisomerase 1 and 2 different?
relieve the twists in front of the replication fork by forming a break on the DNA backbone
BONUS: topoisomerase I gives a nick in one strand, II breaks both strands
Explain Nick translation
polymerase activity and exonuclease activity happen at the same time and same direction
This domain forms an active site that only accommodates a watson-crick base pair.
The closing of a finger domain in the DNA polymerase
sorry
All newly synthesized strands begin with ___. It is made of ___ made by ____
primers; RNA by primase
Which strand has RNA primer? Which strand has Okazaki fragments?
both strands have RNA primers, lagging strand has Okazaki fragments
What does the cancer drug Etopside (VP16) do?
Inhibit topoisomerase II to treat cancer
topoisomerase II breaks both DNA strands to relieve supercoiled DNA before the replication fork
Which of the following is not necessary for DNA replication?
template DNA, primer strand, dNTP, RNA polymerase
RNA polymerase
What ion coordinates the DNA polymerase reaction?
MG2+
How do DNA polymerases ensure accuracy of replication?
1. by the fit of the incoming nucleotide (if it fits, catalysis of phosphodiester bond occurs)
2. proofreading (3'-5' exonuclease activity of polymerase will remove the incorrect nucleotide)
How many subunits are in DNA helicases? What is the role of this protein?
6 subunits (hexameric), it hydrolyzes ATP to separate the parental strands
What replicative protein keeps the polymerase in contact with the growing chain? How do they affect processivity?
sliding clamps; increase (it increases the number of nucleotide additions catalyzed by polymerase before dissociation)
Which of the following is true with regard to DNA primase?
A- it is inhibited by helicase
B- it requires 3'OH for synthesis
C- it synthesizes RNA primers for lag strand synthesis
D- it removes RNA primer to replace with DNA primer
C
How does DNA polymerase grow the strand?
Add dNTPs to the free 3'OH of the primer or the growing daughter strand
Select the correct statement (select all that apply)
A. DNA Polymerase I has 3'-5' endonuclease activity and 5'-3' endonuclease activity.
B. DNA Polymerase III only has 5'-3' exonuclease activity.
C. DNA Polymerase I has both 3'-5' and 5'-3' exonuclease activity.
D. DNA Polymerase III does not have 5'-3' exonuclease activity
C and D are correct
sorry this question was mean
Explain the function of single stranded DNA binding proteins.
They bind to the parental single strands and prevent annealing and secondary structure formation. They fall off the strand when contacted with polymerase
What is the trombone model of DNA replication?
when the lagging strand and its template strand form a loop when DNA Polymerase initiates Okazaki fragment synthesis from an RNA primer
Each replication fork requires both leading and lagging strand synthesis because...
DNA templates are antiparallel but yet the DNA polymerases only work in one direction
THROWING YOU A BONE FOR SOME POINTS
WHATS THE CENTRAL DOGMA OF BIOLOGY
DNA TO RNA (TRANSCRIPTION) TO PROTEIN (TRANSLATION)