DNA Synthesis, Repair & Recombination 1 Flashcards
In contrast to DNA synthesis, DNA polymerases read a DNA template in what direction?
3’–>5’
Prokaryotes have 3 DNA polymerases. What are their names?
Pol I
Pol II
Pol III
In the process of DNA replication the resut is 2 daughter molecules. This is done in order to achieve semiconservative replication. What is this phenomenon?
One strand is parental (conserved in the 2 daughter helicies) and one strand is newly synthesized.
In eukaryotes, replication can begin at multiple different sites on the genomic DNA. However in prokaryotes it is different. How?
Prokaryotes have a single origin of replication
In both prokaryotes as well as eukaryotes replication is bidrectional. However, in order to begin this process there are 2 other requirements. What are they?
Strands must be separated (melted) at the “start site”
Separated strands form a V-like structure otherwise known as a replication fork
As a part of the “pre-priming” complex there is a protein that is responsible for binding to and melting (separting) the dsDNA. What is the name of this protein?
DnaA protein
Also as a part of the pre-priming complex is a protein that is responsible for the unwinding of the double helix. What is the name of this protien?
DNA Helicase
Once the dsDNA is unwinded, there are proteins whose only job is to ensure that this is maintained. What is the name of these proteins and how do they accomplish this task?
ssDNA-binding (single stranded binding) proteins- literally just bind to the strand in order to keep it separated from the other strand.
* They also protect the ssDNA from nucleases
During the process of unwinding DNA there can be a mechanical problem which may interfere with the process of replication later on. What is this problem and what is the solution it?
Formation of Positive Supercoils
Solution is DNA topoisomerases => remove supercoils and facilitate transcription
During the process of DNA replication, there is a leading strand and a lagging strand. How does one go about differentiating between the 2?
Leading strand => being synthesized continuously in the direction of the replication fork
Lagging strand => being synthesized discontinuously in the direction away from the replication fork - Okazaki fragments (small DNA fragments) copied near replication fork
In order to initiate synthesis the DNA polymerase requires what?
RNA primer
=>made by primarse (RNA pol)
Which DNA pol is responsible for elongation of DNA during DNA synthesis?
DNA Polymerase III - major enzyme responsible for proofreading during replication
While elongation of prokaryotic DNA is taking place, the lagging strand is elongated in a unique fashion (besides 3’–>5’) what is it? List all four components involved and the function of each one?
DNA pol III –> elongates lagging strand starting at RNA primer until encountering next RNA primer.
DNA pol I –> excises RNA primer one ribonucleotide at a time and then fills gap with DNA (deoxyribonucleotides).
RNA primer–> acts as target for DNA pol III in making of okazaki fragments
DNA ligase–> links okazaki fragments togther, thereby completing lagging strand (requires ATP)
In eukaryotic replication RNA primers are removed by what protein?
RNAse H
At the ends of eucharyotic chromosomes, there is a region of highly repetative DNA (TTAGGG) known as a telomere. What are some of the functions of the telomere?
- Act as buffer, consumed during cell division
- Protect ends of chromosome from nucleases
- Limit cells to a fixed number of divisions (anti-cancer)
- Replenish lost DNA
Ribonucleoprotein complex which is RNA-dependent DNA polymerase adn contains TERC which is complementary to a repetative sequence in telomere. What is the name of this structure?
Telomerase
What is the significance of high telomerase activity?
Although it is not the cause of cancer, it is a contributing factor to indefinite cell proliferation (immortal cells)
X-rays which produce free radicals from H2O is a good example of what type of DNA damage?
Indirect
Cigarette smoke which when oxidized in the body adducting to guanine residues is a good example of what type of DNA damage?
Direct
Explain the mechanism of xeroderma pigmentosum, that is what central process is dysfunctional/absent? What is the mode of inheritance? What bases are building up in excess?
Nucleotide excision repair sytsem is defective so cells are unable to repair (UV-) damaged DNA which leads to skin cancer.
Autosomal recessive
Pyrimidines (TC)
In the case of a double stranded break there are 2 manners in which repair can take place. The first is one that which has a higher chance of altering the original DNA sequence. What is the mechanism by which it works?
Nonhomologous end joining
-can result in deletions or insertions
In the case of double stranded breaks the second method of repair is more complex but preferred as it is better able to restore the original DNA sequence. What is the name of this method?
Homologous recombination
In BRCA2 (cause of breast, ovarian, and prostate cancer) what is the central process missing or affected?
DNA repair by homologous recombination
This enzyme is known as the retroviral enzyme as it is able to synthesize DNA from an RNA template. What is the name of this enzyme?
Reverse transcriptase
In the treatment of retroviral infections providers will use a drug that utilizes what mechanism? Give an example and why it works.
Reverse transcriptase inhibitors (nucleotide analogs)
ex: Replacement of hydroxyl group by AZT
- Reverse transcriptase has higher affinity for AZT than DNA pol
From lecture we learned about a reverse transcriptase inhibitor whcih is able to terminate chain growth when incorporated into DNA by reverse transcriptase. What is the name of this compound?
DDL (didanosine)
From lecture we learned about a reverse transcriptase inhibitor which inhibits the synthesis of thymine nucleotides required for DNA replication by irreversibly inhibiting thymidylate synthase. What is the name of this compound?
5’-fluorouracil
In general most chemotherapeutic agents target one of two processes concerned with nucleic acid metabolism. What are the 2 processes? (Don’t overthink this)
Nucleotide synthesis or DNA replication
Acyclovir is a prodrug which means what?
It is administered in an essentially deactivated form but becomes activated once incorporated into viral DNA effectively resulting in chain termination/blockage of viral replication.
