DNA Synthesis, Repair & Recombination 1

Question 1

In contrast to DNA synthesis, DNA polymerases read a DNA template in what direction?

Answer 1

3’–>5’

Question 2

Prokaryotes have 3 DNA polymerases. What are their names?

Answer 2

Pol I

Pol II

Pol III

Question 3

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?

Answer 3

One strand is parental (conserved in the 2 daughter helicies) and one strand is newly synthesized.

Question 4

In eukaryotes, replication can begin at multiple different sites on the genomic DNA. However in prokaryotes it is different. How?

Answer 4

Prokaryotes have a single origin of replication

Question 5

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?

Answer 5

Strands must be separated (melted) at the “start site”

Separated strands form a V-like structure otherwise known as a replication fork

Question 6

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?

Answer 6

DnaA protein

Question 7

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?

Answer 7

DNA Helicase

Question 8

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?

Answer 8

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

Question 9

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?

Answer 9

Formation of Positive Supercoils

Solution is DNA topoisomerases => remove supercoils and facilitate transcription

Question 10

During the process of DNA replication, there is a leading strand and a lagging strand. How does one go about differentiating between the 2?

Answer 10

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

Question 11

In order to initiate synthesis the DNA polymerase requires what?

Answer 11

RNA primer

=>made by primarse (RNA pol)

Question 12

Which DNA pol is responsible for elongation of DNA during DNA synthesis?

Answer 12

DNA Polymerase III - major enzyme responsible for proofreading during replication

Question 13

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?

Answer 13

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)

Question 14

In eukaryotic replication RNA primers are removed by what protein?

Answer 14

RNAse H

Question 15

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?

Answer 15

• 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

Question 16

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?

Answer 16

Telomerase

Question 17

What is the significance of high telomerase activity?

Answer 17

Although it is not the cause of cancer, it is a contributing factor to indefinite cell proliferation (immortal cells)

Question 18

X-rays which produce free radicals from H2O is a good example of what type of DNA damage?

Answer 18

Indirect

Question 19

Cigarette smoke which when oxidized in the body adducting to guanine residues is a good example of what type of DNA damage?

Answer 19

Direct

Question 20

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?

Answer 20

Nucleotide excision repair sytsem is defective so cells are unable to repair (UV-) damaged DNA which leads to skin cancer.

Autosomal recessive

Pyrimidines (TC)

Question 21

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?

Answer 21

Nonhomologous end joining

-can result in deletions or insertions

Question 22

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?

Answer 22

Homologous recombination

Question 23

In BRCA2 (cause of breast, ovarian, and prostate cancer) what is the central process missing or affected?

Answer 23

DNA repair by homologous recombination

Question 24

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?

Answer 24

Reverse transcriptase

Question 25

In the treatment of retroviral infections providers will use a drug that utilizes what mechanism? Give an example and why it works.

Answer 25

Reverse transcriptase inhibitors (nucleotide analogs)

ex: Replacement of hydroxyl group by AZT
- Reverse transcriptase has higher affinity for AZT than DNA pol

Question 26

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?

Answer 26

DDL (didanosine)

Question 27

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?

Answer 27

5’-fluorouracil

Question 28

In general most chemotherapeutic agents target one of two processes concerned with nucleic acid metabolism. What are the 2 processes? (Don’t overthink this)

Answer 28

Nucleotide synthesis or DNA replication

Question 29

Acyclovir is a prodrug which means what?

Answer 29

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.