L2- DNA Replication and Repair

Question 1

What kind of bond is most critical for DNA recognition by proteins?

Answer 1

Hydrogen bonding.

Question 2

On which part of the DNA helix do proteins typically make contact with DNA bases?

Answer 2

In the major groove of DNA.

Question 3

Many proteins contain ____ (structural motif) that can fit in the ____ (location) of DNA to play a role in site specific binding.

Answer 3

α-helices, major groove.

Question 4

What is the origin recognition complex (ORC) and what is its function?

Answer 4

The ORC is a group of proteins that binds DNA at origins of replication. It helps initiate DNA replication in eukaryotes.

Question 5

What is a helicase and what is its function?

Answer 5

It is an enzyme that unzips double stranded DNA to form two single strands by hydrolyzing the hydrogen bonds between the two DNA strands.

Question 6

What is the function of human single stranded DNA binding proteins (SSBs)?

Answer 6

To stabilize single stranded DNA by preventing re-annealing.

Question 7

What is the function of Topoisomerase I?

Answer 7

Topo I is an enzyme that removes DNA supercoiling by breaking a single DNA strand, allowing the DNA structure to relax. It then covalently re-connects the DNA strands where they were originally cut.

Question 8

What disease associated with leukemia is caused by a deficiency of a cellular DNA helicase?

Answer 8

Bloom’s Syndrome.

Question 9

What syndrome associated with pre-mature aging is caused by a defective helicase?

Answer 9

Werner’s syndrome.

Question 10

In which direction does the DNA polymerase that synthesizes the leading strand of DNA read its template?

Answer 10

5’ to 3’ (all DNA and RNA polymerases synthesize oligonucleotides in this direction).

Question 11

What are Okazaki fragments and in which direction are they synthesized?

Answer 11

Okazaki fragments are short fragments of DNA that constitute the DNA lagging strand during replication. They are synthesized in the 5’ to 3’ direction.

Question 12

List three Human DNA polymerases.

Answer 12

Pol-α, Pol-δ, and Pol-ε.

Question 13

What is the function of a primase?

Answer 13

It associates with DNA polymerase α. The resulting complex synthesizes a short RNA strand that serves as a primer for other DNA polymerases.

Question 14

What is DNA Pol ε and what is its function?

Answer 14

It is a high fidelity polymerase with 3’ - 5’ exonuclease proofreading activity. It is required for leading strand synthesis and is PCNA dependent.

Question 15

What is the function of DNA Pol δ and what other enzyme does it require for proper function?

Answer 15

It synthesizes the lagging strand during DNA replication with high fidelity due to its exonuclease activity. It requires PCNA to remain attached to the DNA template.

Question 16

What is the function of Poly α?

Answer 16

It works with a primase to make the DNA primers required to initiate DNA-synthesis by pol ε and pol δ, which in turn synthesize the leading and lagging strands, respectively.

Question 17

What is the function of Proliferating Cell Nuclear Antigen (PCNA)?

Answer 17

PCNA form a clamp around a DNA polymerase and prevents it from dissociating from the template DNA strand.

Question 18

What is the function of the minichromosome maintenance complex (MCM)?

Answer 18

It unzips double stranded DNA, resulting in the formation of single strands (MCM is the human DNA helicase complex).

Question 19

What is the function of replication factor C (RFC)?

Answer 19

RFC helps to load DNA poly ε and DNA poly δ onto the template DNA.

Question 20

What is the function of single strand binding proteins (SSBs)?

Answer 20

SSBs prevent single stranded DNA fragments from re-annealing. Note that human SSBs are often abbreviated RPA.

Question 21

What is the function of DNA ligases?

Answer 21

They covalently join (ligate) DNA ends and Okazaki fragments to one another.

Question 22

What is the function of DNA Polymerase γ?

Answer 22

It synthesizes mitochondrial DNA.

Question 23

What is the function of DNA Polymerase β?

Answer 23

It maintains the integrity of the genome by participating in excision repair. (Do not confuse this with RNA polymerase β, which synthesizes mRNA!)

Question 24

Acyclovir is used to inhibit the polymerase of what class of viruses?

Answer 24

Herpes simplex viruses

Question 25

Which enzyme is inhibited by the drug azidothymine (AZT)?

Answer 25

An HIV reverse transcriptase

Question 26

List the four stages of the cell cycle.

Answer 26

G1 (growth), S (DNA synthesis), G2 (more growth) and M (Mitosis, which itself is divided into several stages).

Question 27

What is p53 and what is its function?

Answer 27

It is a tumor suppressor protein that is active at the G1/S checkpoint to prevent cells with DNA damage from replicating.

Question 28

What syndrome is associated with inherited mutant forms of the p53 tumor suppressor gene?

Answer 28

Li-Fraumeni syndrome.

Question 29

What process does a cell undergo if its genome is so damaged that it cannot be repaired?

Answer 29

Apoptosis.

Question 30

Name three DNA repair pathways.

Answer 30

Mismatch repair, Excision repair, Removal of Uracil from DNA.

Question 31

Name the three proteins used in prokaryotic mismatch repair.

Answer 31

Mut S, Mut H, and Mut L.

Question 32

Name two human proteins that are involved in mismatch repair.

Answer 32

hMSH and hMLH.

Question 33

What are the functions of Mut S and Mut H in bacteria?

Answer 33

Mut S recognizes mismatched base pairs while Mut H catalyzes the incision of the section of the strand containing the mismatched base pairs.

Question 34

Name three diseases associated with trinucleotide repeats.

Answer 34

Fragile-X syndrome, Myotonic Dystrophy, and Huntington’s Disease.

Question 35

What are the main steps of excision repair in E.coli?

Answer 35

Incision, Excision, Resynthesis and Ligation.

Question 36

What complex of proteins is responsible for the repair of pyrimidine dimers in bacteria?

Answer 36

uvrABC.

Question 37

Which DNA repair mechanism is defective in Xeroderma Pigmentosum?

Answer 37

The excision repair system. As a result, UV-induced DNA damage cannot be effectively repaired.

Question 38

Deamination of adenine and cytosine by nitrous acid causes these bases to turn into _____ and ______, respectively

Answer 38

Hypoxanthine and uracil.

Question 39

What is the major site of alkylation on DNA bases?

Answer 39

The N7 of guanine. This results in a loss of the guanine residue.

Question 40

What are intercalators and what do they cause?

Answer 40

They are polycyclic rings that have the ability to insert themselves between bases of DNA, causing physical distortion of the DNA, ultimately leading to the addition or loss of base pair(s).

Question 41

What is the functional difference between DNA Poly δ and DNA ligase with respect to lagging strand synthesis?

Answer 41

DNA Poly δ removes the RNA primers at every Okazaki fragment and fills in the gaps between the fragments. DNA ligase covalently binds the completed Okazaki fragments to one another.