HRR: maintenance of the genome

Question 1

what is semiconservative replication

Answer 1

each DNA molecule consists of a parent strand and a daughter strand

Question 2

Name three important elements of DNA replication

Answer 2

it needs to be fast, accurate, and bidirectional

Question 3

Bonds formed with DNA polymerase are __ to __

Answer 3

3 to 5

Question 4

Describe the 4 main characteristics of the DNA polymerase reaction.

Answer 4

-Synthesis of DNA is primed, meaning it needs a free 3’ hydroxyl for the polymerase to work.
-DNA synthesis always occurs 5 to 3
-Synthesis is template directed, meaning complementary base pair binding is required before forming the 3 to 5 bonds
-Template is always read 3 to 5

Question 5

Specify the domains of DNA polymerase I and describe their corresponding functions in DNA replication in prokaryotes.

Answer 5

-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

-III: main one; synthesizes leading and lagging strands

Question 6

Define the functions of the a, b and e subunits of DNA polymerase III in DNA replication.

Answer 6

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

Question 7

What is in the central component of DNA polymerase III?

Answer 7

the clamp loader and helicase; the unit connects the 2 core enzymes

Question 8

Explain the role of 5 ́ to 3 ́ exonuclease activity of DNA polymerase I during replication.

Answer 8

5 to 3: removes primer
3 to 5: proofreading
5 to 3: forming phosphodiester bonds at 10-20 nucleotides per second

Question 9

Specify the 3 main mechanisms that contribute to the high fidelity of DNA replication.

Answer 9

-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

Question 10

Describe initiation of DNA synthesis in prokaryotes

Answer 10

-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.

Question 11

Describe a replication fork and identify the leading and lagging strands, the template strand, and the direction of fork movement.

Answer 11

The replication fork has a leading strand and a lagging strand. The leading is 5 to 3, and lagging is 3 to 5.

Question 12

describe synthesis of the leading strand in the replication fork

Answer 12

The leading strand is primed once, and DNA polymerase continuously synthesizes in the 5 to 3 directions

Question 13

describe the synthesis of the lagging strand in the replication fork

Answer 13

The lagging strand has to be primed several times and is made in smaller pieces called Okazaki fragments. This is because DNA can only be made in 5 to 3 direction, but the lagging strand runs 3 to 5

Question 14

Differentiate between a replication bubble and an origin of replication.

Answer 14

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.

Question 15

what is the function of primase in DNA replication?

Answer 15

enters with helicase/polymerase. It is complementary to the template and allows the DNA polymerase to begin synthesis via a free 3’ hydroxyl group.

Question 16

Which strand “loops” during synthesis? What is the function of this?

Answer 16

The lagging strand: it allows the pol III to synthesize both stands at the same time. The clamp on the loop with dissociate and reassociate to release the slack on the loop while forming Okazaki fragments.

Question 17

Explain the role of DNA ligase in the synthesis of the lagging strand.

Answer 17

It catalyzes the formation of the phosphodiester bond between Okazaki fragments

Question 18

What are the main DNA polymerases in eukaryotes

Answer 18

Alpha: generates RNA-DNA primers to initiate lagging strand synthesis

Gamma: main enzyme for synthesizing the lagging strand and helps fill the gaps between Okazaki fragments

Epsilon: main enzyme for synthesizing the leading strand

Question 19

What is PCNA in eukaryotic DNA synthesis

Answer 19

A sliding clap protein that allows for processivity of polymerases epsilon and gamma

Question 20

In eukaryotes, which topoisomerase addresses tangles behind the replication fork?

Answer 20

Topoisomerase II

Question 21

Describe initiation of DNA synthesis in eukaryotes

Answer 21

As opposed to having one replication bubble, we have multiple per DNA strand. The bubbles ultimately come together and fuse.

Question 22

22. Describe the mechanism by which telomerases “cap” the ends of DNA with telomeres.

Answer 22

-A telomerase brings its RNA template to the parent strand with 3’ overhang

-The telomerase preforms reverse transcription, synthesizing in the 3’ to 5’ direction

-The telomerase translocate along the new strand and repeats the process, lengthening the strand

-The other strand synthesizes via complementary base pairing to the telomere

Question 23

Specify the functions of telomeres

Answer 23

-Protects the chromosomes from degradation
-Prevents the ends of DNA joining by ligase
-Prevents homologous recombination of chromosome ends by recombination enzymes.

Question 24

what are telomeres

Answer 24

Repeating DNA sequences at the ends of chromosomes that allow the lagging strand to loop. This allows for the entire strand to replicate without losing DNA, thus protecting the strand

Question 25

Do tumor cells have higher or lower telomere activity than normal somatic tissue cells

Answer 25

higher