DNA Replication

Question 1

Define the term semi-conservative.

Answer 1

Both parental DNA strands are used as templates for replication, resulting in each daughter cell obtaining one strand of parent DNA. This ensures both daughter cells have the exact same genetic information as the parent.

Question 2

What is euchromatin and how does it appear?

Answer 2

Areas of transitionally active DNA, which appears less condensed.

Question 3

What is heterochromatin?

Answer 3

Areas of inactive DNA that appears dense, tightly packed together, and near the nuclear periphery.

Question 4

At the beginning of packaging, DNA is wrapped around these positively charged proteins.

Answer 4

Histones

Question 5

What is a nucleosome bead?

Answer 5

Complex formed when DNA wraps twice around the histone octamer.

Question 6

What is the purpose of post-translational modification of histones during packaging?

Answer 6

PTM of histones influences chromatin structure. By changing structure, these modification dictate whether, how, and when DNA can be transcribed. (EX: acetylation, methylation, phosphorylation)

Question 7

What post-translational modification of histones neutralizes charges, makes DNA more accessible, and promotes transcription?

Answer 7

Acetylation. Conversely, methylation strengthens interactions between histones and DNA to prevent transcription.

Question 8

In what stage of the cell cycle is DNA replicated?

Answer 8

S Phase

Question 9

How is the cell cycle tightly regulated?

Answer 9

Cyclin dependent kinases (CDKs) become active at different parts of the cell cycle and phosphorylate proteins that activate that stage of the cell cycle.

Question 10

What is the function of proto-ongogenes?

Answer 10

A signaling pathway in the cell cycle that promotes cell proliferation.

Question 11

What proteins control checkpoints in the cell cycle and check for DNA stability?

Answer 11

Tumor Supressor

Question 12

DNA replication is bi-directional, however, the DNA polymerase only functions in one direction. What direction is this?

Answer 12

Replication is in the 5’ –> 3’. This means that the DNA polymerase reads the template strand in the 3’ –> 5’ direction.

Question 13

DNA replication utilizes many origin points in order to be efficient. Does replication at all sites happen simultaneously?

Answer 13

No, different origins may be activated at different times.

Question 14

In what regions of the DNA are origin points more often located?

Answer 14

While there are not specific points when replication origins are created, they more often appear in areas of DNA with right A-T linkages. A-T has fewer hydrogen bonds than G-C making them more susceptible to breakage.

Question 15

What is the function of licensing? What is the process to license DNA?

Answer 15

Origin points are licensed during the G1 stage of the cell cycle to ensure that points of origin are not utilized more than once during replication. An Origin Recognition Complex binds to origins throughout the cell cycle. Cdt1 and Cdc6 proteins, only available in G1, then recruit Msm helicase. The ORC-Msm complex licenses the origin. Phosphorylation of ORC-Msm by a CDK activates the Msm’s helicase function. ORC is displaced by the DNA Polymerase, but quickly rebinds. The other components of the complex cannot bind the phosphorylated version of ORC, which prevents re-licensing until the next G1 phase.

Question 16

What protein relieves coiling and tension ahead of the replication fork?

Answer 16

Topoisomerases

Question 17

How is single-stranded DNA kept stable during replication?

Answer 17

Single-stranded binding proteins bind to single-stranded DNA to prevent parental strands from reannealing with each other or themselves.

Question 18

What is the name of a bacterial topoisoerase?

Answer 18

Gyrase (makes double-stranded breaks)

Question 19

What is the role of topoisomerases in cancer treatment?

Answer 19

Inhibition of topoisomerases stops DNA replication and eventually leads to cell death. This can be a target of some chemotherapy treatments.

Question 20

What is needed for the DNA polymerase to begin replication?

Answer 20

The DNA polymerase must bond a 3’ OH to begin replication. A primase synthesizes a short RNA primer, which is later replaced by DNA.

Question 21

How is DNA edited if an incorrect nucleotide is added?

Answer 21

The DNA polymerase exhibits a 3’ –> 5’ exonuclease ability, which enables it to proofread and edit incorrectly added nucleotides.

Question 22

How does replication of the leading strand differ from that of the lagging strand?

Answer 22

The leading strand is replicated continuously in the direction of the replication fork, with fewer primers. Since the lagging strand begins at the replication fork and moves toward the origin, DNA is replicated discontinuously into Okasaki fragments, which later must be joined together.

Question 23

What is the name of replicated segments of lagging strand DNA?

Answer 23

Okazaki fragments

Question 24

What is used to remove RNA primers placed to initiate replication by the DNA polymerase?

Answer 24

RNAse

Question 25

What is the function of DNA ligase?

Answer 25

Uses ATP to make the final phosphodiester bond and seal any nicks in the replicated DNA.

Question 26

What keeps the DNA polymerase attached to the DNA strands for replication and regulates its processitivity?

Answer 26

PCNA (Proliferating Cell Nuclear Antigen). Without PCNA, DNA polymerase would unpredictably fall off the DNA strand and be unable to replicated long strands of DNA in an efficient manner.

Question 27

What is PCNA (Proliferating Cell Nuclear Antigen)?

Answer 27

A sliding clamp that regulates the processtivity of DNA polymerase.

Question 28

What is the function of DNA polymerase alpha?

Answer 28

Synthesizes primer and initiates DNA synthesis

Question 29

What is the function of DNA polymerase delta?

Answer 29

Synthesizes DNA on the lagging strand

Question 30

What DNA polymerase synthesizes DNA on the leading strand?

Answer 30

DNA Polymerase Epsilon

Question 31

What DNA polymerase synthesizes mitochondrial DNA?

Answer 31

DNA Polymerase Gamma

Question 32

What is the function of DNA Polymerase III in bacterial cells?

Answer 32

Synthesizes most DNA

Question 33

What is the function of DNA Polymerase I in bacterial cells?

Answer 33

Removes primers and fills in gaps between Okazaki fragments

Question 34

What is the name of the ends of chromosomes that provides protection, but does not code for any proteins?

Answer 34

Telomeres

Question 35

What is the function of telomeres?

Answer 35

They mark the ends of chromosomes and protects DNA from degradation. Without telomeres, chromosomes would be fused together.

Question 36

What happens when telomeres become too short?

Answer 36

They cell will stop replicating and activated a cell cycle checkpoint. The cell will then enter a stage called senescence.

Question 37

What is the function of telomerase? Where is it found?

Answer 37

Telomerase maintains the length of telomeres on the parent strand using an RNA template. It is expressed in germ cells, stem cells, and most cancer cells.

Question 38

What happens when a cell enters senescence?

Answer 38

The cell continues to live, but eventually dies from genomic instability. In a very small number of cells, genomic rearrangements result in telomerase activity that then allows the cell to proliferate indefinitely.

Question 39

Why do dideoxynucleotides (ddNTP) terminate DNA synthesis?

Answer 39

ddNTPs lack a 3’OH group, which is required to form the phosphodiester bond with the 5’ phosphate group with the next nucleotide.

Question 40

How does telomerase maintain telomers?

Answer 40

A ribozyme uses its own RNA template to extend the parental DNA via reverse transcriptase.

Question 41

What is Bloom’s syndrome?

Answer 41

Disorder caused by a mutation of the helicase. Symptoms include short stature, photosensitivity, and increased risk of cancer.