Ch 6: DNA replication and Repair

Question 1

Consider the process that a cell uses to replicate its double-stranded DNA before undergoing call division. Which statement describes the DNA in the resulting daughter cells?

Answer 1

The double helix in each daughter cell consists of one parent strand and one newly synthesized strand

Question 2

DNA mismatch repair typically corrects what percent of errors?

Answer 2

99%

Question 3

Which of the following best defines a mutation?

Answer 3

Permanent change in a DNA sequence

Question 4

When is homologous recombination, which can flawlessly repair double-strand DNA breaks, most likely to occur?

Answer 4

After the cell’s DNA has been replicated: duplicated chromosomes are still physically close to each other so the intact one can provide a template for the damaged chromosome

Question 5

Overview of DNA replication

Answer 5

Two strands of a DNA double-helix are pulled apart at replication origins, producing y-shaped replication forks. DNA polymerases at each form move away from replication origins, synthesizing new, complementary DNA strands on each parent strand

Question 6

DNA polymerase error rate

Answer 6

DNA plymerase makes one error in about every 10^7 nucleotides, in part because it proofreads its own mistakes as it goes

Question 7

Direction of DNA synthesis

Answer 7

Can only be done in the 5’ to 3’ direction, so there is a leading strand that is synthesized continuously, and a lagging strand that is back-stitched together, forming discontinuous strands that are later joined by DNA ligase

Question 8

How does the replication process get started?

Answer 8

DNA synthesis is primed by an RNA polymerase called primase, which makes short lengths of RNA primers that are then elongated by DNA polymerase. The primers are subsequently removed and replaced with DNA

Question 9

What happens to telomeres after replication?

Answer 9

They would get shortened with each replication, but an enzyme called telomerase replicates and lengthens the telomeres

Question 10

Once DNA is replicated, how do mistakes get noticed?

Answer 10

mismatch repair proteins scan the strand, increasing the accuracy from 1 mistake in every 10^7 nucleotides to 1 in every 10^9

Question 11

Homologous recombination

Answer 11

A way that double-strand breaks can be repaired flawlessly. An undamaged duplicate homologous chromosome is used to guide the repair.

It can also repair a broken replication fork

During meiosis, this results in an exchange of genetic material between the maternal and paternal homologs

Question 12

Nonhomologous end joining

Answer 12

An error prone mechanism for rapidly repairing double-strand breaks in DNA by rejoining the two broken ends. Often results in a loss of information at the site of repair.

Question 13

Cancer

Answer 13

disease caused by abnormal and uncontrolled cell proliferation, followed by invation and colonization of body sites normally reserved for other cells.

Successful repair mechanisms help protect against cancers

Question 14

DNA helicase

Answer 14

Enzyme that pries open the DNA double helix, using energy derived from ATP hydrolysis. Used to expose DNA single strands for DNA replication

Question 15

DNA ligase

Answer 15

Enzyme that seals nicks that arise in phosphodiester backbone of a DNA molecule.

Can also be used in the laboratory to join together two DNA fragments

Question 16

DNA polymerase

Answer 16

Enzyme that catalyzes the synthesis of a DNA molecule from a DNA template

Question 17

Mismatch repair

Answer 17

Mechamism for recognizing and correcting incorrectly pairs nucleotides

Question 18

mutation

Answer 18

a randomly produced, permanent change in the nucleotide sequence of DNA

Question 19

Okazaki fragment

Answer 19

Short length of DNA, including an RNA primer, that is produced on the lagging strand during DNA replication. The primer is removed, and the ends are joined together by DNA ligase to form a continuous strand.

Question 20

Primase

Answer 20

and RNA polymerase that uses DNA as a template to produce a short RNA fragment that serves as a primer for DNA synthesis

Question 21

proofreading

Answer 21

the process by which DNA polymerase corrects its own errors as it moves along DNA

There is a hypothesis that the ease of proofreading in one direction is why there is directionality in DNA replications.

Question 22

Replication origin

Answer 22

Nucleotide sequence at which DNA replication is initiated

Question 23

telomerase

Answer 23

Enzyme that elongates telomeres, synthesizing the repetitive nucleotide sequences found at the end of eukaryotic chromosomes

Cancer cells cannot grow unless they have telomerase, so many cancer cells will over express telomerase

Question 24

DNA replication basics

Answer 24

1) requires an origin site (tells the DNA where to start replicating)
2) requires a primer: a short strand of DNA or RNA to start binding the new strand to
3) requires a template: lets it know what to bind next
4) adds nucleotides in the 5’ to 3’ direction

Question 25

What happens at each origin of replication?

Answer 25

two replication forms move in opposite directions.

Question 26

What bonds form between the DNA molecules on the same strand?

Answer 26

phosphodiester bonds

Question 27

what is a nick?

Answer 27

a break in on backbone of a double-strand DNA helix

this is easier to repair than a break in both strands

Question 28

How is the lagging strand synthesized?

Answer 28

1) There is a previous RMA primer and a previous Okazaki fragment
2) new RNA primer is synthesized by primase
3) DNA polymerase adds nucleotides to 3he 3’ end of new RNA primer to synthesize the next okazaki fragment
4) the previous DNA primer is removed by nucleases and replaced with DNA by repair polymerase
5) the nick is sealed by DNA ligase

Question 29

What is the mechanism to remove knockout genes in bacteria?

Answer 29

takes advantage of the backstitching mechanism, but instead of an okazaki fragment, is stitches in the DNA that you want it do

a phage: a virus that infects bacteria, has a mechanism to do this.

Another application is getting bacteria to produce proteins for us

Question 30

Why would it be desirable to knockout a gene?

Answer 30

If a gene causes a disease, this could correct the disease.

It can also help create drought-resistant, flood-resistant food, etc

Research

Question 31

How do bacterial chromosome replicate?

Answer 31

They typically have only one origin of replication, but can still replicate very rapidly because they can start making the next copy before they finish the first

Question 32

DNA replication completion in eukaryotes (linear DNA)

Answer 32

the leading strand can replicate all the way to the end, but the lagging strand has no 3’ hydroxyl group to backstitch the last part, because the primer is an RNA strand that needs to be removed.

This would cause the end to shorten after each replication, but telomerase adds repetitive sequences to the end of the lagging strand

When mature cells have very long telomerase, it signals them to stop making telomerase, which causes the genomes to shorten.

Question 33

What is the winding problem in DNA replication?

Answer 33

splitting apart and unwinding strands in the middle of a very long molecule will cause the helix to get tighter and tighter, putting stress on it. topoisomerase makes a transient nick that allows the helix to rotate freely, relieving the pressure

Question 34

topoisomerase

Answer 34

the enzyme that makes a transient nick in DNA as it is being replicated, relieving the torsional stress of unwinding the strands and allowing it to rotate freely

Question 35

Strand-directed mismatch repair

Answer 35

MutS and MutL will recognize a mismatch, and will the look for a nick in the DNA, and remove the part between the mismatch and the nick to resynthesize. The incorrect strand is the new strand, which is most likely to be the one with the nick.

Question 36

What are the two major mechanisms that prevent errors in DNA replication?

Answer 36

proofreading and mismatch repair

Question 37

Cancer is caused by uncontrolled growth of cells. What are a few reasons that problems in DNA repair mechanisms can lead to cancer?

Answer 37

If the replication is not accurate, then mutations will arise. IF the mutations affect control mechanisms, uncontrolled growth can start

Question 38

What repairs happen after the replication process?

Answer 38

1) basic excision repair
2) nucleotide excision repair

Question 39

What are the applications of nonhomologous and homologous end recombination?

Answer 39

They can introduce mutations into the genome.

Homologous recombination helps inset a desired gene into a genome (as long as you can introduce the gene into the cell).

Non homologous end joining deults in deletions of base pairs at the site of the break

Question 40

Why is it harder to repair DNA if replication were to proceed from 3’ to 5’?

Answer 40

When the incorrect nucleotide is removed during proofreading, further polymerization is blocked because there is no triphosphate group to provide energy for polymerization

Question 41

What is an HIV virus?

Answer 41

a retrovirus that carries RNA which, with the help of reverse transcriptase in the host, is transcribed into DNA and integrated into the host genome to reproduce itself

Question 42

Do all organisms have double-stranded DNA for their genome?

Answer 42

No, viruses can have: single stranded DNA, single-stranded RNA, double-stranded DNA, double-stranded RNA, single-stranded circular DNA, double-stranded circular DNA, double-stranded DNA with each end covalently sealed, and double-stranded DNA with covalently links terminal proteins

Question 43

What other ways can DNA be mutated, other than during replication?

Answer 43

1) Depurination: thermal collisions with other molecules can remove a purine base from a nuclotide.

2) Demination: A common reaction with water molecules causes the loss of an amino group

3) Thymine dimer: UV radiation promotes covalent linkages between adjacent pyrimidine