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Cell Biology > Ch 6: DNA replication and Repair > Flashcards

Ch 6: DNA replication and Repair Flashcards

1
Q

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?

A

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

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2
Q

DNA mismatch repair typically corrects what percent of errors?

A

99%

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3
Q

Which of the following best defines a mutation?

A

Permanent change in a DNA sequence

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4
Q

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

A

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

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5
Q

Overview of DNA replication

A

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

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6
Q

DNA polymerase error rate

A

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

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7
Q

Direction of DNA synthesis

A

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

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8
Q

How does the replication process get started?

A

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

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9
Q

What happens to telomeres after replication?

A

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

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10
Q

Once DNA is replicated, how do mistakes get noticed?

A

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

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11
Q

Homologous recombination

A

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

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12
Q

Nonhomologous end joining

A

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.

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13
Q

Cancer

A

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

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14
Q

DNA helicase

A

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

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15
Q

DNA ligase

A

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

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16
Q

DNA polymerase

A

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

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17
Q

Mismatch repair

A

Mechamism for recognizing and correcting incorrectly pairs nucleotides

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18
Q

mutation

A

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

19
Q

Okazaki fragment

A

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.

20
Q

Primase

A

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

21
Q

proofreading

A

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.

22
Q

Replication origin

A

Nucleotide sequence at which DNA replication is initiated

23
Q

telomerase

A

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

24
Q

DNA replication basics

A

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

25
Q

What happens at each origin of replication?

A

two replication forms move in opposite directions.

26
Q

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

A

phosphodiester bonds

27
Q

what is a nick?

A

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

this is easier to repair than a break in both strands

28
Q

How is the lagging strand synthesized?

A

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

29
Q

What is the mechanism to remove knockout genes in bacteria?

A

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

30
Q

Why would it be desirable to knockout a gene?

A

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

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

Research

31
Q

How do bacterial chromosome replicate?

A

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

32
Q

DNA replication completion in eukaryotes (linear DNA)

A

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.

33
Q

What is the winding problem in DNA replication?

A

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

34
Q

topoisomerase

A

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

35
Q

Strand-directed mismatch repair

A

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.

36
Q

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

A

proofreading and mismatch repair

37
Q

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

A

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

38
Q

What repairs happen after the replication process?

A

1) basic excision repair
2) nucleotide excision repair

39
Q

What are the applications of nonhomologous and homologous end recombination?

A

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

40
Q

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

A

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

41
Q

What is an HIV virus?

A

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

42
Q

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

A

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

43
Q

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

A

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

Cell Biology (24 decks)

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