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SF:Biochemistry > DNA Replication > Flashcards

DNA Replication Flashcards

1
Q

Describe the three steps of DNA replication.

A
  1. Double-stranded DNA is separated.
  2. DNA that is complementary to the unwound/separated DNA is made.
  3. RNA primers are replaced with DNA by a special DNA polymerase.
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2
Q

Define the origin of replication.

A

The origin of replication is a little bubble rich in AT bonds where the DNA separates to create two replication forks.

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3
Q

How does the unzipping of DNA progress during replication?

A

The unzipping progresses in both directions away from the origin of replication, allowing replication to occur in both directions and reducing the time needed for the process.

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4
Q

What enzymes are involved in separating DNA strands?

A

Topoisomerase unwinds the DNA, helicase unzips the DNA by breaking hydrogen bonds, and single-strand binding proteins (SSB) stabilize the unwound DNA by binding to it.

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5
Q

Explain the role of single-strand binding proteins (SSB) in DNA replication.

A

SSBs are responsible for keeping DNA unwound after helicase and stabilize single-stranded DNA by binding to it.

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6
Q

Identify the enzyme that unwinds DNA during replication.

A

Topoisomerase is the enzyme that unwinds DNA.

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7
Q

What is the function of helicase in DNA replication?

A

Helicase unzips the DNA by breaking the hydrogen bonds between the strands.

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8
Q

Describe the stability of single-stranded DNA.

A

Single-stranded DNA is unstable and prone to degradation by DNA nucleases.

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9
Q

How does DNA polymerase synthesize new DNA?

which direction?

A

DNA polymerase synthesizes new DNA in the 5’ to 3’ direction, requiring a template and a primer.

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10
Q

Explain the process of creating a new DNA strand from the Leading Strand.

A

An RNA primer is placed on the leading strand by DNA Primase, and DNA Polymerase III expands the strand in the 5’ to 3’ direction.

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11
Q

What is the direction of the leading strand during DNA replication?

A

The leading strand goes in the 3’ to 5’ direction.

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12
Q

How is a new DNA strand created from the Lagging strand?

A

DNA Primase places an RNA primer near the replication fork, and DNA Polymerase III expands the strand in the 5’ to 3’ direction, creating Okazaki fragments.

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13
Q

What are Okazaki fragments?

A

Okazaki fragments are short segments of DNA synthesized on the lagging strand during DNA replication.

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14
Q

How are RNA primers replaced during DNA replication?

A

RNA primers are removed and replaced by DNA through the activity of DNA polymerase I.

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15
Q

What role does DNA ligase play in DNA replication?

A

DNA ligase seals the nicks that remain after the RNA primers are replaced with DNA.

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16
Q

Define specific coupling in DNA replication.

A

Specific coupling ensures that nucleotides are incorporated with correct base-pairing along the separated strands (A with T, G with C).

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17
Q

Why is DNA replication considered semi-conservative?

A

DNA replication is considered semi-conservative because it produces two double-stranded DNA molecules, each containing one original strand and one newly synthesized strand.

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18
Q

List the enzymes involved in DNA replication.

A

The enzymes involved in DNA replication include Helicase and Primase, among others.

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19
Q

Describe the role of DNA Helicase in DNA replication.

A

DNA Helicase uses hydrolysis of ATP to unwind the DNA helix at the replication fork, allowing the resulting single strands to be copied.

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20
Q

Define the function of Topoisomerases in DNA replication.

A

Topoisomerases relax the super-coiling that results from unwinding the DNA helix.

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21
Q

How does Primase contribute to DNA replication?

A

Primase synthesizes RNA primers that act as templates for future Okazaki fragments to build on.

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22
Q

Explain the function of Single-stranded binding proteins (SSBPs).

A

Single-stranded binding proteins bind to the separated strands of DNA to prevent them from re-annealing.

23
Q

What is the role of DNA polymerase I in DNA replication?

A

DNA polymerase I synthesizes nucleotides onto primers on the lagging strand, forming Okazaki fragments, and removes primers from the fragments to replace the gap with relevant nucleotides.

24
Q

Describe the function of DNA polymerase III during DNA replication.

A

DNA polymerase III follows the replication fork, adding new nucleotides in the 5′ to 3′ direction, while proofreading and removing incorrect nucleotides.

25
Q

How does proofreading work? Explain the 3’-5’ exonuclease.

A

Some DNA polymerases (III) can proofread DNA as it adds nucleotides to make sure it added the right one. It just checks the width of the DNA and if there’s a bulge, it cuts out the mistaken nucleotide.

26
Q

Some DN polymerase have 5’->3’ exonucleases too. What do they do?

A

They take out RNA primers and replace them with DNA. Ligase later glues these sections together.

27
Q

How does DNA ligase assist in DNA replication?

A

DNA ligase helps to anneal strands by joining Okazaki fragments together.

28
Q

Describe the role of Telomerase in DNA structure.

A

Telomerase lengthens telomeres of linear eukaryotic DNA.

29
Q

How many origins of replication do prokaryotes typically have?

A

Prokaryotes usually have a single origin of replication for their single, circular DNA.

30
Q

How many origins of replication are found in eukaryotes?

A

Eukaryotes have multiple origins of replication across their numerous linear chromosomes.

31
Q

Explain the End Replication Problem.

A

The End Replication Problem occurs because Primase lays down primers to help replicate DNA, leading to regions near the 3’ end of the original DNA strand that never get replicated, resulting in the gradual shortening of DNA.

32
Q

Describe the role of telomeres in DNA replication.

A

Telomeres are regions of repetitive DNA segments at the end of the DNA that help solve the End Replication Problem by providing a buffer zone, as the end of DNA that isn’t replicated isn’t useful.

33
Q

How does telomerase contribute to DNA replication?

A

Telomerase is an enzyme that can expand telomeres, thereby addressing the End Replication Problem by maintaining the length of telomeres during DNA replication.

34
Q

Define the End Replication Problem in the context of DNA.

A

The End Replication Problem refers to the difficulty in fully replicating the ends of linear DNA molecules, which can lead to the loss of important genetic information during cell division.

35
Q

What are the two solutions the body has to address the End Replication Problem?

A

The body’s first solution is the presence of telomeres, and the second solution is the enzyme telomerase, which can expand telomeres.

36
Q

Describe the Hayflick limit.

A

The Hayflick limit refers to the number of times a normal somatic human cell can divide before cell division stops, due to the shortening of telomeres.

37
Q

How do telomeres affect DNA replication?

A

Telomeres protect and stabilize the coding regions of DNA, but as DNA replication occurs, telomeres shorten, eventually leading to a limit on cell division.

38
Q

Define telomeres and their function.

A

Telomeres are repetitive nucleotide sequences at the ends of chromosomes that protect and stabilize the coding regions of DNA during replication.

39
Q

What happens to cells when they reach the Hayflick limit?

A

When cells reach the Hayflick limit, they stop replicating due to the telomeres reaching their shortest allowable length.

40
Q

Explain the relationship between DNA replication and telomere length.

A

As DNA replication occurs multiple times, telomeres shorten, which eventually limits the number of times a cell can divide.

41
Q

DNA Damage: Thymine Dimers

A

UV light can cause intrastrand thymine dimers.
Fix: Nucleotide Excison Repair

42
Q

DNA Damage: Xeroderma Pigmentosa

A

Lack NER pathway so can’t fix many DNA mutations. Super sensitive to UV light
Skin Cancer
Die early

43
Q

DNA Damage: DNA Deamination

A

Cytosine gets deaminated into Uracil

44
Q

DNA Damage: Alkylation

A

This is the most common form of DNA damage and it happens on its own.

45
Q

DNA Damage: DNA Intercolators

A

Inserts into DNA double hexid and causes frameshift mutations

46
Q

DNA Repair: Nucleotide Excision Repair

A

Just measures diameter of helix and cuts it out a chunk and replaces it

46
Q

DNA Repair: Base Excision Repair

A

Super Specific
Uses glycosylase, AP endonucleases, and DNA pol 5’–>3’ exonuclease + others

47
Q

DNA Repair: Mismatch Repair

A

Some proteins are able to recognize the new (not yet methylated) strand and check for mistakes. MSH and MutL recognize the mutation and methylation spot.

Issues with this lead to HNPCC (colon cancer)

48
Q

Homologous Recombination

A

Cross over between sister chromatids
Double Strand Break Repair (DSBR)
Synthesis dependent single strand annealing

49
Q

Why are BRCA1 and BRCA2 mutations relevant?

A

These genes are involved in homologous recombination and DSBR.
Leads to different cancers (breast, ovarian, pancreatic)

50
Q

Why is Fanconi Anemia relevant?

A

Due to mutations in any of 17 genes that are involved in homologous recombination

51
Q

Describe the RecQ helicase disorders

A

Premature aging and cancer
Bloom: excessive HR
Werner: no DSBR

52
Q

Burkitt’s Lymphoma

A

Recombination causes the promotor of a sequence in B cells to line up with a cell growth gene (Myc)

SF:Biochemistry (14 decks)

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