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Molecular Biology > Ch 11-DNA Replication > Flashcards

Ch 11-DNA Replication Flashcards

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1
Q

Semiconservative

A

Each daughter complex conserves one strand of parental DNA, and the other strand is totally new

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2
Q

Origin of replication

A

The nucleotide sequence or site in DNA replication is initiated

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3
Q

Replication fork

A

The point where the parental duplex separates and the daughter duplexes form, the site of new DNA synthesis

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4
Q

DNA polymerase

A

Enzyme that synthesis DNA, only goes 5’->3’ (when extending dna)

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5
Q

Semidiscontinuous

A

Only one daughter strand is synthesized continuously, the other is synthesized in a series of fragments(Okazaki) that way it can also be done 5’->3’ despite the fork being the opposite direction

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6
Q

Leading strand

A

Continuous synthesizing of daughter strand (same direction as replication fork 5’->3’

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7
Q

Lagging strand

A

Discontinuous synthesizing of daughter strand (runs 3’->5’) but it is synthesized in fragments so it can be done in the same direction as the fork (5’->3’)

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8
Q

Requirements for DNA pol:

A

1) has a template strand to guide it
2) primer strand
- complementary to template
- contains free 3’OH

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9
Q

Insertion site

A

A site within active site of DNA pol where the template nucleotide & incoming dNTPs are positioned

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10
Q

Post insertion site

A

A site within active site of DNA pol where the primer 3’terminal base pair is positioned

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11
Q

Nucleases

A

Enzymes that degrade DNA

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12
Q

Exonucleases

A

Cut DNA from the ends

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13
Q

Endonucleases

A

Cut DNA at internal positions

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14
Q

DNA has 2 different endonucleas activities:

A

1) degrades DNA 3’-5’

2) degrades DNA 5’-3’

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15
Q

Proofreading

A

Exonuclease (3’-5’) removes incorrect dNMP (mismatched nucleotides) and improved error in DNA pol

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16
Q

Which DNA pol has 5’-3’ exonuclease activity?

A

Pol I

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17
Q

What is a major source of error in DNA pol?

A

Including dNTP tautmers

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18
Q

Nick translation

A

A concerted process of 5’-3’ excision and DNA polymerization that shifts a discontinuity in the phosphodiester backbone between 3’ hydroxyl of one nucleotide and the 5’ phosphate of the adjacent nucleotide along a DNA strand

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19
Q

Distributive synthesis

A

The enzymatic synthesis of a biological polymer in which the enzyme dissociates from the substrate after the addition of each monomeric unit

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20
Q

Processive synthesis

A

The enzymatic synthesis of a biological polymer in which the enzyme adds multiple subunits w/o dissociating from the substrate

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21
Q

Processivity #

A

Avg # of nucleotides incorporated before the enzyme dissociates from DNA

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22
Q

Pol III holoenzyme

A

Replicated both leading and lagging strands

-has 3 pol cores: 2 beta sliding clams and clamp loader

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23
Q

Beta sliding clamp

A

Ring shaped homodimer encircles and sides along duplex DNA of the pol III core it is attached to, greatly increases processivity if DNA synthesis

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24
Q

Clamp loader

A

Assembled beta clamp onto DNA

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25
Q

DNA helicase

A

Unwind duplex

-can act as replication fork (ring shaped hexamers)

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26
Q

Topoisomerases

A

Enzyme that cuts one or both strands of dna to unwind it then releases it
-used in supercoils

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27
Q

Primase

A

Synthesis RNA primers

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28
Q

Do DNA pol in eukaryotes have proofreading?

A

No because they do not have 3’-5’ exonucleases, so they make more mistakes then in bacteria

29
Q

Replicon

A

Total length of DNA replicated from one origin

-in bacteria replicon is entire chromosome

30
Q

Initator protein

A

Binds specific sites at the origin, is an example of a protein encoded by a slow-stop gene

31
Q

Open complex

A

A complex assembled on E.coli origin of replication, oriC, at an early stage of replication initiation

32
Q

Dam methylated (DNA adenine methyltransferase)

A

Recognizes both strands of palindromic sequence GATC and methylates the N^6 position of A residues on both strands of the GATC site

33
Q

SeqA

A

Binds hemimethylated DNA and prevents DnaA from re-binding the replicated origin and initiating another replication

34
Q

Origin recognition complex (ORC)

A

Eukaryotic initiator

-ATP is required for ORC binding to the origin

35
Q

Ter sites

A

Termination sites in eukaryotes

36
Q

End replication problem

A

The inability of DNA pol to o replicate the final segment of DNA at the 3’OH end of the lagging strand where there is no primer to provide a free 3’OH group

37
Q

Does end replication problem happen in circular DNA?

A

No because it has no ends

38
Q

Telomeres

A

Ends of the linear eukaryotic chromosomes
-contain repeats
Ex: human DNA has TTAGGG repeated in the telomeres on our chromosomes

39
Q

Telomerase reverse transcriptase (TERT)

A

The protein components of telomerase

40
Q

Telomerase RNA (TR)

A

RNA component of telomerase

41
Q

T-loop

A

Telomere Koop. A looped structure in mammalian telomeres, in which the single strand 3’ end of the chromosome folds back and hybridized to a duplex portion of the telomere

42
Q

Why does the cell replicate DNA?

A

DNA is replicated so that the daughter cell can receive an identical copy of the genome

  • stores genomic info is handed down to the next generation. It is central to life and evolution, without it there would be no transfer of info across generations.
  • initiation is key because once replication begins it does not stop until the entire DNA molecule is successfully duplicated
43
Q

What is the template of replication?

A

DNA

44
Q

What is the result of Replication?

A

DNA

45
Q

How much of the chromosome is replicated in one round?

A

One round of DNA replication produces two chromatids in each duplicated chromosome

-single round creates four chromatids for each type of chromosome

46
Q

What is the origin of replication and how does it differ between prokaryotes and eukaryotes?

A

The initiation site of replication. Eukaryotes have many and prokaryotes only have one.

47
Q

What does it mean that replication occurs bidirectionally? What would be the benefit of bidirectional replication?

A

Replicating DNA in two directions at the same time resulting in a leading strand( continuous, replication occurs quicker), and a lagging strand(discontinuous, replication occurs slower)

48
Q

What does it mean that replication is semidiscontinuous?

A

One daughter strand is synthesized continuously(leading) while the other is madre as a series of discontinuous fragments(lagging, Okazaki fragments). One strand moves in the same direction as the replication fork(leading, 5’-3’) and the other moves in the opposite direction (lagging, 3’-5’) but is synthesized from the 5’-3’ direction

49
Q

DNA is synthesized in the 5’-3’ direction, why does this result in both a lagging and leading strand?

A

Because the leading strand is synthesized in the same direction as the replication fork whereas the lagging strand is synthesized in the opposite direction

50
Q

What is an Okazaki fragment?

A

Small fragments in the lagging strand, it is primed at 5’ end by a short RNA and joined together by ligases after the replication fork has passed.

51
Q

How many active sites does DNA POL have?

A

One

-it interacts with all 4 dNTPs

52
Q

Why does the use of dNTP as opposed to a dNDP make the process of nucleotide synthesis virtually unable to be reversed?

A

In dNDP, the reverse reaction could easily be initiated because Pi, the molecule that would initiate the reverse reaction is abundant in the cell. DNTP would ensure no reverse reaction because PPi is eliminated by pyrophosphatase.

53
Q

Once the dNMP is incorporated, what other interactions stabilize it?

A

Non-covalent base pairing and base-stacking interactions

54
Q

What is the result of nucleotide removal?

A

When an incorrect dNMP is incorporated, the 3’-5’ exonuclease removes the mismatched nucleotide, giving the polymerase a second chance to incorporate the correct one

  • only pol I has this
  • not a reverse reaction
55
Q

Proofreading:

A

When a pol mispairs a base, the pol repositions the mispaired 3’ terminus into the 3’-5’ exonuclease site. The exonuclease hydrolyzes the mispaired base and the 3’ terminus repositions back to the pol site. The pol corrects the nucleotide base

56
Q

How often does a mutation occur that can be contributed to replication?

A

Only a single error is acquired in every 100 to 1,000 new cells

57
Q

Function of Pol I:

A

-repairs any damage with DNA, it it also serves to connect Okazaki fragments by deleting RNA primers or DNA lesions and replacing the strand with DNA(exonuclease activity)

-organized into 3 domains:
Proofreading exonuclease (3’-5’)

At a nick, the gap between lagging fragments and pol I degrade the RNA primer in the 5’-3’ direction, releasing rNMPs and extends 3’ terminus with dNTPs in the same direction. DNA ligase can then seal the fragments

58
Q

E.coli has 5 DNA pols. what are the major processes they are involved in and which are 2 sloppy?

A

Pol I: Okazaki fragment processing and DNA repair
Pol II: translesion synthesis (involved in DNA repair)
Pol III: chromosome replication (replicase)
Pol IV: translesion synthesis
Pol IV: translesion synthesis

Sloppy pols: IV and V, they lack 3’-5’ proofreading exonuclease and incorporate the wrong nucleotides

59
Q

Difference between open and closed form of DNA pol:

A

In open form, dNTP binds to the fingers domain in the closed form the fingers domain undergoes a 40 degree rotation that moves the dNTP into base-pairing position with the template and forms an active site cavity that fits the shape of a correct Watson crock base pair

60
Q

What is the significance of a mismatch resulting in the polymerase stalking?

A

Stalling of catylysis by an incorrectly incorporated dNTP buys time for the mismatched primer strand terminus to relocate to the 3’-5’ exonuclease domain for proofreading

-correct base pairs fit in active site, incorrect don’t

61
Q

What is the replisome?

A

Pol III holoenzyme + the helicase + primase

62
Q

What is the function of dna pol alpha, beta, epsilon?

A

Alpha- primase activity

Beta and epsilon- responsible for genome replication (epsilon lagging strand, beta leading strand)

63
Q

What does the MCM complex do?

A

Activated by cycling-dependent kinase

-primes chromatin for dna replication by binding origins of dna replication during the late M phase to early G1 phase of the cell cycle

64
Q

What are the role of cyclin-dependent kinases in the initiation of replication in eukaryotes?

A
  • phosphorylates certain target proteins, are central to the separation of cell phases
  • inactivated the origin of recognition complex by phosphorylating one of its subunits
65
Q

What is the function of the Ter sites and Tus proteins in replication termination? Which forks do they stop?

A

Tus binds tightly to the Ter site and blocks the advance of the replication fork. G stopping DNAB helicase

-replication forks are stopped when approaching the Ter-tus complex from one direction (nonpermissive direction)

66
Q

Is telomerase active in most somatic cells?

A

Most somatic cells have little to no telomerase

67
Q

Function of shelterin proteins:

A

Protects telomeres against chromosome joining and regulates telomere length

-TRF1 and TRF2 (telomere repeat factors 1 and 2)

68
Q

Is it believed that active telomerase in cells is healthy?

A

No

Molecular Biology (4 decks)

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