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Genes > DNA Replication and Transfer > Flashcards

DNA Replication and Transfer Flashcards

1
Q

Define replicon

A

Unit of genome where DNA is replicated = each containing an origin for replication initiation

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2
Q

Define origin

A

Sequence of DNA where replication is initiated

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3
Q

Define plasmid

A

Autonomous circular DNA that makes up a separate replicon

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4
Q

Define single-copy replication

A

Replicates once every time bacterial chromosome replicates

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5
Q

Define multi-copy replication

A

Greater number of copies per individual bacterial cell

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6
Q

Describe the replication fork

A

Replication fork = initiated at origin and moves along DNA

Bidirection

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7
Q

When is replication bidirectional?

A

When 1 origin creates 2 replication forks that move in opposite directions

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8
Q

Describe a bacterial genome

A

Usually a single circular replicon
Replicate bidirectionally from single origin

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9
Q

How do replica chromosomes split into daughter cells?

A

Decatenated

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10
Q

What does oriC contain?

A

11 palendromic GATC reapeats
Methylated on ADENINE on both strands

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11
Q

What enzyme methylates the adenine in palindromic oriC?

A

Dam methylase

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12
Q

What type of DNA is produced from replication?

A

Hemimethylated DNA = cannot initiate replication

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13
Q

What does the origin need to initiate replication?

A

Only fully methylated origins can initiate replication

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14
Q

How long before new origin is remethylated?

A

13 minute delay until methylated by Dam methylase

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15
Q

What is required for delaying rereplication?

A

SeqA = binds to hemimethylated DNA
Prevents origin being remethylated

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16
Q

For initiation to occur what is needed?

A

There must be membrane or cell wall synthesis

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17
Q

What is the effect of penicillin?

A

Inhibits cell wall synthesis = blocking replication initiation

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18
Q

What is the bacteria licensing factor?

A

DnaA = inactivated or destroyed after one round of replication

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19
Q

What does DnaA need to perform its role?

A

ATP

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20
Q

What is the role of DnaA-ATP?

A

Melts DNA by binding short repeated sequence that is fully methylated

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21
Q

What is the role of DnaB?

A

ATP hydrolysis-dependent 5’to3’ helicase

22
Q

What is the role of DnaC?

A

Chaperone = represses the helicase activity of DnaB

23
Q

What is the DnaB/C complex called and where does it bind?

A

Prepriming complex that binds origin

Helicase is inactive until DnaC leaves

24
Q

What is the role of DnaG?

A

Primase = binds to helicase complex

25
Q

What does a primase do?

A

Synthesizes an RNA chain
Providing priming end for DNA replication

26
Q

What forms the replication fork?

A

Hexamer of DnaB = helicase

27
Q

What is gyrase and where does it bind?

A

Type II topoisomerase
Binds ahead of replication fork = relieves strain placed in the double helix as it unravels

28
Q

How does DNAp carry out proofreading?

A

3’ to 5’ exonuclease that excises incorrectly paired bases

29
Q

What is processitivity?

A

Tendancy to remain on a single template rather than dissociate and re-associate

30
Q

What has a 5’ to 3’ exonuclease?

A

DNAp I

31
Q

What does DNAp need to initiate DNA synthesis?

A

RNA primer = synthesized by primase

32
Q

What sub-complexes does DNAp holoenzyme have?

A

Each monomeric unit has
Catalytic core, dimerization subunit and processivity component

33
Q

What is one catalytic core associated with?

A

One core = associated with one template strand

34
Q

What is the role of the clamp loader?

A

Places processivity subunit on DNA
These two subunits for a beta clamp around DNA

35
Q

What is the role of dimerizing subunit t?

A

Links the two catalytic cores together

36
Q

What happens to the clamp on the leading and lagging strand?

A

Leading strans is processive because its clamp keeps it on DNA

Clamp on lagging strand dissociates at end of each Okazaki fragment and reassembles for next fragment

37
Q

How are each Okazaki fragments initiated?

A

Helicase DnaB is responsible for interacting with primase DnaG to initiate

38
Q

What is the role of DNAp I?

A

Removes RNA primer = using 5’ to 3’ exonuclease
Replaces it with DNA

39
Q

What happens when a replication fork reaches damaged DNA and how can bacteria avoid death?

A

Replication fork stalls and may collapse

Lesion bypass or homologous recombination

40
Q

How does lesion bypass work?

A

Error-prone DNAp IV = replicates past the lesion allowing replication to continue

This may produce mutations in the sequence

41
Q

What are the 3 gene transfer processes in prok?

A

Transformation = naked DNA
Conjugation = bacteria-mediated
Transduction = phage-mediated

42
Q

What is an epsiome?

A

Segment of DNA = can exist and replicate either autonomously in the cytoplasm or as part of chromosome

43
Q

What are two methods of gene transfer via transformation?

A

CaCl2 then heatshock
Electroporation

44
Q

What is conjugation?

A

Process where genetic material is transferred by F plasmid
F = fertility factor

45
Q

What is the free F factor?

A

Replicon maintained at the level of 1 plasmid
It can be integrated into bacterial chromosome

46
Q

What are tra genes and where are they located?

A

Encoding transfer function = pilus synthesis and assembly, cell pairing nicking at oriT
Located in an operon

47
Q

What is the mechanism of conjugation?

A

Rolling circle mechanism
Nick at origin by TraY/I
TraY/I unwinds DNA
Elongation of growing strand displaces old strand
After one revolution displaced strand reaches unit length
TraI bound single strand enters recipient

48
Q

What strains are made when F integrates into bacterial chromosome?

A

High-frequency of recombination strains

Plasmid must recombine with bacterial chromosome to become a Hfr cell

49
Q

What happens in Hfr x F- mating?

A

F- cells almost never acquire F+ phenotype
Because only the first part of F is transferred

50
Q

What is an exconjugant?

A

Each of the cells that separates after conjugation has taken place

51
Q

What are prototrophs vs auzotrophs?

A

Prototrophs
Wild-type strain = has minimal requirement for nutrient supplements

Auxotrophs
Mutant strain = lost ability to synthesize nutrients (amino acids)

52
Q
A

Genes (6 decks)

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