Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

Applied Genetics > Plasmid structure and replication > Flashcards

Plasmid structure and replication Flashcards

You may prefer our related Brainscape-certified flashcards:
Biology 101 flashcards
1
Q

how do bacterial plasmids form

A

self replicating

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

where is bacterial plasmids

A

Extrachromosomal not part of genomal material

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

are plasmids needed for bacteria survival

A

Dispensable to cells (in general bacteria can survive without plasmids)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

why do some bacteria have plasmids

A

Carry functional genes – selective advantage

in some environments

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

what are the forms of plasmids

A

ds circular DNA (CCC, covalently closed circular)
ds linear DNA (Streptomyces)
ss circular DNA (Myxococcus)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

what is the GC content % like in bacterial plasmid compared to host

A

% GC may be different to host (acquired not evolved)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

what is cryptic bacterial plasmid

A

no known function, do not change the phenotype of the host cell

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

what is the phenotypic bacterial plasmid

A

gives the cell an additional property e.g antibiotic-resistance

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

what are phenotypic plasmids

A

Lots of genes held on plasmids that are not needed by the cell all of the time

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

what is catabolic gene - bacterial plasmid

A

using energy sources e.g. toulene degredation
Catabolic genes “break down” something. E.g. toluene - a colourless liquid hydrocarbon present in coal tar and petroleum and used as a solvent and in organic synthesis – harmful to animals/humans

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

what is antibiotic resistance genes - bacterial plasmid

A

fighting off competitors

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

what is virulence genes - bacterial plasmid

A

accessing new nutrient sources

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

how can plasmids be moved

A

Conjugation, Mobilisation
Transformation
Transduction

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

what is bacterial movement important for

A

bacterial evolution

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

how can plasmids be exchanged

A

Plasmids can be exchanged between cells to move these traits between cells

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

which cells can plasmids pass into

A

Plasmids can be exchanged between cells, not just cells of the same type, they can pass bacteria to different types of bacteria – move traits between cells

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

what is the physical structure of plasmids

A

Most commonly used plasmids are covalently closed circular (CCC) molecules
all bases are joined by phosphodiester bonds
B-form DNA there are 10.4 bp per turn of the molecule
This is termed “Relaxed” DNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

what is DNA like inside cells

A

supercoiled
tightly wound/twisted DNA with compact structure
Compact so it fits in the cell
Extent of supercoiling also helps regulate gene expression

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

what causes relaxed DNA to untwist

A

DNA gyrase

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

what causes supercoiled DNA to twist

A

DNA topoisomerases

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

what does DNA gyrase do

A

essential bacterial enzyme that catalyzes the ATP-dependent negative super-coiling of double-stranded closed-circular DNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

how is DNA supercoiling regulated

A

enzymes DNA gyrase and topoisomerase can introduce fewer or more twists into DNA structure

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

what is positive supercoiling

A

Positive supercoiling is a force on DNA in right hand direction, same direction of DNA double helix

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

what does supercoiling cause

A

causes DNA to form a more compact structure

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
Q

what does enzyme DNA gyrase or topoisomerase II do

A

enzyme DNA gyrase or topoisomerase II functions to add negative supercoils to bacterial DNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
26
Q

what does DNA gyrase bind to in supercoiling, effect

A

DNA gyrase binds to circular, supercoiled DNA molecule

alleviates one positive supercoil. Gyrase first introduces a double-stranded break in DNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
27
Q

what happens when segment of DNA once broken in DNA supercoiling

A

segment of DNA passes through break to opposite side of gyrase protein
movement of DNA needs ATP hydrolysis by gyrase, and introduces a negative supercoil into DNA molecule

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
28
Q

how is DNA gyrase released

A

break in strands repaired, gyrase is released from DNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
29
Q

what effect does DNA gyrase do

A

DNA molecule with one positive supercoil now has one negative supercoil

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
30
Q

how does plasmid DNA separate from chromosomal DNA

A

supercoiling of plasmid DNA allows us to separate it from chromosomal DNA by physical methods
e.g. CsCl (Cesium Chloride density gradient centrifugation) density gradient

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
31
Q

what happens to chromosomal DNA during cell lysis

A

Chromosomal dna is usually broken into fragments during cell lysis, but plasmids are usually small enough to be isolated intact in supercoiled form

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
32
Q

what is CsCl

A

Cesium Chloride density gradient centrifugation

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
33
Q

how do plasmids move in agrose gel

A

On agarose gels, supercoiled DNA runs faster than relaxed (or open circular) DNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
34
Q

why does CCC DNA look smaller than relaxed DNA

A

Compact structure of CCC DNA makes it appear smaller than relaxed DNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
35
Q

how do we know if DNA was cut from supercoiled

A

If try to cut DNA and doesn’t work will stay supercoiled and will therefore migrate differently on the gel to one that was cut

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
36
Q

what is a replicon

A

segment of DNA to be replicated and the proteins needed in the process. Each replicon contains an origin of replication (oriV)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
37
Q

what is replicon responsible for

A

copy number
incompatibility
host range

38
Q

what is oriV

A

plasmid origin of replication

39
Q

what does plasmid replication require

A

some plasmid encoded genes and some chromosomally encoded genes

40
Q

what is copy number in bacterial plasmids

A

how many copies of a plasmid there are in the cell

41
Q

what is incompatibility in bacterial plasmids

A

whether certain plasmids can live together, if they’re compatible

42
Q

what is host range in bacterial plasmids

A

which host cells can this plasmid live in, can survive in all, need certain features in host cell, some plasmids can be recognised by more hosts than others

43
Q

what are the basic features of plasmids

A

phenotypic genes
cryptic genes
oriV

44
Q

what are phenotypic genes

A

can give cell selective advantage

45
Q

what are cryptic genes

A

no phenotype can be seen

46
Q

what is oriV

A

origin of replication, allows the host cell to copy the plasmid DNA

47
Q

what type of replication is DNA

A

semiconservative – half (semi) of the original DNA molecule is conserved during replication

48
Q

what are the types of semiconservative replication

A

theta form

rolling circle replication

49
Q

what is theta form replication

A

Used for replicating the bacterial chromosome and many plasmids

50
Q

what is rolling circle replication (RCR)

A

Used to replicate some plasmids, bacteriophage genomes, and some circular RNA genomes of viroids

51
Q

what happens in theta form replication

A

Unwinding of DNA
DNA helicase remove supercoiling = single stranded DNA
End up with a bubble, replication fork(s)
Forms two double stranded products

52
Q

what is bidirectional

A

If have two replication forks

53
Q

what is unidirectional

A

If have one replication fork

54
Q

which replication is fastest

A

Is quicker to copy if have two replication forks

bidirectional

55
Q

what does primase do

A

makes each RNA primer

56
Q

what happens in bidirectional DNA replication initiation

A

Form a bubble
Proteins that bind to ssDNA
When unwound by DNA gyrase, bubble have two pieces of ssDNA, want to stabilise and protect the ssDNA
Primase comes in, the primers added on both sides and DNA polymerase can extend them to form new strands
Leading strand 5’ to 3’ direction
Lagging 3’ to 5’ so has to make it backwards in fragments then they are joined

57
Q

what are the key features of theta replication

A

Requires a circular DNA template
Can be uni- or bi-directional
Produces 2 circular DNA molecules
Requires an RNA primer (gets replication started)

58
Q

how is the bacterial chromosome replicated in theta replication

A

bacterial chromosome is replicated similarly to plasmid DNA, but they are replicated independently and regulated differently

59
Q

what molecules are needed in plasmid ColE1 replication

A

RNAII
Rnase H
RNAI
Rop protein

60
Q

what does RNAII molecule do in plasmid ColE1 replication

A

processed to form primer for DNA synthesis

61
Q

what does Rnase H do in plasmid ColE1

A

cleaves 3’ end of RNAII molecule in region complementary to oriV sequence
(Rnase H is a cellular enzyme that cleaves RNA paired with DNA)

62
Q

what does RNAI do in plasmid ColE1 replication

A

can pair with RNAII (antisense RNA)

63
Q

what does Rop do in plasmid ColE1 replication

A

protein stabilises RNAI/RNAII hybrid, thereby preventing cleavage/further replication when Rop is at high levels

64
Q

what happens in plasmid ColE1 replication after cell division

A

concentration of Rop per cell decreases (cytoplasmic content shared between the 2 cells)

65
Q

what effect does low Rop have in plasmid ColE1 replication

A

allows plasmid replication to initiate/start again

66
Q

what effect does an increase in plasmid ColE1 replication

A

Rop increases again

plasmid replication stops again… process repeats

67
Q

when is plasmid copy number constant

A

under constant physiological conditions

68
Q

what is a high copy number

A

often 50-100 per cell

69
Q

what is a medium copy number

A

5-20 per cell

70
Q

what is a low copy number

A

1-2 per cell, generally large

71
Q

what controls bacterial plasmid copy number

A

speed of replication initiation at oriV and how quickly it is completed

72
Q

what does bacterial plasmid controls for copy number require

A

plasmid-encoded functions (rep or cop genes)

73
Q

which plasmids have a low metabolic burden

A

Small plasmids have high copy number

74
Q

which plasmids have a high metabolic burden

A

Large have small copy number

75
Q

what can influence bacterial plasmid number

A

Copy number can be influenced by some of the plasmid encoded genes such as rep or cop and physiological conditions

76
Q

what determines the host range of a plasmid

A

determined by the ability of the replicon to be recognised and activated by different host cells

77
Q

what must plasmids do to allow their replication

A

must interact with host cell proteins to allow their replication (e.g. helicase, anchoring proteins, DNA polymerase, primase)

78
Q

which cells do plasmids replicate in

A

plasmids are only replicated in cells which recognise their oriV site

79
Q

what is the host range for gram-negative bacteria

A

bacterial plasmids can be either narrow or broad host range

80
Q

what is the host range for gram-positive bacteria

A

bacterial plasmids are usually narrow host range

81
Q

what are shuttle vectors (plasmids)

A

broad range plasmids that can replicate in Gram-positive AND Gram-negative bacteria

82
Q

what are the eukaryotic and prokaryotic bacterial plasmid host range

A

shuttle vectors have two different origins and will replicate in two different cell types

83
Q

what are eukaryotic/prokaryotic shuttle vectors useful for

A

useful for eukaryotic exogenous protein expression – prokaryotic replication for plasmid generation and amplification in bacteria. Eukaryotic replication for expression of cloned genes in eukaryotic cells

84
Q

what happens in plasmid partitioning when low copy number

A

One generation to the next is vertical transmission
Par genes regulate the process specifically for low copy number plasmids
One of the par proteins can polymerase itself and keep adding monomers in till it forms a long chain which pushes the two plasmids apart – so one plasmid in each cell, quite physical process
Ensure both daughter cells have a plasmid

85
Q

what happens in plasmid partitioning when high copy number

A

random partitioning

Don’t need par process, wont necessarily have par proteins

86
Q

what is vertical transmission

A

plasmids replicate and cells divide, plasmids are passed from generation to generation

87
Q

why may plasmids be maintained

A

maintained in a population if there is either (a) a selective advantage, or (b) no disadvantage, to the host cell

88
Q

what does cured mean

A

Cells that have lost a plasmid

89
Q

what is plasmid incompatibility

A

inability of two particular plasmids to be maintained in the same host cell (competition)
Used to classify bacterial plasmids - every plasmid belongs to an incompatibility (Inc) group

90
Q

what causes plasmid incompatibility in low copy number plasmids

A

related partitioning systems

91
Q

what causes plasmid incompatibility in high copy number plasmids

A

due to unequal partitioning

Applied Genetics (20 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions