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MICR335 section B > lecture 3 > Flashcards

lecture 3 Flashcards

1
Q

how is the chromosome compacted?

A

Compacted in an orderly and hierarchical fashion with a functional three dimensional form to allow replication , recombination, segregation, and transcription

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2
Q

what is the genetic map?

A

organization of the chromosome within the bacteial cell

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3
Q

what controls the chromosome architecture?

A

Controlled by specialized proteins

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4
Q

what are some methods for visualizing the bacterial chromosome?

A

cryo electron tomography
super-resolution microscopies

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5
Q

what is the structure of the chromosome?

A

Overall curved shape
- bundles at the central core and low-debsuty regions

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6
Q

what are the features of cryo electron tomography?

A

bacteria within native condition
has biological context
is high resolution

Low contract
is just a snapshot

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7
Q

what are the features of super-resolution microscopies?

A

The bacteria are live
Has functional context
it is fast and easy

Has low resolution
hard labeling

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8
Q

what is the structural organisation of the bacterial chromosome?

A
  • The chromosome is compacter in an orderly and hierarchical fashion in lockstep with DNA replication
  • It is not enclosed by a membrane
  • The organization of the chromosome within the bacterial cell recapitulates the genetic map
  • The chromosome is organized at different scales
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9
Q

what are CIDs?

A

Chromosome interaction domains

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10
Q

what are features the chromosome interaction domains?

A
  • insulated from flanking regions, self interactions
  • 10^2-10^3 kbp
  • boundaires between CIDs: highly expressed genes
  • HEG- house keeping genes (ribosomal gene cluster)
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11
Q

how does the number of CIDs differ?

A

depending on growth conditions

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12
Q

what are the important positions within the bacterial chromosome?

A
  • replication (oriC) - one pole
    The replication terminus (ter) - opposite pole
    pole-anchoring proteins
  • Left and right chomosomal arms
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13
Q

what determines chromosome configuration?

A

Chromosome configuration is different in different bacteria and depends on the growth conditions

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14
Q

what does the ori-ter pattern determine?

A

Each daughter cell inherits a full copy of the genome

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15
Q

what happens during replication to the DNA?

A

During replication the new DNA moves to its relative position

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16
Q

what shape are bacterial chromosome?

A

Most bacterial chromosomes are circular but some are linear

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17
Q

what is the role of MatP in E.coli?

A

Keeps Ter in a compacted form
MatP binds to 13-bp matS sites present exclusively in the ~800-kb Ter macrodomain

MatP binds the matS site as a dimer
interacts with membranes

18
Q

what is the function of NAPs?

A

They govern DNA organization

19
Q

how is eukaryotic DNA organized?

A

Genomic DNA is condensed using histones (identical repeating octamers)

20
Q

how is bacterial DNA organized?

A

organized plectonemic supercoiled using specific proteins

21
Q

what are NAPs?

A

nucleoid-associated proteins

22
Q

what are the structural maintenance complexes of chromosomes?

A
  • ‘hinge’ dimerization domain
  • an antiparallel coiled-coil ‘arm’ extending between the hinge and head domains
  • ATPase ‘head’ domain
  • Kleisin-interacting winged tandem elements (kite)
23
Q

what are DNA loop extrusion mechanisms?

A
  • embracing a pair of DNA segments in a signle ring
  • dimerization of two rings
24
Q

what are the structure of histone-like nucleoid structuring protein (H-NS)?

A

-small polypeptide; binds the DNA minor groove using a C-terminal arginine hook motif
- AT rich segments
- head-to-head: H-NS-DNA filaments
- Tail-to-tail DNA-H-NS-DNA bridges
- can occlude RNAP binding sites or transcription activators-> gene epxression

25
Q

what are the features of heat stable protein form E.coli U93 strain?

A
  • two subunits (alpha and beta) -> homo and heterodimers
  • Flexible hinge: range of different angles
  • abundant: 30,000 copies/cell
  • can make octamers (spiral structures)
26
Q

what do integration host factors do?

A

make a hairpin in the DNA strand at 160 degrees

27
Q

what causes DNA light bending?

A

Fis

28
Q

what is Fis?

A

Factor for inversion stimulation

29
Q

what are the features of Fis?

A
  • highly expressed gene during rapid cell division
  • conserved in most gram-negative bacteria
  • bending the DNA by 50-60 degrees
  • stable, long-lived nucleoprotein complexes
  • can regulated transcription
30
Q

what can modulate the structure of NAPs?

A

additional proteins

31
Q

what induces supercoiling?

A

RNAP induces +/- supercoiling

32
Q

how is dsDNA topologically constrained?

A

dsDNA circular molecule is topologically constrained- no rotation of the free ends

  • genome organizes in plectonemic supercoils constrained by NAPs
33
Q

what is plectonemic supercoiling?

A

a cut in one domain will only relax that domain and not others

34
Q

how do topoisomerases bind and cut DNA?

A

One DNA strand- type 1
both DNA strands- type II

35
Q

what happens when supercoiled DNA unravels?

A

once it uncoils it will reform in a circle

36
Q

what mediates chromosome condensation?

A

condensation mediated by supercoiling and NAPs

37
Q

what is bulk chromosome segragation?

A

the orderly compaction of the replicated sisters along adjacent DNA segments

38
Q

what facilitates the origin of segregation?

A

the origin of segregation is facilitated by a highly conserved partitioning system

39
Q

how to topoisomerases work in chromosome segragation?

A

Topoisomerases (IV) enriched ahead of replication forks and transcription bubbles

40
Q

how do environmental conditions affect DNA organization?

A
  • the chromosome structure changes with environmental conditions
  • Conformational changes induced by ligands
    Mg stabilizes H-NS helix conformation
  • temperature reduces H-NS oligomerizations and dissociation from DMA
  • Usually NAPs present in lower level in starved cells
    DNA adopts a crystalline structure
41
Q

what are important things to remember?

A
  • bacterial chromosome is compacted
  • bacterial chromosome is hierarchically organized
  • various methods are used to study DNA organization
  • NAPs are modelling the DNA
  • NAPs expression and structure respond to environmental stimuli
42
Q

how does Mg affect chromosomes?

A

stabilizes H-NS helix conformation

MICR335 section B (4 decks)

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