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Molecular Genetics > Chromatin > Flashcards

Chromatin Flashcards

1
Q

what is the packaging of DNA?

A
  • the condensed state of the DNA is the result of interactions with basic proteins
  • high density
  • packaged with positively charged proteins to enable supercoiling the negative phosphodiester backbone in DNA
  • means no transcription is occurring
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2
Q

what is the density of DNA in bacteria? in eukaryotic nucleus? in T4 phages?

A
  • bacteria = 10 mg/mL
  • eukaryotes = 100 mg/mL
  • T4 = 500 mg/mL
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3
Q

what does packaging relate to?

A
  • expression
  • condensed means there is no transcription
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4
Q

packaging ratios

A
  • length of DNA divided by the length of the unit that contains it
  • unpackaged DNA to packaged DNA
  • lower the ratio the less active transcription is occurring
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5
Q

what is the packaging ratio of interphase chromatin?

A

1,000 - 2,000

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6
Q

what is the packaging ratio of mitosis?

A

5,000 - 10,000

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7
Q

how do you calculate packaging ratios?

A
  • 46,000,000 bp = 14 um unpackage v 2 um packaged
  • 14,000 / 2 = 7,000 packaging ratio
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8
Q

what is DNA density?

A
  • mass of DNA per volume
  • for example, bacteria has a DNA density of 10 mg/mL
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9
Q

what are the different types of genomes?

A
  • virus = TMV, phage fd and T4, and adenovirus
  • prokaryote = e. coli
  • eukaryote = mitochondria and nucleus
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10
Q

what is the length of the human genome compared to the bacterial genome?

A
  • humans = 1.8 m (5.9 ft) / 6 x106 kb
  • bacteria = 1.3 m (4.2 ft) / 4.2x103 kb
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11
Q

what are the types of viral packaging and what viruses are they associated with?

A
  • filamentous = TMV and phage fd
  • icosadedron = adenovirus and phage T4
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12
Q

what is the bacterial genome?

A
  • 80% DNA by mass
  • unfolded by agents that act on RNA or proteins
  • condensing proteins are not completely understood
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13
Q

how is bacterial genome organized?

A
  • independent domains or loops that contain 40 bp per loop
  • genome is supercoiled and organized into loops
  • nucleoid has 100 independent negatively charged super coiled domains
  • 1 super coil contains 100 bp
  • each loop contains 10 - 40 bases
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14
Q

supercoiling density

A
  • 1 supercoil per 100 bp
  • 100 loops of fibers per genome
  • enough to influence melting of DNA promoters
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15
Q

what proteins are involved in DNA binding in bacteria?

A
  • HU, IHF, H1, and protein P
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16
Q

HU

A

dimer that condenses DNA into bead-like structure

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17
Q

IHF

A

integration host factor

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18
Q

H1

A

interacts with bent DNA
- not the same H1 in eukaryotes

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19
Q

protein P

A

resembles protamine (found in sperm); very basic

20
Q

what is the eukaryotic genome comprised of?

A
  • 50% DNA
  • 10% RNA
  • the rest is proteins, with half of the proteins histones
21
Q

how is the eukaryotic genome organized?

A
  • loops of DNA about 60 kb but can range from 20-200
  • composed of scaffold proteins
22
Q

MAR

A
  • matrix attachment region
  • DNA binds to nuclear matrix within nuclear membrane
  • appear to be associated with scaffold proteins
  • heterochromatin is strongly associated here
23
Q

euchromatin

A
  • much less densely packed and dispersed
  • only small portion transcribed
  • more likely to be transcribed, does not mean it will be
24
Q

heterochromatin

A
  • inactive
  • two kinds: facultative and constitutive
25
Q

constitutive heterochromatin

A
  • regions that are not expressed, remain condensed
  • structural and remain near centromeres
26
Q

facultative heterochromatin

A
  • entire chromosomes that are inactive in one cell lineage in the female
  • mosaic in cells, one cell can have a different active X chromosome than another
27
Q

what are the 10, 30, and 50 nm fibers?

A
  • 10 nm = beads on a string
  • 30 nm = compact beads on a string
28
Q

why is the beads on a string model no longer accurate past the 30 nm fiber?

A
  • based on the hierarchal model that is no longer accurate because is only present in isolated DNA and does not occur naturally
  • beads on a string are all packaged at different densities and not that organized
29
Q

explain scaffolding

A
  • the mitotic chromosome is comprised of consecutive loops formed by condensin 1 and 2
  • mega loops nested within smaller loops all situated on a backbone
  • condensin 2 forms the primary loops while condensin 1 forms sub-loops
  • first structure wraps around over and over with other to form a large structure
30
Q

condensin 1

A

within primary loops to form subloops

31
Q

condensin 2

A
  • spirals that form the central structure of the condensed chromosome
32
Q

lampbrush chromosomes

A
  • highly extended conformation at 400 - 800 um (normal is 15-20)
  • found in amphibians like newt and frog
  • have extended meiosis for several months
  • found within normal DNA with loops that are heavily transcribed
  • contains ribonucleoproteins
33
Q

polytene chromosomes

A
  • drosophila larval salivary glands interphase nuclei
  • more than 5,000 bands with a packaging ration more than 20
  • comprised of parallel fibers running longitudly that result in the chromosome doubling up to 9 times
  • transcriptionally active bands are puffed forming balbiani rings
34
Q

what occurs in puff and balbiani rings?

A

intense RNA synthesis
- can tell the order based on short to long

35
Q

what is a centriole?

A
  • involved in the development of spindle fibers for cell division
  • not found in all organisms
36
Q

what is a centrosome?

A
  • eukaryotic segregation device
  • no DNA sequence but epigenetic modifications
37
Q

what are MTOCs?

A
  • microtubular organizing center
  • found at centrioles at the poles and on each chromosome at the center
38
Q

what is a kinetochore?

A
  • 400 nm fiber found at centromere that is attached to the microtubules during mitosis
  • provides MTOC for chromosome
39
Q

what is the unusual yeast kinetochore?

A

Dam 1

40
Q

budding yeast centromere structure

A

point centromere

41
Q

insects, mammals, and plant centromere structure

A

regional centromeres

42
Q

nematodes centromere structure

A

holocentric chromosome

43
Q

regional chromosomes

A
  • contain a centromere specific histone H3 variant and repetitive DNA
  • alternating pattern of H3 octamers and CenH3 tetrameres
  • the Cen H3 tetramers recruit proteins that form the kinetochore
  • location seems to be epigenetically controlled
44
Q

why is the regional centromere more beneficial over the point centromere?

A

the point centromere can only accommodate a single turn of DNA

45
Q

chromatin

A

a complex chiefly of DNA and histone in eukaryotic cells that is usually dispersed in the interphase nucleus and condensed into chromosomes in mitosis and meiosis

46
Q

interphase nucleus

A

no condensed chromosomes
- chromosomes occupy specific territories within the nucleus and are not entangled

47
Q

acentric fragment

A

does not get attached to mitotic spindle

Molecular Genetics (28 decks)

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