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DNA organization Flashcards

1
Q

Prokaryotes - DNA organization

A
  • dsDNA
  • single circular DNA molecule
  • single chromosome
  • possible plasmids (extra chromosomal structures)
  • found in nucleoid region (no nucleus)
  • associate with histone like DNA binding proteins (NOT HISTONE)
  • supercoiled
  • can undergo horizontal gene transfer
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2
Q

Eukaryotes - DNA organization

A
  • dsDNA
  • multiple linear chromosomes: found in nucleus and single long dsDNA molecules
  • circular chromosomes: found in mitochondria and chloroplasts
  • chromatin (DNA associated with histones, non-histone chromosome proteins and RNA)
  • have more DNA
  • more complex protein association
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3
Q

purpose of supercoiling

A

allows for DNA to fit into the cell

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4
Q

how does supercoiling work

A

DNA twists and untwists, bond angles strain and dsDNA twist back on itself

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5
Q

what is positive supercoiling

A

more twists - overwound

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6
Q

where is positive supercoiling found

A

ahead of transcription and replication bubbles - in thermophilic organisms

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7
Q

what is negative supercoiling

A

less twists - underwound
- most common in DNA cells

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8
Q

what is topiosomerase

A
  • highly conservative family of proteins
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9
Q

what does topoisomerase do

A

cuts DNA, either positively or negatively twists and reseals the DNA

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10
Q

type I topoisomerase

A

nicks/cuts one strand

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11
Q

type 2 topoisomerase

A

nicks both strands
- also called DNA gyrase

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12
Q

2nm DNA

A
  • each chromosome consists of single, long strand of DNA
  • still not compact enough
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13
Q

11nm DNA

A

winds around histones to form nucleosomes

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14
Q

histones role in 11nm DNA

A

positively charged proteins that allows histone to bind and neutralize DNA; rich in lysine and arginine

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15
Q

5 types of histone proteins

A
  1. H2A
  2. H2B
  3. H3
  4. H4
  5. H1
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16
Q

what histone proteins form an octamer

A

H2A, H2B, H3, H4

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17
Q

what histone protein is linker DNA

A

H1

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18
Q

linker DNA

A

short segments of DNA that joins nucleosomes together in chromatin

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19
Q

histone chaperone proteins

A

help construct the nucleosome

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20
Q

30nm DNA

A

nucleosomes pack into 30nm chromatin fiber

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21
Q

chromatin fibers in 30nm DNA

A

DNA + histone + RNA
- nucleosomes are coiled and stacked with the help of non-histone proteins
- requires H1 (associated with linker DNA) to form
- DNA can become 6x more compact
- dominant form of chromatin observed during interphase

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22
Q

condensins

A

create chromatin loops

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23
Q

what are condensins

A

non-histone chromosomal protein with multiple subunits - have ring shape that form around nucleosomes (studded DNA)

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24
Q

condensins move along chromatin strands and

A

cause supercoiling

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25
DNA topoisomerase III
non-histone protein
26
function of DNA topoisomerase III
relaxes DNA supercoiling to prevent tangles and breaks
27
300nm DNA
chromatin fibers arrange into irregular loops assisted by condensins and cohesions
28
700nm DNA
looped chromatin coils further
29
1400nm DNA
chromosome during metaphase
30
when is DNA more compact
during metaphase
31
when is DNA less compact and what does it allow
during interphase - allows for gene expression and DNA replication
32
DNA organization
- nucleosomes are not evenly spaced - arrangement is dynamic and can change in response to stimulus
33
euchromatin
open and accessible to transcription where genes can be expressed
34
when is euchromatin observed
interphase
35
heterochromatin
tightly packed, closed and inaccessible to transcription where genes are silenced
36
when is heterochromatin observed
during all phases
37
what are the two heterochromatin
constitutive and faculative
38
constitutive heterochromatin
present in all cells at the same position on chromosomes - repetitive DNA
39
where is constitutive heterochromatin found
centromeres and telomeres
40
faculative heterochromatin
vary between cell type, developmental stages or between homologous chromosomes - euchromatin can become heterochromatin - X inactivation in mamalian cells
41
what does faculative heterochromatin have?
an active and inactive state
42
nucleosome compelx
physical block that prevents other proteins from recognizing and binding to DNA
43
chromatin remodeling complex
opens regions of the chromatin so that promotor regions or DNA replication origins can be recognized
44
what do the 4 core histone proteins have
tails of amino acids that extend from subunit that binds DNA
45
specific amino acids can receive modifying chemical groups:
1. methyl groups 2. acetyl groups 3. phosphate groups 4. ubiquitin groups
46
specific enzymes can ___-
catalyze the addition and the removal of the modifying groups
47
sugar phosphate backbone of DNA
carries a negative charge
48
positive charge of histone core proteins
allows histone to bind to DNA
49
charge of histone tails
positive
50
histone tails are modified or the positive charge decreases
association with DNA becomes weaker and nucleosomes can move
51
histone modification - acetylation
use histone acetyltransferase (HAT)
52
histone acetyltransferase (HAT)
transfers acetyl group to lysine using cofactor enzyme (CoA)
53
acetyl group
neutralizes the positive charge of lysine of H3, H2A and H2B
54
acetylation of lysine
attracts HAT activity which facilitates the spread of histone aceylation
55
histone deacetylases (HDAC's)
remove acetyl groups
56
nucleosome spacing increases
gene expression increases
57
histone modification - methylation
uses histone methyltransferases (HMTs)
58
histone methyltransferases (HMTs)
PRC2 (polycomb repressive complex 2) transfers methyl group to lysine and arginine using a methyl donor (SAM)
59
methyl groups properties
- do not change charge - can block access to genes - can increase expression
60
where are methyl groups
most commonly on H3 and H4
61
histone demethylases
removes methyl groups
62
Barr Bodies

Genetics (4 decks)

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