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CMMB 411 > topic 4 > Flashcards

topic 4 Flashcards

1
Q

compare prokaryote and eukaryote genomic structure

A

prok:
- nucleoid
- less compact
- single circular chromosome + plasmid

euk:
- nucleus
- highly compact
- multiple linear chromosomes
- haploid or diploid

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2
Q

what is gene density?

A
  • average number of genes per megabase (Mb) of genomic DNA
  • less dense in more complicated organisms due to larger genome size (more introns, not just more genes)
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3
Q

4 parts of a euk chromosome

A
  • kinetochore
  • centromeres
  • telomeres
  • origins of replication
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4
Q

what is a centromere

A

DNA sequences that are required for the formation of kinetochore complex. 1 centromere/chromosome

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5
Q

what is the kinetochore

A

protein complex that forms on the centromeres for interacting with spindles during chromosome segregation in cell division

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6
Q

what are telomeres and their key features

A

TG-rich repeats that cap ends of chromosome, protect from damage and loss.
2 pairs per chromosome

features:
- distinguish the chromosome ends from chromosome and other DNA breakage sites (i.e. prevent frequent DNA recombination and degradation)
- serve as a specialized origin of replication for replicating ends of chromosomes

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7
Q

what is the origin of replication

A

sites where DNA replication machinery assembles and begins replication; many origins per chromosome

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8
Q

goals of gap phases

A

provides time for cells to achieve two goals:
- prepare for next phase of cell cycles
- check completion of previous phase (cell cycle checkpoint)

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9
Q

Key Events in the S Phase

A
  • each chromosome of a duplicated pair = chromatid (sister chromatids)
  • DNA replication begins at origins, spreads in both directions
  • cohesin = protein that forms rings to hold sister chromatids together
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10
Q

Mitotic Events

A

● a kinetochore forms on each chromosome, connects to spindles, which are connected to the microtubule organizing centre (MTOC or centrosomes)
● cohesin is cleaved
● sister chromatids separate to opposite poles

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11
Q

during what phase are chromosomes less compact?

A

interphase
(G1+S+G2)

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12
Q

when are chromosomes most compact

A

during mitosis
(chromosome condensation)
to facilitate their segregation
- M phase is max condensation

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13
Q

what is the role of cohesin? condensin?

A

cohesin: required for holding the 2 sister chromatids
condensin: required for chromosome condensation

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14
Q

when does attachment happen during mitosis? meiosis?

A

mitosis - M phase
meiosis
- monovalent attachment during M1
- bivalent attachment during M2

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15
Q

Advantages of DNA packing

A
  • protect DNA from damaging
  • proper segregation during cell division
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16
Q

Disadvantages of DNA packing

A

reduces accessibility to cellular machinery needed for cell function
e.g., DNA replication, transcription, repair, and recombination

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17
Q

what is a nucleosome and how compact are they

A
  • building blocks of chromosomes
    ● composed of 8 histone proteins + ~2 rounds of DNA wrapped around each histone core
    ● 6X compaction
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18
Q

what is micrococcal nuclease (MNase):

A
  • sequence-nonspecific nuclease
  • cleaves protein-free DNA rapidly and protein-associated DNA poorly
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19
Q

what proteins comprise histones

A
  • highly basic (arginine and lysine rich) proteins
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20
Q

H3 and H4 form a ______?
H2A and H2B form a ______?

A

tetremer
heterodimer

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21
Q

does a nucleosome have any symmetry?

A

~two fold symmetry in two axes in the complex

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22
Q

Where does the H3 - H4 tetramer bind?
how does this impact the structure?

A

binds to middle + ends of DNA → DNA constraint and being extensively bent

  • hydrogen bonds provide the energy to bend the DNA
23
Q

what groove do histones bind?

A

minor (sequence independent)

24
Q

Where does histone modification take place?
what is the purpose of this?

A

N tails of histones
- regulate nucleosome functions

25
how is eukaryote DNA packed and what undoes this packaging?
negative supercoil topoisomerases
26
what is gyrase?
- prokaryote topoisomerase - negative superhelicity, costs ATP
27
what is reverse gyrase?
- prokaryote topoisomerase - keeps the genome positively supercoiled, costs ATP
28
heterochromatin vs euchromatin
hetero - tightly packed, more organized eu - loose
29
heaviest histone? what is its function?
H1, linker histone - further condensation - high in lysine and argenine
30
what are 2 models for 30nm chromatin fibre? what do they require?
a. solenoid - 1 helix b. zigzag - 2 helix - need H1 - makes less accessible for DNA-dependent enzymes
31
10 vs 30nm fibres
10nm - 1 histone 30nm - connected by H1
32
How compact is DNA with nucleosome + 30-nm fiber?
~40X of DNA compaction
33
what is the function of topoisomerase 2?
- holds DNA at the base of loops – ensures the loops are topologically isolated from one another
34
What enzyme ensures DNA loops are isolated from one another?
topo II
35
function of Structural Maintenance of Chromosome name 2 examples
- condenses and holds sister chromatids after duplication - provides foundation for interactions between nuclear scaffold and chromosomal DNA - cohesion, condensin
36
3 steps to minimize DNA entanglement (cohesin+condensin)
1. Cohesin generates + stabilizes DNA loops to organize interphase chromatin into topological domains. then 2. Topo II forms knots, inter or intra molecular DNA interlinks to introduce random DNA strand passages (increase chromatin compaction) or 3. Condensin uses its DNA loop- extrusion activity to constrict DNA entanglements.
37
What is H2A.X?
- H2A variant – phosphorylated - found at site of dsb – phosphorylated H2A.X can be recognized by DNA repair enzymes
38
What does CENP-A do?
- replaces histone H3 in centromeric nucleosomes - serve as a binding site for kinetochore protein(s) (has tails that stick out) (makes more condensed)
39
Histone Varient:
- H2A.X - attract DNA repair - CENP-A - maintain kinetochore attachment - protamine. - tight sperm - H3.3 - locks open
40
role of protamine
- tighter DNA packaging for sperm’s streamline shape * protects sperm’s DNA from damage * helps epigenetic resetting
41
con of histone binding
DNA binding proteins don't like, sterically hinders DNA access, prevents genes from being expressed
42
Factors Regulating Chromatin Accessibility:
* dynamic nature of histone octamer-DNA interactions * nucleosome-remodeling complexes and DNA-binding proteins bent DNA and restrict nucleosome at certain positions * modifications of histone N-terminal tails these factors can be combined
43
3 types of nucleosome/chromatin-remodeling
sliding ejection dimer exchange
44
how can you allow the DNA-binding site to remain accessible for regulatory proteins?
restricting nucleosome location - located in linker region
45
how does nucleosome positioning impact a southern blot?
If they're positioned evenly after the cut site, the blot will reveal distinct bands where each histone resides
46
How can histone N-terminal tail can be modified? (4)
acetylation (lysines) phosphorylation (serines) methylation (lysines, arginines) ubiquitination (lysines)
47
How does acetylation impact DNA condensation?
- reduces +ve charge - decreases affinity for negatively charged DNA backbone - bromodomain binds, making less compact
48
how does methylation impact histone binding?
- can lead to gene repression (Lys9) or activation (lys4) - recruit other machinery that modify the histone
49
what interacts with methylated histones?
chromo-domain-TUDOR domains and PHD-finger containing proteins interact methylated histone tail
50
histone-DNA interaction is dynamic and is achieved by: (6)
1. specific DNA regions 2. competition between histones and specific DNA- binding proteins 3. interaction of nucleosome with chromatin-remodeling proteins 4. modification of histone N-terminal tails by histone-modifying enzymes 5/6. combinatorial modification of histone N-terminal tails, and interaction with chromatin-remodeling complexes to change accessibility of DNA
51
replication of DNA during S-phase requires partial disassembly of the______?
nucleosome
52
Do daughter chromosomes contain old or new histones
both!
53
how do old histones get modified to match the new histones
- old modified H3-H4 tetramer recruits histone modifying enzymes to add similar mods to adjacent nucleosomes of daughter chromosome - mechanism is important for maintaining cell identity from one generation to the next
54
What charge do histone chaperones have and how does this effect the histone?
- negatively charge proteins - form complexes with histones and escort them to the site of nucleosome assembly

CMMB 411 (3 decks)

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