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MOLGEN > Ch 8 Lecture (Chromatin) > Flashcards

Ch 8 Lecture (Chromatin) Flashcards

1
Q

nucleosome

A

The basic structural subunit of chromatin, consisting of 200 bp of DNA and an octamer of histone proteins
Serves as the first level of chromatin organization
Packed 6X

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2
Q

histones

A

DNA binding proteins that are part of nucleosome structure

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3
Q

Histone tails

A

Flexible N- or C-terminal regions of the core histones that extend beyond the surface of the nucleosome
Are often extensively post-translationally modified

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4
Q

10 nm fiber

A

A fiber generated from the linear array of nucleosomes

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5
Q

30nm fiber

A

A coil of nucleosomes
40X packing
Basic level of organization in chromatin
Requires interactions of histone tails and linker histones

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6
Q

linker histones

A

A family of histones that are not components of the nucleosome core that bind nucleosomes and/or linker DNA
Histone H1

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7
Q

micrococcal nuclease

A

cleaves linker DNA and releases individual nucleosomes from chromatin

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8
Q

there is one nucleosome every

A

200 base pairs

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9
Q

what proteins are the octomer of core histone proteins

A

A pair of H2A, H2B, H3, and H4
Stable H32-H42 tetramer associates with two stable H2A-H2B dimers

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10
Q

histone proteins are

A

small, basic, and lysine and arginine rich

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11
Q

what histone proteins are highly conserved

A

H3 and H4

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12
Q

what histone proteins are not highly conserved

A

H2A and H2B

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13
Q

DNA is coiled around the histone how many times

A

1.6

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14
Q

Interdigitation of histone proteins is facilitated via the interaction of

A

histone folds

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15
Q

histone folds

A

Conserved structure of 3 -helices
Two short helices on end and one long helix in middle separated by loops

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16
Q

what facilitates heterodimer formation

A

loop to loop interactions

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17
Q

What binds to the middle 60bp and the entry/exit points of the DNA

A

H3-H4 tetramer

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18
Q

what stabilizes the DNA on the bottom of the nucleosome

A

H2A-H2B dimers

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19
Q

Association between DNA and the nucleosome is facilitated by

A

142 hydrogen bonds

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20
Q

intrinsic positioning

A

AT-rich regions position with minor groove towards octamer
GC-rich regions position with minor groove facing away from octamer

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21
Q

what on the histones help “lock” the DNA on the nucleosome

A

The N-terminal tails

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22
Q

Histone tails are distributed … around the nucleosome disc

A

evenly

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23
Q

histone tails

A

Each histone has a flexible N-terminal tail
H2A and H2B also have flexible C-terminal tails
Structures not well defined via molecular imaging
Conformation can be altered greatly by posttranslational modification
The tails (especially H4) interact with the H2A-H2B dimer of an adjacent nucleosome

24
Q

linker histone

A

Help link neighboring nucleosomes into higher order chromatin structure
A set of closely related proteins that show variation between tissues and species
H1 histone

25
nucleosome+ linker histone =
chromatosome
26
H1 histone
Interacts with two distinct regions of DNA Linker DNA at one end of nucleosome Middle of nucleosome-bound DNA found at dyad axis Produces a more defined angle of DNA entry and exit from nucleosome Produces a zig-zag appearance of “beads on a string”
27
30nm fiber structure
Condensed zigzag structure Facilitated by histone tail-to-tail interactions Especially the H4 tail Also requires the H1 histone Linker DNA passes through the central axis of the fiber
28
All core histones except H4 are members of families of
histone variants
29
histone variants vary in
in their polypeptide chain length, amino acid sequence, and pattern of stable histone modifications
30
histone modifications
Covalent modifications to the amino acid side chains of histone proteins
31
variants often involve changes in
the histone tails
32
CenH3/CENP-A
Replaces H3 in nucleosomes of DNA regions associated with the kinetochore
33
H3.3
Expressed throughout the cell cycle Some histone variants are primarily expressed only in the S phase Available for assembly at regions of active transcription “Replacement” histone
34
H2AX
Present in 10-15% of multicellular eukaryote nucleosomes H2AX tails are a target of phosphorylation events associated with DNA damage, repair, and cell cycle arrest Phosphorylated -H2AX is recognized by repair enzymes
35
histones are covalently modified by
Methylation Acetylation Phosphorylation Ubiquitylation ADP-ribosylation
36
histone modifications happen
Usually in tails All reversible May be transient or stable
37
acetylation
Neutralizes the positive charge of lysine Releases histone tails from DNA Increases accessibility of DNA to transcriptional machinery Newly synthesized histones lose acetylation after incorporation into chromatin
38
methylation
Lysine or arginine Can be mono-, di-, or tri- Several types of trimethylated lysine modifications are important components of heterochromatin
39
phosphorylation
adding phosphates on serine or threonine
40
what is the memory effect
Modifications can remain long after transcription factors are gone can be passed down to descendant cells
41
how are histone modifying enzymes recruited
by transcription factories
42
There are over ... known coordinated sets of histone modifications in mammalian cells
15
43
what modifications turn gene expression on and are in highly accessible, open chromatin
H4K4me3 and H3K9ac
44
what modifications turn gene expression off and are found in heterochromatin
H3K9me3 and H3K27me3
45
After modification, histones and nucleosomes can be bound by
chromatin binding proteins
46
bromodomains recognize
acetylated lysines
47
chromodomains, PHD domains, and Tudor domains recognize
methylated residues
48
SANT domain recognizes
unstructured tails
49
ING PHD domain
Specifically recognizes H3K4me3 Also recognizes the 6 amino acids in the N-terminal tail of H3
50
reader protein complex
Nucleosome binding proteins that contain multiple binding domains that allow the protein to recognize a specific combination of histone modifications
51
Reader complexes may be attached to ...that can make histone modifications
writer enzymes
52
reader-writer complexes
will bind a specific chromatin region and modify neighboring nucleosomes
53
reader write complexes work until
it meets a barrier insulator region
54
what complex can erase modifications
reader-eraser
55
Reader-writer complexes are involved in
heterochromatin spreading

MOLGEN (28 decks)

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