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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
Q

nucleosome+ linker histone =

A

chromatosome

26
Q

H1 histone

A

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
Q

30nm fiber structure

A

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
Q

All core histones except H4 are members of families of

A

histone variants

29
Q

histone variants vary in

A

in their polypeptide chain length, amino acid sequence, and pattern of stable histone modifications

30
Q

histone modifications

A

Covalent modifications to the amino acid side chains of histone proteins

31
Q

variants often involve changes in

A

the histone tails

32
Q

CenH3/CENP-A

A

Replaces H3 in nucleosomes of DNA regions associated with the kinetochore

33
Q

H3.3

A

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
Q

H2AX

A

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
Q

histones are covalently modified by

A

Methylation
Acetylation
Phosphorylation
Ubiquitylation
ADP-ribosylation

36
Q

histone modifications happen

A

Usually in tails
All reversible
May be transient or stable

37
Q

acetylation

A

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
Q

methylation

A

Lysine or arginine
Can be mono-, di-, or tri-
Several types of trimethylated lysine modifications are important components of heterochromatin

39
Q

phosphorylation

A

adding phosphates on serine or threonine

40
Q

what is the memory effect

A

Modifications can remain long after transcription factors are gone
can be passed down to descendant cells

41
Q

how are histone modifying enzymes recruited

A

by transcription factories

42
Q

There are over … known coordinated sets of histone modifications in mammalian cells

A

15

43
Q

what modifications turn gene expression on and are in highly accessible, open chromatin

A

H4K4me3 and H3K9ac

44
Q

what modifications turn gene expression off and are found in heterochromatin

A

H3K9me3 and H3K27me3

45
Q

After modification, histones and nucleosomes can be bound by

A

chromatin binding proteins

46
Q

bromodomains recognize

A

acetylated lysines

47
Q

chromodomains, PHD domains, and Tudor domains recognize

A

methylated residues

48
Q

SANT domain recognizes

A

unstructured tails

49
Q

ING PHD domain

A

Specifically recognizes H3K4me3
Also recognizes the 6 amino acids in the N-terminal tail of H3

50
Q

reader protein complex

A

Nucleosome binding proteins that contain multiple binding domains that allow the protein to recognize a specific combination of histone modifications

51
Q

Reader complexes may be attached to …that can make histone modifications

A

writer enzymes

52
Q

reader-writer complexes

A

will bind a specific chromatin region and modify neighboring nucleosomes

53
Q

reader write complexes work until

A

it meets a barrier insulator region

54
Q

what complex can erase modifications

A

reader-eraser

55
Q

Reader-writer complexes are involved in

A

heterochromatin spreading

molgen (28 decks)

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