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Nuclear envelope made up of

Outer and inner nuclear membranes

1

Where is nuclear lamina? What binds to it?

On inside of inner nuclear membrane. Peripheral heterochromatin binds to it.

2

What is a continuation of the outer nuclear membrane

Endoplasmic reticulum

3

What is a chromosome. What does it do?

A single DNA molecule.
Function:
Maintain genetic info
Replicate genetic info
Segregate genetic info

4

What is chromatin made of

DNA
Histones
Non-histone proteins

5

How many histones in nucleosome

Eight

6

What links Nucleosomes? What is length between them?

Linker DNA.
200 nucleotide pairs of FNA

7

What does nuclease do

Digest linker DNA

8

What is the diameter of a nucleosome

11 nm

9

How many times does DNA wrap around nucleosome core

1.67 times

10

How is DNA coiled in Nucleosomes

Negatively

11

How big are histones? How are thy structured?

102-133 aa
Histone fold at C terminus

12

What is the charge of histones

Positive

13

What are histones enriched in? What is their PI?

Enriched in arginine and lysine. pIs range from 9.8 to 10.25

14

How foes histone bind to DNA

Via various noncovalent bonds

15

What extends from nucleosome. What does it have?

Amino-terminal tails. Have numerous covalent modifications.

16

What encodes histones

Multigene families expressed during DNA replication

17

Are histones found in bacteria

No, but in archaea yes

18

Are histones present in all eukaryotes

All but dinoflagellates

19

What do archaea histone-like proteins assemble

Tetramers that protect ~60bp of DNA from nuclease digestion

20

How is chromatin remodeled

ATP-dependent DNA translocate a anchor on histone October and move DNA around the nucleosome

21

What is the function of chromatin remodeling complexes

-work with histone chaperones to remove and replace histones
-assemble Nucleosomes on newly-replicates DNA
-assist in DNA repair
-condense chromatin to form heterochromatin
-regulate gene expression by altering chromatin structure at promoters
-modify transcription elongation

22

Isotonic buffer

Has same ionic conditions as inside cell

23

How is 30nm fiber extracted from cells

Using isotonic buffers

24

How are Nucleosomes stacked

In 30 nm fibers

25

What are 30 nm fibers formed by

Interaction of histone tails
Linker histone H1 (1 per nucleosome)

26

Qualities of epigenetic inheritance

Phenotypes not based on changes in DNA sequence
Genes may lie within different chromatin structures:
-euchromatic or heterochromatin

27

Euchromatin

Less condensed, active in gene expression

28

Heterochromatin

Highly condensed, gene expression repressed

29

What happens to gene expression if structural gene is not barred from heterochromatin

Structural gene may be inactivated

30

Result of chromosome rearrangement

Allows heterochromatin to spread into structural gene

31

Result of acetylation of lysine on N terminal (histone) tails

Loosens chromatin structure

32

What does acetyl group do to lysine

Removes its positive charge and reduced the affinity of the tails for adjacent Nucleosomes

33

Histone acetyl transferase

Adds acetyl group to lysine

34

Histone deacetylase

Removes acetyl group from lysine

35

Lysine methyl transferase and demethylase

Add and remove methyl groups to lysine, respectively

36

Arginine methyl transferase

Adds methyl group to arginine

37

What does serine phosphorylation do to a histone

Gives it a negative charge

38

Types of histone modifications

Code "writer"
Code "eraser"
Code "reader or effector"

39

Code "writer"

Enzyme that adds a modification

40

Code "eraser"

Enzyme that removes a modification

41

Code "reader or effector"

Enzyme that recognizes the modification and translates it into a specific outcome

42

Which trimethylations are associated with transcriptional repression

H3K9, H3K27, and H4K20. Enriched in heterochromatin.

43

Which methylations are associated with transcriptional activation

H3K4, H3K36, H3K79. Enriched in euchromatic

44

MLL

Histone methyl transferase. h3K4Me. Over expression resulting from gene fusions in hematopoietic stem cells are associated with leukemia

45

Trans effect

Invites other molecules to come and bind? Positive feedback loop and self propagating. Changes both chromosomes.

46

Cis effect

Affects only one chromosomal copy. Depends on transcription regulators synthesized in cytosol.

47

To loosen chromatin, you need an acetyl group. To tighten then you need

A methyl group or more

48

How does histone deacetylase propagate heterochromatin?

Removes acetyl group from H3 tail lysine 9 so that histone methyl transferase can methyl H3K9

49

How does HP1 chromo domain work

It is a reader. It reads the histone code. Binds H3K9Me3

50

What does Chromatin remodeling complex do to promote heterochromatin

It is ATP dependent. Uses ATP to shift DNA on Nucleosomes

51

How is heterochromatin structure stabilized

Oligomerization of HP1

52

What is loss of HP1 associated with

Several cancers

53

Chromatin immunoprecipitation

To identify DNA sequence to which a modified histone or regulatory protein will bind

54

Antibodies can be used to identify DNA bound by 3

Gene regulatory protein
Modified histone
Chromatin-associated protein