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Cell Biology > Lecture 5 Slides > Flashcards

Lecture 5 Slides Flashcards

0
Q

Where is nuclear lamina? What binds to it?

A

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

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1
Q

Nuclear envelope made up of

A

Outer and inner nuclear membranes

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2
Q

What is a continuation of the outer nuclear membrane

A

Endoplasmic reticulum

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3
Q

What is a chromosome. What does it do?

A 
A single DNA molecule.
Function:
Maintain genetic info
Replicate genetic info
Segregate genetic info
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4
Q

What is chromatin made of

A

DNA
Histones
Non-histone proteins

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5
Q

How many histones in nucleosome

A

Eight

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6
Q

What links Nucleosomes? What is length between them?

A

Linker DNA.

200 nucleotide pairs of FNA

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7
Q

What does nuclease do

A

Digest linker DNA

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8
Q

What is the diameter of a nucleosome

A

11 nm

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9
Q

How many times does DNA wrap around nucleosome core

A

1.67 times

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10
Q

How is DNA coiled in Nucleosomes

A

Negatively

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11
Q

How big are histones? How are thy structured?

A

102-133 aa

Histone fold at C terminus

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12
Q

What is the charge of histones

A

Positive

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13
Q

What are histones enriched in? What is their PI?

A

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

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14
Q

How foes histone bind to DNA

A

Via various noncovalent bonds

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15
Q

What extends from nucleosome. What does it have?

A

Amino-terminal tails. Have numerous covalent modifications.

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16
Q

What encodes histones

A

Multigene families expressed during DNA replication

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17
Q

Are histones found in bacteria

A

No, but in archaea yes

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18
Q

Are histones present in all eukaryotes

A

All but dinoflagellates

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19
Q

What do archaea histone-like proteins assemble

A

Tetramers that protect ~60bp of DNA from nuclease digestion

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20
Q

How is chromatin remodeled

A

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

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21
Q

What is the function of chromatin remodeling complexes

A
  • 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
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22
Q

Isotonic buffer

A

Has same ionic conditions as inside cell

23
Q

How is 30nm fiber extracted from cells

A

Using isotonic buffers

24
Q

How are Nucleosomes stacked

A

In 30 nm fibers

25
Q

What are 30 nm fibers formed by

A

Interaction of histone tails

Linker histone H1 (1 per nucleosome)

26
Q

Qualities of epigenetic inheritance

A

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

27
Q

Euchromatin

A

Less condensed, active in gene expression

28
Q

Heterochromatin

A

Highly condensed, gene expression repressed

29
Q

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

A

Structural gene may be inactivated

30
Q

Result of chromosome rearrangement

A

Allows heterochromatin to spread into structural gene

31
Q

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

A

Loosens chromatin structure

32
Q

What does acetyl group do to lysine

A

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

33
Q

Histone acetyl transferase

A

Adds acetyl group to lysine

34
Q

Histone deacetylase

A

Removes acetyl group from lysine

35
Q

Lysine methyl transferase and demethylase

A

Add and remove methyl groups to lysine, respectively

36
Q

Arginine methyl transferase

A

Adds methyl group to arginine

37
Q

What does serine phosphorylation do to a histone

A

Gives it a negative charge

38
Q

Types of histone modifications

A

Code “writer”
Code “eraser”
Code “reader or effector”

39
Q

Code “writer”

A

Enzyme that adds a modification

40
Q

Code “eraser”

A

Enzyme that removes a modification

41
Q

Code “reader or effector”

A

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

42
Q

Which trimethylations are associated with transcriptional repression

A

H3K9, H3K27, and H4K20. Enriched in heterochromatin.

43
Q

Which methylations are associated with transcriptional activation

A

H3K4, H3K36, H3K79. Enriched in euchromatic

44
Q

MLL

A

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

45
Q

Trans effect

A

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

46
Q

Cis effect

A

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

47
Q

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

A

A methyl group or more

48
Q

How does histone deacetylase propagate heterochromatin?

A

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

49
Q

How does HP1 chromo domain work

A

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

50
Q

What does Chromatin remodeling complex do to promote heterochromatin

A

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

51
Q

How is heterochromatin structure stabilized

A

Oligomerization of HP1

52
Q

What is loss of HP1 associated with

A

Several cancers

53
Q

Chromatin immunoprecipitation

A

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

54
Q

Antibodies can be used to identify DNA bound by 3

A

Gene regulatory protein
Modified histone
Chromatin-associated protein

Cell Biology (35 decks)

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