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Molecular Biology > Ch 10-nucleosomes, Chromatin, And Chromosome Structure > Flashcards

Ch 10-nucleosomes, Chromatin, And Chromosome Structure Flashcards

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1
Q

Chromatin

A

Chromosome material, consists of both DNA and protein

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2
Q

Histones

A

The family of basic proteins that associate tightly w/DNA in the chromosomes of all eukaryotic cells

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3
Q

Nucleosomes

A

In eukaryotes, the structural unit for packaging chromatin, consists of a DNA strand wound around a histone core

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4
Q

Cross linking

A

The use of a small chemical agent w/two reactive groups to covalently link molecules that are in close proximity

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5
Q

Histone octamer

A

The complex of 2 copies of each of the four core histones the forms the histone core of nucleosome

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6
Q

Histone core

A

H2A, H2B, H3, H4

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7
Q

Histone fold motif

A

A protein structural motif formed from 3 alpha hélices connected by two loops. Histone diners are instrumental in the tight wrapping of the DNA helix around the histone core in nucleosomes.
each histone contains a histone-fold motif

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8
Q

Histone tails

A

The flexible, disordered N-terminal ends of the histone proteins that comprise the histone core. These ends protrude from the nucleosome and contact adjacent nucleosomes
-sp1 is no effective in presence of higher levels of H1 (think about pic of gel)

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9
Q

Linker histone

A

H1, binds to the linker DNA adjacent to the nucleosome

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10
Q

30 nm filament

A

A higher-order if nucleosomes seen in condensed chromosomes

-tails are required

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11
Q

2 models for nucleosome arrangement in 30 nm filament:

A

1) solenoid model

2) zigzag model

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12
Q

Solenoid model

A

Nucleosome adopts a spiral shape, in which the flat sides of adjacent nucleosome disks are next to each other. Linker DNA is thought to bend in filament in this model

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13
Q

Zigzag model

A

Zigzag histone pairs stack on each other and twist about a central axis

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14
Q

Chromosomal scaffold

A

Proteinaceous residue after extraction of histone from chromosomes, consisting mainly of SMC proteins

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15
Q

Nucleoid

A

In bacteria, the nuclear zone that contains the chromosome but has no surrounding membrane

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16
Q

Chromatin remodeling complex

A

A protein complex with ATPase activity that translocates nucleosomes among the DNA making certain regions of DNA more or less accesible to transcription factors

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17
Q

Histone modifying enzymes

A

A class of enzymes that covalently modify the N-terminal tails of histones

18
Q

Epigenetic inheritance

A

The inheritance of characteristics acquired by means that do not involve the nucleotide sequence of the parental chromosomes

Ex: covalent modifications of histones

19
Q

Histone chaperones

A

Acidic proteins required for the assembly of histone octamers on DNA

-bins either H3 -> H4 or H2A -> H2B

20
Q

Histone acetlytransferases (HATs)

A

Acetylate Lys residues

21
Q

Histone deacetylases (HDACs)

A

Remove acetyl groups from histones

-usually results in transcriptional repression

22
Q

Bromodomain

A

A protein structural domain that recognizes and binds to certain acetylated lys residues in proteins

  • open
  • lys residues un larger multi protein complex, ie: chromatin remodeling complex
  • histone tail modification
  • stabilized open state
23
Q

Chromodomain

A

A protein structural motif that recognizes and binds methylated lys residues in proteins

  • stabilized closed state
  • methylation can result in activation or deactivation depending on the aa and location
24
Q

Histone code

A

A hypothetical code in which successive covalent modifications of histone tails and DNA trigger chromatin remodeling and transcriptional activation events

25
Q

Which amino acid residues predominate in the histone octamer and why?

A

Lysine and arginine predominate because they are positively charged

26
Q

What is linker DNA?

A

The DNA not wrapped around the histone octamer and served as a linker between nucleosomes, to which H1 binds

27
Q

How many base pairs does linker DNA have?

A

20-90 bp

28
Q

Approximately how much DNA is wrapped around a histone?

A

200 bp

  • the DNA sequence influences how the DNA can wrap around the histone. A-T rich regions alternating with G-C rich regions allows the DNA to naturally bend around the histone structure
  • histone octamers assemble particularly well with sequences where 2 or more A-T base pairs are staggered at 10bp intervals because DNA is naturally bent
29
Q

How do histone tails influence chromosome condensation? What are the potential effects of modifying the histone tails?

A
  • the unstructured Gail (N-terminus) is able to interact with neighboring nucleosomes
  • chemical modifications to the tails affect how the nucleosome binds DNA
  • required for filament formation
  • tails are flexible, but don’t contribute strength to DNA binding. They form intermolecular contacts with nucleosome particles into a higher order chromatin structure. The tighter the inter nucleosome connections mediated by the histone tails, the less accessible DNA is to transcription factors and other proteins
30
Q

How does H1 differ from the other histones? How does it associate with DNA?

A
  • H1 is a linker histone
  • H1 has DNA binding regions associated with its globular domain
  • H1 controls the location of the entrance and exit of the DNA which is associated with the nucleosome; plays a role in transcription regulation
  • removal of H1 causes the chromatin to be looser
31
Q

What is the function of Sp1? How is the function influenced by the presence of histone H1?

A
  • Sp1 activates transcription
  • activators are not required for transcription
  • presence of histones do not inhibit transcription
  • darker bands means you have more transcripts
  • H1 can outcompete the effects of an activator
32
Q

How do nucleosomes play a role in transcriptional regulation?

A

Nucleosomes generally repress transcription by sterically preventing the access of regulatory proteins to promoter sequences

-H1 participates in this activity by stabilizing the nucleosomes on the DNA and promoting higher-order chromatin structure that further compacts nucleosomal DNA

33
Q

What is the function of the chromatin remodeling complex (CRC)?

A
  • slide nucleosomes
  • remove the nucleosome
  • replace the nucleosome
34
Q

What is the function of histone modifying enzymes (HME)? What is the difference between cis acting and trans acting histone modifying enzymes?

A

HME affect chromatin structure:

  • cis: directly acts (no middle man)
  • trans: uses a secondary (intermediate protein)
  • histone modifying proteins stick methyl groups to loosen DNA strands

Cis: closed-open

35
Q

3 possible results from the action of the chromatin remodeling complex (CRC):

A
  • eject the nucleosome
  • move the nucleosome
  • change out the variants
36
Q

Where on the histone do the majority of modifications occur?

A

Histone tails

37
Q

Would histone acetyltranserases (HATs) be an example of of a CRC or HME?

A
  • HATs modify histone subunits and acetylate specific residues in a histone tail
  • acetylation of lysine residues
  • acetylation = activation
  • methylase
  • cis interactions are histone modifying enzyme
  • HAT would be an HME
38
Q

What are the different types of modifications that have been observed on histones?

A
  • acetylation of lysines
  • methylation of lysine, arginine
  • phosphorylation of serine
  • ubiquitination of lysine
39
Q

Acetylation of specific lysine residues by HATs results in the activation of transcription. Why might the attachment of an acetyl group to a lysine have this effect on transcription?

A

Acetyl groups can be added to lysine to neutralize the positive groups on histone and loosen the DNA

40
Q

Are histone modifications reversible?

A

Yes

41
Q

Since both marked and unmarked nucleosomes are distributed between the replicated strands of DNA how can this result in the passing of the message by CRC?

A
  • marked is modified by DNA
  • more acetylated histones have a “louder” message to pass on
  • CRC (bromodomain HAT in figure) detect acetylated histones and makes all histones acetylated and can actively transcribe

Molecular Biology (4 decks)

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