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Nucleic Acid Biochem II > 23 Chromatin > Flashcards

23 Chromatin Flashcards

331-352 734-736

1
Q

What is chromatin?

A

The filamentous material of chromosomes, comprised of DNA with associated histones and non-histone proteins

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2
Q

When does a chromosome consist of two sister chromatids joined at their centromere?

A

Metaphase

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3
Q

What is the nuclear matrix?

A

A fibrillar network of protein that remains in the region of the nucleus after eukaryotic cells are treated with detergent and Dnase I. Includes the lamins that makes up the nuclear lamina

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4
Q

What are 4 functions of chromatin?

A

1) to package DNA into a smaller volume to fit in the cell,
2) to strengthen the DNA to allow mitosis,
3) to prevent DNA damage, and
4) to control gene expression and DNA replication

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5
Q

What are the three levels of chromatin organization?

A
  • DNA wraps around histone proteins forming nucleosomes; the “beads on a string” structure (euchromatin).
  • Multiple histones wrap into a 30 nm fibre consisting of nucleosome arrays in their most compact form (heterochromatin).
  • Higher-level DNA packaging of the 30 nm fibre into the metaphase chromosome (during mitosis and meiosis).
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6
Q

How big is the diameter of chromatin filaments? What is the structure of this filament?

A

30 nm diameter helical structure called a solenoid

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7
Q

What are regions of the genome that attach to the nuclear matrix called?

A

Matrix association regions (MARs) or scaffold attachment regions (SARs)

Both mean the same thing and these regions have lower gene expression

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8
Q

Starting at helical DNA and ending at metaphase chromosomes, label the forms of chromatin that can be observed

A
  • Duplex DNA
  • Beads on a string form of chromatin (DNA + histones = nucleosomes)
  • 30 nm chromatin fiber of packed nucleosomes (solenoid)
  • Chromosomes scaffold is attached to solenoid chromatin fibres (interphase scaffold-associated chromatin)
  • Condensed scaffold associated chromatin
  • Metaphase chromosome
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9
Q

How wide is a metaphase chromosome?

A

1400 nm

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10
Q

How wide is condensed scaffold associated chromatin?

A

700 nm

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11
Q

How wide is looped chromatin tightly attached to chromosome scaffolds?

A

300 nm

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12
Q

How wide is a chromatin fibre of packed nucleosomes?

A

30 nm

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13
Q

How wide are nucleosomes?

A

11 nm

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14
Q

How wide is duplex DNA?

A

2 nm

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15
Q

What is a bacterial nucleoid?

A

DNA complexed with basic proteins (not histones)

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16
Q

Is nucleoid DNA relaxed or supercoiled?

A

Highly supercoiled and stretched out

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17
Q

Is the bacterial nucleoid free floating or tethered to the cell membrane?

A

Tethered to the cell membrane

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18
Q

What are non-supercoiled loops of DNA in the nucleoid called?

A

Broken loops

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19
Q

What are the three components of a nucleoid?

A
  • A protein core
  • Supercoiled DNA loops attached to protein core
  • Broken loops attached to protein core
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20
Q

What is gene rich (active) portion of the genome called?

A

Euchromatin

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21
Q

What is genetically inactive chromatin called?

A

Heterochromatin

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22
Q

What is one difference between euchromatin and heterochromatin?

A

Euchromatin is lightly staining and heterochromatin is darkly staining

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23
Q

What are the two types of heterochromatin?

A
  • Constitutive heterochromatin

- Facultative heterochromatin

24
Q

What is constitutive heterochromatin?

A

DNA containing no genes, always present in a compacted form (eg. centromeric and telomeric DNA) and comprised of A/T rich repetitive DNA sequence

25
Q

What is facultative heterochromatin?

A

DNA that contains genes that are differentially active/inactive in a certain tissues or cells during certain period of development.

26
Q

When a fibroblast becomes a fibrocyte, what form of chromatin will probably change in terms of gene expression?

A

Facultative heterochromatin

27
Q

Where does DNA methylation primarily occur?

A

Primarily in C residues that are 5’ to G residues (CpG islands)

eg. 5’ CpG 3’

Found at a higher density near gene promoters in vertebrate genomes

28
Q

Methylation is associated with ____ of gene activity

A

repression

29
Q

What is the only methylated base in eukaryotic DNA?

A

5-methylcytosine in eukaryotes and N6-methyladenine in prokaryotes

30
Q

What are Dnase I hypersensitive sites?

A

Region of the genome susceptible to digestion by nucleases

31
Q

Dnase I hypersensitive sites are associated with actively or non-actively transcribed regions of the genome?

A

Dnase I hypersensitive sites are associated with actively transcribed regions of the genome

32
Q

What does Dnase I do at Dnase I hypersensitive sites (2 things)?

What is the purpose of this?

A
  • Removes nucleosomes
  • Remodels nucleosomes

Allows transcription apparatus to access nucleosome bound DNA

33
Q

What are the fundamental units of chromatin structure?

A

Histones

34
Q

What are the five main proteins of a histone?

A
  • H1
  • H2A
  • H2B
  • H3
  • H4
35
Q

What two amino acids are histones rich in? Why?

A

Lysine and arginine

These are basic amino acids

36
Q

Which histone protein is associated with linker DNA?

A

H1

37
Q

Which histones make up the histone octamer?

A
  • H2A
  • H2B
  • H3
  • H4

Two each of these make up the histone octamer

38
Q

All known eukaryotic H4 sequences are 102 amino acids in length. What does this say about the evolution of histones?

A

They are very conserved across eukaryotic evolution

39
Q

How many bp of DNA are wrapped around the histone octamer?

A

146 bp

40
Q

How many turns does DNA make around the histone octamer? Is this right handed or left handed?

A

About 1.7 left-hand turns

41
Q

What is the natural state for eukaryotic genes in chromatin?

A

Repression (gene OFF) from the condensed chromatin solenoid fibre

42
Q

When a gene is ON, what is the chromatin structure?

A

Chromatin is decondensed and there is usually a mediator bridge between activators and the Pol II complex which somewhat holds chromatin decondensed.

43
Q

Repressors are to condensed chromatin as activators are to _____?

A

Decondensed chromatin

44
Q

how to transcription factors and initiation complexes bind DNA in the presence of nucleosomes?

A

Gene/cell/tissue specific PROTEIN FACTORS that enable promoter regions to be able to accept the transcription machinery through chromatin remodelling.

ANSWER: Histone/nucleosome modification through chromatin remodelling by protein factors.

45
Q

How does the actively transcribing RNA polymerase complex pass through arrays of nucleosomes?

A

Addition of polymerase elongation factors to the transcription complex.

Some of these function as nucleosome remodelling factors which temporarily displace the nucleosomes.

46
Q

What does acetylation of histones at their N-terminal domain cause?

A

Causes histones to decrease in positive charge, thereby relaxing how strongly DNA is bound to them. Also reduces nucleosomes affinity for each other to create 30 nm fibres

This allows for greater gene expression.

47
Q

What does deacetylation of histones at their N-termal domain cause?

A

Takes away acetylation of histone cores, which restores their positive charge and therefore causes DNA to more tightly bind to histones.

48
Q

Is the basic domain or the histone fold domain acetylated/deacetylated for changes in gene expression?

A

The basic domain is acetylated or deacetylated

49
Q

What proteins acetylate histones?

A

HATs (histone acetyltransferases) use acetyl-coenzyme A to acetylize hisones

50
Q

Histone acetyltransferase transfers acetyl moieties to what residues in the N-terminal regions of each of the core histones?

A

Lysine residues

51
Q

HAT (histone acetyltransferase) activity can be seen in some of what transcription factors?

A

TAFs (TATA binding associated factors)

52
Q

What proteins remove acetyl groups from histones?

A

Histone deacetylases

53
Q

What are chromatin remodeling factors (chromatin remodelling machines)?

A
  • Protein complexes that enable promoter regions to accept/interact with the transcription apparatus
54
Q

What do chromatin remodeling factors do?

A

Alter nucleosome assembly and positioning on the DNA

55
Q

What regions of DNA do chromatin remodelling factors interact with? (3)

A
  • Regions of methylated DNA
  • DNA binding factors
  • Histone tails

Nucleic Acid Biochem II (8 decks)

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