02. Chromatin Structure — Levels of Organization & Histones

Question 1

What is the nucleoid in bacteria?

Answer 1

• The bacterial ‘chromosome’ consists of supercoiled and relaxed DNA.
• In loops called domains.
• Compacted via HU proteins and supercoiling.

Question 2

What is restricted vs. unrestricted supercoiling?

Answer 2

• Restricted — around a protein, no tension
• Unrestricted — free, high tension

Question 3

Describe eukaryotic chromatin.

Answer 3

• Beads on a string.
• Chromosomes are singular linear DNA molecules.
• Together they make up the genome.

Question 4

Describe the levels of organization that make up the chromosome.

Answer 4

• Nucleosome — the ‘bead’. Contains a core particle: octet of histones wrapped by DNA.
  
  • Histones consist of 5 subunits:
    
    • H1 — linker protein that ‘staples’ nucleosomes tighter; associates with DNA + octet in the linker region between nucleosomes, wraps DNA tighter around nucleosome.
    • H2A, H2B, H3, H4 — form an octet that interacts with DNA via electrostatic interactions
• Fibres — nucleosomes + linker DNA condensed into 10-30 nm fibers.
• Chromosome — fibres condense into metaphase chromosomes via attachment to scaffolding proteins.
• Chromatin — organized into territories.

Question 5

Describe the different kinds of chromatin.

Answer 5

• Euchromatin — transcriptionally active DNA.
• Heterochromatin — transcriptionally inactive DNA.
  
  • Constitutive — highly condensed, repetitive DNA.
    
    • Telomeres (end of a chromosome)
    • Centromere (attachment point)
  • Facultative — inactive in particular tissues.

Question 6

What are the different kinds of chromatin elements?

Answer 6

• Locus control regions — control chromatin condensation
• Matrix associated regions — AT-rich
• Insulators — regulatory sequences

Question 7

What are some non-histone proteins involved in chromatin organization?

Answer 7

• DNA replication proteins
• Proteins that bind to matrix/scaffold attachment regions.
• Structural maintenance proteins.

Question 8

What role do histone tails play in transcription/replication?

Answer 8

• Modification of histone tails provides signals to transcription + replication proteins.
  
  • Methylation — (in)activation of genes
  • Ubiqutinylation — non-destructive
  • Phosphorylation — active genes
  • Acetylation — active genes — needed for transcription
• Proteins read histone tail modifications to ‘read’ chromatin