Chapter 12: Organization of DNA

Where is DNA found in prokaryotes like E. coli? How do small bacteria fit so much genetic material inside a tiny cell? 

• In the nucleoid, a compacted region of the cell containing the bacterial chromosome.

• DNA is folded, bent, and compacted with the help of DNA-binding proteins such as HU and H-NS.

What is supercoiling?

• Supercoiling is the contortion of circular DNA to relieve underwinding or overwinding strain, making the molecule more compact.

What is a twist in DNA? Why can it cause DNA to writhe? 

• Twist (T) is the number of helical turns in a DNA molecule.

• If the DNA is underwound or overwound, energetic strain causes the DNA to writhe, forming supercoils to relieve stress.

What is positive supercoiling? Where is it found in nature?

• DNA is overwound, forming right-handed supercoils.

• Found in hyperthermophilic archaea to stabilize DNA at high temperatures.

What is negative supercoiling? Where is it found in nature? 

• DNA is underwound, forming left-handed supercoils.

• Found in most bacterial and viral circular DNAs (e.g., E. coli, SV40).

Most DNA in cells is ______________________ supercoiled. 

• negatively

What do topoisomerases do? What is the difference between Type 1 and Type 2?

• Enzymes that cut DNA strands, change supercoiling, then reseal the strands

• Type 1: cuts one strand to relieve supercoiling.

• Type 2: cuts both strands to introduce negative supercoils (e.g., DNA gyrase in bacteria).

Linear or circular? ___________________ chromosomes found in nucleus. ___________________ chromosomes found in mitochondria and chloroplasts. 

1. linear

2. circular

What is C-value? What is C-value paradox? 

1. The C-value is the amount of DNA contained within a haploid genome (one complete set of chromosomes) 

2. The C-value paradox refers to the observation that organisms with similar complexity can have vastly different genome sizes.

   1. This paradox arises because much of the DNA in many organisms is noncoding (repetitive DNA, introns, transposable elements), so genome size does not correlate directly with organismal complexity

What is chromatin? 

• Chromatin is the material that makes up chromosomes, consisting of DNA wrapped around proteins called histones.

What are histones? 

• Positively charged proteins (H1, H2A, H2B, H3, H4) that bind negatively charged DNA to help pack it into nucleosomes.

List the higher order chromatin structures in Eukaryotes.

• Nucleosome – DNA (~147 bp) wrapped around a histone octamer (2×H2A, H2B, H3, H4).

• “Beads-on-a-string” (10 nm fiber) – Nucleosomes connected by linker DNA (~20–80 bp), forming a linear structure.

• 30 nm fiber – Nucleosomes coil into a thicker fiber, stabilized by linker histone H1.

• Looped domains – 30 nm fiber forms loops (~50–200 kb), attached to a scaffold of non-histone proteins.

• Topologically associated domains (TADs) – Loops organize into functional domains that interact more frequently internally than with neighboring domains.

• Chromosome – The fully condensed mitotic chromosome, visible under a microscope during cell division.

Know the 3 components of the 10nm nucleosome. 

1. DNA (~200 bp per nucleosome, 147 bp in core particle).
   

2. Histone octamer (2× H2A, 2× H2B, 2× H3, 2× H4).
   

3. Linker DNA associated with H1.

Packing along the chromosome is less uniform during _______________________.

• Interphase (chromatin is partially decondensed)

Euchromatin is ________________ causing higher levels of transcription due to packed _______________. 2. Heterochromatin is _______________ causing lower levels of transcription due to being packed ________________; therefore, genes are more likely to be _________________. 3. Histones are octamers. They contain ____________ of each subunit ______, _______, ________, _________. 

 Euchromatin is ___less condensded__ causing higher levels of transcription due to being packed loosley_. 2. Heterochromatin is highly condensed__ causing lower levels of transcription due to being packed tightly; therefore, genes are more likely to be inactive_. 3. Histones are octamers. They contain 2 of each subunit ___H2A___, H2B__, ____H3____, _____H4____.

What does H1 do? 

• Binds linker DNA between nucleosomes, promoting higher-order folding

What do we mean by histones are highly conserved? 

• Amino acid sequences of histones are very similar across species, reflecting their essential structural role.

What are the two types of heterochromatin? Define and provide examples of each.

1. Constitutive heterochromatin: always condensed, gene-poor (e.g., centromeres, telomeres).
   
   

2. Facultative heterochromatin: can switch between active/inactive (e.g., Barr body/X inactivation).

Does the chromatin of an interphase cell differ from a metaphase cell? How so? 

Yes:

• Interphase: decondensed, dispersed in nucleus.
  
  

• Metaphase: highly condensed, visible as chromosomes.

Which is more likely to have higher gene expression: heterochromatin or euchromatin? Why? 

• Euchromatin, because DNA is less tightly packed, accessible to transcription machinery.

Define and provide examples of unique-sequence DNA and repetitive DNA sequences? 

1. Unique-sequence DNA: one or few copies, often protein-coding genes.
   
   

2. Repetitive DNA: multiple copies, often structural or regulatory, e.g., satellite DNA

Define the centromere and identify its function.

• Region where spindle fibers attach during cell division; maintains chromosome movement.

Define the telomere and identify its function.

• End of linear chromosome, protects against degradation and prevents fusion with other chromosomes.