Nucleosome

When Chromosomes are lysed gently, a 250 Ǻ thick chromatin network is obtained.
After treatment with reagents like EDTA or sodium citrate, which remove the calcium ions, 100 Ǻ thick fibres are obtained, indicating thereby that each 250 Ǻ thick fibres is composed of two 100 Ǻ. The 100 Ǻ fibres are composed of DNA and protein.
When the protein portion is digested by pronase, the DNA double helix is exposed. In conjunction with histones the DNA duplex contracts a great deal and becomes considerably thick to form the 100 Ǻ fibre.
The 250 Ǻ fibres, which are sometimes branched, are perhaps formed due to the foldings of a 100 Ǻ fibre. How the 250 Ǻ fibers are organized to form the chromosomes is still a mystery, but the organization of 100 Ǻ fibers is more or less known.

Olius and Olius (1973) and woodcock (1973) exposed isolated nuclei to hypotonic buffers and centrifuged them through a formaldehyde solution onto a grid.
When seen through the electron microscope, such preparations appeared as beads on a string.
They suggested that the beaded structure represents highly compact particles of DNA and histones in a regular repeating array.
These particles, 70 to 90 Ǻ across, were later called nucleosome by Oudet et al. (1975).
Nucleosome (or nu bodies) have now been crystallized and subjected to neutron-scattering, X-ray diffraction, nuclease digestion and high resolution electron microscopy.
These studies suggest that four out of the five types of histone molecules found in eukaryotic cells, associate with each other to form dimers, which in turn associate to form an octamer.
The DNA double helix, about 140 nucleotide pairs long, is wrapped around the octamer, forming approximately 1¾ turns around the histone octamer.
This core particle is discoid or oblate and adjacent particles are connected by the intercore DNA helix.
Treatment of chromatin with micrococcal nuclease cuts the connecting double-stranded DNA to generate nucleosomal monomers, each containing about 160 base pairs of DNA. Further digestion removes the spacer helix and results into the core nucleosome with about 140 base pairs.
The size of DNA fragments from diverse cell types indicates that the nucleosome structure is the same whereas there is a wide variation in the size of the spacer. Prolonged digestion results into subnucleosomal particles.

Chromatin → Nucleosomal monomers Containing the spacer DNA (160 base pairs) → Core nucleosomes (140 base pairs) → Subnucleosomal particles

Four (H2A, H2B, H3, and H4) out of the five types of histones are associated with the nucleosome core.
Equimolar amounts of these four inner histones can be used to reconstruct nucleosomes.
Mixtures of H3 and H4 also permit the organization of nucleosome-like particles, but individual histones or mixtures of H2A and H2B fail to do so. Thus, H3 and H4 appear to play a crucial role in the organization of nucleosomes.
The 140 base pair long DNA associated with the core nucleosome is frequently cut by DNase I at approximately 20, 40, 50, 100, 120 and 130 bases from the 5’ end, indicating thereby that these are the sites which are not in close association with the inner histones and are therefore more prone to nuclease digestion.

H1 has been found to be associated with the spacer region.
The size of H1 histone and its content of basic amino acids control the length of the spacer DNA.
It is believed to control the super-nucleosomal organization (e.g. coiling and supercoiling of the helix) in the chromosomes.
The 200-300 Ǻ wide chromatin fibres become thinner after the removal of H1 histones and reagents which bring about cross-linking result into polymerization of H1 molecules.
It has been suggested that H1-H1 contacts are possibly responsible for the stabilization of the 200-300 Ǻ thick chromatin thread.
As soon as these contacts are severed by the removal or modification of H1 histones, the nucleosomal beads on a string can be clearly seen.

Nucleosome has a packaging function, organizing the constituent DNA into a structure about six fold shorter than the DNA duplex.
Folding of these DNA results into a close-packed alignment of nucleosomes and shortens the DNA by another factor of 5 or 10 into 200-300 Ǻ thick fibres.
The entire eukaryotic DNA, whether transcriptionally active or inactive, is organized into nucleosomes.
Chromatin structure and nucleosomal conformation is altered in some unknown way at the time of transcription.
This is essential to expose the DNA for RNA synthesis.

🔹 PART A: Basic Concept of Nucleosome

Q1. The term “nucleosome” was first coined by:
A. Olius and Woodcock
✅ B. Oudet et al.
C. Watson and Crick
D. Hershey and Chase

Q2. The appearance of chromatin as “beads on a string” was first observed by:
✅ A. Olius and Woodcock
B. Franklin and Wilkins
C. Watson and Crick
D. Pauling and Corey

Q3. Each bead in the “beads on a string” model represents:
✅ A. Nucleosome
B. Chromatid
C. Histone tail
D. Satellite

Q4. Nucleosome core particles are approximately:
A. 30–40 Å wide
✅ B. 70–90 Å wide
C. 200–250 Å wide
D. 300 Å wide

Q5. Nucleosomes contain:
✅ A. DNA and histone proteins
B. RNA and histone proteins
C. Lipids and DNA
D. RNA and centromeres

🔹 PART B: DNA-Histone Interaction & Structure

Q6. The core histones involved in nucleosome formation include all EXCEPT:
A. H2A
B. H3
✅ C. H1
D. H4

Q7. The nucleosome core contains how many base pairs of DNA?
✅ A. ~140 bp
B. 100 bp
C. 250 bp
D. 70 bp

Q8. Histone H1 is associated with:
✅ A. Spacer DNA between nucleosomes
B. Inner core of nucleosome
C. Telomeric regions
D. Replication fork

Q9. Each nucleosome core is made of:
✅ A. Histone octamer
B. Tetramer
C. Hexamer
D. Pentamer

Q10. The histone octamer is composed of:
A. H1 x 4
B. H2A, H2B x 2 only
✅ C. 2 x (H2A, H2B, H3, H4)
D. All 5 types of histones

🔹 PART C: Nucleosome Assembly & Function

Q11. The DNA wraps around the histone octamer making:
✅ A. 1¾ turns
B. ½ turn
C. 2 turns
D. 1 full turn

Q12. Spacer DNA in nucleosomes contains approximately:
✅ A. ~20 bp
B. ~140 bp
C. ~40 bp
D. ~20–60 bp

Q13. Micrococcal nuclease digestion first releases:
✅ A. Nucleosomal monomers
B. Chromosomes
C. Centromeres
D. Polysomes

Q14. Further digestion of nucleosomal monomers results in:
A. mRNA
B. Histone fragments
✅ C. Core nucleosome
D. Exon only

Q15. Subnucleosomal particles are formed after:
✅ A. Prolonged nuclease digestion
B. ATP hydrolysis
C. Transcription
D. Translation

🔹 PART D: Advanced Structure and Histone Roles

Q16. H1 histone helps in:
✅ A. Higher-order DNA coiling
B. DNA replication
C. Transcription only
D. Ribosome formation

Q17. H1 histone affects:
A. Centromere size
✅ B. Spacer DNA length
C. Telomere shape
D. Protein synthesis

Q18. Which of the following histones is not part of the nucleosome core?
✅ A. H1
B. H4
C. H3
D. H2B

Q19. Which two histones alone can form nucleosome-like particles?
✅ A. H3 and H4
B. H2A and H2B
C. H1 and H2A
D. H2B and H4

Q20. The DNase I cutting pattern on core DNA indicates:
✅ A. Loose association regions
B. No binding sites
C. Ribosomal RNA presence
D. Presence of centrioles

🔹 PART E: DNA Compaction

Q21. Nucleosomes shorten DNA length by:
A. 2 times
✅ B. 6 times
C. 10 times
D. 100 times

Q22. Further coiling of nucleosomes creates chromatin fibers of width:
A. 70 Å
B. 100 Å
✅ C. 200–300 Å
D. 500 Å

Q23. What stabilizes the 200–300 Å chromatin thread?
A. Telomerase
✅ B. H1–H1 contact
C. Histone H3
D. RNA polymerase

Q24. Upon removal of H1, the chromatin appears as:
A. Tight spiral
✅ B. Beads on a string
C. Dense heterochromatin
D. Looped domains

Q25. Which of the following causes polymerization of H1?
✅ A. Cross-linking reagents
B. DNase
C. RNAase
D. ATPase

🔹 PART F: Chromatin Remodeling and Activity

Q26. Nucleosome structure changes during:
✅ A. Transcription
B. DNA methylation
C. Cell death
D. Telomere shortening

Q27. The chromatin state in transcriptionally active genes is:
A. Permanently condensed
B. In heterochromatin
✅ C. Relaxed/open
D. Looped tightly

Q28. During gene expression, nucleosomes:
A. Become more compact
✅ B. Undergo remodeling
C. Shrink
D. Are destroyed

Q29. Transcription requires the exposure of:
A. Centromere
B. Telomere
✅ C. DNA from nucleosomes
D. Histones only

Q30. Which histone is modified most commonly for transcriptional regulation?
✅ A. H3
B. H1
C. H2B
D. H4

🔹 PART G: PYQs (NEET / CUET / UPSC Style)

Q31. (NEET 2020) Nucleosome consists of:
A. Only DNA
✅ B. DNA + histone octamer
C. RNA + DNA
D. Lipids + DNA

Q32. (CUET 2022) Beads on a string appearance is due to:
A. Telomeric DNA
✅ B. Nucleosome
C. Centrioles
D. rRNA

Q33. Which histone regulates supercoiling of DNA?
✅ A. H1
B. H4
C. H2B
D. H3

Q34. (UPSC 2020) Which histones can form tetramers alone?
✅ A. H3 & H4
B. H1 & H2A
C. H2A & H2B
D. H4 & H2B

Q35. (CUET 2023) DNA in core nucleosome is:
A. 100 bp
✅ B. ~140 bp
C. 300 bp
D. ~200 bp

🔹 PART H: Conceptual & Fact-Based

Q36. The chromatin structure is consistent across:
✅ A. All cell types
B. Prokaryotes only
C. Somatic cells only
D. Ribosomes

Q37. Spacer DNA is most variable in:
✅ A. Length
B. Base composition
C. Histone content
D. RNA transcription

Q38. Nucleosomes are absent in:
✅ A. Prokaryotes
B. Eukaryotes
C. Fungi
D. Plants

Q39. Basic unit of DNA packaging in eukaryotes:
A. Histone
✅ B. Nucleosome
C. Ribosome
D. Operon

Q40. The protein responsible for tightening DNA into 100 Å fiber is:
✅ A. Histone
B. Telomerase
C. RNA
D. Centromere

🔹 PART I: Experimental Insight

Q41. Treatment with EDTA or sodium citrate yields:
✅ A. 100 Å chromatin fibers
B. 250 Å chromatin fibers
C. Nucleosomes
D. Ribosomes

Q42. The removal of calcium ions leads to:
✅ A. Thinner chromatin structure
B. Cell lysis
C. DNA replication
D. Transcription

Q43. Which reagent digests chromatin proteins?
✅ A. Pronase
B. DNase
C. Ligase
D. Protease K

Q44. Histone octamers are:
✅ A. Oblate/discoid
B. Linear
C. Helical
D. Cuboidal

Q45. Which technique can be used to study nucleosome structure?
A. Spectrophotometry
✅ B. Neutron scattering
C. Centrifugation only
D. PCR

🔹 PART J: Miscellaneous

Q46. Nucleosome is stable because of:
✅ A. Histone-DNA interaction
B. mRNA pairing
C. Telomerase binding
D. rRNA alignment

Q47. Length of nucleosomal DNA (with linker):
A. 100 bp
✅ B. ~160 bp
C. 300 bp
D. 90 bp

Q48. Core nucleosome contains:
✅ A. DNA tightly bound to histones
B. Loosely bound DNA
C. Only RNA
D. Replication fork

Q49. Spacer DNA connects:
✅ A. Two nucleosomes
B. Telomeres and centromeres
C. Exons
D. Transposons

Q50. Function of nucleosome in eukaryotic genome:
✅ A. DNA packaging and regulation
B. Protein synthesis
C. tRNA splicing
D. Cell signaling