NUCLEOSOME ORGANIZATION
- This model was proposed by Kornberg and Thomas in 1974 to explain the structure of chromatin fibres.
- This has been widely accepted all over the world.
- According to this model, chromatin is composed of a repeating unit called nucleosome.
Important points of this model are as follows:
- Chromatin fibres of a chromosome are made up of DNA and histone proteins.
- The repeating unit of chromatin is called nucleosome.
- It is a disc-like structure 11nm in diameter and 6 nm in height.
- The core of a nucleosome is made up of an octamer of proteins having two molecules each of H2A, H2B, H3 and H4 histones.
- Around this octamer, a DNA segment having the length of 200 base pairs is wound round making one 3/4 turns.
- This segment of DNA in chromatin fibre is nuclease resistant.
- The structure of the nucleosome is invariable in all the eukaryotes.
- P. Oudet et al. (1975) worked extensively on the structure of nucleosomes and proposed that the length of the DNA segment in the core of nucleosome is 146 base pairs.
- Two nucleosome units are joined with a segment of DNA, which is called linker.
- It consists of 50-70 base pairs.
- H1 histone is associated with this linker DNA which makes a connection between two adjacent nucleosomes.
- The nucleosome model explains the ‘string of beads’ concept of chromatin.
- This is just opposite to the concept of ‘beads on string’ explaining the interrelationship of genes and chromosomes.
- Aron Clug (1977-80) made further electron microscopic studies of chromosomes and chromatin and proposed the ‘Solenoid model of nucleosome’.
- This model describes the dense compaction of DNA in chromosomal chromatids.
- It further illustrates that chromatin fibers tightly coil in a chromosome and form lump-like structures.
- The average diameter of this chromatin lump is 300 Å in which several nucleosomes of 100 Å diameter are found.
- As has been mentioned earlier each nucleosome is made up of protein octamer around which a DNA segment of 200 base pairs was found forming one3/4 turn.
- Through the process of supercoiling, such nucleosomes with the help of linker DNA easily form the solenoid-like structure.
SOLENOID MODEL:
- It was also shown that an 11 nm wide fiber of nucleosomes gets coiled upon itself to form – 30 nm wide helix with five or six nucleosomes per helix.
- In this helix successive nucleosome units came close together, so that their center to center distance was about 10 nm.
- This 30 nm structure was called a solenoid.
- Formation of solenoid from nucleosomes can be compared with winding of a cable on a spool and then folding of wrapped spools.
- It was also proved that H1 protein helped in folding of 110 A wide fiber into 300 armstrong wide solenoid,
- It has been shown that H1 molecules aggregate by cross linking to form polymers and may thus control the formation of solenoids.
- The above account gives patterns of coiling and packing of DNA. Since 60 nm along
- DNA is coiled in a nucleosome, only 6nm long, and then nucleosomes are coiled in 30 nm wide solenoid fibers, giving DNA a packing ratio of 1:50.
- However, in highly condensed chromosomes, the packing ratio is actually 1:5000, which is 100 times greater than provided by solenoid, which would take place by further coiling and folding of solenoid.
Ubiquitination, acetylation, methylation and phosphorylation of histones in the nucleosome.
- The histone proteins, which are integral parts of nucleosomes undergo a variety of modifications to bring about decondensation of chromatin, to allow access of DNA replication or transcription machinery to naked DNA.
- These modifications include ubiquitination, acetylation, methylation and phosphorylation of some specific amino acid residues of histones.
- Acetylation and methylation occur on the free amino groups of lysines residues. Methylation also occurs on arginine and histidine.
- Similarly, phosphorylation occurs on the hydroxyl group of serine and histidine.
- Methylation and acetylation remove the positive charge on NH3+, while phosphorylation introduces a negative charge in the form of phosphate group.
1-10: Basic Concepts of Nucleosome Organization
- Who proposed the nucleosome model of chromatin organization?
a) Watson and Crick
b) Kornberg and Thomas
c) Oudet and Clug
d) Franklin and Wilkins
✅ Answer: b) Kornberg and Thomas - The fundamental unit of chromatin organization is called:
a) Histone
b) Nucleosome
c) Chromatid
d) Linker DNA
✅ Answer: b) Nucleosome - The core of a nucleosome consists of:
a) Five histone proteins
b) Two molecules each of H2A, H2B, H3, and H4
c) H1 histone only
d) Non-histone proteins
✅ Answer: b) Two molecules each of H2A, H2B, H3, and H4 - Histone H1 is associated with:
a) The core nucleosome
b) Linker DNA
c) DNA polymerase
d) RNA transcription
✅ Answer: b) Linker DNA - The diameter of a nucleosome is:
a) 30 nm
b) 11 nm
c) 6 nm
d) 50 nm
✅ Answer: b) 11 nm - How many base pairs of DNA wrap around a nucleosome core?
a) 146 bp
b) 200 bp
c) 50 bp
d) 100 bp
✅ Answer: a) 146 bp - The total length of DNA per nucleosome, including linker DNA, is:
a) 146 bp
b) 200 bp
c) 100 bp
d) 50 bp
✅ Answer: b) 200 bp - Which of the following is not a histone protein found in the nucleosome core?
a) H2A
b) H2B
c) H5
d) H4
✅ Answer: c) H5 - The nucleosome model supports the ‘string of beads’ concept. What does this mean?
a) DNA is in a circular form
b) DNA wraps around histones in repeating units
c) Chromatin is highly condensed
d) Genes are evenly spaced along DNA
✅ Answer: b) DNA wraps around histones in repeating units - The enzyme nuclease is used to study chromatin structure because it:
a) Cleaves non-histone proteins
b) Degrades RNA molecules
c) Digests unprotected DNA
d) Modifies histones
✅ Answer: c) Digests unprotected DNA
11-20: Solenoid Model and Higher Order Chromatin Structure
- Who proposed the solenoid model of nucleosome organization?
a) Kornberg and Thomas
b) Oudet et al.
c) Clug
d) Watson and Crick
✅ Answer: c) Clug - The solenoid model explains:
a) DNA base pairing
b) DNA supercoiling in chromatin
c) Ribosome formation
d) DNA replication
✅ Answer: b) DNA supercoiling in chromatin - What is the diameter of a solenoid chromatin fiber?
a) 11 nm
b) 30 nm
c) 50 nm
d) 100 nm
✅ Answer: b) 30 nm - How many nucleosomes are present per turn in the solenoid structure?
a) 3
b) 5-6
c) 10-12
d) 15
✅ Answer: b) 5-6 - What role does H1 histone play in solenoid formation?
a) It helps fold nucleosomes into 30 nm fibers
b) It directly binds to DNA bases
c) It unwinds chromatin
d) It breaks chromatin fibers
✅ Answer: a) It helps fold nucleosomes into 30 nm fibers - The packing ratio of DNA in the solenoid model is:
a) 1:10
b) 1:50
c) 1:1000
d) 1:5000
✅ Answer: b) 1:50 - What is the center-to-center distance between adjacent nucleosomes in the solenoid model?
a) 5 nm
b) 10 nm
c) 30 nm
d) 50 nm
✅ Answer: b) 10 nm - In highly condensed chromosomes, the DNA packing ratio increases to:
a) 1:100
b) 1:500
c) 1:5000
d) 1:10,000
✅ Answer: c) 1:5000 - What is the significance of nucleosome supercoiling?
a) Helps in DNA condensation
b) Aids in gene transcription
c) Protects DNA from damage
d) All of the above
✅ Answer: d) All of the above - How is the solenoid model different from the ‘beads on string’ model?
a) Solenoid model is more compact
b) ‘Beads on string’ model represents loosely packed chromatin
c) Solenoid model involves higher-order folding
d) All of the above
✅ Answer: d) All of the above
21-30: Histone Modifications in Chromatin Regulation
- Which histone modification removes the positive charge from histones?
a) Methylation
b) Acetylation
c) Ubiquitination
d) Phosphorylation
✅ Answer: b) Acetylation - Methylation of histones occurs on which amino acid residues?
a) Lysine and arginine
b) Serine and threonine
c) Proline and histidine
d) Glycine and leucine
✅ Answer: a) Lysine and arginine - Histone phosphorylation introduces what type of charge?
a) Positive
b) Negative
c) Neutral
d) No change
✅ Answer: b) Negative - Which modification activates gene transcription?
a) Histone acetylation
b) Histone methylation
c) Histone ubiquitination
d) Histone phosphorylation
✅ Answer: a) Histone acetylation - Histone deacetylation leads to:
a) Gene activation
b) Gene silencing
c) mRNA degradation
d) Chromosome fragmentation
✅ Answer: b) Gene silencing
31-40: Chromatin Structure and Function
- The main function of chromatin is to:
a) Store energy
b) Regulate gene expression
c) Convert DNA into RNA
d) Break down proteins
✅ Answer: b) Regulate gene expression - The histone proteins found in nucleosomes are:
a) Acidic proteins
b) Basic proteins
c) Neutral proteins
d) Non-protein molecules
✅ Answer: b) Basic proteins - Histone octamer is composed of:
a) H1, H2A, H2B, H3, H4
b) Two molecules each of H2A, H2B, H3, and H4
c) H1 and non-histone proteins
d) H3 and H4 only
✅ Answer: b) Two molecules each of H2A, H2B, H3, and H4 - What is the charge of histones in nucleosomes?
a) Negative
b) Positive
c) Neutral
d) Varies with modification
✅ Answer: b) Positive - Which of the following statements is true about linker DNA?
a) It is 10-20 base pairs long
b) It connects adjacent nucleosomes
c) It is associated with histone H3
d) It is part of the histone octamer
✅ Answer: b) It connects adjacent nucleosomes - The major function of histone H1 is to:
a) Bind to core DNA
b) Organize linker DNA
c) Unwind the nucleosome
d) Degrade chromatin
✅ Answer: b) Organize linker DNA - In eukaryotes, chromatin exists in two forms:
a) Euchromatin and heterochromatin
b) DNA and RNA
c) Linear and circular
d) Histone and non-histone proteins
✅ Answer: a) Euchromatin and heterochromatin - Euchromatin is characterized by:
a) Tightly packed chromatin
b) Active gene transcription
c) Gene silencing
d) No histone proteins
✅ Answer: b) Active gene transcription - Heterochromatin is characterized by:
a) Loosely packed DNA
b) Inactive gene transcription
c) High levels of acetylation
d) No nucleosomes
✅ Answer: b) Inactive gene transcription - What is the function of nucleosome positioning?
a) Enhances DNA stability
b) Regulates access to transcription factors
c) Controls DNA methylation
d) Prevents chromatin condensation
✅ Answer: b) Regulates access to transcription factors
41-50: Chromatin Compaction and Higher-Order Organization
- The first level of chromatin organization is:
a) Nucleosome formation
b) DNA looping
c) Solenoid structure
d) Chromosome formation
✅ Answer: a) Nucleosome formation - The second level of chromatin folding is:
a) DNA compaction
b) Solenoid structure
c) Nucleosome positioning
d) Gene transcription
✅ Answer: b) Solenoid structure - Which higher-order structure compacts chromatin beyond the solenoid model?
a) 300 nm looped domains
b) 700 nm metaphase chromatin
c) Both a and b
d) None of the above
✅ Answer: c) Both a and b - Chromatin fibers form loops attached to a:
a) Histone H1 scaffold
b) Nuclear matrix
c) Cytoplasm
d) Nucleolus
✅ Answer: b) Nuclear matrix - The final level of chromatin packing is observed in:
a) Interphase
b) Metaphase chromosomes
c) Ribosomes
d) Mitochondria
✅ Answer: b) Metaphase chromosomes - What is the function of topoisomerase in chromatin?
a) Unwinds DNA
b) Breaks and rejoins DNA strands
c) Condenses chromatin
d) Modifies histones
✅ Answer: b) Breaks and rejoins DNA strands - How is chromatin structure regulated during the cell cycle?
a) Histone modifications
b) ATP-dependent remodeling
c) Both a and b
d) None of the above
✅ Answer: c) Both a and b - Chromatin condensation increases during:
a) Interphase
b) Mitosis
c) Transcription
d) DNA repair
✅ Answer: b) Mitosis - The primary function of chromatin compaction is to:
a) Allow efficient DNA storage
b) Regulate gene expression
c) Facilitate DNA replication
d) All of the above
✅ Answer: d) All of the above - In what phase does chromatin become highly compact?
a) S-phase
b) Metaphase
c) G1 phase
d) G2 phase
✅ Answer: b) Metaphase