Chromatin, Practice Problems and FAQs

You know that whatever we do; physically and physiologically are controlled by our brain. Just like the brain controls our body functions, which is that organelle that controls all the functions of a cell? Yes, it is the nucleus. Hence the nucleus is called the brain of the cells. The information for synthesising all the proteins needed for the cell and for the nucleus are present inside the nucleus. So what is that particular structure present in the nucleus which carries the information needed to synthesise proteins and thereby transferring the genetic information from one generation to the next generation? They are called chromosomes. If you consider the structure of a chromosome, you can see the two arms connected together by a centromere and kinetochore. Is this a stable structure for a chromosome? Do you think we can see the chromosome just like we explained in every cell? The answer can be no!!!

GIF: Synthesis of protein in a cell

There are different stages in the life of a cell. We can divide each stage depending on the changes happening inside the cell and this sequence of events in the life of a cell is called the cell cycle. The two major phases of the cell cycle are M - phase and interphase. M phase is the mitotic phase. But the tasks to be completed before cell division takes place, like the cell growth and the copying of genetic material (DNA) happens in the interphase. So in the interphase the genetic materials can be seen in the form of thread that spread inside the nucleus. They are called chromatin fibres, which later condense to form chromosomes. Now you will be excited to know more about the structure and functions of chromatin. We are going to discuss chromatin in detail in this article.

Fig: Cell cycle

Table of contents

• Nucleus
• Discovery of chromatin
• Chemical composition of chromatin
• Types of chromatin
• Differences between euchromatin and heterochromatin
• Functions of chromatin
• Practice Problems
• FAQs

Nucleus

Nucleus is the most conspicuous and principal organelle of the cell which possesses all the genetic information for controlling the activities of the cell. In the structure of an interphase nucleus we can observe the following:

• Nuclear envelope
• Nuclear matrix
• Nucleoplasm
• Nucleolus
• Chromatin reticulum

Nuclear envelope

It is the double membranous covering of a nucleus, which separates the cytoplasm and nuclear material. It possesses the outer and inner nuclear membranes with a perinuclear space.

Fig: Nuclear envelope

Nuclear matrix

It is the intermediate filaments of laminin in the nucleoplasm, which is the transparent semifluid substance.

Nucleolus

It is the dense and spherical structure seen in the nucleoplasm which is attached to the chromatin at a specific region called Nucleolar Organiser Region (NOR).

Chromatin reticulum

Apart from these nuclear materials, there is a stained thread like fibres seen in the nucleoplasm of stained cells and these are called chromatin fibres. It appears in the form of fine overlapping and coiled fibres which appears to produce a network called chromatin network or nuclear reticulum. If the cell is living, but unstained, the chromatin fibres can not be observed.

Fig: Structure of the nucleus

Discovery of chromatin

Chromatin was first observed by Walther Flemming, a German biologist in 1879. He found this while studying the mitotic cell divisions in the salamander embryo cells. The salamanders possess very large chromosomes. He used the basic stain called aniline dyes and found the stained threads in the nucleoplasm and called it ‘chromatin’.

Fig: Walther Flemming and his observations

Chromosome

During cell division, the chromatin fibres condense to form thick chromosomes. The number of chromosomes differ in different organisms. In higher groups of organisms, the number of chromosomes are specific, but their shapes vary. Chromosomes possess centromere or primary constriction or kinetochore, chromatin, chromatids, telomere, chromomere, secondary constriction, chromonema, and matrix.

Fig: Condensation of chromatin to form chromosome

Chemical composition of chromatin

Even though the chromatin is visible as a thread like structure, the chemical composition of chromatin is not simple. The chemical composition of the chromatin fibres include the following:

• Chromatin consists of a continuous linear DNA duplex strand.
• Associated basic proteins, histones or protamines are present in the chromatin.
• Protamines are rich in arginine.
• A small amount of RNA is also present.
• It also possesses inorganic components such as salts.
• Acidic nonhistone proteins are also present in chromatin.
• Some complex proteins, the enzymes like DNA-polymerase and RNA polymerase can also be observed in the chromatin fibres.
• It also possesses some phosphorus containing organic components.

Types of chromatin fibres

The staining process of chromatin fibres are done during the interphase stage of the cell cycle. Interphase is the longest preparatory phase of the cell cycle before cell division starts. Since the cell grows during this time and duplicates its DNA, before entering the mitosis, the structure of chromatin fibres will be easily identifiable. Chromatin fibres are of two types on the basis of location and intensity of staining. They are as follows:

• Euchromatin
• Heterochromatin

Fig: Types of chromatin in the nucleus

Euchromatin

The metabolically or transcriptionally active form of chromatin is called euchromatin. They are lightly stained and loosely packed chromatin fibres. It has a bead on string appearance under electron microscope and each bead is called a nucleosome and the thread is the DNA.

Fig: Euchromatin

Nucleosome

A nucleosome is considered as a section of DNA which is wrapped around a core of proteins and is the basic repeating subunit of chromatin packaged inside the nucleus of a cell. This model of the chromatin organisation was proposed by Roger Kornberg in 1974. It is the most accepted model of chromatin organisation.

Structure of nucleosome

A nucleosome has a complex structure and the major four parts are as follows:

• Core particle
• Double stranded DNA fragment
• Linker DNA
• H1 protein

Core particle or nu body

The core particle or nu body of a nucleosome is formed of 8 histone molecules and called a histone octamer. The histone proteins are positively charged basic proteins. A protein acquires charge due to the abundance of amino acid residues with charged side chains. The histone proteins are rich in amino acids like lysines and arginines. The core particle has two H2A molecules, two H2B molecules, two H3 molecules, and two H4 molecules that are arranged side by side. In this arrangement their positively charged ends are present towards the outside.

Double stranded DNA

The DNA which is wrapped around the core particles will be double stranded and it has 146 nucleotide pairs and forms 1.75 coils.

Linker DNA or interbead

The DNA which connects the two adjacent nucleosomes is called linker DNA or interbead. It is about 60 base pairs long.

H1 protein

The H1 histone protein helps to pack other histone molecules through the core DNA. It specifically binds to the site where the core DNA enters and exits the nucleosome. It also helps to join the two nucleosomes along with the linker DNA.

Fig: Structure of nucleosome

Chromatosome

The core particles of the nucleosome and H1 histone are together called chromatosomes. They possess mono-nucleosomes containing ∼160 bp and H1.

Solenoid structure of chromosome

When the nucleosome folds up and stalks to form a helix, then it is called a solenoid structure. Six nucleosomes make a solenoid. The diameter of a solenoid structure is 30 nm. This solenoid model of DNA was proposed first by Aaron Klug and John Finch in 1976. They used X-ray diffraction patterns and electron microscopy images to determine this model. The solenoid structure is stabilised by the H1 histones.

Fig: Solenoid structure of chromosome

Heterochromatin

The darkly stained and densely packed part of chromatin are called heterochromatin. It is gene-poor, and transcriptionally silent.

Fig: Heterochromatin

Types of heterochromatin

There are two types of heterochromatin and they are as follows:

• Constitutive heterochromatin
• Facultative heterochromatin

Constitutive heterochromatin

The hyper condensed or invariably heterochromatic regions of chromosomes containing repetitive sequences of DNA are called constitutive heterochromatin. It occurs near the centromeric region and telomeres of all the chromosomes and are genetically inactive. It serves as a structural element of the chromosome. It is present in all cells and is stable. It can be observed in all the stages of the life cycle and is mainly made up of satellite DNA.

Fig: Constitutive heterochromatin

Facultative heterochromatin

The heterochromatin which is reversible and are formed only in certain cells temporarily in certain stages of the life cycle are called facultative heterochromatin. An example for heterochromatinization is the formation of the Barr body. Barr bodies are formed by the condensation of one of the two X chromosomes (XX) in female mammals. Sex chromatin is the term used for this condensed X chromosome. Supercoiling or condensation of chromatin results in taking up more stain and is called heteropycnosis. Facultative chromosomes are made up of LINE (long interspersed nuclear elements) sequences. LINE sequence is a group of non-LTR (long terminal repeat) retrotransposons and is more common in the genome of most eukaryotes.

Fig: Facultative heterochromatin

Differences between constitutive and facultative heterochromatin

The major differences between the constitutive and facultative heterochromatin are as follows:

Differences between euchromatin and heterochromatin

The major differences between the euchromatin and heterochromatin are as follows:

Functions of chromatin

The major functions of chromatin are as follows:

• The primary function of chromatin is to pack the long DNA molecules into compact and dense structures.
• The nucleosome model prevents the tangling (twist together into a mass) of DNA strands.
• It plays an important role in reinforcing the DNA during division of cells.
• It prevents the damage of DNA.
• It helps in regulating gene expression and DNA replication.
• The proper segregation of the chromosomes in anaphase of mitosis and meiosis is facilitated by chromatin fibres.

• The characteristic shape of chromosomes is due to the high concentration of the chromatin and it helps in the splitting of sister chromatids.

Practice Problems

1. The stained thread like fibres seen in the nucleoplasm of stained cells are ________________.

1. nuclear matrix
2. nucleolus
3. chromatin
4. chromosome

Solution: Nucleus is one of the organelle that carries the genetic material. The genetic material gets transferred to the newly formed cells during cell division. The structure of a nucleus has five major parts. These are nuclear envelope, nuclear matrix, nucleoplasm, nucleolus and chromatin reticulum. Nuclear envelope is the double membranous covering of a nucleus, which separates the cytoplasm and nuclear material. Nuclear matrix is the intermediate filaments of laminin in the nucleoplasm, which is the transparent semifluid substance. Nucleolus is the dense and spherical structure seen in the nucleoplasm which is attached to the chromatin at a specific region called Nucleolar Organiser Region (NOR). Apart from these nuclear materials, there are stained thread like fibres seen in the nucleoplasm of stained cells and they are called chromatin fibres. Chromatin is the uncondensed form of the nucleoprotein complex and the condensed form of the nucleoprotein complex is called chromosomes. Hence the correct option is c.

2. Given below are the statements regarding the chemical composition of the chromatin. Find out the correct statements.

I) Chromatin consists of a continuous linear DNA duplex strand.

II) Associated basic proteins, histones or protamines are present in the chromatin.

III) Small amount of RNA is present in the chromatin.

IV) Inorganic components such as salts are present in the chromatin.

1. I, II, III, IV
2. I, II, III
3. I and III
4. I and IV

Solution: The stained fibres that resemble threads seen in the nucleoplasm of stained cells are called chromatin. It appears in the form of fine overlapping and coiled fibres which appears to produce a network called chromatin network or nuclear reticulum. Even though the chromatin is visible as a thread like structure, the chemical composition of chromatin is not simple. Chromatin consists of a continuous linear DNA duplex strand with associated basic proteins, histones or protamines. It also possesses a small amount of RNA in the structure. It possesses inorganic components such as salts. Acidic nonhistone proteins, some complex proteins, enzymes like DNA-polymerase and RNA polymerase can also be observed in the chromatin fibres. Some phosphorus containing organic components are also present in it. So all the statements given in the question are correct. Hence the correct option is a.

3. Match the types of chromatin in column A with their characters in column B.

1. I - i, II - ii, III - iii
2. I - ii, II - iii, III - i
3. I - i, II - iii, III - ii
4. I - iii, II - ii, III - i

Solution: Chromatin fibres are of two types on the basis of location and intensity of staining. They are euchromatin and heterochromatin.

• Euchromatin - It is the metabolically or transcriptionally active form of chromatin. They are lightly stained and loosely packed chromatin fibres. It has a bead on string appearance under electron microscope and each bead is called a nucleosome and the thread is the DNA.
• Heterochromatin - It is the darkly stained and densely packed part of chromatin. It is gene-poor, and transcriptionally silent. There are two types of heterochromatin and they are constitutive heterochromatin and facultative heterochromatin.
  • Constitutive heterochromatin - It is the hyper condensed or invariably heterochromatic regions of chromosomes containing repetitive sequences of DNA. It occurs near the centromeric region and telomeres of all the chromosomes and are genetically inactive. They are made up of satellite DNA.
  • Facultative heterochromatin - It is the heterochromatin which is reversible and formed only in certain cells temporarily in certain stages of the life cycle. An example for heterochromatinization is the formation of the Barr body. Hence the correct option is b.

Fig: Chromatin

4. Which histone protein helps to join the two nucleosomes along with the linker DNA?

1. H1
2. H2A
3. H2B
4. H3

Solution: The metabolically or transcriptionally active form of chromatin is called euchromatin. They are lightly stained and loosely packed chromatin fibres. It has a bead on string appearance under electron microscope and each bead is called a nucleosome. A nucleosome has a complex structure and the major four parts of a nucleosome are core particle, double stranded DNA fragment, linker DNA and H1 protein. The core particle or nu body of a nucleosome is formed of 8 histone molecules called histone octamer. It has two H2A molecules, two H2B molecules, two H3 molecules, and two H4 molecules that are arranged side by side. The H1 histone protein helps to pack other histone molecules through the core DNA. It also helps to join the two nucleosomes along with the linker DNA. Hence the correct option is a.

FAQs

1. What are the differences between chromatin and chromosomes?

Answer: Chromosomes and chromatin are observed inside the nucleus at different stages of cell cycle. The major difference between chromatin and chromosomes are as follows:

2. What is CENPA?

Answer: CENPA is also called centromere protein A. It is a protein in humans that is encoded by the CENPA gene. CENPA is a histone H3 variant and is a critical factor that determines the position of kinetochores on each chromosome in most of the eukaryotes.

3. Is heterochromatin present in bacteria?

Answer: Heterochromatin is associated with eukaryotic organisms. But bacteria have certain areas with densely protein occupied chromatin. This will silence the gene expression. Euchromatin is present in both eukaryotes and prokaryotes.

4. Are histones present in heterochromatin?

Answer: Heterochromatin has its own specific and modified histones which can form attachments between nuclear envelope and chromosomes. The common examples of histones in heterochromatin are H3K9me2, H3K9me3, and H3K27me3. In addition to this, the linker histone H1, that binds the intervening linker DNA and nucleosomes are also seen in heterochromatin.

YOUTUBE LINK: https://www.youtube.com/watch?v=tdoS1Iglj38 (54:58- 59:10)