Chromosomal Theory of Inheritance: Observations and Inheritance

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Mendel’s Laws of Inheritance and Chromosomal Theory of Inheritance – Mechanisms of Chromosome Segregation in Meiosis

After the rediscovery of Mendelism in 1900, the concept of heredity was verified by different experiments. Mendel’s theory of segregation had been accepted by scientists without confusion, but the other theory, i.e., the law of Independent Assortment, was criticized by many, yet the theory was not rejected fully. However, along with such investigations, scientists tried to see the nature of the hereditary determinants that were described as factors by Mendel. The chromosome theory of inheritance is the outcome of such investigations and the proposer of this theory were Walter Sutton and Theodor Boveri (1903). The chromosome theory of inheritance states that the chromosome is the bearer of hereditary material or genes and the transmission of genes from one generation to the other is facilitated by the transmission of the chromosomes.

Discovery of Chromosome Theory of Inheritance

Walter Sutton and Theodor Boveri (1903) independently realized that the chromosomes show the same hereditary pattern from parents to progeny as the hereditary components (Mendelian factors) are transmitted following Mendelian principles. Based on some discoveries they pointed out that the alleles of a gene segregate as the homologous chromosomes of a diploid organism segregate during meiosis to form gametes and the chromosomes of two sets may also be assorted at random during meiosis to form gametes. This indicates that the genes of different homologs may be assorted at random showing their independent segregation.

Such concepts of Sutton and Bovery were nourished by the cell theory of Sleiden and Schwann, the organization of the cell nucleus as suggested by Brown, events of fertilization as revealed by Hartwig and Strasburger, observation of cell division by Schneider and Flemming and equal distribution of chromosomes in the daughter cells from division as revealed by Von Beneden. The researchers also identified that different species of plants and animals contain chromosomes in specific numbers and in all the body cells of such organisms the same number of chromosomes may be observed. The gametes of the diploid organisms contain half the chromosome number as observed in their body cells and at fertilization when the two gametes unite to form the zygote, the diploid state is achieved with the restoration of diploid chromosome number as found in the body cells.

From all these discoveries Sutton and Bovery became able to realize that a pair of homologous chromosomes of a diploid set during the formation of gamete segregate and each of them enters into different gametes. This indicates that one of the pair of homologs enters into one gamete. The chromosomes of the two sets during their segregation assort at random and enter into gametes in every possible combination. Therefore, the behaviour of the hereditary determinants, the Mendelian factor (Gene), is parallel to the bahaviour of the homologous chromosomes at segregation as well as at independent assortment. Indirectly this supports the idea that genes are present on chromosomes, i.e., the chromosomes are the bearer of the hereditary units.

Several Fundamental Principles Related to Chromosome Theory of Inheritance

Several fundamental principles are related to the chromosome theory of inheritance and these are:

• Chromosomes contain genetic material.
• Chromosomes are duplicated for their equal transmission from parents to the progeny.
• Chromosomes are found in homologous pairs and they are present in the nucleus of all eukaryotic cells and the homologous chromosomes segregate during the formation of gametes in meiosis.
• During gamete formation chromosomes (non-homologous) segregate independently.
• Each parent contributes one set of chromosomes to its offspring and the set of chromosomes carries full gene complement.
• During gamete formation during meiosis, the chromo¬somes segregate and enter into gametes as the Mendelian factors segregate during gametogenesis.
• The chromosome pairs segregate independently and may be assorted at random. This behaviour is equivalent to the independent assortment of Mendelian factors during gametogenesis.

Therefore, the behaviour of the heredity determinants, the Mendelian factor (Gene), is parallel to the behaviour of the homologous chromosomes during their segregation. Indirectly this supports the idea that genes are present on chromosomes, i.e., the chromosomes are the bearer of the hereditary units. The parallel aspects of Mendelian discoveries and the behavior of the chromosomes may be enumerated in the following way.

Parallelism of Mendelian Concepts and Chromosome Theory of Inheritance:

Mendelian Concept	Chromosome Behaviour
1. Factors for a character are present in pair in a cell.	1. Homologous chromosomes are present in pair in a cell.
2. Each factor of a pair, maintains its identity and individuality throughout the life period of the organism.	2. Chromosomes of a pair maintain their structural identity and individuality throughout the life period of the organism.
3. Factors in a pair are independent of their existence and segregate independently during gamete formation.	3. Chromosomes of the pair are independent and they segregate independently during gamete formation.
4. Two or more pairs of factors during their independent segregation assort at random.	4. Chromosomes of all the pairs segregate independently in a random fashion during their segregation.
5. Blending of a pair of factors (Genes) does not occur.	5. Blending of the pair of chromosomes does not occur.

Evidence in Favour of Chromosome Theory of Inheritance

McClung (1902) observed in certain insects that if it is a male a specific chromosome (known as X chromosome) is single in a cell, but if it is female the same chromosome is two in number. Wilson and his colleagues (1905) observed in Pronetor sp. that male contains 13 chromosomes and female contains 14 chromosomes. In this unequal distribution, the difference is found only in the number of X chromosomes and the female contains a pair of X chromosomes, while the male contains only one X chromosome in the body cell. The male Pronetor may form two types of male gametes, one containing the X chromosome and the other without the X chromosome. The female Pronetor may form identical gametes and all containing one X chromosome. A female gamete being fertilized by a male gamete lacking the X chromosome may produce male progeny only. From these observations, it becomes apparent that the sex-determining factors are associated with the X chromosome, and transmission of these factors accompanies the transmission of the X chromosome.

In man, the differentiation of the male sex depends on the presence of the Y chromosome. For this reason, the individual with either XO or XX chromosome combination appears as female. These facts suggest that the genetic determinant for the male sex is present on the Y chromosome. In 1910 Morgan followed the inheritance of the white eye feature in Drosophila melanogaster for several generations and he came to the conclusion that the gene for the white eye feature of Drosophila melanogaster is present on the X chromosome. Later on, in 1916 C.B Bridges, a student of Morgan, could be able to prove that the gene for white eye feature in fruit flies is actually present on the X chromosome.

When Bridges crossed one white-eyed female with a red-eyed male, he obtained astonishingly an abnormal result. Among every 2000 progeny, he scored on a white-eyed female fly or one red-eyed male. White-eyed female flies and red-eyed male flies were stated to be matroclinous and patroclinous respectively. The unusual white-eyed females were, however, fertile but the males having red eyes were sterile. When he allowed the white-eyed female of the F1 generation to cross with the normal red-eyed males, again white-eyed females were produced and in the F2 generation, the number of white-eyed females was about 4%. He then investigated to know the number of chromosomes in the unusual F1 and F2 white-eyed female and red-eyed male progeny. On investigation, he observed that the white-eyed females contained two X chromosomes, along with one Y chromosome. While the red-eyed males though contained one X chromosome, but no Y chromosome.

To explain the origin of the unusual female and male progeny of the F1 and F2 generation Bridges pointed out the occurrence of non-disjunction when during the formation of gametes in female parents, two X chromosomes failed to segregate from each other. However, he called the event of non-disjunction in the production of unusual F1 progeny as primary non-disjunction and that associated with the formation of unusual files of F2 generation as secondary non-disjunction.

During non-disjunction when two X chromosomes fail to separate, an abnormal female gamete with two X chromosomes and a gamete with no X chromosome may be formed. The female gamete with two X chromosomes when fertilized by a normal Y-bearing male gamete, the XXY female may be produced. The F1 XXY female with a white eye feature was actually produced in this way. On the other hand, the null-X female gamete being fertilized by the X-bearing male gamete could produce the F1 red-eyed male progeny. XXY female was matroclinous as she obtained the white eye feature from her mother and the XO red-eyed male was patroclinous having inherited the red eye gene from her father.

If the gene for the white eye feature is considered as w, and its normal allele for red eye colour is w⁺, then the genotype of the parental white female and red-eyed male may be indicated as X^wX^w and X^w+Y respectively. On the basis of this, the F1 white female and the red male may be indicated as X^wX^wY and X^w+O respectively. The event of non-disjunction in the parental female and production of F1 progeny may be shown in the following diagram:

Bridges also carried out a crossing involving the white-eyed female of the F1 generation and normal male and in this case, he obtained again white-eyed females and red-eyed males unusually showing their appearance by about 4%. This could be possible due to secondary non-disjunction. Bridges pointed out that in XXY female files of the F1 generation, the segregation of X chromosomes occurs in two different ways. In one way during meiosis, one X chromosome goes to one pole and the other pole gets X and Y chromosomes together. As a result, X and XY-bearing female gametes may be produced.

In the second case, both the X chromosomes go to one pole, while the Y chromosome goes to the other pole. Therefore, in the second case, XX and Y types of female gametes may be produced. Bridges suggested that in the XXY female of F, generation either XX or XY may come in pairing. Therefore, when XX comes in pairing the Y chromosome remains free. On the other hand, when XY comes in pairing the X chromosome remains free. He observed that in about 16% of cases X and Y come in pairing and in about 84% of cases two X chromosomes show pairing and non-disjunction. Therefore, the proportion at which the different gametic types may appear as a result of secondary non-disjunction may be shown in the following diagram. The formation of F2 white females and red males from F1 white females may also be shown by a checkerboard.

Bridges analyzed the results of his experiments of non-disjunction and came to the conclusion that the w gene is present on the X chromosome. The experimental result also indicated that the segregation of the genes determining the eye colour in Drosophila melanogaster is associated with the segregation of X chromosomes in females.

Chromosomal Segregation During Meiosis

Such concepts of Sutton and Boveri were nourished by the cell theory of Sleiden and Schwann, the organization of the cell nucleus as suggested by Brown, events of fertilization as revealed by Hartwig and Strasburger, observation on cell division by Schneider and Flemming, and equal distribution of chromosomes in the daughter cells from division as revealed by Von Beneden. Sutton pointed out that chromo¬somes followed Mendel’s rules – the first clear argument for the chromosome theory of heredity and this was revealed by him from his works on chromosomes of grasshopper Brachystola sp. Sutton regarded chromosomes as units of heredity, but he could not point out that several alleles must reside in one chromosome and therefore be inherited as a unit. During the time of Mendel’s rediscovery in 1900, it was realized by many cytologists that the chromosomes in meiosis and fertilization obey Mendel’s laws.

The German Cytologist T. Boveri said that he had the same idea at the same time as Sutton. Boveri was able to elucidate the chromosome behavior in inheritance from his works on sea urchins. Wilson (1925) considered the chromosome theory of heredity as the Sutton-Boveri hypothesis. Boveri was a leading figure during this discovery but Sutton was a young graduate student totally unknown in the world of cytology and genetics.

Chromosomes and Genes

Chromosome theory of inheritance states that the chromosomes bear the genes and through the transmission of chromosomes inheritance of genes from one generation to the other becomes possible. Therefore, to realize the inheritance of genes through generation an idea on the structure and organization of chromosomes should be developed. Not only that how the chromosomes influence the expression of characters in the living organisms should also be studied.

Chromosome and its Organization

During cell division of eukaryotic cells, some filamentous and rod-shaped bodies are developed from the nuclear reticulum those are constituted of proteins and nucleic acid. They are self-replicating and participate in heredity, mutation, and evolution of species in the living world. These very special filamentous or rod-shaped nuclear bodies of the eukaryotic cells carrying genetic material (DNA) are known as chromosomes. Flemming (1879) called these nuclear filamentous bodies chromatin.

W. Waldeyer (1888) named these bodies as chromosomes. Beneden and Boveri (1889) proposed that the chromosome number of all the species is constant. Boveri (1902) opinioned that the chromosomes are the carriers of hereditary materials. The word ‘Chromosome’ is derived from the Greek word ‘Chrome’ means color and ‘Soma’ means body, i.e., colored body.

Number of Chromosomes

In any given species, the number of chromosomes is constant. In the reproductive cells or gametes (spermatozoan or ovum), there is a haploid (n) number of chromosomes. However, in the somatic cell, there are two sets of diploid chromosomes (2n). In the endosperm nucleus, there is a triploid number (3n) of chromosomes. The total of genes present in the haploid set of chromosomes is called the genome. The roundworm of a horse named Ascaris megalocephaly univalent exhibits the least number of chromosomes. In their body cells, there are only two chromosomes. The protozoan form Aulacantha contains the highest number of chromosomes (Chromosome no. 1600). The plant species Spirogyra and Ustilago show two chromosomes in their haploid set (n = 2). In the plant species named Ophioglossum, the chromosome number (2n) is 1260. The somatic cell of man contains 46 chromosomes.

Number of Chromosomes in Some Eukaryotes:

• Number of chromosomes in the reproductive cell: Haploid (n)
• Number of chromosomes in the somatic cell: Diploid (2n)
• Number of chromosomes in endosperm cell: Triploid (3n)
• Number of chromosomes in Ascaris megalocephala univalens: 2n = 2
• Number of chromosomes in Protozoa: Aulacantha: 2n = 1600
• Total genes in a haploid set of chromosomes: Genome

Importance of Chromosome

The chromosomes are very important with respect to the hereditary transmission of characters in living organisms. They are not only significant cellular constituents, but they also regulate cellular functions. Several important functions of the chromosomes are as follows:

• Chromosomes carry genetic materials or genes.
• The chromosomes act as vehicles in the transmission of genetic material from generation to generation.
• The chromosomes control almost all chemical and physiological activities of the cell as well as of the organism.
• During cell division, the chromosomes may develop recombination by way of crossing over, thereby enhancing the trend of evolution.

Types of Chromosome

Viral Chromosome
A viral chromosome represents only one molecule of DNA or RNA. It is also known as the viral genome. The nucleic acid molecule may be circular or linear. The virus-containing DNA as its genome is called a DNA virus. On the other hand, a virus containing RNA is called arbovirus. The DNA or RNA of a virus may be single or double-stranded.

1. DNA Virus:
   • Single Stranded DNA (ss DNA):
     • Linear ss DNA – Parvovirus
     • Circular ss DNA – Φ × 174, Coliphage M-13
   • Double-Stranded DNA:
     • Linear ds DNA – T4 bacteriophage, Herpes virus, Pox virus.
     • Circular ds DNA – SV-40, Polioma virus.
2. RNA Virus:
   • Single-stranded RNA (ss RNA): TMV, Bacteriophage R-17.
   • Double-stranded RNA (ds RNA): Reo Virus, Retro Virus (virus containing the gene for production of reverse transcriptase), Raus sarcoma virus.

Prokaryotic or Bacterial Chromosome
The genetic material of bacteria is formed of a single circular chromosome. This is a naked double-stranded DNA molecule. This is also known as the nucleoid. The bacterial chromosome or nucleoid is about 1 pm long and contains 80% DNA and little RNA and protein. The DNA of E. coli contains about 4 million nucleotide pairs and its molecular weight is 2.8 × 10⁹.

Plasmid:
Sometimes a bacterium may contain one or more circular extrachromosomal DNA and this extrachromosomal DNA is known as a plasmid. William Hays and Joshua Lederberg in 1952 first observed plasmid DNA. Plasmids usually carry antibiotic-resistance genes. Plasmids may be isolated very easily and they may be introduced in a bacterium by mechanical method. In modern research of genetic engineering, the use of plasmid is very important.

Eukaryotic Chromosome
During late prophase, chromosomes are produced from nuclear chromatin. A chromosome is principally a histone-chromatin complex. Usually, a chromosome is filamentous and rod-shaped. Based on functional status, chromosomes may be of two types autosomes and sex chromosomes.

• Autosome: In sexually reproducing animals, the chromosomes which remain equally present in males and females, are known as autosomes. In a man, there are 46 chromosomes, and out of that 44 are autosomes.
• Sex Chromosome (also Allosome or Heterochromosome): In sexually reproducing organisms, chromosomes other than the autosomes are called sex chromosomes or allosomes. The X-chromosomes of females and X and Y chromosomes of males are of this type. Sex determination in animals is controlled by these chromosomes in many animals.

Differences between Autosome and Sex Chromosome:

Autosome	Sex Chromosome
1. Equally present in males and females.	1. Unequally present in males and females.
2. Principally associated with the expression of somatic characters.	2. Principally associated with sex determination.
3. They are many in number in most cases.	3. They are few in number and usually one pair.
4. There is no difference in the number of the two sexes.	4. They differ by number in the male and female sexes.

Differences between Prokaryotic and Eukaryotic Chromosome:

Prokaryotic Chromosome	Eukaryotic Chromosome
1. Primitive type found only in bacteria, blue-green algae, and Mycoplasma.	1. Typical in structure, found in all plant and animal cells.
2. One in number.	2. More than one in number in a cell.
3. Circular DNA.	3. Chromosome contains linear DNA.
4. Histone protein absent.	4. Histone present.
5. Chromosomes remain naked.	5. Chromosomes remain enclosed within a membrane.
6. Chromosomes directly associate with the cytoplasm.	6. No direct contact between chromosome and cytoplasm.

Shape of Chromosome

Though a chromosome looks rod-shaped during the metaphase stage of cell division, its shape may vary at anaphase depending upon the presence of a centromeric location. It may be I, J, L, or V-shaped on the basis as described.

Size of Chromosome

Chromosomes may vary in size. The length of the chromosome may vary from 0.2 – 0.50 μm and the diameter may vary from 0.2 – 20 μm. In man, the length of a chromosome maybe 6 pm. However, in some vertebrates, the lampbrush chromosome developed in the oocytes, and the polytene chromosomes of the insects are the longest in size. Such chromosomes are called giant chromosomes. A giant chromosome may be about 2 mm in length. Among the plants, the longest chromosome (about 32 pm) is observed in Trillium.

Structure of Chromosome or Morphology of Chromosome

The metaphase chromosome exhibits the following structures:
(i) The chromatids represent a pair of coiled filaments aligned side by side and attached at the centromeric position. Each of the chromatids contains a long chromatin filament called chromonema (Vejdovsky, 1912) (Pl-Chromonemata). With regard to the structural organization of the chromonema thread, there are two views:

(a) Dangler String or Radial Loop Model: According to this model (Laemmli, 1977), the metaphase chromosome is more compact when the diameter of a chromosome arm is about 1 μm. Under an electron microscope, the cross-section of a chromosome exhibits a radial arrangement of the chromatin fiber. Besides this, when histones are removed from chromatin, the scaffold is produced from chromosomes.

The scaffold is a structure formed of a non-histone protein core containing many DNA loops arising from it. From the features of the scaffold, it is presumed that probably a 3000 A thick chromatin fiber remains oriented in the form of radial loops to give the structure of a comparatively thick chromosome arm.

(b) Solenoid Model: Klug in 1976 proposed this model. According to this model, 100 A primary fiber coils in the form of the solenoid to form 300A fiber, and at each side of this fiber six nucleosomes are associated. These nucleo- somes may remain in stable condition by HI histone.

(ii) Chromomere:
The chemical components of the chromonema are not equal in concentration in all the regions. At different regions, these exhibit more concentration and these highly concentrated regions of the chromonema are known as chromomeres. The regions in between the chromomeres take lighter staining and these regions are called inter-chromomeric regions.

(iii) Primary Constriction:
The centromere-associated region of a chromosome that takes more stain and that forms a constricted region is called the centromere.

(iv) Kinetochore:
The disc-shaped structure at the centromere is called a kinetochore. The kinetochore is mainly formed of protein and its diameter is about 0.20 – 0.23 µm. It is associated with 4 – 40 microtubules which are concerned with chromosome movement. On two chromatids of a chromosome, there are two kinetochores. During the formation of the spindle apparatus, the spindle microtubules are attached to the kinetochores.

(v) Centromere:
The centromere represents the region of the primary constriction that connects the two chromatids together and this region gets connected with the spindle fiber during cell division. The chromosomal segments at the sides of the centromere are known as chromosome arms. Each centromere is formed of four spherical small bodies and these are known as centromeric chromomeres.

The number of centromeres may vary in chromosomes. A chromosome with one centromere is called a monocentric chromosome, with two centromeres is called a dicentric chromosome, and with more than two or more centromeres is called a polycentric chromosome. Sometimes, a chromosome may lack a centromere and it is known as an acentric chromosome. However, according to the location of the centromere, the chromosome may be of four types:

• Telocentric Chromosome: When the centromere of a chromosome is present at the terminal region of a chromosome.
• Acrocentric Chromosome: When the centromere is present subterminally in a chromosome.
• Metacentric Chromosome: When the centromere is located in the middle of a chromosome composing two equal arms of the chromosome.
• Sub-metacentric Chromosome: When the centromere is located on the chromosome somewhere away from the center of the chromosome forming two unequal arms of a chromosome.

(vi) Pellicle or Matrix:
The chromatids of a chromosome are said to be immersed in a jelly-like viscous fluid called a matrix. The matrix is said to be enclosed within a membrane called a pellicle. However, according to the modern view, the pellicle and matrix are totally absent in the chromosome.

(vii) Telomere:
The terminal end of a chromosome arm is called Telomere.

(viii) Secondary Constriction:
Any constriction along the chromosome arm except the centromere is known as secondary constriction. The secondary constriction plays a role in the formation of nucleolus and therefore, it is also known as Nucleolar Organizer (NOR).

(ix) Satellite:
Sometimes the terminal part of a chromosome may be bulb-like forming a knob. Such a portion of a chromosome is called a satellite. The chromosome containing a satellite is called a sat-chromosome.

Differences between Primary Constriction and Secondary Constriction:

Primary Constriction	Secondary Constriction
1. Centromere is associated with chromosomal constriction.	1. Chromosomal constriction other than the primary constriction is known as secondary constriction.
2. This contains a centromere.	2. This contains a nucleolar organizer.
3. It connects the chromosome with the spindle fiber.	3. It produces nucleolus in the cell.

Differences between Chromatid and Chromatin:

Chromatid	Chromatin
1. Appears during late prophase and early metaphase.	1. Appears during interphase and early prophase.
2. Condensed structure and more psychotic.	2. Slender thread-like, less condensed, and less psychotic.
3. Elongated paired identical coiled threads attached at the centromere.	3. Elongated thin uncoiled single thread containing chromomeres.

Differences between Chromosome and Chromatid:

Chromosome	Chromatid
The self-replicating nuclear chromatin fiber composed of protein and nucleic acid is known as a chromosome.	Each of the paired coiled chromatin fibers is identical in nature and remains connected with each other at the centromeric region is known as a chromatid.

Differences between Centromere and Chromomere:

Centromere	Chromomere
1. It is part of a chromosome and is usually single in number in a chromosome.	1. It is the condensed portion of the chromonema thread and is usually many in number in a chromosome.
2. It is present at the primary constriction of a chromosome.	2. They are present all along the chromonema thread in serial order almost at equal intervals.
3. Usually one in number, though in some cases two or more such structures may be present.	3. Always many in number in a chromosome.
4. It is the constricted structure in a chromosome.	4. These are swelled structures in a chromonema.
5. During cell division, this region is attached to the spindle fiber.	5. It is attached to the chromonema.

Chemical Structure of Chromosome

A chromosome is principally formed of proteins (histones and non-histones), nucleic acid (DNA & RNA), and several metallic ions (Ca, Mg, and Fe). Primarily chromosome is constituted of 90% DNA and basic proteins and 10% RNA and acidic proteins. Basic proteins are usually histones, which may be arginine, histidine, and lysine-rich in nature. The acidic proteins are usually tryptophan and tyrosine rich. Histones are of five different types, namely HI, H2A, H2B, H3, and H4. Histones are combined with DNA from nucleohistone. One double-stranded DNA being combined with histones forms chromatin. In each chromatid, there is a single DNA molecule in a longitudinal orientation.

In a large chromosome, DNA is about 1 meter long, but a metaphase chromosome is microscopic. How such a long DNA molecule is housed in a very small microscopic metaphase chromosome, is a pertinent question. To explain chromosome organization, the nucleosome model was proposed by scientists. The nucleosome model states that the DNA thread having a dimension of about 2 nm wraps around several histones to form nucleosomes forming a basic thread of 10 nm diameter. Several nucleosomes being associated develop a chromatin thread of 30 nm dimension which again orients in the form of radial loops to form metaphase chromosomes having a dimension of about 0.5 µm.

The amount of DNA present in the chromosomes of a cell in any species is known as C-Value and C-Value differs in different organisms. For example, the C-Value of several species is given below. It actually represents the amount of DNA in a haploid set of chromosomes in a species.

Chromatid	Chromatin
Humans (Homo sapiens)	3.5 picogram
Fruit fly (Drosophila melanogaster)	0.18 picogram
Locust (Locusta migratoria)	4.6 picogram
Frog (Rana tigrina)	4.2 picogram
Yeast (Saccharomyces cerevisiae)	0.03 picogram

Chemical Constituents of Chromosome:
DNA – 40%
RNA – 1.5%
Lipid – In trace amount
Ca²⁺, Mg²⁺, Fe²⁺ – in trace amount
Histones & Other Proteins – 50%

Chemical Constituents in Chromosomes:

Major	Types	Ingredients	Character
Nucleic Acid	DNA RNA	–	DNA in the form of a coiled helix
Protein	Histones	H1, H2A, H2B, H3 and H4	H1, H2A & H2B are lysine rich H3 & H4 are arginine-rich
	Non-histone proteins	Phosphoproteins, DNA polymerase, RNA polymerase, DPN Pyrophosphorylase, and nucleoside triphosphatases	Tryptophan and tyrosine rich
Metallic Ions	Divalent Cations	Mg++, Ca++, etc	Help in DNA Histone Linking

Structure of DNA

The structural organization of DNA could not be revealed prior to 1953 when James Watson and Francis Crick proposed DNA double helix model. Their model was based on the X-ray crystallographic analysis of Wilkins and Franklin and the chemical analysis of Chargaff et. al. (1950). For this discovery, Watson and Crick along with Wilkins obtained Nobel Prize in 1962.

The DNA Double Helix Model:
The proposed DNA double helix model by Watson and Crick may be described by the following points.

• The DNA molecule is macromolecular in organization having two polynucleotide chains.
• Two polynucleotide strands in DNA are aligned side by side maintaining a specific distance and they remain oriented in an anti-parallel fashion.
• The polynucleotide strands are organized in the form of a right-handed helix surrounding an imaginary central axis which may be comparable to a spiral staircase.
• Of the two polynucleotide strands, one is complementary to the other because the sequence of purine and pyrimidine of one strand determines the sequence of pyridine and purine of the other strand. The number of purine bases on one strand equals the number of pyrimidines on the other strand, (i.e., A + G = T + C). This equivalence of purine and pyrimidine of DNA is known as Chargaff’s rule.
• In the alignment of purine and pyrimidine of two DNA polynucleotide strands, adenine of one strand pairs with thymine of the other strand by two hydrogen bonds, and guanine of one strand pairs with cytosine of the other strand by three hydrogen bonds. The pattern of hydrogen bonding between purine and pyrimidine in the DNA molecule is called Watson-Crick’s base pairing rule.
• The nucleotides in the polynucleotide strand are stacked one above the other and in this organization, the nitrogenous bases are directed towards the inner side of the helix and the sugar-phosphate backbone remains at the outer side of the helix.
• The helix diameter is about 20A° and the nucleotide strands remain 10A° away from the imaginary axis. One complete turn of the helix covers 34A° and within this helix segment, there may be 10 base pairs being present equidistantly. Therefore, the distance between two adjacent base pairs is about 3.4A°.
• Along the whole length of the helix, two grooves may be observed, one is called the major groove and the other is called the minor groove. The major groove is directed towards the inner face of the helix and the minor groove is directed towards the outer side of the helix. The major groove is 11.7A° wide and 8.8A° deep, while the minor groove is 5.7A° wide but 7.5A° deep.
• In paired condition guanine and cytosine spans a distance of about 10.8A° and adenine and thymine spans a distance of about 11.1A°.
• The bases remain at a right angle to the helix axis, but on the horizontal line, each of them remains in a slightly tilted condition forming a definite angle. In this respect, the bases form the angle as G : 52°, C : 50°, T : 50° and A : 51°.

General Composition of Nucleic Acids:
In general, DNA or RNA may be stated as a polymer of unit components named nucleotides. On hydrolysis by acids, the polymer in the nucleic acid is broken down into nucleotides. The nucleotides in DNA or RNA are ligated sequentially one after another to produce a long chain called polynucleotide. The polynucleotide gives a structure to either RNA or DNA.

Nucleotides:
One nucleotide is formed of three basic components namely nitrogenous base, pentose sugar, and phosphoric acid.

1. Nitrogenous base: Nitrogenous bases in the nucleic acids are of two principal categories namely purine and pyrimidine. The purine molecules are double-ring components and the pyrimidines are single-ring components.
   • Purine: Purine found in the nucleic acids are of two types namely adenine and guanine. Adenine and guanine are available in both DNA and RNA. However, adenine is chemically known as 6-amino purine and guanine is known as 2-amino. 6 oxy-purine.
   • Pyrimidine: Pyrimidines in nucleic acids are available in three forms namely Uracil. Thymine and Cytosine. All the molecules are single-ring components. Uracil is chemically known as 2, 4 deoxy pyrimidines, thymine is known as 2, 4, di-oxy, 5 methyl pyrimidine, and cytosine is known as 2 oxy 4-amino pyrimidine.
2. 5 Carbon Sugar: 5 carbon sugar of nucleic acid is also known as pentose sugar. The sugar in its ring configuration contains the 5th carbon outside the ring. Other 4 carbon atoms are present within the ring. The pentose sugar present in DNA lacks one oxygen at the 2’ position, therefore, the sugar in DNA is called deoxyribose sugar.
3. Phosphoric Acid: Phosphoric Acid or H₃PO₄ is an important part of a nucleotide. It helps the nucleotides to be joined together.

The Nucleosome Model:
The nucleosome represents the basic structural and functional unit of chromatin and it consists of nine histone proteins and about 200 base pairs of DNA. Nucleosome structure was revealed first by Roger Kornberg in 1974. When chromatin is digested with micrococcal nuclease complex containing 200 base pair DNA was produced and based on this finding he proposed that chromatin is composed of repeating 200 bases per unit, the nucleosomes. Further digestion of chromatin with the same nuclease was found to produce that correspond to beads visible under an electron microscope and these beads are called nucleosome core particles. A close look at such particles exhibited that about 146 bp DNA wraps a histone core by 1.65 turns. Four types of histones are found to be present in the core particle and they are H2A, H2B, H3, and H4. Each histone fraction is present in pair and therefore in the core histone, there are 8 histone particles.

Therefore, the core particle contains histone octamer, sur-rounding which 146 bp DNA wraps it by 1.65 turns. At the exit point of DNA from the histone octamer, there is another histone, HI that requires about 20bp DNA to remain in position. Taking together histone octamer and HI histone 166 base pair of DNA remains combined with the histones and with this a chromatin sub-unit called chromatosome is formed. HI serves as the sealing material to hold the DNA surrounding the histone octamer. In the chromatin two histone beads are joined by a linker DNA which varies from 8 to 114 bp in length. The histone core is surrounded by DNA in a negatively supercoiled fashion when some terminal segments of histones pass over and between the turns of DNA.

The tails of the histone molecules that protrude from the nucleosome are accessible to enzymes to remove the chemical groups such as methyl and acetyl groups associated with gene expression. The packaging of DNA into nucleosomes results shortening of the fiber length about sevenfold. By this activity, 1 meter-long DNA becomes just 14 centimeters (about 6 inches) long in a “beads on a string” configuration. Halffoot-long chromatin is still too long to fit into the nucleus. Therefore, chromatin fiber is further coiled into shorter, thicker fiber forming “30-nanometer fiber”, because it is about 30 nanometers in diameter.

In the case of humans the length of the chromosomes ranges from 1 – 10 µm and a single chromosome contains a single DNA. The largest human metaphase chromosome is about 10 × 0.5 μm and it contains about 85 µm long DNA. Therefore, the DNA of this chromosome has to undergo 10⁴ dmes condensation for its accommodation in a chromosome of 10 μm long. Isolated chromatin from the interphase cell when examined by electron microscope, it was found to consist of a series of ellipsoid beads (-11 nm × 6.5 nm) connected by thin threads. Again partial digestion of chromatin with micrococcal nuclease yields small fragments containing DNA and histones and in this fragment, about 200 bp DNA remain associated. Electron microscopic observation of isolated metaphase chromosomes showed coiled folded fibers forming a shape in aggregation. The fibers have an average dimension of 30 nm.

However, one histone-depleted metaphase chro¬mosome exhibited a central scaffold or core in the form of a metaphase chromosome associated with a huge pool or halo of DNA. From all these observations it appears that DNA in the chromosome remains associated with proteins in highly condensed conditions and this condensation is promoted through at least three levels of organization. In the first level of organization beads on a string configuration may be formed. At the second level of organization chromatin as a fiber of 30 nm dimension may be developed and at the third level of organization the shape of a metaphase chromosome having about 1 pm thickness may be achieved.

Structure of Nucleosome:
(a) First level of organization – Formation of 11 nm Chromatin Fiber: Chemical analysis of chromatin has revealed that it is formed of DNA and protein of which basic protein histone remains in maximum amount. The proportional distribution of DNA and histones appears to be about 1 : 1 with minor variation in different species of organisms. Therefore, chromatin is principally composed of DNA and histone proteins. In the structural organization of chromosomes, non-histone proteins contribute to some extent.

In the first level of organization DNA being complexed with histones forms 11 nm thick chromatin fibers which appear as beads on a string configuration. The beads-on-a-string configuration represents the first level of organization of chromatin within cells. Partial digestion of chromatin fiber with micrococcal nuclease was found to produce repeating units containing about 200 bp DNA and nine histones forming a single bead on a chromatin fiber. The repeating units of chromatin fiber have been named nucleosomes. Based on this observation, the nucleosome model in chromosome organization was proposed by Kornberg in 1974.

(b) Chromatin Second Level of Organization: In the second level of organization the chromatin fiber achieves a much thicker dimension when the chromatin fiber becomes 30 nm in dimension. How the primary chromatin fiber achieves a dimension of 30 nm that remains unknown. However, there are two models explaining the mechanism to promote the formation of 30 nm chromatin fiber from 11 nm chromatin fiber. The models are the solenoid model and the zig-zag model. If the meta-phase chromosome is viewed under a scanning electron microscope 30 nm chromatin fibers may be visible on the surface of the chromatids of the chromosomes.

Klug proposed the formation of solenoids in the formation of 30 nm chromatin fiber from the basic primary chromatic fiber. According to this model, the primary chromatin fiber with nucleosomes forms a coiled orientation with 6 nucleosomes per turn and the structure may be stabilized by the intervention of H1 histone. It has been found that if H1 histone is removed from 30 nm chromatin fiber its organization is disrupted. However, some investigators found with the help of cryoelectron microscopy that 30 nm chromatin fiber appeared less tightly packed zigzag structure. Nucleosomes in linear orientation form 11 nm chromatin fiber and this promotes 5-7 fold compaction of DNA. But when the fiber achieves a 30 nm dimension its condensation further increases by another 7 fold.

(c) Third Level of Compaction – Formation of Metaphase Chromosome: During metaphase, a chromosome is highly condensed when its thickness may reach about 1 pm. Metaphase chromosome observed under scanning electron microscope shows an aggregation of 30 nm chromatin fibers in the form of loops on the surface of the chromatids as if radial loops of 30 nm fibers remain oriented surrounding a central core. Such an orientation of chromatin fiber makes the chromosome enough thick and in this condition, the solenoid becomes 100 times more condensed promoting condensation of DNA about 5000 – 10000 times, i.e., packing ratio equivalent to 10000: 1.

Histone plays a significant role in the packing of 30 nm chromatin fiber with the formation of the structure of a metaphase chromosome. When the metaphase chromosome is treated with polyanion dextran sulphate, histones are removed from the chromatin fiber and then a central scaffold is left as a skeleton structure surrounding which huge DNA remains oriented as hollow and extended loops. The scaffold is formed of non-histone protein and its structure is identical to a metaphase chromosome with two chromatids attached at the centromeric position.

Therefore, each chromosome at metaphase contains two scaffolds attached at the centromeric position. The DNA loops in the scaffold measure about 25 μm and a loop originates from a specific point of the scaffold. If the 25 μm DNA loop is condensed at a ratio 40 : 1, then its length is reduced to about 0.6 pm, and at metaphase, it may promote the formation of a chromosome of 1 μm thickness. The radial loop formation of some matrix attachment proteins (MARs) and Scaffold proteins attachment proteins (SARs) play a significant role. The radial loop formation requires some matrix attachment proteins (MARs) and Scaffold proteins attachment proteins (SARs) play a significant role.

Chromatin Formation:
Chromatin fiber of 30 nm dimension interacts with matrix proteins like MARs or SARs so as to achieve a higher order of interaction. Due to such interactions, DNA becomes attached to the Matrix Associate protein or Scaffold Associated Protein at specific points as a result of which radial loops of DNA may be formed surrounding the scaffold protein. Mars as well as SARs of DNA is AT-rich and may bind with non-histone proteins of Matrix or Scaffold forming looped of DNA. The regions for attachment of the DNA with non-histone proteins are present in between the genes for expression. The non-histone proteins have no role in chromosome compaction but they may have some role in gene expression. The compaction of DNA in chromosomes occurs in steps and the steps of DNA packing in the chromosome may be shown by the flowing diagram.

Chromatin Modification During Interphase and Functional State:
Processes such as transcription and replication need two strands of DNA to go apart temporarily to operate polymerase activity on the DNA template. However, the presence of nucleosomes and the folding of chromatin into 30-nanometer fibers become barriers to the enzymes that unwind and copy DNA. It is therefore important for cells to have means of opening up chromatin fibers and/or removing histones transiently to permit transcription and replication to proceed. Generally speaking, there are two major mechanisms by which chromatin is made more accessible:

• Histones may be modified by the addition of acetyl, methyl, or phosphate groups (Fischle et al., 2005).
• Displacement of histones may occur by chromatin remodeling complexes that exposed DNA sequences to polymerases and other enzymes (Smith & Peterson, 2005). It is to be noted here that these events are reversible and therefore, altered chromatin may reverse back to its compact state after transcription and/or replication.

Karyotype

Chromosomes as may be observed in an organism may be called the karyotype of the organism. Identification of an organism, its classification, and naming are important aspects in the study of living organisms and the discipline of these studies is known as taxonomy. The study of chromosomes from different organisms thus may be called karyology. Karyological analysis with regard to their total number, number in a set of chromosomes, genes they contain, their behaviors, etc. may be used in taxonomical identification also and based on a study of chromosomes identification of species is known as cytotaxonomy.

• Karyotype represents a profile of total chromosome complement in a cell of an organism arranged in order from descending order of length and grouped according to the similarity in their structure concerning length, centromeric position, and banding pattern along the chromosome arms.
• In other words, karyotype denotes the picture of all the chromosomes of a cell on an organism arranged in pairs and according to their descending order of length and similarity in appearance, centromeric position, banding pattern as well as other physical characteristics.
• After the preparation of metaphase chromosomes from the somatic cell of an organism, they are stained with some suitable dye. Then the chromosomes are studied under a microscope to identify the homologous pairs and similarities among the chromosomes so that they may be arranged in order to prepare a karyotype.

As indicated before different species of animals and plants contain distinct numbers of chromosomes and chromosomes of a species contain different G band orientations as revealed through staining through G banding because the chromosomes differ by the constitution of genes. As karyotype may be one of the identifying criteria for the members of a species, karyotype may be individualistic identification of a member of species especially with regard to any abnormality related to the genic constitution of the individual that may be expressed through a chromosomal complement of the member.

In the case of humans, such a study is very important for the identification of chromosomal abnormalities simply for clinical purposes. In the human population, there are different types of chromosomal abnormalities known as chromosomal aberrations that may be detected by karyotype study or analysis. Genetical defects that may be expressed through the chromosomes of an individual may come to our use simply to reduce the genetic load of the human population when the genetic defects are incurable by any means. The study of the karyotype of the fetus in the maternal uterus may inform us about the future of the baby in the womb.

Karyotype is the representation of the genome of the individual and therefore, it is the expression of the genome of an individual thus it may be a parameter for the identification of a member of a species or an indication of genetic defect in the human individual. Simply the metaphase chromosomes of an individual are prepared by standard method and the chromosomes are stained by a suitable dye for their study under a light microscope. The individual chromosome of a set of chromosomes may be identified through meticulous study under a microscope and their photograph is taken for the presentation of the chromosomes in the karyogram.

Normally one cell of the body of any individual contains two sets of chromosomes and therefore, in the full set of chromosomes in a metaphase plate each chromosome remains in pair. The identical chromosomes in the set are called homologous chromosomes. The homologous chromosomes are arranged serially from largest to smallest in series over a plain white paper and this is known as a karyogram. The karyogram is the representation of the karyotype of an individual. Simple morphological analysis of the metaphase chromosomes is the basis for the karyotype study of any individual.

In cattle how a karyotype may be prepared has been shown in the above diagrams. Chromosomes of the metaphase plate are arranged to prepare the karyotype by arranging the chromosome in order based on their similarity. In human karyotype preparation also follow a similar method. Commonly cultured lymphocyte culture is used to obtain metaphase chromosomes and the karyotype is prepared in the following manner.

Human Karyotype:
A karyotype from a normal human exhibits 23 pairs of chromosomes out of these chromosomes 22 pairs represent autosomes and one pair represents sex chromosomes. The karyotype of a female may be denoted as 46, XX meaning a female normally contains 22 pairs of autosomes and one pair of X chromosomes. On the other hand, a normal male shows a karyotype as 46, XY, meaning the male contains 22 pair of autosomes along with sex chromosomes as X and Y. Any deviation of these karyotypic characteristics denotes an abnormality in the human subject.

In the human karyotype, each chromosome is numbered based on its size. The largest chromosome is designated as chromosome 1. Therefore chromosome 18 or 22 is one of the smallest chromosomes in the human karyotype. Each chromosome has a characteristic banding pattern detectable by staining the chromosomes with Giemsa’s stain. The centromere, the primary constriction on the chromosome, and the banding pattern make each chromosome recognizable to a trained eye. If the centromere on the chromosome is not at the middle then the chromosome will contain two unequal arms, one is long, the q arm, and the other is short, the p arm. The banding pattern and the centromere on different human chromosomes may be indicated by the following diagram.

Metaphase chromosomes from humans are arranged on the basis of their appearance. Cytogeneticists have classified them into seven groups A, B. C, D, E, F, and G. The chromosomes of different groups and the basis for their classification may be indicated in the following table.
Groups of Human Chromosomes and their Characteristic Features:

Group	Chromosome	Description
A	1 – 3	Largest; 1 & 3 metacentric and 2 is sub-metacentric
B	4 & 5	Large; sub-metacentric with two arms very different in size
C	6 – 12 & X	Medium Size; Submetacentric
D	13 – 15	Medium Size; Acrocentric with satellites
E	16 – 18	Small; 16 is metacentric but 17 & 18 sub-metacentric
F	19 & 20	Small metacentric
G	21, 22 & Y	Small acrocentric with satellites on 21 and 22 but not on Y

Criteric based on which organisms belonging to non-identical species differ:

• The absolute size of the chromosomes.
• Centromeric position.
• Number of chromosomes.
• Position of secondary constriction.
• Distribution of heterochromatin.
• Banding pattern.

Applications of Karyotype:
Karyotype analysis is useful for many purposes as indicated below:

• For identification of chromosomal aberrations.
• To study cellular functions.
• To find out the taxonomic relationship between the species.
• To gather information about past evolutionary events.

Importance of Karyotype Study:

• Detect whether the chromosomes of an adult are normal or not.
• Detect whether a baby in the maternal womb carries any chromosome abnormality.
• Determination of the sex of the fetus.
• Detection of type of cancer.

Idiogram

Drawing of the photograph of chromosomes of a cell of an organism is known as an idiogram. Therefore, an ideogram is the graphic or diagrammatic representation of a karyotype exhibiting the number, relative sizes, and morphological features of the chromosomes in a species. Idiogram usually represents the gametic chromosomes (n) of a species. For humans, the idiogram may be presented in the following manner.

Euchromatin and Heterochromatin

Chromosomal materials are known as chromatin which may be categorized into euchromatin and heterochromatin.

Euchromatin
The portion of the chromatin that remains active in the interphase nucleus and is less psychotic because of the extended state is known as Euchromatin.

Structure of Euchromatin:
Structurally euchromatin is a less compact region of the chromosome and represents 11 nm chromatin fiber with the presence of beads at regular intervals along the fiber. The beads are the nucleosomes of the chromatin fiber. This region of the chromosome represents the exon and DNA in this region remains unmethylated. During the S phase, this region replicates first. This region is also transcriptionally active.

Functions of Euchromatin:

• The Euchromatin region remains involved in transcription. Hence, this region forms mRNA.
• The region permits the recruitment of RNA polymerase and gene-regulatory proteins.

Heterochromatin
The region of the chromatin that remains inactive in the interphase nucleus and due to highly compact organization takes more stain, is known as heterochromatin. The chromosome region that is functionally inactive is known as the heterochromatic region. Normally the chromatin in this region remains condensed. However, the region that remains inactive at some stage of cellular life may be active at other times. Heterochromatin may be of two types namely Facultative heterochromatin and Constitutive heterochromatin. The heterochromatin that is active at a certain stage and becomes active at some other stage of cellular life is known as facultative heterochromatin. On the other hand, when a chromosomal region remains permanently inactive during the whole life of the cell it is called constitutive heterochromatin. The centromere region of the chromosome represents the constitutive heterochromatin. In the cell, the heterochromatin region takes more stain.

Functions of Heterochromatin:

• Heterochromatin may control the expression of the gene adjacent to it.
• In the cell, the control of genes may be organized by heterochromatinization.
• Chromosomal length and dimension are determined by heterochromatin.

Differences between Euchromatin and Heterochromatin:

Euchromatin	Heterochromatin
1. Appear as a loosely packed chromosomal region.	1. Appears as a condensed packed chromosomal region.
2. Takes less stain during chromosomal staining.	2. Takes more stains during chromosomal staining.
3. Genes in this region are active.	3. Genes in this region remain inactive.
4. Shows early replication at the S phase.	4. Shows late replication at the S phase.
5. This is high in transcriptional activity.	5. This is low in transcriptional activity.

The Parallelism between Genes and Chromosomes

After the rediscovery of Mendelism in 1900, the concepts of heredity were verified by different experiments. Mendel’s Theory of Segregation had been accepted by scientists without confusion, but the other theory, i.e., the law of Independent Assortment, was criticized by many, yet the theory was not rejected fully. However, along with such investigations, scientists tried to see the nature of the hereditary determinants which were described as factors by Mendel. The chromosome theory of inheritance is the outcome of such investigations and the proposers of this theory were Walter Sutton and Theodore Boveri (1903). Chromosome theory of inheritance states that the chromosome is the bearer of hereditary material or the genes residing on the chromosome and the transmission of genes from one generation to the other is facilitated by the transmission of the chromosomes.

Some Aspects that Support Parallelism of Chromosomes and Genes

• In every cell of a diploid organism, there are two sets of chromosomes and in each cell, there are two genes for a particular character.
• During meiosis-I, two sets of chromosomes are separated to go into different gametes, and a pair of genes is also segregated into the gametes during the meiotic separation of chromosomes.
• The Mendelian genes retain their identity throughout the whole life of the organism and the chromosomal configurations also remain unchanged throughout the life of an organism.
• Chromosomes in a cell during meiosis not only segregate but also assort at random during gametogenesis. This is true for the genes of the chromosomes.
• In the gametes, genes are present only in one set of chromosomes, and the gamete carries only one copy of a pair of genes as present in diploid organisms.

Relationship between Gene and Chromosome:

Gene	Chromosome
1. Each gene is present in pair in a cell.	1. In a diploid cell, each chromosome is available in pair.
2. Each pair of genes segregate during gamete formation.	2. The homologous pair of chromosomes segregate during gamete formation.
3. Each gamete carries one gene of a characteristic feature.	3. Each gamete carries one chromosome of the homologous pair.
4. A gene maintains its existence in the organism throughout its life period.	4. A chromosome also maintains its existence throughout the life period of an individual.
5. Genes show independent assortment during gamete formation.	5. The chromosomes of an individual assort independently during gamete formation.

Genes with respect to Chromosomes

From the above discussion, it appears that a chromosome represents a rather long thread-like structure made of principally DNA and protein and this chromosome carries the genes for characters. In this context question arises what is the nature of a gene and what is its dimension and also how it acts to express a character? Mendelian concepts gave the idea that a gene is some sort of particulate material that in later analysis has been realized to be present on chromosomes. Morgan and his student, Sturtevant discovered that genes are linked to chromosomes and they are having specifically defined locations over a chromosome called locus. Subsequently, mobile genetic elements were discovered suggesting that some genes may move from one position to the other. Still, the idea prevails that the majority of the genes occupy a specific location of a chromosome.

Chromosomes contain mainly DNA and protein of which DNA only acts as genetic material, while DNA is a continuous chain of polynucleotides. A gene represents a part of DNA that in most cases produces a polypeptide chain for protein. The part of DNA that may promote the formation of protein for specific functions in living organisms, is a gene and this part of DNA is nothing but a strand of polynucleotides. Any change in this polynucleotide chain (by base substitution, deletion, or addition) results in a change in the polynucleotide chain in DNA leading to defective (Altered) expression in a character.

Different Types of Genes

1. Autosomal Genes: The genes that are present on the autosomes.
Ex. The genes for baldness, albinism, alkaptonuria, etc.

2. Sex Chromosomal Gene: The genes that are present on the X chromosome.
Ex. The gene for hemophilia and color blindness.

3. Holandric Gene: The gene which is present on the Y chromosome of males.
Ex. Hypertrichosis.

4. Jumping gene: The gene of a chromosome that can change its position. These are also known as transposable genetic elements or transposons.
Ex. AC/DS element in maize.

5. Pseudogene: The part of DNA that is structurally identical with some gene but remains inactive. Such a gene is known as a pseudogene.

6. Lethal gene: The gene which in expression causes the death of the organism is known as the lethal gene.

7. Selfish gene: The gene which remains suppressed in the living organism and retains the probability of expression in the future, is known as the selfish gene.

8. Oncogene: The gene which results in cancer in the organism is known as oncogene.

9. Split gene: The gene which is composed of intron and exon and where the exon part is involved in the expression of the gene is known as a split gene.

10. Transgene: The gene which may be transferred from one organism to the other is called transgene.

Functions of Genes

• Genes are the identity of a chromosome and genes compose a chromosome.
• Genes of a chromosome determine some characteristics. Therefore, lacking a chromosome an organism faces severe complexity.
• Genes present over a chromosome are in linear order and they determine the length of a chromosome.
• Genes of a chromosome are linked and the linked genes tend to be inherited in block.
• In higher organisms, the Y chromosome is responsible for maleness.

Some changes in the chromosomes resulting the synthesis of defective proteins due to mutation in different genes in humans:

Defect	Type of Change in DNA	Chromosomal Relation	Expressed Character
1. Sickle Cell Anaemia	A-T → T-A Conversion	β-globin gene in human chromosome 11	Defective β-polypeptide chain of haemoglobin with valine in place of glutamic acid.
2. Cystic Fibrosis	Trinucleotide deletion	CF gene in human chromosome 7	∆F508 deletion causes the synthesis of defective CFTR protein.
3. Huntington’s Disease	The addition of trinucleotide (CAG) repeats in the HTT gene	HTT gene in human chromosome 4	Defective HD protein with long polyglutamine region.

Special Types of Chromosomes

In both plants and animals, there are certain types of chromosomes that are not equivalent in size and shape to the metaphase chromosomes. Though they are also microscopic in nature yet they are large enough in comparison to the mitotic chromosomes. These chromosomes are sometimes called giant chromosomes. There are two forms of giant chromosomes namely polytene chromosomes and lampbrush chromosomes, one develops during the interphase stage of the cell cycle in some organisms, and the other at the diplotene stage of meiotic cell division in some amphibians.

Besides these, in certain cases, minute extra chromosome complements are encountered in some species and they are called B chromosomes or supernumerary chromosomes. Hence, these types of chromosomes may be called special types of chromosomes. If we have no idea about these chromosomes encountered in the living world our knowledge about chromosome structure and organization will be incomplete. A discussion about these chromosomes, therefore, may be made as under.

Polytene Chromosome

Polytene chromosomes appear as long ribbon-like bodies with an alternate arrangement of bands and interband when each chromosome is very large in comparison, to their normal counterpart. For this reason, they are considered as giant chromosomes. These chromosomes represent the organization of the cellular chromatin materials in the form of ribbon-like extended bodies at interphase nuclei with several unique features that are not observed in the metaphase chromosomal bodies in the cell.

Among a number of their unique features, the multistrandedness of the chromosomal bodies, giant configuration, mosaic assemblage of euchromatin and heterochromatin, active Balbiani ring structures, differential display of segmental arrangement of individual chromosomes and extensive response to environmental conditions appear to be some notable properties of these chromosomes. Because of the presence of many DNA strands that are quite long the chromosomes are not only very large but also much thick being a thousand times more in dimension in comparison to their metaphase counterparts. Polytene chromosomes are gigantic structures occurring in certain larval tissues of dipteran flies, especially in the salivary gland cell nuclei. Balbiani (1881) published the first description of these giant chromosomes in the salivary gland cell nuclei of midges of the genus Chironomus.

Polytene chromosomes are strictly confined to certain types of somatic tissues in the insects belonging to the order Diptera (Crane-flies, midges, mosquitoes, houseflies, and Drosophila, etc.). Usually, they acquire their largest size in the spherical nuclei of the larval salivary gland cells, but similar nuclei frequently exist in other tissues such as the lining cells of the gut and its derivatives, the Malpighian tubules as well as the muscle, the fat body cells, ovarian nurse cells, etc. Though polytene chromosomes appear in a number of living eukaryotic organisms as insects of the other Diptera, Collembola, infusorians, and mammals the polytene chromosomes of Chironomids in most cases appear to be unique with their separate and distinct existence. Polytene chromosomes are now considered to be very important objects for the analysis of numerous features of interphase chromosome organization and the genome as a whole. Moreover, according to Ashburer (1970), polytene chromosomes are a ‘system in which differential gene activity and its control can be analyzed directly at the level of the genes themselves’.

Discovery of Polytene Chromosomes
Balbiani in 1881 first noticed polytene chromosomes in the salivary gland cells of Chironomus, but he could not able to identify them as chromosomes. In fruit flies, Drosophila, these chromosomes were observed by Heitz and Bauer. The name polytene chromosome was introduced by Koller in 1930. Rambousek in 1912 identified the relation of polytene chromosomes with regular metaphase chromosomes.

Occurrence of Polytene Chromosome
Polytene chromosomes are developed in the interphase nuclei of some organisms and they are the chromatin bodies during the developmental stage of animals especially in dipterous flies and they appear in the salivary gland cells. Cells in the Malpighian tubules, intestine, hypoderm, and muscles of Chironomus plumosus also develop polytene chromosomes.

General Organization
Morphology: Polytene chromosomes in their classical configuration appear as very long ribbon-like bodies in the interphase cell nucleus. On staining with suitable chromatin-specific dye each chromosome exhibits many bands and interbands of variable sizes. The bands appear as deeply stained dark stripes over the chromosome arm when the interband is lightly stained or clear areas between the bands. Over the chromosome arm, there may be several constricted sites and several swelled regions called puffs. In some regions, the puffs may be highly enlarged showing transcriptional activities. These sites are called Balbiani rings.

The number of polytene chromosomes appears to be equivalent to the haploid number of chromosomes as found in an organism. During the formation of the polytene chromosome, the homologous chromosomes come in pairing and the replication of individual chromosomes occurs but the duplicated chromatids do not separate. The process is called endoreduplication or endomitosis. Thereby, gradually the chromosome becomes thicker forming the broad polytene chromosome. The polytene chromosomes appear as isolated chromosomal bodies but in some organisms, all the chromosomes are fused together at their centromeres forming a chromocentre. From which chromosomal arms radiate around the chromocenter. Such chromosomal organization may be found in D. melanogaster. On the other hand in most of the species of Chironomus, polytene chromosomes in the cell remain as isolated bodies. Usually, the centromere of a polytene chromosome appears as a heavily pycnotic broadband and the centromeric region may be stained by C banding procedure.

On the basis of the morphological features a polytene chromosome carries the following structures namely-

1. Band
2. Interband
3. Puff
4. Constriction
5. Balbiani ring

1. Bands:
Over the polytene chromosome series of bands are observed and these bands are the condensed chromatin mass that appeared as a result of condensation of chromatin at the region. Because of the condensation of chromatin at the bands the regions represent inactive sites of chromosomes and are, therefore, heterochromatin mass along a chromosome. The bands along a chromosome vary in dimension and therefore, some bands are thick and others are slender. The thicker bands correspond to more chromatin mass condensed at a site, whereas the thin band represents less chromatin mass condensed at the site.

The number of bands over a chromosome also varies and usually longer polytene chromosome contains more number of bands than the shorter chromosome. The organization of bands over a chromosome is rather irregular and in some regions several bands may remain in clusters. Though a band over a polytene chromosome represents the inactive site at times the same region may be active when the band is fizzled out forming an extended puff. The bands remain separated by the presence of an interband that is comparatively less stained when a chromosome is treated with a chromatin-specific dye. However, the pattern of bands and interbands in every polytene chromosome of a species is specific and this pattern is also specific to any developmental stage of the organism.

Individual chromatid at specific sites becomes condensed due to the coiling of the chromatin thread at the site. This condensed site of a chromatid is called a chromomere. For all the chromatids thickening of the chromatin fiber appears at the same site and chromomeres of all the chromatin threads when forming the chromomeres at the same site of the chromatins appear as a thick band on the polytene chromosome.

2. Interbands:
In between two bands over a polytene chromosome, the unstained or feebly stained comparatively clear area is known as an interband. The interband represents the euchromatic site and therefore, active regions of the chromosome. Because at the interband region, chromatin remains in the extended state the regions appear to be uncondensed and less pycnotic. As the band region varies in dimension so also the interbands also vary in dimension. The interband are arranged alternately with the bands on the chromosome.

3. Puff:
Along the length of the polytene chromosome at some regions, the ribbon-like chromosome may produce swelled segments and this swelled segment of the polytene chromosome is called the puff. The puff regions are, therefore, broad in comparison to the adjacent segment of the same chromosome. The swelled segment on a chromosomal region may arise due to two possibilities as-

• due to more activity, the chromatin of a region may be extended forming a swelled structure or
• due to more replication at some specific region, the chromatin quantity of a region may be increased forming swelled segment.

4. Constriction:
Along the chromosome arm at certain regions, distinct constrictions may arise and constrictions are usually associated with bands. The constrictions over the polytene chromosome represent the site with the presence of less number of chromatin threads that usually develop due to repeated rounds of replication of a chromosome. Thus a constricted site may be a site of a low level of replication.

5. Balbiani Ring:
The Balbiani ring represents the most active site on a polytene chromosome. The region is highly swelled and associated with the production of RNA at the region. The DNA fibers are extended laterally for the ring-like structures along the Balbini ring and the DNA at the ring participates in the process of transcription producing mRNA for translation. The Balbiani ring region has been observed to be a modification of the band structure on a chromosome in necessity and therefore, the Balbiani ring is not a permanent structure on the polytene chromosome. Experimentally it has been found that under induction a Balbiani ring may be produced at a specific site of the polytene chromosome.

Some Common Features of Polytene Chromosome
Cells producing polytene chromosomes are associated with several common features as-

• Complete block of mitotic cell division.
• The cell cycle comprises only two phases synthetic phase (S) and the inter-synthetic phase (G).
• After replication of DNA, newly formed DNA fails to separate.
• The nuclear membrane and nucleolus remain intact during the causation of replication cycles.
• Cells promoting the formation of polytene chromosomes seem to be intimately associated with intense secretory function.

Lampbrush Chromosome

Lampbrush chromosome represents a special form of meiotic chromosome in bivalent form having many DNA loops on either side of the axis of the chromosome showing gene activity during the diplotene stage of dividing cell nuclei of oocytes in some female animals. Because of their lampbrush-like appearance with sufficiently large dimensions, the chromosomes are named lampbrush chromosomes.

Discovery of Lampbrush Chromosome
Walter Flemming (1882) was the first person to observe the lampbrush chromosomes in the oocytes of Ambystoma mexicanum, a species of salamander. After about 10 years of this, Ruchert obtained these chromosomes from the oocytes of dogfish and he is credited for naming this type of chromosome.

Occurrence of Lampbrush Chromosome
These are the largest known chromosomes found in the yolk-rich oocyte nuclei of certain vertebrates such as fishes, amphibians, reptiles, and birds. They can be seen with the naked eye and are characterized by fine lateral loops, arising from the chromomeres, during the first prophase (diplotene) of meiosis.

General Organization
Morphology: Lampbrush chromosome appears as a looped structure with two axes each having many laterals extended loops at both sides. One lampbrush chromosome in the oocytes of salamanders measures about 5900 (tm in length. Such chromosome appears in the diplotene of meiotic prophase I. Hence, one lampbrush chromosome is actually a bivalent structure when two homologous chromosomes are associated together. Each component chromosome of the bivalent becomes much extended and produces lateral loops from both of its sides.

Due to its large configuration, the lampbrush chromosome is called the giant chromosome. The chromosomes may be dissected out from the oocyte nucleus intact and they are even visible to the naked eye.

Component Parts of Lampbrush Chromosome

1. Axis:
The two homologous chromosomes of the bivalent in meiotic chromosome form the axis of the lampbrush chromosome. Hence, the axis represents two components and each representing one of the bivalent chromosomes. Each of the bivalent again is formed of two chromatids, hence, together the axis comprises four chromatids when each chromatid contains one DNA thread. Along the longitudinal axis series of bead-like structures are visible and these are thickening of DNA in the chromatids called chromomeres. From each chromomere lateral loops originate at two sides and thus many such loops may be encountered along the whole length of the axis.

2. Chromomere:
Chromomere is the tight folder DNA thread and the region is transcriptionally inactive. At the chromomere region, the DNA fiber exhibits unfolding to form lateral loops.

3. Lateral Loops:
Lateral loops are formed of DNA and lateral loops show their active participation in RNA synthesis. Each loop in turn developed from an axis of a single DNA molecule, which remains coated with a matrix of nascent RNA and proteins. The matrix is asymmetrical when it is thicker at one end of the loop. RNA synthesis begins at the thinner end and proceeds toward the thicker end. The majority of the DNA, however, does not contain loops and in these DNA regions, gene expression cannot occur. The loop region contains about 5-10% of the DNA in a chromosome.

Because of the formation of a loop, the mass of a chromomere is reduced. The centromere of the lampbrush chromosome represents an elongated PAS+ve chromomere and the region does not contain any loop. A typical loop may contain about 50,000 – 2,00,000 base pairs of DNA. However, there are also reports of loops containing much more DNA. The puffs in the polytene chromosomes are equivalent to lampbrush loops.

Functions of Lampbrush Chromosome

• The Lampbrush chromosome shows full gene activity at the chromosomal level similar to the polytene chromosome.
• But the difference is that when the lampbrush chromosome shows gene activity at the divisional stage, the polytene chromosome shows gene activity at the interphase stage.
• The Lampbrush chromosome may have a role in yolk synthesis in the egg.
• Because of the formation of the lampbrush chromosome, the nuclear volume is increased.
• Lampbrush chromosomes may help in detecting the location of a particular gene on a chromosome.
• Lampbrush chromosome through a light on the organization of a chromosome.
• Lampbrush chromosomes contribute to the cytological mapping of the individual chromosomes.