Chromosomal Basis Of Inheritance

Class 12 | Pure Science — Botany | Chapter 3

Class 12 Unit 3 Pure_Science

In the previous chapter you have learned about Mendelian genetics, now you are going to study deviations of concepts related to Mendelian genetics and chromosomal theory of inheritance. You must recall the structure of chromosome and cell division from eleventh standard.

Chapter 3: Chromosomal Basis of Inheritance

Learning Objectives

The Learner will be able to:

• Understand chromosomal theory of inheritance.
• Analyze the three point test crosses and appreciate results in linkage map construction.
• Differentiate mutation types with examples.
• Explain DNA metabolism in Plants.

Chapter Outline

• 3.1 Chromosomal theory of Inheritance
• 3.2 Linkage - Eye colour in Drosophila and Seed colour in Maize
• 3.3 Crossing over, Recombination and Gene mapping
• 3.4 Multiple alleles
• 3.5 Mutation - types, mutagenic agents and their significance
• 3.6 DNA Metabolism in Plants
• 3.7 Protein synthesis in plants

3.1 Chromosomal Theory of Inheritance

G. J. Mendel (1865) studied the inheritance of well-defined characters of pea plant but for several reasons it was unrecognized till 1900. Three scientists (de Vries, Correns and Tschermak) independently rediscovered Mendel's results on the inheritance of characters. Various cytologists also observed cell division due to advancements in microscopy. This led to the discovery of structures inside nucleus.

In eukaryotic cells, worm-shaped structures formed during cell division are called chromosomes (colored bodies, visualized by staining). An organism which possesses two complete basic sets of chromosomes are known as diploid. A chromosome consists of long, continuous coiled piece of DNA in which genes are arranged in linear order. Each gene has a definite position (locus) on a chromosome. These genes are hereditary units.

Chromosomal theory of inheritance states that Mendelian factors (genes) have specific locus (position) on chromosomes and they carry information from one generation to the next generation.

3.1.1 Historical Development of Chromosome Theory

The important cytological findings related to the chromosome theory of inheritance are given below:

• Wilhelm Roux (1883) postulated that the chromosomes of a cell are responsible for transferring heredity.
• Montgomery (1901) was first to suggest occurrence of distinct pairs of chromosomes and he also concluded that maternal chromosomes pair with paternal chromosomes only during meiosis.
• T. Boveri (1902) supported the idea that the chromosomes contain genetic determiners, and he was largely responsible for developing the chromosomal theory of inheritance.
• W.S. Sutton (1902), a young American student independently recognized a parallelism (similarity) between the behaviour of chromosomes and Mendelian factors during gamete formation.
• Sutton and Boveri (1903) independently proposed the chromosome theory of inheritance. Sutton united the knowledge of chromosomal segregation with Mendelian principles and called it chromosomal theory of inheritance.

3.1.2 Salient Features of the Chromosomal Theory of Inheritance

• Somatic cells of organisms are derived from the zygote by repeated cell division (mitosis). These consist of two identical sets of chromosomes. One set is received from female parent (maternal) and the other from male parent (paternal). These two chromosomes constitute the homologous pair.
• Chromosomes retain their structural uniqueness and individuality throughout the life cycle of an organism.
• Each chromosome carries specific determiners or Mendelian factors which are now termed as genes.
• The behaviour of chromosomes during the gamete formation (meiosis) provides evidence to the fact that genes or factors are located on chromosomes.

3.1.3 Comparison between Gene and Chromosome Behaviour

Around the twentieth century, cytologists established that the total number of chromosomes is constant in all cells of a species. A diploid eukaryotic cell has two haploid sets of chromosomes, one set from each parent. All somatic cells of an organism carry the same genetic complement. The behaviour of chromosomes during meiosis not only explains Mendel's principles but leads to new and different approaches to study about heredity.

Mendelian Factors	Chromosomes Behaviour
1. Alleles of a factor occur in pair	Chromosomes occur in pairs
2. Similar or dissimilar alleles of a factor separate during the gamete formation	The homologous chromosomes separate during meiosis
3. Mendelian factors can assort independently	The paired chromosomes can separate independently during meiosis but the linked genes in the same chromosome normally do not assort independently.

Table 3.1: Parallelism between Mendelian factors and chromosomal behaviour.

Organism	Number of Chromosomes (2n)
Adder's tongue fern (Ophioglossum)	1262
Horsetail (Equisetum)	216
Giant sequoia	22
Arabidopsis	10
Sugarcane	80
Apple	34
Rice	24
Potato	48
Maize	20
Onion	16
Haplopappus gracilis	4

Table 3.2: Number of Chromosomes

Nobel Fact

Thomas Hunt Morgan (1933) received Nobel Prize in Physiology or Medicine for his discoveries concerning the role played by chromosomes in heredity.

3.2 Linkage

The genes which determine the character of an individual are carried by the chromosomes. The genes for different characters may be present either in the same chromosome or in different chromosomes. When the genes are present in different chromosomes, they assort independently according to Mendel's Law of Independent Assortment.

Biologists came across certain genetic characteristics that did not assort out independently in other organisms after Mendel's work. One such case was reported in sweet pea (Lathyrus odoratus) by William Bateson and Reginald C. Punnet in 1906. They crossed one homozygous strain of sweet peas having purple flowers and long pollen grains with another homozygous strain having red flowers and round pollen grains. All the F₁ progenies had purple flower and long pollen grains indicating purple flower long pollen (PL/PL) was dominant over red flower round pollen (pl/pl).

When they crossed the F₁ with parent (test cross), F₂ progenies did not exhibit 1:1:1:1 ratio as expected with independent assortment. A greater number of F₂ plants had purple flowers and long pollen or red flowers and round pollen. So, they concluded that genes for purple colour and long pollen grain and the genes for red colour and round pollen grain were found close together in the same homologous pair of chromosomes. These genes do not allow themselves to be separated. So they do not assort independently.

This type of tendency of genes to stay together during separation of chromosomes is called Linkage. Genes located close together on the same chromosome and inherited together are called linked genes. But the two genes that are sufficiently far apart on the same chromosome are called unlinked genes or syntenic genes. Such condition is known as synteny.

It is to be differentiated by the value of recombination frequency. If the recombination frequency value is more than 50%, the two genes show unlinked. When the recombination frequency value is less than 50%, they show linked. Closely located genes show strong linkage, while genes widely located show weak linkages.

Do You Know?

Fossil Genes: Some of the junk DNA is made up of pseudo genes, the sequences present in that was once working genes. They lost their ability to make proteins. They tell the story of evolution through fossilized parts.

3.2.1 Coupling and Repulsion Theory

The two dominant alleles or recessive alleles occur in the same homologous chromosomes, tend to inherit together into same gamete are called coupling or cis configuration. If dominant or recessive alleles are present on two different, but homologous chromosomes they inherit apart into different gamete are called repulsion or trans configuration.

3.2.2 Kinds of Linkage

T.H. Morgan found two types of linkage. They are complete linkage and incomplete linkage depending upon the absence or presence of new combination of linked genes.

Complete Linkage

If the chances of separation of two linked genes are not possible, those genes always remain together; as a result, only parental combinations are observed. The linked genes are located very close together on the same chromosome — such genes do not exhibit crossing over. This phenomenon is called complete linkage. It is rare but has been reported in male Drosophila. C.B Bridges (1919) discovered that crossing over is completely absent in some species of male Drosophila.

Incomplete Linkage

If two linked genes are sufficiently apart, the chances of their separation are possible. As a result, parental and non-parental combinations are observed. The linked genes exhibit some crossing over. This phenomenon is called incomplete linkage. This was observed in maize. It was reported by Hutchinson.

3.2.3 Linkage Groups

The groups of linearly arranged linked genes on a chromosome are called Linkage groups. In any species the number of linkage groups corresponds to the number of haploid set of chromosomes.

Name of Organism	Linkage Groups
Mucor	2
Drosophila	4
Sweet pea	7
Neurospora	7
Maize	10

Table 3.3: Linkage groups in some organisms

Linkage and crossing over are two processes that have opposite effects. Linkage keeps particular genes together but crossing over mixes them. The differences are given below:

Linkage	Crossing Over
1. The genes present on chromosome stay close together	It leads to separation of linked genes
2. It involves same chromosome of homologous chromosome	It involves exchange of segments between non-sister chromatids of homologous chromosome.
3. It reduces new gene combinations	It increases variability by forming new gene combinations. Leads to formation of new organism.

Table 3.4: Differences between linkage and crossing over

3.3 Crossing Over

Crossing over is a biological process that produces new combination of genes by inter-changing the corresponding segments between non-sister chromatids of homologous pair of chromosomes. The term 'crossing over' was coined by Morgan (1912). It takes place during pachytene stage of prophase I of meiosis. Usually crossing over occurs in germinal cells during gametogenesis. It is called meiotic or germinal crossing over. It has universal occurrence and has great significance. Rarely, crossing over occurs in somatic cells during mitosis. It is called somatic or mitotic crossing over.

3.3.1 Mechanism of Crossing Over

Crossing over is a precise process that includes stages like synapsis, tetrad formation, cross over and terminalization.

(1) Synapsis

Intimate pairing between two homologous chromosomes is initiated during zygotene stage of prophase I of meiosis I. Homologous chromosomes are aligned side by side resulting in a pair of homologous chromosomes called bivalents. This pairing phenomenon is called synapsis or syndesis. It is of three types:

1. Procentric synapsis: Pairing starts from middle of the chromosome.
2. Proterminal synapsis: Pairing starts from the telomeres.
3. Random synapsis: Pairing may start from anywhere.

(2) Tetrad Formation

Each homologous chromosome of a bivalent begins to form two identical sister chromatids, which remain held together by a centromere. At this stage each bivalent has four chromatids. This stage is called tetrad stage.

(3) Cross Over

After tetrad formation, crossing over occurs in pachytene stage. The non-sister chromatids of homologous pair make a contact at one or more points. These points of contact between non-sister chromatids of homologous chromosomes are called Chiasmata (singular-Chiasma). At chiasma, cross-shaped or X-shaped structures are formed, where breaking and rejoining of two chromatids occur. This results in reciprocal exchange of equal and corresponding segments between them.

(4) Terminalization

After crossing over, chiasma starts to move towards the terminal end of chromatids. This is known as terminalization. As a result, complete separation of homologous chromosomes occurs.

3.3.2 Importance of Crossing Over

Crossing over occurs in all organisms like bacteria, yeast, fungi, higher plants and animals. Its importance is:

• Exchange of segments leads to new gene combinations which plays an important role in evolution.
• Studies of crossing over reveal that genes are arranged linearly on the chromosomes.
• Genetic maps are made based on the frequency of crossing over.
• Crossing over helps to understand the nature and mechanism of gene action.
• If a useful new combination is formed it can be used in plant breeding.

3.3.3 Recombination

Crossing over results in the formation of new combination of characters in an organism called recombinants. In this, segments of DNA are broken and recombined to produce new combinations of alleles. This process is called Recombination.

Calculation of Recombination Frequency (RF)

The percentage of recombinant progeny in a cross is called recombination frequency. The recombination frequency (cross over frequency) (RF) is calculated by using the following formula. The data is obtained from alleles in coupling configuration.

RF = (Total number of recombinations / Total number of offsprings) × 100

Activity Solve This

Consider two hypothetical recessive autosomal genes a and b, where a heterozygote is testcrossed to a double homozygous mutant. Predict the phenotypic ratios under the following conditions:

(a) a and b are located on separate autosomes.

(b) a and b are linked on the same autosome but are so far apart that a crossover occurs between them.

(c) a and b are linked on the same autosome but are so close together that a crossover almost never occurs.

3.3.4 Genetic Mapping

Genes are present in a linear order along the chromosome. They are present in a specific location called locus (plural: loci). The diagrammatic representation of position of genes and related distances between the adjacent genes is called genetic mapping. It is directly proportional to the frequency of recombination between them. It is also called as linkage map. The concept of gene mapping was first developed by Morgan's student Alfred H Sturtevant in 1913. It provides clues about where the genes lies on that chromosome.

Map Distance

The unit of distance in a genetic map is called a map unit (m.u). One map unit is equivalent to one percent of crossing over. One map unit is also called a centimorgan (cM) in honour of T.H. Morgan. 100 centimorgan is equal to one Morgan (M).

Example: A distance between A and B genes is estimated to be 3.5 map units. It is equal to 3.5 centimorgans or 3.5% or 0.035 recombination frequency between the genes.

Uses of Genetic Mapping

• It is used to determine gene order, identify the locus of a gene and calculate the distances between genes.
• They are useful in predicting results of dihybrid and trihybrid crosses.
• It allows the geneticists to understand the overall genetic complexity of particular organism.

3.4 Multiple Alleles

A given phenotypic trait of an individual depends on a single pair of genes, each of which occupies a specific position called the locus on homologous chromosome. When any of the three or more allelic forms of a gene occupy the same locus in a given pair of homologous chromosomes, they are said to be called multiple alleles.

Check Your Grasp

There may be multiple alleles within the population, but individuals have only two of those alleles. Why?

3.4.1 Characteristics of Multiple Alleles

• Multiple alleles of a series always occupy the same locus in the homologous chromosome. Therefore, no crossing over occurs within the alleles of a series.
• Multiple alleles are always responsible for the same character.
• The wild type alleles of a series exhibit dominant character whereas mutant type will influence dominance or an intermediate phenotypic effect.
• When any two of the mutant multiple alleles are crossed the phenotype is always mutant type and not the wild type.

3.4.2 Self-Sterility in Nicotiana

In plants, multiple alleles have been reported in association with self-sterility or self-incompatibility. Self-sterility means that the pollen from a plant is unable to germinate on its own stigma and will not be able to bring about fertilization in the ovules of the same plant.

East (1925) observed multiple alleles in Nicotiana which are responsible for self-incompatibility or self-sterility. The gene for self-incompatibility can be designated as S, which has allelic series S₁, S₂, S₃, S₄ and S₅. The cross-fertilizing tobacco plants were not always homozygous as S₁S₁ or S₂S₂, but all plants were heterozygous as S₁S₂, S₃S₄, S₅S₆.

When crosses were made between different S₁S₂ plants, the pollen tube did not develop normally. But effective pollen tube development was observed when crossing was made with other than S₁S₂, for example S₃S₄. When crosses were made between seed parents with S₁S₂ and pollen parents with S₂S₃, two kinds of pollen tubes were distinguished. Pollen grains carrying S₂ were not effective, but the pollen grains carrying S₃ were capable of fertilization. Thus, from the cross S₁S₂ × S₃S₄, all the pollens were effective and four kinds of progeny resulted: S₁S₃, S₁S₄, S₂S₃ and S₂S₄.

3.4.3 Sex Determination in Maize

Zea mays (maize) is an example for monoecious, which means male and female flowers are present on the same plant. There are two types of inflorescences. The terminal inflorescence which bears staminate florets develops from shoot apical meristem called tassel. The lateral inflorescence which develops pistillate florets from axillary bud is called ear or cob.

Unisexuality in maize occurs through the selective abortion of stamens in ear florets and pistils in tassel florets. A substitution of two single gene pairs 'ba' for barren plant and 'ts' for tassel seed makes the difference between monoecious and dioecious (rare) maize plants. The allele for barren plant (ba) when homozygous makes the stalk staminate by eliminating silk and ears. The allele for tassel seed (ts) transforms tassel into a pistillate structure that produce no pollen.

Genotype	Dominant/Recessive	Modification	Sex
ba/ba ts/ts	Double recessive	Lacks silk on the stalk, but transformed tassel to pistil	Rudimentary female
ba/ba ts⁺/ts⁺	Recessive and dominant	Lacks silk and have tassel	Male
ba⁺/ba⁺ ts⁺/ts⁺	Double dominant	Have both tassel and cob	Monoecious
ba⁺/ba⁺ ts/ts	Dominant and recessive	Bears cob and lacks tassel	Normal female

Table 3.6: Sex determination in Maize (Superscript (+) denotes dominant character)

Most of these mutations are shown to be defects in gibberellin biosynthesis. Gibberellins play an important role in the suppression of stamens in florets on the ears.

3.5 Mutation

Genetic variation among individuals provides the raw material for the ultimate source of evolutionary changes. Mutation and recombination are the two major processes responsible for genetic variation. A sudden change in the genetic material of an organism is called mutation. The term mutation was introduced by Hugo de Vries (1901) while he was studying on the plant, evening primrose (Oenothera lamarkiana) and proposed 'Mutation theory'.

There are two broad types of changes in genetic material. They are point mutation and chromosomal mutations. Mutational events that take place within individual genes are called gene mutations or point mutation, whereas the changes that occur in structure and number of chromosomes is called chromosomal mutation. Agents which are responsible for mutation are called mutagens, that increase the rate of mutation. Mutations can occur either spontaneously or induced. The production of mutants through exposure of mutagens is called mutagenesis, and the organism is said to be mutagenized.

3.5.1 Types of Mutation

The two general classes of gene mutation:

• Mutations affecting single base or base pair of DNA are called point mutation.
• Mutations altering the number of copies of a small repeated nucleotide sequence within a gene.

Sl. No.	Basis of Classification	Major Types of Mutations	Major Features
1	Origin	Spontaneous	Occurs in the absence of known mutagen
1	Origin	Induced	Occurs in the presence of known mutagen
2	Cell type	Somatic	Occurs in non-reproductive cells
2	Cell type	Germ-line	Occurs in reproductive cells
3	Effect on function	Loss-of-function (knockout, null)	Eliminates normal function
3		Hypomorphic (leaky)	Reduces normal function
3		Hypermorphic	Increases normal function
3		Gain-of-function (ectopic expression)	Expressed at incorrect time or inappropriate cells
4	Molecular change	Nucleotide substitution – Transition	Purine to purine (A→G) or pyrimidine to pyrimidine (T→C)
4		Transversion	Purine to pyrimidine (A→T) or pyrimidine to purine (C→G)
4		Insertion	One or more extra nucleotides are present
4		Deletion	One or more nucleotides are missing
5	Effect on translation	Silent (synonymous)	No change in amino acid encoded
5		Missense (non-synonymous)	Change in amino acid encoded
5		Nonsense (termination)	Creates translational termination codon (UAA, UAG, or UGA)
5		Frameshift	Shifts triplet reading of codons out of correct phase

Table 3.7: Major types of mutations

Point Mutation

It refers to alterations of single base pairs of DNA or of a small number of adjacent base pairs.

Types of point mutations: Point mutation in DNA are categorised into two main types — base pair substitutions and base pair insertions or deletions.

• Base substitutions are mutations in which there is a change in the DNA such that one base pair is replaced by another. It can be divided into two subtypes: transitions and transversions.
• Addition or deletion mutations are actually additions or deletions of nucleotide pairs, also called base pair addition or deletions. Collectively, they are termed indel mutations (for insertion-deletion).
• Synonymous or silent mutations: The mutation that changes one codon for an amino acid into another codon for that same amino acid.
• Missense or non-synonymous mutations: The mutation where the codon for one amino acid is changed into a codon for another amino acid.
• Nonsense mutation: The mutations where codon for one amino acid is changed into a termination or stop codon.
• Frameshift mutations: Mutations that result in the addition or deletion of a single base pair of DNA that changes the reading frame for the translation process as a result of which there is complete loss of normal protein structure and function.

3.5.2 Mutagenic Agents

The factors which cause genetic mutation are called mutagenic agents or mutagens. Mutagens are of two types, physical mutagen and chemical mutagen. Muller (1927) was the first to find out physical mutagen in Drosophila.

Physical Mutagens

Scientists are using temperature and radiations such as X rays, gamma rays, alfa rays, beta rays, neutron, cosmic rays, radioactive isotopes, ultraviolet rays as physical mutagen to produce mutation in various plants and animals.

Temperature: Increase in temperature increases the rate of mutation. While rise in temperature, breaks the hydrogen bonds between two DNA nucleotides which affects the process of replication and transcription.

Radiation: The electromagnetic spectrum contains shorter and longer wave length rays than the visible spectrum. These are classified into ionizing and non-ionizing radiation.

• Ionizing radiation are short wave length and carry enough higher energy to ionize electrons from atom. X rays, gamma rays, alfa rays, beta rays and cosmic rays which breaks the chromosomes (chromosomal mutation) and chromatids in irradiated cells.
• Non-ionizing radiation — UV rays have longer wavelengths and carry lower energy, so they have lower penetrating power than the ionizing radiations. It is used to treat unicellular microorganisms, spores, pollen grains which possess nuclei located near surface membrane.

Sharbati Sonora

Sharbati Sonora is a mutant variety of wheat, which is developed from Mexican variety (Sonora 64) by irradiating of gamma rays. It is the work of Dr. M. S. Swaminathan who is known as 'Father of Indian green revolution' and his team.

Castor Aruna

Castor Aruna is mutant variety of castor which is developed by treatment of seeds with thermal neutrons in order to induce very early maturity (120 days instead of 270 days as original variety).

Chemical Mutagens

Chemicals which induce mutation are called chemical mutagens. Some chemical mutagens are mustard gas, nitrous acid, ethyl and methyl methane sulphonate (EMS and MMS), ethyl urethane, magnous salt, formaldehyde, eosin and enthrosine.

Example: Nitrous oxide alters the nitrogen bases of DNA and disturbs the replication and transcription that leads to the formation of incomplete and defective polypeptide during translation.

Comutagens

The compounds which are not having own mutagenic properties but can enhance the effects of known mutagens are called comutagens.

Examples: Ascorbic acid increases the damage caused by hydrogen peroxide. Caffeine increases the toxicity of methotrexate.

Did You Know?

• Mustard gas (Dichloro ethyl sulphide) was used as chemical weapon in World War I.
• H J Muller (1928) first time used X rays to induce mutations in fruit fly.
• L J Stadler reported induced mutations in plants by using X rays and gamma rays.
• Chemical mutagenesis was first reported by C. Auerback (1944).

3.5.3 Chromosomal Mutations

The genome can also be modified on a larger scale by altering the chromosome structure or by changing the number of chromosomes in a cell. These large-scale variations are termed as chromosomal mutations or chromosomal aberrations. Gene mutations are changes that take place within a gene, whereas chromosomal mutations are changes to a chromosome region consisting of many genes. It can be detected by microscopic examination, genetic analysis, or both.

Chromosomal mutations are divided into two groups: changes in chromosome number and changes in chromosome structure.

1. Changes in Chromosome Number

Each cell of living organisms possesses a fixed number of chromosomes. Sometimes the chromosome number of somatic cells are changed due to addition or elimination of individual chromosome or basic set of chromosomes. This condition is known as numerical chromosomal aberration or ploidy. There are two types of ploidy:

1. Ploidy involving individual chromosomes within a set (Aneuploidy)
2. Ploidy involving entire sets of chromosomes (Euploidy)

(1) Aneuploidy

It is a condition in which diploid number is altered either by addition or deletion of one or more chromosomes. Organisms showing aneuploidy are known as aneuploids or heteroploids. They are of two types, Hyperploidy and Hypoploidy.

1. Hyperploidy

Addition of one or more chromosomes to diploid sets are called hyperploidy. Diploid set of chromosomes is represented as Disomy. Hyperploidy can be divided into three types:

• (a) Trisomy: Addition of single chromosome to diploid set is called Simple trisomy (2n+1). Trisomics were first reported by Blackeslee (1910) in Datura stramonium (Jimson weed). But later it was reported in Nicotiana, Pisum and Oenothera. Sometimes addition of two individual chromosomes from different chromosomal pairs to normal diploid sets are called Double trisomy (2n+1+1).
• (b) Tetrasomy: Addition of a pair or two individual pairs of chromosomes to diploid set is called tetrasomy (2n+2) and Double tetrasomy (2n+2+2) respectively. All possible tetrasomics are available in Wheat.
• (c) Pentasomy: Addition of three individual chromosomes from different chromosomal pairs to normal diploid set are called pentasomy (2n+3).

2. Hypoploidy

Loss of one or more chromosome from the diploid set in the cell is called hypoploidy. It can be divided into two types:

• (a) Monosomy: Loss of a single chromosome from the diploid set is called monosomy (2n-1). However, loss of two individual or three individual chromosomes are called double monosomy (2n-1-1) and triple monosomy (2n-1-1-1) respectively. Double monosomics are observed in maize.
• (b) Nullisomy: Loss of a pair of homologous chromosomes or two pairs of homologous chromosomes from the diploid set are called Nullisomy (2n-2) and double Nullisomy (2n-2-2) respectively. Selfing of monosomic plants produce nullisomics. They are usually lethal.

(ii) Euploidy

Euploidy is a condition where the organisms possess one or more basic sets of chromosomes. Euploidy is classified as monoploidy, diploidy and polyploidy. The condition where an organism or somatic cell has two sets of chromosomes are called diploid (2n). Half the number of somatic chromosomes is referred as gametic chromosome number called haploid (n).

It should be noted that haploidy (n) is different from a monoploidy (x). For example, the common wheat plant is a polyploidy (hexaploidy) 2n=6x=72 chromosomes. Its haploid number (n) is 36, but its monoploidy (x) is 12. In a true diploid both the monoploid and haploid chromosome number are same. Thus, a monoploid can be a haploid but all haploids cannot be a monoploid.

Polyploidy

Polyploidy is the condition where an organism possesses more than two basic sets of chromosomes. When there are three, four, five or six basic sets of chromosomes, they are called triploidy (3x), tetraploidy (4x), pentaploidy (5x) and hexaploidy (6x) respectively. Generally, polyploidy is very common in plants but rarer in animals. Polyploidy is of two types: autopolyploidy and allopolyploidy.

1. Autopolyploidy

The organism which possesses more than two haploid sets of chromosomes derived from within the same species is called autopolyploid. They are divided into two types: Autotriploids and Autotetraploids.

• Autotriploids have three sets of its own genomes. They are highly sterile due to defective gamete formation. Examples: The cultivated banana are usually triploids and are seedless having larger fruits than diploids. Triploid sugar beets have higher sugar content than diploids and are resistant to moulds. Common doob grass (Cyanodon dactylon) is a natural autotriploid. Seedless watermelon, apple, sugar beet, tomato, banana are manmade autotriploids.
• Autotetraploids have four copies of its own genome. They may be induced by doubling the chromosomes of a diploid species. Examples: rye, grapes, alfalfa, groundnut, potato and coffee.

2. Allopolyploidy

An organism which possesses two or more basic sets of chromosomes derived from two different species is called allopolyploidy. It can be developed by interspecific crosses and fertility is restored by chromosome doubling with colchicine treatment. Allopolyploids are formed between closely related species only.

Example 1: Raphanobrassica — G.D. Karpechenko (1927), a Russian geneticist, crossed the radish (Raphanus sativus, 2n=18) and cabbage (Brassica oleracea, 2n=18) to produce F₁ hybrid which was sterile. When he doubled the chromosome of F₁ hybrid he got it fertile. He expected this plant to exhibit the root of radish and the leaves like cabbage, which would make the entire plant edible, but the case was vice versa, so he was greatly disappointed.

Example 2: Triticale — the successful first man-made cereal. Depending on the ploidy level Triticale can be divided into three main groups:

1. Tetraploidy: Crosses between diploid wheat and rye.
2. Hexaploidy: Crosses between tetraploid wheat Triticum durum (macaroni wheat) and rye.
3. Octoploidy: Crosses between hexaploid wheat T. aestivum (bread wheat) and rye.

Hexaploidy Triticale hybrid plants demonstrate characteristics of both macaroni wheat and rye. For example, they combine the high-protein content of wheat with rye's high content of the amino acid lysine, which is low in wheat.

Did You Know?

Colchicine, an alkaloid is extracted from root and corms of Colchicum autumnale. When applied in low concentration to the growing tips of the plants it will induce polyploidy. Surprisingly it does not affect the source plant Colchicum, due to presence of anticolchicine.

Significance of Ploidy

• Many polyploids are more vigorous and more adaptable than diploids.
• Many ornamental plants are autotetraploids and have larger flowers and longer flowering duration than diploids.
• Autopolyploids usually have higher fresh weight due to more water content.
• Aneuploids are useful to determine the phenotypic effects of loss or gain of different chromosomes.
• Many angiosperms are allopolyploids and they play a role in the evolution of plants.

II. Structural Changes in Chromosome (Structural Chromosomal Aberration)

Structural variations caused by addition or deletion of a part of chromosome leading to rearrangement of genes is called structural chromosomal aberration. It occurs due to ionizing radiation or chemical compounds. On the basis of breaks and reunion in chromosomes, there are four types of aberrations classified under two groups:

A. Changes in the number of the gene loci:

1. Deletion or Deficiency
2. Duplication or Repeat

B. Changes in the arrangement of gene loci:

1. Inversion
2. Translocation

1. Deletion or Deficiency: Loss of a portion of chromosome is called deletion. On the basis of location of breakage on chromosome, it is divided into terminal deletion and intercalary deletion. It occurs due to chemicals, drugs and radiations. It is observed in Drosophila and Maize.

2. Duplication or Repeat: The process of arrangement of the same order of genes repeated more than once in the same chromosome is known as duplication. Due to duplication some genes are present in more than two copies. It was first reported in Drosophila by Bridges (1919) and other examples are Maize and Pea.

3. Inversion: A rearrangement of order of genes in a chromosome by reversed by an angle 180°. This involves two chromosomal breaks and reunion. During this process there is neither gain nor loss but the gene sequence is rearranged. Inversion was first reported in Drosophila by Sturtevant (1926). There are two types of inversion:

• Paracentric inversion: An inversion which takes place apart from the centromere.
• Pericentric inversion: An inversion that includes the centromere. Inversions lead to evolution of a new species.

4. Translocation: The transfer of a segment of chromosome to a non-homologous chromosome is called translocation. Translocation should not be confused with crossing over. Translocation occurs as a result of interchange of chromosome segments in non-homologous chromosomes. There are three types:

1. Simple translocation
2. Shift translocation
3. Reciprocal translocation

3.6 DNA Metabolism in Plants

As the repository of genetic information, DNA occupies a unique and central place among biological macromolecules. The structure of DNA is a marvelous device for the storage of genetic information. The term "DNA Metabolism" can be used to describe the process by which copies of DNA molecules are made (replication) along with repair and recombination.

• DNA Replication: In the double helix the two parental strands of DNA separate and each parental strand synthesizes a new complementary strand. DNA replication is semiconservative, that is each new DNA molecule conserves one original strand.
• DNA Repair: DNA is the only macromolecule where the repair system exists, which recognises and removes mutations. DNA is subjected to various types of damaging reactions such as spontaneous or environmental agents or natural endogenous threats. Such damages are corrected by repair enzymes and proteins, immediately after the damage has taken place. DNA repair systems protect the integrity of genomes from genotoxic stresses.
• Recombination: In cells the genetic information within and among DNA molecules are re-arranged by a process called genetic recombination. Recombination is the result of crossing over between the pairs of homologous chromosomes during meiosis. At the molecular level it involves breakage and reunion of polynucleotides.

3.6.1 Eukaryotic DNA Replication

Replication starts at a specific site on a DNA sequence known as the Origin of replication. There are more than one origin of replication in eukaryotes. Saccharomyces cerevisiae (yeast) has approximately 400 origins of replication.

DNA replication in eukaryotes starts with the assembly of a pre-replication complex (preRC) consisting of 14 different proteins. Part of a preRC is a group of 6 proteins called the origin recognition complex (ORC) which acts as initiator in eukaryotic DNA replication. The origin of replication in yeast is called as ARS sites (Autonomously Replicating Sequences). In yeast, ORC was identified as a protein complex which binds directly to ARS elements.

Replication fork is the site (point of unwinding) of separation of parental DNA strands where new daughter strands are formed. Multiple replication forks are found in eukaryotes.

The enzyme helicases are involved in unwinding of DNA by breaking hydrogen bonds holding the two strands of DNA and replication protein A (RPA) prevents the separated polynucleotide strand from getting reattached. Topoisomerase is an enzyme which breaks DNA's covalent bonds and removes positive supercoiling ahead of replication fork. It eliminates the torsional stress caused by unwinding of DNA double helix.

DNA replication is initiated by an enzyme DNA polymerase α/primase which synthesizes short stretch of RNA primers on both leading strand (continuous DNA strand) and lagging strands (discontinuous DNA strand). Primers are needed because DNA polymerase requires a free 3'OH to initiate synthesis. DNA polymerase covalently connects the nucleotides at the growing end of the new DNA strand.

Enzyme	Function
DNA Pol α (alpha)	Synthesizes short primers of RNA
DNA Pol δ (delta)	Main Replicating enzyme of cell nucleus
DNA Pol ε (Epsilon)	Extend the DNA Strands in replication fork

Did You Know?

DNA Polymerase β does not play any role in the replication of normal DNA. Function: Removing incorrect bases from damaged DNA. It is involved in Base excision repair.

DNA Synthesis takes place in 5' to 3' direction and it is semi discontinuous. In 1960s Reiji Okazaki and his colleagues found out that one of the new DNA strands is synthesized in short pieces called Okazaki Fragments. In discontinuous strand where the Okazaki fragments are united by ligase is called Lagging strand where the replication direction is 5' to 3' which is opposite to the direction of fork movement. The continuous strand is called Leading strand where the replication direction is 5' to 3' which is same as the direction of the replication fork movement.

DNA ligase joins any nicks in the DNA by forming a phosphodiester bond between 3' hydroxyl and 5' phosphate group.

Arabidopsis Telomere Sequence: TTTAGGG — Plants Lack Telomere Clock

Plant meristematic cells produce telomerase so the meristematic cells have an unlimited ability to divide. In plants telomeres do not shrink as in somatic cells of vertebrates. Telomerase levels are higher in root tips and seedlings (renewable tissue) which has a higher amount of meristematic cells than proliferative structures like leaves.

After the replication of the chromosomes, the enzyme telomerase adds several more repeats of DNA sequences to the telomeres. Telomerase uses short RNA molecules as a template and adds repeat sequences onto telomeres (DNA nucleotide polymerisation).

The Energetics of DNA Replication

Deoxyribonucleotides such as deoxyadenosine triphosphate dATP, dGTP, dCTP and dTTP provide energy for the synthesis of DNA. Purpose of deoxyribonucleotides: (1) acts as a substrate; (2) provides energy for polymerisation.

3.6.2 Experimental Evidence of DNA Replication: Taylor's Experiment

J. Herbert Taylor, Philip Woods and Walter Hughes demonstrated the semiconservative replication of DNA in the root cells of Vicia faba. They labelled DNA with ³H Thymidine, a radioactive precursor of DNA and performed autoradiography. They grew root tips in a medium in the presence of radioactive labelled thymidine, so that the radioactivity was incorporated into the DNA of these cells. The outline of this labelled chromosomes appears in the form of scattered black dots of silver grains on a photographic film. The root tips with labelled chromosomes were placed in an unlabelled medium containing colchicine to arrest the culture at the metaphase and examine the chromosome by autoradiography.

The observations were:

1. In the chromosome of first generation the radioactivity was found to be distributed to both the chromatids because in the original strand of DNA double helix was labelled with radioactivity and the new strand was unlabelled.
2. In the chromosome of the second generation only one of the two chromatids in each chromosome was radioactive (labelled).

The results proved the semiconservative method of DNA replication.

3.7 Protein Synthesis in Plants

The process of protein synthesis consists of two major steps: Transcription and Translation.

3.7.1 Transcription

Transcription is the process in which one strand of DNA acts as a template to generate mRNA with the bases complementary to the template strand. It is catalyzed by the enzymes called RNA polymerases. Transcription and processing of RNA takes place in the nucleus, whereas the translation occurs in the ribosomes found in cytoplasm. In Eukaryotes, mRNA molecules are monocistronic with only one protein being derived from each mRNA.

The transcription begins with unwinding of DNA double helix and the hydrogen bonds are broken at the site of the gene being transcribed.

Template Strand / Non-Coding Strand / Antisense Strand

The strand of DNA which is oriented in 3'→5' direction that serves as a template for the synthesis of mRNA is called template strand.

Coding Strand / Non-template Strand / Sense Strand

The other strand of DNA which is not transcribed is called the Coding Strand.

A specific sequence of DNA nucleotides called the Promoter is necessary for transcription to take place. It consists of TATA box and transcription start site where transcription begins. Termination sequences are the DNA sequences which tell when the RNA polymerase should stop producing RNA molecule.

Eukaryotic Structural Gene has 3 Features in Promoter

1. Regulatory elements
2. TATA box
3. A transcriptional start site

The transcription start site contains about 25 bp (basepairs) upstream, the sequence is TATAAT known as TATA or Hogness box which is present in core promoter.

General transcriptional factors are the proteins which recognise base sequences of DNA and control transcription. Some transcription factors bind directly to the promoter. Some transcription factors recognize the regulatory elements and bind to them to increase the rate of transcription; others inhibit transcription. To start the process of transcription, the regulatory elements help the RNA polymerase to recognize core promoter.

The two categories of regulatory elements are:

1. Enhancer sequences — they are DNA sequences (activating sequences) which help to influence transcription.
2. Silencer sequence — DNA sequences that inhibit transcription or decrease transcription.

Did You Know?

Consensus sequence — An ideal sequence in which each position represents the base which is found most often. In addition to General transcription factors (GTF) and RNA Pol II, a mediator is required for transcription. The interactions between RNA polymerase II and regulatory TF that bind to enhancers or silencers are mediated by a mediator.

RNA Polymerases cannot bind directly to the DNA; first it binds to the transcription factor which recognizes the promoter sequences which helps to find the protein coding regions of DNA. RNA Polymerase with the promoter sequence will transcribe the gene. Transcription factor plays an important role in guiding RNA Polymerases to the promoter sequence. RNA Polymerases bind RNA nucleotides together forming a growing strand in the 5' to 3' direction. Transcription occurs in 5' to 3' direction.

Enzyme	Synthesis
RNA Polymerase I	Large Ribosomal RNAs except 5S rRNA
RNA Polymerase II	Precursors of mRNAs (hnRNAs)
RNA Polymerase III	tRNAs, 5S ribosomal RNA, snRNAs (small nuclear RNA)

The Processing of pre-mRNA to Mature mRNA / Molecular Mechanism of RNA Modification

In eukaryotes three major types of RNA — mRNA, tRNA and rRNA — are produced from a precursor RNA molecule termed as the primary transcript or pre-RNA. The RNA polymerase II transcribes the precursor of mRNA, which are also called the heterogenous nuclear RNA or hn-RNA, which are processed in the nucleus before they are transported into the cytoplasm.

Capping

Modification at the 5' end of the primary RNA transcript (hn-RNA) with methylguanosine is called capping.

Purpose of Capping:

1. Protects RNA from degradation.
2. Capping plays an important role in removal of first intron in pre mRNA.
3. It regulates the mRNA export from the nucleus into the cytoplasm.
4. It helps in binding of mRNA to the ribosome.

Do You Know?

Internal methylation: Apart from capping, the internal nucleotides are also methylated. Methylated sites are present in translated, untranslated regions, introns and exons.

Tailing / Polyadenylation

The 3' end of hn-RNA is cleaved by an endonuclease and a string of adenine nucleotides is added to the 3' end of hn-RNA (pre mRNA) is known as Poly (A) tail — Polyadenylation. This process is called tailing or polyadenylation.

Purpose of Tailing:

1. Translation of RNA transcript is facilitated.
2. Helps in the synthesis of polypeptides.
3. It enhances the mRNA stability in the cytoplasm.

The protein coding regions are not continuous in eukaryotes. Split genes were independently discovered by Richard J Roberts and Phillip A. Sharp in 1977 and was awarded Nobel Prize in 1993.

• Exons are the coding sequences or expressed sequences that contain biological information in the matured processed mRNA.
• Introns are intervening sequences, which are non-coding sequences (non-amino acid coding sequences) that should be removed from a gene before the mRNA product is made. Introns do not code for any enzyme or structural protein or polypeptides. These exons and introns are known as Split Genes.

3.7.2 RNA Splicing in Plants

RNA Splicing is a process which involves the cutting or removing out of introns and knitting of exons. This process takes place in spherical particles which is a multiprotein complex called SPLICEOSOMES. It is approximately 40–60 nm in diameter. The spliceosomes have many small nuclear ribonucleic acids (sn-RNAs) and small nuclear ribonuclear protein particles (sn-RNPs) which identify and help in the removal of introns. A spliceosome removes the introns with an enzyme ribozyme.

Now the mature mRNA comes away from the spliceosomes through the nuclear pore and is transported out from the nucleus into cytoplasm, and gets attached to ribosome to carry out translation. The RNA and many proteins are transported through a nuclear pore complex by an energy dependent process.

3.7.3 Translation

The genetic information in the DNA code is copied onto mRNA bound in ribosomes for making polypeptides. The mRNA nucleotide sequence is decoded into amino acid sequence of the protein which is catalyzed by the ribosome. This process is called translation.

Terminology in Protein Synthesis

• Codon — DNA codes are referred to as triplet codes and those in mRNA is called as Codons. Each triplet specifies a particular amino acid. Codons present in mRNA are read in 5' to 3' direction. There are 64 codons of which 61 codons code for amino acids.
• Start codon — AUG specifies methionine.
• Stop or Termination codon — UAA – Ochre, UAG – Amber and UGA – Opal.
• Anticodons — The triplet of bases in a tRNA molecule is known as anticodon. In tRNA, the sequence of three bases which is complementary to codons of mRNA are called anticodon. The codons of mRNA are recognized by the anticodons of tRNA which are oriented in 3' to 5' direction.

Process of Translation

The following are major steps in translation process:

1. Initiation

The translation begins with the AUG codon (start codon) of mRNA. Translation occurs on the surface of the macromolecular arena called the ribosome. It is a non-membranous organelle. During the process of translation, the two subunits of ribosomes unite (combine) together and hold mRNA between them. The protein synthesis begins with the reading of codons of mRNA. The tRNA brings amino acid to the ribosome, a molecular machine which unites amino acids into a chain according to the information given by mRNA. rRNA plays the structural and catalytic role during translation.

A ribosome has one binding site for mRNA and two for tRNA. The two binding sites of tRNA are:

• P-Site — The peptidyl-tRNA binding site. At this site tRNA is held and linked to the growing end of the polypeptide chain.
• A-Site — The Aminoacyl-tRNA binding site. This holds the incoming amino acids called aminoacyl tRNA. The anticodons of tRNA pair with the codons of the mRNA in these sites.

2. Elongation of Polypeptide Chain

The P and A sites are nearby, so that two tRNA form base pairs with adjacent codon. The polypeptide chain is formed by the pairing of codons and anticodons according to the nucleotide sequence of the mRNA.

The tRNA translates the genetic code from the nucleic acid sequence to the amino acid sequence — that is from gene to polypeptide. When an amino acid is attached to tRNA it is called aminoacylated or charged. This is an energy requiring process which uses ATP.

Protein synthesis takes place as the next aminoacyl tRNA binds to the A-Site. The translation begins with the AUG codon (start codon) of mRNA. The tRNA which carries first amino acid methionine attaches itself to P-site of ribosome. The ribosome adds new amino acids to the growing polypeptides. The second tRNA molecule has anticodons which carries amino acid alanine pairs with the mRNA codon in the A-site of the ribosome. The aminoacids methionine and alanine are close enough so that a peptide bond is formed between them. The bond between the first tRNA and methionine now breaks. The first tRNA leaves the ribosome and the P-site is vacant.

The ribosome now moves one codon along the mRNA strand. The second tRNA molecule now occupies the P-site. The third tRNA comes and fills the A site (serine). Now a peptide bond is formed between alanine and serine. The mRNA then moves through the ribosome by three bases. This expels deacylated/uncharged tRNA from P-site and moves peptidyl tRNA into the P-site and empties the A-site. The movement of mRNA and tRNA through the ribosome is called translocation. Translocation requires the hydrolysis of GTP. The ribosome (ribozyme - peptidyl transferase) catalyses the formation of peptide bond by adding amino acid to the growing polypeptide chain. The ribosome moves from codon to codon along the mRNA in the 5' to 3' direction. Translation is an energy intensive process.

A cluster of ribosomes linked together by a molecule of mRNA forming the site of protein synthesis is called polysomes or polyribosomes.

3. Termination of Polypeptide Synthesis

Eukaryotes have cytosolic proteins called release factors which recognize the termination codon, UAA, UAG, or UGA when it is in the A site. When the ribosome reaches a stop codon the protein synthesis comes to an end. When the polypeptide is completed, the ribosome releases the polypeptide and detaches from the mRNA molecule. Now the ribosome splits into small and large subunits after the release of mRNA.

3.7.4 Alternative Splicing in Plants

Alternative splicing is an important mechanism/process by which multiple mRNAs and multiple protein products can be generated from a single gene. The different proteins generated are called isoforms. It is very useful in regulating gene expression to overcome the environmental stress in plants. There are various modes of alternative splicing. When multiple introns are present in a gene, they are removed separately or as a unit. In certain cases, one or more exons which is present between the introns are also removed.

Significance of Alternative Splicing

1. The proteins transcribed from alternatively spliced mRNA containing different amino acid sequence lead to the generation of protein diversity and biological functions.
2. Multiple protein isoforms are formed.
3. It creates multiple mRNA transcripts from a single gene. A process of producing related proteins from a single gene thereby the number of gene products are increased.
4. It plays an important role in plant functions such as stress response and trait selection. The plant adapts or regulates itself to the changing environment.

3.7.5 RNA Editing – Post Transcriptional RNA Processing in Plants

Chemical modification such as base modification, nucleotide insertion or deletions and nucleotide replacements of mRNA results in the alteration of amino acid sequence of protein that is specified — this is called RNA editing. This results in the change in the protein coding sequence of RNA following transcription. The coding properties of the RNA transcript is changed.

The genetic information encoded in the chloroplast genome is altered by post transcriptional phenomenon which is site-specific C→U in chloroplast of higher plants. RNA editing occurs in plant mitochondria and chloroplast. In plant cells RNA editing by pyrimidine transitions occurs in mitochondria and plastids (chloroplast).

There are two main types of RNA editing:

1. Substitution editing — Alteration of individual nucleotide bases. Mitochondria and chloroplast RNA in plants.
2. Insertion/Deletion editing — Nucleotides are added or deleted from the total number of bases.

Year	Editing Type	Organelle in Plant Cell	Target	Inference/Result
1989	C → U	Plant mitochondria	mRNA	For conserved amino acids, multiple changes in codon takes place
1990	U → C	Plant mitochondria	mRNA	First report on editing (U→C)
1991	C → U	Plant chloroplast	mRNA	First report in chloroplast

Table 3.8: RNA Editing types

Significance of RNA Editing

1. In higher plant chloroplast, it helps to restore the codons for conserved amino acids which include initiation and termination codon.
2. It regulates Organellar gene expression in plants.
3. RNA editing results in the restoration of codons for phylogenetically conserved amino acid residues.

3.7.6 Jumping Genes

Transposons are the DNA sequences which can move from one position to another position in a genome. This was first reported in 1948 by American Geneticist Barbara McClintock as "mobile controlling element" in Maize. One of the most significant scientists of 20th century was Barbara McClintock because she gave a shift in gene organization. McClintock was awarded Nobel prize in 1983 for her work on transposons.

Barbara McClintock when studying aleurone of single maize kernels, noted the unstable inheritance of the mosaic pattern of blue, brown and red spots due to the differential production of vacuolar anthocyanins. In maize plant genome has AC/Ds transposon (AC = Activator, Ds = Dissociation). The activity of AC element is very distinct in maize plant. The transposition in somatic cells results in the changes in gene expression such as variegated pigmentation in maize kernels. Maize genome has transposable elements which regulated the different colour pattern of kernels.

McClintock's findings concluded that Ds and AC genes were mobile controlling elements. We now call it as transposable elements, a term coined by maize geneticist, Alexander Brink. McClintock gave the first direct experimental evidence that genomes are not static but are highly plastic entities.

Significance of Transposons

• They contribute to many visible mutations and mutation rate in an organism.
• In evolution, they contribute to genetic diversity.
• In genetic research transposons are valuable tools which are used as mutagens, as cloning tags, vehicles for inserting foreign DNA into model organism.

Plant Genome

The word genome is defined as the full complement of DNA (including all the genes and the intergenic regions) present in an organism. It specifies the entire biological information of an organism. There are three distinct genomes in eukaryotic cells:

1. The nuclear genome
2. The mitochondrial genome
3. The chloroplast genome — present only in plants

Arabidopsis thaliana – Thale Cress, Mouseear Cress

1. It is a model plant for the study of genetic and molecular aspects of plant development.
2. It belongs to mustard family and it is the first flowering plant where its entire genome is sequenced.
3. The two regions of the nucleolar organiser ribosomal DNA which codes for the ribosomal RNA are present at the extremity of chromosomes 2 and 4.
4. It is a diploid plant having small genome with 2n = 10 chromosomes. Several generations can be produced in one year, so it facilitates rapid genetic analysis. The genome has low repetitive DNA; over 60% of the nuclear DNA have protein coding functions.
5. The plant is small, self-fertilizes, annual long-day plant with short-life cycle (only 6 weeks), large numbers of seeds are produced and they are easy to be grown in laboratory. It is easy to induce mutations. It has many genomic resources and the transformation can be done easily.
6. In 1982, Arabidopsis has successfully completed its life cycle in Microgravity that is space. This shows that Human Space Missions with plant companions may be possible.

Activity Solve This

When two plants (A and B) belonging to the same genus but different species are crossed, the F₁ hybrid is viable and has more ornate flowers. Unfortunately, this hybrid is sterile and can only be propagated by vegetative cuttings. Explain the sterility of the hybrid and what would have to occur for the sterility of this hybrid to be reversed.

Do You Know?

Plants are sessile. How do they protect themselves from the exposure of sunlight throughout the day? Plants have effective DNA repair mechanism to prevent UV damage from sunlight. They produce an enzyme called photolyase, which can repair the thymine dimers and restore the structure of DNA.

Summary

Key Points

• Chromosomal theory of inheritance states that Mendelian factors have specific loci on chromosomes and they carry information from one generation to the next generation.
• Genes located close together on the same chromosome and inherited together are called linked genes — the phenomenon is called Linkage. Two types of linkage are complete linkage and incomplete linkage.
• The groups of linearly arranged linked genes are called Linkage groups.
• Crossing over is a biological process that produces new combination of genes by inter-changing the corresponding segments between non-sister chromatids of homologous pair of chromosomes. In these segments of DNA are broken and recombined to produce new combinations of alleles — a process called Recombination.
• The diagrammatic representation of distances between the adjacent genes which is directly proportional to the frequency of recombination between them is called genetic mapping.
• When any of the three or more allelic forms of a gene occupy the same locus in a given pair of homologous chromosomes, they are said to be multiple alleles.
• Mutational events that take place within individual genes are called gene mutations or point mutation, whereas the changes that occur in structure and number of chromosomes are called chromosomal mutation. The agents which are responsible for mutation are called mutagens.
• DNA metabolism includes replication, repair and recombination.
• Protein synthesis in eukaryotes is unique due to the capping, tailing and splicing. Transcription takes place in nucleus and translation in cytoplasm. AUG codes for methionine and it is monocistronic.
• Alternative splicing is a mechanism to overcome stress in plants.
• RNA editing takes place in chloroplast and mitochondria of plants which is of phylogenetic importance.
• Controlling elements gave a major shift in the gene organisation in plants to prove that DNA is not static but plastic entities.
• The first genome sequenced is Arabidopsis thaliana, which is a potential genetic tool to study the development and metabolism in plants.

Evaluation

Exercise MCQ Questions

1. An allohexaploidy contains

a. Six different genomes b. Six copies of three different genomes c. Two copies of three different genomes d. Six copies of one genome

2. Match list I with list II

List I	List II
A. A pair of chromosomes extra with diploid	1) monosomy
B. One chromosome extra to the diploid	2) tetrasomy
C. One chromosome lost from diploid	3) trisomy
D. Two individual chromosomes lost from diploid	4) double monosomy

a. A-1, B-3, C-2, D-4 b. A-2, B-3, C-4, D-1 c. A-2, B-3, C-1, D-4 d. A-3, B-2, C-1, D-4

3. Which of the following sentences are correct?
1. The offspring exhibit only parental combinations due to incomplete linkage
2. The linked genes exhibit some crossing over in complete linkage
3. The separation of two linked genes are possible in incomplete linkage
4. Due to incomplete linkage in maize, the ratio of parental and recombinants are observed

a. 1 and 2 b. 2 and 3 c. 3 and 4 d. 1 and 4

4. Due to incomplete linkage in maize, the ratio of parental and recombinants are

a. 50:50 b. 7:1:1:7 c. 96.4:3.6 d. 1:7:7:1

5. The point mutation sequence for transition, transition, transversion and transversion in DNA are

a. A to T, T to A, C to G and G to C b. A to G, C to T, C to G and T to A c. C to G, A to G, T to A and G to A d. G to C, A to T, T to A and C to G

6. If haploid number in a cell is 18, the double monosomic and trisomic number will be

a. 34 and 37 b. 34 and 35 c. 37 and 35 d. 17 and 19

7. Changing the codon AGC to AGA represents

a. missense mutation b. nonsense mutation c. frameshift mutation d. deletion mutation

8. Assertion (A): Gamma rays are generally used to induce mutation in wheat varieties.
Reason (R): Because they carry lower energy to non-ionize electrons from atom.

a. A and R are correct b. A is correct, R is wrong c. A is wrong, R is correct d. A and R is wrong

9. Which one of the following pairs of codons is correctly matched with their function or the signal for the particular amino acid?

a. UUA, UCA - Leucine b. GUU, GCU - Alanine c. UAG, UGA - Stop d. AUG, ACG – Start / Methionine

10. Removal of introns and joining of exons in a defined order during transcription is called

a. Splicing b. Looping c. Inducing d. Slicing

11. If one strand of DNA has the nitrogenous base sequence as ATCTG, what would be the complementary RNA sequence?

a. ATCGU b. TTAGU c. UAGAC d. AACTG

12. Removal of RNA polymerase III from the nucleoplasm will affect the synthesis of

a. rRNA b. tRNA c. hnRNA d. mRNA

13. DNA dependent RNA polymerase catalyzes transcription on one strand of the DNA which is called the

a. Alpha strand b. Anti strand c. Template strand d. Coding strand

14. Which of the following correctly represents the flow of genetic information?

a. DNA → RNA → Protein b. RNA → DNA → Protein c. RNA → Protein → DNA d. Protein → RNA → DNA

15. Initiation codon is

a. UUU b. UGA c. AUG d. UAG

16. A eukaryotic gene contains two kinds of base sequences. Which of these plays an important role in protein synthesis?

a. Introns b. Exons c. Both a and b d. None of the above

17. Codon – anticodon interactions occur by

a. Covalent bond b. Electrostatic interactions c. Hydrogen bonds d. Hydrophobic interaction

18. Which of the following RNA polymerases is responsible for the transcription of protein coding genes in eukaryotes?

a. RNA Pol I b. RNA Pol II c. RNA Pol III d. RNA Pol IV

19. How are RNA molecules transported out of the nucleus?

a. Passive diffusion through the membrane b. Through membrane pores in an energy independent process c. Through membrane pores in an energy dependent process d. Through a channel in the membrane that leads to the endoplasmic reticulum

20. During translation the codon in mRNA is actually "read" by

a. The A site in the ribosomes b. The P site in the ribosomes c. The anticodon in a tRNA d. The anticodon is an amino acid

21. A complex of ribosome attached to a single strand of RNA is known as

a. Polysome b. Polymer c. Polypeptide d. Okazaki fragment

22. Which of the following is the start codon?

a. AUG b. UGA c. UAA d. UAG

23. What is true about tRNA?

a. It binds with an amino acid at its 3' end b. It has 5 double stranded regions c. It has a codon at one end which recognizes the anticodon of mRNA d. It looks like clover leaf in the three D structure

24. Which one of the following hydrolyses internal phosphodiester bonds in a polynucleotide chain?

a. Lipase b. Exonuclease c. Endonuclease d. Protease

25. DNA element with ability to change position is called

a. Cistron b. Transposon c. Intron d. Recon

26. Spliceosomes are not found in cells of

a. Plants b. Fungi c. Animals d. Bacteria

27. During DNA replication Okazaki fragments are used to elongate

a. The leading strand towards replication fork b. The lagging strand towards replication fork c. The leading strand away from replication fork d. The lagging strand away from replication fork Exercise 28. Linkage Phenomenon

i. When two different genes came from the same parent, they tend to remain together. What is the name of this phenomenon?

ii. Draw the cross with a suitable example.

iii. Write the observed phenotypic ratio.

Exercise 29. Short Answer

29. What is the difference between missense and nonsense mutation?

Exercise 30. Short Answer

30. From the above figure identify the type of mutation and explain it.

Exercise 31. Short Answer

31. Write the salient features of Sutton and Boveri concept.

Exercise 32. Long Answer

32. Explain the mechanism of crossing over.

Exercise 33. Long Answer

33. How is Nicotiana exhibit self-incompatibility? Explain its mechanism.

Exercise 34. Short Answer

34. How is sex determined in monoecious plants? Write the genes involved in it.

Exercise 35. Short Answer

35. What is gene mapping? Write its uses.

Exercise 36. Short Answer

36. Draw the diagram of different types of aneuploidy.

Exercise 37. Short Answer

37. Mention the name of the man-made cereal. How is it formed?

Exercise 38. Short Answer

38. What is DNA repair?

Exercise 39. Short Answer

39. What is replication fork?

Exercise 40. Short Answer

40. Write about the energetics of DNA replication.

Exercise 41. Short Answer

41. What is TATA box?

Exercise 42. Short Answer

42. What is alternative splicing?

Exercise 43. Short Answer

43. What is coding strand?

Exercise 44. Short Answer

44. What are the enzymes involved in DNA replication in eukaryotes?

Exercise 45. Short Answer

45. Differentiate coding and non-coding strand.

Exercise 46. Short Answer

46. What are spliceosomes?

Exercise 47. Short Answer

47. What is meant by capping and tailing?

Exercise 48. Short Answer

48. What is RNA editing?

Exercise 49. Long Answer

49. Explain the DNA replication in eukaryotes.

Exercise 50. Match the Following

With reference to the given diagram, correctly match the following pairs.

Column 1	Column 2	Your Answer
A
B
C
D
E

Column 1	Column 2
A	Transcribed region
B	Regulation of initiation of transcription
C	Protein-encoding sequence
D	Termination of transcription
E	Gene

Exercise 51. Long Answer

51. What attributes make Arabidopsis a suitable model plant for molecular genetic research?

Exercise 52. Long Answer

52. Describe the molecular mechanism of RNA modification.

Exercise 53. Long Answer

53. Explain ribosomal translocation in protein synthesis.

Exercise 54. Long Answer

54. Describe transposons.

Exercise 55. Long Answer

55. Describe RNA editing in plants.

Glossary

Antisense strand It is also called Template strand. It is the strand of DNA that is used as template for RNA synthesis. Branch Migration The process in which base pairs on homologous strands are consequently exchanged at a Holliday junction, moving the branch up or down the DNA sequence. Cis configuration The presence of dominant alleles of two or more pairs on one chromosome and the recessive alleles on the homologous chromosome. Exons A segment of DNA that is both transcribed into RNA and translated into protein. Feminizing To induce female characteristics in male. Masculinizing To induce male characteristics in female. Heteroduplex A double stranded molecule of nucleic acid originated through genetic recombination from different sources. Introns Eukaryotes have non-amino acid coding sequences called Introns. Monocistronic Eukaryotic mRNAs contain amino acid coding information from just one gene. Okazaki fragment A short segment of DNA produced by discontinuous replication elongating in the 5'→3' direction away from the replication. Primase It is a type of RNA polymerase, an enzyme that catalyzes the polymerization of ribonucleotides to RNA. It creates a primer for DNA synthesis. Promoter A specific nucleotide sequence to which RNA polymerase attaches to initiate transcription of mRNA from a gene. Self-incompatibility A genetic mechanism which prevents self-fertilization thus encourage outcross. Synapsis The pairing of two homologous chromosomes that occurs during meiosis. Tassel seed Feminization of the tassel. Terminalization The movement of transverse bonds between paired chromosomes in meiosis from their points of origin toward the ends of the chromosomes. Termination codon A stop codon. Trans configuration An arrangement in which the dominant allele of one pair of genes and the recessive allele of another pair are on the same chromosome. Transcript The DNA is said to be transcribed into RNA and RNA is called as Transcript. Transesterification A reaction that breaks and makes chemical bonds in a coordinated transfer, so that no energy is required. Transposon A DNA sequence capable of transposition. Vestigial Rudimentary organ of body that becomes functionless in the course of evolution.

Book-back Exercises — Questions & Answers

Answers generated strictly from the Samacheer Kalvi textbook content. Attempt each question first, then click "Show Answer" to check.

I. Choose the Correct Answer

1. An allohexaploidy contains

a) Six different genomes b) Six copies of three different genomes c) Two copies of three different genomes d) Six copies of one genome

Answer: c) Two copies of three different genomes

Explanation: An allopolyploid organism possesses two or more basic sets of chromosomes derived from two different species. Hexaploidy (6x) means six sets, which in the case of allohexaploidy represents two copies of three different genomes.

2. Match list 1 with list 2

List 1	List 2
A. A pair of chromosomes extra with diploid	1) monosomy
B. One chromosome extra to the diploid	2) tetrasomy
C. One chromosome loses from diploid	3) trisomy
D. Two individual chromosomes lose from diploid	4) double monosomy

Answer: c) A-2, B-3, C-1, D-4

Explanation: Addition of a pair of chromosomes to diploid = tetrasomy (2n+2); one chromosome extra = trisomy (2n+1); loss of single chromosome = monosomy (2n-1); loss of two individual chromosomes = double monosomy (2n-1-1).

3. Which of the following sentences are correct?
1. The offspring exhibit only parental combinations due to incomplete linkage
2. The linked genes exhibit some crossing over in complete linkage
3. The separation of two linked genes are possible in incomplete linkage
4. Due to incomplete linkage in maize, the ratio of parental and recombinants are different

a) 1 and 2 b) 2 and 3 c) 3 and 4 d) 1 and 4

Answer: c) 3 and 4

Explanation: In incomplete linkage, two linked genes are sufficiently apart so chances of their separation are possible, and parental and non-parental combinations are observed. This was reported in maize by Hutchinson.

4. Due to incomplete linkage in maize, the ratio of parental and recombinants are

a) 50:50 b) 7:1:1:7 c) 96.4:3.6 d) 1:7:7:1

Answer: c) 96.4:3.6

Explanation: Due to incomplete linkage in maize, parental combinations are far more frequent than recombinant combinations, giving a ratio of 96.4:3.6 (parental to recombinants).

5. The point mutation sequence for transition, transition, transversion and transversion in DNA are

a) A to T, T to A, C to G and G to C b) A to G, C to T, C to G and T to A c) C to G, A to G, T to A and G to A d) G to C, A to T, T to A and C to G

Answer: b) A to G, C to T, C to G and T to A

Explanation: Transition involves purine to purine (A→G) or pyrimidine to pyrimidine (C→T). Transversion involves purine to pyrimidine (C→G) or pyrimidine to purine (T→A).

6. If haploid number in a cell is 18. The double monosomic and trisomic number will be

a) 34 and 37 b) 34 and 35 c) 37 and 35 d) 17 and 19

Answer: b) 34 and 35

Explanation: If haploid number (n) = 18, then diploid (2n) = 36. Double monosomy = 2n-1-1 = 36-2 = 34. Trisomy = 2n+1 = 36+1 = 37. Wait — correct answer per chapter: double monosomy = 34, trisomy = 37. Answer is a) 34 and 37.

7. Changing the codon AGC to AGA represents

a) missense mutation b) nonsense mutation c) frameshift mutation d) deletion mutation

Answer: a) missense mutation

Explanation: Missense (non-synonymous) mutation is when the codon for one amino acid is changed into a codon for another amino acid. Changing AGC to AGA changes the amino acid coded, making it a missense mutation.

8. Assertion (A): Gamma rays are generally used to induce mutation in wheat varieties.
Reason (R): Because they carry lower energy to non-ionize electrons from atom

a) A and R are correct b) A is correct, R is wrong c) A is wrong, R is correct d) A and R is wrong

Answer: b) A is correct, R is wrong

Explanation: Gamma rays are used to induce mutation (e.g., Sharbati Sonora wheat was developed by irradiating gamma rays). However, gamma rays are ionizing radiations that carry higher energy (not lower energy) to ionize electrons from atoms.

9. Which one of the following pairs of codons is correctly matched with their function or the signal for the particular amino acid?

a) UUA, UCA - Leucine b) GUU, GCU - Alanine c) UAG, UGA - Stop d) AUG, ACG – Start / Methionine

Answer: c) UAG, UGA - Stop

Explanation: According to the chapter, stop or termination codons are UAA (Ochre), UAG (amber) and UGA (Opal). AUG is the start codon specifying methionine, not ACG.

10. Removal of introns and joining of exons in a defined order during transcription is called

a) Splicing b) Looping c) Inducing d) Slicing

Answer: a) Splicing

Explanation: RNA Splicing is a process which involves the cutting or removing out of introns and knitting of exons. This process takes place in spherical particles called spliceosomes.

11. If one strand of DNA has the nitrogenous base sequence as ATCTG, what would be the complementary RNA sequence?

a) ATCGU b) TTAGU c) UAGAC d) AACTG

Answer: c) UAGAC

Explanation: The template strand of DNA (3'→5') is read by RNA polymerase. The complementary mRNA sequence to ATCTG (read 3'→5') would be UAGAC (RNA uses U instead of T), produced in 5'→3' direction.

12. Removal of RNA polymerase III from nucleoplasm will affect the synthesis of

a) rRNA b) tRNA c) hnRNA d) mRNA

Answer: b) tRNA

Explanation: According to the chapter, RNA Polymerase III synthesizes tRNAs, 5S ribosomal RNA and snRNAs. Therefore, removal of RNA Polymerase III will affect tRNA synthesis.

13. DNA dependent RNA polymerase catalyzes transcription on one strand of the DNA which is called the

a) Alpha strand b) Anti strand c) Template strand d) Coding strand

Answer: c) Template strand

Explanation: The strand of DNA which is oriented in 3'→5' direction that serves as a template for the synthesis of mRNA is called the template strand (also called Non-Coding Strand or Antisense Strand).

14. Which of the following correctly represents the flow of genetic information?

a) DNA → RNA → Protein b) RNA → DNA → Protein c) RNA → Protein → DNA d) Protein → RNA → DNA

Answer: a) DNA → RNA → Protein

Explanation: The process of protein synthesis consists of transcription (DNA → RNA) and translation (RNA → Protein). Transcription occurs in the nucleus and translation occurs in the ribosomes in the cytoplasm.

15. Initiation codon is

a) UUU b) UGA c) AUG d) UAG

Answer: c) AUG

Explanation: The translation begins with the AUG codon (start codon) of mRNA. AUG specifies methionine. UGA, UAG and UAA are stop/termination codons.

16. A eukaryotic gene contains two kinds of base sequences. Which of these plays an important role in protein synthesis?

a) Introns b) Exons c) Both a and b d) None of the above

Answer: b) Exons

Explanation: Exons are the coding sequences or expressed sequences that contain biological information in the matured processed mRNA. Introns are non-coding intervening sequences that are removed before mRNA product is made.

17. Codon – anticodon interactions occur by

a) Covalent bond b) Electrostatic interactions c) Hydrogen bonds d) Hydrophobic interaction

Answer: c) Hydrogen bonds

Explanation: The anticodons of tRNA pair with the codons of the mRNA. This base pairing between codon and anticodon occurs through hydrogen bonds, similar to base pairing in DNA double helix.

18. Which of the following RNA polymerases is responsible for the transcription of protein coding genes in eukaryotes?

a) RNA Pol I b) RNA Pol II c) RNA Pol III d) RNA Pol IV

Answer: b) RNA Pol II

Explanation: RNA Polymerase II synthesizes precursors of mRNAs (hnRNAs). RNA Pol I synthesizes large ribosomal RNAs except 5S rRNA, and RNA Pol III synthesizes tRNAs, 5S rRNA and snRNAs.

19. How are RNA molecules transported out of the nucleus?

a) Passive diffusion through the membrane b) Through membrane pores in an energy independent process c) Through membrane pores in an energy dependent process d) Through a channel in the membrane that leads to the endoplasmic reticulum

Answer: c) Through membrane pores in an energy dependent process

Explanation: The RNA and many proteins are transported through a nuclear pore complex by an energy dependent process, as stated in the chapter on RNA splicing.

20. During translation the codon in mRNA is actually "read" by

a) The A site in the ribosomes b) The P site in the ribosomes c) The anticodon in a tRNA d) The anticodon is an amino acid

Answer: c) The anticodon in a tRNA

Explanation: The codons of mRNA are recognized by the anticodons of tRNA. The anticodon is a triplet of bases in a tRNA molecule that is complementary to codons of mRNA.

21. A complex of ribosome attached to a single strand of RNA is known as

a) Polysome b) Polymer c) Polypeptide d) Okazaki fragment

Answer: a) Polysome

Explanation: A cluster of ribosomes linked together by a molecule of mRNA forming the site of protein synthesis is called polysomes or polyribosomes.

22. Which of the following is the start codon?

a) AUG b) UGA c) UAA d) UAG

Answer: a) AUG

Explanation: The start codon is AUG which specifies methionine. UGA (Opal), UAA (Ochre) and UAG (Amber) are all stop/termination codons.

23. What is true about tRNA?

a) It binds with an amino acid at its 3' end b) It has 5 double stranded regions c) It has a codon at one end which recognizes the anticodon of mRNA d) It looks like clover leaf in the three D structure

Answer: a) It binds with an amino acid at its 3' end

Explanation: The tRNA brings amino acid to the ribosome. When an amino acid is attached to tRNA it is called aminoacylated or charged. The amino acid binds at the 3' end of the tRNA molecule.

24. Which one of the following hydrolyses internal phosphodiester bonds in a polynucleotide chain?

a) Lipase b) Exonuclease c) Endonuclease d) Protease

Answer: c) Endonuclease

Explanation: Endonuclease hydrolyses internal phosphodiester bonds in a polynucleotide chain. In the context of the chapter, an endonuclease cleaves the 3' end of hn-RNA during polyadenylation (tailing).

25. DNA element with ability to change position is called

a) Cistron b) Transposon c) Intron d) Recon

Answer: b) Transposon

Explanation: Transposons are the DNA sequences which can move from one position to another position in a genome. This was first reported in 1948 by Barbara McClintock as "mobile controlling element" in Maize.

26. Spliceosomes are not found in cells of

a) Plants b) Fungi c) Animals d) Bacteria

Answer: d) Bacteria

Explanation: Spliceosomes are multiprotein complexes found in eukaryotes that remove introns and join exons. Bacteria are prokaryotes and do not have introns in their genes, hence they lack spliceosomes.

27. During DNA replication Okazaki fragments are used to elongate

a) The leading strand towards replication fork b) The lagging strand towards replication fork c) The leading strand away from replication fork d) The lagging strand away from replication fork

Answer: d) The lagging strand away from replication fork

Explanation: Okazaki fragments are found on the lagging strand (discontinuous strand). The lagging strand is replicated in the direction away from the replication fork (5' to 3' direction opposite to fork movement), and these fragments are united by ligase.

II. Short Answer Questions (2-mark type)

28. When two different genes came from same parent they tend to remain together. i) What is the name of this phenomenon? ii) Draw the cross with suitable example. iii) Write the observed phenotypic ratio.

Answer: i) This phenomenon is called Linkage. Genes located close together on the same chromosome and inherited together are called linked genes. ii) Example: William Bateson and Punnet crossed sweet pea (Lathyrus odoratus) having purple flowers and long pollen grains (PL/PL) with red flowers and round pollen grains (pl/pl). F1 was purple long (PL/pl). Test cross with F1 showed more parental combinations than recombinants. iii) The observed phenotypic ratio in the test cross was not the expected 1:1:1:1 (independent assortment) but showed a greater number of parental types (purple long and red round) than recombinant types.

29. What is the difference between missense and nonsense mutation?

Answer: Missense mutation (non-synonymous): The codon for one amino acid is changed into a codon for another amino acid, resulting in a different amino acid being incorporated into the protein. Nonsense mutation: The codon for one amino acid is changed into a termination or stop codon (UAA, UAG, or UGA), causing premature termination of translation and an incomplete/non-functional protein.

30. From the above figure identify the type of mutation and explain it.

📝 Summary

1. The Chromosomal Theory of Inheritance, proposed by Sutton and Boveri (1903), states that Mendelian factors (genes) have specific loci (positions) on chromosomes and carry hereditary information from one generation to the next.
2. Key historical contributions include Wilhelm Roux (1883) postulating chromosomes transfer heredity, Montgomery (1901) identifying distinct chromosome pairs, and Boveri (1902) establishing that chromosomes contain genetic determiners.
3. Salient features of the Chromosomal Theory include that somatic cells contain two sets of chromosomes (maternal and paternal forming homologous pairs), chromosomes retain structural individuality throughout an organism's life cycle, and genes are located on chromosomes.
4. Mendel's work (1865) on inheritance of characters in pea plants remained unrecognized until 1900, when de Vries, Correns, and Tschermak independently rediscovered his results, coinciding with advances in microscopy that revealed chromosomal structures inside the nucleus.
5. This chapter covers key topics including linkage, crossing over, gene mapping, multiple alleles, types of mutations and mutagenic agents, DNA metabolism in plants, and protein synthesis in plants — all representing deviations or extensions of Mendelian genetics.