Sexual Reproduction in Flowering Plants

A flower is a modified shoot specialised for sexual reproduction. Its four whorls are the calyx (sepals), corolla (petals), androecium (stamens, the male part) and gynoecium (pistils or carpels, the female part). A typical stamen has a filament and a bilobed anther; each lobe has two thecae, so the anther is dithecous and tetrasporangiate (four microsporangia). The wall of a microsporangium has four layers: epidermis, endothecium, middle layers, and the innermost tapetum, which nourishes the developing pollen grains.

Inside each microsporangium, diploid pollen mother cells (PMCs) undergo meiosis (microsporogenesis) to form tetrads of haploid microspores, which mature into pollen grains. A pollen grain has a tough outer exine of sporopollenin (one of the most resistant organic materials known, so pollen fossilises well) with germ pores, and an inner intine. Mature grains contain a larger vegetative cell and a smaller generative cell, which divides to form two male gametes. In most angiosperms pollen is shed at this 2-celled stage.

The gynoecium has a stigma, style and ovary. Each ovule is attached by a funicle at the hilum and has protective integuments, a micropyle, a chalaza at the base, and the nucellus holding the megaspore mother cell. In megasporogenesis the megaspore mother cell divides by meiosis into four megaspores, of which three degenerate and one functional megaspore undergoes three mitotic divisions to form the 8-nucleate, 7-celled embryo sac (female gametophyte): an egg apparatus (egg cell plus two synergids), three antipodals, and a large central cell with two polar nuclei.

Pollination and Pollen–Pistil Interaction

Pollination is the transfer of pollen from anther to stigma. By source of pollen it is classed as: autogamy (same flower; in cleistogamous flowers such as Viola, Oxalis and Commelina the flowers never open, guaranteeing assured seed set), geitonogamy (another flower of the same plant; genetically like autogamy but functionally cross-pollination as it needs a pollinating agent), and xenogamy (flowers of different plants; the only type that brings genetically different pollen, giving variation).

Agents may be abiotic or biotic. Wind-pollinated flowers produce large quantities of light, non-sticky pollen, and have well-exposed stamens, large feathery stigma and often a single ovule per ovary (maize cob). Water-pollination occurs in about 30 genera such as Vallisneria and Hydrilla; in Vallisneria the female flower reaches the surface while male flowers or pollen float to it. Animals (bees, butterflies, moths, flies, beetles, birds, bats) are attracted by colour, scent and rewards like nectar and edible pollen; the Yucca–moth and Ophrys–bee systems show remarkable co-evolution.

Plants promote outbreeding through asynchronous release of pollen and stigma receptivity, different positions of anther and stigma, self-incompatibility (genetic inhibition of pollen germination or tube growth), and unisexual flowers (monoecious castor and maize; dioecious papaya). After landing, the stigma recognises pollen; compatible pollen germinates and the pollen tube grows through the style to the ovule, usually entering through the micropyle. In plant breeding, emasculation (removal of anthers from a bisexual flower before dehiscence) and bagging allow controlled crosses.

Double Fertilisation, Seed and Fruit Formation

The pollen tube releases two male gametes into one synergid. One fuses with the egg cell (syngamy) to form the diploid zygote; the other fuses with the two polar nuclei (triple fusion) to form the triploid primary endosperm nucleus (PEN). Because two fusions happen, the event is called double fertilisation, unique to flowering plants. The PEN develops into endosperm, which nourishes the developing embryo; it usually develops before the embryo (free-nuclear type as in coconut water, or cellular type).

The zygote forms the embryo through the proembryo, globular and heart-shaped stages. A dicot embryo has an embryonal axis and two cotyledons, with the part above the cotyledons the epicotyl (ending in the plumule) and below it the hypocotyl (ending in the radicle). A monocot embryo has one cotyledon (scutellum), with the plumule covered by coleoptile and the radicle by coleorhiza. After fertilisation, the integuments harden into the seed coat, the ovule becomes the seed and the ovary becomes the fruit with its wall called the pericarp. Seeds may be endospermic (castor, coconut) or non-endospermic (pea, groundnut) where cotyledons store food, and in some, such as black pepper, a remnant nucellus persists as perisperm.

In some plants the fruit forms without fertilisation (parthenocarpy, as in banana). Apomixis produces seeds without fertilisation, a way to preserve hybrid vigour, and polyembryony (several embryos in a seed) occurs in citrus and mango. A false fruit (apple, strawberry, cashew) includes other floral parts such as the thalamus. Seeds can remain viable for very long periods, with a record of a date palm seed about 2000 years old.

Human Reproductive Systems

The male reproductive system includes a pair of testes held in the scrotum, which keeps them 2–2.5 °C below body temperature (necessary for sperm production). Each testis has about 250 compartments (lobules) containing coiled seminiferous tubules, lined by male germ cells (spermatogonia) and supporting Sertoli cells; between tubules are Leydig (interstitial) cells that secrete androgens. Sperm pass from seminiferous tubules to rete testis, vasa efferentia, epididymis, vas deferens, ejaculatory duct and urethra. Accessory glands are the seminal vesicles, prostate and bulbourethral glands; their secretions form seminal plasma rich in fructose, calcium and enzymes.

The female reproductive system has paired ovaries, oviducts (fallopian tubes: infundibulum with fimbriae, ampulla, isthmus), uterus (perimetrium, myometrium, endometrium), cervix and vagina, with external genitalia (mons pubis, labia, hymen, clitoris). Each ovary contains follicles at different stages, and at birth there are about 2 million follicles, of which only 60,000–80,000 remain at puberty. The uterus opens through the cervix into the vagina (birth canal). Mammary glands (15–20 lobes with alveoli, ducts and lactiferous ducts) produce milk after delivery.

Gametogenesis, Menstrual Cycle and Fertilisation

Spermatogenesis: spermatogonia (2n = 46) multiply by mitosis; some grow into primary spermatocytes (2n), which undergo meiosis I to form two secondary spermatocytes (n), and meiosis II to form four haploid spermatids. Spermiogenesis transforms spermatids into sperms with a head (nucleus capped by acrosome), neck, middle piece (mitochondria) and tail. It starts at puberty under GnRH, which stimulates LH (acting on Leydig cells to release androgens) and FSH (acting on Sertoli cells). A healthy ejaculate contains about 200–300 million sperm, of which at least 60% should be normal and 40% motile.

Oogenesis begins during embryonic life: oogonia become primary oocytes that enter meiosis I and stay arrested at prophase I until puberty. Each month under FSH one follicle grows; before ovulation the primary oocyte completes meiosis I, giving a large secondary oocyte and a tiny first polar body. The secondary oocyte starts meiosis II but is arrested at metaphase II; it completes meiosis only if sperm entry occurs, giving an ovum and a second polar body. Thus one primary oocyte yields one ovum, whereas one primary spermatocyte yields four sperms.

The menstrual cycle (~28 days) has menstrual (days 1–5, shedding of endometrium), follicular/proliferative (growth of follicle and endometrium under FSH and oestrogen), ovulation (around day 14, triggered by an LH surge), and luteal/secretory phases (the ruptured follicle becomes the corpus luteum, secreting progesterone to maintain the endometrium). If pregnancy does not occur, the corpus luteum degenerates and menstruation starts. Menarche is the first cycle; menopause occurs around 50 years.

Fertilisation occurs in the ampulla–isthmus junction. Sperm contact triggers changes in the zona pellucida that block other sperm (block to polyspermy), and acrosomal enzymes help penetration. The zygote undergoes cleavage to form a morula (8–16 cells) and then a blastocyst with outer trophoblast and an inner cell mass (which forms the embryo); the blastocyst implants into the endometrium. The placenta, formed by the trophoblast and uterine tissue, exchanges nutrients and gases and secretes hCG, hPL, oestrogen, progesterone and relaxin. Gestation lasts about nine months, and parturition is induced by oxytocin and a foetal ejection reflex; colostrum, rich in antibodies (IgA), is the first milk.

Reproductive Health and Assisted Reproduction

Reproductive health means total well-being in all aspects of reproduction (physical, emotional, behavioural and social). India started family-planning programmes in 1951 and today the Reproductive and Child Health (RCH) programme provides education, healthcare and awareness. Important issues are sex education, prevention of sexually transmitted infections (STIs) such as gonorrhoea, syphilis, genital herpes, chlamydiasis, trichomoniasis, hepatitis-B and HIV/AIDS, safe delivery, and control of population growth. STI risk can be lowered by using condoms, avoiding multiple partners and early treatment. Female foeticide through misuse of amniocentesis is illegal and the test is allowed only to detect genetic disorders.

Contraceptive methods: natural (periodic abstinence, withdrawal, lactational amenorrhoea), barrier (condoms, diaphragms, cervical caps), intra-uterine devices (copper-releasing CuT, Multiload 375, hormone-releasing LNG-20; copper ions suppress sperm motility), oral pills (combined progestogen–oestrogen, and the non-steroidal weekly pill Saheli), injectables and implants, emergency contraception, and surgical sterilisation (vasectomy in males, tubectomy in females). Medical termination of pregnancy (MTP), legalised in India in 1971 and revised since, is safest in the first trimester and must be done by registered medical practitioners.

Infertility may be treated by assisted reproductive technologies (ART). In IVF (in vitro fertilisation, “test-tube baby”), ova and sperm are combined in a laboratory; the zygote or early embryo (up to 8 blastomeres) is transferred into the fallopian tube (ZIFT), and an embryo of more than 8 blastomeres into the uterus (IUT). GIFT transfers ova into the fallopian tube, ICSI injects a sperm directly into an ovum, and artificial insemination (AI/IUI) introduces semen into the vagina or uterus.

Mendelian Inheritance and Genetic Crosses

Gregor Mendel studied seven contrasting traits in the garden pea (tall/dwarf, round/wrinkled seed, yellow/green seed, etc.). He chose pea because it has clear contrasting characters, short life cycle, many offspring, and easily controlled pollination. From his experiments he formulated three laws. The law of dominance: in a heterozygote, one factor (the dominant allele) masks the other. The law of segregation: the two alleles of a gene separate during gamete formation so each gamete carries only one (explained by meiosis; gametes are “pure”). The law of independent assortment: in a dihybrid cross, alleles of different genes assort independently, as long as the genes lie on different chromosomes.

Key terms: allele (alternate form of a gene), homozygous / heterozygous, genotype (allele combination), phenotype (observable trait). A test cross crosses an individual with dominant phenotype to the homozygous recessive to reveal whether it is homozygous (all offspring dominant) or heterozygous (1 : 1 ratio). Monohybrid F₂: phenotypic ratio 3 : 1, genotypic ratio 1 : 2 : 1. Dihybrid F₂: phenotypic 9 : 3 : 3 : 1, with 9 genotypes. Probability rules: multiply for independent events (product rule), add for alternative outcomes (sum rule).

Extensions of Mendelian Genetics

Many traits deviate from simple dominance. In incomplete dominance the heterozygote is intermediate: in snapdragon (Antirrhinum) and Mirabilis, red × white gives pink F₁, and the F₂ shows 1 red : 2 pink : 1 white (phenotypic and genotypic ratios coincide). In codominance both alleles are expressed in the heterozygote, as with the AB blood group. Multiple alleles (more than two alleles in a population, though any individual carries two) are exemplified by ABO blood groups: alleles Iᴬ, Iᴮ and i. Iᴬ and Iᴮ are dominant over i and codominant with each other.

Pleiotropy means one gene affects several traits (phenylketonuria causes mental retardation, reduced hair and skin pigmentation). Polygenic inheritance means several genes contribute to one trait with a continuous range, as in human height and skin colour. Pedigree analysis traces traits in families. Mendelian disorders include autosomal recessive conditions (sickle-cell anaemia, cystic fibrosis, phenylketonuria, thalassaemia), autosomal dominant (Huntington’s, myotonic dystrophy) and X-linked recessive (haemophilia, colour blindness). In sickle-cell anaemia, a single base substitution changes the sixth amino acid of the β-globin chain from glutamic acid to valine (HbS). Thalassaemia is a quantitative defect in globin chain synthesis (α on chromosome 16, β on chromosome 11). Chromosomal disorders arise from aneuploidy: Down syndrome (trisomy 21; 47 chromosomes), Turner syndrome (45, XO), Klinefelter syndrome (47, XXY).

Chromosomal Theory, Linkage and Recombination

Sutton and Boveri (1902) noted that chromosomes behave like Mendel’s factors, pairing and segregating at meiosis, leading to the chromosomal theory of inheritance. Thomas Hunt Morgan tested it using the fruit fly Drosophila melanogaster, which is ideal for genetics: it grows easily on simple media, has a short life cycle (about 12 days), produces many progeny, shows clear sexual dimorphism, and has many visible hereditary variations.

Morgan found that two genes on the same chromosome do not assort independently, and called this linkage. When he crossed yellow-bodied, white-eyed females with brown-bodied, red-eyed males, the two recessive traits stayed together in F₂ with only 1.3% recombinants (tightly linked), whereas white eyes and miniature wings showed 37.2% recombinants (less tightly linked). Recombinants are produced by crossing over between non-sister chromatids of homologous chromosomes in meiosis I. The closer two genes are, the less likely a crossover occurs between them. Alfred Sturtevant used recombination frequency as a measure of distance and created the first genetic maps; one map unit (centimorgan) corresponds to 1% recombination.

Sex Determination and Sex-Linked Inheritance

Henking (1891) observed an X body in some sperm and not others, which led to the idea of sex chromosomes. XX–XY mechanism (humans, Drosophila): females are XX (homogametic) and males XY (heterogametic); half the sperm carry X and half carry Y while all eggs carry X, so the father’s sperm determines the child’s sex. XX–XO (grasshopper): males have a single X. ZZ–ZW (birds): females are heterogametic (ZW) and the egg determines sex. In honey bees haplodiploidy operates: the queen and workers are diploid (32 chromosomes) from fertilised eggs, whereas drones are haploid (16) from unfertilised eggs by parthenogenesis.

Genes on the X chromosome show X-linked inheritance. In haemophilia (blood fails to clot normally) and red-green colour blindness, the recessive allele on X is expressed in males (X^hY) because they have only one X. A heterozygous female is a carrier; she is affected only if both her X chromosomes carry the allele, which requires an affected father and a carrier or affected mother. Characteristic features are that the trait is more common in males, is transmitted through carrier mothers to sons, and there is no father-to-son transmission. Sex chromosome aneuploidy gives Turner (XO) and Klinefelter (XXY) syndromes.

DNA Replication and Molecular Inheritance

Evidence that DNA is the genetic material came from Griffith’s transformation experiment (1928: dead virulent pneumococci transformed living non-virulent bacteria), Avery, MacLeod and McCarty (1944: the transforming principle is DNA, since DNase destroyed it), and the Hershey–Chase experiment (1952: bacteriophages labelled with ³²P in DNA or ³⁵S in protein; only ³²P entered bacteria, proving DNA is inherited). Watson and Crick’s double helix has two antiparallel polynucleotide chains with sugar–phosphate backbones, bases paired A = T (2 hydrogen bonds) and G ≡ C (3), a pitch of 3.4 nm with 10 base pairs per turn (0.34 nm apart).

Replication is semiconservative, shown by Meselson and Stahl (1958) using ¹⁵N-labelled E. coli grown in ¹⁴N medium and separated by caesium chloride density gradient centrifugation: after one generation all DNA was of hybrid density, and after two generations half was hybrid and half light. Replication starts at the origin; helicase opens the strands; DNA-dependent DNA polymerases add nucleotides only in the 5′ → 3′ direction. The leading strand is made continuously, whereas the lagging strand is made in short Okazaki fragments that are joined by DNA ligase. E. coli (4.6 × 10⁶ bp) replicates in about 18 minutes.

In eukaryotes, DNA is packaged around histone octamers (two each of H2A, H2B, H3 and H4, positively charged) as nucleosomes, with about 200 bp of DNA per nucleosome and histone H1 locking linker DNA. The nucleosome string forms chromatin; loosely packed euchromatin is active and densely packed heterochromatin is generally inactive.

Transcription and RNA Processing

The central dogma states that information flows DNA → RNA → protein (with reverse transcription in some viruses). Transcription copies one strand of DNA into RNA by DNA-dependent RNA polymerase. The strand that serves as template runs 3′ → 5′ and the RNA is made 5′ → 3′; the other strand, the coding strand, has the same sequence as RNA except that T is replaced by U. A transcription unit has a promoter (binding site for RNA polymerase), a structural gene and a terminator.

In bacteria, a single RNA polymerase makes all RNAs, with the σ factor for initiation and the ρ factor for termination; the mRNA is often polycistronic and translation can start before transcription ends. In eukaryotes three polymerases act: RNA pol I (rRNAs 28S, 18S, 5.8S), pol II (precursor of mRNA, hnRNA) and pol III (tRNA, 5S rRNA, snRNA). Eukaryotic genes are split genes with coding exons and non-coding introns. The primary transcript (hnRNA) undergoes splicing (introns removed, exons joined), capping (methyl guanosine triphosphate at the 5′ end) and tailing (200–300 adenylate residues at the 3′ end) to become mature mRNA that exits the nucleus.

Genetic Code and Translation

The genetic code is the set of rules by which nucleotide triplets (codons) in mRNA specify amino acids. Of 64 codons, 61 code for amino acids and 3 (UAA, UAG, UGA) are stop codons; AUG codes for methionine and also acts as the start codon. The code is triplet, degenerate (several codons for one amino acid), unambiguous (each codon one amino acid), non-overlapping, comma-less and nearly universal. Marshall Nirenberg, Har Gobind Khorana (synthetic RNA polymers) and Severo Ochoa (enzyme polynucleotide phosphorylase) helped decode it.

Translation occurs on ribosomes. tRNA is the adapter: its clover-leaf structure has an anticodon loop that pairs with the codon and an acceptor end that binds a specific amino acid (charging requires ATP, catalysed by aminoacyl-tRNA synthetase). Ribosomes have small and large subunits made of rRNA and proteins; the rRNA acts as a ribozyme to form peptide bonds. The steps are initiation (small subunit binds mRNA at the start codon and initiator tRNA carrying methionine; large subunit joins), elongation (aminoacyl-tRNAs enter, peptide bonds form, ribosome moves along mRNA 5′ → 3′) and termination (a release factor recognises a stop codon). mRNA has untranslated regions (UTRs) on both ends that aid efficient translation. Mutations alter the code: a point mutation may change a single amino acid (sickle-cell) and a frame-shift (insertion or deletion of bases not in multiples of three) changes all codons downstream.

Regulation of Gene Expression

All cells of an organism carry the same genome, but different genes are active in different cells and at different times. In eukaryotes, regulation operates at the level of transcription (chromatin state, promoters and enhancers), RNA processing, transport, and translation. In prokaryotes, regulation mainly controls transcription, using the operon concept proposed by François Jacob and Jacques Monod for the lac operon of E. coli.

The lac operon has structural genes z (β-galactosidase, which splits lactose into glucose and galactose), y (permease, which increases lactose entry) and a (transacetylase), all under one promoter and operator, plus a regulatory gene i producing the repressor protein. When lactose is absent, the repressor binds the operator and blocks RNA polymerase, so the genes are off. When lactose (the inducer, as allolactose) is present, it binds the repressor, changing its shape so it cannot bind the operator; transcription proceeds and the enzymes are made. This is negative regulation, and it is economical because enzymes are made only when needed. In the presence of glucose, expression of the operon is also reduced.

Human Genome, DNA Fingerprinting and Genomics

The Human Genome Project (HGP) (1990–2003) aimed to sequence all the base pairs of the human genome (about 3 × 10⁹ bp), identify genes, store data in databases, and address ethical, legal and social issues. Two approaches were used: expressed sequence tags (ESTs) identifying genes expressed as RNA, and sequence annotation of the whole genome. DNA fragments were cloned in BAC and YAC vectors and sequenced by the automated Sanger method, with bioinformatics needed to handle the data.

Salient features: only a small portion (less than 2%) codes for proteins; the estimated gene number is a few tens of thousands (older textbooks say about 30,000, newer estimates 20,000–25,000); the average gene has about 3000 bases, and the largest known human gene is dystrophin (2.4 million bases); chromosome 1 has the most genes (2968) and the Y chromosome the fewest (231); repeated sequences make up much of the genome; and about 1.4 million SNPs (single-nucleotide polymorphisms) were identified, useful for tracing disease genes and human history. Human DNA sequences are about 99.9% identical between individuals.

DNA fingerprinting (Alec Jeffreys) exploits variation in VNTRs (variable number of tandem repeats), repeated short sequences that differ in number among individuals. Steps: isolate DNA, digest with restriction enzymes, separate fragments by gel electrophoresis, transfer to a membrane (Southern blotting), hybridise with a labelled VNTR probe, and detect by autoradiography. Uses include forensic investigations, paternity disputes and genetic diversity studies. Because genetic data are sensitive, privacy and consent matter.

Evidence and Mechanisms of Evolution

The Oparin–Haldane theory proposed that life arose from non-living organic molecules in the reducing atmosphere of early Earth; Miller and Urey (1953) simulated it by sending electric discharge through CH₄, H₂, NH₃ and water vapour at 800 °C, producing amino acids. Evidence for evolution includes: palaeontological (fossils in rock strata, determined by radioactive dating); comparative anatomy and morphology (homologous organs have the same origin but different functions, such as the forelimbs of whale, bat, cheetah and human, showing divergent evolution; analogous organs have similar function but different origin, such as the wings of butterfly and bird, or flippers of penguin and dolphin, showing convergent evolution); embryology; biogeography (Darwin’s finches in the Galápagos and Australian marsupials show adaptive radiation); and molecular similarities in DNA and proteins.

Lamarck proposed the inheritance of acquired characters through use and disuse (now rejected). Darwin proposed natural selection: populations show heritable variation; more offspring are produced than can survive; individuals better adapted leave more offspring (“fitness”), so favourable traits spread. Hugo de Vries’s mutation theory proposed large sudden changes (saltation). Classic examples are industrial melanism in the peppered moth (dark forms increased in polluted areas where light-lipped forms were more visible to predators) and the evolution of antibiotic resistance. Human evolution: Dryopithecus and Ramapithecus (ape-like), Australopithecus (~2 million years ago), Homo habilis (brain 650–800 cc), Homo erectus (~900 cc), Neanderthals (~1400 cc) and Homo sapiens (modern humans, arose in Africa).

Population Genetics and Evolutionary Change

The Hardy–Weinberg principle says that allele and genotype frequencies in a population remain constant from generation to generation if no evolutionary force acts. For two alleles with frequencies p and q (p + q = 1), genotype frequencies are p² (homozygous dominant), 2pq (heterozygous) and q² (homozygous recessive), and p² + 2pq + q² = 1. The conditions are a very large population, random mating, and no mutation, migration or selection. A departure from equilibrium indicates that evolution is occurring.

Evolutionary forces include mutation (new alleles), gene flow (migration of alleles between populations), genetic drift (random changes in allele frequency, strongest in small populations; the founder effect occurs when a few individuals start a new population), genetic recombination, and natural selection, which may be stabilising (extreme phenotypes removed), directional (one extreme favoured) or disruptive (both extremes favoured). Long-term divergence and reproductive isolation lead to speciation. Individuals do not evolve in their lifetime; populations evolve.

Human Health, Pathogens and Disease

Health is a state of complete physical, mental and social well-being. Infectious diseases are caused by pathogens. Bacterial diseases include typhoid (Salmonella typhi, diagnosed by the Widal test), pneumonia (Streptococcus pneumoniae, Haemophilus influenzae), dysentery, plague and diphtheria. Viral: common cold (rhinoviruses), dengue and chikungunya (mosquito-borne). Fungal: ringworm (Microsporum, Trichophyton, Epidermophyton). Protozoan: malaria (Plasmodium) and amoebiasis (Entamoeba histolytica). Helminth: ascariasis (Ascaris) and filariasis (Wuchereria, spread by Culex).

Malaria: the female Anopheles mosquito injects sporozoites; they multiply in liver cells, then infect red blood cells, which burst and release the toxin haemozoin, causing recurrent chills and high fever; gametocytes in blood are taken up by mosquitoes, where fertilisation occurs. P. falciparum causes the most serious malignant malaria. Prevention depends on hygiene, clean water and food, vector control (draining stagnant water, nets, insecticides) and vaccination where available.

Cancer is uncontrolled cell division. Oncogenes and carcinogens (physical, chemical, biological) can transform cells; malignant tumours invade other tissues (metastasis), whereas benign tumours do not. Detection uses biopsy, radiography, CT and MRI; treatment includes surgery, radiation, chemotherapy and immunotherapy. AIDS is caused by HIV, a retrovirus with an RNA genome that infects helper T cells, weakening immunity; it spreads by sexual contact, infected blood, shared needles and from mother to child, and is detected by ELISA. Drug and alcohol abuse involves opioids (heroin from morphine of Papaver somniferum), cannabinoids (Cannabis sativa), cocaine (Erythroxylum coca) and tobacco (nicotine), with serious health and social effects; adolescents need education, counselling and medical support.

Immunity, Vaccination and Immune Memory

Innate immunity is present from birth and non-specific, with four types of barriers: physical (skin, mucus lining), physiological (stomach acid, saliva, tears), cellular (neutrophils, monocytes, natural killer cells, macrophages that phagocytose microbes) and cytokine barriers (virus-infected cells secrete interferons). Acquired (adaptive) immunity is pathogen-specific and has memory: the first (primary) response is of low intensity, and the second (secondary) response on re-exposure is much faster and stronger. It involves two kinds of lymphocytes: B cells secrete antibodies (humoral immunity), and T cells mediate cell-mediated immunity (important in graft rejection).

An antibody has four polypeptide chains (two heavy, two light; H₂L₂). The main classes are IgA, IgM, IgE and IgG. Active immunity arises when the body makes its own antibodies after infection or vaccination (slow, long-lasting); passive immunity comes from readymade antibodies (colostrum IgA to the infant, antitetanus serum, antivenom; immediate but short-lived). Vaccination (Edward Jenner’s cowpox/smallpox work) introduces weakened or inactivated pathogens or antigenic proteins so that memory B and T cells are created; recombinant vaccines such as hepatitis B are made in yeast. Allergy is an exaggerated response to allergens through IgE, with mast cells releasing histamine and serotonin. In autoimmunity the body attacks its own cells (rheumatoid arthritis). The lymphoid organs are primary (bone marrow, thymus, where lymphocytes mature) and secondary (spleen, lymph nodes, tonsils, Peyer’s patches, MALT).

Microbes in Human Welfare

Household products: lactic acid bacteria (Lactobacillus) convert milk to curd by producing acid that coagulates and partially digests milk proteins; they also increase vitamin B₁₂. Dough for idli and dosa is fermented by bacteria; bread dough rises because Saccharomyces cerevisiae (baker’s yeast) releases CO₂. Toddy comes from fermented sap. In cheese-making, bacteria curdle milk; Swiss cheese has large holes due to CO₂ released by Propionibacterium sharmanii, and Roquefort is ripened by specific fungi.

Industrial products: Saccharomyces cerevisiae (brewer’s yeast) ferments malted cereals and fruit juices to give beer, wine, whisky, brandy and rum. Antibiotics: Alexander Fleming discovered penicillin (from Penicillium notatum) in 1928; Chain and Florey established its use. Organic acids: citric acid (Aspergillus niger), acetic acid (Acetobacter aceti), butyric acid (Clostridium butylicum), lactic acid (Lactobacillus). Enzymes and bioactive molecules: lipases (detergents), pectinases and proteases (clearing fruit juices), streptokinase (Streptococcus; clot buster), cyclosporin A (Trichoderma polysporum; immunosuppressant), and statins (Monascus purpureus; lower blood cholesterol).

Sewage treatment: primary treatment physically removes floating and suspended solids; secondary (biological) treatment uses aerobic microbes forming flocs in aeration tanks, lowering the BOD (biochemical oxygen demand, the amount of oxygen consumed by microbes to oxidise organic matter); the settled activated sludge is partly recycled and the rest goes to anaerobic digesters, where bacteria (Methanobacterium) produce biogas (methane, CO₂, H₂S). Biocontrol uses Bacillus thuringiensis (Bt) against caterpillars, Trichoderma against plant pathogens and baculoviruses against insects. Biofertilisers include Rhizobium (legume root nodules), Azotobacter, Azospirillum, cyanobacteria (Anabaena, Nostoc) and mycorrhizal fungi (Glomus) that improve phosphorus uptake.

Principles of Recombinant DNA Technology

Biotechnology rests on two core techniques: genetic engineering (altering the genetic material of organisms) and bioprocess engineering (growing cells in sterile conditions on a large scale). The first recombinant DNA was made by Stanley Cohen and Herbert Boyer (1972), who linked an antibiotic-resistance gene to a plasmid of Salmonella typhimurium and transferred it to E. coli, where it replicated and expressed. The basic tools are enzymes, vectors and a host organism.

Restriction enzymes (molecular scissors) cut DNA at specific palindromic sequences. The first, Hind II, recognises a specific six-base-pair sequence. Eco RI (from E. coli RY13) cuts between G and A in the sequence 5′-GAATTC-3′, leaving single-stranded overhangs called sticky ends that base pair with complementary ends of other DNA cut with the same enzyme; DNA ligase then joins them. Cloning vectors replicate within the host: plasmids such as pBR322 have an origin of replication (ori), antibiotic-resistance genes (amp^R, tet^R) as selectable markers, and unique restriction sites; bacteriophages and the Ti plasmid of Agrobacterium are used for plants. Insertional inactivation allows identification of recombinants: inserting a gene into the amp or tet gene (or into lacZ, which prevents blue colour with a chromogenic substrate) means that recombinant colonies lose that property.

The host cell must take up the DNA. Bacteria are made competent by treatment with divalent cations such as calcium and a brief heat shock (42 °C); other methods are microinjection (animal cells) and the gene gun or biolistics (plant cells; DNA-coated gold or tungsten particles).

Genetic Engineering Tools and Gene Transfer

The process of recombinant DNA technology has defined steps: (1) isolating DNA from cells, by treating with enzymes (lysozyme for bacteria, cellulase for plants, chitinase for fungi), removing RNA (ribonuclease) and proteins (protease), and precipitating pure DNA with chilled ethanol; (2) cutting with restriction enzymes; (3) separating fragments by gel electrophoresis (DNA is negatively charged and moves toward the anode through an agarose gel matrix; smaller fragments move faster; stained with ethidium bromide and viewed under UV); (4) amplifying the gene by PCR; (5) ligating into the vector; (6) transferring to the host; and (7) obtaining the product.

Polymerase chain reaction (PCR) makes millions of copies of a DNA segment in vitro. Each cycle has three steps: denaturation (about 94 °C, strands separate), annealing (two synthetic primers bind the ends of the target), and extension (thermostable Taq polymerase from Thermus aquaticus, at about 72 °C, extends the primers). After n cycles there are 2ⁿ copies from one template, so 30 cycles give about a billion copies. Large-scale production uses bioreactors (stirred-tank type) with controlled temperature, pH and oxygen, followed by downstream processing (separation, purification, formulation, quality control, clinical trials) before marketing.

Applications of Biotechnology in Medicine and Agriculture

Agriculture: Genetically modified (GM) crops can be pest resistant, herbicide tolerant, more nutritious (Golden Rice rich in vitamin A), or have longer shelf life (Flavr Savr tomato). Bt cotton contains genes from Bacillus thuringiensis that code for Cry proteins (cryIAc and cryIIAb control cotton bollworms; cryIAb controls corn borer). The Bt toxin is produced as an inactive protoxin crystal; in the alkaline pH of an insect’s gut it is solubilised and activated, binds to midgut epithelial cells, creates pores, causing cell swelling, lysis and death. RNA interference (RNAi) protects plants from the nematode Meloidogyne incognita: Agrobacterium vectors introduced genes producing sense and antisense RNA in tobacco roots; these form double-stranded RNA that silences the parasite’s mRNA.

Medicine: Recombinant human insulin (Eli Lilly, 1983, made in E. coli; chains A and B are produced separately and joined by disulphide bonds) replaced animal insulin, avoiding allergy. Gene therapy corrects a gene defect, first used in 1990 for adenosine deaminase (ADA) deficiency. Transgenic animals carry foreign genes, and are used to study gene function, produce human proteins (such as human α-lactalbumin-enriched milk from the cow Rosie), test vaccine safety and chemical toxicity. Early diagnosis uses PCR, recombinant DNA probes and ELISA.

Ethical and legal issues: The Genetic Engineering Approval Committee (GEAC) in India evaluates the safety of GM research. Biopiracy is the use of bio-resources and traditional knowledge by organisations without proper authorisation; patents granted on basmati rice, turmeric and neem triggered strong objections and legal challenges in India.

Organisms and Environmental Adaptations

Ecology studies the interactions of organisms with one another and with their environment. Major abiotic factors are temperature, water, light and soil. Temperature affects enzyme activity and metabolism; eurythermal species tolerate wide ranges and stenothermal species a narrow range; similarly euryhaline and stenohaline organisms tolerate wide or narrow salinity. Biomes such as desert, tropical rain forest and tundra reflect regional climate.

Organisms respond in four ways. Regulate: maintain a constant internal environment (homeostasis) by thermoregulation and osmoregulation, as mammals and birds do, which costs energy. Conform: let body temperature or osmolarity change with surroundings (most animals and nearly all plants). Migrate: temporarily move away, such as Siberian cranes coming to Keoladeo National Park, Bharatpur. Suspend: hibernation, aestivation, diapause in zooplankton, bacterial spores and seeds.

Adaptations are heritable features enhancing survival and reproduction. The kangaroo rat of North American deserts meets its water needs by internal fat oxidation and concentrates its urine. Opuntia has spines (reduced leaves), a thick cuticle, sunken stomata and CAM photosynthesis. By Allen’s rule, mammals in colder regions have shorter ears and limbs to minimise heat loss. Seals have a thick blubber layer. At high altitude, people may get altitude sickness (nausea, fatigue, heart palpitations); the body acclimatises by increasing red blood cell production, decreasing haemoglobin’s binding affinity, and breathing faster.

Population Ecology and Species Interactions

A population is a group of individuals of one species in a given area. Its attributes include birth rate (natality), death rate (mortality), sex ratio, age distribution (age pyramids may be expanding, stable or declining) and density. Population size changes by natality (B), mortality (D), immigration (I) and emigration (E): N_t+1 = N_t + [(B + I) − (D + E)]. With unlimited resources, growth is exponential (J-shaped): dN/dt = rN, with N_t = N₀e^rt, where r is the intrinsic rate of natural increase. With limited resources growth is logistic (S-shaped): dN/dt = rN[(K − N)/K], approaching the carrying capacity (K).

Species interactions: predation (controls prey, maintains diversity; the prickly pear cactus in Australia was controlled by the cactus-feeding moth Cactoblastis); competition (Gause’s competitive exclusion principle: two closely related species competing for the same limited resources cannot coexist indefinitely; resource partitioning, as in MacArthur’s warblers, allows coexistence; Connell’s barnacle experiment); parasitism (ectoparasites and endoparasites; brood parasitism by cuckoo); commensalism (orchid on a mango branch, cattle egret with cattle); and mutualism (lichens, mycorrhizae, fig–wasp pollination, Mediterranean orchid Ophrys).

Ecosystem Structure and Productivity

An ecosystem is a functional unit of nature combining the biotic community with its abiotic surroundings. Structure includes species composition and stratification (vertical layering in forests). Productivity is the rate of biomass production. Gross primary productivity (GPP) is the total organic matter produced by photosynthesis; net primary productivity (NPP) is GPP minus the respiratory loss (R): NPP = GPP − R. NPP is the biomass available to consumers. The annual NPP of the biosphere is about 170 billion tonnes (dry weight), of which oceans contribute only about 55 billion tonnes despite covering most of Earth. Secondary productivity is the rate of formation of new organic matter by consumers.

Decomposition involves fragmentation (by detritivores such as earthworms), leaching, catabolism (enzymatic breakdown by bacteria and fungi), humification (formation of dark-coloured humus, resistant to microbial action) and mineralisation (release of inorganic nutrients). Decomposition is faster with nitrogen- and sugar-rich litter and in warm, moist conditions, but slower with lignin and chitin or at low temperature and anaerobic conditions. Nutrient cycling: in the carbon cycle, about 71% of global carbon is dissolved in oceans and the atmosphere holds only about 1%; the phosphorus cycle has no gaseous phase. Ecological succession is the orderly replacement of communities, primary (on bare rock) or secondary (after disturbance), reaching a stable climax community. Ecosystem services (clean air and water, pollination, climate regulation) were valued by Robert Costanza and colleagues at about US$ 33 trillion per year.

Food Chains, Food Webs and Ecological Pyramids

The sun is the source of energy; about 50% of incident solar radiation is photosynthetically active radiation (PAR), and plants capture only 2–10% of PAR. Energy flows in one direction through trophic levels: producers (first), primary consumers (herbivores), secondary consumers and tertiary consumers. Feeding relationships form a grazing food chain (GFC) beginning with producers, and a detritus food chain (DFC) beginning with dead organic matter; in aquatic ecosystems the GFC is the major conduit of energy, whereas in terrestrial ecosystems the DFC is dominant. Interlinked chains form a food web.

According to Lindeman’s 10% law, only about 10% of the energy at one trophic level passes to the next; the rest is lost as heat or used in respiration, which limits food chains to 4–5 levels. Ecological pyramids show trophic structure: the pyramid of numbers is upright in grassland but can be inverted (one tree supporting many insects); the pyramid of biomass is upright in land ecosystems but inverted in the sea (small standing crop of phytoplankton supports larger zooplankton biomass); the pyramid of energy is always upright because energy is lost at each step. Pyramids do not show food-web complexity or account for species in several levels.

Biodiversity Patterns and Biological Value

Biodiversity is the variety of life at three levels: genetic diversity (within a species, such as the many varieties of rice or mango), species diversity (variety of species in a region; the Western Ghats have more amphibian species than the Eastern Ghats) and ecosystem diversity (variety of habitats, such as deserts, rain forests, mangroves, coral reefs). More than 1.5 million species have been described, and Robert May’s estimate of the global total is about 7 million. India has only 2.4% of the world’s land area but about 8.1% of its species diversity.

Patterns: species diversity generally decreases from the equator toward the poles (latitudinal gradient); for instance Colombia near the equator has about 1400 bird species, New York about 105, Greenland about 56. Tropical regions are richer because they have had longer evolutionary time, more stable and less seasonal climates and more solar energy for productivity; the Amazon rain forest is the richest, with over 40,000 plant species. Species–area relationship (Alexander von Humboldt): within a region, species richness increases with area at a decreasing rate, giving a rectangular hyperbola; on a log scale it is a straight line: log S = log C + Z log A, with slope Z typically 0.1–0.2 regardless of taxon or region (and 0.6–1.2 for very large areas such as continents).

Value: narrowly utilitarian (food, firewood, fibre, medicines such as reserpine from Rauwolfia vomitoria), broadly utilitarian (ecosystem services; the Amazon forest contributes about 20% of the oxygen produced on land by photosynthesis, pollination, climate regulation, aesthetic value) and ethical (every species has a right to exist). Biodiversity hotspots are regions with very high species richness and endemism that are under threat; there are 34 globally, and three overlap India: the Western Ghats and Sri Lanka, Himalaya, and Indo-Burma.

Threats to Biodiversity and Conservation Strategies

More than 800 species have become extinct in the last 500 years (the dodo, quagga, Steller’s sea cow, thylacine, passenger pigeon), and extinction rates today are far higher than natural background rates, so many scientists speak of a “sixth extinction”. The main causes, called the “evil quartet”, are: (1) habitat loss and fragmentation, the most important cause (the Amazon rain forest has been cleared for soya-bean cultivation and cattle ranching); (2) overexploitation (hunting, overfishing); (3) alien species invasions (the Nile perch introduced into Lake Victoria led to extinction of over 200 cichlid fish species; invasive plants such as Parthenium, Lantana and water hyacinth Eichhornia); and (4) co-extinctions (extinction of a dependent species when its partner species disappears, such as a parasite with its host, or a pollinator with its plant).

Conservation strategies: in situ (on site) conservation protects whole ecosystems in their natural habitats: national parks, wildlife sanctuaries, biosphere reserves, biodiversity hotspots and sacred groves. Ex situ (off site) conservation protects threatened species outside their natural habitat: zoological parks, botanical gardens, wildlife safari parks, cryopreservation of gametes, in vitro fertilisation, tissue culture, and seed banks. The IUCN Red List categorises species by threat level. International efforts include the Convention on Biological Diversity (Earth Summit, Rio de Janeiro, 1992) and the World Summit on Sustainable Development (Johannesburg, 2002), which pledged to reduce biodiversity loss. Local communities, such as those that protect sacred groves, play a major role.

Environmental Biology and Sustainable Ecosystem Management

Air pollution control includes the electrostatic precipitator (removes over 99% of particulate matter by charging particles and collecting them on plates) and the scrubber (removes gases such as sulphur dioxide by passing exhaust through water or lime). Catalytic converters fitted to vehicles contain platinum–palladium and rhodium catalysts that convert unburnt hydrocarbons to CO₂ and water, carbon monoxide to CO₂, and nitric oxide to nitrogen; they require unleaded petrol. Bharat Stage emission norms limit pollutants from vehicles.

Water pollution: organic waste raises BOD, and nutrient enrichment causes eutrophication, the accelerated ageing of lakes with algal blooms that deplete oxygen and kill fish. Biomagnification is the increase in concentration of a non-degradable toxicant (such as DDT or mercury) at successive trophic levels; DDT may rise from about 0.003 ppb in water to 25 ppm in fish-eating birds, causing eggshell thinning and population declines. Other issues are solid waste, e-waste and radioactive waste.

Global climate and ozone: greenhouse gases (CO₂ about 60% of the enhanced effect, CH₄ about 20%, CFCs and N₂O) trap heat, causing global warming, melting ice and rising sea levels. Chlorofluorocarbons deplete stratospheric ozone, producing the Antarctic ozone hole and increasing harmful UV-B, which damages DNA and causes skin cancer and cataract; the Montreal Protocol (1987) phases out ozone-depleting substances. Sustainable management includes reforestation, the Chipko movement (Sunderlal Bahuguna and others; based on the sacrifice of Amrita Devi Bishnoi in 1731), Joint Forest Management with local communities, rainwater harvesting, and the three Rs: reduce, reuse and recycle.

Important Scientists and Discoveries

Handy numbers and ratios

• Monohybrid F₂: 3 : 1 phenotypic, 1 : 2 : 1 genotypic. Dihybrid F₂: 9 : 3 : 3 : 1. Test cross heterozygote: 1 : 1.
• Embryo sac: 8 nuclei, 7 cells. Endosperm: 3n. PMC → 4 pollen grains. Primary oocyte → 1 ovum.
• Codons: 64 total; 61 sense; 3 stop (UAA, UAG, UGA); AUG start. Human genome ≈ 3 × 10⁹ bp.
• Hardy–Weinberg: p² + 2pq + q² = 1. PCR copies = 2ⁿ. Energy transfer between trophic levels ≈ 10%.
• Species–area: log S = log C + Z log A with Z ≈ 0.1–0.2. Hotspots: 34 worldwide, 3 in India.

Exam strategy

• Draw and label. Diagrams of the flower, embryo sac, nephron-like structures, replication fork, lac operon and food webs are repeatedly asked; neat labelling carries marks.
• Use exact terms. Write “secondary oocyte”, “primary endosperm nucleus”, “coding strand”, “template strand”, “autogamy” and “geitonogamy” precisely rather than general phrases.
• Practise genetics problems. Always write gametes, set up the Punnett square, then state genotypic and phenotypic ratios separately.
• Link cause and effect. For ecology and environment answers, explain why (for example, why pyramids invert or why DDT thins eggshells).
• Memorise the lists. Pathogens and diseases, microbes and their products, and biotechnology tools are short factual lists that gain easy marks.
• Revise with tables. Make comparison tables (mitosis vs meiosis style): spermatogenesis vs oogenesis, innate vs adaptive immunity, in situ vs ex situ conservation.