Words to know

The flower: who's who

Parts of a flower:

• Androecium (male) = all the stamens. Each stamen = filament (stalk) + anther (makes pollen).
• Gynoecium (female) = all the pistils. Each pistil = stigma (receives pollen) + style (tube) + ovary (contains ovules).

Male side: anther and pollen

• A typical anther has 2 lobes, and each lobe has 2 chambers (theca), so it is bilobed and dithecous.
• So an anther has 4 microsporangia (pollen sacs).
• Wall of the microsporangium, outside to inside: epidermis → endothecium → middle layers → tapetum.
• The tapetum is the innermost layer. It feeds the developing pollen.

How pollen is made (microsporogenesis)

Microspore mother cell (2n) → meiosis → microspore tetrad (4 cells, n) → each microspore becomes a pollen grain.

Pollen grain: a tough little packet

• Exine is the hard outer wall, made of sporopollenin. It is one of the toughest natural materials: it survives high heat, strong acids and alkalis, and no enzyme can break it. That is why pollen is found preserved as fossils.
• Germ pores are gaps in the exine where there is no sporopollenin. The pollen tube comes out through them.
• Intine is the thin inner wall, made of cellulose and pectin.
• Inside a mature pollen grain there are 2 cells:
  • Vegetative cell: big, has food, and forms the pollen tube.
  • Generative cell: small, divides to make 2 male gametes.
• About 60% of flowering plants shed pollen at this 2-celled stage.

Female side: ovule and embryo sac

• The ovary contains ovules, attached to a cushion called the placenta.
• Parts of an ovule: funicle (stalk), hilum, integuments (coverings), micropyle (small opening), chalaza (base) and nucellus (food tissue).

How the embryo sac is made

Megaspore mother cell (2n) → meiosis → 4 megaspores (n) → 3 degenerate, 1 stays functional → 3 rounds of free-nuclear mitosis → embryo sac with 8 nuclei in 7 cells.

• Only one megaspore survives, so this is called monosporic development.

• Synergids have a filiform apparatus, which works like a "landing guide" that attracts and guides the pollen tube.

Pollination: getting pollen to the stigma

• Chasmogamous flowers open normally.
• Cleistogamous flowers never open, so they always self-pollinate (e.g. Viola, Oxalis, Commelina). They give an assured seed set, even without pollinators.

Who carries the pollen?

• Abiotic (non-living) agents:
  • Wind: light, non-sticky pollen and feathery stigmas (grasses, maize).
  • Water: rare; Vallisneria, Hydrilla and Zostera.
• Biotic (living) agents: mostly insects (especially bees), also birds and bats. Their flowers are large, colourful, fragrant and rich in nectar.

Outbreeding devices: stopping self-pollination

Plants want variety, so many have tricks to avoid selfing:

1. Pollen release and stigma readiness happen at different times.
2. Anther and stigma are at different positions.
3. Self-incompatibility: the pistil rejects its own pollen (a genetic lock).
4. Unisexual flowers:
   • Monoecious plants (castor, maize) have male and female flowers on the same plant. This stops autogamy but not geitonogamy.
   • Dioecious plants (papaya) have male and female flowers on different plants. This stops both.

Artificial hybridisation (plant breeding)

• Emasculation means removing the anthers from a flower before they release pollen.
• Bagging means covering the flower with a butter-paper bag so no unwanted pollen gets in.
• The breeder then dusts the chosen pollen on the stigma and bags the flower again.

Double fertilisation (a favourite exam topic)

The pollen tube brings 2 male gametes. Both of them fuse with something, so it's called double fertilisation. This happens only in flowering plants (angiosperms).

• Syngamy: male gamete 1 + egg (n) → zygote (2n) → becomes the embryo.
• Triple fusion: male gamete 2 + 2 polar nuclei (n + n) → primary endosperm nucleus, PEN (3n) → becomes the endosperm (food).

After fertilisation: what becomes what

Endosperm: the baby's lunch box

• Endosperm forms before the embryo, because the baby needs food first!
• Most common type: free-nuclear (many nuclei, no walls yet).
• Coconut: the water is free-nuclear endosperm and the white kernel is cellular endosperm.
• Non-albuminous seeds use up all the endosperm (pea, groundnut).
• Albuminous seeds keep some endosperm (wheat, maize, castor).
• Perisperm is leftover nucellus (black pepper, beet).

The embryo

• The zygote grows: proembryo → globular → heart-shaped → mature embryo.
• A monocot embryo (like grass) has 1 cotyledon called the scutellum. The shoot tip is covered by the coleoptile and the root tip by the coleorhiza.

Fruits and seeds: fun facts

• False fruits grow from the thalamus as well as the ovary (apple, strawberry, cashew).
• Parthenocarpic fruits grow without fertilisation, so they have no seeds (banana).
• Oldest seeds: a Lupinus arcticus seed germinated after about 10,000 years, and a date palm (Phoenix dactylifera) seed after about 2,000 years.

Apomixis and polyembryony

• Apomixis means forming seeds without fertilisation (some grasses, Asteraceae). It is useful for farmers because hybrid seeds made this way stay the same every year, so farmers don't need to buy new hybrid seed every season.
• Polyembryony means more than one embryo in one seed (citrus, mango).

30-second revision

• Anther = 4 microsporangia; tapetum feeds the pollen.
• Exine = sporopollenin (the toughest material). Germ pores have no sporopollenin.
• Embryo sac = 7 cells, 8 nuclei (monosporic).
• Xenogamy = the only pollination type that brings new genes.
• Double fertilisation = syngamy (2n zygote) + triple fusion (3n PEN).
• Ovary → fruit, ovule → seed, integuments → seed coat.

The whole story in 7 steps

1. Gametogenesis: making sperms and eggs.
2. Insemination: sperms are transferred into the female.
3. Fertilisation: sperm + egg → zygote.
4. Cleavage and implantation: the embryo attaches to the uterus wall.
5. Gestation (pregnancy): the baby grows for about 9 months.
6. Parturition: birth of the baby.
7. Lactation: the mother feeds milk.

Male reproductive system

• Testes (2) are the sperm factories. They sit outside the body in a skin pouch called the scrotum.
• The scrotum keeps the testes 2–2.5 °C cooler than the body, because sperms need a cooler temperature to form.
• Each testis has about 250 compartments called testicular lobules. Each lobule has 1–3 seminiferous tubules, where the sperms are made.

The sperm's journey out

Seminiferous tubules → rete testis → vasa efferentia → epididymis (sperms stored and mature) → vas deferens → ejaculatory duct → urethra → outside.

• Accessory glands: 2 seminal vesicles, 1 prostate and 2 bulbourethral glands.
• Their fluid is seminal plasma. It is rich in fructose (energy for sperms), calcium and enzymes.
• Semen = sperms + seminal plasma.

Female reproductive system

• Ovaries (2) make the eggs and the hormones estrogen and progesterone.
• Oviduct (fallopian tube) has 3 parts: infundibulum (funnel with finger-like fimbriae that catch the egg) → ampulla (wide part) → isthmus (narrow part).
• Fertilisation happens at the ampullary–isthmic junction.
• Uterus (womb): where the baby grows. Its wall has 3 layers:

• Mammary glands (breasts) make milk. Each has 15–20 lobes full of milk-making cells (alveoli).

Making gametes (gametogenesis)

Spermatogenesis: making sperms

Spermatogonium (2n) → grows → primary spermatocyte (2n) → meiosis I → 2 secondary spermatocytes (n) → meiosis II → 4 spermatids (n) → spermiogenesis → 4 sperms (n).

• Spermiogenesis means spermatids changing into sperms (they get a tail).
• Spermiation means the release of sperms from the seminiferous tubules.

Hormones control it all

• The hypothalamus releases GnRH, which acts on the anterior pituitary.
• The anterior pituitary releases:
  • LH → acts on Leydig cells → they make testosterone.
  • FSH → acts on Sertoli cells → they help spermiogenesis.

Parts of a sperm

• One ejaculation releases 200–300 million sperms. For normal fertility, at least 60% must have normal shape and at least 40% must swim strongly.

Oogenesis: making eggs

• It starts before birth. Millions of egg mother cells (oogonia) form in each ovary of the unborn baby girl, and no new ones are made after birth.
• Many follicles die between birth and puberty. At puberty, only 60,000–80,000 primary follicles are left in each ovary.
• Follicles grow: primary → secondary → tertiary (with a fluid space called the antrum) → Graafian follicle (mature).
• The secondary oocyte is released at ovulation. It is covered by the zona pellucida layer.

The menstrual cycle (about 28 days)

• If no fertilisation: the corpus luteum dies → progesterone falls → the endometrium breaks down → the next period starts.
• Menarche is the first period (at puberty). Menopause is when periods stop, around 50 years.

Fertilisation and implantation

1. The sperm meets the egg at the ampullary–isthmic junction.
2. The sperm enters; changes in the zona pellucida block other sperms.
3. The egg (secondary oocyte) finishes meiosis II.
4. The zygote (2n) forms.
5. Cleavage (mitosis) → morula (8–16 cells) → blastocyst.
6. Implantation: the blastocyst embeds in the endometrium.

• Blastocyst has 2 parts:
  • Trophoblast (outer layer): sticks to the uterus and helps form the placenta.
  • Inner cell mass: becomes the baby. It has stem cells that can form any tissue.

Boy or girl?

• The mother's eggs all carry X.
• The father's sperms are 50% X and 50% Y.
• X egg + X sperm = XX → girl. X egg + Y sperm = XY → boy.

Pregnancy: the baby grows

• Placenta is the link between mother and baby. It gives food and oxygen and removes waste. It is joined to the baby by the umbilical cord.
• Placenta also makes hormones: hCG, hPL, estrogens, progestogens and relaxin.

Three germ layers

Month-by-month milestones

Birth and breastfeeding

• Parturition (birth) is started by signals from the fully grown baby and the placenta. This is called the foetal ejection reflex.
• It causes the release of oxytocin, which makes the uterus muscles squeeze. Squeezing causes more oxytocin, and so on, until the baby is born.
• Colostrum is the first milk after birth. It is full of IgA antibodies, which protect the newborn.

30-second revision

• Testes are in the scrotum, 2–2.5 °C cooler than the body.
• Sertoli = nurse cells; Leydig = testosterone.
• Fertilisation happens at the ampullary–isthmic junction.
• LH surge → ovulation (day 14); corpus luteum → progesterone.
• Zygote → morula → blastocyst → implantation.
• The father decides the baby's sex (X or Y sperm).
• Oxytocin → birth; colostrum → IgA antibodies.

India's efforts

• India was one of the first countries to start a nationwide family planning programme, in 1951.
• Today it is part of the RCH (Reproductive and Child Health Care) programme.
• Schools teach sex education to remove myths and give correct information.

Population explosion

• Why it grew: fewer deaths, fewer mothers and babies dying (lower MMR and IMR), and more people reaching reproductive age.
• Ways to control it: encourage small families, use contraceptives, and raise the marriage age. The legal marriage age is 18 for girls and 21 for boys.

Contraception (birth control)

There are 5 groups of methods: natural, barrier, IUDs, oral pills, injections and implants, and surgical (permanent).

How each method works

Medical Termination of Pregnancy (MTP)

• MTP means ending a pregnancy on purpose, before the baby is fully grown.
• Legal in India since 1971 (MTP Act), with an amendment in 2017 to reduce illegal abortions.
• It is relatively safe during the first trimester (up to 12 weeks).
• Big risk: illegal abortions by untrained people are dangerous and can kill.

Sexually Transmitted Infections (STIs)

Infections that spread through sexual contact. They are also called VD (venereal diseases) or RTI (reproductive tract infections).

• Hepatitis B and HIV can also spread by sharing needles and blood transfusion, and from mother to baby.
• If not treated, STIs can cause PID (pelvic inflammatory disease), abortions, stillbirths, ectopic pregnancy (the baby grows outside the uterus), infertility and even cancer of the reproductive tract.
• Prevention: avoid sex with unknown or multiple partners, always use condoms, and see a doctor early if in doubt.

Infertility and ART (Assisted Reproductive Technologies)

Some couples can't have children. Science can help using ART, techniques that help the sperm and egg meet.

• Low sperm count → AI / IUI: semen is placed in the vagina or uterus.
• Sperm can't enter the egg → ICSI: a sperm is injected straight into the egg.
• Female can't make eggs → GIFT: a donor egg is placed in her fallopian tube.
• IVF + ET ("test tube baby"): the egg and sperm meet in the lab, then the embryo is transferred:
  • embryo with up to 8 cells → ZIFT (into the fallopian tube)
  • embryo with more than 8 cells → IUT (into the uterus)

30-second revision

• Family planning started in India in 1951; now under RCH.
• Amniocentesis for sex determination is banned.
• CuT reduces sperm motility; Saheli = weekly, non-steroidal (CDRI Lucknow).
• Emergency contraception: within 72 hours.
• MTP is legal since 1971 and safest in the first 12 weeks.
• Incurable STIs: Herpes, Hepatitis B, HIV.
• ZIFT (≤ 8 cells, tube), IUT (> 8 cells, uterus), GIFT (donor egg), ICSI (injected sperm).

Words to know

Why did Mendel choose peas?

• Pea plants are easy to grow and have a short life cycle.
• They have many clear, opposite traits (tall/dwarf, green/yellow).
• They self-pollinate naturally but can also be cross-pollinated by hand.
• Mendel studied 7 pairs of contrasting traits from 1856 to 1863.

Monohybrid cross: one trait at a time

Mendel crossed a pure tall (TT) plant with a pure dwarf (tt) plant.

Parents TT (tall) × tt (dwarf) → F1: all Tt (all tall) → self-pollinate Tt × Tt → F2: TT, Tt, Tt, tt → 3 tall : 1 dwarf (genotype 1 TT : 2 Tt : 1 tt).

Punnett square for F1 × F1 (Tt × Tt):

Test cross: find the hidden genotype

A tall plant could be TT or Tt. To find out, cross it with a dwarf (tt) plant:

• If all the offspring are tall → the plant was TT.
• If half are tall and half dwarf (1 : 1) → the plant was Tt.

Mendel's 3 laws

Dihybrid cross: two traits together

Mendel crossed round yellow (RRYY) seeds with wrinkled green (rryy) seeds. The F1 were all RrYy (round yellow). In the F2:

• 4 types of gametes from each parent: RY, Ry, rY, ry. That gives a 4 × 4 = 16 box Punnett square.
• This cross proved the Law of Independent Assortment.

When Mendel's rules bend: exceptions

1. Incomplete dominance: blending

• In the snapdragon (dog flower, Antirrhinum): red (RR) × white (rr) → pink (Rr) in F1.
• F2 = 1 red : 2 pink : 1 white. Here the phenotype ratio is the same as the genotype ratio (1:2:1).

2. Co-dominance: both show

• ABO blood groups in humans are controlled by the gene I, which has 3 alleles: Iᴬ, Iᴮ and i.
• Iᴬ and Iᴮ are co-dominant (both show together as AB). i is recessive.
• This also shows multiple alleles (more than 2 alleles for one gene in a population).

3. Pleiotropy and polygenic inheritance

Chromosomal theory of inheritance

• Sutton and Boveri said genes are on chromosomes, and chromosomes move in pairs like Mendel's factors.
• Thomas Hunt Morgan proved it using fruit flies (Drosophila).

• Linkage: genes on the same chromosome tend to be inherited together.
• Recombination: new combinations appear when linked genes separate (by crossing over).
• Tight linkage gives few recombinants; loose linkage gives more.
• Alfred Sturtevant used recombination frequency to make the first gene maps.

Sex determination: boy or girl?

Mutation

• A mutation is a change in DNA.
• Point mutation: one base changes. Example: sickle-cell anaemia.
• Frameshift mutation: a base is added or deleted, which shifts the whole reading frame.
• Mutagens: things that cause mutation, such as UV rays and some chemicals.

Pedigree analysis

A pedigree is a family tree that shows how a trait is passed down. It helps track genetic diseases.

Genetic disorders

A. Mendelian disorders (a single gene change)

B. Chromosomal disorders (whole chromosome changes)

• Aneuploidy: one chromosome extra or missing, caused by failed separation during cell division.
• Polyploidy: whole extra sets of chromosomes. Common in plants.

30-second revision

• Monohybrid 3:1 (phenotype), 1:2:1 (genotype); dihybrid 9:3:3:1; test cross 1:1.
• Incomplete dominance: snapdragon → pink (1:2:1).
• ABO blood groups = co-dominance + multiple alleles (3-6-4).
• Morgan → Drosophila → linkage; Sturtevant → gene maps.
• Birds: female ZW. Honey bee male: haploid (16).
• Haemophilia and colour blindness: X-linked recessive. Sickle-cell: Glu6Val.
• Down's = 21 trisomy; Klinefelter = XXY; Turner = XO.

The central dogma: DNA → RNA → Protein

DNA → transcription → mRNA → translation → protein. DNA also copies itself by replication.

Structure of DNA

Building block: the nucleotide

• Nucleotide = nitrogen base + sugar + phosphate.
• Nucleoside = nitrogen base + sugar (no phosphate).
• Purines (2 rings): Adenine, Guanine.
• Pyrimidines (1 ring): Cytosine, Thymine (in DNA), Uracil (in RNA instead of T).

The double helix (Watson and Crick, 1953)

• DNA is a twisted ladder: the sides are sugar–phosphate and the steps are base pairs.
• The two strands run in opposite directions (antiparallel): one 5'→3', the other 3'→5'.
• A = T (2 hydrogen bonds) and G ≡ C (3 hydrogen bonds).
• Pitch (one full turn) = 3.4 nm, with 10 base pairs per turn, so the distance between two base pairs = 0.34 nm.
• Chargaff's rule: in DNA, A = T and G = C, so purines = pyrimidines.
• Watson and Crick built their model using X-ray pictures by Maurice Wilkins and Rosalind Franklin.

How 2 metres of DNA fits in a nucleus: packaging

DNA double helix → wraps around a histone octamer (8 histones) → nucleosome (~200 bp) → "beads on a string" → chromatin fibre → chromosome (seen during cell division).

• Histones are positively charged (rich in lysine and arginine), so they hold negatively charged DNA like a magnet.
• Euchromatin: loosely packed and active (genes are read).
• Heterochromatin: tightly packed and inactive.

Proving DNA is the genetic material

• Viruses with radioactive DNA (³²P) infected bacteria → radioactivity was found inside the bacteria.
• Viruses with radioactive protein (³⁵S) infected bacteria → radioactivity stayed outside the bacteria.
• Conclusion: DNA, not protein, enters the bacteria and carries the genetic information.

Why DNA is better than RNA as genetic material

• RNA has an extra 2'-OH group, which makes it reactive and unstable.
• RNA mutates faster.
• DNA is double-stranded and stable. That's why DNA stores information, while RNA mostly carries messages.
• RNA was probably the first genetic material ("RNA world"), and some RNAs work as enzymes (ribozymes).

DNA replication: making a copy

• DNA copies itself in a semi-conservative way: each new DNA has 1 old strand + 1 new strand.
• Proved by Meselson and Stahl (1958) using heavy nitrogen (¹⁵N) and normal nitrogen (¹⁴N) in E. coli.

1. Start: all DNA has heavy ¹⁵N (band at the bottom of the tube).
2. After 1 generation in ¹⁴N: all DNA is hybrid ¹⁵N/¹⁴N (one middle band).
3. After 2 generations in ¹⁴N: half is hybrid and half is light ¹⁴N (a middle band and a top band).

The replication team (enzymes)

• Leading strand: made continuously.
• Lagging strand: made in short pieces called Okazaki fragments, which ligase joins.
• Replication starts at a point called the origin of replication (ori), and happens in the S phase of the cell cycle.

Transcription: DNA → RNA

• Only one strand of DNA is used as a template.
  • Template strand (3'→5'): read to make RNA.
  • Coding strand (5'→3'): same sequence as the RNA, with T in place of U.
• A transcription unit has 3 parts: promoter (start signal) → structural gene → terminator (stop signal).

RNA processing in eukaryotes

The first copy (hnRNA) is edited before it leaves the nucleus:

hnRNA (exons + introns) → splicing (remove introns, join exons) → capping (add a methyl guanosine cap at the 5' end) → tailing (add a poly-A tail at the 3' end) → mRNA.

The genetic code

• Worked out by George Gamow, Har Gobind Khorana and Marshall Nirenberg.
• Severo Ochoa's enzyme (polynucleotide phosphorylase) helped make RNA for the experiments.

Translation: RNA → protein

• tRNA is the "adapter". One end has the anticodon (it reads the mRNA codon); the other end carries the matching amino acid. Its 2D shape is a clover leaf and its 3D shape is an inverted L.
• Ribosome is the protein factory. In bacteria, its 23S rRNA works as an enzyme (a ribozyme) that makes the peptide bonds.

1. Charging: each tRNA picks up its amino acid (uses ATP).
2. Initiation: the ribosome binds the mRNA at the start codon AUG.
3. Elongation: amino acids join one by one by peptide bonds.
4. Termination: at a stop codon, the protein is released.

• UTRs (untranslated regions) are extra parts at both ends of mRNA that are not translated.

Gene regulation: the lac operon

• Proposed by Jacob and Monod in E. coli.
• Regulator gene (i) makes a repressor protein.
• Structural genes:
  • z → β-galactosidase (breaks lactose)
  • y → permease (lets lactose into the cell)
  • a → transacetylase
• Lactose is the inducer. It switches the operon on.
• This is negative regulation, because the repressor switches it off.

Human Genome Project (HGP)

• A huge international project from 1990 to 2003 to read all human DNA.
• Methods: ESTs (Expressed Sequence Tags) to find genes that are expressed, and sequence annotation (read everything, then find what each part does). Vectors used: BAC and YAC. Sequencing method by Frederick Sanger.

DNA fingerprinting

• Developed by Alec Jeffreys.
• Uses VNTRs (Variable Number of Tandem Repeats): short DNA sequences that repeat a different number of times in different people, so everyone's pattern is unique (except identical twins).

1. Isolate DNA (from blood, hair, skin).
2. Cut it with restriction enzymes.
3. Separate the pieces by gel electrophoresis.
4. Transfer them to a nylon membrane (Southern blotting).
5. Hybridise with a labelled VNTR probe.
6. Autoradiography shows the band pattern.

• Uses: solving crimes (forensics), paternity disputes, and studying population diversity and evolution.

30-second revision

• DNA: antiparallel; A=T (2 bonds), G≡C (3 bonds); 10 bp per turn, 3.4 nm pitch.
• Human DNA ≈ 2.2 m long; nucleosome = histone octamer + ~200 bp.
• Griffith → transformation; Avery → DNA; Hershey–Chase (³²P) → DNA is the genetic material.
• Meselson–Stahl → semi-conservative replication.
• Pol I rRNA, Pol II mRNA, Pol III tRNA. Splicing, capping, tailing.
• Stop codons: UAA, UAG, UGA; start: AUG (Met).
• lac operon: z, y, a; lactose = inducer; negative regulation.
• HGP: ~30,000 genes, 99.9% same; DNA fingerprinting uses VNTRs.

Earth's history in one timeline

Origin of life

• Spontaneous generation (life from rotting matter) was an old idea. Louis Pasteur disproved it: life comes only from pre-existing life.
• Oparin and Haldane said the first life came from non-living organic molecules (like RNA and proteins) through chemical evolution.

Miller's experiment (1953)

Flask with CH₄, H₂, NH₃ and water vapour → heated to 800 °C with electric sparks → amino acids formed.

Evidence for evolution

1. Fossils (palaeontology)

• Fossils are remains of old organisms preserved in rocks. Different rock layers have different life forms, showing how life changed over time.

2. Comparative anatomy

3. Natural selection seen in action

• Industrial melanism (England): before factories, light (white-winged) moths were more common on light, lichen-covered trees. After industrialisation, smoke killed the lichens and darkened the tree trunks, so dark moths were better hidden from birds and became more common.
• Resistance: use of herbicides, pesticides and antibiotics has selected resistant weeds, insects and bacteria within a short time.

Adaptive radiation

• Darwin's finches on the Galápagos Islands: from seed-eating ancestors, finches evolved different beaks to eat seeds, insects and more.
• Australian marsupials (kangaroo, koala, Tasmanian wolf and more) evolved from one ancestor on the same continent.
• When adaptive radiation happens in different places and gives similar-looking animals (e.g. placental wolf and Tasmanian wolf, a marsupial), it is convergent evolution.

Theories of evolution

Darwin's natural selection, step by step

1. Overproduction: organisms produce many offspring.
2. Limited resources → struggle for existence.
3. Variation: no two individuals are the same.
4. Survival of the fittest: better-suited individuals survive.
5. They reproduce more and pass on useful traits.
6. Over many generations → new species.

• Fitness in Darwin's sense means reproductive fitness: leaving more offspring, not being the strongest!
• Alfred Wallace, working in the Malay Archipelago, reached the same conclusion.

Hardy–Weinberg principle

• If p = frequency of allele A and q = frequency of allele a:
  • p + q = 1
  • p² + 2pq + q² = 1 (p² = AA, 2pq = Aa, q² = aa)

5 factors that disturb the balance:

1. Gene migration (gene flow)
2. Genetic drift (chance changes)
3. Mutation
4. Genetic recombination
5. Natural selection

• Founder effect: a small group moves to a new place. By chance, its allele frequencies are different from the original population, so the new group can become a new species.

Three types of natural selection

A quick story of plant and animal evolution

• Plants: early land plants (like Zosterophyllum, Psilophyton) → ferns and seed ferns → gymnosperms → angiosperms (flowering plants).
• Animals: jawless fish (~350 mya) → lobefins (like the coelacanth, the ancestor of amphibians) → amphibians → reptiles → dinosaurs, birds and mammals.

Human evolution

30-second revision

• Miller: CH₄, H₂, NH₃, water vapour + sparks → amino acids.
• Homologous = same origin, divergent; analogous = same function, convergent.
• Industrial melanism: dark moths survived better after pollution.
• Darwin's finches and Australian marsupials = adaptive radiation.
• Fitness = reproductive fitness.
• Hardy–Weinberg: p² + 2pq + q² = 1; 5 disturbing factors (MGMRN).
• Brain size: habilis 650–800 → erectus 900 → Neanderthal 1400 cc.

Common diseases in humans

The malaria parasite's life cycle

1. An infected female Anopheles bites → sporozoites enter the blood.
2. Sporozoites reach the liver and multiply.
3. They then attack red blood cells and multiply there.
4. RBCs burst and release haemozoin → chills and high fever.
5. Some parasites become gametocytes (male and female).
6. A mosquito bites the patient and sucks up the gametocytes.
7. Fertilisation happens in the mosquito's stomach.
8. New sporozoites form and move to the mosquito's salivary glands, ready to infect the next person.

• Humans are the intermediate host (asexual reproduction happens in us).
• The mosquito is the definitive host (sexual reproduction happens there).

Preventing infectious diseases

• Personal hygiene: clean body, clean drinking water, clean food.
• Public hygiene: proper disposal of waste and sewage.
• Control mosquitoes: no stagnant water; spray insecticides; use mosquito nets and screens.
• Put the fish Gambusia in ponds. It eats mosquito larvae.
• Vaccines and antibiotics.

Immunity: the body's army

• Innate immunity (inborn, non-specific):
  • Physical barrier: skin, mucus
  • Physiological barrier: stomach acid, saliva, tears
  • Cellular barrier: neutrophils, monocytes, natural killer cells, macrophages
  • Cytokine barrier: interferons
• Acquired immunity (specific, has memory):
  • Humoral: B cells make antibodies
  • Cell-mediated: T cells attack directly

Innate immunity: 4 barriers

• Physical barrier: skin, and the mucus lining of the nose, gut and airways, which traps germs.
• Physiological barrier: stomach acid, saliva and tears kill germs.
• Cellular barrier: white blood cells like PMNL-neutrophils, monocytes, natural killer cells and macrophages eat or kill germs.
• Cytokine barrier: virus-infected cells release interferons, which protect nearby cells from the virus.

Acquired immunity

• It is specific (one germ at a time) and has memory.
• Primary response: the first time we meet a germ, the response is slow and weak.
• Secondary response: the next time, the response is fast and strong, thanks to memory cells. This is also called the anamnestic response.

Structure of an antibody

• Each antibody has 4 chains: 2 heavy + 2 light, written as H₂L₂.
• Types of antibodies: IgA, IgM, IgE, IgG (and IgD).

Active vs passive immunity

When immunity goes wrong

• Allergy: the body over-reacts to harmless things (allergens) like dust, pollen or animal hair.
  • Involves IgE antibodies and chemicals like histamine and serotonin from mast cells.
  • Treated with antihistamines, adrenaline and steroids.
• Autoimmunity: the body attacks its own cells. Example: rheumatoid arthritis.

Lymphoid organs

• MALT (mucosa-associated lymphoid tissue) makes up about 50% of all lymphoid tissue in the body.

AIDS

• AIDS = Acquired Immuno Deficiency Syndrome. It is caused by HIV, a retrovirus (it has RNA as its genetic material).
• Spreads through: unsafe sex, infected blood, sharing needles, and from an infected mother to her baby.
• Does NOT spread by: touching, hugging, sharing food or mosquito bites.

How HIV destroys the immune system

1. HIV enters the body and gets into a macrophage.
2. Reverse transcriptase makes viral DNA from the viral RNA.
3. The viral DNA joins the host DNA; the macrophage keeps making new viruses (an "HIV factory").
4. The new viruses attack helper T-cells.
5. The number of helper T-cells keeps falling.
6. The immune system fails → infections such as TB (Mycobacterium) and Toxoplasma.

• Test: ELISA (enzyme-linked immunosorbent assay).
• Treatment: anti-retroviral drugs only slow down the disease; they don't cure it.
• Awareness: NACO (National AIDS Control Organisation) and NGOs educate people. World AIDS Day is 1 December.

Cancer

• Causes (carcinogens):
  • Physical: X-rays, gamma rays (ionising radiation) and UV rays (non-ionising)
  • Chemical: tobacco smoke and other chemicals
  • Biological: oncogenic viruses. Genes called proto-oncogenes (c-onc) in normal cells can also turn into cancer genes.
• Detection: biopsy, blood tests, X-ray, CT scan, MRI, and antibodies against cancer antigens.
• Treatment: surgery, radiation therapy, chemotherapy and immunotherapy (e.g. α-interferon, which boosts the immune system).

Drugs and alcohol abuse

• Barbiturates, amphetamines, benzodiazepines and LSD are sometimes used as medicines, but are often misused.
• Tobacco: contains nicotine, which makes the adrenal gland release adrenaline, raising blood pressure and heart rate. Smoking increases carbon monoxide in the blood, so less oxygen reaches the body.

Why teens are at risk, and how to stay safe

• Adolescence (about 12–18 years) is a time of curiosity, stress and peer pressure.
• Warning signs: falling grades, skipping school, losing interest in hobbies, mood swings, changes in sleep and eating.
• How to prevent it:
  1. Avoid undue peer pressure. It's OK to say NO.
  2. Education and counselling.
  3. Talk to parents and friends.
  4. Watch for danger signs.
  5. Get professional and medical help.

30-second revision

• Typhoid → Salmonella typhi, Widal test. Malaria → Plasmodium, female Anopheles, haemozoin.
• Filariasis → Wuchereria, Culex. Ringworm → fungi.
• Gambusia fish eats mosquito larvae.
• Innate barriers: physical, physiological, cellular, cytokine (PPCC).
• Antibody = H₂L₂. B cells → antibodies; T cells → CMI and graft rejection.
• HIV → macrophage → helper T cells ↓. ELISA test. 1 December.
• Cancer: contact inhibition lost; malignant tumours spread (metastasis).

Where microbes help us

Useful microbes help us in six areas: household products, industrial products, sewage treatment, biogas production, biocontrol and biofertilisers.

1. Microbes in household products

2. Microbes in industry

Fermented drinks

• Brewer's yeast (Saccharomyces cerevisiae) ferments fruit juices and grains.
• Without distillation: wine and beer.
• With distillation: whisky, brandy and rum (they have more alcohol).

Antibiotics

• Antibiotic means "against life". Antibiotics are chemicals made by microbes that kill or stop disease-causing microbes.

Chemicals, enzymes and medicines

3. Microbes in sewage treatment

1. Primary treatment (physical): filtering and settling remove grit, soil and pebbles. The settled solids form primary sludge; the liquid on top is the primary effluent.
2. Secondary treatment (biological): the effluent is aerated. Aerobic microbes grow as flocs and eat the organic matter, so the BOD falls.
3. The flocs settle as activated sludge:
   • a small part goes back into the aeration tank as inoculum;
   • most goes to anaerobic sludge digesters, where bacteria produce biogas.
4. The treated water is released into rivers.

• Flocs are clumps of bacteria + fungal threads, like tiny "cleaning teams".
• BOD (Biochemical Oxygen Demand): the amount of oxygen that microbes would use to break down all the organic matter in one litre of water.

• The Ministry of Environment and Forests started the Ganga Action Plan and the Yamuna Action Plan to save these rivers from pollution.

4. Microbes in biogas production

• Biogas is mostly methane (CH₄), with some CO₂ and H₂S. It burns well and is used for cooking and lighting.
• It is made by methanogens (e.g. Methanobacterium). These bacteria live without oxygen (anaerobic).
• They are found in cow dung (gobar) and in the rumen (stomach) of cattle, where they help digest cellulose.

Cow dung slurry → digester tank (no oxygen) → methanogens act → biogas (mainly CH₄) for cooking. The spent slurry is used as fertiliser.

• The biogas technology in India was developed mainly by IARI (Indian Agricultural Research Institute) and KVIC (Khadi and Village Industries Commission).

5. Microbes as biocontrol agents

• IPM (Integrated Pest Management): using many eco-friendly methods together instead of only chemicals.

6. Microbes as biofertilisers

30-second revision

• Curd → Lactobacillus (LAB), vitamin B₁₂ ↑. Swiss cheese holes → Propionibacterium sharmanii.
• Penicillin → Fleming (Penicillium notatum); Chain and Florey.
• Citric acid → Aspergillus niger; statins → Monascus; cyclosporin A → Trichoderma; streptokinase → clot buster.
• Sewage: primary (physical) → secondary (biological, flocs) → activated sludge → biogas. High BOD = high pollution.
• Biogas = methane, made by methanogens (Methanobacterium); IARI and KVIC.
• Biocontrol: Bt, Trichoderma, baculoviruses, ladybird. Biofertilisers: Rhizobium, Azotobacter, Glomus, Anabaena.

Two core techniques

• EFB (European Federation of Biotechnology) definition: "the integration of natural science and organisms, cells, parts thereof, and molecular analogues for products and services."

The 3 basic steps of genetic modification

1. Identify the DNA with the useful gene.
2. Introduce it into a host organism.
3. Keep the new DNA in the host and pass it on to the host's offspring.

The toolkit

• Restriction enzymes: "molecular scissors"
• DNA ligase: "molecular glue"
• Vectors: carriers such as plasmids and bacteriophages
• Competent host: e.g. E. coli

1. Restriction enzymes: molecular scissors

• They cut DNA at specific sequences.
• The first one discovered was Hind II. It always cuts at a particular 6 base-pair sequence.
• Exonucleases cut nucleotides from the ends of DNA. Endonucleases cut inside the DNA at specific points.

How they are named: EcoRI

Palindromes: restriction enzymes recognise palindromic sequences. These read the same on both strands in the 5'→3' direction (like the words "MADAM" or "RACECAR").

EcoRI site:   5' — G ↓A A T T C — 3'
              3' — C T T A A↑ G — 5'

After cutting:
              5' — G           A A T T C — 3'
              3' — C T T A A           G — 5'
                   └── sticky ends ──┘

• EcoRI cuts between G and A on each strand, leaving short single-stranded overhangs called sticky ends.
• Sticky ends easily stick to matching ends from the same enzyme. DNA ligase then seals them.

2. Gel electrophoresis: sorting DNA pieces by size

1. DNA pieces are placed in wells of an agarose gel.
2. An electric current is switched on. DNA (negative) moves towards the anode (+).
3. Small pieces move fast and far; big pieces move slowly.
4. The gel is stained with ethidium bromide and viewed under UV light → orange bands.
5. The band is cut out (elution) to get the pure DNA piece.

• Agarose comes from seaweed.
• DNA is negatively charged (because of the phosphate groups), so it moves towards the positive electrode (anode).

3. Cloning vectors: the delivery trucks

A vector carries the foreign gene into the host. Usually a plasmid (small circular DNA in bacteria) or a bacteriophage (a virus that infects bacteria).

What a good vector needs:

Finding the right cells: insertional inactivation

1. The foreign gene is inserted into the vector's lacZ gene, which breaks it (insertional inactivation).
2. Bacteria are grown on a plate with a chromogenic substrate.
3. White (colourless) colonies = recombinants (lacZ broken, no colour).
4. Blue colonies = non-recombinants (lacZ works and makes the blue colour).

Vectors for plants and animals

• Agrobacterium tumefaciens causes crown gall disease in plants. Its Ti plasmid is disarmed (made harmless) and used to carry useful genes into plants.
• Retroviruses can be disarmed and used to carry genes into animal cells.

4. Competent host: getting DNA into cells

DNA can't cross cell membranes on its own (it is hydrophilic), so we make cells "competent":

The complete process of recombinant DNA technology

1. Isolate DNA: break the cells with enzymes, remove RNA and protein, add chilled ethanol → DNA threads appear.
2. Cut DNA with restriction enzymes; check by gel electrophoresis.
3. Amplify the gene with PCR (make millions of copies).
4. Ligate: join the gene into a vector with DNA ligase.
5. Insert the recombinant DNA into a host; select the transformants.
6. Grow the host on a large scale in bioreactors → product.
7. Downstream processing: purify, add preservatives, test.

Step 1 detail: breaking open cells

• Then RNA is removed with ribonuclease and proteins with protease.
• Chilled ethanol makes the pure DNA come out as fine threads, which can be lifted out (spooling).

Step 3 detail: PCR, the DNA photocopier

PCR = Polymerase Chain Reaction. It makes millions of copies of a gene in a few hours. Each cycle has 3 steps:

1. Denaturation: heating (~94 °C) separates the DNA strands.
2. Annealing: on cooling, the primers bind.
3. Extension: Taq polymerase builds the new strands.
4. The cycle is repeated about 30 times.

• Taq polymerase comes from the bacterium Thermus aquaticus, which lives in hot springs. The enzyme doesn't get destroyed by heat.
• Primers are short DNA pieces that mark where to start copying.
• Copies double every cycle: after n cycles there are about 2ⁿ copies. About 30 cycles give about 1 billion copies!

Step 6 detail: bioreactors

• Bioreactors are large tanks (100–1000 litres) where the host cells grow and make the product.
• The most common type is the stirred-tank bioreactor. It has:
  • an agitator (stirrer) to mix,
  • an oxygen delivery system (sparger, which bubbles air),
  • a foam control system,
  • temperature and pH control,
  • a sampling port.
• Continuous culture: used medium is drained out and fresh medium added, which keeps the cells in their most active log (exponential) phase.

Step 7: downstream processing

• Separation and purification of the product.
• Formulation with preservatives.
• Clinical trials (for medicines) and quality control testing.

30-second revision

• First rDNA: Cohen and Boyer (1972), Salmonella typhimurium plasmid.
• EcoRI = E. coli RY13, first enzyme. Palindrome GAATTC, sticky ends.
• DNA runs to the anode; small pieces go farther; ethidium bromide + UV; elution.
• Vector needs ori, selectable marker, cloning sites. pBR322: ampR, tetR.
• Blue–white selection: white = recombinant (lacZ broken).
• Ti plasmid of Agrobacterium for plants; Ca²⁺ + heat shock for bacteria.
• PCR: denature → anneal → extend (Taq polymerase); 2ⁿ copies.
• Stirred-tank bioreactor; downstream processing.

Biotechnology in agriculture

Three ways to grow more food:

1. Agrochemical-based agriculture (fertilisers and pesticides)
2. Organic agriculture
3. Genetically engineered crop-based agriculture (GM crops)

What are GMOs?

Benefits of GM plants:

• They tolerate stresses such as cold, drought, salt and heat.
• They need fewer chemical pesticides.
• They reduce losses after harvest.
• They use soil minerals more efficiently.
• They can give more nutritious food, e.g. Golden Rice (rich in vitamin A).

Bt cotton: a plant that protects itself

• Bt = Bacillus thuringiensis, a soil bacterium that makes a protein toxic to certain insects.
• The Bt gene was put into cotton, so the plant makes the toxin itself and kills pests that eat it.

How the Bt toxin kills insects

1. The bacterium makes the toxin as an inactive protoxin (crystal protein).
2. An insect eats the plant.
3. The alkaline pH of the insect gut dissolves the crystals.
4. The protoxin becomes an active toxin.
5. The toxin binds the midgut lining and makes pores.
6. The cells swell and burst → the insect dies.

Bt genes (called cry genes):

Pest-resistant plants using RNA interference (RNAi)

• Problem: the nematode (roundworm) Meloidogyne incognita attacks tobacco roots and reduces the crop.
• Solution: RNA interference (RNAi), a natural defence method found in all eukaryotes.

1. Nematode-specific genes are put into tobacco using Agrobacterium.
2. The plant makes both sense and antisense RNA.
3. These pair up to form double-stranded RNA (dsRNA).
4. When the nematode feeds, the dsRNA silences its matching mRNA.
5. The needed protein is not made → the nematode dies.

Biotechnology in medicine

1. Genetically engineered insulin

• Insulin controls blood sugar. Diabetic patients need insulin injections.
• Earlier, insulin came from the pancreas of slaughtered cattle and pigs, which caused allergies in some patients.
• Insulin structure: 2 short chains, A and B, joined by disulphide bridges.
• In the body it is first made as pro-insulin, which has an extra piece called the C-peptide. The C-peptide is removed to make mature insulin.

1. DNA sequences for chain A and chain B are made separately.
2. Each is put into an E. coli plasmid.
3. E. coli makes chain A and chain B.
4. The chains are extracted and joined by disulphide (S–S) bonds.
5. Result: human insulin (Humulin).

• Made in 1983 by the US company Eli Lilly.

2. Gene therapy

• First used in 1990 on a 4-year-old girl with ADA (adenosine deaminase) deficiency. ADA is an enzyme needed for the immune system to work.

1. Lymphocytes are taken from the patient's blood.
2. They are grown in the lab.
3. A working ADA gene is inserted using a retrovirus vector.
4. The cells are put back into the patient.
5. This is not permanent: lymphocytes die, so the treatment must be repeated.

• Permanent cure: put the ADA gene into bone marrow cells at an early embryonic stage.
• Other treatments for ADA deficiency: bone marrow transplant and enzyme replacement therapy.

3. Molecular diagnosis

• Normal tests find a disease only after symptoms appear, when there are many germs.
• New techniques detect it early, when there are very few germs or small changes:
  • PCR: copies tiny amounts of germ DNA until it can be detected (e.g. HIV in suspected AIDS patients, cancer gene mutations).
  • ELISA: based on antigen–antibody reactions (e.g. HIV test).
  • Probes + autoradiography: a radioactive single-stranded DNA/RNA probe sticks to the matching DNA. A mutated gene won't show up on the photographic film because the probe can't bind to it.

Transgenic animals

Transgenic animals have a foreign gene added to their DNA. More than 95% of all transgenic animals are mice.

Ethical issues

• GEAC (Genetic Engineering Approval Committee): an Indian government body that checks whether GM research is valid and whether GM organisms are safe for public use.

Biopiracy

• Basmati rice: India has 27 documented varieties of Basmati. In 1997, an American company (RiceTec) got a patent on Basmati rice and grain in the USA.
• Turmeric and neem were also patented abroad, even though Indians had used them for centuries.
• India has about 2,00,000 varieties of rice alone.
• India's Parliament passed the second amendment of the Indian Patents Bill to stop this.

30-second revision

• GM crops: stress-tolerant, fewer pesticides, Golden Rice (vitamin A).
• Bt toxin: inactive protoxin → alkaline gut → pores → death. cryIAc/cryIIAb → bollworm; cryIAb → corn borer.
• RNAi: dsRNA silences Meloidogyne incognita mRNA in tobacco.
• Insulin: chains A and B made separately in E. coli (Eli Lilly, 1983).
• Gene therapy: ADA deficiency (1990), lymphocytes + retrovirus.
• Molecular diagnosis: PCR, ELISA, probes. Rosie (1997): human α-lactalbumin.
• GEAC checks GM safety; biopiracy: Basmati, turmeric, neem.

Levels of ecology

Organism (one tiger) → population (all tigers in a forest) → community (all species in the forest) → biome (a large region, e.g. tropical forest).

Organism and its environment

Major abiotic (non-living) factors

How organisms respond to stress

1. Regulate: keep the body constant (homeostasis). Birds and mammals (thermoregulation).
2. Conform: the body changes with the surroundings. 99% of animals and almost all plants.
3. Migrate: move away for a while. Siberian birds visit Keoladeo National Park, Bharatpur.
4. Suspend: slow down and wait. Hibernation (winter), aestivation (summer), diapause (zooplankton), spores and seed dormancy.

Adaptations: cool survival tricks

Populations

A population is a group of individuals of the same species living in an area.

Population attributes

• Birth rate (natality) and death rate (mortality): per capita births and deaths.
• Sex ratio: e.g. 60% females, 40% males.
• Population density (N): how many live in an area. It can be measured by counting, per cent cover, biomass, or indirectly (e.g. tiger pug marks and faecal pellets).

Age pyramids

What changes population size?

• Increase the population: natality (births) and immigration (coming in).
• Decrease the population: mortality (deaths) and emigration (going out).

N(t+1) = Nt + [(B + I) − (D + E)]

Population growth models

• r = intrinsic rate of natural increase. Examples: Norway rat 0.015, flour beetle 0.12; for India's human population in 1981, r = 0.0205.
• K = carrying capacity: the maximum population the environment can support.

Life history variation

• Some species breed only once in their life (Pacific salmon, bamboo). Most breed many times (birds, mammals).
• Some make many small offspring (oysters, pelagic fishes). Others make few large offspring (birds, mammals).

Population interactions

Predation

• Predators control prey populations and keep species diversity high.
• Prickly pear cactus spread wildly in Australia until a cactus-eating moth was brought in to control it.
• When the starfish Pisaster was removed from a coast in America, more than 10 species of invertebrates died out within a year.
• How prey defend themselves:
  • Camouflage: insects and frogs blend in.
  • Poison: the monarch butterfly is distasteful to birds because of chemicals it gets by eating a poisonous weed as a caterpillar.
  • Thorns: Acacia and cactus.
  • Toxic chemicals: Calotropis makes cardiac glycosides, so cattle don't eat it.

Competition

• Gause's Competitive Exclusion Principle: two closely related species competing for the same resource can't live together forever. The weaker one is eliminated.
• Resource partitioning: species avoid competition by sharing differently. MacArthur showed that 5 species of warblers live on the same tree by feeding at different heights and times.

Parasitism: tricky parasites

• Brood parasitism: the cuckoo (koel) lays its eggs in a crow's nest. Its eggs look like the crow's eggs, so the crow raises the cuckoo chicks!
• Ectoparasites live outside the host (lice on humans, ticks on dogs, Cuscuta on plants). Endoparasites live inside (liver fluke, tapeworm).
• The human liver fluke needs two intermediate hosts (a snail and a fish) to complete its life cycle.

Mutualism: best friends

• Fig and wasp: the female wasp pollinates the fig flower while laying eggs in it. The fig feeds the wasp's larvae.
• Ophrys orchid (sexual deceit): one petal looks like a female bee. Male bees try to mate with it and carry pollen to the next flower.

30-second revision

• Eury = wide, steno = narrow tolerance.
• Responses: regulate, conform, migrate, suspend (hibernation, aestivation, diapause).
• Kangaroo rat: internal fat oxidation. Allen's rule: short ears and limbs in the cold.
• Age pyramids: triangle = expanding, bell = stable, urn = declining.
• Exponential = J (dN/dt = rN); logistic = S (dN/dt = rN(K−N)/K), K = carrying capacity.
• Mutualism (+,+), competition (−,−), predation and parasitism (+,−), commensalism (+,0), amensalism (−,0).
• Gause's principle; MacArthur's warblers; Ophrys (sexual deceit); cuckoo (brood parasite).

Structure of an ecosystem

• Biotic (living) components:

  • Producers: green plants
  • Consumers: animals
  • Decomposers: fungi and bacteria

• Abiotic (non-living) components: sunlight, water, soil, temperature and air.

• Stratification: plants grow in vertical layers. In a forest: tall trees (top) → shrubs → herbs and grasses (bottom).

• Ecosystems can be terrestrial (forest, grassland, desert) or aquatic (pond, lake, sea). They can also be man-made, like a crop field or an aquarium.

Productivity: how much food plants make

Yearly NPP (organic matter, dry weight):

Decomposition: nature's recycling

1. Fragmentation: detritivores (earthworms) break detritus into small pieces.
2. Leaching: water-soluble nutrients sink into the soil.
3. Catabolism: bacterial and fungal enzymes break it down chemically.
4. Humification: dark, spongy humus forms (it decays very slowly).
5. Mineralisation: humus slowly releases inorganic nutrients.

Energy flow

• The Sun is the only source of energy for almost all ecosystems (except deep-sea hydrothermal vent ecosystems).
• Less than 50% of sunlight is PAR (photosynthetically active radiation, the light plants can use).
• Plants capture only 2–10% of PAR. But this small amount runs the whole living world!
• Energy flow is one-way (unidirectional): Sun → producers → herbivores → carnivores. It never flows backwards.

The 10% law (Lindeman)

Only about 10% of energy passes to the next level. The rest is lost as heat (respiration) at each step.

Food chains and food webs

• A food web is many food chains linked together, which is more realistic.
• Standing crop = the mass of living material at each level at a given time.

Trophic levels:

1. 1st level: producers
2. 2nd level: primary consumers (herbivores)
3. 3rd level: secondary consumers (carnivores)
4. 4th level: tertiary consumers (top carnivores)

Ecological pyramids

Limitations of ecological pyramids:

• They don't show a species that belongs to 2 or more trophic levels.
• They assume a simple food chain, not a food web.
• They don't include saprophytes (decomposers), even though decomposers are very important.

Ecological succession

• Sere = the whole sequence of communities. Each stage is a seral stage (seral community).

Succession on land (xerarch) vs in water (hydrarch)

• Xerarch (on bare rock): lichens (pioneers; they secrete acids that break the rock) → mosses (bryophytes) → herbs → shrubs → forest (climax).
• Hydrarch (in water): phytoplankton (pioneers) → rooted submerged plants → floating plants → reed swamp → marsh meadow → scrub → forest (climax).

30-second revision

• NPP = GPP − R. Earth's NPP ≈ 170 billion tons; oceans ≈ 55 billion tons.
• Decomposition: fragmentation → leaching → catabolism → humification → mineralisation.
• Only 2–10% of PAR is captured; energy flow is unidirectional; 10% law.
• GFC starts with living plants; DFC with detritus.
• Energy pyramid is always upright. Biomass pyramid is inverted in the sea; number pyramid is inverted for a tree.
• Primary succession: no soil, slow; secondary: soil present, faster.
• Pioneers: lichens (xerarch), phytoplankton (hydrarch). Both end in a mesic climax.

Three levels of biodiversity

The word "biodiversity" was made popular by the biologist Edward Wilson.

• Genetic diversity (variety within a species): Rauwolfia vomitoria in the Himalayas makes different amounts of reserpine; India has more than 50,000 rice and 1,000 mango varieties.
• Species diversity (variety of species): the Western Ghats have more amphibian species than the Eastern Ghats.
• Ecological diversity (variety of ecosystems): India has deserts, rainforests, mangroves, coral reefs, wetlands, estuaries and alpine meadows.

How many species are there?

• IUCN (2004): a little more than 1.5 million species have been described so far.
• Robert May's estimate of the total number of species on Earth: about 7 million.
• More than 70% of all recorded species are animals. Plants (including algae, fungi, bryophytes, gymnosperms and angiosperms) make up no more than 22%.
• Among animals, insects are the biggest group, about 70% of all animals. That means 7 out of every 10 animals are insects!

Patterns of biodiversity

1. Latitudinal gradient: more life near the equator

Diversity decreases as we go from the equator towards the poles.

Why are the tropics so rich?

1. Long, undisturbed history: the tropics were not frozen by ice ages, so species had millions of years to evolve.
2. Stable climate: the tropics are less seasonal and more constant and predictable, so species can specialise.
3. More solar energy: more sunlight → more productivity → more food for more species.

2. Species–area relationship

• Alexander von Humboldt found that as the area increases, the number of species increases, but only up to a limit.

• On a log scale the relationship is a straight line: log S = log C + Z log A

  • S = species richness, A = area, Z = slope (regression coefficient), C = Y-intercept.

• Z is usually 0.1 to 0.2 for small regions, whatever the group or area.

• For very large areas (like whole continents), Z is much steeper: 0.6 to 1.2.

Why is biodiversity important?

Stability of ecosystems

• David Tilman's experiments on outdoor plots: plots with more species had less year-to-year change in total biomass, and higher productivity.

The rivet popper hypothesis

Loss of biodiversity

• The IUCN Red List (2004) records 784 extinctions in the last 500 years, including 338 vertebrates, 359 invertebrates and 87 plants.
• Recent extinctions:
  • Dodo (Mauritius)
  • Quagga (Africa)
  • Thylacine (Australia)
  • Steller's sea cow (Russia)
  • 3 subspecies of tiger (Bali, Javan and Caspian)
• We are now in the sixth mass extinction. It is happening 100 to 1,000 times faster than before humans, and humans are the cause.

What happens when biodiversity is lost?

• Plant production decreases.
• The ecosystem becomes less stable during disturbances like drought.
• Some processes change: water use, pest and disease cycles.

Causes: the "Evil Quartet"

Why should we conserve biodiversity?

How do we conserve biodiversity?

• In-situ (protect it in its natural home): biodiversity hotspots; biosphere reserves, national parks and wildlife sanctuaries; sacred groves.
• Ex-situ (protect it outside its natural home): zoos, botanical gardens and wildlife safari parks; cryopreservation of gametes, seed banks and tissue culture.

In-situ conservation

• Biodiversity hotspots are regions with very high species richness and many endemic species (found nowhere else), which are under threat.
  • There are 34 hotspots in the world.
  • India has 3 hotspots: the Western Ghats and Sri Lanka, Indo-Burma, and the Himalaya.
  • Hotspots cover less than 2% of Earth's land, but protecting them could reduce mass extinctions by up to 30%.
• Protected areas in India: 14 biosphere reserves, 90 national parks and 448 wildlife sanctuaries (as given in NCERT).
• Sacred groves: forests protected by local people for religious and cultural reasons. Some rare plants survive only here.

Ex-situ conservation

• Zoological parks, botanical gardens and wildlife safari parks.
• Cryopreservation: gametes of threatened species are frozen and kept alive for a long time using liquid nitrogen at −196 °C.
• In vitro fertilisation and tissue culture to grow plants in labs.
• Seed banks store seeds of many plant varieties.

International efforts

30-second revision

• 3 levels: genetic, species, ecological (Edward Wilson).
• ~1.5 million described (IUCN 2004); ~7 million estimated (Robert May). Insects are about 70% of animals.
• India: 2.4% of land, 8.1% of species; one of 12 mega-diversity countries.
• Diversity falls from equator to poles (time, stability, energy).
• log S = log C + Z log A; Z = 0.1–0.2 (small areas), 0.6–1.2 (continents).
• Rivet popper (Ehrlich); stability (Tilman).
• Evil Quartet: habitat loss (biggest), over-exploitation, alien species (Nile perch), co-extinctions.
• India's 3 hotspots: Western Ghats–Sri Lanka, Indo-Burma, Himalaya. Earth Summit 1992; WSSD 2002.

Important scientists

Important abbreviations

Numbers you must remember

Top memory tricks

Diagrams to practise

Board exams often ask you to draw and label these. Practise each one from your NCERT textbook at least 3 times:

1. T.S. of an anther and the structure of a pollen grain
2. Embryo sac (7 cells, 8 nuclei)
3. L.S. of a flower showing pollen tube growth
4. Human male and female reproductive systems
5. Sperm and ovum
6. Menstrual cycle hormone graph
7. Seminiferous tubule and Graafian follicle
8. DNA double helix and the replication fork
9. lac operon (with and without lactose)
10. Antibody structure (H₂L₂)
11. pBR322 vector
12. Growth curves (J and S) and age pyramids
13. Ecological pyramids

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