Environmental Issues 

• One of the major environmental problem is pollution
• defined as any undesirable change in physical, chemical or biological characteristics of air, land or water
• Agents bringing out such undesirable change called pollutants

 Air pollution

• Caused mainly due to burning of fossil fuels in industries and automobiles
• Harmful to all living organisms (plants, animals and humans)
• Can be solved by -
• fitting filters in smokestacks and smelters
• using electrostatic precipitators
• using scrubbers to remove gases such as SO2 
• using CNG to reduce vehicular pollution
• fitting catalytic converters to vehicles

 Green house effect

• Natural phenomenon which keeps the earth’s atmosphere warm
• CO₂, methane, etc. known as greenhouse gases
• Absorb the heat of sun and the earth and emit it back to the earth’s surface
• Increased concentration of gases leads to the heating up of the earth’s surface (global warming)
• Cosequences include
  • melting of polar ice caps
  • rise in the sea level
  • ​submerging of the coastal areas

 Ozone depletion

• Ozone found in the stratosphere layer
• Important for protection against UV rays of sun
• Depletion in ozone rsulted in formation of ozone hole
• Caused due to CFCs which react with the ozone moleclues
• Leads to diseases like skin cancer and snow blindness
• Montreal protocol signed to control the emission of CFC's

 Water pollution

• Essential component for the existence of life

 Pollution caused by pollutants like -

• domestic sewage
• industrial effluents
• oil spills
• thermal waste water discharge
• agrochemicals (chemicals used in agriculture like pesticides and fertilisers)

 Effect of pollution

• leads to eutrophication of water bodies
• eutrophication refers to ageing of a water body due to nutrient enrichment of its water
• reduces the oxygen content of water bodies
• results in the loss of indigenous flora and fauna
• another effect includes biomaginification
• toxic substances not metabolised and thus accumulate in the organism
• toxins passed from one trophic level to other

 Can be solved by-

• treating raw sewage with biological and other methods
• denitrifying nitrogen fertilizers with the help of microbes
• practicing organic farming to deal with problems of agrochemicals
• using Integrated wastewater management as practised in Arcata, California

 Solid wastes

• Refers to all the unwanted undesired materials thrown into the dustbin
• Waste could be biodegradable or non-biodegradable
• Waste can be categorised as
  • Municipal solid waste - includes waste from homes, offices, schools, store etc.
  • Hospital waste - wastes generated from hospitals
  • e-wastes - includes irreparable computers and electronic goods

 Can be solved by -

• Segregating waste into biodegradable and non biodegradable
• Reuse and recycling of non biodegradable wastes
• Recycling e-wastes
• Using biodegradable waste for generating compost

 Polyblend, an example of efficient use of plastic waste

• blends of polyblend and bitumen used to lay roads
• increases the life of roads

 Nuclear wastes

• Nuclear energy considered an efficient non-polluting source of energy
• Problem with disposing of the nuclear wastes
• Highly hazardous and can lead to mutations in the genetic structure
• Requires proper and safe disposal 

 Deforestation

• Conversion of forested areas to non-forested ones
• Done for the purpose of 
  • obtaining wood
  • converting forests into agriculual land
  • creating space to accomodate the growing human population
• Chipko movement and Bishnois contributed to the conservation of forests

Molecular Basis of Inheritance

 Structure of DNA

• Long polymer of deoxyribonucleotides
• Length of DNA defined by number of nucleotides present in it

 Structure of polynucleotide chain

• Polynucleotide a combination of several nucleotides
• Nucleotides are made up of three components
  • nitrogen base
    • are of two types -
    • purines - adenine and guanine
    • pyrimidine - thymine, cytosine and uracil
  • pentose sugar
  • phosphate group
• Two nucleotides joined together by phosphodiester bond
• Two polynucleotide chain form one DNA molecule
• Both strands of DNA are anti parallel and complimentory

 Packaging of DNA helix

• Prokaryotes - 
  • DNA held in a region called nucleoid by some proteins.
• Eukaryotes -
  • DNA wrapped around positively charged proteins (histones)
  • Forms a structure called nucleosome

 Search for genetic material
Transforming principle carried out by Frederick Griffith
Avery, MacLeod and McCarty worked to show that tranforming principle was DNA
Experiment by Hershey and Chase proved DNA is the genetic material

 Replication

• Process of producing two identical replicas of DNA from original DNA
• DNA replicates in semiconservatibe mode
• Experimentally proved by Meselson and Stahl
• Replication occurs in S phase of cell cycle
• Enzyme involved - DNA polymerase (DNA dependent DNA polymerase)
• Energy required for replication provided by dNTPs
  • dNTPs have dual purpose − Act as substrates and provide energy also
• Replication initiates at specific regions in DNA called origin of replication
• Continuous replication occurs on one strand whereas discontinuous replication on the other strand

 Transcription

• Process of copying genetic information from one strand of DNA into RNA
• Transcription unit has components -
  • promoter
  • structural gene
  • terminator
• Promoter and terminator flank the structural gene
• Strand with 3' to 5' polarity called template strand
• Strand with 5' to 3' polarity called coding strand
• Transcription occurs in three steps
  • Initiation
  • Elongation
  • Termination

 Genetic Code

• Directs the sequence of amino acids during synthesis of proteins
• Salient features of genetic code:
  • Codon is triplet
  • Codons are unambiguous
  • Codons are degenerate 
  • Genetic code is universal
  • Codons are read continuous
  • AUG has dual functions − Codes for Methionine and acts as a start codon

 Mutation

• Alteration of DNA sequence
• Results in change in genotype and phenotype of organisms
  • include insertions, deletions, and rearrangements
• Insertion or deletion of single base pair disturbs entire reading frame in mRNA
• Such mutations called frameshift mutations

 Translation

• Refers to the process of polymerisation of amino acids to form a polypeptide
• Main role played by tRNA and ribosomes
• Ribosomes have two sub-units
• Translational unit has components -
  • start codon
  • stop codon
  • mRNA
• mRNA has Untranslated Regions (UTR's) which are not translated
• Translation includes steps -
  • Initiation
  • Elongation
  • Termination

 Gene Regulation

• Gene regulation can occur at different levels -
  • Transcriptional level (formation of primary transcripts)
  • Processing level (splicing)
  • Transport of mRNA from nucleus to cytoplasm
  • Translational level
• Regulation can also occur by metabolic, physiological, or environmental conditions 

 Human Genome Project

• Joint venture of US Department of Energy and National Institute of Health (NIH); later joined by Welcome Trust (UK)
• Launched in 1990, completed in 2003
• Aimed towards determination of complete DNA sequence of humans
• Two methods used to identify genes
  • ESTs
  • Annotation 
• Various features observed based on the above project on human genomes

 DNA Fingerprinting

• A method for comparing the DNA sequences of any two individuals
• Specific regions called repetitive DNA sequences used for comparative study.
• Repetitive DNA separated from bulk genomic DNA since it appears as a distinct peak during density gradient centrifugation.
• Technique initially designed by Alec Jeffreys
• Used satellite DNA as probe
• Methodology
  • isolation and treatment with restriction endonucleases
  • separation by gel elecetrophoresis
  • hybridisation with a n VNTR probe
  • detection by radioautography

Applications of DNA Fingerprinting

• widely used in forensics 
• forms the basis of paternity testing 
• used for studying genetic diversity in a population and evolution

 

Evolution

 Origin of life

• Origin of life on earth is explained by Big Bang Theory
• States that a huge explosion followed by a series events resulted in the formation of galaxies
• Believed that earth was formed 4.5 millions years ago
• Theories of evolution:
  • Panspermia: believed by Greeks that units of life brought to earth and other planets from outside
  • Theory of Spontaneous generation: Stated that life could originate from decaying and rotting matter
  • Theory rejected by Louis Pasteur
• Experiment performed by Louis Pasteur to show life comes from pre-exiting life
• Theory of Spontaneous generation rejected by Louis Pasteur
• Oparin and Haldane proposed that first forms of life originated from pre-existing non-living organic molecules
• He also stated that formation of life preceded by chemical evolution
• Miller demonstrated an experiment to prove Oparin and Haldanes theory

 Adaptive radiation

• Process of evolution starting from a single point and radiating in different directions 
• Example: evolution of the Australian marsupials from a single ancestor

 Evidences of evolution

• Fossils: Represent plants and animals that lived millions of years ago and are now extinct. 

• Comparative anatomy and morphology: Shows evidences of the similarities and differences between living forms of present day and that of prehistoric times.
  Some examples of comparative anatomy and morphology -

• Homologous organs
• Analogous organs
• Adaptive melanism

 Biological evolution

• Darwin's theory of evolution based on natural selecton and branching descent
  • nautal selection - natures choses the fittest of organims to survive
• Lamark's theory of evolution
  • Proposed that evolution occurred due to use and disuse of organs

 Mechnaism of evolution

• Hugo deVries gave the idea of mutations
• Worked on evening primrose
• Stated that evolution was a result of mutations and not minor changes
• Believed mutations caused specaiton and gave the term saltation

 Hardy-Weinberg Equillibrium

• States that the allele frequency in a population is stable and is constant from generation to generation unless disturbances such as mutations, non-random mating etc. are introduced
• Hardy-Weinberg equation is expressed as:
  • p² + 2pq + q² = 1
  • p = frequency of the "A" allele
  • q = frequency of the "a" allele in the population
• Hardy-Weinberg equation used to measure whether the observed genotype frequencies in a population differ from the frequencies predicted by the equation
• Any difference in the frequencies indicates the extent of evolutionary change
• Factors which affect Hardy Weinberg equillibrium
  • Gene flow or gene migration
  • Genetic drift (changes occurring by chance)
  • Mutation
  • Genetic recombination
  • Natural selection
• Genetic drift leads to founder effect

 A brief account of evolution

• First forms of life appeared almost 2000 million years ago on earth
• Invertebrates formed around 500 mya
• Around 320 mya sea weeds and plants evoloved and existed
• Coelocanth a lobed fish found in South Afirca 
• considered to be the first organisms which evolved into amphibious organism
• Biggest land reptiles are dinosaurs
• Largest dinosaur - Tyranasaurus rex
• Mass extinction of dinosaurs
• Evolution of mammals begins

 Origin and evolution of man
 

Year	Evolution
15 million years ago	Dryopithecus (ape-like) and Ramapithecus (man-like)
3 − 4 million years ago	Man-like primates
2 million years ago	Australopithecus, also called Homo habilis
1.5 million years ago	Homo erectus
1,000 − 40, 000 years ago	Neanderthal man
75, 000 − 10, 000 years ago	Homo sapiens

Principles of Inheritance and Variation

 Mendel’s work

• Proposed that heredity controlled by genes
• Performed experiments on garden peas (Pisum sativum)
• Used seven contrasting pairs of characters or traits
• Divided traits into two categories

• Homozygous: when the factors or genes of a trait are similar e.g.,TT or tt
• Heterozygous: when the factors or genes of a trait are different e.g., Tt
• ​Performed two types of crosses -
  • Monohybrid cross: involves only one pair of contrasting characters
  • Dihybrid cross: involves two pairs of contrasting characters

• Law of dominance 
• Law of segregation

• Incomplete dominance - shown by Antirrhinum
• Co-dominance - shown in case of blood groups in humans

• Considered two different characters simultnoeusly
• Gave the Law of independant Assortment

• Sutton and Boveri gave the Chromosomal Theory of Inheritance
• Experimental verification of the theory given by Thomas Hunt Morgan
• Used Drosophila melanohaster to work on
• Morgan gave the concept of linkage and recombination

 Sex determination

• Two types of chromosomes exist in animals
  • autosomes -  chromosomes other than sex chromosomes
  • sex chromosomes - chromosomes involved in determination of sex
• Different types of sex determination occur in different organisms
• XO type - insects like Grasshopper
• XY type - in humans
• ZW type - in some brids

 Mutation 

• Refers to a phenomenon which results in changes in alteration of DNA sequences
• Leads to changes in genotype and phenotype of an organism
• Change in single base pair of DNA called point mutation
• Substances which induce mutations are called mutagens

 Genetic disorders
Are of two types -
 Mendelian disorders

• Characterized by mutation in a single gene
• Mode of inheritance follows the principles of Mendelian genetics​​​
• ​Examples of Mendelian disorders include
  • Haemophilia
  • Sickle cell anaemia
  • Phenylketonuria

• Caused due to
• absence or excess of one or more chromosomes
• abnormal arrangement of one or more chromosomes
• Examples of chromosomal disorders
  • Down's Syndrome
  • Klinefelter's Syndrome
  • Turner's Syndrome
     

Ecosystem

• Consists of community of organisms and their physical environment
• Mainly of two types -
  • Terrestrial
  • Aquatic 

 Different components of ecosystem include

• Productivity
• Decomposition
• Energy Flow 
• Nutrient cycling

 Productivity

• Productivity - rate of production of biomass at any trophic level at any given interval of time
• Primary productivity - amount of biomass produced per unit area in a certain time period by plants through photosynthesis
• Gross productivity - rate of production of organic matter by green plants per unit time per unit area
• Net primary productivity - difference between gross primary productivity and the loss due to respiration 
• Secondary productivity - rate of formation of organic matter by consumers

 Decomposition

• Process of breakdown of organic matter into inorganic substances
• Dead remains of plants and animals known as detritus
• Steps of decomposition include
• Fragmentation
• Leaching
• Catabolism
• Humification
• Mineralisation

 Energy Flow

• Refers to the flow of energy through different trophic levels
• Plants called producers as they produce food
• Animals depend on plants for food so called consumers
• Food chain represents a linear sequence of organisms through which nutrients are passed from one generation to another
• Plants are known as producers
• Animals which feed on plants called primary consumers
• Animals which feed on primary consumers called secondary consumers
• Each animal occupies one trophic level
• Energy transferred according to 10% energy law of energy transfer

 Ecological pyramids

• Ecological pyramids classified as -
  • Pyramid of energy
  • Pyramid of number
  • Pyramid of biomass 
• Pyramids are always in upright position for all ecosystems
• Pyramid of biomass can be inverted in some ecosystems

 Nutrient Cycling

• Also known as biogeochemical cycles
• Refers to the movement of nutrients through different components of the ecosystem
• Nutrient cycles are of two types -
• Gaseous - examples, nitrogen and carbon cycle
• Sedimentary - examples, sulphur and phosphorous cycle

 Ecological succession

• Term used to define the gradual and predictable change in the species composition of an area
• Entire sequence of communities that change successively in a given area called sere.
• Final community which emerges after the changes and is in equillibrium with the environment called climax community
• Species which invade a bare area called pioneer species
• Succession is of two types -
  • Primary - succession starts in an area where no living organisms existed
  • Secondary - succession starts in an area which lost all its living organisms
• Succession shown by plants can be of two types
• Hydrarch - takes place in wetter areas and progresses from hydric to mesic conditions
• Xerarch - takes place in dry areas and progresses from xeric to mesic conditions

 Ecosystem Services

• Refers to the products obtained from biological processes
• Examples of ecoystem services provided by a healthy forest ecosystem
  • purify air and water
  • cycle nutrients
  • provide wildlife habitat etc.

Strategies for Enhancement in Food Production

 Animal husbandry

• Refers to the agricultural practice of breeding and raising livestock

  Includes two components -
  Management of farms and farm animals

• Includes management of dairy farm animals and poultry  
• Focus on
  • maintaining clean and hygeinic environment
  • proper food and adequate amount of water
  • regular visits to vet

 Animal breeding

• aims at increasing the yield of animals and increasing the quality of products
• inbreeding refers to breeding carried out between animals of the same breed
• outbreeding refers to breeding carried out between animals of different breeds
• Continued inbreeding leads to inbreeding depression
• Out crossing refers to mating animals of the same breed 
  • but should not have any common ancestors for 5-6 genrations on both the sides
• Cross breeding- Superior males of one breed mated with superior females of other breed
• MOET (Multiple Embryo transfer technology) a technique used for herd improvement

  Bee-keeping

• refers to maintanince of bees and their hives for the production of honey
• most commonly used species include Apis indica

  Fisheries

• Deals with catching, processing or selling of fish and other aquatic organisms
• Important source of income

  Plant Breeding

• refers to manipulation of plant species to create desired plant types
• Steps involved in breeding -
  • collection of variablity
  • Evaluation and selection of parents
  • Cross hybridisation among selected parents
  • Selecting and testing of superior recombinants
  • testing, release and commercialisation of new cultivars
• Sonalika and Kalyan - high yielding varities of wheat
• Himgiri - disease resistant variety of wheat
• Pusa Gaurav - insect resistant variety of Brassica
• Biofortification - breeding crops with higher levels of vitamins and minerals, proteins or healthier fats
  • Example is Atlas 66, a wheat variety with higher protein content

 Single Cell protein

• Microbes which can be grown on industrial scale as proetin source
• Advantages -
  • easily grown on wastes such as molasses
  • rich sources of proteins, fats, carbohydrates
  • higher rate of biomass production and growth

 Tissue culture

• culturing plants from tissues
• plant parts which used to generate a new plant called explant
• capacity to generate a whole plant from an explant called totipotency
• technique used to produce several copies of plants through tissue culture called micropropogation
• technique can also be used to obtain virus free plants
• Somatic hybridisation techniques used to produce hybrids (somatic)
• Produced by fusion of protoplasts from two plants of different variety 

Human Health and Disease

   Diseases

• Can be broadly categorised as 
• Infectious - can be transmitted from one person to other
• Non infectious - not transmitted from one person to other
• Disease causing organisms called pathogens
• Some common infectious diseases -
  • Bacterial diseases -Typhoid, pneumonia
  • Viral diseases - Common cold
  • Protozoan diseases - Malaria and Amoebiasis
  • Fungal diseases - Ringworms
  • Diseases caused by worms - Ascariasis and Elephantiasis

  Immunity

• Refers to the ability of a host to defend itself from foreign antigens

 Two types of immunity
  Innate immunity - present at the time of birth

• Consists of 4 types of barriers -
  • Physical barriers
  • Physiological barriers
  • Cellular barriers
  • Cytokine barriers

 Acquired immunity - pathogen specific and characterised by memory

• Mediators of acquired immunity include
  • B lymphocytes and T lymphocytes
  • B lymphocytes produce proteins called antibodies
  • T lymphocytes do not produce antibodies but help B lymphocytes to do so
• Antibodies made up of two heavy and two light chains
• Immunity can also be categorised as active and passive
• Active immunity - immunity provided by antibodies produced by the host on encountering a foreign antigen
• Passive immunity - immunity provided by ready made antibodies that are directly injected into the host
  • Used in cases where quick immune response required

 Allergies

• Exaggerated response of the immune system to certain antigens
• Substances producing such responses called allergens
• IgE antibody mediates allergic responses

 Immune system

• Includes lymphoid organs, tissues, cells and antibodies
• Lymphoid organs - sites of origin and maturation of lymphocytes
• Are of two types -
  • Primary lymphoid organs - site where immature differenciate into antigen-sensitive lymphocytes
  • Secondary lymphoid organs - site of interaction of lymphocytes with antigen

 AIDS

• Caused by HIV retro virus
• HIV has RNA genome
• Transmitted by -
  • sexual contact with affected person
  • transfusion of conatimnated blood blood products
  • sharing infected needles
  • from mother to child
• HIV affects the helper T lymphocytes
• Can be detected using ELISA
• Can be prevented by creating awareness about the disease

 Cancer

• Refers to a condition where abnormal cells divide in an uncontrollable manner
• Cancerous loose their ability of contact inhibition
• Cancerous cells give rise to tumors
• Tumors are of two types -
  • Benign - remain confined to one region and do not spread to other parts of the body
  • Malignant - can spread to the different parts of the body
  • Malignant tumors show metastasis
• Causes -
  • due to biological, chemical physical carcinogens
  • oncogenic viruses
  • activation of proto oncogenes
• Can be detected by biopsy, histopathological studies, MRI, radiography, CT
• Treatment includes -
  • surgery, radiation therapy and immunotherapy

 Drugs and Alcohol Abuse

• Commonly abused drugs include opiods, cannabinoids and coca alkaloids
  • Opioids obtained from latex of Papaver somniferum plant
  • Cannibinoids obtained from inflorescence of Cannabis sativa
  • Coca alkaloid/cocaine obtained from Erythroxylum coca plant
• Other drugs like barbiturates, amphetamines etc have medical importance
• Use of these drugs other than medical puropses constitutes drug abuse
• Drug abuse severely affects the health of an individual
• Affects the  physical, psychological, emotional and social health
• Alcohol abuse also a major concern

Biotechnology: Principles and Processes

 Biotechnology 

• refers to the techniques of using live organisms or enzymes from organisms to produce products and processes
• two things which enabled the growth of modern technology
  • genetic engineering
  • maintaining aseptic environment

 Tools of recombinant DNA technology

 Restriction enzymes

• Cut DNA at specific position
• Are of two types -
• Endonucleases - cut at a specific position within the DNA sequence
• Exonucleases - remove nucleotides from the ends of the DNA
• ​Restriction enzymes produce two types of cuts -
• Blunt ends 
• Sticky ends 
• Fragments of DNA separated by gel electrophoresis
• Separated on the basis of size of fragments on agarose gel

 Cloning vectors

• Features important in vectors -
• origin of replication - sequence from where replication begins
• selectable marker - helps in selection of transformed and non-transformed cells
• cloning sites - sites recognised by restriction enzymes which help in cloning

 Competent host

• Cells made compotent (prepared) to take up the recombinant DNA
• Techniques used to introduce recombinant DNA into cells -
• treatment with calcium chloride
• micro injection
• biolistics/gene gun

Processes of recombinant DNA technology

 Isolation of genetic material

• Genetic material (DNA) isolated and purified using enzymes

  Cutting of DNA

• DNA cut at specific positions using restriction enzymes
• Cut DNA ligated to the vector by ligase enzyme

  Amplification of gene of interest

• Refers to the process of generating copies of genes of interest
• Done by using PCR
• PCR involves three steps - denaturation, annealing and extension
• Enzyme dependent process 

  Insertion of recombinant DNA into the host cell

• Host cell made compotent to take up the recombinant DNA
• Transformed cells selected with the help of selectable marker

  Obtaining foreign gene product - 

• Cells producing the recombinant protein are cultured
• Cultured in continuous culture system

 Downstream processing -

• Refers to steps of processes for obtaining the final product

Reproduction in Organisms

 Reproduction
Process of giving rise to young ones which are similar to the organism

  Asexual reproduction -

• Requires only a single parent
• Occurs by various methods like - binary fission, multiple fission, budding
• Common asexual reproductive structures are - zoospores, conidia, buds, gemmules
• In plants asexual reproduction termed as vegetative reproduction/vegetative propogation
• Vegetative propogation occurs with the help of structures called vegetative propogules
• Examples are rhizome, runner, sucker, tubers, offsets and bulbs

  Sexual reproduction -

• Involves formation of male and female gametes 
• Gametes produced by the same individual or different individuals of opposite sex

Events in sexual reproduction divided into 3 phases -

 Pre-fertilization events
Refers to events of sexual reproduction prior to fusion of gametes

 Gametogenesis -

• Process of formation of gametes
• Gametes are always haploid
• Can be of two types -
• homogametes - male and female gametes have similar appearances
• heterogametes - male and female gametes are morphologically distinct
• Fungi and plants may be categorised as -
• Homothallic/monoecious - both male and female sex organs present in the same individual
• Heterothallic/dioecious -  male and female sex organs present in different individuals
• Animals with bisexual condition known as hermaphrodites.

 Gamete transfer - 

• Male and female gametes need to be brought physically together
• Requires a medium such as water
• In seed plants, pollen grains act as carriers of male gametes
• Transfer of pollen grains from anther to stigma of a flower known as pollination

  Fertilisation - 
Process of fusion of male and female gametes

• Results in the formation of a zygote
• Can be of two types -
• External fertilisation - fusion of male and female gamete occurs outside the body of the organism
• Internal fertilisation - fusion of male and female gamete occurs inside the body of the organism

 Post fertilization event
Refers to the events in sexual reproduction after the formation of zygote

 Zygote

• Vital link which ensures continuity of species from one generation to another
• Zygote may be formed externally or internally

 Embryogenesis

• Process of development of embryo from zygote
• Zygote undergoes cell division and cell differentiation
• On the basis of development of zygote, organisms may be classified as -
• Oviparous - development of zygote takes place outside the body
• Viviparous - development of zygote takes place inside the body
• Zygote formed inside the ovule in plants
• Zygote develops into embryo
• Ovules develop into seeds
• Ovary develops into fruits

Biodiversity and Conservation

• Biodiversity - According to Edward Wilson, biodiversity described as the combined diversity at all levels of biological organisation.
• Importance of biodiversity explained by Paul Ehrlich using 'Rivet popper hypothesis'

 Biological diversity classified as - 

• Genetic diversity - refers to diversity at genetic level
• Species diversity - refers to diversity at species level
• Ecological diversity - refers to diversity at ecosystem level

 Causes of biodiversity losses

• Habitat loss and fragmentation
• Over-exploitation
• Alien speceis invasion
• Co-extinctions

 Reasons to conserve biodiversity -

• Narrow utilitarian - states that biodiversity should be conserved as humans drive innumerable benefits from it
• Broadly utilitarian - states that biodiversity should be conserved as it has a major role in any ecosystem services that nature provides
• Ethical utilitarian - states that biodiversity should be conserved as the planet belongs to them as much as it belongs to us

 Methods of biodiversity conservation

 In-situ conservation -

• Threatened/endangered species protected in their natural environment
• Examples include biosphere reserves, wildlife sanctuaries, and national parks 
• Biodiversity hotspots - regions with very high levels of species richness

 Ex-situ conservation -

• Threatened species of plants and animals taken out of their habitats and kept in special settings
• Examples inlcude zoological parks, wildlife parks, botanical garden

Organisms and Population

• Organisms survive in an environment
• Environment is composed of biotic and abiotic factors
• Abiotic factors include -
  • temperature
  • water
  • light
  • soil

Responses to abiotic factors

• Organisms undertake various strategies to regulate the responses to abiotic factors -
• Regulate 
• Conform 
• Migrate
• Suspend

Adaptations

• Attributes which allow organisms to survive and reproduce in a habitat
• Example - Opuntia
• sunken stomata, leaves reduced to spine
• Mammals in colder climates have shorter ears and limbs to minimise heat loss (Allen's rule)

 Populations

 Population attributes

• Attributes which define a population are 
• birth rate
• death rate
• Age pyramid - plot representing the age distribution in a population
• Age pyramids can be expanding, stable or declining

 Population growth

• Factors which affect population density
  • Natality 
  • Mortality
  • Immigration
  • Emigration

 Growth models -
Exponential growth - type of growth shown by organisms when the resources are unlimited
Logistic growth - type of growth shown by organisms when the resources are limited or finite leading to competition between individuals and survival of the fittest
more realistic type of model



 Population Interactions

• Predation-
• One species is benefitted while the other is harmed
• One species acts as predator while the other acts as prey
• Predator benefits while prey is harmed
• Predators act as conduits of energy
• Keep the prey population in check
• Competition-
• Occurs when related or unrelated species compete for the same resources
• Both species are harmed
• Gause's 'Competitive Exclusion Principle' - states that two closely related species cannot co-exist indefinitely and the competitively inferior one will be eliminated eventually
• Parasitism -
• One species is benefitted while the other is harmed
• parasites harm the host
• Parasites characterised as -
  • ectoparasites - live outside the host
  • endoparasites - live inside the host
• Special type of parasitism in birds -
  • brood parasitism - parasitic bird lays egg in the nest of the host and allows the host to incubate them
  • reduces the chances of detection of foreign eggs by the host
• Commensalism -
• One species is benefitted while the other is neither harmed nor benefitted
• example - clown fish living in the tentacles of sea anemone 
  • clown fish gets from its predators but sea anemone has no benefit
• Mutualism
• Both the species are benefited
• Example - lichens (algae + fungi), mycorrhizae (fungi + roots of higher plants)
• Ophrys shows sexual deceit to get pollinated

 Microbes in Human Welfare

• Various applications of microbes include

 Microbes in household products -

• Lactic acid bacteria (LAB) - production of curd
• Saccharomyces cereviciae - production of alcohol and breads
• Propionibacterium shermanii - production of Swiss cheese

 Microbes in Industrial Products -

 Fermented beverages -

• Saccharomyces cerevisiae - used in production of alcohol, whiskey, rum etc.

 Antibiotics-

• Penicillium notatum - used to produce penicillin (first antibiotic)

 Chemicals, enzymes etc. -

• Aspergillus niger - used in the production of citric acid
• Acetobacter aceti - used in the production of acetic acid
• Clostridium butyricum - used in the prouction of lactic acid
• Lipases - enzymes used in detergents formulations
• Pectinases - used in clearing of bottled juices
• Streptokinase (produced by Streptococcus) - used as  clot buster

  Microbes in sewage treatment -

• Play an important role in treatment of sewage
• Aerobic microbes used during secondary treatment
• Used in anerobic sludge digestors

  Microbes in production of biogas -

• Methanogens - bacteria which produce methane gas along with CO₂ and H₂
• Found in rumen of cattle and anerobic sludge
• Cattle dung rich in methanogens and hence used in the production of biogas

  Microbes as bioconrol agents -

• Microbes can be used for biological control of pests and diseases
• Genes from Bacillus thuringienses used to develop Bt-cotton
• Bt-cotton resistant to insects (lepideptoreans and dipterians)
• Fungus Trichoderma effective against various other plant pathogens
• Baculoviruses effective against various pathogens

  Microbes as biofertilisers -

• Biofertilisers refer to the organisms which enrich the nutrient quality of the soil
• Rhizobium - fixes nitrogen for leguminous plants
• Cyanobacteria - fixes nitrogen in paddy fields
• Other examples include Anabena and Azotobacter 

Biotechnology and Its Applications

• Has applications in agriculture, medicine, animal breeding, waste treatment, bioremediation etc.
• Genetically Modified Organisms - organisms whose genes have been altered by manipulation 
• Advantages of GMO -
• tolerant to abiotic stresses
• reduced post harvest losses
• increased efficiency of mineral usage
• enhanced nutritional value

  Agriculture -

 Insect resistant plants

• Example: Bt cotton
• Gene from bacterium Bacillus thuringiensis inserted into the cotton plant
• Gene produces a toxin which kills insects like lepidopterans and dipterans
• Toxin produced in inactive form which gets activated by the alkaline pH in the gut of the insect
• Toxin coded by the cry gene

 Pest resistant plants

• Provides resistance to plants against pests like Meloidegyne incognita
• Technique used is RNA interference
• Specific mRNA is silenced (prevents translation) due to a complimentory dsRNA
• Suppresses the translation of the target RNA

  Medicine

 Genetically engineered insulin

• Hormone which controls the blood glucose levels
• First synthesized by the company Eli lily
• Gene coding for the two chains of insulin introduced into E. coli
• Both chains produced separately, extracted 
• Chains combined by disulphide bonds to finally form the human insulin

 Gene therapy

• First gene therapy given for adenosine deaminase deficiency
• Adenosine deaminase enzyme important for the functioning of the immune system
• Other techniques do exist but are not completely curative 
• In gene therapy -
• functional ADA cDNA added to the lymphocytes
• lymphocytes returned to the patients
• Periodic infusion required as the cells are immortal

 Molecular diagnosis

• Many biotechnological techniques used in the detection of pathogens
• Techniques include PCR, ELISA etc.
• Help in early diagnosis (even before the symptoms appear)

 Transgenic animals

• Refers to animals whose DNA has been manipulated
• Transgenic animals used for the purpose of
• studying normal physiology and development
• studing diseases
• biological products
• vaccine safety
• chemical safety testing

Reproductive Health

• Refers to total well being in all aspects of reproduction
• Tests designed to determine the sex of the foetus based on chromosomal pattern

 Methods of contraception classified as

 Natural methods 

• Periodic abstinence - avoiding coitus from 10-17 day of the menstrual cycle (period when ovulation is expected)
• Coitus interruptus - withdrawing penis from the vagina before ejaculation
• Lactational amenorrhea - based on the fact that ovulation does not occur till the mother breastfeed the child fully

 Barrier methods

• Condoms - used by males to cover the penis
• Cervical caps, vaults and diaphragms - barriers used by females
• Intra uterine devices (IUD's) - inserted into uterus through vagina by doctors or nurses
  • Includes Cu-T, Lippes loop etc.

 Drugs

• Administration of drugs orally by females
• Combination of progesteron or estrogen-progesteron
• Used as pills

 Surgical methods

• Vasectomy - In male, small part of vas deferens removed or tied up through a small incision
• Tubectomy - In females, small part of fallopian tube removed or tied up through a small incision

  Medical Termination of Pregnancy (MTP) -

• Refers to intentional/voluntary termination of pregnancy before full term
• Considered safe upto first trimester/12 weeks

  Sexually Transmitted Diseases (STD's) -

• Also called veneral diseases, reproductive tract infections
• Infections/diseases which spread through sexual intercourse
• Can also be spread through other means (sharing of needles, blood transfusion etc.)
• Includes diseases like AIDS, hepaptitis-B, genital warts, gonorrhea, syphilis etc

  Infertility

• Refers to the inability of an individual to reproduce naturally
• Can be treated by ART's (Assisted Reproductive Technologies)

  ART's include -

• In vitro fertilisation (IVF) - fertilisation occurs outside the body followed by embryo transfer
  • Zygote intro Fallopian Transfer (ZIFT) - transfer of zygote or embryo (upto 8 blastomere) in the fallopian tube
  • Intra Uterine Transfer (IUT) -transfer of embryo (more than 8 blastomeres) in the uterus
• Gamete Intra Fallopian Transfer(GIFT) - transfer of ovum from a healthy donor to the fallopian tube of another female who cannot produce the ovum but can provide a suitable environment for fertilisation
• Intra Cytoplasmic Sperm Injection (ICSI) - under in vitro conditions, sperm is directly injected into the ovum
• Artificial Insemination (AI) - semen collected either from the husband or a healthy donor injected into the vagina/ uterus of a female (Intra Uterine Insemination)

Human Reproduction

• Human reproductive system divided into male and female reproductive system

 Male reproductive system

 Includes - testes, accessory glands and external genitalia

  Testes

• Situated in within a pouch called scrotum
• Each testes divided into compartments called testicular lobules
• each  testicular lobular has one to three semniferous tubules
• Semniferous tubules lined with two thypes of cells -
• male germ cells (spermatogonia)- eventually form the sperms
• Sertoli cells - provide nutrition to germ cells
• Interstitial spaces outside semeniferous tubules contain Leydig cells
• Secrete male hormones called androgens

  Male sex accessory ducts include -

• rete testes, vasa efferentia, epididymis and vas deferens
• Play role in transporting sperms from testes to outside through urtehra

  Male accessory glands include -

• paired seminal vesicles, prostate and paired bulborethral gland
• Secretions constitute seminal plasma rich in fructose, calcium and certain enzymes
• Help in lubrication of the penis

 Female Reproductive System

 Consists of pair of ovaries, oviducts, uterus, cervix, vagina and external genitalia

 Ovaries

• Primary female sex organs
• produce female gametes called ovum
• Covered by an epithelium which encloses the ovarian stroma
• Female accessory ducts include - oviducts, uterus, vagina

  Female external genitalia include -

• mons pubis, labia majora, labia minora, hymen and clitoris
• Mammary glands characteristics of females

 Gametogenesis

• Process of formation of male and female gametes
• Process of gamete formation in males called spermatogenesis
• ​Process of gamete formation in females called oogenesis

 Spermatogenesis

• Process of formation of sperms from immature germ cells/spermatogonia

• Sperm composed of neck, middle piece and tail

 Oogenesis

• Process of formation of mature female gamete

 Menstrual Cycle

• Reproductive cycle in female primates
• Begins at puberty and ends at menarche
• Cycle begins with mensuration and known as menstrual phase
• Followed by follicular phase
  • development of follicles
  • hormones involved LH and FSH
  • finally rupture of Graffian follicle and release of ovum
• Followed by luteal phase
  • Grafian follicle transforms into corpus luteum
  • corpus luteum secretes proesterone
  • required to maintain pregnancy
• In absence of pregnancy, corpus luteum dgenerates
• New menstrual cycle starts again

 Fertilisation and Implantation

• Fertitilisation refers to the process of fusion of male and female gametes
• Occurs in the ampullary region in females
• Sperm comes in contact with the ovum
• Induces certain changes to block entry of other sperms
• Haploid nucleus of sperm fuses with haploid ovum
• Results in the formation of a zygote
• Zygote starts undergoing mitotic division and move from oviduct to the uterus
• Zygote divides and forms 2,4,8,16 daughter cells called blastomeres
• Embryo with 8-16 blastomeres called morula
• Morula divided to form blastocyst
• Blastocycts implanted in the uterus, a process called implantation

 Pregnancy and Embryonic Development

• Structural and Functional unit between mother and embryo called placenta
  • Roles -
  • facilitates supply of oxygen and nutrients to placenta
  • removal of carbon dioxide and excretory wastes produced by embryo
  • also acts as an endocrine tissue
  • produces hormones like hCG, hPL, estrogens etc.
• Further development of foetus occurs
• Human pregnancy lasts for 9 months

 Parturition and lactation

• Expulsion of the baby due to vigoruos contractions of the uterus referred to as parturition
• Parturition a result of foetal ejection reflex
• At end of pregnancy, mammary glands start producing milk
  • a process referred to as lactation

 Sexual Reproduction in Flowering Plants

 Pre-fertilisation

Reproductive structures in flowers

• Male reproductive structures known as androceium
• Female reproductive structures known as gynoceium

 Androceium -

• Consists of stamen, filament and anther
• Anther-
• Bilobed and dithecous
• Four sided consisting of 4 microsporangia present at the two corners
• Microsporangia develops into pollen sacs and microspores develope into pollen grains
• Process of formation of microspores known as microsporogenesis
• Pollen grains covered with two layers - exine and intine
• Contain two types of cells - vegetative and generative cell

 Gynoceium

• Consists of stigma, style and ovary
• Ovules are found in the ovary and called megasporangia
• Process of formation of megaspores from megaspore mother cells known as megasporogenesis

 Pollination

• Transfer of pollen grains from the anther to the stigma
• Different types of pollination -
• Autogamy - transfer of pollen grains from anther to the stigma of the same flower
• Geitonogamy - transfer of pollen grains from the anther to stigma of another flower of the same plant
• Xeinogamy - trasfer of pollen grains from the anther to the stigma of a different flower
• Pollination occurs with the help of pollinating agents - water, wind, insects, animals
• Plants prevent self pollination by developing outbreeding devices
• Artificial hybridization an important procedure in plant breeding
• Involves two major steps - emasculation and bagging

 Double fertilisation

• Two fertilisation occurs at the same time
• One male gamete fuses with the egg cell
• Other male gamete fuses with the two polar nuclei

 Post fertilisation 

  Seed

• Final product of sexual reproduction 
• Formed from ovules
• Consists of seed coat, cotyledons and embryo
• Can be of two types
• Albuminous - have residual endosperm
• Non albuminous - have no residual endosperm

  Fruits develop from ovaries

• Can be of two types - 
• False fruits - thalamus contributes to fruit formation
• True fruits - develop only from ovary
• Fruits which develop wihtout fertilisation called parthenocarpic fruit
• Mechanism of producing seeds without fertilisation termed as apomixis
• Occurance of more than one embryo termed as polyembryony