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Concept of Life Sciences. Part I and 2

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 Contents
Preface ....................................................................................................................... xxxiii

UNIT-1: MOLECULES AND THEIR INTERACTION RELAVENT TO

BIOLOGY ...................................................................................... 1-152
1. STRUCTURE OF ATOMS, MOLECULES AND CHEMICAL BONDS ................................... 3
I. STRUCTURE OF ATOM ..................................................................................................... 3
1. Subatomic Particles ...................................................................................................... 4
(a) Discovery of Electrons ......................................................................................... 4
(b) Discovery of Protons ........................................................................................... 6
(c) Discovery of Neutrons ......................................................................................... 8
2. Atomic Models ............................................................................................................ 8
(a) Thomson Model ................................................................................................... 8
(b) Rutherford’s Model .............................................................................................. 9
(c) Bohr’s Model ...................................................................................................... 10
3. Atomic Number and Mass Number ........................................................................... 13
4. Concept of Valency .................................................................................................... 14
5. Isobars and Isotopes ................................................................................................. 14
II. STRUCTURE OF MOLECULES ........................................................................................ 15
1. Molecular Shapes ...................................................................................................... 18
2. Hybridization .............................................................................................................. 19
3. Molecular Orbitals ..................................................................................................... 24
3. Bond Angles .............................................................................................................. 27
4. Resonance .................................................................................................................. 29
5. Isomers ....................................................................................................................... 30
III. STRUCTURE OF CHEMICAL BONDS ............................................................................. 35
1. Ionic Bond ................................................................................................................. 36
2. Covalent Bond ........................................................................................................... 40
3. Metallic Bond ............................................................................................................. 44
4. Hydrogen bond .......................................................................................................... 45
vi

2. COMPOSITION, STRUCTURE AND FUNCTION OF BIOMOLECULES ......................... 53

1. Carbohydrates ................................................................................................................... 53
2. Proteins ............................................................................................................................ 58
3. Lipids ............................................................................................................................ 65
4. Nucleic Acids .................................................................................................................... 67
5. Vitamins ............................................................................................................................ 69
3. STABILIZING INTERACTIONS ............................................................................................ 73
1. Van Der Waals Interaction ................................................................................................ 74
2. Electrostatic Interaction .................................................................................................... 75
3. Hydrogen Bond ................................................................................................................. 76
4. Hydrophobic Interaction ................................................................................................... 77
4. PRINCIPLES OF BIOPHYSICAL CHEMISTRY ................................................................... 79
1. pH ............................................................................................................................ 79
2. Buffers ............................................................................................................................ 80
3. Reaction Kinetics .............................................................................................................. 84
4. Thermodynamics ............................................................................................................... 88
5. Colligative Properties ........................................................................................................ 90
5. BIOENERGETICS AND ATP SYNTHESIS ............................................................................ 92
I. BIOENERGETICS .............................................................................................................. 92
1. Concept of Gibbs Free Energy .................................................................................. 92
2. ATP Hydrolysis ......................................................................................................... 94
3. Steps in ATP Hydrolysis ........................................................................................... 94
4. Other High–Energy Phosphorylated compounds ..................................................... 96
II. GLYCOLYSIS ..................................................................................................................... 97
III. OXIDATIVE PHOSPHORYLATION ................................................................................ 102
1. Structure of Mitochondria ....................................................................................... 102
2. Electron Transport Chain (ETC) .............................................................................. 102
3. ATP Synthesis ......................................................................................................... 104
IV. COUPLED REACTIONS .................................................................................................. 106
V. GROUP TRANSFER REACTIONS AND BIOLOGICAL GROUP TRANSDUCERS ....... 106
6. PRINCIPLES OF CATALYSIS ............................................................................................. 108
1. Enzymes .......................................................................................................................... 108
2. Classification Of Enzymes ............................................................................................... 109
3. Factors Affecting Enzyme Activity ................................................................................. 109
4. Enzyme Kinetics .............................................................................................................. 110
5. Enzyme Catalysis ............................................................................................................ 111
6. Enzyme Regulation .......................................................................................................... 113
 vii

7. CONFORMATION OF PROTEINS ......................................................................................116

1. The Peptide Bond and Ramachandran Plot .................................................................... 117
2. Secondary Structure of Proteins ..................................................................................... 119
3. Tertiary and Quartenary Structure of Proteins ............................................................... 120
4. Protein Folding ................................................................................................................ 121
8. CONFORMATION OF NUCLEIC ACIDS ........................................................................... 122
I. CONFORMATION OF NUCLEIC ACIDS ....................................................................... 122
1. DNA Helix ................................................................................................................ 122
2. tRNA ........................................................................................................................ 124
II. STABILITY OF NUCLEIC ACIDS ................................................................................... 126
III. STABILITY OF PROTEINS ............................................................................................. 127
9. METABOLISM OF BIOMOLECULES ................................................................................ 129
I. METABOLISM OF CARBOHYDRATES ........................................................................ 129
II. METABOLISM OF LIPIDS ............................................................................................. 139
III. METABOLISM OF AMINO ACIDS ............................................................................... 141
IV. METABOLISM OF NUCLEIC ACID ............................................................................... 144
V. VITAMINS AND METABOLISM ................................................................................... 150

UNIT-2: CELLULAR ORGANIZATION ....................................... 153-230

1. MEMBRANE STRUCTURE AND FUNCTION .................................................................... 155
I. MEMBRANE MODELS .................................................................................................. 155
1. Gorter-Grendel Model .............................................................................................. 155
2. Danielli-Davson Model ............................................................................................ 156
3. Fluid Mosaic Model ................................................................................................ 156
II. MEMBRANE PROTEINS ................................................................................................ 157
III. TRANSPORT ACROSS MEMBRANES .......................................................................... 158
1. Simple Diffusion ....................................................................................................... 158
2. Osmosis .................................................................................................................... 158
3. Transport Proteins ................................................................................................... 159
IV. PROTEIN SORTING ........................................................................................................ 160
V. MECHANISMS OF INTRACELLULAR TRANSPORT .................................................. 162
1. Transportation of Synthesized Proteins .................................................................. 162
2. Transport Vesicles ................................................................................................... 166
3. Role of Microtubules ............................................................................................... 168
VI. ELECTRICAL PROPERTIES OF MEMBRANES ............................................................. 169
2. STRUCTURAL ORGANIZATION AND FUNCTION OF INTRACELLULAR
ORGANELLES ...................................................................................................................... 172
I. THE CELL WALL ............................................................................................................ 173
viii

II. NUCLEUS ........................................................................................................................ 178

III. MITOCHONDRIA ........................................................................................................... 180
IV. GOLGI BODIES ............................................................................................................... 181
V. ENDOPLASMIC RETICULUM ....................................................................................... 182
VI. PEROXISOMES ............................................................................................................... 185
VII. PLASTIDS ....................................................................................................................... 186
VIII.VACUOLES ...................................................................................................................... 190
IX. CYTOSKELETON AND CELL MOTILITY ..................................................................... 191
3. ORGANIZATION OF GENES AND CHROMOSOMES ..................................................... 195
I. OPERON CONCEPT ........................................................................................................ 196
II. UNIQUE AND REPETITIVE DNA .................................................................................. 197
III. SPLIT OR INTERRUPTED GENES ................................................................................. 199
IV. GENE FAMILIES ............................................................................................................. 199
V. STRUCTURE OF CHROMATIN AND CHROMOSOMES ............................................. 201
VI. TRANSPOSONS .............................................................................................................. 204
4. CELL DIVISION AND CELL CYCLE .................................................................................. 208
I. MITOSIS AND ITS SIGNIFICANCE .............................................................................. 208
II. PRE-MITOTIC PHASES .................................................................................................. 208
1. G1 Phase .................................................................................................................. 209
2. S Phase ..................................................................................................................... 209
3. G2 Phase .................................................................................................................. 210
III. STAGES OF MITOSIS .................................................................................................... 210
1. Prophase .................................................................................................................. 210
2. Metaphase ............................................................................................................... 211
3. Anaphase ................................................................................................................. 211
4. Telophase ................................................................................................................. 212
5. Cytokinesis ............................................................................................................... 213
IV. MEIOSIS AND ITS SIGNIFICANCE ............................................................................... 214
V. STEPS IN MEIOSIS ......................................................................................................... 214
Meiosis I ......................................................................................................................... 214
1. Prophase I ................................................................................................................ 214
2. Metaphase I ............................................................................................................. 217
3. Anaphase I ............................................................................................................... 217
4. Telophase I ............................................................................................................... 218
Meiosis II ........................................................................................................................ 219
1. Prophase II ............................................................................................................... 219
2. Metaphase II ............................................................................................................ 220
 ix

3. Anaphase II ............................................................................................................. 220

4. Telophase II and Cytokinesis .................................................................................. 221
VI. REGULATION OF MEIOSIS AND CONTROL OF CELL CYCLE ................................... 222
1. Cyclin-Dependent Protein Kinase (Cdks) ................................................................ 222
2. Cyclins ..................................................................................................................... 222
5. MICROBIAL PHYSIOLOGY ............................................................................................... 224
I. GROWTH RATE AND GROWTH YIELD ....................................................................... 224
II. STRATEGIES OF CELL DIVISION ................................................................................. 225
1. Binary fission ........................................................................................................... 225
2. Budding .................................................................................................................... 226
3. Filamentation ............................................................................................................ 226
4. Sporulation ............................................................................................................... 227
III. STRESS RESPONSE ........................................................................................................ 229
1. Heat Shock Response .............................................................................................. 229
2. Acid Stress Response ............................................................................................. 230
3. Less Nutrient Availability ........................................................................................ 230

UNIT-3: FUNDAMENTAL PROCESSES .................................... 231-330

1. DNA REPLICATION REPAIR AND RECOMBINATION .................................................... 233
I. DNA REPLICATION ....................................................................................................... 233
1. Meselson and Stahl Experiment .............................................................................. 234
2. The Process of Replication ...................................................................................... 236
II. FIDELITY OF REPLICATION ......................................................................................... 240
III. EXTRACHROMOSOMAL REPLICONS ......................................................................... 241
1. Rolling Circle Replication ......................................................................................... 242
2. Conjugation .............................................................................................................. 242
IV. DNA DAMAGE AND REPAIR MECHANISMS ............................................................ 246
1. Light Dependent Repair ........................................................................................... 246
2. Excision Repair ......................................................................................................... 246
V. HOMOLOGOUS RECOMBINATION .............................................................................. 249
VI. SITE SPECIFIC RECOMBINATION ................................................................................ 250
2. RNA SYNTHESIS AND PROCESSING ............................................................................... 252
I. TRANSCRIPTION ........................................................................................................... 252
1. Transcription Factors ............................................................................................... 253
2. Formation of Initiation Complex .............................................................................. 259
3. RNA Polymerases .................................................................................................... 261
4. Capping .................................................................................................................... 264
5. Elongation and Termination ..................................................................................... 265
x

II. RNA PROCESSING ......................................................................................................... 270

1. Pre-mRNA Processing .............................................................................................. 270
2. RNA Splicing ............................................................................................................ 271
3. RNA Editing ............................................................................................................. 274
III. STRUCTURE AND FUNCTION OF DIFFERENT TYPES OF RNA ............................... 277
1. mRNA ....................................................................................................................... 279
2. tRNA ........................................................................................................................ 280
3. rRNA ........................................................................................................................ 282
IV. RNA TRANSPORT .......................................................................................................... 284
3. PROTEIN SYNTHESIS AND PROCESSING ...................................................................... 287
I. THE RIBOSOME ............................................................................................................. 288
II. TRANSLATION .............................................................................................................. 289
1. The Genetic Code .................................................................................................... 290
2. Initiation of Translation ........................................................................................... 291
3. Elongation ................................................................................................................ 296
4. Termination ............................................................................................................... 298
5. Untranslated Regions .............................................................................................. 301
6. Translational Proofreading ....................................................................................... 301
7. Translational Inhibitors ............................................................................................ 302
8. Post Translational Modification of Proteins ........................................................... 304
4. CONTROL OF GENE EXPRESSION .................................................................................. 308
I. PHAGES AND VIRUSES ................................................................................................. 308
1. Lysis ......................................................................................................................... 310
2. Lysogeny .................................................................................................................. 311
II. IN PROKARYOTES ........................................................................................................ 314
1. Transcriptional Level ............................................................................................... 315
2. Alternative Sigma Factors ....................................................................................... 316
3. Repressors and Activators ...................................................................................... 317
III. IN EUKARYOTES ........................................................................................................... 321
1. Promoters and Enhancers ........................................................................................ 322
2. Transcriptional Activators and Repressors ............................................................. 323
3. DNA Methylation .................................................................................................... 325
4. RNA Interference (RNAi) and miRNA ..................................................................... 326
IV. ROLE OF CHROMATIN ................................................................................................. 328
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UNIT-4: CELL COMMUNICATION AND CELL SIGNALLING ..... 331-503

1. HOST PARASITE INTERACTION ...................................................................................... 333
I. PATHOGEN RECOGNITION ........................................................................................... 333
II. PATHOGEN PENETRATION .......................................................................................... 334
1. Pre-Penetration Stage ............................................................................................... 334
2. Penetration Stage – .................................................................................................. 335
3. Post-Penetration Stage ............................................................................................. 337
III. ALTERATION OF HOST CELL BEHAVIOUR AFTER PATHOGEN ENTRY .................. 338
IV. VIRAL TRANSFORMATION ......................................................................................... 340
V. PATHOGEN INDUCED DISEASES ................................................................................. 343
1. Common Infections in Plant .................................................................................... 343
2. Diseases Caused In Animals ................................................................................... 348
VI. CELL-TO-CELL FUSION IN NORMAL AND ABNORMAL CELLS .............................. 354
2. CELL SIGNALLING ............................................................................................................. 362
I. HORMONES AND THEIR RECEPTORS ........................................................................ 363
II. CELL SURFACE RECEPTORS ........................................................................................ 368
III. SIGNALLING THROUGH G-PROTEIN COUPLED RECEPTOR (GPCR) ........................ 371
IV. SIGNAL TRANSDUCTION PATHWAYS ....................................................................... 374
V. SECOND MESSENGERS ................................................................................................. 376
VI. REGULATION OF SIGNALLING PATHWAYS ............................................................... 378
1. Multiple G Proteins Transduce Signals to Different Effector Proteins ................... 378
2. Glycogenolysis Is Promoted by Multiple Second Messengers .............................. 378
3. Insulin and Glucagon Work Together to Maintain a Stable Blood Glucose Level ... 380
VII. TWO COMPONENT SYSTEMS ..................................................................................... 381
1. Bacteria ..................................................................................................................... 381
2. Plants ........................................................................................................................ 383
VIII.NORMAL SIGNALLING AND LIGHT SIGNALLING IN PLANTS ................................ 384
IX. BACTERIAL CHEMOTAXIS .......................................................................................... 387
X. QUORUM SENSING ....................................................................................................... 388
3. CELLULAR COMMUNICATION ......................................................................................... 391
I. REGULATION OF HEMATOPOIESIS ............................................................................ 391
II. GENERAL PRINCIPLES OF CELL COMMUNICATION ................................................ 394
III. CELL ADHESION AND ROLE OF DIFFERENT ADHESION MOLECULES .................. 397
IV. NEUROTRANSMISSION AND ITS REGULATION ....................................................... 405
4. CANCER ......................................................................................................................... 407
I. GENETIC REARRANGEMENTS ..................................................................................... 407
II. ONCOGENES AND TUMOUR SUPPRESSOR GENES ................................................... 411
xii

III. CANCER AND THE CELL CYCLE ................................................................................. 415

IV. VIRUS INDUCED CANCER ............................................................................................ 416
V. METASTASIS ................................................................................................................. 419
VI. INTERACTION OF CANCER CELLS WITH NORMAL CELLS .................................... 420
VII. APOPTOSIS AND CANCER ........................................................................................... 424
VIII.THERAPEUTIC INTERVENTIONS OF UNCONTROLLED CELL GROWTH ................. 427
1. Radiation Therapy ................................................................................................... 427
2. Gene Therapy ........................................................................................................... 429
3. Immunotherapies ...................................................................................................... 430
4. Drug Therapies ........................................................................................................ 431
5. Bacterial Therapy and Virotherapy .......................................................................... 433
5. INNATE AND ADAPTIVE IMMUNE SYSTEM .................................................................... 435
I. CELLS AND MOLECULES INVOLVED IN INNATE AND ADAPTIVE IMMUNITY .... 435
1. Components of Innate Immunity ............................................................................. 436
2. Components of Acquired or Adaptive Immunity .................................................... 438
II. ANTIGENS ...................................................................................................................... 442
III. B AND T CELL EPITOPES ............................................................................................. 445
IV. ANTIBODY STRUCTURE AND FUNCTION ................................................................. 446
V. GENERATION OF ANTIBODY DIVERSITY ................................................................... 448
VI. MONOCLONAL ANTIBODIES ....................................................................................... 451
VII. ANTIBODY ENGINEERING ............................................................................................ 453
VIII.ANTIGEN ANTIBODY INTERACTIONS ....................................................................... 455
1. Interaction Kinetics .................................................................................................. 455
2. Nature of Bonds ...................................................................................................... 455
3. Factors Affecting the Interactions ........................................................................... 456
IX. MHC MOLECULES, ANTIGEN PROCESSING AND PRESENTATION ......................... 457
1. MHC I ...................................................................................................................... 457
2. MHC II ..................................................................................................................... 460
X. ACTIVATION AND DIFFERENTIATION OF LYMPHOCYTES ..................................... 463
1. B Cells ...................................................................................................................... 463
2. T Cells ...................................................................................................................... 466
XI. CELL RECEPTORS ........................................................................................................... 469
1. B Cell Receptor ............................................................................................................ 469
2. T Cell Receptor ............................................................................................................ 470
XII. PRIMARY AND SECONDARY IMMUNE MODULATION ........................................... 473
XIII. THE COMPLEMENT SYSTEM ..................................................................................... 475
1. Classical Pathway .................................................................................................... 475
 xiii

2. Alternative Pathway ................................................................................................ 475

3. Lectin Pathway ......................................................................................................... 476
XIV. TOLL LIKE RECEPTORS .............................................................................................. 477
XV. CELL MEDIATED EFFECTOR FUNCTIONS ............................................................... 479
XVI. INFLAMMATION ........................................................................................................ 481
XVII. HYPERSENSITIVITY AND AUTOIMMUNITY ............................................................ 483
XVIII. IMMUNE RESPONSES TO COMMON DISEASES .................................................... 486
1. Tuberculosis ............................................................................................................ 486
2. Malaria ..................................................................................................................... 489
3. HIV 492
XXI. CONGENITAL AND ACQUIRED IMMUNODEFICIENCES ......................................... 494
1. Defective Microbial Activities of Phagocytes ......................................................... 495
2. Severe Combined Immunodeficiencies (SCID) ........................................................ 496
3. Acquired Immunodeficiency .................................................................................... 497
XIX. VACCINES ..................................................................................................................... 498

UNIT-5: DEVELOPMENTAL BIOLOGY ........................................ 505-630

1. BASIC CONCEPTS OF DEVELOPMENT .......................................................................... 507
I. POTENCY AND STEM CELLS ....................................................................................... 507
1. Potency .................................................................................................................... 507
II. INDUCTION, COMPETENCE AND COMMITMENT : SPECIFICATION AND CELL
FATE DETERMINATION ................................................................................................ 509
III. CELL DIFFERENTIATION .............................................................................................. 514
1. Cell-cell Interaction .................................................................................................. 515
2. Cell–Matrix Interactions ........................................................................................... 516
3. Polarity and Shape of the cell ................................................................................. 517
4. Oxygen Tension ....................................................................................................... 517
IV. MORPHOGENETIC GRADIENTS ................................................................................... 518
V. CELL FATE AND CELL LINEAGES ................................................................................ 521
VI. STEM CELLS .................................................................................................................. 521
VII. GENOMIC EQUIVALENCE AND CYTOPLASMIC DETERMINANTS .......................... 525
1. Metaplasia ................................................................................................................ 525
2. Amphibian Cloning .................................................................................................. 526
3. Cytoplasmic Determinants ....................................................................................... 527
VIII.IMPRINTING ................................................................................................................... 529
IX. MUTANTS AND TRANSGENICS IN ANALYSIS OF DEVELOPMENT ........................ 533
xiv

2. GAMETOGENESIS, FERTILIZATION AND EARLY DEVELOPMENT ............................ 539

I. GAMETOGENESIS .......................................................................................................... 539
1. Gamete ...................................................................................................................... 539
2. Spermatogenesis ...................................................................................................... 541
3. Oogenesis ................................................................................................................ 543
II. SPERM-EGG RECOGNITION .......................................................................................... 544
III. EMBRYO SAC DEVELOPMENT AND DOUBLE FERTILIZATION IN PLANTS .......... 547
IV. EMBRYOGENESIS IN PLANTS ...................................................................................... 551
V. SEED DEVELOPMENT AND GERMINATION ............................................................... 555
VI. ESTABLISHMENT OF SYMMETRY IN PLANTS ......................................................... 558
VII. ZYGOTE FORMATION, CLEAVAGE AND BLASTULA FORMATION ........................ 561
VIII.EMBRYONIC FIELDS ...................................................................................................... 563
IX. GASTRULATION AND FORMATION OF GERM LAYERS IN ANIMALS .................. 564
3. MORPHOGENESIS AND ORGANOGENESIS IN ANIMALS ............................................ 568
I. CELL AGGREGATION AND DIFFERENTIATION IN DICTYOSTELIUM ..................... 568
1. Life Cycle ................................................................................................................. 568
2. Aggregation ............................................................................................................. 570
3. Differentiation .......................................................................................................... 570
II. AXES AND PATTERN OF FORMATION OF DROSOPHILA, AMPHIBIA
AND CHICK .................................................................................................................... 572
1. Drosophila ................................................................................................................ 572
2. Amphibia .................................................................................................................. 575
3. Chick ........................................................................................................................ 577
III. ORGANOGENESIS – VULVA FORMATION IN Caenorhabditis elegans ..................... 579
IV. EYE LENS INDUCTION .................................................................................................. 583
V. LIMB DEVELOPMENT AND REGENERATION IN VERTEBRATES ............................. 584
1. Apical Ectodermal Ridge .......................................................................................... 585
2. The ZPA ................................................................................................................... 586
3. Regeneration ............................................................................................................ 587
VI. DIFFERENTIATION OF NEURONS ............................................................................... 590
VII. POST EMBRYONIC DEVELOPMENT:
LARVAL FORMATION AND METAMORPHOSIS ........................................................ 592
1. Larval Stage ............................................................................................................. 592
2. Metamorphosis ........................................................................................................ 593
VIII.ENVIRONMENTAL REGULATION OF NORMAL DEVELOPMENTAL ........................ 596
IX. SEX DETERMINATION .................................................................................................. 600
 xv

4. MORPHOGENESIS AND ORGANOGENESIS IN PLANTS .............................................. 604

I. ORGANIZATION OF SHOOT AND ROOT APICAL MERISTEM ................................ 604
1. Shoot Apical Meristem ............................................................................................ 605
2. Root Apical Meristem .............................................................................................. 606
3. Theories Of Apical Meristem Differentiation .......................................................... 607
II. SHOOT AND ROOT DEVELOPMENT ........................................................................... 609
1. Root .......................................................................................................................... 609
2. Shoot ........................................................................................................................ 609
III. LEAF DEVELOPMENT AND PHYLLOTAXY ................................................................ 611
IV. TRANSITION TO FLOWERING: FLORAL MERISTEMS AND
FLORAL DEVELOPMENT IN ARABIDOPSIS AND ANTIRRHINUM .......................... 614
5. PROGRAMMED CELL DEATH, AGINGAND SENESCENCE ........................................... 622
I. PROGRAMMED CELL DEATH ...................................................................................... 622
II. AGEING AND SENESCENCE ......................................................................................... 626

UNIT-6: SYSTEM PHYSIOLOGY PLANT ..................................... 631-777

1. PHOTOSYNTHESIS ............................................................................................................. 633
I. LIGHT HARVESTING COMPLEXES .............................................................................. 639
II. THE PHOTOSYNTHETIC ELECTRON TRANSPORT .................................................... 642
III. PHOTOPROTECTIVE MECHANISMS ........................................................................... 648
IV. CARBON DIOXIDE FIXATION PATHWAYS ................................................................ 651
1. C3 or Calvin Cycle ....................................................................................................... 652
2. C4 Cycle or Hatch and Slack Pathway ........................................................................ 654
3. Cam Pathway or Crassulacean Acid Metabolism Pathway ........................................ 655
2. RESPIRATION AND PHOTORESPIRATION ..................................................................... 658
I. CITRIC ACID CYCLE ...................................................................................................... 661
II. PLANT MITOCHONDRIAL ELECTRON TRANSPORT AND ATP SYNTHESIS .......... 664
III. ALTERNATIVE OXIDASE .............................................................................................. 672
IV. PHOTORESPIRATORY PATHWAY ................................................................................ 676
3. NITROGEN METABOLISM ................................................................................................. 681
I. NITRATE AND AMMONIUM ASSIMILATION ............................................................ 683
II. AMINO ACID BIOSYNTHESIS ...................................................................................... 690
4. PLANT HORMONES ........................................................................................................... 697
I. TYPES OF PLANT HORMONES, STORAGE AND FUNCTIONS ................................. 697
1. Auxin ........................................................................................................................ 697
2. Cytokinins ................................................................................................................ 698
3. Gibberellins ............................................................................................................... 698
4. Ethylene ................................................................................................................... 700
5. Abscisic Acid ........................................................................................................... 701
xvi

II. BIOSYNTHESIS OF PLANT HORMONES ..................................................................... 701

1. Auxins ...................................................................................................................... 701
2. Cytokinin .................................................................................................................. 701
3. Gibberellin ................................................................................................................ 704
4. Ethylene ................................................................................................................... 705
5. Abscisic Acid ........................................................................................................... 708
III. TRANSPORT OF PLANT HORMONES ......................................................................... 709
IV. MECHANISM OF ACTION ............................................................................................ 712
1. Auxin ........................................................................................................................ 712
2. Cytokinin .................................................................................................................. 714
3. Gibberellins ............................................................................................................... 715
4. Ethylene ................................................................................................................... 716
5. Abscisic Acid ........................................................................................................... 717
5. SENSORY PHOTOBIOLOGY ............................................................................................. 719
I. STRUCTURE, FUNCTION AND MECHANISM OF ACTION ....................................... 719
1. Phytochromes .......................................................................................................... 719
2. Crytpochromes ......................................................................................................... 722
3. Phototropins ............................................................................................................ 726
II. STOMATAL MOVEMENT ............................................................................................. 728
III. PHOTOPERIODISM AND BIOLOGICAL CLOCKS ........................................................ 731
6. SOLUTE TRANSPORT AND PHOTOASSIMILATORY TRANSLOCATION ................. 736
I. WATER TRANSPORT .................................................................................................... 736
1. Soil to Roots to Leaves ........................................................................................... 737
2. Water Potential ......................................................................................................... 741
3. Transpiration ............................................................................................................ 742
II. SOLUTE TRANSPORT ................................................................................................... 745
III. PHLOEM TRANSPORT .................................................................................................. 749
1. Structure ................................................................................................................... 749
2. Transport of Photosynthates from Source to Sink ................................................. 750
3. Factors Affecting Phloem Transport ....................................................................... 753
IV. LOADING AND UNLOADING OF PHOTOASSIMILATES ........................................... 755
1. Source-Path-Sink System ......................................................................................... 755
2. Loading and Unloading ........................................................................................... 756
7. SECONDARY METABOLITES ............................................................................................ 758
I. CLASSIFICATION AND FUNCTIONS ........................................................................... 759
1. Terpenes ................................................................................................................... 759
2. Phenolics .................................................................................................................. 761
3. Nitrogen Containing Compounds ............................................................................ 763
 xvii

II. BIOSYNTHESIS OF SECONDARY METABOLITES ...................................................... 765

1. Terpenoids ............................................................................................................... 765
2. Phenolics .................................................................................................................. 766
3. Nitrogen Containing Compounds ............................................................................ 768
8. STRESS PHYSIOLOGY ....................................................................................................... 770
I. PLANT DEFENSE AGAINST BIOTIC STRESSES ......................................................... 770
II. PLANT DEFENSE AGAINST ABIOTIC STRESSES ....................................................... 773

UNIT-7: SYSTEM PHYSIOLOGY ANIMAL ................................. 779-922

1. BLOOD AND CIRCULATION ............................................................................................. 781
I. BLOOD CORPUSCLES, HAEMOPOEISIS AND FORMED ELEMENTS ........................ 781
II. BLOOD VOLUME AND ITS REGULATION .................................................................. 786
III. HAEMOGLOBIN ............................................................................................................. 787
IV. OVERVIEW OF BLOOD AND IMMUNITY .................................................................... 789
V. HEMOSTASIS ................................................................................................................. 791
2. CARDIOVASCULAR SYSTEM ............................................................................................ 800
I. COMPONENTS OF THE CARDIOVASCULAR SYSTEM .............................................. 800
II. ANATOMY OF THE HEART ......................................................................................... 803
III. MYOGENIC HEART MECHANISM ............................................................................... 808
IV. ECG .......................................................................................................................... 809
V. THE CARDIAC CYCLE ................................................................................................... 812
1. Phases ...................................................................................................................... 812
2. Heart Sounds ........................................................................................................... 815
VI. BLOOD PRESSURE ......................................................................................................... 816
VII. NEURAL AND CHEMICAL REGULATION ................................................................... 818
3. RESPIRATORY SYSTEM .................................................................................................... 820
I. RESPIRATION SYSTEMS IN DIFFERENT ANIMAL SPECIES ..................................... 823
1. Direct Diffusion ........................................................................................................ 823
2. Skin And Gills .......................................................................................................... 824
3. Tracheal Systems ..................................................................................................... 825
4. In Mammals .............................................................................................................. 825
II. TRANSPORT AND EXCHANGE OF GASES ................................................................. 826
1. Oxygen Transport .................................................................................................... 826
2. Carbon Dioxide Transport ....................................................................................... 829
III. NEURAL AND CHEMICAL REGULATION ................................................................... 831
4. NERVOUS SYSTEM ............................................................................................................. 833
I. NEURONS ....................................................................................................................... 834
II. ACTION POTENTIAL .................................................................................................... 836
xviii

III. GROSS NEUROANATOMY OF THE BRAIN AND SPINAL CORD ............................. 838
1. The Brain .................................................................................................................. 839
2. Spinal Cord ............................................................................................................... 843
IV. CENTRAL AND PERIPHERAL NERVOUS SYSTEM ..................................................... 845
V. NEURAL CONTROL OF MUSCLE TONE AND POSTURE ........................................... 847
5. SENSE ORGANS .................................................................................................................. 851
I. VISION .......................................................................................................................... 851
II. HEARING ........................................................................................................................ 853
III. TACTILE RESPONSE ...................................................................................................... 858
6. EXCRETORY SYSTEM ........................................................................................................... 860
I. KIDNEYS, NEPHRONS AND URINE FORMATION ...................................................... 860
1. Kidney ...................................................................................................................... 861
2. Nephron ................................................................................................................... 862
3. Urine Formation ....................................................................................................... 864
II. MICTURITION ................................................................................................................ 865
III. BLOOD PRESSURE AND VOLUME ............................................................................... 866
IV. REGULATION OF WATER BALANCE, ELECTROLYTE BALANCE
AND ACID-BASE BALANCE ........................................................................................ 868
1. Regulation of Water Balance ................................................................................... 868
2. Electrolyte Balance ................................................................................................... 871
3. Acid-base Balance ................................................................................................... 874
7. THERMOREGULATION ....................................................................................................... 876
I. THERMAL NEUTRAL ZONE OR COMFORT ZONE .................................................... 877
II. BODY TEMPERATURE AND REGULATION ................................................................ 879
III. ACCLIMATIZATION ...................................................................................................... 884
8. STRESS AND ADAPTATION .............................................................................................. 886
I. ADAPTATION TO TERRESTRIAL HABITATS ............................................................ 886
II. ADAPTATION TO MARINE HABITAT ........................................................................ 887
III. NEUROBIOLOGY OF STRESS ADAPTATION .............................................................. 888
9. DIGESTIVE SYSTEM ........................................................................................................... 892
I. JOURNEY OF FOOD THROUGH THE GI TRACT ......................................................... 893
II. CHEMICAL DIGESTION AND ABSORPTION ............................................................... 895
1. Digestion and Absorption of Carbohydrates .......................................................... 895
2. Digestion and Absorption of Proteins .................................................................... 898
3. Digestion and Absorption of Lipids ........................................................................ 899
4. Digestion and Absorption of Nucleic Acids ........................................................... 900
5. Absorption of Minerals ........................................................................................... 901
6. Absorption of Vitamins ............................................................................................ 901
II. ENERGY BALANCE AND BASIC METABOLIC RATE ................................................ 902
 xix

10. ENDOCRINOLOGY AND REPRODUCTION ..................................................................... 906

I. ENDOCRINE GLANDS ................................................................................................... 906
II. HORMONES .................................................................................................................... 908
1. Types of Hormones ................................................................................................. 908
2. Action of Hormones ................................................................................................ 910
3. Hormones and Diseases .......................................................................................... 912
III. REPRODUCTION ............................................................................................................ 915
1. Gametogenesis ......................................................................................................... 915
2. Hormonal Control ..................................................................................................... 917

UNIT-8: INHERITANCE BIOLOGY ............................................. 923-1058

1. MENDELIAN PRINCIPLES .................................................................................................. 925
I. HISTORY OF MENDEL ................................................................................................... 925
II. MENDEL’S LAWS OF INHERITANCE ........................................................................... 927
1. Law of Dominance ................................................................................................... 927
2. Law of Segregation .................................................................................................. 930
3. Law of Independent Assortment ............................................................................. 930
2. CONCEPT OF GENE ............................................................................................................ 931
I. ALLELE .......................................................................................................................... 931
II. MULTIPLE ALLELES ...................................................................................................... 932
1. Fur Colour in Rabbits .............................................................................................. 933
2. Wing Type in Drosophila ........................................................................................ 933
3. Eye Colour in Drosophila ........................................................................................ 934
4. ABO Blood Group in Man ....................................................................................... 934
III. PSEUDO ALLELES .......................................................................................................... 935
IV. COMPLEMENTATION TEST ......................................................................................... 936
3. EXTENSION OF MENDELIAN PRINCIPLES ..................................................................... 938
I. GENE INTERACTIONS IN CODOMINANCE AND INCOMPLETE DOMINANCE ...... 938
1. Codominance ............................................................................................................ 938
2. Incomplete Dominance ............................................................................................. 939
II. PLEIOTROPY .................................................................................................................. 939
III. GENOMIC IMPRINTING, PENETRANCE AND EXPRESSIVITY, PHENOCOPY ............ 941
1. Genomic Imprinting .................................................................................................. 941
2. Penetrance and Expressivity .................................................................................... 942
3. Phenocopy ............................................................................................................... 942
IV. LINKAGE AND CROSSING OVER ................................................................................. 943
V. SEX LIMITED AND SEX INFLUENCED GENES ........................................................... 948
1. Sex Limited Traits ..................................................................................................... 948
xx

4. GENE MAPPING METHODS ............................................................................................... 950

1. Genetic Linkage ........................................................................................................ 950
2. Recombination Frequency ....................................................................................... 950
I. TETRAD ANALYSIS ...................................................................................................... 952
1. Crossing Over Betwen Centromere And Gene ........................................................ 952
2. Frequency Of Recombination Between Centromere And Gene .............................. 953
3. Detection Of Linkage ............................................................................................... 953
4. Linkage Map Preparation ......................................................................................... 955
II. MAPPING WITH MOLECULAR MARKERS ................................................................ 956
1. Restriction Fragment Length Polymorphism (RFLP) ............................................... 957
2. Variable Number Tandem Repeats (VNTRs) ............................................................ 958
III. MAPPING USING SOMATIC CELL HYBRIDS .............................................................. 958
1. Assigning Genes To Chromosomes ........................................................................ 958
2. Chromosome Mapping ............................................................................................. 961
IV. DEVELOPMENT OF MAPPING POPULATIONS IN PLANTS ...................................... 962
1. Types of Mapping Populations ............................................................................... 963
2. Bulk Segregant Analysis .......................................................................................... 964
3. Combining Markers And Populations ..................................................................... 964
5. EXTRACHROMOSOMAL INHERITANCE ......................................................................... 966
I. INHERITANCE OF CHLOROPLAST GENETIC MATERIAL ......................................... 966
II. MITOCHONDRIAL INHERITANCE ............................................................................... 968
6. MICROBIAL GENETICS ...................................................................................................... 972
I. HORIZONTAL GENE TRANSFER MECHANISMS ....................................................... 972
1. Conjugation .............................................................................................................. 972
2. Transformation ......................................................................................................... 973
3. Transduction ............................................................................................................ 975
II. MAPPING GENES BY INTERRUPTED MATING .......................................................... 977
III. FINE STRUCTURE ANALYSIS OF GENES .................................................................... 977
1. Fine Structure ........................................................................................................... 979
2. Analysis ................................................................................................................... 981
3. Functional Analysis Steps ....................................................................................... 983
7. HUMAN GENETICS .............................................................................................................. 985
I. PEDIGREE ANALYSIS .................................................................................................... 985
1. Autosomal Recessive Disorders .............................................................................. 987
2. Autosomal Dominant Disorders .............................................................................. 988
3. X-Linked Recessive Disorders ................................................................................. 991
4. X-Linked Dominant Disorders ................................................................................. 993
 xxi

II. LOD SCORE AND ANALYSIS ........................................................................................ 994

III. KARYOTYPES AND CHROMOSOMAL DISORDERS ................................................. 998
1. Types ...................................................................................................................... 1000
2. Other Examples ....................................................................................................... 1001
3. Testing ................................................................................................................... 1005
8. QUANTITATIVE GENETICS .............................................................................................. 1006
I. POLYGENIC INHERITANCE ......................................................................................... 1008
II. HERITABILITY AND ITS MEASUREMENTS ............................................................. 1009
III. QTL MAPPING ............................................................................................................. 1012
9. MUTATION ....................................................................................................................... 1018
I. TYPES AND CAUSES OF MUTATIONS ..................................................................... 1020
1. Recessive and Dominant ....................................................................................... 1020
2. Large and Small DNA Alterations ......................................................................... 1022
3. Spontaneous and Induced Mutations ................................................................... 1023
II. DETECTION OF MUTATIONS ..................................................................................... 1025
III. MUTANT TYPES .......................................................................................................... 1030
1. Lethal Mutations .................................................................................................... 1030
2. Conditional Mutations ........................................................................................... 1030
3. Biochemical Mutations .......................................................................................... 1031
4. Loss-of-function And Gain-of-function Mutations ............................................... 1032
IV. INSERTIONAL MUTAGENESIS ................................................................................... 1033
10. STRUCTURALAND NUMERICALALTERATIONS OF CHROMOSOMES ................... 1037
I. STRUCTURAL ALTERATIONS .................................................................................... 1038
1. Deletions ................................................................................................................ 1038
2. Duplications ........................................................................................................... 1040
3. Inversions .............................................................................................................. 1041
4. Translocations ....................................................................................................... 1043
II. NUMERICAL ABERRATIONS AND GENETIC IMPLICATIONS ................................ 1045
1. Ploidy ..................................................................................................................... 1045
2. Genetic Implications ............................................................................................... 1048
11. RECOMBINATION ............................................................................................................. 1050
I. MECHANISIM OF RECOMBINATION ........................................................................ 1050
II. TYPES OF RECOMBINATION ..................................................................................... 1051
xxii

UNIT-9: DIVERSITY OF LIFE FORMS ..................................... 1059-1162

1. PRINCIPLES AND METHODS OF TAXONOMY ............................................................ 1061
I. TAXONOMY ................................................................................................................. 1061
II. DIVISIONS OF LIFE ...................................................................................................... 1070
1. Kingdom Classification .......................................................................................... 1070
2. Domain Classification ............................................................................................ 1070
III. CLASSIFICATION, SYSTEMATICS AND ZOOLOGICAL NOMENCLATURE ........... 1071
1. Classification .......................................................................................................... 1071
2. Systematics ............................................................................................................ 1071
3. Zoological Nomenclature ....................................................................................... 1072
III. CONCEPT OF SPECIES ................................................................................................. 1073
IV. MICROBIAL TAXONOMY AND CLASSIFICATION .................................................. 1077
1. Polyphasic Approach for Identificaion .................................................................. 1077
2. LEVELS OF STRUCTURAL ORGANIZATION ................................................................ 1081
I. ORGANIZATION OF CELLS ........................................................................................ 1081
II. LEVELS OF ORGANIZATION ...................................................................................... 1083
1. Chemical Level ....................................................................................................... 1083
2. Cellular Level .......................................................................................................... 1084
3. Tissue Level ........................................................................................................... 1084
4. Organ Level ............................................................................................................ 1087
5. Organ System Level ............................................................................................... 1088
III. COMPARITIVE ANATOMY FOR EVIDENCE OF EVOLUTION .................................. 1089
1. Homologous Structures ......................................................................................... 1090
2. Analogous Structures ............................................................................................ 1090
3. Vestigial Structures ................................................................................................ 1091
IV. ADAPTIVE RADIATION: DARWIN’S FINCHES ........................................................ 1093
V. ADAPTIVE MODIFICATIONS ..................................................................................... 1094
1. Structural And Behavioural ................................................................................... 1094
2. Habitat .................................................................................................................... 1094
3. Speciation ............................................................................................................... 1095
4. Coadaptation .......................................................................................................... 1096
3. OUTLINE CLASSIFICATION OF PLANTS, ANIMALS AND MICROORGANISMS ........ 1097
I. CRITERIA FOR CLASSIFICATION .............................................................................. 1097
II. FIVE KINGDOM CLASSIFICATION ............................................................................ 1101
1. Kingdom Monera ................................................................................................... 1102
2. Kingdom Protista ................................................................................................... 1103
3. Kingdom Fungi ...................................................................................................... 1105
4. Kingdom Plantae .................................................................................................... 1108
5. Kingdom Animalia .................................................................................................. 1112
 xxiii

III. MICROBIAL TAXONOMY CONCEPTS ...................................................................... 1117

IV. EVOLUTIONARY RELATIONSHIPS AMONG TAXA : PHYLOGENETIC TREES ....... 1119
4. NATURAL HISTORY OF INDIAN SUBCONTINENT ...................................................... 1122
I. MAJOR HABITAT TYPES OF THE INDIAN SUBCONTINENT AND
THE GEOGRAPHIC ORIGINS OF WILDLIFE .............................................................. 1123
II. MIGRATION OF SPECIES ............................................................................................ 1127
III. COMMON INDIAN MAMMALS AND BIRDS ........................................................... 1128
1. Mammals ................................................................................................................ 1128
2. Birds ....................................................................................................................... 1130
IV. SEASONALITY AND PHENOLOGY ............................................................................ 1131
1. Seasonality ............................................................................................................. 1131
2. Phenology .............................................................................................................. 1131
5. ORGANISMS OF HEALTH AND AGRICULTURAL IMPORTANCE ............................... 1135
I. COMMON PARASITES AND THEIR RESPECTIVE DISEASES
IN HUMANS AND ANIMALS ..................................................................................... 1136
1. Ectoparasites .......................................................................................................... 1136
2. Helminths ............................................................................................................... 1137
3. Protozoa ................................................................................................................. 1141
II. COMMON PARASITES AND PATHOGENS,
AND THEIR RESPECTIVE DISEASES IN CROPS ....................................................... 1144
1. Fungi ...................................................................................................................... 1144
2. Water Molds Or Oomycetes .................................................................................. 1145
3. Bacteria ................................................................................................................... 1146
4. Virus ....................................................................................................................... 1146
5. Parasitic Nematodes ............................................................................................... 1148
6. ORGANISMS OF CONSERVATION CONCERN ............................................................. 1152
I. BIODIVERSITY AND IMPORTANCE OF CONSERVATION ........................................ 1152
1. Rare Endangered Species ...................................................................................... 1154
II. CONSERVATION STRATEGIES ................................................................................... 1158
1. List of Conservation Strategies on a Global Scale ................................................ 1158
2. Conservation Strategies in India ........................................................................... 1159

UNIT-10: ECOLOGICAL PRINCIPLES..................................... 1163-1271

1. THE ENVIRONMENT ......................................................................................................... 1165
I. PHYSICAL ENVIRONMENT ........................................................................................ 1166
II. BIOTIC ENVIRONMENT .............................................................................................. 1167
1. Biotic Components ................................................................................................. 1167
2. Abiotic Components .............................................................................................. 1168
xxiv

2. HABITAT AND NICHE ....................................................................................................... 1170

I. NICHE CONCEPTS ....................................................................................................... 1171
II. RESOURCE PARTITIONING ......................................................................................... 1174
III. CHARACTER DISPLACEMENT .................................................................................. 1175
3. POPULATION ECOLOGY ................................................................................................. 1177
I. CHARACTERISTICS OF A POPULATION .................................................................. 1177
1. Population Density ................................................................................................ 1177
2. Natality ................................................................................................................... 1178
3. Mortality ................................................................................................................ 1179
4. Population Growth and Curves ............................................................................. 1180
5. Age Distributions .................................................................................................. 1182
6. Population Fluctuations ......................................................................................... 1183
II. POPULATION REGULATION ....................................................................................... 1185
1. Density Dependent Limiting Factors ..................................................................... 1185
2. Density Independent Limiting Factors .................................................................. 1186
III. LIFE HISTORY STRATEGIES ....................................................................................... 1187
IV. METAPOPULATION .................................................................................................... 1189
1. Deme ...................................................................................................................... 1190
2. Dispersal ................................................................................................................ 1190
V. INTERDEMIC SELECTION AND EXTINCTION .......................................................... 1192
1. Interdemic Selection ............................................................................................... 1192
2. Age Structured Populations .................................................................................. 1192
4. SPECIES INTERACTIONS ................................................................................................ 1194
I. TYPES OF INTERACTION ........................................................................................... 1194
II. INTERSPECIFIC COMPITITION .................................................................................. 1194
III. HERBIVORY .................................................................................................................. 1195
IV. CARNIVORY ................................................................................................................. 1196
V. POLLINATION .............................................................................................................. 1196
VI. SYMBIOSIS ................................................................................................................... 1198
5. COMMUNITY ECOLOGY .................................................................................................. 1199
I. NATURE OF COMMUNITIES ...................................................................................... 1199
II. COMMUNITY STRUCTURE AND ATRRIBUTES ....................................................... 1199
III. LEVEL OF SPECIES DIVERSITY AND ITS MEASUREMENT .................................... 1200
IV. EDGES AND ECOTONES .............................................................................................. 1202
6. ECOLOGICAL SUCCESSION ........................................................................................... 1204
I. TYPES OF SUCCESSION .............................................................................................. 1205
1. Primary Succession ............................................................................................... 1205
 xxv

2. Secondary Succession ........................................................................................... 1206

II. MECHANISMS OF SUCCESSION ............................................................................... 1208
III. CHANGES INVOLVED IN SUCCESSION ..................................................................... 1211
IV. CONCEPT OF CLIMAX ................................................................................................ 1211
7. ECOSYSTEM ECOLOGY ................................................................................................... 1213
I. ECOSYSTEM STRUCTURE .......................................................................................... 1214
1. Abiotic Components .............................................................................................. 1215
2. Biotic Components ................................................................................................. 1216
II. FUNCTIONS OF ECOSYSTEM ..................................................................................... 1218
III. ENERGY FLOW AND MINERAL CYCLING (C,N,P) .................................................... 1220
IV. PRIMARY PRODUCTIVITY AND DECOMPOSITION ................................................. 1223
V. STRUCTURE AND FUNCTION OF SOME INDIAN ECOSYSTEMS .......................... 1226
8. BIOGEOGRAPHY ............................................................................................................... 1229
I. MAJOR TERRESTRIAL BIOMES ................................................................................ 1230
II. THEORY OF ISLAND BIOGEOGRAPHY ...................................................................... 1235
III. BIOGEOGRAPHICAL ZONES OF INDIA ..................................................................... 1236
9. APPLIED ECOLOGY ......................................................................................................... 1240
I. ENVIRONMENTAL POLLUTION ................................................................................. 1241
II. GLOBAL ENVIRONMENT CHANGE ........................................................................... 1243
III. BIODIVERSITY ............................................................................................................. 1244
IV. BIODIVERSITY CHANGE DRIVERS ............................................................................ 1247
V. BIODIVERSITY MANAGEMENT ................................................................................. 1251
1. ICMM ..................................................................................................................... 1251
2. DCNR ..................................................................................................................... 1252
3. Food and Agriculture Organization of United Nations ......................................... 1252
10. CONSERVATION BIOLOGY ............................................................................................. 1255
I. CONSERVATION MANAGEMENT APPROACHES ..................................................... 1256
II. CASE STUDIES IN INDIA ........................................................................................... 1259
1. Project Tiger ........................................................................................................... 1259
2. Biosphere Reserves ............................................................................................... 1263

UNIT-11: ECOLOGICAL PRINCIPLES ..................................... 1273-1392

1. EMERGENCE OF EVOLUTIONARY THOUGHTS ........................................................ 1275
I. LAMARK– CONCEPTS OF VARIATIONS, ADAPTION,
STRUGGLE, FITNESS AND NATURAL SELECTION .................................................. 1275
II. DARWIN– CONCEPTS OF VARIATIONS, ADAPTION,
STRUGGLE, FITNESS AND NATURAL SELECTION .................................................. 1278
III. MENDELISM ................................................................................................................ 1284
xxvi

IV. SPONTANEITY OF MUTATIONS ................................................................................ 1286

V. THE EVOLUTIONARY SYNTHESIS ............................................................................. 1289
2. ORIGIN OF CELLS AND UNICELLULAR EVOLUTION ................................................ 1291
I. ORIGIN OF BASIC BIOLOGICAL MOLECULES ......................................................... 1291
II. ABIOGENESIS ............................................................................................................... 1291
III. THE OPARIN-HALDANE HYPOTHESIS ..................................................................... 1293
IV. MILLER-UREY EXPERIMENT ...................................................................................... 1293
V. THE ORIGIN AND EVOLUTION OF CELLS ................................................................ 1295
VI. THE FIRST CELL .......................................................................................................... 1295
VII. EVOLUTION OF PROKARYOTES ................................................................................ 1298
VIII.EUKARYOTIC CELLS ................................................................................................... 1299
IX. THE DEVELOPMENT OF MULTICELLULAR ORGANISMS ...................................... 1301
X. THE EVOLUTION OF METABOLISM ......................................................................... 1303
3. PALEONTOLOGY AND EVOLUTIONARY HISTORY .................................................... 1306
I. THE EVOLUTIONARY TIME SCALE .......................................................................... 1306
II. LEARNING THE GEOLOGICAL TIME SCALE ............................................................ 1307
III. THE GEOLOGICAL TIME SCALE ................................................................................ 1310
IV. ORIGINS OF UNICELLULAR AND MULTI CELLULAR ORGANISMS ...................... 1311
V. EVOLUTION OF PLANTS ............................................................................................ 1318
VI. EVOLUTION OF ANIMALS ......................................................................................... 1322
VI. THE EVOLUTION OF HUMANS ................................................................................. 1327
4. MOLECULAR EVOLUTION .............................................................................................. 1331
I. CONCEPTS OF NEUTRAL EVOLUTION ..................................................................... 1331
II. MOLECULAR DIVERGENCE AND MOLECULAR CLOCKS ....................................... 1336
III. TOOLS USED IN PHYLOGENY .................................................................................... 1338
VI. PROTEIN AND NUCLEOTIDE SEQUENCE ANALYSIS .............................................. 1341
V. GENE DUPLICATION AND DIVERGENCE .................................................................. 1344
5. THE MECHANISMS ........................................................................................................... 1347
I. GENE POOL ................................................................................................................... 1348
II. GENE FREQUENCY ....................................................................................................... 1349
III. HARDY-WEINBERG LAW ........................................................................................... 1352
IV. CONCEPTS AND RATE OF CHANGE IN GENE FREQUENCY
THROUGH NATURAL SELECTION ............................................................................ 1355
V. MIGRATION AND RANDOM GENETIC DRIFT ......................................................... 1359
VI. MIGRATION ................................................................................................................. 1361
VII. ADAPTIVE RADIATION .............................................................................................. 1361
VIII.ISOLATING MECHANISMS ........................................................................................ 1362
 xxvii

IX. SPECIATION ................................................................................................................. 1364

X. CONVERGENT EVOLUTION ........................................................................................ 1365
XI. SEXUAL SELECTION ................................................................................................... 1367
XII. COEVOLUTION ............................................................................................................. 1369
6. BRAIN, BEHAVIOR AND EVOLUTION ........................................................................... 1371
I. APPROACHES AND METHODS IN STUDY OF BEHAVIOR ..................................... 1371
II. PROXIMATE AND ULTIMATE CAUSATION ............................................................ 1373
III. INNATE BEHAVIORS: MOVEMENT AND MIGRATION ........................................... 1374
IV. FORAGING .................................................................................................................... 1375
V. COMMUNICATION WITHIN A SPECIES ................................................................... 1376
VI . GROUP SELECTION ..................................................................................................... 1377
VII. KIN SELECTION ........................................................................................................... 1378
VIII.RECIPROCAL ALTRUISM ............................................................................................ 1379
IX. BIOLOGICAL CLOCK ................................................................................................... 1380
X. BEHAVIOURAL DEVELOPMENT ................................................................................ 1381
XI. USE OF SPACE AND TERRITORIALITY .................................................................... 1383
XII. MATING SYSTEMS ...................................................................................................... 1384
XIII. PARENTAL INVESTMENT (PI) .................................................................................. 1388
XIV. REPRODUCTIVE SUCCESS .......................................................................................... 1389
XV. PATERNAL CARE ........................................................................................................ 1391

UNIT-12: APPLIED BIOLOGY ................................................... 1393-1512

1. FERMENTATION TECHONOLOGY ................................................................................. 1395
I. MICROBIAL FERMENTATION .................................................................................... 1395
II. MICROBIAL KINETICS ................................................................................................ 1399
1. Batch Fermentation ................................................................................................ 1399
2. Fed Batch and Continuous Fermentation ............................................................. 1400
III. FERMENTATION PROCESS ......................................................................................... 1402
IV. PRODUCTION OF MICRO AND MACROMOLECULES ............................................. 1402
1. Alcohol Fermentation ............................................................................................ 1403
2. Lactic Acid Fermentation ....................................................................................... 1404
3. Mixed Acid Fermentation ....................................................................................... 1405
4. 2, 3 Butanediol Fermentation ................................................................................. 1405
5. Butanol Fermentation ............................................................................................. 1407
6. Propionic Acid Fermenation .................................................................................. 1407
xxviii

2. IMMUNOLOGYAND TISSUE CULTURE ......................................................................... 1409

I. IMMUNOLOGICAL APPLICATIONS ........................................................................... 1410
1. Vaccines ................................................................................................................. 1410
2. Diagnosis ............................................................................................................... 1411
II. TISSUE AND CELL CULTURE METHODS FOR PLANTS AND ANIMALS .............. 1417
1. Cell Culture ............................................................................................................. 1417
2. Animal Cell Culture ................................................................................................ 1420
3. Tissue Culture ........................................................................................................ 1423
3. TRANSGENE TECHNOLOGY ........................................................................................... 1426
I. TRANSGENIC ANIMALS ............................................................................................. 1426
1. Importance ............................................................................................................. 1426
2. Discovery ............................................................................................................... 1426
3. Application ............................................................................................................. 1427
II. TRANSGENIC PLANTS ................................................................................................ 1431
1. Reasons to Make Transgenic Plants ..................................................................... 1431
2. Steps Involved in Production of Transgenic Plants ............................................. 1432
3. Applications ........................................................................................................... 1437
III. MOLECULAR APPROACHES TO DIAGNOSIS AND STRAIN DENTIFICATION .... 1441
4. GENOMICS ....................................................................................................................... 1446
I. APPLICATIONS OF GENOMICS IN AGRICULTURE .................................................. 1446
1. Sequencing of Plant Genomes ............................................................................... 1447
2. Genomics of Farm Animals .................................................................................... 1449
3. Sequencing Of Agricultural Pathogens ................................................................. 1449
II. APPLICATION OF GENOMICS IN HEALTH ............................................................... 1450
5. BIODIVERISTY RESORUCES .......................................................................................... 1453
I. DEFINITION OF BIO-RESOURCES .............................................................................. 1453
II. BIODIVERSITY ............................................................................................................. 1455
III. BIODIVERSITY OF INDIA ........................................................................................... 1457
6. PLANT AND ANIMAL BREEDING .................................................................................... 1467
I. PLANT BREEDING ....................................................................................................... 1467
II. ANIMAL BREDING ...................................................................................................... 1470
III. SELECTIVE BREEDING OR ARTIFICIAL SELECTION ................................................ 1473
7. BIOREMEDIATION ............................................................................................................ 1491
I. PHYTOREMEDIATION ................................................................................................. 1495
8. BIOLOGICAL SENSORS .................................................................................................. 1499
I. PROPERTIES OF A BIOSENSOR .................................................................................. 1500
II. COMPONENTS AND WORKING PRINCIPLE OF BIOSENSORS ............................... 1501
 xxix

III. TYPES ........................................................................................................................ 1502

1. Electrochemical Biosensors ................................................................................... 1502
2. Physical Biosensors ............................................................................................... 1503
3. Optical Biosensors ................................................................................................. 1505
4. Wearable Biosensors ............................................................................................. 1506
5. Genetically Encoded Biosensors ........................................................................... 1507
IV. APPLICATIONS ............................................................................................................ 1507
1. In Food Processing, Monitoring, Food Authenticity, Quality and Safety ........... 1507
2. In Fermentation Processes ..................................................................................... 1509
3. In the Medical Field ............................................................................................... 1510
4. For Military Purposes ............................................................................................ 1512
V. FUTURE SCOPE ............................................................................................................ 1512

UNIT-13: METHODS IN BIOLOGY ........................................... 1513-1676

1. MOLECULAR BIOLOGY AND RECOMBINANT DNA METHODS ............................... 1515
I. ISOLATION AND PURIFICATION OF RNA, DNA (GENOMIC AND PLASMID)
AND PROTEINS, DIFFERENT SEPARATION METHODS .......................................... 1515
II. ANALYSIS OF RNA, DNA AND PROTEINS BY ONE
AND TWO-DIMENSIONAL GEL ELECTROPHORESIS .............................................. 1522
III. MOLECULAR CLONING OF DNA OR RNA FRAGMENTS IN BACTERIAL AND
EUKARYOTIC SYSTEMS. EXPRESSION OF RECOMBINANT PROTEINS USING
BACTERIAL, ANIMAL AND PLANT VECTORS. ISOLATION OF SPECIFIC
NUCLEIC ACID SEQUENCES ..................................................................................... 1524
IV. GENERATION OF GENOMIC AND CDNA LIBRARIES IN PLASMID, PHAGE,
COSMID, BAC AND YAC VECTORS. (PLEASE REFER UNIT-8
CHAPTER 3,4,9,10,11 & UNIT3-CHAPTER 1) ............................................................. 1532
V. IN VITRO MUTAGENESIS AND DELETION TECHNIQUES, GENE KNOCKS
OUT IN BACTERIAL AND EUKARYOTIC ORGANISMS.
(UNIT 3- CHAPTER 3 & 4 AND 1ST PART OF UNIT 13) .......................................... 1532
VI. PROTEIN SEQUENCING METHODS, DETECTION OF POST TRANSLATION
MODIFICATION OF PROTEINS. DNA SEQUENCING METHODS, STRATEGIES
FOR GENOME SEQUENCING. (UNIT3-CHAPTER 3& 4) ............................................ 1532
VII. METHODS FOR ANALYSIS OF GENE EXPRESSION AT RNA AND PROTEIN
LEVEL, LARGE SCALE EXPRESSION, SUCH AS MICRO ARRAY BASED
TECHNIQUES ................................................................................................................ 1532
1. Microarray Expression Analysis ............................................................................ 1533
2. Microarray for Mutation Analysis ......................................................................... 1533
3. Comparative Genomic Hybridization ...................................................................... 1533
VIII.ISOLATION, SEPARATION AND ANALYSIS OF CARBOHYDRATE
AND LIPID MOLECULES ............................................................................................. 1534
xxx

IX. ISOLATION, SEPARATION AND ANALYSIS OF CARBOHYDRATE

AND LIPID MOLECULES ............................................................................................. 1537
X. RFLP, RAPD AND AFLP TECHNIQUES ...................................................................... 1547
2. HISTOCHEMICALAND IMMUNO TECHNIQUES ........................................................... 1551
I. HOW IS ANTIBODIES PRODUCED? ........................................................................... 1551
II. ELISA ........................................................................................................................ 1552
III. RIA (RADIOIMMUNOASSAY) .................................................................................... 1554
IV. WESTERN BLOT .......................................................................................................... 1555
V. IMMUNOPRECIPITATION (IP) .................................................................................... 1561
VI. IMMUNOFLUORESCENCE MICROSCOPY ................................................................. 1562
VII. FLOW CYTOMETERS .................................................................................................. 1565
VIII.IN SITU LOCALIZATION BY TECHNIQUES SUCH AS FISH AND GISH ................. 1566
3. BIOPHYSICAL METHOD .................................................................................................. 1570
I. MOLECULAR ANALYSIS UTILIZING UV/VISIBLE SPECTROSCOPY ....................... 1570
II. FLUORESCENCE ........................................................................................................... 1572
III. CIRCULAR DICHROISM .............................................................................................. 1577
IV. ELECTRON SPIN RESONANCE ................................................................................... 1583
V. MOLECULAR STRUCTURE DETERMINATION USING X-RAY DIFFRACTION
AND NMR .................................................................................................................... 1584
VI. SURFACE PLASMON RESONANCE ........................................................................... 1587
4. STATISTICAL METHODS ................................................................................................. 1590
I. DESCRIPTIVE STATISTICS .......................................................................................... 1590
II. PROBABILITY DISTRIBUTIONS (BINOMIAL, POISSON AND NORMAL) .............. 1590
III. SAMPLING DISTRIBUTION; DIFFERENCE BETWEEN PARAMETRIC AND
NON-PARAMETRIC STATISTICS ............................................................................... 1593
IV. CONFIDENCE INTERVAL ............................................................................................. 1597
V. ERRORS ........................................................................................................................ 1600
VI. LEVELS OF SIGNIFICANCE; REGRESSION AND CORRELATION ............................ 1601
VII. T-TEST; ANALYSIS OF VARIANCE ............................................................................ 1608
VIII. THE CHI SQUARE STATISTIC ................................................................................... 1610
IX. AN INTRODUCTION TO MULTIVARIATE STATISTICS ........................................... 1612
5. RADIOLABELING TECHNIQUES ..................................................................................... 1614
I. RADIOISOTOPES ......................................................................................................... 1614
II. EXAMPLES OF RADIOISOTOPES IN BIOLOGY ........................................................ 1615
III. INCORPORATION OF RADIONUCLIDES INTO BODY TISSUES
AND INTERNAL EXPOSURES .................................................................................... 1616
IV. HANDLING RADIOACTIVE MATERIALS SAFELY ..................................................... 1618
 xxxi

6. MICROSCOPIC TECHNIQUES ......................................................................................... 1623

7. ELECTROPHYSIOLOGICAL METHODS ......................................................................... 1635
I. SINGLE NEURON RECORDING ................................................................................... 1635
II. PATCH CLAMP ELECTROPHYSIOLOGY .................................................................... 1638
III. EGC: ELECTROCARDIOGRAM .................................................................................... 1649
IV. BRAIN ACTIVITY RECORDING .................................................................................. 1653
V. LESION AND STIMULATION OF BRAIN ................................................................... 1657
VI. PHARMACOLOGICAL TESTING ................................................................................ 1659
VII. CAT (COMPUTED AXIAL TOMOGRAPHY) .............................................................. 1660
VIII.PET (POSITRON EMISSION TOMOGRAPHY) ............................................................ 1660
IX. MRI (MAGNETIC RESONANCE IMAGING) ............................................................... 1661
X. FUNCTIONAL MAGNETIC RESONANCE IMAGING (fMRI) ..................................... 1662
8. METHODS IN FIELD BIOLOGY ....................................................................................... 1663
I. POPULATION SIZE AND DENSITY ............................................................................ 1663
II. METHODS OF ESTIMATING POPULATION DENSITY OF PLANTS ....................... 1665
III. RANGING PATTERNS .................................................................................................. 1666
IV. SAMPLING METHODS IN THE STUDY OF BEHAVIOR ........................................... 1669
V. HABITAT CHARACTERIZATION: GROUND AND REMOTE SENSING METHODS ... 1672

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