Pathfinder Publication

Life Sciences : Fundamentals and Practice

Sixth edition

ISBN: 978-81-906427-0-5 (paperback)

Copyright © 2017 by Pathnder Publication, all rights reserved.

This book contains information obtained from authentic and highly

regarded sources. Reasonable efforts have been made to publish reliable data
and information, but the author and the publisher cannot assume responsibility
for the validity of all materials or for the consequences of their use.
No part of this book may be reproduced by any mechanical, photographic, or
electronic process, or in the form of a phonographic recording, nor it may be
stored in a retrieval system, transmitted, or otherwise copied for public or
private use, without written permission from the publisher.

Publisher : Pathnder Publication

Production editor : Ajay Kumar
Copy editor : Jomesh Joseph
Illustration and layout : Pradeep Verma
Cover design : Monu
Marketing director : Arun Kumar
Production coordinator : Murari Kumar Singh

Pathfinder Publication
A unit of Pathnder Academy Private Limited, New Delhi, India.
pathnderpublication.in
Life Sciences have always been a fundamental area of science. The exponential increase in
the quantity of scientific information and the rate, at which new discoveries are made, require
very elaborate, interdisciplinary and up-to-date information and their understanding. This
sixth edition of Life sciences, Fundamentals and practice includes extensive revisions of the
previous edition. We have attempted to provide an extraordinarily large amount of information
from the enormous and ever-growing field in an easily retrievable form. It is written in clear
and concise language to enhance self-motivation and strategic learning skill of the students
and empowering them with a mechanism to measure and analyze their abilities and the
confidence of winning. We have given equal importance to text and illustrations. The sixth edition
has a number of new figures to enhance understanding. At the same time, we avoid excess detail,
which can obscure the main point of the figure. We have retained the design elements that have
evolved through the previous editions to make the book easier to read. Sincere efforts have been
made to support textual clarifications and explanations with the help of flow charts, figures and
tables to make learning easy and convincing. The chapters have been supplemented with self-tests
and questions so as to check one’s own level of understanding. Although the chapters of this book
can be read independently of one another, they are arranged in a logical sequence. Each page is
carefully laid out to place related text, figures and tables near one another, minimizing the need
for page turning while reading a topic. We have given equal importance to text and illustrations
as well. We hope you will find this book interesting, relevant and challenging.
Acknowledgements
Our students were the original inspiration for the first edition of this book, and we remain continually
grateful to them, because we learn from them how to think about the life sciences, and how to
communicate knowledge in most meaningful way. We thank, Dr. Diwakar Kumar Singh and Mr. Ajay
Kumar, reviewers of this book, whose comments and suggestions were invaluable in improving
the text. Any book of this kind requires meticulous and painstaking efforts by all its contributors.
Several diligent and hardworking minds have come together to bring out this book in this complete
form. We are much beholden to each of them and especially to Dr. Neeraj Tiwari. This book is a
team effort, and producing it would be impossible without the outstanding people of Pathfinder
Publication. It was a pleasure to work with many other dedicated and creative people of Pathfinder
Publication during the production of this book, especially Pradeep Verma.
1.1 Amino acids and Proteins 1

1.1.1 Optical properties 3

1.1.2 Absolute configuration 4

1.1.3 Standard and non-standard amino acids 5

1.1.4 Titration of amino acids 7

1.1.5 Peptide and polypeptide 12

1.1.6 Peptide bond 13

1.1.7 Protein structure 16

1.1.8 Denaturation of proteins 20

1.1.9 Solubilities of proteins 21

1.1.10 Simple and conjugated proteins 22

1.2 Fibrous and globular proteins 22

1.2.1 Collagen 23

1.2.2 Elastin 24

1.2.3 Keratins 25
1.2.4 Myoglobin 25

1.2.5 Hemoglobin, Hb 27

Oxygen transport 28

Functional differences between Mb and Hb 30

Factors affecting the affinity of Hb for oxygen 30

1.2.6 Models for the behavior of allosteric proteins 31

1.3 Protein folding 33

1.3.1 Molecular chaperones 34

1.3.2 Amyloid 35
1.3.3 Ubiquitin mediated protein degradation 36

1.3.4 N-end rule 38

1.4 Protein sequencing and assays 39

1.5 Nucleic acids 47

1.5.1 Nucleotides 47

1.5.2 Chargaff’s rules 51

1.6 Structure of dsDNA 53

1.6.1 B-DNA 53

1.6.2 Z-DNA 54
 1.6.3 Triplex DNA 55

1.6.4 G-quadruplex 56

1.6.5 Stability of the dsDNA helix 57

1.6.6 DNA denaturation 57

1.6.7 Quantification of nucleic acids 59

1.6.8 Supercoiled forms of DNA 59

Linking number 60

1.6.9 DNA: A genetic material 61

1.7 RNA 63

1.7.1 Alkali-catalyzed cleavage of RNA 64

1.7.2 RNA World hypothesis 65

1.7.3 RNA as genetic material 65

1.8 Carbohydrates 66

1.8.1 Monosaccharide 66
1.8.2 Epimers 68

1.8.3 Cyclic forms 68

1.8.4 Derivatives of monosaccharide 70

1.8.5 Disaccharides and glycosidic bond 71

1.8.6 Polysaccharides 73

1.8.7 Glycoproteins 75

1.8.8 Reducing and non-reducing sugar 76

1.9 Lipids 76

1.9.1 Fatty acids 77

1.9.2 Triacylglycerol and Wax 78

1.9.3 Phospholipids 79

1.9.4 Glycolipids 81

1.9.5 Steroid 82

1.9.6 Eicosanoid 82

1.9.7 Plasma lipoproteins 84

1.10 Vitamins 84

1.10.1 Water-soluble vitamins 85

Thiamine (Vitamin B1) 85

Riboflavin (Vitamin B2) 85

Niacin 86

Biotin 86

Pantothenic acid 87

Folic acid 87

Cobalamin (Vitamin B12) 87

Pyridoxine (Vitamin B6) 88

Ascorbic acid (Vitamin C) 88

1.10.2 Fat-soluble vitamins 89

Vitamin A (Retinol) 89
 Vitamin D 89

Vitamin K 90

Vitamin E 90

1.11 Reactive oxygen species and antioxidant 91

1.12 Enzymes 92
1.12.1 Naming and classification of enzyme 93

1.12.2 How enzymes operate? 94

1.12.3 Catalytic strategies 96

1.12.4 Enzyme kinetics 97

1.12.5 Enzyme inhibition 104

1.12.6 Regulatory enzymes 107

1.12.7 Isozymes 110

1.12.8 Zymogen 110

1.12.9 Ribozyme 111

1.12.10 Examples of enzymatic reactions 111

2.1 Bioenergetics 119

2.2 Metabolism 124

2.3 Respiration 125

2.3.1 Aerobic respiration 125

2.3.2 Glycolysis 126

2.3.3 Pyruvate oxidation 131

2.3.4 Krebs cycle 133

2.3.5 Anaplerotic reaction 136

2.3.6 Oxidative phosphorylation 136

2.3.7 Inhibitors of electron transport 141

2.3.8 Electrochemical proton gradient 142

2.3.9 Chemiosmotic theory 143

2.3.10 ATP synthase 144

2.3.11 Uncoupling agents and ionophores 146

2.3.12 ATP-ADP exchange across the inner mitochondrial membrane 146

2.3.13 Shuttle systems 147

2.3.14 P/O ratio 149

2.3.15 Fermentation 150

2.3.16 Pasteur effect 152

2.3.17 Warburg effect 152

2.3.18 Respiratory quotient 152

2.4 Glyoxylate cycle 153

2.5 Pentose phosphate pathway 154
2.6 Entner-Doudoroff pathway 156

2.7 Photosynthesis 157

2.7.1 Photosynthetic pigment 157

2.7.2 Absorption and action spectra 161

2.7.3 Fate of light energy absorbed by photosynthetic pigments 162

2.7.4 Concept of photosynthetic unit 164

2.7.5 Hill reaction 164

2.7.6 Oxygenic and anoxygenic photosynthesis 164

2.7.7 Concept of pigment system 165

2.7.8 Stages of photosynthesis 167

2.7.9 Light reactions 168

2.7.10 Prokaryotic photosynthesis 174

2.7.11 Non-chlorophyll based photosynthesis 176

2.7.12 Dark reaction: Carbon reduction and fixation cycle 176

2.7.13 Starch and sucrose synthesis 180

2.8 Photorespiration 181

2.8.1 C4 cycle 182

2.8.2 CAM pathway 184

2.9 Carbohydrate metabolism 187

2.9.1 Gluconeogenesis 187

2.9.2 Glycogen metabolism 192

2.10 Lipid metabolism 197

2.10.1 Synthesis and storage of triacylglycerols 197

2.10.2 Biosynthesis of fatty acid 199

2.10.3 Fatty acid oxidation 202

2.10.4 Biosynthesis of cholesterol 210

2.10.5 Steroid hormones and Bile acids 211

2.11 Amino acid metabolism 213

2.11.1 Amino acid synthesis 213

2.11.2 Amino acid catabolism 216

2.11.3 Molecules derived from amino acids 221

2.12 Nucleotide metabolism 222

2.12.1 Nucleotide synthesis 222

2.12.2 Nucleotide degradation 229

3.1 What is a Cell? 235

3.2 Structure of eukaryotic cells 236

3.2.1 Plasma membrane 236

3.2.2 ABO blood group 244

3.2.3 Transport across plasma membrane 246

3.3 Membrane potential 253

3.4 Transport of macromolecules across plasma membrane 263

3.4.1 Endocytosis 263

3.4.2 Fate of receptor 268

3.4.3 Exocytosis 268

3.5 Ribosome 269

3.5.1 Protein targeting and translocation 271

3.6 Endoplasmic reticulum 272

3.6.1 Endomembrane system 276

3.6.2 Transport of proteins across the ER membrane 277

3.6.3 Transport of proteins from ER to cis Golgi 281

3.7 Golgi complex 283

3.7.1 Transport of proteins through cisternae 284

3.7.2 Transport of proteins from the TGN to lysosomes 285

3.8 Vesicle fusion 286

3.9 Lysosome 287

3.10 Vacuoles 289

3.11 Mitochondria 290

3.12 Plastids 293

3.13 Peroxisome 294

3.14 Nucleus 295

3.15 Cytoskeleton 299

3.15.1 Microtubules 299

3.15.2 Kinesins and Dyneins 302

3.15.3 Cilia and Flagella 303

3.15.4 Centriole 305

3.15.5 Actin filament 306

3.15.6 Myosin 307

3.15.7 Muscle contraction 309

3.15.8 Intermediate filaments 312

3.16 Cell junctions 314

3.17 Cell adhesion molecules 317

3.18 Extracellular matrix of animals 318

3.19 Plant cell wall 320

3.20 Cell signaling 322

3.20.1 Signal molecules 323

3.20.2 Receptors 323

3.20.3 GPCR and G-proteins 325

3.20.4 Ion channel-linked receptors 334

3.20.5 Enzyme-linked receptors 334

3.20.6 Nitric oxide 341

3.20.7 Two-component signaling systems 342
 3.20.8 Chemotaxis in bacteria 343

3.20.9 Quorum sensing 344

3.20.10 Scatchard plot 345

3.21 Cell Cycle 347

3.21.1 Role of Rb protein in cell cycle regulation 356

3.21.2 Role of p53 protein in cell cycle regulation 358

3.21.3 Replicative senescence 360

3.22 Mechanics of cell division 360

3.22.1 Mitosis 360

3.22.2 Meiosis 367

3.22.3 Nondisjunction and aneuploidy 371

3.23 Apoptosis 374

3.24 Cancer 377

Molecular basis of cancer 379

Proto-oncogenes 380

Tumor suppressor genes 382

Carcinogen 383

Retinoblastoma 384

Oncovirus or tumor virus 385

Retroviral oncogenes 385

4.1 General features of Prokaryotes 391

4.2 Phylogenetic overview 392

4.3 Structure of bacterial cell 393

Staining 393

Cell Wall 395

Outer membrane 397

Glycocalyx 398

Plasma membrane 399

Cytoplasm 399

Surface appendages 400

Endospores 402

4.4 Bacterial genome: Bacterial chromosome and plasmid 403

4.5 Bacterial nutrition 408

4.5.1 Culture media 409

4.5.2 Bacterial growth 410

4.6 Horizontal gene transfer and genetic recombination 413

4.6.1 Transformation 414

4.6.2 Transduction 416