Biotechnology A problem approach PDF

Preview

Summary

Biotechnology A problem approach Third edition Pranav Kumar Former faculty, Department of Biotechnology Jamia Millia Islamia, New Delhi, India Usha Mina Scientist, Division of Environmental Sciences Indian Agricultural Research Institute (IARI), New Delhi, India Pathfinder Publication New Delhi, In...

Description

Biotechnology A problem approach Third edition

Pranav Kumar Former faculty, Department of Biotechnology Jamia Millia Islamia, New Delhi, India

Usha Mina Scientist, Division of Environmental Sciences Indian Agricultural Research Institute (IARI), New Delhi, India

Pathfinder Publication New Delhi, India

Pranav Kumar Former faculty, Department of Biotechnology Jamia Millia Islamia, New Delhi, India

Usha Mina Scientist, Division of Environmental Sciences Indian Agricultural Research Institute (IARI), New Delhi, India

Biotechnology A problem approach, Third edition ISBN: 978-93-80473-00-0 (paperback) Copyright © 2014 by Pathfinder 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 : Pathfinder Publication Production editor : Ajay Kumar Copy editor : Jomesh Joseph Illustration and layout : Pradeep Verma Cover design : Pradeep Verma Marketing director : Arun Kumar Production coordinator : Murari Kumar Singh Printer : Ronit Enterprises, New Delhi, India

Pathfinder Publication A unit of Pathfinder Academy Private Limited, New Delhi, India. www.thepathfinder.in 09350208235

Preface The present century has been considered as one that belongs to biotechnology. This branch of science has been viewed as something vital for life with numerous scientific applications in several fields of human endeavours. The branch of science is significant for mankind that many of the big discoveries of the second half of the last century and early this century would not have been possible in the absence of our accomplishments in this discipline. Biotechnology – A problem approach, covers fundamentals and techniques. This book provides a balanced introduction to all major areas of the subject. The chapters such as Biomolecules and catalysis, Bioenergetics and metabolism, Cell structure and functions, Immunology, Bioinformatics and Bioprocess engineering were selected in a sharply focused manner without overwhelming or excessive detail. 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 knowledge.

Acknowledgements Our students were the original inspiration for the first edition of this book, and we remain continually grateful to all of them, because we learn from them how to think about the life sciences and how to communicate knowledge in most meaningful way. We thank, Abhai Kumar, Rizwan Ansari, Lekha Nath, Harleen Kaur and Mr. Ajay Kumar, reviewers of this book, whose comment 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. 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.

Pranav Kumar Usha Mina

iii

This page intentionally left blank.

Contents Chapter

1

Biomolecules and Catalysis 1.1

1.2

1.3

Amino acids and Proteins

1

1.1.1

Optical properties

2

1.1.2

Absolute configuration

1.1.3

Standard and non-standard amino acids

1.1.4

Titration of amino acids

8

1.1.5

Peptide and polypeptide

11

1.1.6

Peptide bond

1.1.7

Protein structure

1.1.8

Denaturation of proteins

1.1.9

Solubilities of proteins

1.1.10

Simple and conjugated proteins

5

12 14

Fibrous and globular proteins

18 19 20

20

1.2.1

Collagen

1.2.2

Elastin

1.2.3

Keratins

1.2.4

Myoglobin

1.2.5

Hemoglobin

1.2.6

Models for the behavior of allosteric proteins

Protein folding

21 22 23 23 25 29

31

1.3.1

Molecular chaperones

1.3.2

Amyloid

32

33

1.4

Protein sequencing and assays

1.5

Nucleic acids

1.6

4

34

42

1.5.1

Nucleotides

1.5.2

Chargaff’s rules

Structure of dsDNA

42 46

47

1.6.1

B-DNA

47

1.6.2

Z-DNA

49

1.6.3

Triplex DNA

1.6.4

G-quadruplex

1.6.5

Stability of the double helical structure of DNA

1.6.6

Thermal denaturation

1.6.7

Quantification of nucleic acids

1.6.8

Supercoiled forms of DNA

1.6.9

DNA: A genetic material

49 50 51 53 53 56

v

51

1.7

1.8

1.9

1.10

1.11

RNA

58

1.7.1

Alkali-catalyzed cleavage of RNA

1.7.2

RNA world hypothesis

1.7.3

RNA as genetic material

Carbohydrates

61 61

63

1.8.1

Monosaccharide

1.8.2

Epimers

1.8.3

Cyclic forms

1.8.4

Derivatives of monosaccharide

1.8.5

Disaccharides and glycosidic bond

1.8.6

Polysaccharides

1.8.7

Glycoproteins

1.8.8

Reducing and non-reducing sugar

Lipids

60

63

64 65 67

70 72 73

73

1.9.1

Fatty acids

1.9.2

Triacylglycerol and Wax

1.9.3

Phospholipids

1.9.4

Glycolipids

1.9.5

Steroid

1.9.6

Eicosanoid

1.9.7

Plasma lipoproteins

Vitamins

74 75

76 78

79 79 81

82

1.10.1

Water-soluble vitamins

1.10.2

Fat-soluble vitamins

Enzymes

82 86

89

1.11.1

Naming and classification of enzyme

1.11.2

What enzyme does?

1.11.3

How enzymes operate?

1.11.4

Enzyme kinetics

1.11.5

Enzyme inhibition

1.11.6

Regulatory enzymes

1.11.7

Isozymes

106

1.11.8

Zymogen

107

1.11.9

Ribozyme

108

92

94 102 105

2

Bioenergetics and Metabolism 2.1

Bioenergetics

2.2

Metabolism

90

91

1.11.10 Examples of enzymatic reactions

Chapter

68

117 122

vi

108

2.3

Respiration

123

2.3.1

Aerobic respiration

123

2.3.2

Glycolysis

2.3.3

Pyruvate oxidation

2.3.4

Krebs cycle

2.3.5

Anaplerotic reaction

2.3.6

Oxidative phosphorylation

2.3.7

Inhibitors of electron transport

2.3.8

Electrochemical proton gradient

2.3.9

Chemiosmotic theory

2.3.10

ATP synthase

2.3.11

Uncoupling agents and ionophores

2.3.12

ATP-ADP exchange across the inner mitochondrial membrane

2.3.13

Shuttle systems

2.3.14

P/O ratio

2.3.15

Fermentation

148

2.3.16

Pasteur effect

150

2.3.17

Warburg effect

2.3.18

Respiratory quotient

124 129

131

139 140

141

144 144

145

147

150

Glyoxylate cycle

2.5

Pentose phosphate pathway

2.6

Entner-Doudoroff pathway

2.7

Photosynthesis

2.9

135

142

2.4

2.8

134

151

151 152 154

154

2.7.1

Photosynthetic pigment

155

2.7.2

Absorption and action spectra

2.7.3

Fate of light energy absorbed by photosynthetic pigments

2.7.4

Concept of photosynthetic unit

2.7.5

Hill reaction

2.7.6

Oxygenic and anoxygenic photosynthesis

2.7.7

Concept of pigment system

2.7.8

Stages of photosynthesis

2.7.9

Light reactions

2.7.10

Prokaryotic photosynthesis

2.7.11

Non-chlorophyll based photosynthesis

2.7.12

Dark reaction: Calvin cycle

2.7.13

Starch and sucrose synthesis

158

161

162

Photorespiration

178

2.8.1

C4 cycle

179

2.8.2

CAM pathway

163 165

165

180

Carbohydrate metabolism

182

2.9.1

182

Gluconeogenesis

162

vii

171

174 177

173

160

2.9.2 2.10

2.11

2.12

Glycogen metabolism

Lipid metabolism

187

192

2.10.1

Synthesis and storage of triacylglycerols

2.10.2

Biosynthesis of fatty acid

2.10.3

Fatty acid oxidation

2.10.4

Biosynthesis of cholesterol

2.10.5

Steroid hormones and Bile acids

Amino acid metabolism

194

198 205 206

208

2.11.1

Amino acid synthesis

2.11.2

Biological nitrogen fixation

2.11.3

Amino acid catabolism

2.11.4

Molecules derived from amino acids

Nucleotide metabolism

208 211 214 220

221

2.12.1

Nucleotide synthesis

2.12.2

Nucleotide degradation

Chapter

192

221 228

3

Cell Structure and Functions 3.1

What is a Cell?

234

3.2

Structure of eukaryotic cells

235

3.2.1

Plasma membrane

235

3.2.2

ABO blood group

3.2.3

Transport across plasma membrane

243 245

3.3

Membrane potential

3.4

Transport of macromolecules across plasma membrane

3.5

3.4.1

Endocytosis

3.4.2

Fate of receptor

3.4.3

Exocytosis

Ribosome 3.5.1

3.6

3.7

252 262

262 266

267

268

Protein targeting and translocation

Endoplasmic reticulum

269

270

3.6.1

Endomembrane system

3.6.2

Transport of proteins across the ER membrane

3.6.3

Transport of proteins from ER to cis Golgi

Golgi complex

275

280

281

3.7.1

Transport of proteins through cisternae

3.7.2

Transport of proteins from the TGN to lysosomes

3.8

Vesicle fusion

3.9

Lysosome

3.10

Vacuoles

275

285 286

288

viii

283 284

3.11

Mitochondria

3.12

Plastids

3.13

Peroxisome

3.14

Cytoskeleton

288

291 292 293

3.14.1

Microtubules

293

3.14.2

Kinesins and Dyneins

3.14.3

Cilia and Flagella

3.14.4

Centriole

3.14.5

Actin filament

3.14.6

Myosin

3.14.7

Muscle contraction

3.14.8

Intermediate filaments

296

299 299

301 302

3.15

Cell junctions

3.16

Cell adhesion molecules

3.17

Extracellular matrix of animals

3.18

Plant cell wall

3.19

Nucleus

3.20

Cell signaling

3.22

306

307 310 311

312

314 317

3.20.1

Signal molecules

3.20.2

Receptors

3.20.3

GPCR and G-proteins

3.20.4

Ion channel-linked receptors

3.20.5

Enzyme-linked receptors

3.20.6

Nitric oxide

3.20.7

Two-component signaling systems

3.20.8

Chemotaxis in bacteria

3.20.9

Quorum sensing

Cell Cycle

318

319 321 330 330

336

3.20.10 Scatchard plot 3.21

296

337

338

339 340

342

3.21.1

Role of Rb protein in cell cycle regulation

3.21.2

Role of p53 protein in cell cycle regulation

3.21.3

Replicative senescence

Mechanics of cell division

348

348

3.22.1

Mitosis

348

3.22.2

Meiosis

355

3.22.3

Nondisjunction and aneuploidy

3.23

Apoptosis

3.24

Cancer

3.25

Stem cells

362 365 372

ix

361

346 347

Chapter

4

Prokaryotes and Viruses 4.1

General features of Prokaryotes

4.2

Phylogenetic overview

4.3

Structure of bacterial cell

4.4

Bacterial genome : Bacterial chromosome and plasmid

4.5

Bacterial nutrition

4.6

377

378 378

393

4.5.1

Culture media

395

4.5.2

Bacterial growth

395

Horizontal gene transfer and genetic recombination 4.6.1

Transformation

4.6.2

Transduction

4.6.3

Conjugation

402 406

Bacterial taxonomy

4.8

General features of important bacterial groups

4.9

Archaebacteria

415

4.10

Bacterial toxins

416

4.11

Control of microbial growth

4.12

Virus

422

4.12.1

Bacteriophage (Bacterial virus)

4.12.2

Life cycle of bacteriophage

4.12.3

Plaque assay

4.12.4

Genetic analysis of phage

4.12.5

Animal Viruses

4.12.6

Plant viruses

Prions and Viroid 4.13.1

Chapter

399

400

4.7

4.13

389

411 413

418

423

424

427 430

433 443

444

Bacterial and viral disease

445

5

Immunology 5.1

Innate immunity

5.2

Adaptive immunity

5.3

Cells of the immune system

5.4

448 450

5.3.1

Lymphoid progenitor

5.3.2

Myeloid progenitor

452 453 455

Organs involved in the adaptive immune response 5.4.1

Primary lymphoid organs

5.4.2

Secondary lymphoid organs/tissues

5.5

Antigens

5.6

Major-histocompatibility complex

456

458 462

x

457

456

5.7

5.6.1

MHC molecules and antigen presentation

5.6.2

Antigen processing and presentation

5.6.3

Laboratory mice

465

467

Immunoglobulins : Structure and function

468

5.7.1

Basic structure of antibody molecule

5.7.2

Different classes of immunoglobulin

5.7.3

Action of antibody

5.7.4

Antigenic determinants on immunoglobulins

468 470

473

5.8

B-cell maturation and activation

5.9

Kinetics of the antibody response

5.10

Monoclonal antibodies and Hybridoma technology 5.10.1

481

Engineered monoclonal antibodies

Organization and expression of Ig genes

5.12

Generation of antibody diversity

5.13

T-cells and CMI

482

483 485

491

494

Superantigens

504

5.14

Cytokines

5.15

The complement system

5.16

Hypersensitivity

5.17

Autoimmunity

5.18

Transplantation

5.19

Immunodeficiency diseases

5.20

Failures of host defense ...