Fundamentals of Biochemistry A Textbook H.P.GAJERA Assistant Professor Deparbnent of Biochemistry College of Agriculture Junagadh Agricultural University Junagadh, Gujarat, India - 362 001 S.V.PATEL Associate Research Scientist Deparbnent of Biochemistry College of Agriculture Junagadh Agricultural University Junagadh, Gujarat, India - 362 001 B. A. GOLAKIYA Professor & Head Deparbnent of Biochemistry College of Agriculture Junagadh Agricultural University Junagadh, Gujarat, India - 362 001 International Book Distributing Co. (Publishing Division) Published by INTERNATIONAL BOOK DISTRIBUTING CO. (Publishing Division) Khushnuma Complex Basement 7, Meerabai Marg (Behind Jawahar Bhawan) Lucknow 226001 U.P. (INDIA) TeI. : 91-522-2209542, 2209543, 2209544, 2209545 Fax: 0522-4045308 E-Mail: [email protected] First Edition 2008 ISBN: 978-81-8189-165-5 © Publisher All Rights Reserved No part of this publication may be reproduced, stored in a retrieval system, or h"ansmitted, in any form or by any means, electronic, mechanical, photocopying, recording or otherwise, without the prior written permission of the publisher. Composed & Designed at : Panacea Computers 2nd Floor, Agarwal Sabha Bhawan, Subhash Mohal Sadar Cantt., Lucknow-226 002 Phone: 0522-2483312, 9335927082, 9452295008 E-mail: [email protected] Printed at: Salasar Imaging Systems C-7/5, Lawrence Road Industrial Area Delhi -110035 Tel. : 011-27185653, 9810064311 Dr. B. K. Kikani Junagadh Agricultural University Junagadh-362001 Vice-chancellor FOREWORD Biochemistry is a gateway of all the branches of life science. It's a field of enormous interest and utility. Biochemistry is a study of the molecule of life. Our understanding of the molecular nature of life is growing at an incredible rate. It is difficult to embody all the information related to this subject in a single collection. If at all it has been done than the user will be discouraged by its volume. It is than even more tough task to encapsulate huge bulk of literature in a small handy book. This effort is done by our team in the Department of Biochemistry, Junagadh Agricultural University, Junagadh, Gujarat, India. The tools of biochemistry have been used to explain biological processes such as origin of life, cell development, cell differentiation, metapolisms, energy dynamics, origin and cause of diseases and even human behaviors. The principles of biochemistry are now reaching into chemistry, the health sciences, nutrition, agriculture, physiology, immunology, neurology, cell biology, biotechnology, nanotechnology, ecology, computer science and psychology. Not only the biochemistry expanding; other disciplines are using the tools of biochemistry to solve their unique problem. Thus biochemistry is seated at the core of other branches of science. This particular branch is engaged in understanding the nature and properties of the life throbbing around us. It is at the threshold where non living biomolecules through some intricate forces starts dancing while getting alive; and we call it a living being. This science has yet to fill up a knowledge gap about secret of life itself. This text book is a distillation of the years of experiences of our faculty members affiliated with teaching and research. Hopefully a complete grasp of the principle of biochemistry can be obtained by simply reading this book. This collection entitled FUNDAMENTALS OF BIOCHEMISTRY: A TEXTBOOK will cater the need of a large segment of people who have a scientific bend. Date: 20/06/2007 Place: Junagadh (B.K.Kikani) Junagadh Agricultural University Dr. D. B. Kuchhadiya Junagadh- 362 001 Director of Research and Dean P.G. Studies PREFACE As such the subject of Biochemistry is vast in its content. Its a tough task to pack up it in a single volume. While preparing a brief note of this subject our faculty members worked for more than 12 hours in a day behind each and every chapter even at final stage. They summarized the content without loosing the essense of the concept. I found it beautifully narrated with 145 figures & photographs, 30 tables containing total 322 text pages. While reading any subject our mind do summarize its major points. This book has been able to develop as a ready reckoner. Its my pleasure that our faculty mambers are mastering the art of scientific writing. There is vacume in the area of lucid and lucrative scientific documentation. If we want to propagate the scientific knowledge we should present it in a more simple form, in a pictorial and diagrammatic manner. It should be more graphical and photographica1. I think our team working at the Biochemistry and Biotechnology Department of Junagadh Agricultural University has to some extent fulfilled the above contention while preparing this book entitled "FUNDAMENTALS OF BIOCHEMISTRY: A TEXTBOOK" . I have no doubt that this collection will be appreciated by the students, teachers, researchers and professionals dealing with biosciences. Date: 20/06/2007 Place: Junagadh (D.B.Kuchhadiya) v CONTENTS Sr. No Topics Page No 1. Introduction 1 Origin of Life 1 The Elements of Life 3 Biomolecules to Cell 5 Cells and Organells 7 Water 16 History of Biochemistry 20 2. Carbohydrates 43 Nature and Nomenclature 43 Classification of Carbohydrates 44 Monosaccharides 44 Oligosaccharides 54 Storage Polysachharides 58 Structural Polysachharides 61 Chemical Properties of Carbohydrates 67 3. Lipids and membranes 77 Classification of Lipids 77 Fatty Acids 78 Simple Lipids 80 Compound Lipids 82 Properties of Fat 88 Constants of Fats and Oils 89 Biological Membranes 91 4. Nucleic acids 113 Nucleic Acids Building Blocks 113 Nucleotide Composition 115 Types and Functions of Nucleic Acids 115 Primary Structure of Nucleic Acids 115 Secondary Structure of Nucleic Acids 116 Complementarity 118 DNA and Inheritance 122 5. Amino acids and proteins 139 Chemistry of Amino Acids 139 Classification of Amino Acids 145 Essential Amino Acids 146 vii Properties of Amino Acids 146 Peptides 148 Classification of Proteins 148 Conformation of Proteins 154 Physical and Chemical Properties of Proteins 161 Myoglobin and Hemoglobin 162 Allosterism and Regulation 166 6. Enzymes and Kinetics 181 Characteristics of Enzymes 181 Classification of Enzymes 182 Cofactor 184 Mechanism of Enzyme Action 185 Enzyme Kinetics and Inhibitors 187 Isoenzymes 196 Enzyme Regulation 196 7. Vitamins and Co-enzymes 225 Fat soluble Vitamins 225 Water Soluble Vitamins 226 Co-enzymes 227 8. Introduction to Metabolism 257 Metabolism Pathways 257 Characteristics of Path ways 257 Organic Reaction in Metabolisms 258 Thermodynamicas in Metabolism 259 9. Carbohydrate Metabolism 275 Glycolysis 276 Gluconeogenesis 292 Pyruvate Metabolism 295 Kreb's TCA Cycle 297 Glycogen Metabolism 303 Pentose Phosphate Pathway 308 Mytochondrial Electron Transport System 312 Mitochondrial T ransport/ Comunica tion 316 10. Lipid metabolism 343 Oxidation of Fatty Acids 345 Ketone Bodies Metabolism 351 Fatty acid Biosynthesis 357 viii Triacylglycerol Biosynthesis 364 Regulation of Fatty Acid Metabolism 365 11. Nucleic acid metabolism 379 Purine Metabolism 379 Pyrimidine Metabolism 383 RNA Synthesis 386 DNA Synthesis 397 12. Amino acid and Protein metabolism 427 Protein Catabolism 427 Amino Acid Metabolism 428 Urea Cycle 432 Protein Synthesis 439 Protein Metabolism and Nitrogen Economy 450 13. Photosynthesis 467 The Chloroplast 467 Light Reaction of Photosynthesis 470 Dark Reaction of Photosynthesis 478 Photorespirat ion 482 14. General Biochemistry Glossry 501 15. Suggested Readings 535 16. Common Important Abbreviations 537 17. Index 545 ix