মুখ্য Textbook of Biochemistry for Medical Students

Textbook of Biochemistry for Medical Students

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The seventh edition of this book is a comprehensive guide to biochemistry for medical students. Divided into six sections, the book examines in depth topics relating to chemical basics of life, metabolism, clinical and applied biochemistry, nutrition, molecular biology and hormones. New chapters have been added to this edition and each chapter includes clinical case studies to help students understand clinical relevance. A 274-page free booklet of revision exercises (9789350906378), providing essay questions, short notes, viva voce and multiple choice questions is included to help students in their exam preparation. Free online access to additional clinical cases, key concepts and an image bank is also provided. Key points *Fully updated, new edition providing students with comprehensive guide to biochemistry *Includes a free booklet of revision exercises and free online access *Highly illustrated with nearly 1500 figures, images, tables and illustrations *Previous edition published in 2010
Jaypee Brothers Medical Publishers
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আপনি একটি বুক রিভিউ লিখতে পারেন এবং আপনার অভিজ্ঞতা শেয়ার করতে পারেন. অন্যান্য পাঠকরা আপনার পড়া বইগুলির বিষয়ে আপনার মতামত সম্পর্কে সর্বদা আগ্রহী হবে. বইটি আপনার পছন্দ হোক বা না হোক, আপনি যদি নিজের সৎ ও বিস্তারিত চিন্তাভাবনা ব্যক্ত করেন তাহলে অন্যরা তাদের জন্য উপযুক্ত নতুন বইগুলি খুঁজে পাবে.
Textbook of


Textbook of

for Medical Students
(Seventh Edition)
Free online access to
Additional Clinical Cases, Key Concepts & Image Bank

Distinguished Professor
Department of Biochemistry
College of Medicine, Amrita Institute of Medical Sciences
Kochi, Kerala, India
Principal, College of Medicine
Amrita Institute of Medical Sciences, Kerala, India
Dean, Sikkim Manipal Institute of Medical Sciences
Gangtok, Sikkim, India

Sreekumari S MBBS MD

Professor and Head
Department of Biochemistry
Sree Gokulam Medical College and Research Foundation
Thiruvananthapuram, Kerala, India

Kannan Vaidyanathan MBBS MD

Professor and Head
Department of Biochemistry
Pushpagiri Institute of Medical Sciences and Research Center
Thiruvalla, Kerala, India


New Delhi • London • Philadelphia • Panama

Jaypee Brothers Medical Publishers (P) Ltd

Jaypee Brothers Medical Publishers (P) Ltd
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© 2013, DM Vasudevan, Sreekumari S, Kannan Vaidyanathan; 
All rights reserved. No part of this book may be reproduced in any form or by any means without the prior permission of the publisher.
Inquiries for bulk sales may be solicited at: jaypee@jaypeebrothers.com
This book has been published in good faith that the contents provided by the authors contained herein are original, and is intended
for educational purposes only. While every effort is made to ensure accuracy of information, the publisher and the authors specifically
disclaim any damage, liability, or loss incurred, directly or indirectly, from the use or application of any of the contents of this work. If not
specifically stated, all figures and tables are courtesy of the authors. Where appropriate, the readers should consult with a specialist or
contact the manufacturer of the drug or device.
Textbook of Biochemistry for Medical Students
First Edition:
Second Edition:
Third Edition:
Fourth Edition:
Fifth Edition:
Sixth Edition:
Seventh Edition:


ISBN 978-93-5090-530-2
Printed at

Dedicated to
With humility and reverence,
this book is dedicated
at the lotus feet of the Holy Mother,
Sri Mata Amritanandamayi Devi

"Today's world needs people who express goodness in their words and deeds.
If such noble role models set the example for their fellow beings, the darkness
prevailing in today's society will be dispelled, and the light of peace and nonviolence will once again illumine this earth. Let us work together towards this goal".
—Mata Amritanandamayi Devi

Preface to the Seventh Edition
We are glad to present the Seventh edition of the Textbook of Biochemistry for Medical Students. Now, this textbook
is entering the 19th year of existence. With humility, we may state that the medical community of India has warmly
received the previous editions of this book. The Medical Council of India has accepted it as one of the standard
textbooks. We are happy to note that this book has also reached in the hands of medical students of neighboring
countries of Nepal, Pakistan, Bangladesh, Sri Lanka, etc. and also to distant countries in Africa and Europe. We are
very proud to report that the Textbook has a Spanish edition, with wide circulation in the Central and South America.
Apart from the medical community, this book has also become popular to other biological group of students in India.
In retrospect, it gives immense satisfaction to note that this book served the students and faculty for the past two
We are bringing out the new edition of the textbook every 3 years. A major addition of this edition is the
incorporation of clinical case studies in almost all chapters. We hope that this feature will help the students to identify
the clinical relevance of the biochemistry. Further, chapters on clinical chemistry have been extensively updated
and clinically relevant points were further added. Rapid progress has been made in the area of molecular biology
during past few years, and these advances are to be reflected in this book also. The major change in this Seventh
edition is that advanced knowledge has been added in almost all chapters, clinical case studies have been added
in relevant chapters; and a few new chapters were added. The print fonts and font size have also been changed for
better readability.
From the First edition onwards, our policy was to provide not only basic essentials but also some of the advanced
knowledge. About 30% contents of the previous editions were not required for a student aiming for a minimum
pass. A lot of students have appreciated this approach, as it helped them to pass the postgraduate (PG) entrance
examinations at a later stage. However, this asset has paved the way for a general criticism that the extra details are
a burden to the average students. Especially, when read for the first time, the student may find it difficult to sort out
the essential minimum from the desirable bulk. In this Seventh edition, advanced topics are given in small prints. In
essence, this book is composed of three complementary books. The bold printed areas will be useful for the student
at the time of revision just before the examinations; regular printed pages are meant for an average first year MBBS
student and the fine printed paragraphs are targeted to the advanced students preparing for the PG entrance.
Essay questions, short notes, multiple choice questions and viva voce type questions are given as a separate book,
but free of cost. These questions are compiled from the question papers of various universities during the last decade.
These questions will be ideal for students for last-minute preparation for examinations. We are introducing the online
study material, which provides concepts of major topic as well as clinical case studies. This shall be updated through
the year. Hence, students are advised to check the web page at regular intervals.
A textbook will be matured only by successive revisions. In the preface for the First edition, we expressed our
desire to revise the textbook every 3 years. We were fortunate to keep that promise. This book has undergone
metamorphosis during each edition. Chemical structures with computer technology were introduced in the Second
edition. Color printing has been launched in the Third edition. The Fourth edition came out with multicolor printing.
In the Fifth edition, the facts were presented in small paragraphs, so as to aid memory. In the Sixth edition, figures
were drastically increased. In this Seventh edition, about 100 case studies are added. In this book, there are about


Textbook of Biochemistry

1100 figures, 230 tables and 200 boxes (perhaps we could call it as illustrated textbook of biochemistry), altogether
making the book more student-friendly. The quality of paper is also improved during successive editions.
We were pleasantly surprised to receive many letters giving constructive criticisms and positive suggestions to
improve the textbook. These responses were from all parts of the country (we got a few such letters from African
and European students also). Such contributors include Heads of Departments, very senior professors, middle
level teachers and mostly postgraduate students. We have tried to incorporate most of those suggestions, within
the constraints of page limitations. In a way, this book thus became multi-authored, and truly national in character.
This is to place on record, our deep gratitude for all those “pen-friends” who have helped us to improve this book.
The first author desires more interaction with faculty and students who are using this textbook. All are welcome to
communicate at his e-mail address <dmvasudevan@yahoo.co.in>
As indicated in the last edition, the first author is in the process of retirement, and would like to reduce the burden
in due course. A successful textbook is something like a growing institution; individuals may come and go, but the
institution will march ahead. Therefore, we felt the need to induce younger blood into the editorial board. Thus, a
third author has been added in the Sixth edition, so that the torch can been handed over smoothly at an appropriate
time later on. In this Seventh edition, the first author has taken less responsibility in editing the book, while the third
author has taken more effort.
The help and assistance rendered by our postgraduate students in preparing this book are enormous. The official
website of Nobel Academy has been used for pictures and biographies of Nobel laureates. Web pictures, without
copyright protection, were also used in some figures. The remarkable success of the book was due to the active
support of the publishers. This is to record our appreciation for the cooperation extended by Shri Jitendar P Vij (Group
Chairman), Mr Ankit Vij (Managing Director) and Mr Tarun Duneja (Director-Publishing) of M/s Jaypee Brothers
Medical Publishers (P) Ltd, New Delhi, India.
We hope that this Seventh edition will be friendlier to the students and be more attractive to the teachers. Now
this is in your hands to judge.

“End of all knowledge must be building up of character”
—Mahatma Gandhi

DM Vasudevan
Sreekumari S
Kannan Vaidyanathan

Preface to the First Edition
There are many textbooks of biochemistry written by Western and Indian authors. Then what is the need for yet another
textbook? Putting this question to ourselves, we have waited for many years before embarking on this project. Most
Western textbooks do not emphasize nutrition and such other topics, which are very vital to an Indian student. While
Indian authors do cover these portions, they sometimes neglect the expanding fields, such as molecular biology
and immunochemistry. Thus, during our experience of more than 25 years in teaching, the students have been seen
compelled to depend on different textbooks during their study of biochemistry. We have tried to keep a balance
between the basic essentials and the advanced knowledge.
This book is mainly based on the MBBS curriculum. However, some advanced portions have also been given in
almost all chapters. These areas will be very beneficial to the readers preparing for their postgraduate entrance
Chapters on diabetes, cancer and AIDS are included in this book. During their clinical years, the students are
going to see such cases quite more often, hence knowledge of applied biochemistry of these diseases will be very
helpful. The authors, themselves medical graduates, have tried to emphasize medical applications of the theoretical
knowledge in biochemistry in almost all the chapters.
A few questions have been given at the end of most of the chapters. These are not comprehensive to cover all the
topics, but have been included only to give emphasis to certain points, which may otherwise be left unnoticed by
some students.
We are indebted to many persons in compiling this textbook. We are highly obliged to Dr ANP Ummerkutty,
Vice-Chancellor, University of Calicut, for his kind gesture of providing an introduction. Dr M Krishnan Nair, Research
Director, Veterinary College, Trichur, has provided his unpublished electron micrographs for this book. Dr MV
Muraleedharan, Professor of Medicine, and Dr TS Hariharan, Professor of Pharmacology, Medical College, Thrissur,
have gone through the contents of this book. Their valuable suggestions on the applied aspects of biochemistry have
been incorporated. Two of our respected teachers in biochemistry, Professor R Raghunandana Rao and Professor GYN
lyer (both retired) have encouraged this venture. Professor PNK Menon, Dr S Gopinathan Nair, Assistant Professor,
Dr Shyam Sundar, Dr PS Vasudevan and Mr K Ramesh Kumar, postgraduate students of this department, have helped
in collecting the literature and compiling the materials. Mr Joby Abraham, student of this college has contributed
the sketch for some of the figures. Professor CPK Tharakan, retired professor of English, has taken great pains to
go through the entire text and correct the usage of English. The secretarial work has been excellently performed
by Mrs Lizy Joseph. Many of our innumerable graduate and postgraduate students have indirectly contributed by
compelling us to read more widely and thoroughly.
Our expectation is to bring out the new edition every 3 years. Suggestions to improve the contents are welcome
from the teachers.
“A lamp that does not glow itself cannot light another lamp”
—Rabindranath Tagore

DM Vasudevan
Sreekumari S

SECTION A: Chemical Basis of Life

Biochemical Perspective to Medicine


Biomolecules 4; Study of metabolic processes 5; Stabilizing forces in molecules 5; Water: the universal solvent 6;
Principles of thermodynamics 7; Donnan membrane equilibrium 8


Subcellular Organelles and Cell Membranes


Subcellular organelles 10; Nucleus 10; Endoplasmic reticulum 11; Golgi apparatus 12; Lysosomes 12; Peroxisomes 13;
Mitochondria 13; Plasma membrane 14; Specialized membrane structures 16; Transport mechanisms 17


Amino Acids: Structure and Properties


Classification of amino acids 24; Properties of amino acids 27;
General reactions of amino acids 29; Peptide bond formation 31


Proteins: Structure and Function


Structure of proteins 34; Study of protein structure 39; Physical properties of proteins 41;
Precipitation reactions of proteins 41; Classification of proteins 42; Quantitative estimation 44


Enzymology: General Concepts and Enzyme Kinetics


Classification of enzymes 48; Co-enzymes 49; Mode of action of enzymes 51; Michaelis-Menten theory 53; Fischer's template theory 53;
Koshland's induced fit theory 53; Active site or active center of enzyme 54; Thermodynamic considerations 54; Enzyme kinetics 55;
Factors influencing enzyme activity 56; Specificity of enzymes 65; Iso-enzymes 66


Chemistry of Carbohydrates


Nomenclature 69; Stereoisomers 70; Reactions of monosaccharides 73; Disaccharides 76; Polysaccharides 78;
Heteroglycans 79; Mucopolysaccharides 80; Glycoproteins and mucoproteins 81


Chemistry of Lipids


Classification of lipids 83; Fatty acids 84; Saturated fatty acids 85; Unsaturated fatty acids 85;
Trans fatty acids 86; Neutral fats 87; Phospholipids 89

SECTION B: General Metabolism

Overview of Metabolism


Experimental study of metabolism 97; Metabolism 98; Metabolic profile of organs 99


Major Metabolic Pathways of Glucose


Digestion of carbohydrates 105; Absorption of carbohydrates 106; Glucose metabolism 107;
Glycolysis 108; Metabolic fate of pyruvate 115; Gluconeogenesis 117


Other Metabolic Pathways of Glucose
Glycogen metabolism 123; Degradation of glycogen (glycogenolysis) 124; Glycogen synthesis (glycogenesis) 125;
Glycogen storage diseases 128; Hexose monophosphate shunt pathway 129; Oxidative phase 130; Non-oxidative phase 130;
Glucuronic acid pathway of glucose 134; Polyol pathway of glucose 135



Textbook of Biochemistry


Metabolic Pathways of Other Carbohydrates


Fructose metabolism 137; Galactose metabolism 138; Metabolism of alcohol 140; Metabolism of amino sugars 142; Glycoproteins 142


Metabolism of Fatty Acids


Digestion of lipids 147; Absorption of lipids 148; Beta oxidation of fatty acids 151; Oxidation of odd chain fatty acids 154; Alpha oxidation 155;
Omega oxidation 155; De novo synthesis of fatty acids 156; Synthesis of triacylglycerols 160; Metabolism of adipose tissue 161;
Fatty liver and lipotropic factors 162; Metabolism of ketone bodies 163; Ketosis 164


Cholesterol and Lipoproteins


Biosynthesis of cholesterol 170; Plasma lipids 173; Chylomicrons 175; Very low density lipoproteins 176;
Low density lipoproteins 177; High density lipoprotein 179; Free fatty acid 181; Formation of bile acids 182


MCFA, PUFA, Prostaglandins and Compound Lipids


Monounsaturated fatty acids 185; Polyunsaturated fatty acids 186; Eicosanoids 188; Prostaglandins 188; Synthesis of compound lipids 191


General Amino Acid Metabolism (Urea Cycle, One Carbon Metabolism)


Digestion of proteins 196; Formation of ammonia 200; Disposal/detoxification of ammonia 203; Urea cycle 203; One-carbon metabolism 207


Simple, Hydroxy and Sulfur-containing Amino Acids (Glycine, Serine, Methionine, Cysteine)


Glycine 210; Creatine and creatine phosphate 211; Serine 213; Alanine 215; Threonine 215;
Methionine 216; Cysteine 217; Cystinuria 219; Homocystinurias 220


Acidic, Basic and Branched Chain Amino Acids (Glutamic Acid, Aspartic Acid, Glutamine, Asparagine,
Lysine, Arginine, Nitric Oxide, Valine, Leucine, Isoleucine)
Glutamic acid 223; Glutamine 224; Glutamate transporters 225; Aspartic acid 226;
Asparagine 226; Arginine 226; Nitric oxide 227; Polyamines 229; Branched chain amino acids 230



Aromatic Amino Acids (Phenylalanine, Tyrosine, Tryptophan, Histidine, Proline) and Amino Acidurias


Phenylalanine 232; Tyrosine 233; Phenylketonuria 236; Alkaptonuria 237; Albinism 238;
Hypertyrosinemias 239; Tryptophan 239; Histidine 243; Proline and hydroxyproline 244; Aminoacidurias 245


Citric Acid Cycle


Regulation of citric acid cycle 253


Biological Oxidation and Electron Transport Chain


Redox potentials 256; Biological oxidation 256; Enzymes and co-enzymes 257; High energy compounds 258;
Organization of electron transport chain 260; Chemiosmotic theory 263


Heme Synthesis and Breakdown


Structure of heme 270; Biosynthesis of heme 271; Catabolism of heme 276; Hyperbilirubinemias 279


Hemoglobin (Structure, Oxygen and Carbon Dioxide Transport, Abnormal Hemoglobins)


Structure of hemoglobin 283; Transport of oxygen by hemoglobin 284; Transport of carbon dioxide 287; Hemoglobin derivatives 289;
Hemoglobin (globin chain) variants 290; Thalassemias 293; Myoglobin 294; Anemias 295; Hemolytic anemia 295

SECTION C: Clinical and Applied Biochemistry

Clinical Enzymology and Biomarkers


Clinical enzymology 301; Creatine kinase 302; Cardiac troponins 303; Lactate dehydrogenase 303;
Alanine amino transferase 305; Aspartate amino transferase 305; Alkaline phosphatase 305;
Prostate specific antigen 306; Glucose-6-phosphate dehydrogenase 307; Amylase 307; Lipase 308; Enolase 308


Regulation of Blood Glucose; Insulin and Diabetes Mellitus
Regulation of blood glucose 311; Reducing substances in urine 316; Hyperglycemic hormones 322;
Glucagon 322; Diabetes mellitus 323; Acute metabolic complications 326




Hyperlipidemias and Cardiovascular Diseases


Atherosclerosis 334; Plasma lipid profile 336; Risk factors for atherosclerosis 336;
Prevention of atherosclerosis 339; Hypolipoproteinemias 341; Hyperlipidemias 342


Liver and Gastric Function Tests


Functions of liver 346; Clinical manifestations of liver dysfunction 348; Studies on malabsorption 359


Kidney Function Tests


Renal function tests 361; Abnormal constituents of urine 364; Markers of glomerular filtration rate 366;
Markers of glomerular permeability 371; Tests for tubular function 373


Plasma Proteins


Electrophoresis 378; Albumin 380; Transport proteins 382;
Acute phase proteins 383; Clotting factors 385; Abnormalities in coagulation 386


Acid-Base Balance and pH


Acids and bases 390; Buffers 392; Acid-base balance 393; Buffers of the body fluids 393; Respiratory regulation of pH 395;
Renal regulation of pH 395; Cellular buffers 397; Disturbances in acid-base balance 397


Electrolyte and Water Balance


Intake and output of water 407; Osmolality of extracellular fluid 408;
Sodium 411; Potassium 413; Chloride 416


Body Fluids (Milk, CSF, Amniotic Fluid, Ascitic Fluid)


Milk 420; Cerebrospinal fluid 421; Amniotic fluid 422; Ascitic fluid 423


Metabolic Diseases


Prenatal diagnosis 424; Newborn screening 427; Laboratory investigations to diagnose metabolic disorders 427


Free Radicals and Antioxidants


Clinical significance 436


Clinical Laboratory; Quality Control


Reference values 439; Preanalytical variables 440; Specimen collection 441; Quality control 443


General Techniques for Separation, Purification and Quantitation


Electrophoresis 446; Chromatography 448; Radioimmunoassay 452; ELISA test 453;
Colorimeter 455; Autoanalyzer 457; Mass spectrometry 458

SECTION D: Nutrition

Fat Soluble Vitamins (A, D, E, K)


Vitamin A 464; Vitamin D (cholecalciferol) 469; Vitamin E 473; Vitamin K 474


Water Soluble Vitamins - 1 (Thiamine, Riboflavin, Niacin, Pyridoxine, Pantothenic Acid, Biotin)


Thiamine (vitamin B1 ) 477; Riboflavin (vitamin B2 ) 479; Niacin 480; Vitamin B6 482; Pantothenic acid 484; Biotin 485


Water Soluble Vitamins - 2 (Folic Acid, Vitamin B12 and Ascorbic Acid)


Mineral Metabolism and Abnormalities


Folic acid 488; Vitamin B12 491; Choline 494; Inositol 495; Ascorbic acid (vitamin C) 495; Rutin 499; Flavonoids 499


Calcium 502; Phosphorus 511; Magnesium 512; Sulfur 513; Iron 514; Copper 520; Iodine 521; Zinc 522; Fluoride 522;
Selenium 522; Manganese 523; Molybdenum 523; Cobalt 523; Nickel 523; Chromium 523; Lithium 524


Textbook of Biochemistry

Energy Metabolism and Nutrition


Importance of carbohydrates 530; Nutritional importance of lipids 531; Importance of proteins 532;
Protein-energy malnutrition 534; Obesity 536; Prescription of diet 538


Detoxification and Biotransformation of Xenobiotics


Phase one reactions 545; Phase two reactions; conjugations 546; Phase three reactions 548


Environmental Pollution and Heavy Metal Poisons


Corrosives 550; Irritants 551; Heavy metal poisons 551; Pesticides and insecticides 553;
Occupational and industrial hazards 553; Air pollutants 553

SECTION E: Molecular Biology

Nucleotides: Chemistry and Metabolism


Biosynthesis of purine nucleotides 563; Uric acid 566; Gout 566; De novo synthesis of pyrimidine 569


Deoxyribonucleic Acid: Structure and Replication


Structure of DNA 574; Replication of DNA 578; DNA repair mechanisms 582




Ribonucleic acid 587; Transcription process 589


Genetic Code and Translation


Protein biosynthesis 596; Translation process 599


Control of Gene Expression


Mutations 612; Classification of mutations 612; Cell cycle 614; Regulation of gene expression 616; Viruses 620


Recombinant DNA Technology and Gene Therapy


Recombinant DNA technology 624; Vectors 626; Gene therapy 629; Stem cells 631


Molecular Diagnostics and Genetic Techniques


Hybridization and blot techniques 633; Polymerase chain reaction 638; Mutation detection techniques 641

SECTION F: Hormones

Mechanisms of Action of Hormones and Signaling Molecules



Hypothalamic and Pituitary Hormones


Hypothalamic neuropeptides 659; Hormones of anterior pituitary 660


Steroid Hormones


Adrenal cortical hormones 664; Sex hormones 669


Thyroid Hormones



Gut Hormones


SECTION G: Advanced Biochemistry

Structure of immunoglobulins 687; Paraproteinemias 690; Complement system 691; Immunodeficiency states 692




Biochemistry of AIDS and HIV


The human immunodeficiency virus 701; Anti-HIV drugs 703


Biochemistry of Cancer


Oncogenic viruses 707; Oncogenes 709; Tumor markers 713; Anticancer drugs 716


Tissue Proteins in Health and Disease


Collagen 720; Elastin 723; Muscle proteins 724; Lens proteins 727; Prions 727; Biochemistry of aging 730


Applications of Isotopes in Medicine


Isotopes 733; Radioactivity 733; Biological effects of radiation 738


Signal Molecules and Growth Factors






Chemical Basis of Life

Chapter 1
Chapter 2
Chapter 3
Chapter 4
Chapter 5
Chapter 6
Chapter 7

Biochemical Perspective to Medicine
Subcellular Organelles and Cell Membranes
Amino Acids: Structure and Properties
Proteins: Structure and Function
Enzymology: General Concepts and Enzyme Kinetics
Chemistry of Carbohydrates
Chemistry of Lipids

Perspective to Medicine
Chapter at a Glance
The reader will be able to answer questions on the following topics:
¾¾History of biochemistry
¾¾Ionic bonds
¾¾Hydrogen bonding

Biochemistry is the language of biology. The tools for
research in all the branches of medical science are mainly
biochemical in nature. The study of biochemistry is
essential to understand basic functions of the body. This
study will give information regarding the functioning of
cells at the molecular level. How the food that we eat is
digested, absorbed, and used to make ingredients of the
body? How does the body derive energy for the normal
day to day work? How are the various metabolic processes
interrelated? What is the function of genes? What is the
molecular basis for immunological resistance against
invading organisms? Answer for such basic questions can
only be derived by a systematic study of biochemistry.
Modern day medical practice is highly dependent on
the laboratory analysis of body fluids, especially the blood.
The disease manifestations are reflected in the composition
of blood and other tissues. Hence, the demarcation of
abnormal from normal constituents of the body is another
aim of the study of biochemistry.

¾¾Hydrophobic interactions
¾¾Principles of thermodynamics
¾¾Donnan membrane equilibrium

The word chemistry is derived from the Greek word "chemi" (the
black land), the ancient name of Egypt. Indian medical science, even from
ancient times, had identified the metabolic and genetic basis of diseases.
Charaka, the great master of Indian Medicine, in his treatise (circa 400
BC) observed that madhumeha (diabetes mellitus) is produced by the
alterations in the metabolism of carbohydrates and fats; the statement
still holds good.
Biochemistry has developed as an offshoot of organic chemistry,
and this branch was often referred as "physiological chemistry". The
term "Biochemistry" was coined by Neuberg in 1903 from Greek
words, bios (= life) and chymos (= juice). One of the earliest treatises in
biochemistry was the "Book of Organic Chemistry and its Applications
to Physiology and Pathology", published in 1842 by Justus von Liebig

460–377 BC

400 BC

500 BC


Textbook of Biochemistry

(1803–73), who introduced the concept of metabolism. The "Textbook
of Physiological Chemistry" was published in 1877 by Felix HoppeSeyler (1825–95), who was Professor of Physiological chemistry at
Strausbourge University, France. Some of the milestones in the develop­
ment of the science of biochemistry are given in Table 1.1.
The practice of medicine is both an art and a science. The word
“doctor” is derived from the Latin root, "docere", which means “to
teach”. Knowledge devoid of ethical back­ground may sometimes be
disastrous! Hippocrates (460 BC to 377 BC), the father of modern
medicine articulated "the Oath”. About one century earlier, Sushrutha
(?500 BC), the great Indian surgeon, enunciated a code of conduct for
the medical practitioners, which is still valid. He proclaims: “You must
speak only truth; care for the good of all living beings; devote yourself to
the healing of the sick even if your life be lost by your work; be simply
clothed and drink no intoxicant; always seek to grow in knowledge; in
face of God, you can take upon yourself these vows.”
Biochemistry is perhaps the most rapidly developing discipline
in medicine. No wonder, the major share of Nobel prizes in medicine
has gone to research workers engaged in biochemistry. Thanks to the
advent of DNA recombinant tech­no­logy, genes can now be transferred
from one person to another, so that many of the genetically determined
diseases are now amenable to gene therapy. Many genes, (e.g. human
insulin gene) have already been transferred to microorganisms for large
scale production of human insulin. Advances in genomics like RNA
interference for silencing of genes and creation of transgenic animals
by gene targeting of embryonic stem cells are opening up new vistas
in therapy of diseases like cancer and AIDS. It is hoped that in future,
the physician will be able to treat the patient, understanding his genetic
basis, so that very efficient "designer medicine" could cure the diseases.
TABLE 1.1: Milestones in history of Biochemistry


Landmark discoveries

Louis Pasteur
Edward Buchner
Fiske and Subbarao
Hans Krebs
Avery and Macleod
Watson and Crick
Paul Berg
Kary Mullis


Isolated urea from urine
Oxidation of food stuffs
Synthesis of urea
Enzyme catalysis theory
Fermentation process
Extracted enzymes
Isolated ATP from muscle
Creatine phosphate
Citric acid cycle
DNA is genetic material
TCA cycle in mitochondria
Structure of DNA
Genetic code in mRNA
Sequenced gene for tRNA
Synthesized the gene
Recombinant DNA technology
Polymerase chain reaction
Human genome project started
Draft human genome
Human genome project completed


ENCyclopedia Of DNA Elements


The large amount of data, especially with regard to single nucleotide
polymorphisms (SNPs) that are available, could be harnessed by
"Bioinformatics". Computers are already helping in drug designing
process. Studies on oncogenes have identified molecular mechanisms of
control of normal and abnormal cells. Medical practice is now depending
more on the science of Medical Biochemistry. With the help of Human
genome project (HGP) the sequences of whole human genes are now
available; it has already made great impact on medicine and related
health sciences.

More than 99% of the human body is composed of 6
elements, i.e. oxygen, carbon, hydrogen, nitrogen, calcium
and phos­phorus. Human body is composed of about 60%
water, 15% proteins, 15% lipids, 2% carbohydrates and
8% minerals. Molecular structures in organisms are built
from 30 small precursors, sometimes called the alphabets
of biochemistry. These are 20 amino acids, 2 purines,
3 pyrimidines, sugars (glucose and ribose), palmitate,
glycerol and choline.
In living organisms, biomolecules are ordered into
a hierarchy of increasing molecular complexity. These
biomolecules are covalently linked to each other to form
macromolecules of the cell, e.g. glucose to glyco­
amino acids to proteins, etc. Major complex biomolecules
are proteins, polysaccharides, lipids and nucleic acids. The
macromole­cules associate with each other by noncovalent
forces to form supramolecular systems, e.g. ribosomes,




Louis Pasteur


Justus von Liebig

Johannes van Albert Lehninger
der Waals
NP 1910,

Chapter 1: Biochemical Perspective to Medicine
Finally at the highest level of organization in the
hierarchy of cell structure, various supramolecular
comple­xes are further assembled into cell organelle. In
prokaryotes (e.g. bacteria; Greek word "pro" = before;
karyon = nucleus), these macromolecules are seen in a
homogeneous matrix; but in eukaryotic cells (e.g. higher
organisms; Greek word "eu" = true), the cytoplasm
contains various subcellular organelles. Comparison of
prokaryotes and eukaryotes are shown in Table 1.2.

Our food contains carbohydrates, fats and proteins as
principal ingredients. These macromolecules are to be
first broken down to small units; carbohydrates to monosaccharides and proteins to amino acids. This process is
taking place in the gastrointestinal tract and is called
digestion or primary metabolism. After absorption, the
small molecules are further broken down and oxidized
to carbon dioxide. In this process, NADH or FADH2 are
generated. This is named as secondary or intermediary
metabolism. Finally, these reducing equi­valents enter the
electron transport chain in the mitochondria, where they
are oxidized to water; in this process energy is trapped as
ATP. This is termed tertiary metabolism. Metabolism is
the sum of all chemical changes of a compound inside the
body, which includes synthesis (anabolism) and breakdown
(catabolism). (Greek word, kata = down; ballein = change).

electrons from the outer most orbit of an electropositive
atom to the outermost orbit of an electronegative atom. This
transfer results in the formation of a ‘cation’ and an ‘anion’,
which get consequently bound by an ionic bond. Common
examples of such compounds include NaCl, KBr and NaF.
With regard to protein chemistry, positive charges are
produced by epsilon amino group of lysine, guanidium
group of arginine and imidazolium group of histidine.
Negative charges are provided by beta and gamma carboxyl
groups of aspartic acid and glutamic acid (Fig.1.3).

Hydrogen Bonds
These are formed by sharing of a hydro­gen between two
electron donors. Hydrogen bonds result from electrostatic

Fig. 1.1: Covalent bond

Covalent Bonds
Molecules are formed by sharing of electrons between
atoms (Fig. 1.1).

Ionic Bonds or Electrostatic Bonds
Ionic bonds result from the electrostatic attraction
between two ionized groups of opposite charges
(Fig.1.2). They are formed by transfer of one or more
TABLE 1.2: Bacterial and mammalian cells
Prokaryotic cell
Eukaryotic cell
Large; 1000 to 10,000 times
Cell wall
Membrane of lipid bilayer
Not defined
Well defined
Organelles Nil
Several; including mitochondria
and lysosomes


Fig. 1.2: Ionic bond

Fig. 1.3: Ionic bonds used in protein interactions


Textbook of Biochemistry

attraction between an electronegative atom and a hydrogen
atom that is bonded covalently to a second electronegative
atom. Normally, a hydrogen atom forms a covalent bond
with only one other atom. However, a hydrogen atom covalently bonded to a donor atom, may form an additional
weak association, the hydrogen bond with an acceptor atom.
In biological systems, both donors and acceptors are usually
nitrogen or oxygen atoms, especially those atoms in amino
(NH2) and hydroxyl (OH) groups.
With regard to protein chemistry, hydrogen releasing
groups are –NH (imidazole, in dole, peptide); –OH (serine,
threonine) and –NH2 (arginine, lysine). Hydrogen accep­ting
groups are COO— (aspartic, glutamic) C=O (peptide); and S–S
(disulphide). The DNA structure is maintained by hydrogen
bonding between the purine and pyrimidine residues.

Johannes van der Waals (1837–1923). He was awarded
Nobel prize in 1910. These are short range attractive
forces between chemical groups in contact. Van der Waals
interactions occur in all types of molecules, both polar and
non-polar. The energy of the van der Waals interaction
is about 1 kcal/mol and are unaffected by changes in
pH. This force will drastically reduce, when the distance
between atoms is increased. Although very weak, van der
Waals forces collectively contribute maximum towards the
stability of protein structure, especially in preserving the
non-polar interior structure of proteins.


These are very weak forces of attraction between all atoms,
due to oscillating dipoles, described by the Dutch physicist

Water constitutes about 70 to 80 percent of the weight of
most cells. The hydrogen atom in one water molecule is
attracted to a pair of electrons in the outer shell of an oxygen
atom in an adjacent molecule. The structure of liquid water
contains hydrogen-bonded networks (Fig. 1.5).
The crystal structure of ice depicts a tetrahedral
arrangement of water molecules. On melting, the molecules
get much closer and this results in the increase in density
of water. Hence, liquid water is denser than solid ice. This
also explains why ice floats on water.
Water molecules are in rapid motion, constantly making
and breaking hydrogen bonds with adjacent molecules.
As the temperature of water increases toward 100°C, the
kinetic energy of its molecules becomes greater than the
energy of the hydrogen bonds connecting them, and the
gaseous form of water appears. The unique properties of
water make it the most preferred medium for all cellular
reactions and interactions.

Fig. 1.4: Hydrophobic interaction

Fig. 1.5: Water molecules hydrogen bonded

Hydrophobic Interactions
Non-polar groups have a tendency to associate with each other
in an aqueous environment; this is referred to as hydrophobic
interaction. These are formed by interactions between
nonpolar hydrophobic side chains by eliminating water
molecules. The force that causes hydrophobic molecules
or nonpolar portions of molecules to aggregate together
rather than to dissolve in water is called the ‘hydrophobic
bond’ (Fig.1.4). This serves to hold lipophilic side chains of
amino acids together. Thus non-polar molecules will have
minimum exposure to water molecules.

Van Der Waals Forces

Chapter 1: Biochemical Perspective to Medicine
a. Water is a polar molecule. Molecules with polar bonds
that can easily form hydrogen bonds with water can
dissolve in water and are termed “hydrophilic”.
b. It has immense hydrogen bonding capacity both with
other molecules and also the adjacent water molecules.
This contributes to cohesiveness of water.
c. Water favors hydrophobic interactions and provides a
basis for metabolism of insoluble substances.
Water expands when it is cooled from 4° C to 0° C,
while normally liquids are expected to contract due to
cooling. As water is heated from 0° C to 4° C, the hydrogen
bonds begin to break. This results in a decrease in volume
or in other words, an increase in density. Hence, water
attains high density at 4° C. However, above 4° C the effect
of temperature predominates.

Thermodynamics is concerned with the flow of heat and
it deals with the relationship between heat and work.
Bioenergetics, or biochemical thermodynamics, is the
study of the energy changes accompanying biochemical
reactions. Biological systems use chemical energy to
power living processes.

First Law of Thermodynamics
The total energy of a system, including its surroundings,
remains constant. Or, ∆E = Q – W, where Q is the heat
absorbed by the system and W is the work done. This is
also called the law of conservation of energy. If heat is
transformed into work, there is proportionality between
the work obtained and the heat dissipated. A system is an
object or a quantity of matter, chosen for observation. All
other parts of the universe, outside the boundary of the
system, are called the surrounding.

Second Law of Thermodynamics
The total entropy of a system must increase if a
process is to occur spontaneously. A reaction occurs
spontaneously if ∆E is negative, or if the entropy of the
system increases. Entropy (S) is a measure of the degree
of randomness or disorder of a system. Entropy becomes
maximum in a system as it approaches true equilibrium.
Enthalpy is the heat content of a system and entropy
is that fraction of enthalpy which is not available to do
useful work.


A closed system approaches a state of equilibrium.
Any system can spontaneously proceed from a state of low
probability (ordered state) to a state of high probability
(disordered state). The entropy of a system may decrease
with an increase in that of the surroundings. The second
law may be expressed in simple terms as Q = T × ∆S,
where Q is the heat absorbed, T is the absolute temperature
and ∆S is the change in entropy.

Gibb's Free Energy Concept
The term free energy is used to get an equation combining
the first and second laws of thermodynamics. Thus, ∆G =
∆H – T∆S, where ∆G is the change in free energy, ∆H is
the change in enthalpy or heat content of the system and ∆S
is the change in entropy. The term free energy denotes a
portion of the total energy change in a system that is
available for doing work.
For most biochemical reactions, it is seen that ∆H is
nearly equal to ∆E. So, ∆G = ∆E – T∆S. Hence, ∆G or
free energy of a system depends on the change in internal
energy and change in entropy of a system.

Standard Free Energy Change
It is the free energy change under standard conditions. It is
designated as ∆G0. The standard conditions are defined for
biochemical reactions at a pH of 7 and 1 M concen­tration,
and differentiated by a priming sign ∆G0´. It is directly
related to the equilibrium constant. Actual free energy
changes depend on reactant and product.
Most of the reversible metabolic reactions are near
equilibrium reactions and therefore their ∆G is nearly zero.
The net rate of near equilibrium reactions are effectively
regulated by the relative concentration of substrates
and products. The metabolic reactions that function far
from equilibrium are irreversible. The velocities of these
reactions are altered by changes in enzyme activity. A
highly exergonic reaction is irreversible and goes to
completion. Such a reaction that is part of a metabolic
pathway, confers direction to the pathway and makes the
entire pathway irreversible.
Laws of thermodynamics have many applications in
biology and biochemistry, such as study of ATP hydrolysis,
membrane diffusion, enzyme catalysis as well as DNA
binding and protein stability. These laws have been used to
explain hypothesis of origin of life.


Textbook of Biochemistry

Three Types of Reactions
A. A reaction can occur spontaneously when ∆G is
negative. Then the reaction is exergonic. If ∆G is of
great magnitude, the reaction goes to completion and
is essentially irreversible.
B. When ∆G is zero, the system is at equilibrium.
C. For reactions where ∆G is positive, an input of energy
is required to drive the reaction. The reaction is termed
as endergonic. (Examples are given in Chapter 5).
Similarly a reaction may be exothermic (∆H is negative),
isothermic (∆H is zero) or endothermic (∆H is positive).
Energetically unfavourable reaction may be driven
forward by coupling it with a favourable reaction.
Glucose + Pi → Glucose-6-phosphate
ATP + H2O → ADP + Pi
(reaction 2)
Glucose + ATP→ Glucose-6-phosphate+ADP (3)
Reaction 1 cannot proceed spontaneously. But the
2nd reaction is coupled in the body, so that the reaction
becomes possible. For the first reaction, ∆G0 is +13.8 kJ/
mole; for the second reaction, ∆G0 is –30.5 kJ/mole. When
the two reactions are coupled in the reaction 3, the ∆G0
becomes –16.7 kJ/mole, and hence the reaction becomes
possible. Details on ATP and other high-energy phosphate
bonds are described in Chapter 20.
Reactions of catabolic pathways (degradation or
oxidation of fuel molecules) are usually exergonic. On the
other hand, anabolic pathways (synthetic reactions or building
up of compounds) are endergonic. Metabolism constitutes
anabolic and catabolic processes that are well co-ordinated.

When two solutions are separated by a membrane
permeable to both water and small ions, but when one of
the compartments contains impermeable ions like proteins,
distribution of permeable ions occurs according to the
calculations of Donnan.



Fig. 1.6: Donnan membrane equilibrium

In Figure 1.6, the left compartment contains NaR,
which will dissociate into Na+ and R¯. Then Na+ can diffuse
freely, but R¯ having high molecular weight cannot diffuse.
The right compartment contains NaCl, which dissociates
into Na+ and Cl¯, in which case, both ions can diffuse freely.
Thus, if a salt of NaR is placed in one side of a
membrane, at equilibrium
Na+ × R¯ × H+ × OH¯ = Na+ × OH¯ × H+
To convey the meaning of the mathematical values, a
hypothetical quantity of each of the ion is also incorporated
in brackets. Initially 5 molecules of NaR are added to the
left compartment and 10 molecules of NaCl in the right
compartment and both of them are ionized (Fig.1.6A).
When equilibrium is reached, the distributions of ions are
shown in Figure 1.6B. According to Donnan's equilibrium,
the products of diffusible electrolytes in both the
compartments will be equal, so that
[Na+] L × [Cl¯ ] L = [Na+] R × [Cl¯ ] R
If we substitute the actual numbers of ions, the formula
9 × 4 in left = 6 × 6 in right
Donnan's equation also states that the electrical
neutrality in each compartment should be maintained. In
other words the number of cations should be equal to the
number of anions, such that
		 In left
: Na+= R¯+ Cl¯; substituting: 9 = 5 + 4
		 In right
: Na+ = Cl¯; substituting: 6 = 6
The equation should also satisfy that the number
of sodium ions before and after the equilibrium are the
same; in our example, initial Na+ in the two compartments
together is 5 + 10 = 15; after equilibrium also, the value is
9 + 6 = 15. In the case of chloride ions, initial value is 10
and final value is also 4 + 6 = 10.
In summary, Donnan's equations satisfy the following
1. The products of diffusible electrolytes in both
compartments are equal.
2. The electrical neutrality of each compartment is
3. The total number of a particular type of ions before
and after the equilibrium is the same.
4. As a result, when there is non-diffusible anion on
one side of a membrane, the diffusible cations are
more, and diffusible anions are less, on that side.

Chapter 1: Biochemical Perspective to Medicine

Clinical Applications of the Equation
1. The total concentration of solutes in plasma will be
more than that of a solution of same ionic strength
containing only diffusible ions; this provides the net
osmotic gradient (see under Albumin, in Chapter 28).
2. The lower pH values within tissue cells than in the
surrounding fluids are partly due to the concentrations
of negative protein ions within the cells being higher
than in surrounding fluids.
3. The pH within red cells is lower than that of the
surrounding plasma is due, in part, to the very high


concentration of negative non-diffusible hemoglobin
ions. This will cause unequal distribution of H+ ions
with a higher concentration within the cell.
4. The chloride shift in erythrocytes as well as higher
concentration of chloride in CSF are also due to
Donnan's effect.
5. Osmolarity of body fluid compartments and sodium
concentration will follow Donnan equation.
6. Different steps of water purification employ the
same principle and may be cited as an example of
industrial application of the equation.

Subcellular Organelles
and Cell Membranes
Chapter at a Glance
The reader will be able to answer questions on the following topics:
¾¾Transport mechanisms
¾¾Endoplasmic reticulum
¾¾Simple and facilitated diffusion
¾¾Golgi apparatus
¾¾Ion channels
¾¾Active transport
¾¾Uniport, symport and antiport
¾¾Plasma membrane

Cells contain various organized structures, collectively
called as cell organelles (Fig.2.1). When the cell membrane
is disrupted, either by mechanical means or by lysing the
membrane by Tween-20 (a lipid solvent), the organized
particles inside the cell are homogenized. This is usually
carried out in 0.25M sucrose at pH 7.4. The organelles
could then be separated by applying differential centrifugal
forces (Table 2.1). Albert Claude got Nobel prize in 1974
for fractionating subcellular organelles.

1. It is the most prominent organelle of the cell. All cells
in the body contain nucleus, except mature RBCs in
circulation. The uppermost layer of skin also may not
possess a readily identifiable nucleus. In some cells,
nucleus occupies most of the available space, e.g.
small lymphocytes and spermatozoa.

Marker Enzymes
Some enzymes are present in certain organelles only; such
specific enzymes are called as marker enzymes (Table 2.1).
After centrifugation, the separated organelles are identified
by detection of marker enzymes in the sample.

NP 1974

NP 1906

de Duve
NP 1974

NP 1974

Chapter 2: Subcellular Organelles and Cell Membranes
2. Nucleus is surrounded by two membranes—the inner
one is called perinuclear membrane with numerous
pores (Fig. 2.2) and the outer membrane is continuous
with membrane of endoplasmic reticulum.
3. Nucleus contains the DNA, the chemical basis of
genes, which governs all the functions of the cell.
The very long DNA molecules are complexed with
proteins to form chromatin and are further organized
into chromosomes.
4. DNA replication and RNA synthesis (transcription)
are taking place inside the nucleus.
5. In some cells, a portion of the nucleus may be seen as
lighter shaded area; this is called nucleolus (Fig. 2.2).
TABLE 2.1: Separation of subcellular organelles
Pellet formed at the
Marker enzyme
centrifugal force of
600–750 x g, 10 min
Mitochondria 10,000–15,000 x g,
Inner membrane:
10 min
ATP Synthase
18,000–25,000 x g,
10 min
35,000–40,000 x g,
30 min
75,000–100,000 x g,
Glucose-6100 min

Fig. 2.1: A typical cell


This is the area for RNA processing and ribosome
synthesis. The nucleolus is very prominent in cells
actively synthesizing proteins. Gabriel Valentine in
1836 described the nucleolus.
6. Vesicular transport across membrane is by endocytosis
and exocytosis. Importin and exportin proteins are
involved, and it is helped by RanGAP proteins.

1. It is a network of interconnecting membranes enclosing channels or cisternae, that are continuous from
outer nuclear envelope to outer plasma membrane.

Fig. 2.2: Nucleus






Textbook of Biochemistry
Under electron microscope, the reticular arrangements will have railway track appearance (Fig. 2.1).
George Palade was awarded Nobel prize in 1974, who
identified the ER.
This will be very prominent in cells actively
synthesizing proteins, e.g. immunoglobulin secreting
plasma cells. The proteins, glycoproteins and
lipoproteins are synthesised in the ER.
Detoxification of various drugs is an important
function of ER. Microsomal cytochrome P-450
hydroxylates drugs, such as benzpyrine, aminopyrine, aniline, morphine, phenobarbitone, etc.
According to the electron microscopic appearance,
the ER is generally classified into rough and smooth
varieties. The rough appearance is due to ribosomes
attached to cytoplasmic side of membrane where the
proteins are being synthesized.
When cells are fractionated, the complex ER is
disrupted in many places. They are automatically
reassembled to form microsomes.

6. ERGIC (Endoplasmic reticulum - Golgi intermediate compartment):
The synthesized protein pass through this compartment before going
to the cis Golgi.

1. Camillo Golgi described the structure in 1898 (Nobel
prize 1906). The Golgi organelle is a network of
flattened smooth membranes and vesicles. It may be
considered as the converging area of endoplasmic
reticulum (Fig. 2.1).
2. While moving through ER, carbohydrate groups are
successively added to the nascent proteins. These
glycoproteins reach the Golgi area.

3. Golgi apparatus is composed of cis, medial and trans cisternae.
Glycoproteins are generally transported from ER to cis Golgi
(proximal cisterna), then to medial Golgi (intermediate cisterna)
and finally to trans Golgi (distal cisterna) for temporary storage.
Trans Golgi is particularly abundant with vesicles containing
glycoproteins. Newly synthesized proteins are sorted first
according to the sorting signals available in the proteins. Then they
are packaged into transport vesicles having different types of coat
proteins. Finally they are transported into various destinations; this
is an energy dependent process.

4. Main function of Golgi apparatus is protein sorting,
packaging and secretion.
5. The finished products may have any one of the
following destinations:
a. They may pass through plasma membrane to
the surrounding medium. This forms continuous



secretion, e.g. secretion of immunoglobulins by
plasma cells.
They reach plasma membrane and form an integral
part of it, but not secreted.
They form a secretory vesicle, where these products
are stored for a longer time. Under appropriate
stimuli, the contents are secreted. Release of
trypsinogen by pancreatic acinar cells and release
of insulin by beta cells of Langerhans are cited as
The synthesized materials may also reach
lysosome packets.
Golgi bodies are fragmented during mitosis, but
get reorganized by interaction with microtubules.
Connective tissue disorders like Sjogren’s
syndrome are found to be associated with antigolgi antibodies.

1. Discovered in 1950 by Christian de Duve (Nobel prize
1974), lysosomes are tiny organelles. Solid wastes
Box 2.1: Clinical applications of lysosomes
1. In gout, urate crystals are deposited around knee joints
(see Chapter 39). These crystals when phagocyto­sed, cause
physical damage to lysosomes and release of enzymes.
Inflammation and arthritis result.
2. Following cell death, the lysosomes rupture releasing the
hydrolytic enzymes which bring about postmortem autolysis.
3. Lysosomal proteases, cathepsins are implicated in tumor
metastasis. Cathepsins are normally restricted to the interior
of lysosomes, but certain cancer cells liberate the cathepsins
out of the cells. Then cathepsins degrade the basal lamina by
hydrolyzing collagen and elastin, so that other tumor cells can
travel out to form distant metastasis.
4. There are a few genetic diseases, where lysosomal enzymes
are deficient or absent. This leads to accumulation of lipids or
polysaccharides (see Chapters 10 and 14).
5. Silicosis results from inhalation of silica particles into the lungs
which are taken up by phagocytes. Lysosomal membrane
ruptures, releasing the enzymes. This stimulates fibroblast
to proliferate and deposit collagen fibers, resulting in fibrosis
and decreased lungs elasticity.
6. Inclusion cell (I-cell) disease is a rare condition in which
lysosomes lack in enzymes, but they are seen in blood. This
means that the enzymes are synthesized, but are not able to
reach the correct site. It is shown that mannose-6-phosphate
is the marker to target the nascent enzymes to lysosomes. In
these persons, the carbohydrate units are not added to the
enzyme. Mannose-6-phosphate deficient enzymes cannot
reach their destination (protein targeting defect).

Chapter 2: Subcellular Organelles and Cell Membranes
of a township are usually decomposed in incinerators.
Inside a cell, such a process is taking place within
the lysosomes. They are bags of enzymes. Clinical
applications of lysosomes are shown in Box 2.2.
2. Endocytic vesicles and phagosomes are fused with
lysosome (primary) to form the secondary lysosome
or digestive vacuole. Foreign particles are pro­
gressively digested inside these vacuoles. Completely
hydrolyzed products are utilized by the cell. As long
as the lysosomal membrane is intact, the encapsulated
enzymes can act only locally. But when the membrane
is disrupted, the released enzymes can hydrolyze
external substrates, leading to tissue damage.
3. The lysosomal enzymes have an optimum pH around 5. These
enzymes are:
a. Polysaccharide hydrolyzing enzymes (alpha-gluco­
alpha-fucosidase, beta-galactosidase, alpha-mannosidase, betaglucuronidase, hyaluronidase, aryl sulfatase, lysozyme)
b. Protein hydrolyzing enzymes (cathepsins, collagenase, elastase,
c. Nucleic acid hydrolyzing enzymes (ribonuclease, deoxyribonuclease)
d. Lipid hydrolyzing enzymes (fatty acyl esterase, phospholipases).

1. The peroxisomes have a granular matrix. They are of
0.3–1.5 mm in diameter. They contain peroxidases and
catalase. They are prominent in leukocytes and platelets.
2. Peroxidation of polyunsaturated fatty acids in vivo
may lead to hydroperoxide formation, R-OOH →
R-OO•. The free radicals damage molecules, cell
membranes, tissues and genes. (see Chapter 33).
3. Catalase and peroxidase are the enzymes present in
peroxisomes, which will destroy the unwanted peroxides
and other free radicals.
Clinical applications of peroxisomes are shown in Box 2.2.

1. They are spherical, oval or rod-like bodies, about
0.5–1 mm in diameter and up to 7 mm in length
(Fig. 2.1). Erythrocytes do not contain mitochondria.
The tail of sper­matozoa is fully packed with
2. Mitochondria are the powerhouse of the cell, where
energy released from oxidation of food stuffs is
trapped as chemical energy in the form of ATP (see
Chapter 20). Metabolic functions of mitochondria are
shown in Table 2.2.
3. Mitochondria have two membranes. The inner mem­
brane convolutes into folds or cristae (Fig. 2.3). The
inner mitochon­drial membrane contains the enzymes
of electron transport chain (see Chapter 20). The
fluid matrix contains the enzymes of citric acid cycle,
urea cycle and heme synthesis.
4. Cytochrome P-450 system present in mitochondrial
inner membrane is involved in steroido­ge­nesis (see
Chapter 52). Superoxide dismutase is present in
cytosol and mitochondria (see Chapter 33).
5. Mitochondria also contain specific DNA. The integral
inner membrane proteins, are made by mitochondrial
protein synthesizing machinery. However, the
majority of proteins, especially of outer membrane
are synthesized under the control of cellular DNA.
The division of mitochondria is under the command
of mitochondrial DNA. Mitochondrial ribosomes
are different from cellular ribosomes. Antibiotics
inhibiting bacterial protein synthesis do not affect
cellular processes, but do inhibit mitochondrial
protein biosynthesis (see Chapter 45).

Box 2.2: Peroxisomal deficiency diseases
1. Deficiency of peroxisomal matrix proteins can lead to
adrenoleukodystrophy (ALD) (Brown-Schilder’s disease)
characterized by progressive degeneration of liver, kidney and
brain. It is a rare autosomal recessive condition. The defect
is due to insufficient oxidation of very long chain fatty acids
(VLCFA) by peroxi­somes (see Chapter 14).
2. In Zellweger syndrome, proteins are not transported into the
peroxisomes. This leads to formation of empty peroxisomes or
peroxisomal ghosts inside the cells. Protein targeting defects
are described in Chapter 46.
3. Primary hyperoxaluria is due to the defective peroxisomal
metabolism of glyoxalate derived from glycine (see Chapter 16).


Fig. 2.3: Mitochondria


Textbook of Biochemistry

6. Mitochondria play a role in triggering apoptosis (see
Chapter 47).

7. Taking into consideration such evidences, it is assumed that
mitochondria are parasites, which entered into cells at a time
when multicellular organisms were being evolved. These parasites
provided energy in large quanti­
ties giving an evolutionary
advantage to the cell; the cell gave protection to these parasites.
This perfect symbiosis, in turn, evolved into a cellular organelle
of mitochondria.
8. Mitochondria are continuously undergoing fission and fusion,
resulting in mixing of contents of mitochondrial particles. Specific
fission and fusion proteins have been identified and abnormalities
in some of these proteins are implicated in diseases like CharcotMarie-Tooth disease.
9. New evidence suggests a role for mitochondria in the genesis of
systemic inflammatory response. The mitochondrial particles
released from damaged tissue may evoke an antigenic response
from the immune system.

10. A summary of functions of organelles is given in
Table 2.2 and Box 2.3.

1. The plasma membrane separates the cell from the
external environment. It has highly selective permea­­
bility properties so that the entry and exit of compounds
are regulated. The cellular metabolism is in turn influ­
enced and probably regulated by the membrane. The
membrane is metabolically very active.
TABLE 2.2: Metabolic functions of subcellular organelles

DNA replication, transcription


Biosynthesis of proteins, glycoproteins,
lipoproteins, drug metabolism, ethanol oxidation,
synthesis of cholesterol (partial)

Golgi body

Maturation of synthesized proteins


Degradation of proteins, carbohydrates, lipids and


Electron transport chain, ATP generation, TCA
cycle, beta oxidation of fatty acids, ketone body
production, urea synthesis (part), heme synthesis
(part), gluconeogenesis (part), pyrimidine
synthesis (part)


Protein synthesis, glycolysis, glycogen metabolism,
HMP shunt pathway, transaminations, fatty acid
synthesis, cholesterol synthesis, heme synthesis
(part), urea synthesis (part), pyrimidine synthesis
(part), purine synthesis

2. The enzyme, nucleotide phosphatase (5' nucleotidase)
and alkaline phosphatase are seen on the outer
part of cell membrane; they are therefore called
3. Membranes are mainly made up of lipids, proteins
and small amount of carbohydrates. The contents of
these compounds vary according to the nature of the
membrane. The carbohydrates are present as glycoproteins and glycolipids. Phospholipids are the most
common lipids present and they are amphipathic in
nature. Cell membranes also contain cholesterol.

Fluid Mosaic Model
The lipid bilayer was originally proposed by Davson and
Danielle in 1935. Later, the structure of the biomembranes
was described as a fluid mosaic model (Singer and
Nicolson, 1972).
A. The phospholipids are arranged in bilayers with the polar head
groups oriented towards the extracellular side and the cytoplasmic
side with a hydrophobic core (Fig. 2.4A). The distribution of
the phospholipids is such that choline containing phospholipids
are mainly in the external layer and ethanolamine and serine
containing phospholipids in the inner layer. Gerd Binnig and
Heinrich Rohrer introduced the scanning electron microscopy in
1981 by which the outer and inner layers of membranes could be
visualized separately. They were awarded Nobel prize in 1986.
B. Each leaflet is 25 Å thick, with the head portion 10 Å and tail 15 Å
thick. The total thickness is about 50 to 80 Å.
C. The lipid bilayer shows free lateral movement of its components,
hence the membrane is said to be fluid in nature. Fluidity enables
the membrane to perform endocytosis and exocytosis.
D. However, the components do not freely move from inner to outer
layer, or outer to inner layer (flip-flop movement is restricted). During
apoptosis (programed cell death), flip-flop movement occurs.
			 This flip-flop movement is catalyzed by enzymes. Flippases
catalyze the transfer of amino phospholipids across the membrane.
Floppases catalyze the outward directed movement, which is

Box 2.3: Comparison of cell with a factory
Plasma membrane
Endoplasmic reticulum
Golgi apparatus

: F ence with gates; gates open
when message is received
: Manager’s office
: Conveyer belt of production units
: Packing units
: Incinerators
: Lorries carrying finished products
: Power generating units

Chapter 2: Subcellular Organelles and Cell Membranes
ATP dependent. This is mainly seen in the role of ABC proteins
mediating the efflux of cholesterol and the extrusion of drugs from
cells. The MDR associated p-glycoprotein is a floppase.

E. The cholesterol content of the membrane alters the
fluidity of the membrane. When cholesterol concentra­
tion increases, the membrane becomes less fluid on
the outer surface, but more fluid in the hydrophobic
core. The effect of cholesterol on membrane fluidity
is different at different temperatures. At temperature
below the Tm, cholesterol increases fluidity and
there-by permeability. At temperatures above the Tm,
cholesterol decreases fluidity.
		 In spur cell anemia and alcoholic cirrhosis, membrane

studies have revealed the role of excess cholesterol. The decrease
in membrane fluidity may affect the activities of receptors and
ion channels. This has been implicated in conditions like LCAT
deficiency, Alzheimer’s disease and hypertension.
			 Fluidity of cellular membranes responds to variations in diet
and physiological states. Increased release of reactive oxygen
species (ROS), increase in cytosolic calcium and lipid peroxidation
have been found to adversely affect membrane fluidity. Anesthetics
may act changing membrane fluidity.

F. The nature of the fatty acids also affects the fluidity of
the membrane, the more unsaturated cis fatty acids
increase the fluidity.

		 The fluidity of the membrane is maintained by the length of
the hydrocarbon chain, degree of unsaturation and nature of the
polar head groups. Trans fatty acids (TFA) decrease the fluidity
of membranes due to close packing of hydrocarbon chains. Cis
double bonds create a kink in the hydrocarbon chain and have
a marked effect on fluidity. Second OH group of glycerol in
membrane phospholipids is often esterified to an unsaturated fatty
acid, monounsaturated oleic or polyunsaturated linoleic, linolenic
or arachidonic.

Fig. 2.4A: The fluid mosaic model of membrane


			 The nature of fatty acids and cholesterol content varies
depending on diet. A higher proportion of PUFA, which increases
the fluidity favors the binding of insulin to its receptor, a transmembrane protein.
The lipids making up components of membranes are of three
major classes that includes glycerophospholipids, sphingolipids,
and cholesterol. Sphingolipids and glycerophospholipids
constitute the largest percentage of the lipid weight of biological
membranes. Proteins that are found associated with membranes
can also be modified by lipid attachment (lipoproteins). The lipid
portion of a lipoprotein anchors the protein to the membrane
either through interaction with the lipid bilayer directly or through
interactions with integral membrane proteins. Lipoproteins
associated with membranes contain one of three types of covalent
lipid attachment. The lipids are isoprenoids such as farnesyl and
geranyl residues, fatty acids such as myristic and palmitic acid, and
glycosylphosphatidyl inositol (GPI).

Membrane Proteins
A. The peripheral proteins exist on the surfaces of the
bilayer (Fig. 2.4B). They are attached by ionic and
polar bonds to polar heads of the lipids.

B. Anchoring of proteins to lipid bilayers: Several peripheral
membrane proteins are tethered to the membranes by covalent
linkage with the membrane lipids. Since the lipids are inserted
into the hydrophobic core, the proteins are firmly anchored. A
typical form of linkage is the one involving phosphatidyl inositol
which is attached to a glycan. This glycan unit has ethanolamine,
phosphate and several carbohydrate residues. This glycan chain
includes a glucose covalently attached to the C terminus of a
protein by ethanolamine and to the phosphatidyl inositol by
glucosamine. The fatty acyl groups of the phosphatidyl inositol
diphosphate (PIP2) are firmly inserted into the lipid membrane
thus anchoring the protein. This is referred to as glycosyl
phosphatidyl inositol (GPI) anchor.

Fig. 2.4B: Proteins are anchored in membrane by different mechanisms


Textbook of Biochemistry

C. Microdomains on membranes: GPI anchored proteins are
often attached to the external surface of plasma membrane at
microdomains called lipid rafts. They are areas on the membrane
having predominantly glycosphingolipids and cholesterol.
The localization and activity of the protein can be regulated by
anchoring and release. Defective GPI anchors are implicated in
Paroxysmal nocturnal hemoglobinuria (PNH). These lipid rafts
are implicated in endocytosis, G protein signaling and binding
of viral pathogens. Lipid rafts are areas on the membrane having
predominantly glycosphingolipids and cholesterol. The GPI
anchors that tether proteins to the membrane are also seen at
the lipid rafts. Membrane proteins may be anchored by covalent
bonding, palmitoylation and myristoylation.
D. Caveolae are flask shaped indentations on the areas of lipid rafts that
are involved in membrane transport and signal transduction. Caveolae
contain the protein caveolin, along with other receptor proteins.
Transport of macromolecules (IgA) from the luminal side occurs
by caveolae mediated transcytosis. The endocytosis of cholesterol
containing lipoproteins may be caveolae mediated. Similarly the
fusion and budding of viral particles are also mediated by caveolae.

E. The integral membrane proteins are deeply embed­
ded in the bilayer and are attached by hydrophobic
bonds or van der Waals forces.
F. Some of the integral membrane proteins span the
whole bilayer and they are called transmembrane
proteins (Fig. 2.4). The hydrophobic side chains of the
amino acids are embedded in the hydrophobic central
core of the membrane. The transmembrane proteins
can serve as receptors (for hormones, growth factors,
neurotransmitters), tissue specific antigens, ion channels,
membrane-based enzymes, etc.
Bacterial Cell Wall
Prokaryotic (bacterial) cells as well as plant cells have a cell wall
surrounding the plasma membrane; this cell wall provides mechanical
strength to withstand high osmotic pressure. Animal cells are devoid
of the cell wall; they have only plasma membrane. Major constituent
of bacterial cell wall is a heteropolysacc­haride, consisting of repeating

units of N-acetyl muramic acid (NAM) and N-acetyl glucosamine
(NAG). This polysaccharide provides mechanical strength to the
plasma membrane. Synthesis of this complex polysaccharide is blocked
by penicillin. This inhibition is responsible for the bactericidal action
of penicillin.

Tight Junction
When two cells are in close approximation, in certain areas, instead
of 4 layers, only 3 layers of plasma membranes are seen. This tight
junction permits calcium and other small molecules to pass through
from one cell to another through narrow hydrophilic pores. Some
sort of communication between cells thus results. Absence of tight
junction is implicated in loss of contact inhibition in cancer cells
(see Chapter 57). Tight junctions also seal off subepithelial spaces
of organs from the lumen. They contain specialized proteins, such as
occludin, claudins and other adhesion molecules.
Most eukaryotic cells are in contact with their neighboring cells and
these interactions are the basis of formation of organs. Cells that abut one
another are in metabolic contact, which is brought about by specialized
particles called gap junctions. Gap junctions are intercellular channels
and their presence allows whole organs to be continuous from within.
One major function of gap junctions is to ensure a supply of nutrients to
cells of an organ that are not in direct contact with the blood supply. Gap
junctions are formed from a type of protein called connexin.

Myelin Sheath
It is made up of the membrane of Schwann's cells, (Theodor Schwann,
1858) condensed and spiralled many times around the central axon. The
cytoplasm of Schwann cells is squeezed to one side of the cell. Myelin is
composed of sphingomyelin, cholesterol and cerebroside. Myelin sheaths
thin out in certain regions (Node of Ranvier) (Anotoine Ranvier, 1878).
Due to this arrangement, the propagation of nerve impulse is wave-like;
and the speed of propagation is also increased. Upon stimulation, there is
rapid influx of sodium and calcium, so that depolarization occurs. Voltage
gradient is quickly regained by ion pumps. The ions flow in and out of
membrane only where membrane is free of insulation; hence the wavelike propagation of impulse. In multiple sclerosis, demyelination occurs
at discrete areas, velocity of nerve impulse is reduced, leading to motor and
sensory deficits.

Microvilli of intestinal epithelial cells and pseudopodia of macrophages
are produced by membrane evagination. This is due to the fluid nature
of membranes.

Membranes of Organelle
Ernst Ruska
NP 1986

NP 1986

NP 1986


Membranes of endoplasmic reticulum, nucleus, lysosomes and outer
layer of mitochondria may be considered as variants of plasma membrane.
Percentage of protein content varies from 20% in myelin sheath to over
70% in the inner membranes of mitochondria.

Chapter 2: Subcellular Organelles and Cell Membranes

Passive Transport

Human body is supported by the skeletal system; similarly the structure
of a cell is maintained by the cytoskeleton present underneath the plasma
membrane. The cytoskeleton is responsible for the shape of the cell, its
motility and chromosomal movements during cell division.
The cytoskeleton is composed of microfilaments, intermediate
filaments and microtubules, forming a network within the cell.
Microfilaments made of G-actin found in almost all cells fuse to form
F-actin and exist as a tangled meshwork of 8–9 nm size. Intermediate
filaments have approximately 10 nm diameter. They form rod like
elongated structures which are stable components of the cytoskeleton.
Examples are keratins found in hair and nails and lamins which provide
support for nuclear membrane. Microtubules contain alpha and beta
tubulin with a diameter of 25 nm. They are essential for formation of
mitotic spindle and participate in exocytosis and endocytosis. Alpha and
beta tubulin molecules polymerize to form cylindrical protofilaments
that assemble into sheets and fibers. They are continuously undergoing
assembly and dissembly. Microtubule associated proteins stabilize their
assembly, e.g. Abnormal aggregation of Tau proteins are found in brain
in degenerative diseases. Vinca alkaloids used as anticancer drugs,
inhibit the formation of mitotic spindle by interfering with the assembly
of microtubules and thus inhibit cell division.

Simple Diffusion

Molecular Motors
Proteins that are responsible for coordinated movements in tissues and
cells are referred to as molecular motors. These may be ATP driven as
in the case of the contractile proteins; actin and myosin in muscle as
well as dynein and tubulin in cilia and flagella. Kinesin, which mediates
movement of vesicles on microtubules also requires ATP.

The permeability of substances across cell membrane
is dependent on their solubility in lipids and not on their
molecular size. Water-soluble compounds are generally
impermeable and require carrier mediated transport.
An important function of the membrane is to withhold
unwanted molecules, while permitting entry of molecules
necessary for cellular metabolism. Transport mechanisms
are classified into:
1. Passive transport
A. Simple diffusion
B. Facilitated diffusion
C. Ion channels are specialized carrier systems.
They allow passage of molecules in accordance
with the concentration gradient.
2. Active transport
3. Pumps can drive molecules against the gradient using


Solutes and gases enter into the cells passively. They
are driven by the concentration gradient. The rate of
entry is proportional to the solubility of that solute in
the hydrophobic core of the membrane. Simple diffusion
occurs from higher to lower concentration. This does not
require any energy. However, it is a very slow process.
Diffusion of gases such as O2, CO2, NO and CO
occurs at a rate that is solely dependent upon concentration
gradients. Lipophilic molecules will also diffuse across
membranes at a rate that is directly proportional to the
solubility of the compound in the membrane.

Facilitated Diffusion
This is a carrier mediated process. (Fig. 2.5). Important
features of facilitated diffusion are:
a. The carrier mechanism could be saturated which is
similar to the Vmax of enzymes.
b. Structurally similar solutes can competitively inhibit
the entry of the solutes.
c. Facilitated diffusion can operate bidirectionally.
d. This mechanism does not require energy but the
rate of transport is more rapid than simple diffusion
e. The carrier molecules can exist in two conformations,
Ping and Pong states. In the pong state, the active sites
are exposed to the exterior, when the solutes bind to the
specific sites. Then there is a conformational change.
In the ping state, the active sites are facing the interior
of the cell, where the concentration of the solute is
minimal. This will cause the release of the solute
molecules and the protein molecule reverts to the pong
state. By this mechanism the inward flow is facilitated,

Fig. 2.5: Facilitated diffusion. The carrier molecule exists in two


Textbook of Biochemistry
but the outward flow is inhibited (Fig. 2.5). Hormones
regulate the number of carrier molecules. For example,
glucose transport across membrane is by facilitated
diffusion involving a family of glucose transporters.
Glucose transport is described in detail in Chapter 9.

They are water channels (Fig. 2.6). They are a family of membrane
channel proteins that serve as selective pores through which water
crosses the plasma membranes of cells. They form tetramers in the
cell membrane, and facilitate the transport of water. They control the
water content of cells. Agre and MacKinnon were awarded Nobel Prize
for Chemistry in 2003 for their contributions on aquaporins and ion
channels. Diseases, such as nephrogenic diabetes insipidus are due to
impaired function of these channels.
Aquaporins (AQP) are a family of channels responsible for the
transport of water across membranes. At least 11 aquaporin proteins have
been identified in mammals with 10 known in humans (termed AQP0
through AQP9). A related family of proteins is called aquaglyceroporins,
which is involved in water transport as well as transport of other small
molecules. AQP9 is the human aquaglyceroporin. Probably the most
significant location of aquaporin expression is in the kidney. The

Peter Agre
NP 2003
b. 1949

NP 2003

Jen Skou
NP 1997
b. 1918

proximal tubule expresses AQP1, AQP7 and AQP8, while collecting
duct expresses AQP2, AQP3, AQP4, AQP6 and AQP8. Loss of function
of renal aquaporins is associated with several disease states; reduced
expression of AQP2 is associated with nephrogenic diabetes insipidus
(NDI), acquired hypokalemia and hypercalcemia.
Channelopathies are a group of disorders that result from
abnormalities in the proteins forming the ion channels or regulatory
proteins. Channelopathies may be acquired or congenital. Congenital
channelopathies may occur due to genetic mutations in sodium,
potassium, chloride and calcium channels. A few examples are Bartter
syndrome, myasthenia gravis, long and short QT syndromes, cystic
fibrosis (chloride channel), Liddle's syndrome (sodium channel) periodic
paralysis (potassium channel) and some types of deafness.

Ion Channels
Membranes have special devices called ion channels
(Fig. 2.9). Ion channels are transmembrane proteins that
allow the selective entry of various ions. Salient features
are enumerated in Box 2.4. These channels are for quick
transport of electrolytes, such as Ca++, K+, Na+ and Cl–.
These are selective ion conductive pores. Ion channels are
specialized protein molecules that span the membranes.
The channels generally remain closed, but in response to
stimulus, they open allowing rapid flux of ions down the
gradient. This may be compared to opening of the gate
of a cinema house, when people rush to enter in. Hence,
this regulation is named as "gated". Such ion channels
are important for nerve impulse propagation, synaptic
transmission and secretion of biologically active substances
from the cells. Ion channels are different from ion transport
pumps described below.

Ligand-Gated Channels
Ligand gated channels are opened by binding of effectors.
The binding of a ligand to a receptor site on the channel

Fig. 2.6: Water channel or aquaporin

Fig. 2.7: Acetylcholine receptor

Chapter 2: Subcellular Organelles and Cell Membranes
results in the opening (or closing) of the channel. The
ligand may be an extracellular signaling molecule or an
intracellular messenger. Clinical applications of channels
are shown in Box 2.5.
a. Acetylcholine receptor (Fig. 2.7) is the best example
for ligand gated ion channel. It is present in postsynaptic membrane. It is a complex of 5 subunits,
consisting of acetylcholine binding site and the ion
channel. Acetylcholine released from the presynaptic
region binds with the receptors on the postsynaptic
region, which triggers opening of the channel and
influx of Na+. This generates an action potential in
the postsynaptic nerve. The channel opens only for
a millisecond, because the acetylcholine is rapidly
degraded by acetylcholinesterase.
b. Calcium channels: Under appropriate stimuli calcium
channels are opened in the sarcoplasmic reticulum
membrane, leading to an elevated calcium level in
the cytosol of muscle cells. Calcium channel blockers


are therefore widely used in the management of

c. Amelogenin, a protein present in enamel of teeth has hydrophobic

residues on the outside. A 27 amino acid portion of amelogenin
functions as a calcium channel. Phosphorylation of a serine residue
of the protein opens the calcium channel, through which calcium
ions zoom through and are funneled to the mineralization front.
The amelogenin is used for the formation of calcium hydroxy
apatite crystals.

Voltage-Gated Channels
Voltage-gated channels (Fig. 2.9) are opened by membrane
depolarization. The channel is usually closed in the ground
state. The membrane potential change (voltage difference)
switches the ion channel to open, lasting less than 25

In voltage-gated channels, the channels open or close in response to
changes in membrane potential. They pass from closed through open to
inactivated state on depolarization. Once in the inactivated state, a channel
cannot re-open until it has been reprimed by repolarization of the membrane.
Voltage-gated sodium channels and voltage gated potassium
channels are the common examples. These are seen in nerve cells and are
involved in the conduction of nerve impulses.
Ion channels allow passage of molecules in accordance with the
concentration gradient. Ion pumps can transport molecules against the


Fig. 2.8: The sodium potassium pump. It brings sodium ions out of

the cells and potassium ions into the cells. Black circle = sodium
ion; green square = potassium ion; pink circle = phosphate. (1)
Cytoplasmic sodium ions (3 numbers) bind to the channel protein.
This favors phosphorylation of the protein along with hydrolysis
of ATP; (2) Phosphorylation causes the protein to change
conformation, expelling the sodium ions across the membrane;
(3) Simultaneously, extracellular potassium ions (2 numbers)
bind to the carrier protein. Potassium binding leads to release
of phosphate group; (4) So, original conformation is restored; (5)
Potassium ions are released into the cytoplasm. The cycle repeats

They are membrane shuttles for specific ions. They
transport antibiotics. Ionophores increase the permeability
of membrane to ions by acting as channel formers.
The two types of ionophores are; mobile ion carriers
(e.g. Valinomycin) and channel formers (e.g. Gramicidin).
They are produced by certain microorganisms and are used
as antibiotics. When cells of higher organisms are exposed
to ionophores, the ion gradient is dissipated. Valinomycin
allows potassium to permeate mitochondria and so it
dissipates the proton gradient; hence, it acts as an uncoupler
of electron transport chain (see Chapter 20).
Box 2.4: Salient features of Ion channels
1. They are transmembrane proteins
2. Selective for one particular ion
3. Regulation of activity is done by voltage-gated, ligand-gated
or mechanically-gated mechanisms
4. Different channels are available for Na+, K+, Ca++ and Cl–
5. Transport through the channel is very quick


Textbook of Biochemistry

Active Transport
The salient features of active transport are:
a. This form of transport requires energy. About 40%
of the total energy expenditure in a cell is used for the
active transport system.
b. The active transport is unidirectional.
c. It requires specialized integral proteins called
d. The transport system is saturated at higher concentrations of solutes.
e. The transporters are susceptible to inhibition by
specific organic or inorganic compounds. General
reaction is depicted in Figures 2.8 and 2.9.

Sodium Pump
It is the best example for active transport. Cell has low
intracellular sodium; but concentration of potassium
inside the cell is very high. This is maintained by sodiumpotassium activated ATPase, generally called as sodium
Box 2.5: Clinical applications of channels
1. Sodium channels: Local anesthetics such as procaine
act on sodium channels both as blockers and on gating
mechanisms to hold the channel in an inactivated state. Point
mutation in sodium channel leads to myotonia, characterized
by increased muscle excitability and contractility.
2. In Liddle's disease, the sodium channels in the renal
epithelium are mutated, resulting in excessive sodium
reabsorption, water retention and elevated blood pressure.
3. Potassium channel mutations in " Long QT syndrome" leads
to inherited cardiac arrhythmia, where repolarization of the
ventricle is delayed, resulting in prolonged QT intervals in ECG.
Potassium channel blockers are used in cardiac arrhythmias
and potassium channel openers as smooth muscle dilators.
4. Chloride channels: The role of GABA and glycine as inhibitory
neurotransmitters is attributed to their ability to open the
chloride channels at the postsynaptic membranes.
5. Cystic fibrosis is due to certain mutations in the CFTR gene
(cystic fibrosis transmembrane regulator protein), which is a
chloride transporting ABC protein.
6. Retina: The excitation of retinal rods by a photon is by closing
of cation specific channels resulting in hyperpolarization of
the rod cell membrane. This light induced hyperpolarization is
the major event in visual excitation (see Chapter 36).
7. Bartter syndrome is due to mutations in potassium and
chloride channels in the renal tubules, especially the ascending
limb. The condition is characterized by hypokalemia and
alkalosis and loss of chloride and potassium in urine.
8. Calcium channel blockers are used in the treatment of

pump. The ATPase is an integral protein of the membrane
(Fig. 2.8). Jen Skou was awarded Nobel Prize in 1997 for
his work on Sodium-Potassium-ATPase. It has binding sites
for ATP and sodium on the inner side and the potassium
binding site is located outside the membrane. It is made
up of two pairs of unequal subunits alpha-2 beta-2. Both
subunits of the pump (alpha and beta) span the whole
thickness of membrane. Details are shown in Figure 2.8.
Clinical applications of sodium pump are shown in Box 2.6.

There are four different types of ATPases, three that transport cations and
one that transports anions.
A-type ATPases transport anions.
P-type ATPases are mostly found in the plasma membrane and are
involved in the transport of H+, K+, Na+, Ca2+, Cd2+, Cu2+ and Mg2+.
F-type ATPases function in the translocation of H+ in the
mitochondria during the process of oxidative phosphorylation.
V-type ATPases are located in acidic vesicles and lysosomes and
have homology to the F-type ATPases.

Calcium Pump
An ATP dependent calcium pump also functions to regulate
muscle contraction. A specialized membrane system called
sarcoplasmic reticulum is found in skeletal muscles, which
regulates the Ca++ concentration around muscle fibers.
In resting muscle the concentration of Ca++ around
muscle fibers is low. But stimulation by a nerve impulse
results in a sudden release of large amounts of Ca++. This
would trigger muscle contraction. The function of calcium
pump is to remove cytosolic calcium and maintain low
cytosolic concentration, so that muscle can receive the
next signal. For each ATP hydrolyzed, 2Ca++ ions are

Uniport, Symport and Antiport
Transport systems are classified as uniport, symport and
antiport systems (Fig. 2.9).
Box 2.6: Clinical applications of sodium pump
The use of cardiotonic drugs like digoxin and ouabain was
prompted by the use of the leaves of the plant foxglove by natives.
They bind to the alpha-subunit and act as competitive inhibitor of
potassium ion binding to the pump. Inhibition of the pump leads
to an increase in Na+ level inside the cell and extrusion of Ca++
from the myocardial cell. This would enhance the contractility
of the cardiac muscle and so improve the function of the heart.
These drugs are now rarely used.

Chapter 2: Subcellular Organelles and Cell Membranes
1. Uniport system carries single solute across the mem­
brane, e.g. glucose transporter in most of the cells.
Calcium pump is another example.
2. If the transfer of one molecule depends on simultaneous
or sequential transfer of another molecule, it is called cotransport system. The active transport may be coupled
with energy indirectly. Here, movement of the substance
against a concentration gradient is coupled with
movement of a second substance down the concentration
gradient; the second molecule being already concentrated
within the cell by an energy requiring process.
3. The cotransport system may either be a symport or
an antiport. In symport, (Fig. 2.9) the transporter
carries two solutes in the same direction across the
membrane, e.g. sodium dependent glucose transport
(see Chapter 9). Phlorhizin, an inhibitor of sodiumdependent cotrans­­port of glucose, especially in the
proximal convoluted tubules of kidney, produces
renal damage and results in renal glycosuria. Amino
acid transport is another example for symport.
4. The antiport system (Fig. 2.9) carries two solutes
or ions in opposite direction, e.g. sodium pump
(Fig. 2.7) or chloride-bicarbonate exchange in RBC
(see Chapter 22). Features of different types of
transport modalities are summarized in Table 2.3.
Clinical Applications
In Hartnup’s disease, transport mechanism for amino acids are defective
in intestine and renal tubules (see Chapter 18). In cystinuria, renal
reabsorption of cystine is abnormal (see Chapter 16). Renal reabsorption
of phosphate is decreased in vitamin D resistant rickets (see Chapter 36).

Fig. 2. 9: Different types of transport systems


Endocytosis is the mechanism by which cells internalize extracellular
macro­molecules, to form an endocytic vesicle. This requires energy
in the form of ATP as well as calcium ions in the extracellular fluid.
Cytoplasmic contractile elements take part in this movement. In general,
plasma membrane is invaginated, enclosing the matter. This forms the
endocytic vesicle (Fig. 2.10). The endocytosis may either be pinocytosis
or phagocytosis.

Pinocytosis literally means ‘drinking by the cell’. Cells take up fluid by
this method. The fluid phase pinocytosis is a nonselective process.

Receptor-Mediated Endocytosis
The selective or adsorptive pinocytosis is receptor-mediated; also
called as absorptive pinocytosis. Low density lipoprotein (LDL) is a
good example. LDL binds to the LDL receptor and the complex is later
internalized. The cytoplasmic side of these vesicles are coated with
filaments; mainly composed of Clathrin. These are called Clathrin
coated pits. Absorption of cholesterol by clathrin coated pit is shown in
TABLE 2.3: Types of transport mechanisms
Ion channels yes

glucose to
sodium pump
glucose to


Textbook of Biochemistry

Chapter 13. After the LDL-receptor complex is internalized, the receptor
molecules are released back to cell surface; but the LDL is degraded by
lysosomal enzymes. Several hormones are also taken up by the cells by
receptor-mediated mechanism. The protein, Dynamin which has GTPase
activity, is necessary for the internalization of clathrin coated pits. Many
viruses get attached to their specific receptors on the cell membranes.
Examples are Influenza virus, Hepatitis B virus, polio virus and HIV.
They are taken up by caveolae-mediated processes. Caveolae-mediated
endocytosis is also known as potocytosis.

Secretory Vesicles and Exocytosis

The term is derived from the Greek word “phagein” which means to eat.
It is the engulfment of large particles such as bacteria by macrophages
and granulocytes. They extend pseudopodia and surround the particles
to form phagosomes. Phagosomes later fuse with lysosomes to form
phagolysosomes, inside which the particles are digested. An active
macrophage can ingest 25% of their volume per hour. In this process,
3% of plasma membrane is internalized per minute. The biochemical
events accompanying phagocytosis is described as respiratory burst
(see Chapter 33).

Under appropriate stimuli, the secretory vesicles or vacuoles move
towards and fuse with the plasma membrane. This movement is created
by cytoplasmic contractile elements; the microtubule system. The inner
membrane of the vesicle fuses with outer plasma membrane, while
cytoplasmic side of vesicle fuses with cytoplasmic side of plasma
membrane. Thus the contents of vesicles are externalized. This process
is called exocytosis or reverse pinocytosis. Release of trypsinogen by
pancreatic acinar cells; release of insulin by beta cells of Langerhans and
release of acetylcholine by presynaptic cholinergic nerves are examples
of exocytosis (Fig. 2.11). Often, hormones are the signal for exocytosis,
which leads to calcium ion changes, triggering the exocytosis.
The most important vesicles are those that contain secreted factors.
Membrane bound proteins (e.g. growth factor receptors) are processed
as they transit through the ER to Golgi apparatus and finally to the
plasma membrane. As these proteins transit to the surface of the cell
they undergo a series of processing events that includes glycosylation.
The vesicles that pinch off from the Golgi apparatus are termed
coated vesicles. The membranes of coated vesicles are surrounded by
specialized scaffolding proteins that will interact with the extracellular
environment. Clathrin coated vesicles contain clathrin and are involved
in transmembrane protein, GLI linked protein and secreted protein
transit to plasma membrane. They are also involved in endocytosis (e.g.
LDL uptake).


Fig. 2.10: Endocytosis

Fig. 2.11: Exocytosis

This is a transport process for macromolecules across cells especially
epithelial cells; Ig A, transferrin and insulin are some of the molecules
thus transported. Transcytosis may be caveolae-mediated. The process
has been implicated in the entry of pathogens into intestinal mucosal
cells and across the blood brain barrier. This process may be an effective
mechanism for targeted drug delivery, especially antibodies and similar

The ABC Family of Transporters
ATP-binding cassette transporters superfamily: All members of this
superfamily of membrane proteins contain a conserved ATP-binding
domain and use the energy of ATP hydrolysis to drive the transport
of various molecules across all cell membranes. There are 48 known
members of this superfamily and they are divided into seven sub-families
designated as ABCA through ABCG.
ABCA1 is involved in the transport of cholesterol out of cells when
HDLs are bound to their cell surface receptor, SR-B1.
ABCB4 is a member of the P-glycoprotein family of multidrug
resistance transporters. Defects in ABCB4 gene are associated with
familial intrahepatic cholestasis type 3 (PFIC3), adult biliary cirrhosis,
and intrahepatic cholestasis.

Chapter 2: Subcellular Organelles and Cell Membranes
ABCB7 is involved in iron homeostasis. Defects in the gene are
associated with X-linked sideroblastic anemia with ataxia (XSAT).
ABCC2 is also called multidrug resistance associated protein 2
(MRP2). Defects in the gene encoding ABCC2 result in Dubin-Johnson’s
syndrome, a type of conjugated hyperbilirubinemia.
ABCD1 is involved in the import and/or anchoring of very long
chain fatty acyl CoA synthetase (VLCFA-CoA synthetase) to the
peroxisome. Defects result in X-linked adrenoleukodystrophy (XALD).
ATP7A and ATP7B are copper transporting ATPases that are related
to SLC31A1. Defects in ATP7A result in Menkes disease and defects in
ATP7B are associated with Wilson’s disease.
SLC11A2 which is also known as DMT1 (divalent metal ion
transporter) is involved in uptake of iron by the apical surface of the
duodenum. In addition to iron, DMT1 is involved in manganese, cobalt,
cadmium, nickel, copper and zinc transport. Defects in DMT1 activity
are associated with hypochromic microcytic anemia with iron overload.
Abnormalities in SLC30A8 result in impaired pancreatic β cell
function leading to defects in insulin secretion. SLC35C1 is fucose
transporter, defects in which result in congenital disorder of glycosylation
(CDG) syndrome. Examples are leukocyte adhesion deficiency syndrome
II (LAD II) leading to immunodeficiency and mental retardation.
SLC40A1 is also known as ferroportin or insulin-regulated gene 1
(IREG1). It is required for the transport of dietary iron across basolateral
membranes of intestinal enterocytes. Defects in SLC40A1 gene are
associated with type 4 hemochromatosis.

1. In a cell, biomolecules are maintained in a state of
‘dynamic’ or ‘steady state’ equilibrium.
2. Cell organelles can be separated by density gradient
3. All cells in the body contain nucleus except mature
4. Endoplasmic reticulum is involved in protein synthesis
and also detoxification of various drugs.
5. Golgi apparatus is primarily involved in glycosylation,
protein sorting, packaging and secretion.


6. Lysosomes are the ‘suicide’ bags, which contain many
hydrolyzing enzymes.
7. Mitochondria, the ‘power house’ of the cell has its own
DNA, can synthesize its own proteins. It is sometimes
referred to as ‘mini cell’.
8. Antibiotics inhibiting bacterial protein biosynthesis
can inhibit mitochondrial protein biosynthesis also.
9. Membranes are mainly composed of lipids
(phospholipids), proteins and a small percentage of
10. Phospholipids, which are amphipathic in nature, are
arranged as bilayers.
11. Cholesterol content and nature of the fatty acid of the
membrane, influences the fluidity.
12. Membrane proteins can be integral, peripheral or
13. Transmembrane proteins serve as receptors, tissue
specific antigens, ion-channels, etc.
14. Transport of molecules across the plasma membrane
could be energy dependent (active) or energy
independent (passive).
15. Ion-channels function for the transport of the ions,
such as Ca2+, K+, Cl–, Na+, etc.
16. Ionophores or transport antibiotics increase permeability
of membranes by acting as channel formers. They could
be mobile ion carriers (e.g. valinomycin) or channel
formers (e.g. gramicidin).
17. Na+ K+ ATPase (sodium pump) is an example of active
transport. Cardiotonic drugs like Digoxin and Ouabain
competitively inhibit K+ ion binding. The property is
used to enhance contractility of the cardiac muscle.
18. Transport systems may be Uniport, Antiport or

Amino Acids:
Structure and Properties
Chapter at a Glance
The reader will be able to answer questions on the following topics:
¾¾Classification of amino acids based on structure
¾¾Based on side chain character
¾¾Based on metabolic fate
¾¾Based on nutritional requirements
¾¾Isoelectric point

Proteins are of paramount importance in biological
systems. All the major structural and functional aspects of
the body are carried out by protein molecules. All proteins
are polymers of amino acids. Proteins are composed of a
number of amino acids linked by peptide bonds.
Although about 300 amino acids occur in nature, only
20 of them are seen in human body. Most of the amino
acids (except proline) are alpha amino acids, which means
that the amino group is attached to the same carbon atom to
which the carboxyl group is attached (Fig. 3.1).

Based on Structure
A. Aliphatic amino acids
a. Monoamino monocarboxylic acids:

¾¾Reactions due to carboxyl group
¾¾Reactions due to amino group
¾¾Reactions of SH group
¾¾Peptide bond formation

• Simple amino acids: Glycine, Alanine (Fig. 3.2)
• Branched chain amino acids: Valine, Leucine,
Isoleucine (Fig. 3.3)
• Hydroxyamino acids: Serine, Threonine (Fig. 3.4.)
• Sulfur-containing amino acids: Cysteine,
Methionine (Fig. 3.5)
• Amino acids with amide group: Asparagine,
Glutamine (Fig. 3.6).
b. Monoamino dicarboxylic acids: Aspartic acid,
Glutamic acid (Fig. 3.7).
c. Dibasic monocarboxylic acids: Lysine, Arginine
(Fig. 3.8).
B. Aromatic amino acids:
Phenylalanine, Tyrosine (Fig. 3.9).
C. Heterocyclic amino acids:
Tryptophan (Fig. 3.10), Histidine (Fig. 3.11).
D. Imino acid: Proline (Fig. 3.11).

Chapter 3: Amino Acids: Structure and Properties
E. Derived amino acids:
i. Derived amino acids found in proteins: After
the synthesis of proteins, some of the amino acids
are modified, e.g. hydroxy proline (Fig. 3