PDQ BIOCHEMISTRY - PART 1 pptx

PDQ SERIES ACKERMANN PDQ PHYSIOLOGY CORMACK PDQ HISTOLOGY DAVIDSON PDQ GENETICS JOHNSON PDQ PHARMACOLOGY, 2/e KERN PDQ HEMATOLOGY McKIBBON PDQ EVIDENCE-BASED PRINCIPLES AND PRACTICE NORMAN, STREINER PDQ STATISTICS, 2/e STREINER, NORMAN PDQ EPIDEMIOLOGY, 2/e PDQ (Pretty Darned Quick) PDQ BIOCHEMISTRY R. ROY BAKER, PhD Professor of Biochemistry ROBERT K. MURRAY, MD, PhD Professor Emeritus of Biochemistry both of University of Toronto Faculty of Medicine Toronto, Ontario with illustrations by Erin A. Baker, BSc 2001 BC Decker Inc Hamilton • London Exit BC Decker Inc 20 Hughson Street South P.O. Box 620, L.C.D. 1 Hamilton, Ontario L8N 3K7 Tel: 905-522-7017; 1-800-568-7281 Fax: 905-522-7839; 1-888-311-4987 e-mail: info@bcdecker.com website: www.bcdecker.com © 2001 BC Decker Inc All rights reserved. No part of this publication may be reproduced, stored in a retrieval system, or transmitted, in any form or by any means, electronic, mechanical, photocopy- ing, recording, or otherwise, without prior written permission from the publisher. 01 02 03 04 / PC / 9 8 7 6 5 4 3 2 1 ISBN 1-55009-150-6 Printed in Canada Sales and Distribution Notice: The authors and publisher have made every effort to ensure that the patient care recom- mended herein, including choice of drugs and drug dosages, is in accord with the accepted stan- dard and practice at the time of publication. However, since research and regulation constantly change clinical standards, the reader is urged to check the product information sheet included in the package of each drug, which includes recommended doses, warnings, and contraindications. This is particularly important with new or infrequently used drugs. United States BC Decker Inc P.O. 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Box 878 Kimberton, PA 19442 Tel: 610-827-1640 Fax: 610-827-1671 e-mail: jsco@voicenet.com To Gail and Jean for all their love and support over the years, and to Dr. Bill Thompson, an exceptional scientist and a very courageous gentleman. Preface This book is an introductory overview of biochemistry, a text that emphasizes important features of the discipline in a concise and focused manner. It is meant as an economical, portable, and rapidly accessed com- panion rather than a costly, stationary, weighty, and comprehensive text. We have based this book on lectures given to undergraduate students at the University of Toronto within both the Faculty of Medicine and the Faculty of Arts and Science. As there are few biochemistry texts that serve medical undergraduates or students in related health disciplines, this book discusses many diseases and clinical applications as well as the basics of biochemistry. PDQ Biochemistry can serve as a refresher for those who have taken a bio- chemistry course before or as an introduction for those coming from non- science disciplines. These latter students are in need of a clear and easily understood text. At the same time, both medical students and students in the health sciences may benefit from a concise and well-mapped journey through the science of biochemistry as they will use it as a stepping stone they can revisit en route to a particular specialty. The student, like a visitor to Europe, Latin America, the Middle East, or Asia, will hopefully find this book to be similar to Biochemistry on $25 a Day in its ability to point out relevant sites on the journey and reasonably priced hostels within sight of the Acropolis. The topics in PDQ Biochemistry follow the curriculum presented to our medical students in their first year. This text is divided into eight chapters, with proteins being a central theme running through each. Proteins are well beloved of biochemists, for they are the principal functional elements within the body. Proteins are, in many ways, not just molecules of living organisms but molecules that are “alive”. However, as this text hopes to demonstrate the relevance of proteins within the body, we will show how the proteins participate within their surroundings and not simply as isolated molecules. In Chapter 1, the biochemistry of muscle is presented with an intro- duction to amino acids and protein structure. This chapter features the structures of actin and myosin; the biochemical mechanisms of contrac- tion; structural and functional differences between skeletal, cardiac, and smooth muscle; ion transport across membranes and membrane-based receptors; and the actions of nitric oxide as a vasodilator. Chapter 2 describes plasma proteins, the biochemical basis of edema, metal ion- transporting proteins, the important roles of iron and copper within the body, diseases associated with defects in the handling of these metal ions, and atherosclerosis. In Chapter 3, enzymes are described as dynamic pro- teins that catalyze reactions leading to the generation or destruction of molecules within the body. In addition, we discuss serum or plasma enzymes as markers for various diseases. The biochemical basis of hemo- stasis and thrombosis is discussed in Chapter 4, as are the hemophilias. In Chapter 5, we cover the structure and function of hemoglobin as well as the genetic defect responsible for sickle cell anemia. This chapter also describes the metabolism of the heme group and the biochemistry of jaun- dice and the porphyrias. The importance of vitamins B 12 and folate is addressed in Chapter 6 in relation to megaloblastic anemias. Chapter 7 provides an introduction to metabolism: how enzymes cooperate within pathways and cycles that synthesize or degrade molecules. Hormonal reg- ulation of metabolism, diabetes mellitus, and inborn errors of metabolism, such as phenylketonuria, are also discussed here. In Chapter 8, the use of molecular biology within medicine is outlined, along with an introduction to DNA and RNA and a description of methodologies used in the pursuit of disease genes. In this text, you will find that we have not agonized unduly over chem- ical structures. In the end, it is important from a medical viewpoint to grasp quickly the overall picture and the important biochemical features. We shall be delighted if some of the material in this text is retained by med- ical graduates, and, to that end, we have added certain elements of humor and anecdotes that may serve as aide-mémoire. There are also historical notations of medical relevance that have been included as we believe that an interest in medical science should be balanced by an interest in the humanities. R. Roy Baker Robert K. Murray May 2001 Acknowledgments We wish to acknowledge the invaluable help of Dr. Margaret Rand of the Hos- pital for Sick Children in Toronto, who reviewed Chapter 4 and provided many helpful comments. We are also very grateful to Dr.Alex Marks, who for many years has coordinated the Biochemistry Seminar Program for Year One medical students at the University of Toronto. Preface vii Contents 1 Proteins: Introduction to Proteins and the Biochemistry of Muscle, 1 Basics of Protein Structure, 1 Proteins of Muscle, 9 Biochemistry of Muscle Contraction, 14 Cardiac Muscle Compared with Voluntary Muscle, 22 The Heart and Ion Transport, 23 Smooth Muscle: Comparison with Striated Muscle, 27 Nitric Oxide, 30 Energy Supplies and Muscle Contraction, 31 2 Biochemistry of Plasma Proteins, 35 Characteristics of Plasma Proteins, 39 Albumin, Oncotic Pressure, and Edema, 41 Transport Functions of Plasma Proteins, 44 Lipoproteins, Lipid Transport, and Atherosclerosis, 57 3 Enzymes, 67 Properties of Enzymes, 68 Enzyme Classification and Nomenclature, 79 Measurement of Enzyme Activity (Enzyme Assays), 82 Enzyme Rate and End-Point Analysis, 91 Modulation of Enzyme Activity by Drugs, 93 Diagnostic Enzymology, 93 Use of Enzymes as Therapeutic Agents, 101 4 Hemostasis, 103 Coagulation Pathways, 103 Inhibition of Coagulation, 109 Antibodies to Coagulation Factors, 111 Thrombophilia, 112 Therapeutic Anticoagulants, 112 Hemophilia A and B, 113 Fibrin Polymerization and Clot Formation, 114 Fibrinolysis, 116 Clot Busters and Therapies for Clot Lysis, 120 Platelets in Hemostasis and Thrombosis, 122 5 Hemoglobin, Porphyrias, and Jaundice, 135 Structure of Hemoglobin and Oxygen Binding, 135 Regulation of Oxygen Binding to Hemoglobin, 144 Disorders of Hemoglobin (Hemoglobinopathies), 150 Biosynthesis of Heme and the Porphyrias, 156 Heme Breakdown, Bilirubin, and Jaundice, 163 6 Vitamin B 12 , Folic Acid, and Megaloblastic Anemia, 175 Vitamin B 12 , 176 Folic Acid, 186 7 Metabolism, 195 Digestion and Metabolism, 199 Enzymes and Disease, 200 An Overview of Metabolic Pathways, 202 Regulation of Metabolism, 206 Bioenergetics, 218 Carbohydrate Metabolism, 221 Fat Metabolism, 236 Protein Metabolism, 247 8 Recombinant DNA Technology and its Application to Medicine, 255 Structure of DNA, 256 More Complex Configurations of DNA, 261 Structural Elements Found Within DNA, 263 Mitochondrial DNA, 265 Ribonucleic Acid, 266 Eukaryotic Genes, mRNA, and Transcription, 266 Recombinant DNA (rDNA) Techniques, 271 Restriction Enzymes, 273 Molecular Cloning, 276 Probes in rDNA Technology, 281 Blotting Techniques and the Points of the Compass, 284 Polymerase Chain Reaction, 287 Somatic Cell Hybridization, In Situ Hybridization, and Fluorescence In Situ Hybridization, 290 The Hunt for Disease Genes, 291 Restriction Fragment Length Polymorphisms, 293 The Human Genome Project and the Positional Candidate Approach, 299 Related rDNA Technologies, 301 Future Directions, 303 Questions and Answers Contents ix ? Web Links W PDQ BIOCHEMISTRY Proteins: Introduction to Proteins and the Biochemistry of Muscle In this chapter, we will introduce proteins and some of their prominent features. The specific introductory example will be the proteins of muscle, with emphasis on those involved in muscular contraction. Com- parisons will be made using skeletal, cardiac, and smooth muscle found in the vascular system. We will comment on ion transport, with particular emphasis on cardiac muscle cells, and the involvement of calcium in exci- tation events. Lastly, the role of nitric oxide as a vasorelaxant and the sources of energy for muscular contraction will be considered. The infor- mation presented is of importance to studies of cardiovascular physiology and health, but it will also pave the way for insights into other areas of pro- tein function. BASICS OF PROTEIN STRUCTURE It is valid to ask why biochemists are so “hung up”about proteins. Are there no other molecules in the human body worthy of attention? Well, of course, there are many others, but proteins, like popular political figures, have charisma and glamour. And, unlike popular political figures, they actually get things done, and in a very dynamic manner. Most proteins are functional molecules that play very specific roles in your body, and, indeed, there are thousands of them, rather like all the possible occupations you may have considered in grade school: butcher, baker (pardon the pun), candlestick maker,stockbroker, scientist, newspaper vendor—virtually as many parts as you can find women and men playing in the real world (presumably, we are told, the realm outside the universities). Yet, if you remove the distinctive clothing or tools from each profession, you invariably find that people do 1 1 [...]... linkage of amino acids, that proteins have a dis- Amino Acid A R +NH 3 COO- C H Dipeptide B +NH 3 C H H2O R2 R1 COO- + +NH 3 R1 COO- C H +NH 3 O C H C R2 N H C H COO- Peptide Bond Oligopeptide C Amino Acid #5 Amino Acid #1 R1 +NH 3 O C H C R2 N H C H C R3 O N-Terminal Amino Acid N H C H C R4 O N H O C H C R5 N H C H COO- C-Terminal Amino Acid Figure 1 1 Structure of an amino acid and peptide bonds Amino... I C T Troponins G-Actin Monomer F-Actin Figure 1 6 Schematic diagram of F-actin with its associated proteins F-actin is shown as a double helix of G-actin monomers, with shorter tropomyosin strands and the troponin complex (I-, C-, and T-subunits) Adapted from Murray RK, Granner DK, Mayes PA, Rodwell VW Harper’s biochemistry 25th ed Stamford (CT): Appleton and Lange; 2000 Chapter 1 Proteins: Introduction... degradation, and the energy released is used in muscle contraction The S -1 fragment was found to bind ATP as well as the light myosin chains Interestingly, S -1 could also bind F-actin, and the S -1 fragments actually looked like arrowheads on the surface of the F-actin (remember the arrowheads shown in Figure 1 5) However, this binding to F-actin occurred only when ATP was absent Apparently, the binding of... channel (see Figure 1 11 ), responding to the binding of acetylcholine Ligand-gated channels are often associated with intracellular proteins called G-proteins The activation of G-proteins by the activation of the receptor leads to a variety of intracellular metabolic events that we will consider in Chapter 7 The dihydropyridine receptor of the T-tubule system is 24 PDQ BIOCHEMISTRY a voltage-gated channel... the 8-year-old who realizes Chapter 1 Proteins: Introduction to Proteins and the Biochemistry of Muscle 17 that (1) the candy store is open, and (2) the piggy bank is close at hand, the inevitable factor (the parent) steps in between the young hero and the front door to moderate any rash spending impulses As can be seen in Figure 1 6, F-actin is not alone in the thin filament Draped around the F-actin... permitting communication with the filaments of the component sarcomeres (Figure 1 12 ) The depolarization of the T-tubule system can open up what is termed a slow calcium voltage channel in the membrane of the T-tubule This channel also goes by the name dihy- Chapter 1 Proteins: Introduction to Proteins and the Biochemistry of Muscle 21 dropyridine receptor and is a protein that (like the acetylcholine receptor)... and the ATP is subsequently hydrolyzed by the globular ATPase (Figure 1 8) As a result, myosin changes conformation and is able to bind F-actin with increased affinity This is the basis of the genera- H2O Myosin + ATP Myosin + ADP + Pi Actin Actin Actin - Myosin + ATP Actin - Myosin + ADP + Pi ATP ADP + Pi Actin - Myosin Figure 1 8 Biochemistry of muscle contraction A cycle in which myosin ATPase converts... (see Figure 1 11 ), opening up in response to depolarization events and allowing the passage of calcium ions into the cell There are voltage-gated channels for sodium, potassium, and calcium ions The sodium channel comprises three different types of protein subunits The largest is the α-subunit, which has four major domains that can form a pore for the movement of sodium ions (see Figure 1 11 ) Each of... irreversibly inhibit acetylcholinesterase A B C COO- NH3+ D Figure 1 11 Schematics of channels found within plasma membrane A, Voltage-gated channel, which opens with depolarization and allows the passage of cations B, C, Ligand-gated channel, such as the acetylcholine receptor, that opens in response to ligand ( ) binding, allowing cation movement D, The α-subunit of the Na+ channel This is made up of... diagram Adapted from Ganong WF Review of medical physiology 17 th ed Norwalk (CT): Appleton and Lange; 19 95 16 PDQ BIOCHEMISTRY F-actin is released, and this is the relaxation phase, which depends on the binding of ATP As ATP is once again hydrolyzed by myosin ATPase, the contraction phase begins anew and can result in further motion of the F-actin toward the center of the sarcomere Presuming that you . 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