Basic Sciences Review for Medical Licensure Developed at The University of Oklahoma College of Medicine Suitable Reviews for: United States Medical Licensing Examination (USMLE), Step 1 Biochemistry Third Edition Edited by Thomas Briggs Albert M. Chandler Springer-Verlag New York Berlin Heidelberg London Paris Tokyo Hong Kong Barcelona Budapest Thomas Briggs, Ph.D. Department of Biochemistry and Molecular Biology University of Oklahoma P.O. Box 26901 Oklahoma City, OK 73190 USA Albert M. Chandler, Ph.D. Department of Biochemistry and Molecular Biology University of Oklahoma P.G. Box 26901 Oklahoma City, OK 73190 USA Library of Congress Cataloging-in-Publication Data CIP applied for ISBN-13:978-0-387 -94398-5 e-ISBN- 13:978-1-4612-4200-0 DOl: 10.1007/978-1-4612-4200-0 Printed on acid-free paper. © 1995, 1992, and 1987 Springer-Verlag New York, Inc. All rights reserved. This work may not be translated or copied in whole or in part without the written permission of the publisher (Springer-Verlag New York, Inc., 175 Fifth Avenue, New York, NY 10010, USA), except for brief excerpts in connection with reviews or schol arly analysis. Use in connection with any form of information storage and retrieval, elec tronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed is forbidden. The use of general descriptive names, trade names, trademarks, etc., in this publication, even if the former are not especially identified, is not to be taken as a sign that such names, as understood by the Trade Marks and Merchandise Marks Act may accordingly be used freely by anyone. While the advice and information in this book are believed to be true and accurate at the date of going to press, neither the authors nor the editors nor the publisher can accept any legal responsibility for any errors or omissions that may be made. The publisher makes no warranty, express or implied, with respect to the material contained herein. Production managed by Laura Carlson; manufacturing supervised by Joe Quatela. Camera-ready copy prepared by the authors. 987654321 ISBN 0-387-94398-6 Springer-Verlag New York Berlin Heidelberg Preface to the (')~~ In 1973, the University of Oklahoma College of Medicine instituted a requirement for passage of the Part I National Boards for promotion to the third year. To assist students in preparation for this examination, a two-week review of the basic sci ences was added to the curriculum in 1975. Ten review texts were written by the faculty: four in anatomical sciences and one each in the other six basic sciences. Self-instructional quizzes were also developed by each discipline and adminis tered during the review period. The first year the course was instituted the Total Score performance on National Boards Part I increased 60 points, with the relative standing of the school chang ing from 56th to 9th in the nation. The performance of the class since then has remained near the national candidate mean. This improvement in our own stu dents' performance has been documented (Hyde et al: Performance on NBME Part I examination in relation to policies regarding use of test. J. Med. Educ. 60: 439-443, 1985). A questionnaire was administered to one of the classes after they had completed the Boards; 82% rated the review books as the most beneficial part of the course. These texts were subsequently rewritten and made available for use by all stu dents of medicine who were preparing for comprehensive examinations in the Basic Medical Sciences. Since their introduction in 1987, over 300,000 copies have been sold. Obviously these texts have proven to be of value. The main reason is that they present a concise overview of each discipline, emphasizing the content and concepts most appropriate to the task at hand, i.e., passage of a comprehen sive examination covering the Basic Medical Sciences. The recent changes in the licensure examination that have been made to create a Step l/Step 2/Step 3 process have necessitated a complete revision of the Oklahoma Notes. This task was begun in the summer of 1991 and has been on going over the past three years. The book you are now holding is a product of that revision. Besides bringing each book up to date, the authors have made every effort to make the tests and review questions conform to the new format of the National Board of Medical Examiners. Thus we have added numerous clinical vignettes and extended match questions. A major revision in the review of the Anatomical Sciences has also been introduced. We have distilled the previous editions' content to the details the authors believe to be of greatest importance and have combined the four texts into a single volume. In addition a book about neu rosciences has been added to reflect the emphasis this interdisciplinary field is now receiving. I hope you will find these review books valuable in your preparation for the licen sure exams. Good luck! Richard M. Hyde, Ph.D. Executive Editor Preface to the Third Edition This book is intended to be a quick review for those who are studying for their licensure examination in Biochemistry (USMLE, Step 1). As in the first two edi tions, we have left out a great deal of detail in the interest of making the book digestible in a reasonable time and to keep the price affordable. Those who need a more thorough reference should consult any of several excellent and up-to-date texts that are now available. Significant improvements in this edition, besides a general updating and correc tion of the text, are as follows: • Test Questions. In addition to many new sample questions, we have supplied an annotation for each, to explain briefly why the selected answer is correct. Although this took up extra space in the book, we felt the teaching value was worth it. • Medical Genetics. We have added a new broadly based chapter, professionally illustrated, on this rapidly developing field, describing recombinant DNA tech niques and their applications in diagnosis of genetic disease and in gene thera py. The chapter also includes a review of basic genetics and the chemistry of mutations. As before, each part is written by a colleague who is either an expert in the field or an experienced teacher of the topic. The words are the authors' own, but as edi tors we accept responsibility for what to include or omit. We welcome comments and suggestions for future editions. Thomas Briggs Albert M. Chandler Contents Preface to the Oklahoma Notes. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . v Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. vii 1. Amino Acids and Proteins A. Chadwick Cox Amino Acids. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 Protein Structure: General . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 Collagen and Fibrous Proteins. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4 Hemoglobin. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5 Plasma Proteins. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6 Hemostasis and Blood Coagulation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7 Genetic Diseases. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12 Review Questions on Amino Acids and Proteins. . . . . . . . . . . . . . . . . . 14 2. Enzymes A. Chadwick Cox and Wai-Yee Chan Nature of Enzymes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 19 Enzyme Kinetics. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21 Effects of Kinetic Parameters on Enzyme Activity . . . . . . . . . . . . . . . . . 24 General Aspects .. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26 Review Questions on Enzymes. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27 3. Carbohydrates Albert M. Chandler Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31 Structural Aspects of Carbohydrates. . . . . . . . . . . . . . . . . . . . . . . . . . . . 31 Digestion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34 Glycolysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35 Entry of Other Hexoses into the Glycolytic Pathway . . . . . . . . . . . . . . . 38 Metabolism of Pyruvate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39 Regulation of Glycolysis. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 40 Pentose Phosphate Pathway. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 41 Gluconeogene~s............................................ 42 Glycogen Metabolism. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 44 Glycogen Storage Diseases. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47 Hormonal Regulation of Carbohydrate Metabolism. . . . . . . . . . . . . . . . 47 Review Questions on Carbohydrates . ; . . . . . . . . . . . . . . . . . . . . . . . . .. 49 4. Energetics and Biological Oxidation Thomas Briggs Concepts in Biological Oxidation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61 Metabolism of Pyruvate to Carbon Dioxide. . . . . . . . . . . . . . . . . . . . . . . 63 Electron Transfer via the Respiratory Chain. . . . . . . . . . . . . . . . . . . . .. 67 Chemi-Osmotic Theory of Oxidative Phosphorylation. . . . . . . . . . . . . . 71 Review Questions on Energetics and Biological Oxidation . . . . . . . . .. 72 x Contents 5. Amino Acid Metabolism Albert M. Chandler Functions of Amino Acids in Man. . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 80 Essential and Non-Essential Amino Acids . . . . . . . . . . . . . . . . . . . . . .. 80 Nitrogen Balance. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81 Protein Quality ........................................... " 81 Protein Digestion. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81 Amino Acid Absorption. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 82 Amino Acid Degradation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 83 The Urea Cycle (Krebs-Henseleit Cycle) . . . . . . . . . . . . . . . . . . . . . . . .. 84 Excretion of Free Ammonia . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 86 Degradation of the Carbon Skeletons. . . . . . . . . . . . . . . . . . . . . . . . . . . . 87 One-Carbon Fragment Metabolism . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 88 Metabolism of Phenylalanine and Tyrosine . . . . . . . . . . . . . . . . . . . . . . 91 General Precursor Functions of Amino Acids. . . . . . . . . . . . . . . . . . . .. 93 Review Questions on Amino Acid Metabolism . . . . . . . . . . . . . . . . . . . 94 6. Porphyrins Thomas Briggs Structure and Chemistry. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 104 Metabolism. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 105 Disorders of Porphyrin and Heme Metabolism .................. " 106 Genetic Diseases. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 107 Review Questions on Porphyrins. . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 109 7. Lipids Chi-Sun Wang Classification of Lipids. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 113 Functions of Lipids. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 113 Digestion and Absorption of Lipids. . . . . . . . . . . . . . . . . . . . . . . . . . . .. 114 Fatty Acids . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 114 Ketone Bodies. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 121 Triacylglycerols. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 122 Phospholipids. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 123 Glycosphingolipids (Glycolipids) . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 125 Lipoproteins. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 125 Genetic Diseases. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 127 Review Questions on Lipids. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 130 8. Steroids Thomas Briggs Cholesterol: Structure and Chemistry. . . . . . . . . . . . . . . . . . . . . . . . . .. 139 Occurrence and Function. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 140 Biosynthesis of Cholesterol . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 140 Metabolism of Cholesterol. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 142 Action of Steroid Hormones. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 144 Cholesterol Levels. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 145 Disorders of Cholesterol and Steroid Metabolism. . . . . . . . . . . . . . . . .. 146 Cholesterol in Perspective. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 147 Review Questions on Steroids. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 148 9. Membranes Thomas Briggs Overview. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 154 Chemistry and Structure. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 155 Functions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 157 Review Questions on Membranes . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 165 Contents xi 10. Nutrition Thomas Briggs Major Nutrients. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 171 Micronutrients .... . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 174 Review Questions on Nutrition . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 185 11. Purines and Pyrimidines Leon Unger Structure and Nomenclature . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 193 Synthesis of Nucleoside Diphosphates and Triphosphates . . . . . . . . .. 194 Purine Metabolism . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 195 Pyrimidine Metabolism: Biosynthesis. . . . . . . . . . . . . . . . . . . . . . . . . .. 199 Deoxyribonucleotides Are Formed by Reduction of Ribonucleoside Diphosphates by Ribonucleoside Diphosphate Reductase (Ribonucleotide Reductase) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 199 Some Anticancer Drugs Act by Blocking Deoxythmidylate Synthesis. 201 Functions of Nucleotides . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 202 Review Questions on Purines and Pyrimidines . . . . . . . . . . . . . . . . . .. 203 12. Nucleic Acids: Structure and Synthesis Jay Hanas DNA ...................................................... 207 RNA ...................................................... 215 Review Questions on Nucleic Acids .......................... " 219 13. Protein Biosynthesis Jay Hanas and Albert M. Chandler Introduction. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 227 Cellular Machinery. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 227 Information Transfer. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 232 Peptide Bond Formation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 233 Postribosomal Modification of Proteins. . . . . . . . . . . . . . . . . . . . . . . . .. 236 Some Antibiotics Acting as Inhibitors of Protein Synthesis. . . . . . . . .. 238 Review Questions on Protein Biosynthesis ..................... " 239 14. Medical Genetics Sara L. Tobin, with figures by Ann Boughton Basic Genetics. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 247 Mutations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 252 Recombinant DNA Techniques . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 254 Genetic Diagnostic Techniques. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 270 Gene Therapy. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 274 Well-Known Genetic Diseases. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 279 Review Questions on Medical Genetics ....... ; ................. , 280 - 1 - 1. AMINO ACIDS AND PROTEINS A. Chadwick Cox I. AMINO ACIDS A. The 20 Amino Acids. These are coded for in DNA: Alanine (Ala) Leucine (Leu) Arginine (Arg) Lysine (Lys) Asparagine (Asn) Methionine (Met) Aspartic Acid (Asp) Phenylalanine (Phe) Cysteine (Cys) Proline (Pro) Glycine (Gly) Serine (Ser) Glutamine (Gin) Threonine (Thr) Glutamic Acid (Glu) Tyrosine (Tyr) Histidine (His) Tryptophan (Trp) Isoleucine (lie) Valine (Val) B. Stereochemistry The absolute configuration is the L (or S) enantiomer. The carbon adjacent to the carboxyl group is the a-carbon, to which the amino group is attached. Other carbon atoms are also attached to the a-carbon to form an R group. Amino acids differ from one another because they have different a-carbon R groups. C. Classification: According to properties important to protein structure. 1. Hydrophobic (nonpolar): Ala, Cys, Gly, lie, Leu, Met, Phe, Trp, Val. 2. Hydrophilic (polar and form H-bonds except for Pro) • neutral: Asn, Gin, Pro, Ser, Thr, Tyr • acidic (negative charge): Asp, Glu • basic (positive charge): Arg, His, Lys D. Post-translational Modifications Several amino acids can be modified after being incorporated into proteins. Common post-translational modifications include formation of disulfide crosslinks, glycosylation of Ser or Asn residues, and phosphory lation of Ser, Thr and Tyr. The functions of these modifications will be discussed later. - 2 - E. Amino Acids as Ampholytes All the amino acids at neutrality possess both positive and negative charges and are called ampholytes and zwitterions. Because proteins contain mixtures of the acidic and basic amino acid residues indicated above, they are also ampholytes. Each of the ionizable groups on amino acids and proteins behaves accord ing to the same principles that apply to any weak acid. HA .. H+ + A- Ka = [H+][A-] / [HA] This equation can be written in a form that directly relates the concentrations to the pH - the Hen derson-Hasselbalch equation: pH = pKa + Log ([conjugate base] / [conjugate acid]) When the conjugate base and acid are equal in concentration, their ratio is one, the log is zero, so pH = pKa. The pH is buffered best by any ionizable group at or near its pKa. For carboxyl groups, pH = pKa + Log ([COO-] / [COOHD pKa usually in the 2 - 4 range For amino groups, pH = pKa + Log ([NH2 ] / [NH3 +]) pKa usually in the 6 - 10 range In histidine the N is part of an imidazole ring but it acts like an amino group with pKa value around neutral ity. For this reason His can participate in acid and base catalysis and is part of the catalytic mechanism of many enzymes. As these equations indicate, the charge ratio varies with pH. An amino acid that has one amino group and one carboxyl group will be positively charged at low pH values. The net charge will diminish as the pH proceeds through values about the pKa of the carboxyl group, because the latter are becoming negatively charged. It will equal zero at some pH intermediate between the pK values of the two ionizable groups, then will become negative as the pH proceeds through values about the pKa of the amino group because these are losing their positive charge. The pH at which the net charge is zero is called the isoelectric point (pI) be cause the molecules in solution will not migrate in an electric field. Figure 1-1 illustrates the points made above. The figure shows the number of equivalents of NaOH consumed by an amino acid in titrating the solution from pH 0 to pH 14. The amino acid has one basic and two acidic ionizable groups. (The latter, in this example, are too close to resolve clearly). TITRATION OF AMINO ACID 1. How many pKa's are there? The same number as equivalents. (3) EQUIVALENTS OF NaOH ADDED 3.5,--'--------------------, 2. What are their values? The same as the 3 pH at each half equivalence. (About 2, 4, 2.5 and 9 in this example). 2 3. Where is the isoelectric point? With 1.5 two pKa values in the acid region it must be an acidic amino acid and the pI must be in 0.5 the acid region halfway between the two 0~~J__~_~~_~_~_~ __L __~ pKa values, that is, at pH 3. o 2 4 6 8 10 12 14 16 pH Figure 1-1. Titration of an Amino Acid having Three Ionizable Groups.