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CLIFFSQuICKREVIEW Biochemistry II By Frank Schmidt,Ph.D. IDG Books Worldwide, Inc. An International Data Group Company Foster City, CA¤ Chicago, IL¤ Indianapolis, IN ¤ New York, NY About the Author Publisher’s Acknowledgments Frank Schmidt is a professor of Biochemistry at Editorial the University of Missouri-Columbia. Project Editor: Sherri Fugit Acquisitions Editor: Kris Fulkerson Copy Editor: Corey Dalton Technical Editor: Jessica Joy Hollenbeck Editorial Assistant: Laura Jefferson Production Proofreader: Joel Showalter IDG Books Indianapolis Production Department CLIFFSQUICKREVIEW™Biochemistry II Note:If you purchased this book without a cover, you should Published by be aware that this book is stolen property. It was reported as IDG Books Worldwide, Inc. "unsold and destroyed" to the publisher, and neither the An International Data Group Company author nor the publisher has received any payment for this 919 E. Hillsdale Blvd. "stripped book." Suite 400 Foster City, CA 94404 www.idgbooks.com (IDG Books Worldwide Web site) www.cliffsnotes.com (CliffsNotes Web site) Copyright © 2000 IDG Books Worldwide, Inc. All rights reserved. No part of this book, including interior design, cover design, and icons, may be reproduced or transmitted in any form, by any means (electronic, photocopying, recording, or otherwise) without the prior written permission of the publisher. Library of Congress Control Number: 00-103372 ISBN: 0-7645-8562-2 Printed in the United States of America 10 9 8 7 6 5 4 3 2 1 1O/RQ/QX/QQ/IN Distributed in the United States by IDG Books Worldwide, Inc. Distributed by CDG Books Canada Inc. for Canada; by Transworld Publishers Limited in the United Kingdom; by IDG Norge Books for Norway; by IDG Sweden Books for Sweden; by IDG Books Australia Publishing Corporation Pty. 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For general information on IDG Books Worldwide’s books in the U.S., please call our Consumer Customer Service department at 800-762-2974.For reseller information, including discounts and premium sales, please call our Reseller Customer Service department at 800-434-3422. For information on where to purchase IDG Books Worldwide’s books outside the U.S., please contact our International Sales department at 317-596-5530or fax 317-572-4002. For consumer information on foreign language translations, please contact our Customer Service department at 1-800-434-3422, fax 317-572-4002, or e-mail [email protected]. For information on licensing foreign or domestic rights, please phone +1-650-653-7098. For sales inquiries and special prices for bulk quantities, please contact our Order Services department at 800-434-3422 or write to the address above. For information on using IDG Books Worldwide’s books in the classroom or for ordering examination copies, please contact our Educational Sales department at 800-434-2086or fax 317-572-4005. For press review copies, author interviews, or other publicity information, please contact our Public Relations department at 650-653-7000or fax 650-653-7500. For authorization to photocopy items for corporate, personal, or educational use, please contact Copyright Clearance Center, 222 Rosewood Drive, Danvers, MA 01923, or fax 978-750-4470. LIMIT OF LIABILITY/DISCLAIMER OF WARRANTY:THE PUBLISHER AND AUTHOR HAVE USED THEIR BEST EFFORTS IN PREPARING THIS BOOK. THE PUBLISHER AND AUTHOR MAKE NO REPRESENTATIONS OR WARRANTIES WITH RESPECT TO THE ACCURACY OR COMPLETENESS OF THE CONTENTS OF THIS BOOK AND SPECIFICALLY DISCLAIM ANY IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. THERE ARE NO WAR- RANTIES WHICH EXTEND BEYOND THE DESCRIPTIONS CONTAINED IN THIS PARAGRAPH. NO WARRANTY MAY BE CREATED OR EXTENDED BY SALES REPRESENTATIVES OR WRITTEN SALES MATERIALS. THE ACCURACY AND COM- PLETENESS OF THE INFORMATION PROVIDED HEREIN AND THE OPINIONS STATED HEREIN ARE NOT GUARAN- TEED OR WARRANTED TO PRODUCE ANY PARTICULAR RESULTS, AND THE ADVICE AND STRATEGIES CONTAINED HEREIN MAY NOT BE SUITABLE FOR EVERY INDIVIDUAL. NEITHER THE PUBLISHER NOR AUTHOR SHALL BE LIABLE FOR ANY LOSS OF PROFIT OR ANY OTHER COMMERCIAL DAMAGES, INCLUDING BUT NOT LIMITED TO SPECIAL, INCIDENTAL, CONSEQUENTIAL, OR OTHER DAMAGES. Trademarks: Cliffs, CliffsNotes, and all related logos and trade dress are registered trademarks or trademarks of IDG Books Worldwide, Inc. in the United States and other countries. All other brand names and product names used in this book are trade names, service marks, trademarks, or regis- tered trademarks of their respective owners. IDG Books Worldwide, Inc. is not associated with any product or vendor mentioned in this book. is a registered trademark under exclusive license to IDG Books Worldwide, Inc. from International Data Group, Inc. CONTENTS FUNDAMENTAL IDEAS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1 CHAPTER 1:FATTY ACID OXIDATION . . . . . . . . . . . . . . . .3 Fats and Oils . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 Dietary Fat Absorption. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4 Lipids in the bloodstream . . . . . . . . . . . . . . . . . . . . . . . . . . . 7 Tissues and lipids . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8 Hydrolysis of Triacylglyerols . . . . . . . . . . . . . . . . . . . . . . . . . . 9 b eta-Oxidation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9 E Activation: Fatty Acid Fatty Acyl-CoA. . . . . . . . . . . . . . . . 10 Transport: The Role of Carnitine. . . . . . . . . . . . . . . . . . . . . . . 10 The b -Oxidation Helical Scheme for Fatty Acyl-CoA . . . . . . 12 Energy Yield from Fatty Acid Oxidation. . . . . . . . . . . . . . . . . 15 Odd-Numbered Chain and Branched Fatty Acids. . . . . . . . . . 15 Ketone Bodies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17 CHAPTER 2:LIPID BIOSYNTHESIS . . . . . . . . . . . . . . . . . .19 Energy Storage. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19 Fatty Acid Biosynthesis. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19 Initiation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21 Elongation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22 Release. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24 Synthesis of Triacylglycerols. . . . . . . . . . . . . . . . . . . . . . . . . . 28 Cholesterol Biosynthesis and its Control. . . . . . . . . . . . . . . . . 29 Isoprenoid Compounds . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29 HMG CoAReductase . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31 Mevalonate Squalence. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31 Squalene fi Lanosterol . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33 Lanosterol fi Cholesterol . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35 Cholesterol Transport, Uptake, and Control . . . . . . . . . . . . . . 35 BIOCHEMISTRY II iii CONTENTS CHAPTER 3:PHOTOSYNTHESIS . . . . . . . . . . . . . . . . . . . . .39 Metabolic Oxidation and Reduction . . . . . . . . . . . . . . . . . . . . 39 Overall Process of Photosynthesis. . . . . . . . . . . . . . . . . . . . . . 40 Two Photosynthetic reactions . . . . . . . . . . . . . . . . . . . . . . . 41 The chloroplast . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41 Chlorophyll and the action spectrum of photosynthesis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41 Light Reactions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45 Photosystem II. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45 Photosystem I . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48 Cyclic Electron Flow. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48 Z-Scheme of Photosynthesis . . . . . . . . . . . . . . . . . . . . . . . . . . 49 ATPSynthesis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49 Carbohydrate Synthesis. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51 C-3 Photosynthesis. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51 Energetics of Photosynthesis. . . . . . . . . . . . . . . . . . . . . . . . . . 55 Photorespiration. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56 C4 plants . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59 CHAPTER 4:NITROGEN FIXATION,ASSIMILATION, AND ELIMINATION . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .63 Reduced Nitrogen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63 The Nitrogen Cycle . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63 Bacterial Nitrogenase. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64 Ammonium Utilization . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66 Glutamate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66 Glutamine . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67 Glutamate from glutamine. . . . . . . . . . . . . . . . . . . . . . . . . . 67 Further Fates of Incorporated Ammonia . . . . . . . . . . . . . . . . . 68 Glutamine . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70 Carbamoyl phosphate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71 Urea . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72 Biochemistry of the urea cycle . . . . . . . . . . . . . . . . . . . . . . 73 CLIFFSQUICKREVIEW iv CONTENTS CHAPTER 5:AMINO ACID METABOLISM:CARBON . . .77 Principles of Amino Acid Metabolism. . . . . . . . . . . . . . . . . . . 77 1-Carbon Metabolism . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77 Folic acid. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77 Folate antagonists as antimicrobial drugs. . . . . . . . . . . . . . 80 Vitamin B12 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81 Methyltransferases. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 82 Amino Acid Biosynthesis . . . . . . . . . . . . . . . . . . . . . . . . . . . . 84 Nonessential amino acids . . . . . . . . . . . . . . . . . . . . . . . . . . 85 Essential amino acids . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 86 Biosynthesis of aromatic amino acids. . . . . . . . . . . . . . . . . 86 Pathway determination by biochemical genetics . . . . . . . . 88 Feedback inhibition. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 90 Amino acid catabolism . . . . . . . . . . . . . . . . . . . . . . . . . . . . 91 Inborn errors of amino acid metabolism. . . . . . . . . . . . . . . 92 Heme biosynthesis. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 93 CHAPTER 6:PURINES AND PYRIMIDINES . . . . . . . . . . .95 Roles of nucleotides. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 95 Purine and Pyrimidine Structures . . . . . . . . . . . . . . . . . . . . . . 95 Salvage and Biosynthetic Pathways. . . . . . . . . . . . . . . . . . . . . 98 Salvage pathways . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 99 Purine biosynthesis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 101 Degradation of purine nucleotides . . . . . . . . . . . . . . . . . . 106 Pyrimidine Metabolism . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 108 Pyrimidine biosynthesis . . . . . . . . . . . . . . . . . . . . . . . . . . 109 Control. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 110 Deoxynucleotide Synthesis . . . . . . . . . . . . . . . . . . . . . . . . . . 111 Thymidylate synthase . . . . . . . . . . . . . . . . . . . . . . . . . . . . 112 Chemotherapy. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 113 CHAPTER 7:INTEGRATED METABOLISM . . . . . . . . . .117 Metabolic Relationships. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 117 Energy from Glucose. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 117 Proteins and Fatty Acids . . . . . . . . . . . . . . . . . . . . . . . . . . 119 BIOCHEMISTRY II v CONTENTS Exercise and Metabolism. . . . . . . . . . . . . . . . . . . . . . . . . . . . 120 Anaerobic exercise: sprinting . . . . . . . . . . . . . . . . . . . . . . 120 Aerobic metabolism: prolonged exercise . . . . . . . . . . . . . 121 Nutritional state. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 122 Hormonal Regulation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 123 Down regulation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 125 Receptor Types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 126 Cyclic AMP: ASecond Messenger . . . . . . . . . . . . . . . . . . . . 126 Action of cyclic AMP . . . . . . . . . . . . . . . . . . . . . . . . . . . . 129 PI System: Another Second Messanger. . . . . . . . . . . . . . . . . 129 Protein kinase C. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 133 Receptors with Kinase Activity. . . . . . . . . . . . . . . . . . . . . . . 133 Hormone interactions . . . . . . . . . . . . . . . . . . . . . . . . . . . . 134 Hormones that Affect Gene Activity. . . . . . . . . . . . . . . . . . . 135 CHAPTER 8:DNA STRUCTURE,REPLICATION, ANDREPAIR . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .137 DNAand RNAStructures . . . . . . . . . . . . . . . . . . . . . . . . . . . 137 Sugar structures in DNAand RNA. . . . . . . . . . . . . . . . . . 140 DNAStructure. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 141 DNAtertiary structure. . . . . . . . . . . . . . . . . . . . . . . . . . . . 144 DNAReplication Enzymes . . . . . . . . . . . . . . . . . . . . . . . . . . 146 DNApolymerases. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 148 Chromosomal replication . . . . . . . . . . . . . . . . . . . . . . . . . 152 Initiation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 152 Elongation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 155 DNARepair. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 156 DNArepair systems. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 159 DNARecombination and Repair. . . . . . . . . . . . . . . . . . . . . . 161 CHAPTER 9:MOLECULAR CLONING OF DNA . . . . . . .167 Gene Expression . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 167 DNAand Information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 167 DNAHybridization . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 168 Restriction Enzyme Mapping . . . . . . . . . . . . . . . . . . . . . . . . 170 DNAMapping . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 172 Southern Blotting. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 174 CLIFFSQUICKREVIEW vi CONTENTS Molecular Cloning. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 176 Plasmid vectors. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 176 Other types of cloning vectors. . . . . . . . . . . . . . . . . . . . . . 179 Identifying Particular Sequences in a Library. . . . . . . . . . . . 181 The Polymerase Chain Reaction . . . . . . . . . . . . . . . . . . . . . . 183 DNASequence Determination. . . . . . . . . . . . . . . . . . . . . . . . 185 Genomics. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 187 CHAPTER 10:RNA AND TRANSCRIPTION . . . . . . . . . . .189 RNAInformation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 189 RNAFunctions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 192 Messenger RNA. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 192 Transfer RNA. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 194 Ribosomal RNA. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 196 Other Information-Processing RNAs. . . . . . . . . . . . . . . . . . . 197 Transcription . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 197 Transcription in Prokaryotes . . . . . . . . . . . . . . . . . . . . . . . . . 198 Promoter recognition. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 199 The transcription process. . . . . . . . . . . . . . . . . . . . . . . . . . 200 Transcriptional Control in Bacteria. . . . . . . . . . . . . . . . . . . . 204 The Lactose Operon—ACase Study in Regulation . . . . . . . 205 CHAPTER 11:PROTEIN SYNTHESIS . . . . . . . . . . . . . . . .213 Transcription and Translation . . . . . . . . . . . . . . . . . . . . . . . . 213 Fidelity in tRNAAminoacylation . . . . . . . . . . . . . . . . . . . . . 215 Initiation of Protein Synthesis . . . . . . . . . . . . . . . . . . . . . . . . 218 Elongation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 220 Termination of Translation. . . . . . . . . . . . . . . . . . . . . . . . . . . 224 CHAPTER 12:EUKARYOTIC GENES . . . . . . . . . . . . . . . .227 Eukaryotic Information Flow. . . . . . . . . . . . . . . . . . . . . . . . . 227 DNAand Genomes in Eukaryotes. . . . . . . . . . . . . . . . . . . . . 227 Structure of Chromatin . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 228 Chromatin Replication. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 230 Reverse Transcription . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 233 BIOCHEMISTRY II vii CONTENTS Eukaryotic Gene Structure. . . . . . . . . . . . . . . . . . . . . . . . . . . 235 Transcription . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 237 Ribosomal RNAsynthesis. . . . . . . . . . . . . . . . . . . . . . . . . 238 Messenger RNAtranscription. . . . . . . . . . . . . . . . . . . . . . 240 Transfer and 5S ribosomal RNAtranscription . . . . . . . . . 240 RNAProcessing. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 242 Messenger RNAprocessing reactions. . . . . . . . . . . . . . . . 242 RNAcatalysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 248 Eukaryotic Translation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 249 Initiation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 249 Elongation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 250 Protein glycosylation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 252 Eukaryotic Transcriptional Control. . . . . . . . . . . . . . . . . . . . 253 Translational Control. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 257 CLIFFSQUICKREVIEW viii FUNDAMENTAL IDEAS For the purpose of your review, your knowledge of the following fun- damental ideas is assumed: n The scope of biochemistry n Biological energy flow n Protein structure n Weak interactions n Physiological chemistry of oxygen binding n Enzymes n Organization of metabolism n Glycolysis n Tricarboxylic acid cycle n Oxidative phosphorylation n Carbohydrate metabolism II If you need to review any of these topics, refer to CliffsQuickReview Biochemistry I. BIOCHEMISTRY II 1

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