CLIFFSQuICKREVIEW™ Biochemistry I By Frank Schmidt 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, Ph.D., is Professor of Editorial Biochemistry at the University of Missouri- Project Editor: Kathleen A. Dobie Columbia. Since 1978, he has taught biochem- Acquisitions Editor: Kris Fulkerson istry to graduate, medical, undergraduate, and Technical Editor: Cristina Furdui continuing education students. His scholarly Editorial Assistant: Laura Jefferson work is in the areas of RNA biochemistry, the ori- Production Proofreader: Melissa Buddendec gin of life, drug discovery, and inquiry-based sci- IDG Books Indianapolis Production ence education. Department CLIFFSQUICKREVIEW™Biochemistry I 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. 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CONTENTS CHAPTER 1:THE SCOPE OF BIOCHEMISTRY . . . . . . . . .1 Biochemistry is a Contemporary Science . . . . . . . . . . . . . . . . . 2 Extrapolating Biochemical Information . . . . . . . . . . . . . . . . . . 3 Common Themes in Biochemistry . . . . . . . . . . . . . . . . . . . . . . 4 Biochemical reactions involve small molecularstructures . . . . 4 Polymers in Living Systems . . . . . . . . . . . . . . . . . . . . . . . . . . . 6 Cell membranes. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8 Types of Biochemical Reactions . . . . . . . . . . . . . . . . . . . . . . . . 9 Regulating biochemical reactions. . . . . . . . . . . . . . . . . . . . . 9 Large molecules provide cell information. . . . . . . . . . . . . . 10 Weak interactions and structural stability. . . . . . . . . . . . . . 10 Biochemical reactions occur in a downhill fashion. . . . . . . 10 All Organisms are Related. . . . . . . . . . . . . . . . . . . . . . . . . . . . 11 The Common Origin of Organisms. . . . . . . . . . . . . . . . . . . . . 12 CHAPTER 2:THE IMPORTANCE OF WEAK INTERACTIONS . . . . . . . . . . . . . . . . . . . . . . . . . . . . .15 The United Strength of biochemical structures. . . . . . . . . . . . 15 Properties of Water and Biomolecular Structure. . . . . . . . . . . 16 The properties of water and hydrogen bonds . . . . . . . . . . . 16 Hydrogen bonds and biomolecules. . . . . . . . . . . . . . . . . . . 17 The Hydrophobic Effect. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18 Nonpolar molecules and water-solubility. . . . . . . . . . . . . . 18 Membrane associations. . . . . . . . . . . . . . . . . . . . . . . . . . . . 20 Electrostatic and van der Waals Interactions. . . . . . . . . . . . . . 21 Acid-Base Reactions in Living Systems . . . . . . . . . . . . . . . . . 23 pK values and protonation. . . . . . . . . . . . . . . . . . . . . . . . . . 24 Solution pH. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25 Buffer capacity . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26 Biological acid-base equilibria . . . . . . . . . . . . . . . . . . . . . . 27 CHAPTER 3:INTRODUCTION TO BIOLOGICAL ENERGY FLOW . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .29 Types of metabolic reactions. . . . . . . . . . . . . . . . . . . . . . . . . . 29 Enzyme Catalysts. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30 Space and Time Links in Metabolic Reactions . . . . . . . . . . . . 30 Energy Flow. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31 BIOCHEMISTRY I iii CONTENTS Free Energy Calculations. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33 The Cell’s Energy Currency. . . . . . . . . . . . . . . . . . . . . . . . . . . 35 Free-Energy-Driven Transport across Membranes . . . . . . . . . 36 CHAPTER 4:OVERVIEW OF BIOLOGICAL INFORMATION FLOW . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .39 Complexity in Biochemical Genetics . . . . . . . . . . . . . . . . . . . 39 The Central Dogma of Molecular Biology: DNAMakes RNAMakes Protein. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40 DNA, RNA, and nucleotide structure . . . . . . . . . . . . . . . . . . . 41 DNA’s duplex nature. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44 The DNAdouble helix and genetic replication. . . . . . . . . . 47 RNACarries Genetic Information. . . . . . . . . . . . . . . . . . . . . . 49 Messenger RNAspecifies the order of amino acids in proteins. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50 Transfer RNA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51 Ribosomes and translation. . . . . . . . . . . . . . . . . . . . . . . . . . 53 Base-Pairing and the Central Dogma. . . . . . . . . . . . . . . . . . . . 54 Genetic information expression. . . . . . . . . . . . . . . . . . . . . . 54 CHAPTER 5:PROTEIN STRUCTURE . . . . . . . . . . . . . . . . .55 Levels of Protein Structure . . . . . . . . . . . . . . . . . . . . . . . . . . . 55 Amino acids. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56 Amino acid side chains. . . . . . . . . . . . . . . . . . . . . . . . . . . . 57 Hydroxyl and sulfer-containing side chains . . . . . . . . . . . . 60 The cyclic amino acid. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61 Primary struture. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64 Secondary structure. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66 Fibrous and globular proteins . . . . . . . . . . . . . . . . . . . . . . . 70 Tertiary structure. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71 Protein-assisted folding. . . . . . . . . . . . . . . . . . . . . . . . . . . . 73 Quaternary structures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 74 CHAPTER 6:THE PHYSIOLOGICAL CHEMISTRY OF OXYGEN BINDING BY MYOGLOBIN AND HEMOGLOBIN . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .75 The Chemistry of Molecular Oxygen . . . . . . . . . . . . . . . . . . . 75 Hemoglobin and myoglobin . . . . . . . . . . . . . . . . . . . . . . . . 76 CLIFFSQUICKREVIEW iv CONTENTS Myoglobin binds oxygen. . . . . . . . . . . . . . . . . . . . . . . . . . . 77 Binding oxygen to hemoglobin. . . . . . . . . . . . . . . . . . . . . . 79 Physiological conditions and hemoglobin . . . . . . . . . . . . . 81 Acidic conditions and hemoglobin . . . . . . . . . . . . . . . . . . . 81 Temperature. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81 The regulatory compound, 2,3 — bisphosphoglycerate (BPG) and hemoglobin. . . . . . . . . . . . . . . . . . . . . . . . . 82 Fetal hemoglobin . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 82 CHAPTER 7:ENZYMES . . . . . . . . . . . . . . . . . . . . . . . . . . . . .83 Enzymes Are Catalysts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83 Six Types of Enzyme Catalysts . . . . . . . . . . . . . . . . . . . . . . . . 85 The Michaelis-Menten equation . . . . . . . . . . . . . . . . . . . . . 88 Inhibitors of enzyme-catalyzed reactions . . . . . . . . . . . . . . 93 Chemical Mechanisms of Enzyme Catalysis. . . . . . . . . . . . . . 97 The transition state . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 97 Vitamin conversion. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 101 Chymotrypsin: An Enzyme at Work . . . . . . . . . . . . . . . . . . . 102 Enzyme Regulation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 105 Allostery and enzyme regulation. . . . . . . . . . . . . . . . . . . . 105 Covalent Modification. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 106 Phosphorylation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 106 Zymogens . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 107 CHAPTER 8:ORGANIZATION OF METABOLISM . . . .109 Metabolism: ACollection of Linked Oxidation and Reduction Processes. . . . . . . . . . . . . . . . . . . . . . . . . . . 109 Energy production. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 110 Catabolic pathways feed into the TCAcycle. . . . . . . . . . . 111 Biosynthetic reactions versus catabolic reactions. . . . . . . 111 CHAPTER 9:GLYCOLYSIS . . . . . . . . . . . . . . . . . . . . . . . . .113 Six-Carbon Reactions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 115 Glycolysis, ATP, and NADH . . . . . . . . . . . . . . . . . . . . . . . . . 118 Electron transfer to pyruvate. . . . . . . . . . . . . . . . . . . . . . . 121 Ethanol. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 122 BIOCHEMISTRY I v CONTENTS Pyruvate to acetyl-Coenzyme A: The entry point into the TCAcycle. . . . . . . . . . . . . . . . . . . . . . . 123 Glycolysis Regulation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 124 Regulation occurs at the three reactions far from equilibrium. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 125 Glycolysis produces short but high bursts of energy. . . . . 128 CHAPTER 10:THE TRICARBOXYLIC ACID CYCLE . .129 The First Phase of the TCACycle. . . . . . . . . . . . . . . . . . . . . 130 Oxidative decarboxylation . . . . . . . . . . . . . . . . . . . . . . . . 136 The third phase of the TCAcycle . . . . . . . . . . . . . . . . . . . 137 Substrate Availiability, Pyruvate, and the TCACycle. . . . . . 139 CHAPTER 11:OXIDATIVE PHOSPHORYLATION . . . . .141 Oxidative Phosphorylation. . . . . . . . . . . . . . . . . . . . . . . . . . . 142 The energy of oxidation. . . . . . . . . . . . . . . . . . . . . . . . . . . 143 Biochemical reduction and concentration-dependency. . . 145 The oxidation of NADH . . . . . . . . . . . . . . . . . . . . . . . . . . 146 The Electron Transport Chain . . . . . . . . . . . . . . . . . . . . . . . . 147 Complex I and Complex II . . . . . . . . . . . . . . . . . . . . . . . . 147 ATPSynthesis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 150 Mitochondrial Transport Systems . . . . . . . . . . . . . . . . . . . . . 153 Energy Yields from Oxidative Phosphorylation . . . . . . . . . . 155 CHAPTER 12:CARBOHYDRATE METABOLISM II . . .157 The Pentose Phosphate Pathway . . . . . . . . . . . . . . . . . . . . . . 157 Ribulose-5-phosphate . . . . . . . . . . . . . . . . . . . . . . . . . . . . 159 Converting pentoses to sugars. . . . . . . . . . . . . . . . . . . . . . 160 Catabolism of other carbohydrates . . . . . . . . . . . . . . . . . . 162 The Gluconeogenic Pathway. . . . . . . . . . . . . . . . . . . . . . . . . 167 Bypassing the pyruvate kinase step. . . . . . . . . . . . . . . . . . 167 Bypassing the phosphofructokinase and hexokinase steps . . . . . . . . . . . . . . . . . . . . . . . . . 169 Storage of Glucose in Polymeric Form as Glycogen. . . . . . . 170 Cyclic AMP. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 174 CLIFFSQUICKREVIEW vi CHAPTER 1 THE SCOPE OF BIOCHEMISTRY Biochemists discuss chemistry with biologists,and biology with chemists,thereby confusing both groups. Among themselves,they talk about baseball. –Anonymous As the name indicates,biochemistryis a hybrid science:Biology is the science of living organisms and chemistry is the science of atoms and molecules,so biochemistry is the science of the atoms and mole- cules in living organisms. Its domain encompasses all the living world with the unifying interest in the chemical structures and reactions that occur in living systems. Where can you find biochemistry? All through science,medicine,and agriculture. Biochemistry underlies ordinary life in unseen ways:For exam- ple, take a middle-aged man (not very different from the author of this book) who: (cid:2) Takes a drug to lower his serum cholesterol. That drug was developed by a pharmaceutical company’s biochemists to inhibit a key enzyme involved in cholesterol biosynthesis. (cid:2) Shaves with a cream containing compounds that soften his beard. These active agents were developed after studies of the physical properties of keratin,the protein in hair. (cid:2) Eats a breakfast cereal fortified with vitamins identified through nutritional biochemistry. (cid:2) Wears a shirt made from pest-resistant cotton. The cotton plants were bioengineered by biochemists through the trans- fer of genes from a bacterium into plants. (cid:2) Goes fishing after work. The conservation agents who man- age the stream use biochemical information from the DNA (deoxyribonucleic acid) sequences to track the genetics of the fish population. BIOCHEMISTRY I 1 THE SCOPE OF BIOCHEMISTRY (cid:2) Drinks milk before bedtime. His sleep is helped by the amino acids in the milk,which are converted by his brain into molec- ular signals that lead to a resting state in other parts of his brain. All these everyday events depend on an understanding of the chemistry of living systems. The purpose of this book is to provide a quick review of the chemical structures and events that govern so much of daily life. You can use it as a supplement to existing texts and as a review of biochemistry for standardized examinations. Biochemistry is a Contemporary Science In the early nineteenth century,as chemistry became recognized as a scientific discipline,a distinction was made between inorganic and organic chemistry. Organic compounds (those containing carbon and hydrogen) were thought to be made only in living systems. However, in 1828, Friedrich Wöhler in Germany heated an inorganic com- pound,ammonium carbamate,and made an organic one,urea,found naturally in animal urine. Wöhler’s experiment showed that the chemistries of the living and nonliving worlds are continuous: O O C C + − NH O NH H N NH 4 2 2 2 + H O 2 At the end of the nineteenth century,a parallel controversy arose as organic chemists debated whether an intact,living cell was needed to carry out biochemical reactions. Hans Büchner in Germany repro- duced the synthesis of ethanol with a cell-free extract of brewer’s yeast,showing that reactions of living systems can be reproduced in vitro (literally,in glass),that is,away from a living system. Reactions in living cells occur because they are catalyzed by enzymes — the very word enzymeis derived from the Greek word for yeast,zymos. CLIFFSQUICKREVIEW 2 THE SCOPE OF BIOCHEMISTRY Biochemistry became a distinct science in the early twentieth century. In the United States,it arose from the merger of physiologi- cal chemistry and agricultural chemistry. Contemporary biochemistry has three main branches: (cid:2) Metabolismis the study of the conversion of biological mol- ecules,especially small molecules,from one to another —for example, the conversion of sugar into carbon dioxide and water, or the conversion of fats into cholesterol. Metabolic biochemists are particularly interested in the individual enzyme-catalyzed steps of an overall sequence of reactions (called a pathway) that leads from one substance to another. (cid:2) Structural Biochemistry is the study of how molecules in living cells work chemically. For example, structural bio- chemists try to determine how the three-dimensional structure of an enzyme contributes to its ability to catalyze a single metabolic reaction. (cid:2) Molecular Genetics is concerned with the expression of genetic information and the way in which this information contributes to the regulation of cellular functions. These distinctions are somewhat artificial,as contemporary bio- chemistry is intimately connected with other branches of biology and chemistry, especially organic and physical chemistry, physiology, microbiology,genetics,and cell biology. Extrapolating Biochemical Information If the reactions of every organism were different,biochemistry would be a poor science. Contemporary biochemistry depends on the ability to extrapolate information from one system to another. For example, if humans and animals made cholesterol in fundamentally different ways,scientists would have no way to find a compound to treat high cholesterol and prevent heart attacks. It would be impossible BIOCHEMISTRY I 3