Understanding Life. Perspectives from Physical, Organic, and Biological Chemistry. First Edition. By Ronald J. Duchovic

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2 Understanding Life Perspectives from Physical, Organic, and Biological Chemistry First Edition By Ronald J. Duchovic Indiana University Purdue University Fort Wayne

3 Bassim Hamadeh, CEO and Publisher Michael Simpson, Vice President of Acquisitions Jamie Giganti, Managing Editor Jess Busch, Graphic Design Supervisor Angela Kozlowski, Acquisitions Editor Sarah Wheeler, Senior Project Editor Alexa Lucido, Licensing Associate Mandy Licata, Interior Designer Copyright 2015 by Cognella, Inc. All rights reserved. No part of this publication may be reprinted, reproduced, transmitted, or utilized in any form or by any electronic, mechanical, or other means, now known or hereafter invented, including photocopying, microfilming, and recording, or in any information retrieval system without the written permission of Cognella, Inc. First published in the United States of America in 2015 by Cognella, Inc. Trademark Notice: Product or corporate names may be trademarks or registered trademarks, and are used only for identification and explanation without intent to infringe. Printed in the United States of America ISBN: (pbk)/ (br)

4 Contents Chapter 0: A Conceptual Orientation and Invitation How Did Chemistry Begin? 1 Key Concepts 3 A Map or Outline of Concepts 7 Chapter 0 Exercises 9 Chapter 1: Tools of Chemistry Nature of Science 11 The Scientific Method 12 Fundamental Concepts 15 Mathematics 23 The Gaseous State: An Early Measurement of the Way Matter Behaves 39 Chapter 1 Exercises 50 Chapter 2: Origins Early Atomic Theory 56 Three-Particle Model of the Atom 61 Modern Atomic Theory 71 Radioactivity and Radioisotopes 74 Quantum Theory 89 Quantum Mechanics 94 Chapter 2 Exercises 105

5 Chapter 3: The Classical Chemical Paradigm: Part I (Pre-Twentieth Century) Early Terminology 108 Chemical Reactions 111 Solutions 113 Chapter 3 Exercises 123 Chapter 4: The Classical Chemical Paradigm: Part II (Pre-Twentieth Century) Periodic Table 125 Solutions and Electricity 130 Why Do Substances Exist? 133 Understanding Electrolyte Compounds 135 What about Nonelectrolyte Compounds? 135 Polyatomic Ions 136 Multiple Bonds 136 Lewis Structures 137 Limitations of the Lewis Model 138 Putting a Name to the Face 141 Electronegativity 142 Polarity 142 Chapter 4 Exercises 144

6 Chapter 5: Transition from the Classical Chemical Paradigm to the Quantum Paradigm (Early Twentieth Century) The Dance of Charges: Redox, Acid-Base Chemistry, and Buffers Oxidation and Reduction 147 Acids and Bases 149 Chemical Equilibrium 153 Forward or Reverse: Which Way Does the Reaction Go? 156 Weak Acid Ionization Constants 158 Weak Base Ionization Constants 160 The Two Faces of Water 161 Acid and Base Concentrations 164 The ph scale 165 Chapter 5 Exercises 171 Chapter 6: Modern Chemical Bonding Models: Why Is There Something and Not Nothing? Valence Shell Electron Pair Repulsion (VSEPR) 175 Molecular Geometry and Electronic Geometry in VSEPR 176 Molecular Bonding: The Quantum Perspective 179 The Questions 179 Valence Bond (VB) Theory 180 The Answers 181 Hybridization 181 sp Hybrid Orbitals 182 sp 2 Hybrid Orbitals 183 sp 3 Hybrid Orbitals 184

7 More Hybrid Orbitals 184 Molecular Geometry and Electronic Geometry in Valence Bond Theory 185 Sigma Bonds (σ) 186 Pi Bonds (π) 187 Multiple Bonds 187 Molecular Orbital (MO) Theory 191 The Question: Why Is O 2 Paramagnetic? 192 Bonding and Antibonding Molecular Orbitals 193 Sigma and Pi Molecular Orbitals 193 The Answer: Why O 2 Is Paramagnetic 197 Chapter 6 Exercises 198 Chapter 7: Structures in Organic Chemistry and Biochemistry: The Somethings of Atoms Become the Molecules of Life First Steps to Understanding Organic Chemistry 202 The Bonds that Bind the Carbon Atom 207 Functional Groups 208 Hydrocarbons 213 Alkenes and Alkynes 214 Aromatic Hydrocarbons 216 Naming Organic Molecules 217 Naming Alkanes 219 Naming Alkenes and Alkynes 224 Naming Aromatic Hydrocarbons 227 Carbohydrates 230

8 Biological Acids: Fatty, Amino, and Nucleic Acids 249 Amino Acids 254 Nucleic Acids 257 Chapter 7 Exercises 262 Chapter 8: Mirror, Mirror: The Role of Isomers The Wonder of Geometry 267 Constitutional (Structural) Isomers 268 Stereoisomers 271 Left Hands and Right Hands 272 Chiral Molecules 272 Plane Polarized Light and Optical Activity 273 Fischer Projections 276 Glyceraldehyde and the D/L Nomenclature System 277 Amino Acids and Chirality 279 Enantiomers and Diastereomers 281 Cis-Trans Isomers 286 Substituted Cycloalkanes 286 Alkenes 288 Chapter 8 Exercises 290 Chapter 9: Reactivity: Keys to Putting the Somethings Together and Taking Them Apart A New Focus: Chemical Reactivity 291 Condensation 292 Hydrolysis Reactions 298

9 Condensation and Hydrolysis Reactions among Biomolecules 302 Reactions in Retrospect 306 Chapter 9 Exercises 308 Chapter 10: Energy, Entropy, Gibbs Free Energy, Intramolecular Forces, and Kinetics: The Links between Structures and Reactivity Thermodynamics 311 Enthalpy 312 Spontaneity 315 Entropy 315 Entropy and the Second Law of Thermodynamics 317 The Gibbs Free Energy 317 Spontaneity and the Gibbs Free Energy 318 Intermolecular Forces 322 Chemical Kinetics: The Role of Time in Chemistry 331 Enzyme Effects 336 Physical Factors Affecting Enzyme Activity 337 Chapter 10 Exercises 340 Chapter 11: Building Complex Structures The Cell 344 Mitochondria and Ribosome 345 Membranes 348 Hereditary Repositories 354 Protein Structure 358

10 Protein Synthesis 362 Central Dogma 366 LncRNA 367 Epigenetics 367 Chapter 11 Exercises 368 Chapter 12: Metabolism Metabolic Pathways: The Big Picture 371 Key Actors in Metabolism: Important Nucleotides 373 Glycolysis 378 Additional Aspects of Carbohydrate Metabolism 378 Anaerobic Fate of Pyruvate 380 Aerobic Fate of Pyruvate: The Krebs Cycle 381 Summary of ATP Production in Catabolism 384 Lipids as an Energy Source 385 Proteins as an Energy Source 386 Overview of Catabolic Pathways 387 Chapter 12 Exercises 389 Image Credits 391

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