Biochemistry For Dummies

John T. Moore, EdD, and Richard H. Langley, PhD, teach Chemistry at Stephen F. Austin State University. Together they have more than 8.9 x 101 years of science education experience, and they have authored or coauthored oodles of books on chemistry topics.

• Introduction 1About This Book 1Foolish Assumptions 2Icons Used in This Book 3Beyond the Book 3Where to Go from Here 4Part 1: Setting the Stage: Basic Biochemistry Concepts 5Chapter 1: Biochemistry: What You Need to Know and Why 7Why Biochemistry? 7What Is Biochemistry and Where Does It Take Place? 8Types of Living Cells 8Prokaryotes 9Eukaryotes 9Animal Cells and How They Work 10A Brief Look at Plant Cells 12Chapter 2: Seems So Basic: Water Chemistry and pH 15The Fundamentals of H2O 16Let’s get wet! The physical properties of water 16Water’s most important biochemical role: The solvent 18Hydrogen Ion Concentration: Acids and Bases 20Achieving equilibrium 20Understanding the pH scale 21Calculating pOH 23Applying the Brønsted-Lowry theory 23Buffers and pH Control 27Identifying common physiological buffers 27Calculating a buffer’s pH 28Chapter 3: Fun with Carbon: Organic Chemistry 31The Role of Carbon in the Study of Life 31It’s All in the Numbers: Carbon Bonds 33When Forces Attract: Bond Strengths 33Everybody has ‘em: Intermolecular forces 34Water-related interactions: Both the lovers and the haters 35How bond strengths affect physical properties of substances 35Getting a Reaction out of a Molecule: Functional Groups 37Hydrocarbons 37Functional groups with oxygen and sulfur 37Functional groups containing nitrogen 38Functional groups containing phosphorus 39Reactions of functional groups 40pH and functional groups 43Same Content, Different Structure: Isomerism 44Cis-trans isomers 44Chiral carbons 44Part 2: The Meat of Biochemistry: Proteins 47Chapter 4: Amino Acids: The Building Blocks of Protein 49General Properties of Amino Acids 50Amino acids are positive and negative: The zwitterion formation 50Protonated? pH and the isoelectric point 51Asymmetry: Chiral amino acids 52The Magic 20 Amino Acids 53Nonpolar (hydrophobic) and uncharged amino acids 53Polar (hydrophilic) and uncharged amino acids 55Acidic amino acids 57Basic amino acids 57Lest We Forget: Rarer Amino Acids 58Rudiments of Amino Acid Interactions 59Intermolecular forces: How an amino acid interacts with other molecules 59Altering interactions by changing the pH 61Combining Amino Acids: How It Works 62The peptide bond and the dipeptide 63Tripeptide: Adding an amino acid to a dipeptide 64Chapter 5: Protein Structure and Function 65Proteins: Not Just for Dinner 65Primary Structure: The Structure Level All Proteins Have 67Building a protein: Outlining the process 67Organizing the amino acids 68Example: The primary structure of insulin 69Secondary Structure: A Structure Level Most Proteins Have 69The -helix 70The -pleated sheet 71-turns and the -loops 73Tertiary Structure: A Structure Level Many Proteins Have 74Quaternary Structure: A Structure Level Some Proteins Have 75Dissecting a Protein for Study 75Separating proteins within a cell and purifying them 75Digging into the details: Uncovering a protein’s amino acid sequence 78Chapter 6: Enzyme Kinetics: Getting There Faster 83Enzyme Classification: The Best Catalyst for the Job 84Up one, down one: Oxidoreductases 85You don’t belong here: Transferases 86Water does it again: Hydrolases 86Taking it apart: Lyases 87Shuffling the deck: Isomerases 87Putting it together: Ligases 87Enzymes as Catalysts: When Fast Is Not Fast Enough 88All about Kinetics 90Enzyme assays: Fixed time and kinetics 91Rate determination: How fast is fast? 92Measuring Enzyme Behavior: The Michaelis-Menten Equation 94Ideal applications 97Realistic applications 98Here we go again: Lineweaver-Burk plots 98Graphing kinetics data 100Enzyme Inhibition: Slowing It Down 102Competitive inhibition 102Noncompetitive inhibition 103Graphing inhibition 103Enzyme Regulation 104Part 3: Carbohydrates, Lipids, Nucleic Acids, and More, Oh My! 107Chapter 7: What We Crave: Carbohydrates 109Properties of Carbohydrates 110They contain one or more chiral carbons 110They have multiple chiral centers 111A Sweet Topic: Monosaccharides 113The most stable monosaccharide structures:Pyranose and furanose forms 113Chemical properties of monosaccharides 115Derivatives of monosaccharides 117The most common monosaccharides 119The beginning of life: Ribose and deoxyribose 120Sugars Joining Hands: Oligosaccharides 120Keeping it simple: Disaccharides 121Starch and cellulose: Polysaccharides 124The Aldose Family of Sugars 126Chapter 8: Lipids and Membranes 129Lovely Lipids: An Overview 129Behavior of lipids 130Fatty acids in lipids 131A Fatty Subject: Triglycerides 132Properties and structures of fats 132Cleaning up: Breaking down a triglyceride 134No Simpletons Here: Complex Lipids 134Phosphoglycerides 135Sphingolipids 137Sphingophospholipids 137Membranes: The Bipolar and the Bilayer 138Crossing the wall: Membrane transport 139Steroids: Pumping up 142Prostaglandins, Thromboxanes, and Leukotrienes: Mopping Up 143Chapter 9: Nucleic Acids and the Code of Life 145Nucleotides: The Guts of DNA and RNA 146Reservoir of genetic info: Nitrogen bases 146The sweet side of life: The sugars 146The sour side of life: Phosphoric acid 148Tracing the Process: From Nucleoside to Nucleotide to Nucleic Acid 148First reaction: Nitrogen base + 5-carbon sugar = nucleoside 148Second reaction: Phosphoric acid + nucleoside = nucleotide 149Third reaction: Nucleotide becomes nucleic acid 150A Primer on Nucleic Acids 151DNA and RNA in the grand scheme of life 152Nucleic acid structure 152Chapter 10: Vitamins: Both Simple and Complex 155More than One-a-Day: Basics of Vitamins 156To B or Not to B: B Complex Vitamins 156Vitamin B1 (thiamine) 157Vitamin B2 (riboflavin) 158Vitamin B3 (niacin) 159Vitamin B6 (pyridoxine) 160Biotin 160Folic acid 162Pantothenic acid 163The wonders of vitamin B12 163Vitamin A 164Vitamin C 166Vitamin D 166Vitamin E 169Vitamin K 169Chapter 11: Hormones: The Body’s Messengers 171Structures of Some Key Hormones 172Proteins 172Steroids 173Amines 174Now and Later: Prohormones 176Proinsulin 176Angiotensinogen 177Fight or Flight: Hormone Function 177Opening the letter: Hormonal action 178Models of hormonal action 179Part 4: Bioenergetics and Pathways 183Chapter 12: Life and Energy 185ATP: The Energy Pony Express 185ATP and free energy 186ATP as an energy transporter 187It’s Relative: Molecules Related to ATP 190The nucleoside triphosphate family 191As easy as 1, 2, 3: AMP, ADP, and ATP 193Where It All Comes From 193Chapter 13: ATP: The Body’s Monetary System 197Metabolism I: Glycolysis 198Glycolysis: Phase I 198Glycolysis: Phase II 201Releasing the power: Energy efficiency 202Going in reverse: Gluconeogenesis 202Alcoholic fermentation: We’ll drink to that 202Metabolism II: Citric Acid (Krebs) Cycle 204Let’s get started: Synthesis of acetyl-CoA 208Three’s a crowd: Tricarboxylic acids 208Oxidative decarboxylation 209Production of succinate and GTP 210Oxaloacetate regeneration 210Amino acids as energy sources 211Electron Transport and Oxidative Phosphorylation 212The electron transport system 213Oxidative phosphorylation 218Proposed mechanisms 221ATP production 221Involving the fats: β-oxidation cycle 222Not so heavenly bodies: Ketone bodies 224Investing in the Future: Biosynthesis 226Fatty acids 226Membrane lipids 229Amino acids 231Chapter 14: Smelly Biochemistry: Nitrogen in Biological Systems 237Ring in the Nitrogen: Purine 237Biosynthesis of purine 238How much will it cost? 246Pyrimidine Synthesis 247First step: Carbamoyl phosphate 247Next step: Orotate 247Last step: Cytidine 250Back to the Beginning: Catabolism 250Nucleotide catabolism 251Amino acid catabolism 251Heme catabolism 252Process of Elimination: The Urea Cycle 253Amino Acids Once Again 256Metabolic Disorders 257Gout 257Lesch-Nyhan syndrome 257Albinism 258Alkaptonuria 258Phenylketonuria 258Part 5: Genetics: Why We Are What We Are 259Chapter 15: Photocopying DNA 261Let’s Do It Again: Replication 262DNA polymerases 265The current model of DNA replication 265Mechanisms of DNA repair 268Mutation: The good, the bad, and the ugly 270Restriction enzymes 272Mendel Rolling Over: Recombinant DNA 272Patterns: Determining DNA Sequences 273Getting charged up about gel electrophoresis 274Determining the base sequence 275The butler did it: Forensic applications 277Genetic Diseases and Other DNA Testing Applications 279Sickle cell anemia 280Hemochromatosis 280Cystic fibrosis 280Hemophilia 281Tay-Sachs disease 282Chapter 16: Transcribe This! RNA Transcription 283Types of RNA 284RNA Polymerase Requirements 285Making RNA: The Basics 286Promoting transcription of RNA 286Prokaryotic cells 287Eukaryotic cells 291Not a Secret Any Longer: The Genetic Code 294Codons 294Alpha and omega 296Models of Gene Regulation 297The Jacob-Monod (operon) model 298Regulation of eukaryotic genes 300Chapter 17: Translation: Protein Synthesis 305Hopefully Not Lost in Translation 305Who needs translation, anyway? 305Home, home in the ribosome 306The Translation Team 307The team captain: rRNA 307Here’s the snap: mRNA 307Carrying the ball: tRNA 308Charging up the middle: Amino acid activation 310Hooking Up: Protein Synthesis 312Activation 313Initiation 313Elongation 314Termination 315The wobble hypothesis 315Variation in Eukaryotic Cells 316Ribosomes 316Initiator-tRNA 318Initiation 319Elongation and termination 319Part 6: The Part of Tens 321Chapter 18: Ten Great Applications of Biochemistry 323Ames Test 323Pregnancy Testing 324HIV Testing 324Breast Cancer Testing 324Prenatal Genetic Testing 324PKU Screening 325Genetically Modified Foods 325Genetic Engineering 325Cloning 326Gene-Replacement Therapy 326Chapter 19: Ten Biochemistry Careers 327Research Assistant 327Nanotechnologist 328Quality Control Analyst 328Clinical Research Associate 328Technical Writer 329Biochemical Development Engineer 329Forensic Scientist 329Patent Attorney 330Pharmaceutical Sales Representative 330Biostatistician 330Index 331