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 1

About This Book 1

Foolish Assumptions 2

Icons Used in This Book 3

Beyond the Book 3

Where to Go from Here 4

Part 1: Setting the Stage: Basic Biochemistry Concepts 5

Chapter 1: Biochemistry: What You Need to Know and Why 7

Why Biochemistry? 7

What Is Biochemistry and Where Does It Take Place? 8

Types of Living Cells 8

Prokaryotes 9

Eukaryotes 9

Animal Cells and How They Work 10

A Brief Look at Plant Cells 12

Chapter 2: Seems So Basic: Water Chemistry and pH 15

The Fundamentals of H2O 16

Let’s get wet! The physical properties of water 16

Water’s most important biochemical role: The solvent 18

Hydrogen Ion Concentration: Acids and Bases 20

Achieving equilibrium 20

Understanding the pH scale 21

Calculating pOH 23

Applying the Brønsted-Lowry theory 23

Buffers and pH Control 27

Identifying common physiological buffers 27

Calculating a buffer’s pH 28

Chapter 3: Fun with Carbon: Organic Chemistry 31

The Role of Carbon in the Study of Life 31

It’s All in the Numbers: Carbon Bonds 33

When Forces Attract: Bond Strengths 33

Everybody has ‘em: Intermolecular forces 34

Water-related interactions: Both the lovers and the haters 35

How bond strengths affect physical properties of substances 35

Getting a Reaction out of a Molecule: Functional Groups 37

Hydrocarbons 37

Functional groups with oxygen and sulfur 37

Functional groups containing nitrogen 38

Functional groups containing phosphorus 39

Reactions of functional groups 40

pH and functional groups 43

Same Content, Different Structure: Isomerism 44

Cis-trans isomers 44

Chiral carbons 44

Part 2: The Meat of Biochemistry: Proteins 47

Chapter 4: Amino Acids: The Building Blocks of Protein 49

General Properties of Amino Acids 50

Amino acids are positive and negative: The zwitterion formation 50

Protonated? pH and the isoelectric point 51

Asymmetry: Chiral amino acids 52

The Magic 20 Amino Acids 53

Nonpolar (hydrophobic) and uncharged amino acids 53

Polar (hydrophilic) and uncharged amino acids 55

Acidic amino acids 57

Basic amino acids 57

Lest We Forget: Rarer Amino Acids 58

Rudiments of Amino Acid Interactions 59

Intermolecular forces: How an amino acid interacts with other molecules 59

Altering interactions by changing the pH 61

Combining Amino Acids: How It Works 62

The peptide bond and the dipeptide 63

Tripeptide: Adding an amino acid to a dipeptide 64

Chapter 5: Protein Structure and Function 65

Proteins: Not Just for Dinner 65

Primary Structure: The Structure Level All Proteins Have 67

Building a protein: Outlining the process 67

Organizing the amino acids 68

Example: The primary structure of insulin 69

Secondary Structure: A Structure Level Most Proteins Have 69

The -helix 70

The -pleated sheet 71

-turns and the -loops 73

Tertiary Structure: A Structure Level Many Proteins Have 74

Quaternary Structure: A Structure Level Some Proteins Have 75

Dissecting a Protein for Study 75

Separating proteins within a cell and purifying them 75

Digging into the details: Uncovering a protein’s amino acid sequence 78

Chapter 6: Enzyme Kinetics: Getting There Faster 83

Enzyme Classification: The Best Catalyst for the Job 84

Up one, down one: Oxidoreductases 85

You don’t belong here: Transferases 86

Water does it again: Hydrolases 86

Taking it apart: Lyases 87

Shuffling the deck: Isomerases 87

Putting it together: Ligases 87

Enzymes as Catalysts: When Fast Is Not Fast Enough 88

All about Kinetics 90

Enzyme assays: Fixed time and kinetics 91

Rate determination: How fast is fast? 92

Measuring Enzyme Behavior: The Michaelis-Menten Equation 94

Ideal applications 97

Realistic applications 98

Here we go again: Lineweaver-Burk plots 98

Graphing kinetics data 100

Enzyme Inhibition: Slowing It Down 102

Competitive inhibition 102

Noncompetitive inhibition 103

Graphing inhibition 103

Enzyme Regulation 104

Part 3: Carbohydrates, Lipids, Nucleic Acids, and More, Oh My! 107

Chapter 7: What We Crave: Carbohydrates 109

Properties of Carbohydrates 110

They contain one or more chiral carbons 110

They have multiple chiral centers 111

A Sweet Topic: Monosaccharides 113

The most stable monosaccharide structures:

Pyranose and furanose forms 113

Chemical properties of monosaccharides 115

Derivatives of monosaccharides 117

The most common monosaccharides 119

The beginning of life: Ribose and deoxyribose 120

Sugars Joining Hands: Oligosaccharides 120

Keeping it simple: Disaccharides 121

Starch and cellulose: Polysaccharides 124

The Aldose Family of Sugars 126

Chapter 8: Lipids and Membranes 129

Lovely Lipids: An Overview 129

Behavior of lipids 130

Fatty acids in lipids 131

A Fatty Subject: Triglycerides 132

Properties and structures of fats 132

Cleaning up: Breaking down a triglyceride 134

No Simpletons Here: Complex Lipids 134

Phosphoglycerides 135

Sphingolipids 137

Sphingophospholipids 137

Membranes: The Bipolar and the Bilayer 138

Crossing the wall: Membrane transport 139

Steroids: Pumping up 142

Prostaglandins, Thromboxanes, and Leukotrienes: Mopping Up 143

Chapter 9: Nucleic Acids and the Code of Life 145

Nucleotides: The Guts of DNA and RNA 146

Reservoir of genetic info: Nitrogen bases 146

The sweet side of life: The sugars 146

The sour side of life: Phosphoric acid 148

Tracing the Process: From Nucleoside to Nucleotide to Nucleic Acid 148

First reaction: Nitrogen base + 5-carbon sugar = nucleoside 148

Second reaction: Phosphoric acid + nucleoside = nucleotide 149

Third reaction: Nucleotide becomes nucleic acid 150

A Primer on Nucleic Acids 151

DNA and RNA in the grand scheme of life 152

Nucleic acid structure 152

Chapter 10: Vitamins: Both Simple and Complex 155

More than One-a-Day: Basics of Vitamins 156

To B or Not to B: B Complex Vitamins 156

Vitamin B1 (thiamine) 157

Vitamin B2 (riboflavin) 158

Vitamin B3 (niacin) 159

Vitamin B6 (pyridoxine) 160

Biotin 160

Folic acid 162

Pantothenic acid 163

The wonders of vitamin B12 163

Vitamin A 164

Vitamin C 166

Vitamin D 166

Vitamin E 169

Vitamin K 169

Chapter 11: Hormones: The Body’s Messengers 171

Structures of Some Key Hormones 172

Proteins 172

Steroids 173

Amines 174

Now and Later: Prohormones 176

Proinsulin 176

Angiotensinogen 177

Fight or Flight: Hormone Function 177

Opening the letter: Hormonal action 178

Models of hormonal action 179

Part 4: Bioenergetics and Pathways 183

Chapter 12: Life and Energy 185

ATP: The Energy Pony Express 185

ATP and free energy 186

ATP as an energy transporter 187

It’s Relative: Molecules Related to ATP 190

The nucleoside triphosphate family 191

As easy as 1, 2, 3: AMP, ADP, and ATP 193

Where It All Comes From 193

Chapter 13: ATP: The Body’s Monetary System 197

Metabolism I: Glycolysis 198

Glycolysis: Phase I 198

Glycolysis: Phase II 201

Releasing the power: Energy efficiency 202

Going in reverse: Gluconeogenesis 202

Alcoholic fermentation: We’ll drink to that 202

Metabolism II: Citric Acid (Krebs) Cycle 204

Let’s get started: Synthesis of acetyl-CoA 208

Three’s a crowd: Tricarboxylic acids 208

Oxidative decarboxylation 209

Production of succinate and GTP 210

Oxaloacetate regeneration 210

Amino acids as energy sources 211

Electron Transport and Oxidative Phosphorylation 212

The electron transport system 213

Oxidative phosphorylation 218

Proposed mechanisms 221

ATP production 221

Involving the fats: β-oxidation cycle 222

Not so heavenly bodies: Ketone bodies 224

Investing in the Future: Biosynthesis 226

Fatty acids 226

Membrane lipids 229

Amino acids 231

Chapter 14: Smelly Biochemistry: Nitrogen in Biological Systems 237

Ring in the Nitrogen: Purine 237

Biosynthesis of purine 238

How much will it cost? 246

Pyrimidine Synthesis 247

First step: Carbamoyl phosphate 247

Next step: Orotate 247

Last step: Cytidine 250

Back to the Beginning: Catabolism 250

Nucleotide catabolism 251

Amino acid catabolism 251

Heme catabolism 252

Process of Elimination: The Urea Cycle 253

Amino Acids Once Again 256

Metabolic Disorders 257

Gout 257

Lesch-Nyhan syndrome 257

Albinism 258

Alkaptonuria 258

Phenylketonuria 258

Part 5: Genetics: Why We Are What We Are 259

Chapter 15: Photocopying DNA 261

Let’s Do It Again: Replication 262

DNA polymerases 265

The current model of DNA replication 265

Mechanisms of DNA repair 268

Mutation: The good, the bad, and the ugly 270

Restriction enzymes 272

Mendel Rolling Over: Recombinant DNA 272

Patterns: Determining DNA Sequences 273

Getting charged up about gel electrophoresis 274

Determining the base sequence 275

The butler did it: Forensic applications 277

Genetic Diseases and Other DNA Testing Applications 279

Sickle cell anemia 280

Hemochromatosis 280

Cystic fibrosis 280

Hemophilia 281

Tay-Sachs disease 282

Chapter 16: Transcribe This! RNA Transcription 283

Types of RNA 284

RNA Polymerase Requirements 285

Making RNA: The Basics 286

Promoting transcription of RNA 286

Prokaryotic cells 287

Eukaryotic cells 291

Not a Secret Any Longer: The Genetic Code 294

Codons 294

Alpha and omega 296

Models of Gene Regulation 297

The Jacob-Monod (operon) model 298

Regulation of eukaryotic genes 300

Chapter 17: Translation: Protein Synthesis 305

Hopefully Not Lost in Translation 305

Who needs translation, anyway? 305

Home, home in the ribosome 306

The Translation Team 307

The team captain: rRNA 307

Here’s the snap: mRNA 307

Carrying the ball: tRNA 308

Charging up the middle: Amino acid activation 310

Hooking Up: Protein Synthesis 312

Activation 313

Initiation 313

Elongation 314

Termination 315

The wobble hypothesis 315

Variation in Eukaryotic Cells 316

Ribosomes 316

Initiator-tRNA 318

Initiation 319

Elongation and termination 319

Part 6: The Part of Tens 321

Chapter 18: Ten Great Applications of Biochemistry 323

Ames Test 323

Pregnancy Testing 324

HIV Testing 324

Breast Cancer Testing 324

Prenatal Genetic Testing 324

PKU Screening 325

Genetically Modified Foods 325

Genetic Engineering 325

Cloning 326

Gene-Replacement Therapy 326

Chapter 19: Ten Biochemistry Careers 327

Research Assistant 327

Nanotechnologist 328

Quality Control Analyst 328

Clinical Research Associate 328

Technical Writer 329

Biochemical Development Engineer 329

Forensic Scientist 329

Patent Attorney 330

Pharmaceutical Sales Representative 330

Biostatistician 330

Index 331