René Fester Kratz, PhD, teaches biology at Everett Community College in Everett, Washington. She works with other scientists and K–12 teachers to develop science curricula that align with national learning standards and the latest research on human learning.

Introduction 1

About This Book 1

Foolish Assumptions 2

Icons Used in This Book 3

Beyond the Book 3

Where to Go from Here 3

Part 1: The World of the Cell 5

Chapter 1: Exploring the World of the Cell 7

Cells and Viruses: Discovering the Inhabitants of the Microscopic World 7

You: On the cellular level 8

Them: Bacteria and viruses 9

The Life of a Cell: How Cells Get What They Need to Survive and Reproduce 10

Sexual Reproduction: Shuffling the Genetic Deck for the Next Generation 10

DNA to Protein: Following the Instructions in the Genetic Code 11

DNA Technology: Tackling the World’s Problems 11

Chapter 2: Take a Tour inside the Cell 13

Admiring the Unity and Diversity of Cells 13

Finding Common Ground: Structures in All Cells 14

Customs: Plasma membrane 15

A happenin’ place: The cytoplasm 16

The library: DNA-containing region 17

Workbenches: Ribosomes 17

Your Body, Your Cells: Eukaryotic Cells 18

Home office: The nucleus 20

Post office: The endomembrane system 22

The fireplace: Mitochondria 24

In the kitchen: Chloroplasts 26

Scaffolding and railroad tracks: The cytoskeleton 27

Rebar and concrete: Cell walls and extracellular matrices 30

Tiny but Mighty: Prokaryotic Cells 32

Castle walls: The cell wall 33

Ooze, slime, and grappling hooks: Capsules, pili, and fimbriae 33

Outboard motors: Bacterial flagella 33

Chapter 3: Dead or Alive: Viruses 35

Viruses: Hijackers of the Cellular World 35

Just the basics: The structure of viruses 36

Knock, knock, virus calling: How viruses get into cells 37

War on a Microcosmic Scale: Viruses of Bacteria 39

Seek and destroy: The lytic cycle 40

I think I’ll take a little nap: The lysogenic cycle 41

I’ve Got a Cold: Viruses of Eukaryotes 41

Same story, different players 42

Come in and take your coat off 44

There’s more than one way to copy a virus 45

Leaving it all behind 47

Putting it all together 47

HIV and AIDS: Viruses in the real world 48

Part 2: Molecules: The Stuff of Life 51

Chapter 4: Better Living through Chemistry 53

Life Really Matters 53

It’s Elemental: Atoms That Make Up Living Things 54

Exploring subatomic particles 56

Defining elements 56

Comparing isotopes 57

Let’s Bond: How Atoms Are Attracted to Each Other 59

Feeling fulfilled by arranging your electrons just right 60

Holding on: Electronegativity 63

Give and take: Oxidation and reduction 64

Opposites attract: Ionic bonds 65

Sharing is caring: Covalent bonds 65

A molecule by any other picture 66

Don’t hog the toys! Polar covalent bonds 67

Molecular Velcro: Hydrogen bonds 67

Molecular cliques: Hydrophobic interactions 69

Blue Planet: The Ocean inside Your Cells 69

Splitting water 70

Measuring pH 70

Changing pH 71

Maintaining pH 71

Chain, Chain, Chain: Building and Breaking Polymers 72

Identifying the parts and the whole 72

Getting together and breaking up again 73

Dressing for success: Functional groups determine molecular properties 73

Chapter 5: Carbohydrates: How Sweet They Are 77

CH2O: Structure of Carbohydrates 77

Keeping it simple: Monosaccharides 78

Making it complex: Polysaccharides 82

Sticky and Sweet: Functions of Carbohydrates 84

Chapter 6: Proteins: Workers in the Cellular Factory 87

Get into Shape: Levels of Protein Structure 87

Get in line: Primary structure 89

The long and winding road: Secondary structure 91

3D: Tertiary structure 92

Sometimes one is not enough: Quarternary structure 94

Jacks of All Trades: The Many Functions of Proteins 95

Get ’Er Done: Enzymes Make Things Happen 95

Made for each other: Enzymes and substrates 96

Helping hands: Cofactors and Coenzymes 97

Listening to others: Inhibiting enzymes 97

Gatekeepers: Membrane Proteins 100

I’m in Charge: DNA-Binding Proteins 101

Chapter 7: DNA and RNA: Instructions for Life 103

It’s Puzzling: Structure of Nucleic Acids 103

Navigating nucleotides 104

Naming the nucleotide bases 105

Recognizing nucleotides 107

Making DNA and RNA 107

The double helix of DNA 109

Shaping up RNA molecules 110

Breaking the Code: The Function of DNA and RNA 110

Chapter 8: Lipids: Waterproof and Energy Rich 113

Hydrocarbons: Structure of Lipids 113

Saturating fatty acids 114

Forming fats and oils 115

Looking at other types of lipids 116

You Say Fat Like It’s a Bad Thing: Functions of Lipids 119

Part 3: The Working Cell 121

Chapter 9: Hello, Neighbor: How Cells Communicate 123

Shipping and Receiving: Transport across Membranes 123

Getting past the bouncer 124

Which way should I go? 124

Crossing the border 125

Going with the flow 126

It’s an uphill battle 127

Chatting through Cellular Connections 129

Shaking hands through cell-cell attachments 129

Sticking together through thick and thin 131

Jumping the cell-cell gap 131

Sending and Receiving Signals 132

Satellite dishes: Receptors 133

Relaying the message: Signal transduction 133

Amplifying the signal 135

Calming down: Deactivating the signal 137

Chapter 10: Metabolism: Transferring Energy and Matter 139

Revving Up Your Metabolism 139

Stayin’ Alive: Cellular Work and the Laws of Thermodynamics 141

The first law of thermodynamics 141

The second law of thermodynamics 143

Going to work in the cellular factory 147

One Step at a Time: Metabolic Pathways 151

Taking baby steps during chemical reactions 152

Helping hands from enzymes 153

Giving and taking electrons in redox reactions 155

Shuttling electrons with electron carriers 156

Getting what you need at the cellular level 158

Chapter 11: Cellular Respiration: Every Breath You Take 159

Cellular Respiration: An Overview 159

Controlling the burn 161

Transferring energy to ATP 162

Moving electrons to oxygen 162

Taking things one step at a time 163

Gimme a Break: Glycolysis 164

Everybody’s doing it 165

Fine print: The steps of glycolysis 165

Making ATP by substrate-level phosphorylation 167

Living by glycolysis alone: Fermentation 168

The Wheel of Fire: Krebs Cycle 170

Linking glycolysis and Krebs 171

Fine print: The steps of the Krebs cycle 173

More is better: Taking advantage of the Krebs cycle 174

Taking It to the Bank: Chemiosmosis and Oxidative Phosphorylation 174

Transferring electrons along an electron transport chain 175

Transferring energy from food to ATP 177

The steps of the chemiosmotic theory of oxidative phosphorylation 177

Doing the math: How many ATP can you make from the energy in a glucose molecule? 179

Breaking Down Complex Carbohydrates, Proteins, and Fats 180

Finding an on-ramp to the superhighway 180

Feeding complex carbohydrates into the system 181

Burning fat 181

Breaking down proteins 183

It’s a Two-Way Street: Connections between Metabolic Pathways 183

Reversing the flow of matter and energy 184

Packing on the fat 185

Building muscle 185

Cellular respiration in the real world 186

Chapter 12: Photosynthesis: Makin’ Food in the Kitchen of Life 187

Photosynthesis: An Overview 187

Getting what plants need 188

Examining the role of soil 190

Basking in the Sun 190

Capturing the Sun’s energy with pigments 191

Yin and yang: The light reactions and the Calvin cycle 192

Shine on Me: The Light Reactions 194

Transferring light energy to chemical energy 194

The steps of photophosphorylation 196

The Circle of Life: Calvin Cycle 198

The steps of the Calvin cycle 199

Got Food? Photosynthesis in the Real World 201

Chapter 13: Splitsville: The Cell Cycle, Cell Division, and Cancer 203

Reproducing the Cell 203

Drifting Apart: Binary Fission 204

Red Light, Green Light: The Cell Cycle 205

Pausing during Gap 1 206

The S phase and Gap 2 206

The Dance of the Chromosomes: Mitosis 207

Breaking Up Is Hard to Do: Cytokinesis 209

Keeping It under Control 211

Cancer: The Enemy Within 212

Defining cancer 212

Causes of cancer 215

Fighting back 217

Part 4: Genetics: From One Generation to the Next 219

Chapter 14: Meiosis: Getting Ready for Baby 221

Let’s Talk about Sex, Baby: Reproduction 221

Riding the life cycle 222

Counting chromosomes 223

Homologous Chromosomes 224

Going Separate Ways: Meiosis 225

Following the plan 226

An overview of meiosis 226

Shuffling the Genetic Deck: Crossing Over 229

Why Two Divisions Are Better than One 230

It Was All a Mistake: Nondisjunction 231

Chapter 15: Genetics: Talkin’ ’Bout the Generations 233

Pass the Peas, Please: Mendel and Segregation of Single Gene Traits 233

Living like a monk 234

Speaking the lingo 235

Round pea meets wrinkled pea 236

The odds are 3:1 237

Making a prediction 238

Testing an idea 240

Remembering meiosis 241

Playing by the rules 241

Tracing a trait: Pedigrees 243

I Can Go My Own Way: Independent Assortment 245

Round yellow pea meets wrinkled green pea 245

Puzzling over the Punnett 247

Remembering meiosis 248

It’s News to Mendel: Inheritance beyond Simple Dominance 249

Almost Inseparable: Linked Genes 253

Traveling together because of linkage 254

Slipping away through recombination 255

Building a map of a chromosome 255

Mama’s Boy: Sex-Linked Inheritance 257

Explaining the differences 257

Analyzing the pedigree 258

Part 5: Molecular Genetics: How Cells Read the Book of Life 261

Chapter 16: DNA Replication: Doubling Your Genetic Stuff 263

DNA Replication: An Overview 263

Everybody Lend a Hand: Enzymes Involved in DNA Replication 264

It Takes a Village: Events at the Replication Fork 265

Start at the very beginning: Origins of replication 265

Learning to unwind with helicase 266

Putting down some primer 266

Rolling down the line 268

Replacing some tiles 268

Tying up loose ends 268

Finishing the job 269

Keeping It Together: Leading and Lagging Strands 269

Chapter 17: Transcription and Translation: What’s in a Gene? 273

File It under Genes: The Blueprints for RNA and Proteins 273

Defining a gene 274

Going with the flow 274

Make a Copy, Please: Transcription 275

Locating the file 275

Hiring a worker 276

Marking the end 278

Finishing Touches: RNA Processing in Eukaryotes 278

Making a Protein: Translation 280

Reading the code 280

The decoder: tRNA 283

Master craftsman: The ribosome 284

The steps of translation 285

Don’t Drink and Drive: Mutation 288

Everybody makes mistakes 288

Dealing with the consequences 289

Chapter 18: Control of Gene Expression: It’s How You Play Your Cards That Counts 291

Controlling the Situation: Gene Regulation and Information Flow 291

Becoming a specialist 292

Keeping house 293

I Can Be Flexible: Gene Expression in Bacteria 294

Organizing bacterial genes 295

Taking E coli to dinner 295

Looking at lac 296

Feeling repressed 296

Game on: Inducing the lac operon 297

Game over: Repressing the lac operon 298

Advancing to the next level: Catabolite repression of the lac operon 298

The Master Plan: Gene Expression in Eukaryotes 301

Seizing the opportunity 301

Unpacking the plan 302

Controlling transcription 304

Controlling events between transcription and translation 306

Controlling translation and beyond 307

Learning from Experience: Epigenetics 308

Part 6: Molecular Biology: Harnessing the Power of DNA 311

Chapter 19: The Book of You: Reading Your Genes 313

Copying a gene with PCR 313

Sorting molecules using gel electrophoresis 316

Reading a gene with DNA sequencing 318

I Read the Whole Thing: Sequencing Genomes 323

Unleashing the power of genomics 324

Reading the book of life with shotgun sequencing 324

Looking within the human genome 326

Beyond Genomics: Systems Biology and Epigenomes 327

Comparing gene expression with DNA microarrays 328

Mapping the epigenome 330

Chapter 20: Rewriting the Code of Life: Recombinant DNA Technology and Genome Editing 331

Piecing It Together: Recombinant DNA Technology 332

Cutting DNA with restriction enzymes 332

Making cDNA with reverse transcriptase 333

Cloning genes into a library 334

Finding a gene with DNA probes 336

Changing the Plan: Using Recombinant DNA Technology to Solve Problems 337

Making useful proteins through genetic engineering 338

Searching for disease genes 339

Building a “better” plant with genetic engineering 341

Fixing a broken gene with gene therapy 342

Hitting the Bull’s-Eye with Genome Editing 344

Get off my lawn! CRISPR in nature 344

Changing the plan: CRISPR in the lab 346

Part 7: The Part of Tens 349

Chapter 21: Ten Important Rules for Cells to Live By 351

The Cell Theory 351

The First Law of Thermodynamics 352

The Second Law of Thermodynamics 353

The Theory of Evolution by Natural Selection 354

The Law of Conservation of Matter 356

Nucleic Acids Pair in Antiparallel Strands 357

Central Dogma 358

Protein Shape Is Essential to Their Function 358

Law of Segregation 360

Law of Independent Assortment 360

Chapter 22: Ten Ways to Improve Your Grade 361

Monitor Your Learning 361

Study Smarter 362

Actively Participate in Class 363

Schedule Your Study Time 363

Give Your Brain a Well-Rounded Workout during Study Sessions 364

Get Creative with Memory Tricks 365

Recognize the Difference between Levels of Understanding 365

Remember the Supporting Material 366

Use Your First Test as a Diagnostic Tool 366

Get Help Sooner Rather than Later 367

Index 369

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