Table of Contents

Table of Contents

1Principles of Life 1

Life as we know it had a single origin 2

Major steps in the history of life are compatible with known physical and chemical processes 2

Biologists can trace the evolutionary tree of life 4

Life’s unity allows discoveries in biology to be generalized 5

Organization is apparent in a hierarchy of levels from molecules to ecosystems 6

Each level of biological organization consists of systems 7

Biological systems are highly dynamic even as they maintain their essential organization 7

Positive and negative feedback are common in biological systems 8

Systems analysis is a conceptual tool for understanding all levels of organization 8

Genomes encode the proteins that govern an organism’s structure 9

Genomes provide insights into all aspects of an organism’s biology 10

Natural selection is an important process of evolution 10

Evolution is a fact, as well as the basis for broader theory 11

Observing and quantifying are important skills 12

Scientific methods combine observation, experimentation, and logic 12

Getting from questions to answers 12

Well-designed experiments have the potential to falsify hypotheses 13

Statistical methods are essential scientific tools 13

Not all forms of inquiry into nature are scientific 14

Consider the big themes of biology as you read this book 15

PART 1 Cells

2The Chemistry and Energy of Life 18

An element consists of only one kind of atom 19

Electrons determine how an atom will react 19

Covalent bonds consist of shared pairs of electrons 20

Hydrogen bonds may form within or between molecules with polar covalent bonds 23

Polar and nonpolar substances: Each interacts best with its own kind 24

Ionic attractions form between anions and cations 24

Functional groups confer specific properties to biological molecules 25

Macromolecules are formed by the polymerization of smaller molecules 26

Monosaccharides are simple sugars 27

Glycosidic linkages bond monosaccharides 27

Polysaccharides store energy and provide structural materials 27

Fats and oils are triglycerides 29

Phospholipids form biological membranes 30

Metabolism involves reactions that store and release energy 32

Biochemical changes obey physical laws 32

3Nucleic Acids, Proteins, and Enzymes 37

Nucleotides are the building blocks of nucleic acids 38

Base pairing occurs in both DNA and RNA 38

DNA carries information and is expressed through RNA 40

The DNA base sequence reveals evolutionary relationships 41

Amino acids are the building blocks of proteins 42

Amino acids are linked together by peptide bonds 44

Higher-level protein structure is determined by primary structure 44

Protein structure can change 47

An energy barrier must be overcome to speed up a reaction 49

Enzymes bind specific reactants at their active sites 51

Enzymes can be regulated by inhibitors 54

An allosteric enzyme is regulated by changes in its shape 54

Some metabolic pathways can be controlled by feedback inhibition 55

Enzymes are affected by their environment 56

4Cells: The Working Units of Life 60

Cell size can be limited by the surface area-to-volume ratio 61

Cells can be studied structurally and chemically 62

The cell membrane forms the outer surface of every cell 62

Cells are classified as either prokaryotic or eukaryotic 63

Prokaryotic cells share certain features 64

Specialized features are found in some prokaryotes 64

Compartmentalization is the key to eukaryotic cell function 68

Ribosomes are factories for protein synthesis 68

The nucleus contains most of the cell’s DNA 68

The endomembrane system is a group of interrelated organelles 68

Some organelles transform energy 71

Several other membrane-enclosed organelles perform specialized functions 72

Microfilaments are made of actin 73

Intermediate filaments are diverse and stable 73

Microtubules are the thickest elements of the cytoskeleton 74

Cilia and flagella provide mobility 74

Biologists manipulate living systems to establish cause and effect 75

The plant cell wall is an extracellular structure 77

The extracellular matrix supports tissue functions in animals 77

Cell junctions connect adjacent cells 78

5Cell Membranes and Signaling 82

Lipids form the hydrophobic core of the membrane 83

Proteins are important components of membranes 85

Cell membrane carbohydrates are recognition sites 86

Membranes are constantly changing 86

Simple diffusion takes place through the phospholipid bilayer 87

Osmosis is the diffusion of water across membranes 88

Diffusion may be aided by channel proteins 89

Carrier proteins aid diffusion by binding substances 90

Different energy sources distinguish different active transport systems 91

Exocytosis moves materials out of the cell 93

Macromolecules and particles enter the cell by endocytosis 93

Receptor endocytosis often involves coated vesicles 94

Cells are exposed to many signals and may have different responses 95

Receptors can be classified by location and function 96

Many receptors are associated with the cell membrane 96

Cell functions change in response to environmental signals 99

Second messengers can stimulate signal transduction 99

A signaling cascade involves enzyme regulation and signal amplification 100

Signal transduction is highly regulated 101

6Pathways that Harvest and Store Chemical Energy 105

ATP hydrolysis releases energy 106

Redox reactions transfer electrons and energy 107

The processes of NADH oxidation and ATP production are coupled 108

In glycolysis, glucose is partially oxidized and some energy is released 109

Pyruvate oxidation links glycolysis and the citric acid cycle 110

The citric acid cycle completes the oxidation of glucose to CO₂ 111

Energy is transferred from NADH to ATP by oxidative phosphorylation 111

Chemiosmosis uses the proton gradient to generate ATP 111

Chemiosmosis can be demonstrated experimentally 113

Oxidative phosphorylation and chemiosmosis yield a lot of ATP 113

Catabolism and anabolism are linked 116

Catabolism and anabolism are integrated into a system 117

ATP and reduced coenzymes link catabolism, anabolism, and photosynthesis 118

Light energy is absorbed by chlorophyll and other pigments 119

Light absorption results in photochemical change 121

Reduction leads to ATP and NADPH formation 122

PART 2 Genetics

7The Cell Cycle and Cell Division 129

Asexual reproduction by binary fission or mitosis results in genetic constancy 130

Sexual reproduction by meiosis results in genetic diversity 130

Sexual life cycles are diverse 131

Prokaryotes divide by binary fission 132

Eukaryotic cells divide by mitosis followed by cytokinesis 133

Prophase sets the stage for DNA segregation 134

Chromosome separation and movement are highly organized 135

Cytokinesis is the division of the cytoplasm 135

The eukaryotic cell division cycle is regulated internally 138

The cell cycle is controlled by cyclindependent kinases 138

Meiotic division reduces the chromosome number 140

Crossing over and independent assortment generate diversity 140

Meiotic errors lead to abnormal chromosome structures and numbers 145

8Inheritance, Genes, and Chromosomes 150

Mendel used the scientific method to test his hypotheses 151

Mendel’s first experiments involved monohybrid crosses 152

Mendel’s first law states that the two copies of a gene segregate 153

Mendel verified his hypotheses by performing test crosses 154

Mendel’s second law states that copies of different genes assort independently 154

Probability is used to predict inheritance 156

Mendel’s laws can be observed in human pedigrees 157

New alleles arise by mutation 158

Dominance is not always complete 159

Genes interact when they are expressed 160

The environment affects gene action 160

Genes on the same chromosome are linked, but can be separated by crossing over in meiosis 162

Linkage is also revealed by studies of the X and Y chromosomes 164

Some genes are carried on chromosomes in organelles 166

Bacteria exchange genes by conjugation 167

Plasmids transfer genes between bacteria 168

The evolution of drug-resistant bacteria is a major public health problem 168

9DNA and Its Role in Heredity 172

Circumstantial evidence suggested that DNA is the genetic material 173

Experimental evidence confirmed that DNA is the genetic material 174

Four key features define DNA structure 177

The double-helical structure of DNA is essential to its function 177

DNA polymerases add nucleotides to the growing chain 180

Telomeres are not fully replicated in most eukaryotic cells 183

Errors in DNA replication can be repaired 184

The basic mechanisms of DNA replication can be used to amplify DNA in a test tube 185

Mutations can have various phenotypic effects 187

Point mutations are changes in single nucleotides 187

Chromosomal mutations are extensive changes in the genetic material 188

Mutations can be spontaneous or induced 189

Some base pairs are more vulnerable than others to mutation 190

Mutagens can be natural or artificial 191

Mutations have both benefits and costs 191

We attempt to minimize our exposure to mutagens 191

10From DNA to Protein: Gene Expression 194

Observations in humans led to the proposal that genes determine enzymes 195

The concept of the gene has changed over time 195

Genes are expressed via transcription and translation 197

RNA polymerases share common features 198

Transcription occurs in three steps 198

Eukaryotic coding regions are often interrupted by introns 199

Eukaryotic gene transcripts are processed before translation 201

The information for protein synthesis lies in the genetic code 203

Point mutations confirm the genetic code 205

Transfer RNAs carry specific amino acids and bind to specific codons 206

Each tRNA is specifically attached to an amino acid 207

Translation occurs at the ribosome 207

Translation takes place in three steps 208

Polysome formation increases the rate of protein synthesis 209

Signal sequences in proteins direct them to their cellular destinations 211

Many proteins are modified after translation 212

11Regulation of Gene Expression 215

Genes are subject to positive and negative regulation 216

Regulating gene transcription is a system that conserves energy 216

Operons are units of transcriptional regulation in prokaryotes 217

Operator-repressor interactions regulate transcription in the lac and trp operons 218

RNA polymerase can be directed to a class of promoters 220

Viruses use gene regulation strategies to hijack host cells 220

Transcription factors act at eukaryotic promoters 222

The expression of transcription factors underlies cell differentiation 223

Transcription factors can coordinate the expression of sets of genes 224

Eukaryotic viruses can have complex life cycles 225

Modification of histone proteins affects chromatin structure and transcription 226

DNA methylation affects transcription 227

Epigenetic changes can be induced by the environment 228

DNA methylation can result in genomic imprinting 229

Different mRNAs can be made from the same gene by alternative splicing 229

MicroRNAs are important regulators of gene expression 229

Translation of mRNA can be regulated 230

Protein stability can be regulated 231

12Genomes 234

Methods have been developed to rapidly sequence DNA 235

Genome sequences yield several kinds of information 237

Phenotypes can be analyzed using proteomics and metabolomics 238

Prokaryotic genomes are compact 240

Metagenomics reveals the diversity of viruses and prokaryotic organisms 241

Some sequences of DNA can move about the genome 241

Will defining the genes required for cellular life lead to artificial life? 242

Model organisms reveal many characteristics of eukaryotic genomes 243

Gene families exist within individual eukaryotic organisms 246

Eukaryotic genomes contain many repetitive sequences 246

The human genome sequence held some surprises 247

Human genomics has potential benefits in medicine 248

DNA fingerprinting uses short tandem repeats 250

Genome sequencing is at the leading edge of medicine 250

13Biotechnology 253

Restriction enzymes cleave DNA at specific sequences 254

Gel electrophoresis separates DNA fragments 255

Recombinant DNA can be made from DNA fragments 257

Genes can be inserted into prokaryotic or eukaryotic cells 258

A variety of methods are used to insert recombinant DNA into host cells 258

Reporter genes help select or identify host cells containing recombinant DNA 260

DNA fragments for cloning can come from several sources 261

Synthetic DNA can be made in the laboratory 262

DNA sequences can be manipulated to study cause-and-effect relationships 262

Genes can be inactivated by homologous recombination 262

Complementary RNA can prevent the expression of specific genes 263

DNA microarrays reveal RNA expression patterns 264

Expression vectors can turn cells into protein factories 265

Medically useful proteins can be made by biotechnology 266

DNA manipulation is changing agriculture 267

There is public concern about biotechnology 270

14Genes, Development, and Evolution 273

Four key processes underlie development 274

Cell fates become progressively more restricted during development 275

Cell differentiation is sometimes reversible 275

Stem cells differentiate in response to environmental signals 276

Cell fates can be determined by cytoplasmic polarity 280

Inducers passing from one cell to another can determine cell fates 280

Differential gene transcription is a hallmark of cell differentiation 282

Morphogen gradients provide positional information during development 283

Multiple proteins interact to determine developmental programmed cell death 284

Expression of transcription factor genes determines organ placement in plants 284

A cascade of transcription factors establishes body segmentation in the fruit fly 285

Developmental genes in distantly related organisms are similar 288

Genetic switches govern how the genetic toolkit is used 289

Modularity allows for differences in the pattern of gene expression among organisms 290

Mutations in developmental genes can cause major morphological changes 291

Evolution proceeds by changing what’s already there 292

Conserved developmental genes can lead to parallel evolution 293

PART 3 Evolution

15Processes of Evolution 298

Darwin and Wallace introduced the idea of evolution by natural selection 299

Evolutionary theory has continued to develop over the past century 301

Mutation generates genetic variation 302

Selection on genetic variation leads to new phenotypes 303

Natural selection increases the frequency of beneficial mutations in populations 304

Gene flow may change allele frequencies 305

Genetic drift may cause large changes in small populations 305

Nonrandom mating can change genotype or allele frequencies 306

Evolution will occur unless certain restrictive conditions exist 308

Deviations from Hardy-Weinberg equilibrium show that evolution is occurring 309

Stabilizing selection reduces variation in populations 310

Directional selection favors one extreme 311

Disruptive selection favors extremes over the mean 312

Much of molecular evolution is neutral 313

Positive and purifying selection can be detected in the genome 314

Heterozygote advantage maintains polymorphic loci 316

Genome size and organization also evolve 317

Sexual recombination amplifies the number of possible genotypes 318

Lateral gene transfer can result in the gain of new functions 319

Many new functions arise following gene duplication 319

Knowledge of gene evolution is used to study protein function 321

In vitro evolution produces new molecules 321

Evolutionary theory provides multiple benefits to agriculture 321

Knowledge of molecular evolution is used to combat diseases 322

16Reconstructing and Using Phytogenies 325

Phylogenetic trees are the basis of comparative biology 327

Derived traits provide evidence of evolutionary relationships 328

Parsimony provides the simplest explanation for phylogenetic data 329

Phylogenies are reconstructed from many sources of data 331

Mathematical models expand the power of phylogenetic reconstruction 332

The accuracy of phylogenetic methods can be tested 332

Phylogenies are important for reconstructing past events 334

Phylogenies allow us to understand the evolution of complex traits 335

Phylogenies can reveal convergent evolution 336

Ancestral states can be reconstructed 336

Molecular clocks help date evolutionary events 337

Evolutionary history is the basis for modern biological classification 339

Several codes of biological nomenclature govern the use of scientific names 339

17Speciation 343

We can recognize many species by their appearance 344

Reproductive isolation is key 344

The lineage approach takes a long-term view 345

The different species concepts are not mutually exclusive 345

Incompatibilities between genes can produce reproductive isolation 346

Reproductive isolation develops with increasing genetic divergence 346

Physical barriers give rise to allopatric speciation 348

Sympatric speciation occurs without physical barriers 350

Prezygotic isolating mechanisms prevent hybridization between species 351

Postzygotic isolating mechanisms result in selection against hybridization 353

Hybrid zones may form if reproductive isolation is incomplete 354

18The History of Life on Earth 357

Radioisotopes provide a way to date rocks 358

Radiometric dating methods have been expanded and refined 358

Scientists have used several methods to construct a geological time scale 359

The continents have not always been where they are today 360

Earth’s climate has shifted between hot and cold conditions 361

Volcanoes have occasionally changed the history of life 363

Extraterrestrial events have triggered changes on Earth 363

Oxygen concentrations in Earth’s atmosphere have changed over time 363

Several processes contribute to the paucity of fossils 367

Precambrian life was small and aquatic 367

Life expanded rapidly during the Cambrian period 368

Many groups of organisms that arose during the Cambrian later diversified 372

Geographic differentiation increased during the Mesozoic era 373

Modern biotas evolved during the Cenozoic era 373

The tree of life is used to reconstruct evolutionary events 374

PART 4 Diversity

19Bacteria, Archaea, and Viruses 378

The two prokaryotic domains differ in significant ways 380

The small size of prokaryotes has hindered our study of their evolutionary relationships 380

The nucleotide sequences of prokaryotes reveal their evolutionary relationships 381

Lateral gene transfer can lead to discordant gene trees 382

The great majority of prokaryote species have never been studied 383

The low-GC Gram-positives include the smallest cellular organisms 384

Some high-GC Gram-positives are valuable sources of antibiotics 384

Hyperthermophilic bacteria live at very high temperatures 385

Hadobacteria live in extreme environments 385

Cyanobacteria were the first photosynthesizers 385

Spirochetes move by means of axial filaments 386

Chlamydias are extremely small parasites 386

The proteobacteria are a large and diverse group 387

Gene sequencing enabled biologists to differentiate the domain Archaea 387

Most crenarchaeotes live in hot or acidic places 389

Euryarchaeotes are found in surprising places 389

Several lineages of Archaea are poorly known 390

Many prokaryotes form complex communities 390

Microbiomes are critical to the health of many eukaryotes 391

A small minority of bacteria are pathogens 393

Prokaryotes have amazingly diverse metabolic pathways 394

Prokaryotes play important roles in element cycling 395

Many RNA viruses probably represent escaped genomic components 396

Some DNA viruses may have evolved from reduced cellular organisms 399

Viruses can be used to fight bacterial infections 399

20The Origin and Diversification of Eukaryotes 401

The modern eukaryotic cell arose in several steps 402

Chloroplasts have been transferred among eukaryotes several times 404

Alveolates have sacs under their cell membranes 406

Stramenopiles typically have two unequal flagella, one with hairs 408

Rhizarians typically have long, thin pseudopods 409

Excavates began to diversify about 1.5 billion years ago 410

Amoebozoans use lobe-shaped pseudopods for locomotion 412

Some protists have reproduction without sex and sex without reproduction 414

Some protist life cycles feature alternation of generations 414

Phytoplankton are primary producers 415

Some microbial eukaryotes are deadly 415

Some microbial eukaryotes are endosymbionts 416

We rely on the remains of ancient marine protists 417

21The Evolution of Plants 420

Several distinct clades of algae were among the first photosynthetic eukaryotes 421

There are ten major groups of land plants 421

Adaptations to life on land distinguish land plants from green algae 423

Life cycles of land plants feature alternation of generations 424

Nonvascular land plants live where water is readily available 425

The sporophytes of nonvascular land plants are dependent on the gametophytes 426

Vascular tissues transport water and dissolved materials 428

The diversification of vascular plants made land more suitable for animals 428

The earliest vascular plants lacked roots 429

The lycophytes are sister to the other vascular plants 429

Horsetails and ferns constitute a clade 429

The vascular plants branched out 431

Heterospory appeared among the vascular plants 431

Features of the seed plant life cycle protect gametes and embryos 432

The seed is a complex, well-protected package 435

A change in stem anatomy enabled seed plants to grow to great heights 435

Gymnosperms have naked seeds 435

Conifers have cones and lack swimming sperm 437

Angiosperms have many shared derived traits 439

The sexual structures of angiosperms are flowers 439

Flower structure has evolved over time 440

Angiosperms have coevolved with animals 441

The angiosperm life cycle produces diploid zygotes nourished by triploid endosperms 442

Fruits aid angiosperm seed dispersal 443

Recent analyses have revealed the phylogenetic relationships of angiosperms 445

22The Evolution and Diversity of Fungi 450

Unicellular yeasts absorb nutrients directly 451

Multicellular fungi use hyphae to absorb nutrients 451

Fungi are in intimate contact with their environment 452

Saprobic fungi are critical to the planetary carbon cycle 453

Some fungi engage in parasitic or predatory interactions 453

Mutualistic fungi engage in relationships beneficial to both partners 455

Endophytic fungi protect some plants from pathogens, herbivores, and stress 458

Fungi reproduce both sexually and asexually 458

Microsporidia are highly reduced, parasitic fungi 459

Most chytrids are aquatic 460

Some fungal life cycles feature separate fusion of cytoplasms and nuclei 460

Arbuscular mycorrhizal fungi form symbioses with plants 462

The dikaryotic condition is a synapomorphy of sac fungi and club fungi 462

The sexual reproductive structure of sac fungi is the ascus 462

The sexual reproductive structure of club fungi is the basidium 464

Lichen diversity and abundance indicate air quality 466

Fungi record and help remediate environmental pollution 466

Reforestation may depend on mycorrhizal fungi 466

23Animal Origins and Diversity 469

Animal monophyly is supported by gene sequences and cellular morphology 470

Basic developmental patterns and body plans differentiate major animal groups 471

Most animals are symmetrical 473

The structure of the body cavity influences movement 473

Segmentation improves control of movement 473

Appendages have many uses 474

Nervous systems coordinate movement and allow sensory processing 474

Sponges are loosely organized animals 475

Ctenophores are radially symmetrical and diploblastic 477

Placozoans are abundant but rarely observed 478

Cnidarians are specialized carnivores 478

Cilia-bearing lophophores and trochophore larvae evolved among the lophotrochozoans 480

Ecdysozoans must shed their cuticles 487

Arthropod relatives have fleshy, unjointed appendages 491

Chelicerates are characterized by pointed, nonchewing mouthparts 491

Mandibles and antennae characterize the remaining arthropod groups 492

More than half of all described species are insects 494

Echinoderms have unique structural features 498

Hemichordates are wormlike marine deuterostomes 499

Chordate characteristics are most evident in larvae 500

Adults of most lancelets and tunicates are sessile 500

The vertebrate body plan can support large, active animals 501

There are two groups of living jawless fishes 501

Jaws and teeth improved feeding efficiency 503

Fins and swim bladders improved stability and control over locomotion 503

Jointed fins enhanced support for fishes 505

Amphibians adapted to life on land 506

Amniotes colonized dry environments 508

Reptiles adapted to life in many habitats 508

Crocodilians and birds share their ancestry with the dinosaurs 510

The evolution of feathers allowed birds to fly 511

Mammals radiated as non-avian dinosaurs declined in diversity 511

Most mammals are viviparous 512

Two major lineages of primates split late in the Cretaceous 514

Bipedal locomotion evolved in human ancestors 515

Human brains became larger as jaws became smaller 516

PART 5 Plant Form and Function

24The Plant Body 521

Plants develop differently than animals 522

The plant body has an apical-basal axis and a radial axis 523

The plant body is constructed from three tissue systems 524

A hierarchy of meristems generates the plant body 527

The root apical meristem gives rise to the root cap and the root primary meristems 528

The products of the root’s primary meristems become root tissues 528

The root system anchors the plant and takes up water and dissolved minerals 529

The products of the shoot’s primary meristems become shoot tissues 530

Leaves are photosynthetic organs produced by shoot apical meristems 531

Plant organs can have alternative forms and functions 531

25Plant Nutrition and Transport 537

Nutrients can be defined by their deficiency 538

Experiments using hydroponics have identified essential elements 538

Soil provides nutrients for plants 539

Ion exchange makes nutrients available to plants 540

Fertilizers can be used to add nutrients to soil 541

Plants send signals for colonization 542

Mycorrhizae expand the root system 542

Rhizobia capture nitrogen from the air and make it available to plant cells 543

Some plants obtain nutrients directly from other organisms 544

Differences in water potential govern the direction of water movement 545

Water and ions move across the root cell’s cell membrane 546

Water and ions pass to the xylem by way of the apoplast and symplast 547

Water moves through the xylem by the transpiration-cohesion-tension mechanism 548

Stomata control water loss and gas exchange 550

Sucrose and other solutes are carried in the phloem 552

The pressure flow model describes the movement of fluid in the phloem 553

26Plant Growth and Development 555

The seed germinates and forms a growing seedling 556

Several hormones and photoreceptors help regulate plant growth 557

Genetic screens have increased our understanding of plant signal transduction 557

Gibberellins have many effects on plant growth and development 560

The transport of auxin mediates some of its effects 561

Auxin plays many roles in plant growth and development 562

At the molecular level, auxin and gibberellins act similarly 563

Ethylene is a gaseous hormone that promotes senescence 565

Cytokinins are active from seed to senescence 566

Brassinosteroids are plant steroid hormones 566

Abscisic acid acts by inhibiting development 566

Phototropin, cryptochromes, and zeaxanthin are blue-light receptors 568

Phytochrome senses red and far-red light 568

Phytochrome stimulates gene transcription 569

Circadian rhythms are entrained by photoreceptors 570

27Reproduction of Flowering Plants 573

The flower is the reproductive organ of angiosperms 574

Angiosperms have microscopic gametophytes 575

Angiosperms have mechanisms to prevent inbreeding 576

A pollen tube delivers sperm cells to the embryo sac 576

Angiosperms perform double fertilization 577

Embryos develop within seeds contained in fruits 577

Shoot apical meristems can become inflorescence meristems 579

A cascade of gene expression leads to flowering 580

Photoperiodic cues can initiate flowering 580

Plants vary in their responses to photoperiodic cues 580

Night length is the key photoperiodic cue that determines flowering 581

The flowering stimulus originates in the leaf 582

Florigen is a small protein 582

Flowering can be induced by temperature or gibberellins 584

Some plants do not require an environmental cue to flower 584

Angiosperms use many forms of asexual reproduction 585

Vegetative reproduction is important in agriculture 587

28Plants in the Environment 589

Physical barriers form constitutive defenses 590

Induced responses can be general or specific 590

General and specific immunity both involve multiple responses 591

Specific immunity is genetically determined 592

Specific immunity usually leads to the hypersensitive response 592

General and specific immunity can lead to systemic acquired resistance 592

Constitutive defenses are physical and chemical 593

Plants respond to herbivory with induced defenses 594

Why don’t plants poison themselves? 596

Plants don’t always mount a successful defense 596

Some plants have special adaptations to live in very dry conditions 597

Some plants grow in saturated soils 599

Plants can respond to drought stress 599

Plants can cope with temperature extremes 600

Some plants can tolerate soils with high salt concentrations 600

Some plants can tolerate heavy metals 601

PART 6 Animal Form and Function

29Fundamentals of Animal Function 605

Animals need chemical building blocks to grow and to replace chemical constituents throughout life 606

Animals need inputs of chemical-bond energy to maintain their organized state throughout life 606

We quantify an animal’s metabolic rate by measuring heat production or O₂ consumption 607

Physical activity increases an animal’s metabolic rate 608

Among related animals, metabolic rate usually varies in a regular way with body size 609

Animals are classed as regulators and conformers 609

Regulation is more expensive than conformity 610

Homeostasis is a key organizing concept 610

Animals are classed as homeotherms or poikilotherms based on their thermal relationships with their external environment 610

Homeothermy is far more costly than poikilothermy 612

Homeotherms have evolved thermoregulatory mechanisms 613

Hibernation allows mammals to reap the benefits of both regulation and conformity 614

Fluid compartments are separated from one another by physiologically active epithelia and cell membranes 615

Animals exhibit a high degree of division of labor 616

Division of labor requires a rapid transport system 617

Each cell must make its own ATP 617

Animal cells have aerobic and anaerobic processes for making ATP 617

Phenotypic plasticity is common at the biochemical level 618

Phenotypic plasticity also occurs at the scales of tissues and organs 618

Phenotypic plasticity is under genetic control 618

Homeothermy exemplifies negative-feedback control 619

Positive feedback occurs in some cases 620

Biological clocks make important contributions to control 620

30Nutrition, Feeding, and Digestion 624

Food provides energy 625

Chemical energy from food is sometimes stored for future use 626

Food provides chemical building blocks 627

Some nutrients in foods are essential 627

Nutrient deficiencies result in diseases 628

Some animals feed by targeting easily visible, individual food items 629

Suspension feeders collect tiny food particles in great numbers 630

Many animals live symbiotically with microbes of nutritional importance 630

Digestive abilities determine which foods have nutritional value 633

Animals are diverse in the foods they can digest 633

Digestive abilities sometimes evolve rapidly 634

Digestive abilities are phenotypically plastic 635

Several classes of digestive enzymes take part in digestion 635

Processing of food starts in the foregut 636

Food processing continues in the midgut and hindgut 637

The midgut is the principal site of digestion and absorption 637

The hindgut reabsorbs water and salts 638

Hormones help regulate appetite and the processing of a meal 639

Insulin and glucagon regulate processing of absorbed food materials from meal to meal 640

31Breathing 643

The diffusion of gases depends on their partial pressures 644

Diffusion can be very effective but only over short distances 645

Gas transport in animals often occurs by alternating diffusion and bulk flow 646

Breathing is the transport of O₂ and CO₂ between the outside environment and gas exchange membranes 646

Air and water are very different respiratory environments 647

Specialized breathing organs have large surface areas of thin membranes 649

The directions of ventilation and perfusion can greatly affect the efficiency of gas exchange 649

Many aquatic animals with gills use countercurrent exchange 650

Most terrestrial vertebrates have tidally ventilated lungs 651

Birds have rigid lungs ventilated unidirectionally by air sacs 652

Insects have airways throughout their bodies 653

At rest, only a small portion of the lung volume is exchanged 656

The lungs are ventilated by expansion and contraction of the thoracic cavity 656

The breathing rhythm depends on nervous stimulation of the breathing muscles 656

Breathing is under negative-feedback control by CO₂ 658

Breathing is also under control of factors in addition to CO₂ 659

32Circulation 661

Closed circulatory systems move blood through blood vessels 662

In open circulatory systems, blood leaves blood vessels 664

Most fish have the systemic circuit and gill circuit connected in series 665

Mammals and birds have the systemic circuit and lung circuit connected in series 666

Amphibians and most non-avian reptiles have circulatory plans that do not anatomically guarantee series flow 666

Vertebrate hearts are myogenic and multi-chambered 667

The myocardium must receive O₂ 670

An electrocardiogram records the electrical activity of the heart 671

Crustacean hearts are neurogenic and single-chambered 671

Pressure and linear velocity vary greatly as blood flows through the vascular system 673

Animals have evolved arrangements of blood vessels that help them conserve heat 674

Blood flow leaves behind fluid that the lymph system picks up 675

Hemoglobin and hemocyanin are the two principal respiratory pigments 677

Respiratory pigments combine with O₂ reversibly 677

33Muscle and Movement 681

Contraction occurs by a sliding-filament mechanism 682

Actin and myosin filaments slide in relation to each other during muscle contraction 682

ATP-requiring actin–myosin interactions are responsible for contraction 684

Excitation leads to contraction, mediated by calcium ions 685

In vertebrates, muscles pull on the bones of the endoskeleton 688

In arthropods, muscles pull on interior extensions of the exoskeleton 689

Hydrostatic skeletons have important relationships with muscle 690

Muscle power output depends on a muscle’s current rate of ATP supply 691

Muscle cell types affect power output and endurance 692

Training modifies muscle performance 693

Vertebrate cardiac muscle is both similar to and different from skeletal muscle 695

Vertebrate smooth muscle powers slow contractions of many internal organs 695

Some insect flight muscle has evolved unique excitation–contraction coupling 696

Catch muscle in clams and scallops stays contracted with little ATP use 696

Fish electric organs are composed of modified muscle 696

34Neurons, Sense Organs, and Nervous Systems 699

Neurons are specialized to produce electric signals 700

Glial cells support, nourish, and insulate neurons 701

Only small shifts of ions are required for rapid changes in membrane potential 703

The sodium-potassium pump sets up concentration gradients of Na⁺ and K⁺ 704

The resting potential is mainly a consequence of K⁺ leak channels 704

The Nernst equation predicts an ion’s equilibrium potential 704

Gated ion channels can alter the membrane potential 705

Changes in membrane potential can be graded or all-or-none, depending on whether a threshold is crossed 706

An action potential is a large depolarization that propagates with no loss of size 707

Action potentials travel particularly fast in large axons and in myelinated axons 708

Chemical synapses are most common, but electrical synapses also exist 709

The vertebrate neuromuscular junction is a model chemical synapse 710

Many neurotransmitters are known 711

Synapses can be fast or slow depending on the nature of receptors 712

Fast synapses produce postsynaptic potentials that sum to determine action potential production 712

Synaptic plasticity is a mechanism of learning and memory 713

Sensory receptor cells transform stimuli into electric signals 714

Sensory receptor cells depend on specific receptor proteins and are ionotropic or metabotropic 715

Sensation depends on which neurons in the brain receive action potentials from sensory cells 715

Sensation of stretch and smell exemplify ionotropic and metabotropic reception 715

Auditory systems use mechanoreceptors to sense sound pressure waves 717

The photoreceptors involved in vision detect light using rhodopsins 718

The vertebrate retina is a developmental outgrowth of the brain and consists of specialized neurons 719

Some retinal ganglion cells are photoreceptive and interact with the circadian clock 721

Arthropods have compound eyes 722

Animals have evolved a remarkable diversity of sensory abilities 722

The autonomic nervous system controls involuntary functions 725

Spinal reflexes represent a simple type of skeletal muscle control 726

The most dramatic changes in vertebrate brain evolution have been in the forebrain 727

Location specificity is an important property of the mammalian cerebral hemispheres 728

35Control by the Endocrine and Nervous Systems 733

The nervous and endocrine systems work in different ways 734

Nervous systems and endocrine systems tend to control different processes 735

The nervous and endocrine systems work together 735

Chemical signaling operates over a broad range of distances 735

Endocrine cells are neurosecretory or nonneural 736

Most hormones belong to one of three chemical groups 737

Receptor proteins can be on the cell surface or inside a cell 737

Hormone action depends on the nature of the target cells and their receptors 739

A hormonal signal is initiated, has its effect, and is terminated 739

Hypothalamic neurosecretory cells produce the posterior pituitary hormones 740

Hormones from hypothalamic neurosecretory cells control production of the anterior pituitary hormones 741

Endocrine cells are organized into control axes 742

Hypothalamic and anterior pituitary hormones are often secreted in pulses 743

The thyroid gland is essential for normal development and provides an example of hormone deficiency disease 745

Sex steroids control reproductive development 746

36Water and Salt Balance 751

Kidneys make urine from the blood plasma 752

Kidneys regulate the composition and volume of the blood plasma 753

Urine/plasma (U/P) ratios are essential tools for understanding kidney function 753

Our day-to-day urine concentrations illustrate these principles 753

The range of action of the kidneys varies from one animal group to another 754

Extrarenal salt excretion sometimes provides abilities the kidneys cannot provide 754

Most water-breathing aquatic animals excrete ammonia 755

Most terrestrial animals excrete urea, uric acid, or compounds related to uric acid 755

Most invertebrates in the ocean are isosmotic with seawater 756

Ocean bony fish are strongly hyposmotic to seawater 756

All freshwater animals are hyperosmotic to fresh water 757

Some aquatic animals face varying environmental salinities 758

Humidic terrestrial animals have rapid rates of water loss that limit their behavioral options 759

Xeric terrestrial animals have low rates of water loss, giving them enhanced freedom of action 759

Some xeric animals are adapted to live in deserts 759

Fluid enters a nephron by ultrafiltration driven by blood pressure 760

The processing of the primary urine in amphibians reveals fundamental principles of nephron function 761

Mammalian kidneys produce exceptionally high urine concentrations 763

The Malpighian tubules of insects employ a secretory mechanism of producing primary urine 764

37Animal Reproduction 768

Most animals reproduce sexually 769

Gametogenesis in the gonads produces the haploid gametes 771

Fertilization may be external or internal 773

The sex of an offspring is sometimes determined at fertilization 774

Some animals undergo sex change 775

Ova mature in the ovaries and move to the uterus 777

Ovulation is either induced or spontaneous 777

Pregnancy is a specialized hormonal state 779

Male sex organs produce and deliver semen 780

Many contraceptive methods are available 781

Animals often gain flexibility by having mechanisms to decouple the steps in reproduction 782

Some animals can reproduce only once, but most can reproduce more than once 783

Seasonal reproductive cycles are common 784

38Animal Development 787

Egg and sperm make different contributions to the zygote 788

Polarity is established early in development 788

Specific blastomeres generate specific tissues and organs 791

The amount of yolk affects cleavage 792

Cleavage in placental mammals is unique 792

The notochord induces formation of the neural tube 797

Mesoderm forms tissues of the middle layer 800

Extraembryonic membranes form with contributions from all germ layers 802

Extraembryonic membranes in mammals form the placenta 803

Fish also make yolk sacs 803

39Immunology: Animal Defense Systems 809

Innate defenses evolved before adaptive defenses 810

Mammals have both innate and adaptive defenses 811

Barriers and local agents defend the body against invaders 812

Cell signaling pathways stimulate additional innate defenses 813

Inflammation is a coordinated response to infection or injury 813

Inflammation can cause medical problems 814

Adaptive immunity has four key features 816

Macrophages and dendritic cells play a key role in activating the adaptive immune system 817

Two types of adaptive immune responses interact 817

Plasma cells produce antibodies that share a common overall structure 819

Antibody diversity results from DNA rearrangements and other mutations 820

Antibodies bind to antigens and activate defense mechanisms 821

T cell receptors specifically bind to antigens on cell surfaces 822

MHC proteins present antigens to T cells and result in recognition 822

T_H cells contribute to the humoral and cellular immune responses 823

Activation of the cellular response results in death of the targeted cell 823

Regulatory T cells suppress the humoral and cellular immune responses 824

AIDS is an immune deficiency disorder 824

40Animal Behavior 827

Many types of evidence point to the neural basis of behavior 828

Behaviors evolve 829

Despite its neural basis, behavior is not necessarily simplistically deterministic 829

Specific information of critical survival value is often learned during early postnatal development 830

Early experience also has other, more global effects on behavior 831

Toads and frogs have evolved contrasting behavioral specializations that depend on their biochemistry of ATP synthesis 832

Behaviors are often integrated with body size and growth 833

Trail following and path integration are two mechanisms of navigation 834

Animals have multiple ways of determining direction 835

Honey bee workers communicate distance and direction by a waggle dance 837

Migration: Many animals have evolved periodic movements between locations 837

Some societies consist of individuals of equal status 839

Some societies are composed of individuals of differing status 839

Eusociality represents an extreme type of differing status 840

Behavior helps maintain species 841

Animals often behaviorally partition space into territories or home ranges 841

Behavior helps structure relationships among species 842

PART 7 Ecology

41The Distribution of Earth’s Ecological Systems 845

Organisms and their environments are ecological systems 846

Ecological systems can be small or large 846

Ecological systems vary, but in ways that can be understood with scientific methods 847

Variation in solar energy input drives patterns of weather and climate 849

The circulation of Earth’s atmosphere redistributes heat energy 850

Ocean circulation also influences climate 851

Topography produces additional environmental heterogeneity 852

Climate diagrams summarize climates in an ecologically relevant way 853

Similarities in terrestrial vegetation led to the biome concept 854

Climate is not the only factor that molds terrestrial biomes 854

The biome concept can be extended to aquatic environments 856

Barriers to dispersal affect biogeography 857

The movements of continents account for biogeographic regions 858

Phylogenetic methods contribute to our understanding of biogeography 859

We are altering natural ecosystems as we use them 861

We are replacing natural ecosystems with human-dominated ones 861

We are blurring biogeographic boundaries 861

Science provides tools for conserving and restoring ecological systems 862

42Populations 864

Population density and population size are two measures of abundance 865

Abundance varies in space and over time 865

Life histories are diverse 868

Resources and physical conditions shape life histories 869

Species’ distributions reflect the effects of environment on per capita growth rates 870

Multiplicative growth with constant r can generate large numbers very quickly 873

Populations growing multiplicatively with constant r have a constant doubling time 873

Density dependence prevents populations from growing indefinitely 873

Changing environmental conditions cause the carrying capacity to change 874

Technology has increased Earth’s carrying capacity for humans 875

Knowledge of life histories helps us manage populations 878

Knowledge of metapopulation dynamics helps us conserve species 878

43Ecological and Evolutionary Consequences of Interactions within and among Species 882

Interspecific interactions are classified by their effects on fitness 883

The effects of many interactions are contingent on the environment 884

Interspecific interactions can modify per capita growth rates 886

Interspecific interactions affect population dynamics and can lead to extinction 886

Interspecific interactions can affect species distributions 887

Rarity advantage promotes species coexistence 888

Consumer-resource interactions form the core of interaction webs 889

Losses or additions of species can cascade through communities 889

The cascading effects of ecological interactions have implications for conservation 891

Intraspecific competition can increase the carrying capacity 892

Interspecific competition can lead to resource partitioning and coexistence 892

Consumer-resource interactions can lead to an evolutionary arms race 892

Mutualisms involve conflict of interest 894

44Ecological Communities 898

Species composition varies along environmental gradients 900

Several processes cause communities to change over time 900

Energy flux is a critical aspect of community function 903

Community function is affected by species diversity 904

Species richness varies with latitude 906

Species richness varies with the size and isolation of oceanic islands 907

Ecological communities provide humans with goods and services 909

Ecosystem services have economic value 910

Island biogeography suggests strategies for conserving community diversity 911

Trophic cascades suggest the importance of conserving certain species 912

The relationship of diversity to community function suggests strategies for restoring degraded habitats 912

45The Global Ecosystem 916

NPP is a measure of ecosystem function 917

NPP varies predictably with temperature, precipitation, and nutrients 917

The forms and locations of elements determine their accessibility to organisms 920

Movement of matter is driven by biogeochemical processes 920

Water transports materials among compartments 921

Within-ecosystem recycling dominates the global nitrogen cycle 922

Movement of carbon is linked to energy flow through ecosystems 924

Biogeochemical cycles are not independent 926

Earth’s surface is warm because of the atmosphere 926

Recent increases in greenhouse gases are warming Earth’s surface 927

Human activities are contributing to changes in Earth’s radiation budget 928

Rapid climate change presents ecological challenges 929

Changes in seasonal timing can disrupt interspecific interactions 929

Climate change can alter community composition by several mechanisms 930

Extreme weather events also have an impact 931

Appendix A The Tree of Life 936

Appendix B Making Sense of Data: A Statistics Primer 943

Appendix C Some Measurements Used in Biology 953

Glossary G-1

Illustration Credits IC-1

Index I-1