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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
TH 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
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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
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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 956
Glossary G-1
Illustration Credits IC-1
Index I-1
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