1

Evolution, the Themes of Biology, and Scientific Inquiry

1.1

The study of life reveals common themes

1.2

The Core Theme: Evolution accounts for the unity and diversity of life

1.3

In studying nature, scientists make observations and form and test hypotheses

1.4

Science benefits from a cooperative approach and diverse viewpoints

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2

The Chemical Context of Life

2.1

Matter consists of chemical elements in pure form and in combinations called compounds

2.2

An elements properties depend on the structure of its atoms 30

2.3

The formation and function of molecules depend on chemical bonding between atoms

2.4

Chemical reactions make and break chemical bonds

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3

Water and Life

3.1

Polar covalent bonds in water molecules result in hydrogen bonding

3.2

Four emergent properties of water contribute to Earths suitability for life

3.3

Acidic and basic conditions affect living organisms

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4

Carbon and the Molecular Diversity of Life

4.1

Organic chemistry is the study of carbon compounds

4.2

Carbon atoms can form diverse molecules by bonding to four other atoms

4.3

A few chemical groups are key to molecular function

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5

The Structure and Function of Large Biological Molecules

5.1

Macromolecules are polymers, built from monomers

5.2

Carbohydrates serve as fuel and building material

5.3

Lipids are a diverse group of hydrophobic molecules

5.4

Proteins include a diversity of structures, resulting in a wide range of functions

5.5

Nucleic acids store, transmit, and help express hereditary information

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6

A Tour of the Cell

6.1

Biologists use microscopes and the tools of biochemistry to study cells

6.2

Eukaryotic cells have internal membranes that compartmentalize their functions

6.3

The eukaryotic cells genetic instructions are housed in the nucleus and carried out by the ribosomes

6.4

The endomembrane system regulates protein traffic and performs metabolic functions in the cell

6.5

Mitochondria and chloroplasts change energy from one form to another

6.6

The cytoskeleton is a network of fibers that organizes structures and activities in the cell

6.7

Extracellular components and connections between cells help coordinate cellular activities

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7

Membrane Structure and Function

7.1

Cellular membranes are fluid mosaics of lipids and proteins

7.2

Membrane structure results in selective permeability

7.3

Passive transport is diffusion of a substance across a membrane with no energy investment

7.4

Active transport uses energy to move solutes against their gradients

7.5

Bulk transport across the plasma membrane occurs by exocytosis and endocytosis

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8

An Introduction to Metabolism

8.1

An organisms metabolism transforms matter and energy, subject to the laws of thermodynamics

8.2

The free-energy change of a reaction tells us whether or not the reaction occurs spontaneously

8.3

ATP powers cellular work by coupling exergonic reactions to endergonic reactions

8.4

Enzymes speed up metabolic reactions by lowering energy barriers

8.5

Regulation of enzyme activity helps control metabolism

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9

Cellular Respiration and Fermentation

9.1

Catabolic pathways yield energy by oxidizing organic fuels

9.2

Glycolysis harvests chemical energy by oxidizing glucose to pyruvate

9.3

After pyruvate is oxidized, the citric acid cycle completes the energy-yielding oxidation of organic molecules

9.4

During oxidative phosphorylation, chemiosmosis couples electron transport to ATP synthesis

9.5

Fermentation and anaerobic respiration enable cells to produce ATP without the use of oxygen

9.6

Glycolysis and the citric acid cycle connect to many other metabolic pathways

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10

Photosynthesis

10.1

Photosynthesis converts light energy to the chemical energy of food

10.2

The light reactions convert solar energy to the chemical energy of ATP and NADPH

10.3

The Calvin cycle uses the chemical energy of ATP and NADPH to reduce CO2 to sugar

10.4

Alternative mechanisms of carbon fixation have evolved in hot, arid climates

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11

Cell Communication

11.1

External signals are converted to responses within the cell

11.2

Reception: A signaling molecule binds to a receptor protein, causing it to change shape

11.3

Transduction: Cascades of molecular interactions relay signals from receptors to target molecules in the cell

11.4

Response: Cell signaling leads to regulation of transcription or cytoplasmic activities

11.5

Apoptosis integrates multiple cellsignaling pathways

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12

The Cell Cycle

12.1

Most cell division results in genetically identical daughter cells

12.2

The mitotic phase alternates with interphase in the cell cycle

12.3

The eukaryotic cell cycle is regulated by a molecular control system

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13

Meiosis and Sexual Life Cycles

13.1

Offspring acquire genes from parents by inheriting chromosomes

13.2

Fertilization and meiosis alternate in sexual life cycles

13.3

Meiosis reduces the number of chromosome sets from diploid to haploid

13.4

Genetic variation produced in sexual life cycles contributes to evolution

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14

Mendel and the Gene Idea

14.1

Mendel used the scientific approach to identify two laws of inheritance

14.2

Probability laws govern Mendelian inheritance

14.3

Inheritance patterns are often more complex than predicted by simple Mendelian genetics

14.4

Many human traits follow Mendelian patterns of inheritance

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15

The Chromosomal Basis of Inheritance

15.1

Morgan showed that Mendelian inheritance has its physical basis in the behavior of chromosomes: Scientific inquiry

15.2

Sex-linked genes exhibit unique patterns of inheritance

15.3

Linked genes tend to be inherited together because they are located near each other on the same chromosome

15.4

Alterations of chromosome number or structure cause some genetic disorders

15.5

Some inheritance patterns are exceptions to standard Mendelian inheritance

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16

The Molecular Basis of Inheritance

16.1

DNA is the genetic material

16.2

Many proteins work together in DNA replication and repair

16.3

A chromosome consists of a DNA molecule packed together with proteins

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17

Gene Expression: From Gene to Protein

17.1

Genes specify proteins via transcription and translation

17.2

Transcription is the DNA-directed synthesis of RNA: A closer look

17.3

Eukaryotic cells modify RNA after transcription

17.4

Translation is the RNA-directed synthesis of a polypeptide: A closer look

17.5

Mutations of one or a few nucleotides can affect protein structure and function

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18

Regulation of Gene Expression

18.1

Bacteria often respond to environmental change by regulating transcription

18.2

Eukaryotic gene expression is regulated at many stages

18.3

Noncoding RNAs play multiple roles in controlling gene expression

18.4

A program of differential gene expression leads to the different cell types in a multicellular organism

18.5

Cancer results from genetic changes that affect cell cycle control

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19

Viruses

19.1

A virus consists of a nucleic acid surrounded by a protein coat

19.2

Viruses replicate only in host cells

19.3

Viruses, viroids, and prions are formidable pathogens in animals and plants

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20

DNA Tools and Biotechnology

20.1

DNA sequencing and DNA cloning are valuable tools for genetic engineering and biological inquiry

20.2

Biologists use DNA technology to study gene expression and function

20.3

useful for basic research and other applications

20.4

The practical applications of DNA-based biotechnology affect our lives in many ways

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21

Genomes and Their Evolution

21.1

The Human Genome Project fostered development of faster, less expensive sequencing techniques

21.2

Scientists use bioinformatics to analyze genomes and their functions

21.3

Genomes vary in size, number of genes, and gene density

21.4

Multicellular eukaryotes have much noncoding DNA and many multigene families

21.5

Duplication, rearrangement, and mutation of DNA contribute to genome evolution

21.6

Comparing genome sequences provides clues to evolution and development

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22

Descent with Modification: A Darwinian View of Life

22.1

The Darwinian revolution challenged traditional views of a young Earth inhabited by unchanging species

22.2

Descent with modification by natural selection explains the adaptations of organisms and the unity and diversity of life22

22.3

Evolution is supported by an overwhelming amount of scientific evidence

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23

The Evolution of Populations

23.1

Genetic variation makes evolution possible

23.2

The Hardy-Weinberg equation can be used to test whether a population is evolving

23.3

Natural selection, genetic drift, and gene flow can alter allele frequencies in a population

23.4

Natural selection is the only mechanism that consistently causes adaptive evolution

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24

The Origin of Species

24.1

The biological species concept emphasizes reproductive isolation

24.2

Speciation can take place with or without geographic separation

24.3

Hybrid zones reveal factors that cause reproductive isolation

24.4

Speciation can occur rapidly or slowly and can result from changes in few or many genes

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25

The History of Life on Earth

25.1

Conditions on early Earth made the origin of life possible

25.2

The fossil record documents the history of life

25.3

Key events in lifes history include the origins of unicellular and multicellular organisms and the colonization of land

25.4

The rise and fall of groups of organisms reflect differences in speciation and extinction rates

25.5

Major changes in body form can result from changes in the sequences and regulation of developmental genes

25.6

Evolution is not goal orientedMajor changes in body form can result from changes in the sequences and regulation of developmental genes

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26

Phylogeny and the Tree of Life

26.1

Phylogenies show evolutionary relationships

26.2

Phylogenies are inferred from morphological and molecular data

26.3

Shared characters are used to construct phylogenetic trees

26.4

An organisms evolutionary history is documented in its genome

26.5

Molecular clocks help track evolutionary time

26.6

Our understanding of the tree of life continues to change based on new data

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27

Bacteria and Archaea

27.1

Structural and functional adaptations contribute to prokaryotic success

27.2

Rapid reproduction, mutation, and genetic recombination promote genetic diversity in prokaryotes

27.3

Diverse nutritional and metabolic adaptations have evolved in prokaryotes

27.4

Prokaryotes have radiated into a diverse set of lineages

27.5

Prokaryotes play crucial roles in the biosphere

27.6

Prokaryotes have both beneficial and harmful impacts on humans

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28

Protists

28.1

Most eukaryotes are single-celled organisms

28.2

Excavates include protists with modified mitochondria and protists with unique flagella

28.3

The SAR clade is a highly diverse group of protists defined by DNA similarities

28.4

Red algae and green algae are the closest relatives of land plants

28.5

Unikonts include protists that are closely related to fungi and animals

28.6

Protists play key roles in ecological communities

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29

Plant Diversity I: How Plants Colonized Land

29.1

Land plants evolved from green algae

29.2

Mosses and other nonvascular plants have life cycles dominated by gametophytes

29.3

Ferns and other seedless vascular plants were the first plants to grow tall

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30

Plant Diversity II: The Evolution of Seed Plants

30.1

Seeds and pollen grains are key adaptations for life on land

30.2

Gymnosperms bear naked seeds, typically on cones

30.3

The reproductive adaptations of angiosperms include flowers and fruits

30.4

Human welfare depends on seed plants

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31.1

Fungi are heterotrophs that feed by absorption

31.2

Fungi produce spores through sexual or asexual life cycles

31.3

The ancestor of fungi was an aquatic, single-celled, flagellated protist

31.4

Fungi have radiated into a diverse set of lineages

31.5

Fungi play key roles in nutrient cycling, ecological interactions, and human welfare

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32

An Overview of Animal Diversity

32.1

Animals are multicellular, heterotrophic eukaryotes with tissues that develop from embryonic layers

32.2

The history of animals spans more than half a billion years

32.3

Animals can be characterized by body plans

32.4

Views of animal phylogeny continue to be shaped by new molecular and morphological data

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33

An Introduction to Invertebrates

33.1

Sponges are basal animals that lack true tissues

33.2

Cnidarians are an ancient phylum of eumetazoans

33.3

Lophotrochozoans, a clade identified by molecular data, have the widest range of animal body forms

33.4

Ecdysozoans are the most species-rich animal group

33.5

Echinoderms and chordates are deuterostomes

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34

The Origin and Evolution of Vertebrates

34.1

Chordates have a notochord and a dorsal, hollow nerve cord

34.2

Vertebrates are chordates that have a backbone

34.3

Gnathostomes are vertebrates that have jaws

34.4

Tetrapods are gnathostomes that have limbs

34.5

Amniotes are tetrapods that have a terrestrially adapted egg

34.6

Mammals are amniotes that have hair and produce milk

34.7

Humans are mammals that have a large brain and bipedal locomotion

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35

Plant Structure, Growth, and Development

35.1

Plants have a hierarchical organization consisting of organs, tissues, and cells

35.2

Different meristems generate new cells for primary and secondary growth

35.3

Primary growth lengthens roots and shoots

35.4

Secondary growth increases the diameter of stems and roots in woody plants

35.5

Growth, morphogenesis, and cell differentiation produce the plant body

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36

Resource Acquisition and Transport in Vascular Plants

36.1

Adaptations for acquiring resources were key steps in the evolution of vascular plants

36.2

Different mechanisms transport substances over short or long distances

36.3

Transpiration drives the transport of water and minerals from roots to shoots via the xylem

36.4

The rate of transpiration is regulated by stomata

36.5

Sugars are transported from sources to sinks via the phloem

36.6

The symplast is highly dynamic

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37

Soil and Plant Nutrition

37.1

Soil contains a living, complex ecosystem

37.2

Plants require essential elements to complete their life cycle

37.3

Plant nutrition often involves relationships with other organisms

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38

Angiosperm Reproduction and Biotechnology

38.1

Flowers, double fertilization, and fruits are key features of the angiosperm life cycle

38.2

Flowering plants reproduce sexually, asexually, or both

38.3

People modify crops by breeding and genetic engineering

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39

Plant Responses to Internal and External Signals

39.1

Signal transduction pathways link signal reception to response

39.2

Plant hormones help coordinate growth, development, and responses to stimuli

39.3

Responses to light are critical for plant success

39.4

Plants respond to a wide variety of stimuli other than light

39.5

Plants respond to attacks by pathogens and herbivores

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40

Basic Principles of Animal Form and Function

40.1

Animal form and function are correlated at all levels of organization

40.2

Feedback control maintains the internal environment in many animals

40.3

Homeostatic processes for thermoregulation involve form, function, and behavior

40.4

Energy requirements are related to animal size, activity, and environment

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41

Animal Form and Function

41.1

An animals diet must supply chemical energy, organic molecules, and essential nutrients

41.2

The main stages of food processing are ingestion, digestion, absorption, and elimination

41.3

Organs specialized for sequential stages of food processing form the mammalian digestive system

41.4

Evolutionary adaptations of vertebrate digestive systems correlate with diet

41.5

Feedback circuits regulate digestion, energy storage, and appetite

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42

Circulation and Gas Exchange

42.1

Circulatory systems link exchange surfaces with cells throughout the body

42.2

Coordinated cycles of heart contraction drive double circulation in mammals

42.3

Patterns of blood pressure and flow reflect the structure and arrangement of blood vessels

42.4

Blood components function in exchange, transport, and defense

42.5

Gas exchange occurs across specialized respiratory surfaces

42.6

Breathing ventilates the lungs

42.7

Adaptations for gas exchange include pigments that bind and transport gases

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43

The Immune System

43.1

In innate immunity, recognition and response rely on traits common to groups of pathogens

43.2

In adaptive immunity, receptors provide pathogen-specific recognition

43.3

Adaptive immunity defends against infection of body fluids and body cells

43.4

Disruptions in immune system function can elicit or exacerbate disease

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44

Osmoregulation and Excretion

44.1

Osmoregulation balances the uptake and loss of water and solutes

44.2

An animals nitrogenous wastes reflect its phylogeny and habitat

44.3

Diverse excretory systems are variations on a tubular theme

44.4

The nephron is organized for stepwise processing of blood filtrate

44.5

Hormonal circuits link kidney function, water balance, and blood pressure

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45

Hormones and the Endocrine System

45.1

Hormones and other signaling molecules bind to target receptors, triggering specific response pathways

45.2

Feedback regulation and coordination with the nervous system are common in endocrine signaling

45.3

Endocrine glands respond to diverse stimuli in regulating homeostasis, development, and behavior

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46

Animal Reproduction

46.1

Both asexual and sexual reproduction occur in the animal kingdom

46.2

Fertilization depends on mechanisms that bring together sperm and eggs of the same species

46.3

Reproductive organs produce and transport gametes

46.4

The interplay of tropic and sex hormones regulates mammalian reproduction

46.5

In placental mammals, an embryo develops fully within the mothers uterus

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47

Animal Development

47.1

Fertilization and cleavage initiate embryonic development

47.2

Morphogenesis in animals involves specific changes in cell shape, position, and survival

47.3

Cytoplasmic determinants and inductive signals contribute to cell fate specification

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48

Neurons, Synapses, and Signaling

48.1

Neuron structure and organization reflect function in information transfer

48.2

Ion pumps and ion channels establish the resting potential of a neuron

48.3

Action potentials are the signals conducted by axons

48.4

Neurons communicate with other cells at synapses

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49

Nervous Systems

49.1

Nervous systems consist of circuits of neurons and supporting cells

49.2

The vertebrate brain is regionally specialized

49.3

The cerebral cortex controls voluntary movement and cognitive functions

49.4

Changes in synaptic connections underlie memory and learning

49.5

Many nervous system disorders can be explained in molecular terms

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50

Sensory and Motor Mechanisms

50.1

Sensory receptors transduce stimulus energy and transmit signals to the central nervous system

50.2

The mechanoreceptors responsible for hearing and equilibrium detect moving fluid or settling particles

50.3

The diverse visual receptors of animals depend on lightabsorbing pigments

50.4

The senses of taste and smell rely on similar sets of sensory receptors

50.5

The physical interaction of protein filaments is required for muscle function

50.6

Skeletal systems transform muscle contraction into locomotion

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51

Animal Behavior

51.1

Discrete sensory inputs can stimulate both simple and complex behaviors

51.2

Learning establishes specific links between experience and behavior

51.3

Selection for individual survival and reproductive success can explain diverse behaviors

51.4

Genetic analyses and the concept of inclusive fitness provide a basis for studying the evolution of behavior

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52

An Introduction to Ecology and the Biosphere

52.1

Earths climate varies by latitude and season and is changing rapidly

52.2

The structure and distribution of terrestrial biomes are controlled by climate and disturbance

52.3

Aquatic biomes are diverse and dynamic systems that cover most of Earth

52.4

Interactions between organisms and the environment limit the distribution of species

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53

Population Ecology

53.1

Biological processes influence population density, dispersion, and demographics

53.2

The exponential model describes population growth in an idealized, unlimited environment

53.3

The logistic model describes how a population grows more slowly as it nears its carrying capacity

53.4

Life history traits are products of natural selection

53.5

Many factors that regulate population growth are density dependent

53.6

The human population is no longer growing exponentially but is still increasing rapidly

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54

Community Ecology

54.1

Community interactions are classified by whether they help, harm, or have no effect on the species involved

54.2

Diversity and trophic structure characterize biological communities

54.3

Disturbance influences species diversity and composition

54.4

Biogeographic factors affect community diversity

54.5

Pathogens alter community structure locally and globally

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55

Ecosystems and Restoration Ecology

55.1

Physical laws govern energy flow and chemical cycling in ecosystems

55.2

Energy and other limiting factors control primary production in ecosystems

55.3

Energy transfer between trophic levels is typically only 10% efficient

55.4

Biological and geochemical processes cycle nutrients and water in ecosystems

55.5

Restoration ecologists return degraded ecosystems to a more natural state

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56

Conservation Biology and Global Change

56.1

Human activities threaten Earths biodiversity

56.2

Population conservation focuses on population size, genetic diversity, and critical habitat

56.3

Landscape and regional conservation help sustain biodiversity

56.4

Earth is changing rapidly as a result of human actions

56.5

Sustainable development can improve human lives while conserving biodiversity