Decorative notebook illustration

AP Biology

Study Notes

1. Chemistry of Life

1.1.1 Water Molecules, Polarity, and Hydrogen Bonds

1.1.2 Thermal Properties of Water and Homeostasis

1.1.3 Evaporative Cooling and Heat of Vaporization

1.1.4 Cohesion, Adhesion, and Surface Tension

1.1.5 Biological Importance of Water’s Properties

1.2.1 Essential Elements and Biological Macromolecules

1.2.2 Carbon, Hydrogen, and Oxygen in Macromolecules

1.2.3 Nitrogen, Phosphorus, Sulfur, and Macromolecule Structure

1.3.1 Building and Breaking Biological Polymers

1.3.2 Dehydration Synthesis and Polymerization Mechanisms

1.3.3 Hydrolysis and Breakdown of Macromolecules

1.4.1 Monosaccharides and Formation of Polysaccharides

1.4.2 Linear and Branched Carbohydrate Polymers

1.4.3 Structural and Functional Roles of Major Polysaccharides

1.5.1 Lipid Structure, Nonpolarity, and Hydrophobicity

1.5.2 Saturated versus Unsaturated Fatty Acids

1.5.3 Degree of Unsaturation and Lipid Fluidity

1.5.4 Fats: Energy Storage and Insulation

1.5.5 Steroids, Cholesterol, and Phospholipids in Membranes

1.6.1 Nucleotides as Monomers of Nucleic Acids

1.6.2 DNA and RNA as Information Molecules

1.6.3 Directionality and Synthesis of Nucleic Acid Strands

1.6.4 DNA Double Helix and Base Pairing

1.6.5 Structural Differences Between DNA and RNA

1.7.1 Amino Acids and Peptide Bond Formation

1.7.2 Amino Acid Structure and R Groups

1.7.3 Primary Structure and Amino Acid Sequence

1.7.4 Secondary Structure: Alpha-Helices and Beta-Sheets

1.7.5 Tertiary Structure and Stabilizing Interactions

1.7.6 Quaternary Structure and Protein Function

1.1.1 Water Molecules, Polarity, and Hydrogen Bonds

1.1.2 Thermal Properties of Water and Homeostasis

1.1.3 Evaporative Cooling and Heat of Vaporization

1.1.4 Cohesion, Adhesion, and Surface Tension

1.1.5 Biological Importance of Water’s Properties

1.2.1 Essential Elements and Biological Macromolecules

1.2.2 Carbon, Hydrogen, and Oxygen in Macromolecules

1.2.3 Nitrogen, Phosphorus, Sulfur, and Macromolecule Structure

1.3.1 Building and Breaking Biological Polymers

1.3.2 Dehydration Synthesis and Polymerization Mechanisms

1.3.3 Hydrolysis and Breakdown of Macromolecules

1.4.1 Monosaccharides and Formation of Polysaccharides

1.4.2 Linear and Branched Carbohydrate Polymers

1.4.3 Structural and Functional Roles of Major Polysaccharides

1.5.1 Lipid Structure, Nonpolarity, and Hydrophobicity

1.5.2 Saturated versus Unsaturated Fatty Acids

1.5.3 Degree of Unsaturation and Lipid Fluidity

1.5.4 Fats: Energy Storage and Insulation

1.5.5 Steroids, Cholesterol, and Phospholipids in Membranes

1.6.1 Nucleotides as Monomers of Nucleic Acids

1.6.2 DNA and RNA as Information Molecules

1.6.3 Directionality and Synthesis of Nucleic Acid Strands

1.6.4 DNA Double Helix and Base Pairing

1.6.5 Structural Differences Between DNA and RNA

1.7.1 Amino Acids and Peptide Bond Formation

1.7.2 Amino Acid Structure and R Groups

1.7.3 Primary Structure and Amino Acid Sequence

1.7.4 Secondary Structure: Alpha-Helices and Beta-Sheets

1.7.5 Tertiary Structure and Stabilizing Interactions

1.7.6 Quaternary Structure and Protein Function

2. Cells

2.1.1 Ribosomes and Protein Synthesis

2.1.2 The Endomembrane System Overview

2.1.3 Endoplasmic Reticulum Structure and Roles

2.1.4 Golgi Complex and Protein Modification

2.1.5 Mitochondria and ATP Production

2.1.6 Lysosomes Vacuoles and Chloroplasts

2.2.1 Surface Area to Volume Ratio Basics

2.2.2 Cell Size Limits and Material Exchange

2.2.3 Membrane Folds and Surface Area Adaptations

2.2.4 Organism Size Heat Exchange and Metabolism

2.3.1 Phospholipid Bilayer Structure

2.3.2 Membrane Proteins and Their Orientation

2.3.3 The Fluid Mosaic Model Components

2.3.4 Membrane Components and Internal Environment

2.4.1 Selective Permeability and Hydrophobic Interior

2.4.2 Diffusion of Gases and Transport Proteins

2.4.3 Limits on Ion and Polar Molecule Movement

2.4.4 Cell Walls Structure and Permeability

2.5.1 Concentration Gradients and Membrane Permeability

2.5.2 Passive Transport and Diffusion

2.5.3 Active Transport and Energy Use

2.5.4 Endocytosis and Vesicle Formation

2.5.5 Exocytosis and Bulk Secretion

2.6.1 Channel Proteins and Ion Movement

2.6.2 Membrane Polarization and Electrochemical Gradients

2.6.3 Carrier Proteins and Aquaporins

2.7.1 Tonicity and Types of Solutions

2.7.2 Osmosis and Water Potential

2.7.3 Osmoregulation and Homeostasis

2.7.4 Solute Potential Equations and Examples

2.8.1 Energy Use in Membrane Transport

2.8.2 Coordinating Transport for Homeostasis

2.8.3 Transport Mechanisms in Whole Organisms

2.9.1 Membrane Bound Organelles and Compartments

2.9.2 Reducing Competing Reactions by Compartmentalization

2.9.3 Surface Area Increases and Reaction Efficiency

2.10.1 Endosymbiosis and Organelle Origins

2.10.2 Internal Organization in Prokaryotes

2.10.3 Internal Membranes in Eukaryotes

2.1.1 Ribosomes and Protein Synthesis

2.1.2 The Endomembrane System Overview

2.1.3 Endoplasmic Reticulum Structure and Roles

2.1.4 Golgi Complex and Protein Modification

2.1.5 Mitochondria and ATP Production

2.1.6 Lysosomes Vacuoles and Chloroplasts

2.2.1 Surface Area to Volume Ratio Basics

2.2.2 Cell Size Limits and Material Exchange

2.2.3 Membrane Folds and Surface Area Adaptations

2.2.4 Organism Size Heat Exchange and Metabolism

2.3.1 Phospholipid Bilayer Structure

2.3.2 Membrane Proteins and Their Orientation

2.3.3 The Fluid Mosaic Model Components

2.3.4 Membrane Components and Internal Environment

2.4.1 Selective Permeability and Hydrophobic Interior

2.4.2 Diffusion of Gases and Transport Proteins

2.4.3 Limits on Ion and Polar Molecule Movement

2.4.4 Cell Walls Structure and Permeability

2.5.1 Concentration Gradients and Membrane Permeability

2.5.2 Passive Transport and Diffusion

2.5.3 Active Transport and Energy Use

2.5.4 Endocytosis and Vesicle Formation

2.5.5 Exocytosis and Bulk Secretion

2.6.1 Channel Proteins and Ion Movement

2.6.2 Membrane Polarization and Electrochemical Gradients

2.6.3 Carrier Proteins and Aquaporins

2.7.1 Tonicity and Types of Solutions

2.7.2 Osmosis and Water Potential

2.7.3 Osmoregulation and Homeostasis

2.7.4 Solute Potential Equations and Examples

2.8.1 Energy Use in Membrane Transport

2.8.2 Coordinating Transport for Homeostasis

2.8.3 Transport Mechanisms in Whole Organisms

2.9.1 Membrane Bound Organelles and Compartments

2.9.2 Reducing Competing Reactions by Compartmentalization

2.9.3 Surface Area Increases and Reaction Efficiency

2.10.1 Endosymbiosis and Organelle Origins

2.10.2 Internal Organization in Prokaryotes

2.10.3 Internal Membranes in Eukaryotes

3. Cellular Energetics

3.1.1 What Are Enzymes and How Do They Work?

3.1.2 Enzyme Structure and Regulation of Reactions

3.1.3 Active Sites, Substrates, and Enzyme Specificity

3.2.1 Structural Changes and Loss of Enzyme Function

3.2.2 Temperature, pH, and Enzyme Denaturation

3.2.3 Reversible Denaturation and Enzyme Recovery

3.2.4 Substrate and Product Concentrations

3.2.5 Temperature Effects on Reaction Rate

3.2.6 Competitive and Noncompetitive Inhibition

3.3.1 Energy Requirements of Living Systems

3.3.2 Thermodynamics and Biological Order

3.3.3 Energy Coupling in Cellular Processes

3.3.4 Sequential Metabolic Pathways

3.3.5 Conserved Metabolic Pathways and Common Ancestry

3.4.1 Overview of Photosynthesis

3.4.2 Evolution and Significance of Photosynthesis

3.4.3 Chloroplast Structure: Stroma, Thylakoids, and Grana

3.4.4 Light Reactions and Photosystems I and II

3.4.5 Electron Transport and Proton Gradients in Chloroplasts

3.4.6 Chemiosmosis and Photophosphorylation

3.4.7 Calvin Cycle and Carbohydrate Production

3.5.1 Overview of Cellular Respiration and ATP Production

3.5.2 Mitochondrial Structure and Its Role in Respiration

3.5.3 Glycolysis: Splitting Glucose in the Cytosol

3.5.4 Pyruvate Oxidation and the Krebs Cycle

3.5.5 Electron Transport Chain and Proton Gradient

3.5.6 Oxidative Phosphorylation and Heat Production

3.5.7 Fermentation in the Absence of Oxygen

3.5.8 Respiration in Prokaryotes and Eukaryotes

3.1.1 What Are Enzymes and How Do They Work?

3.1.2 Enzyme Structure and Regulation of Reactions

3.1.3 Active Sites, Substrates, and Enzyme Specificity

3.2.1 Structural Changes and Loss of Enzyme Function

3.2.2 Temperature, pH, and Enzyme Denaturation

3.2.3 Reversible Denaturation and Enzyme Recovery

3.2.4 Substrate and Product Concentrations

3.2.5 Temperature Effects on Reaction Rate

3.2.6 Competitive and Noncompetitive Inhibition

3.3.1 Energy Requirements of Living Systems

3.3.2 Thermodynamics and Biological Order

3.3.3 Energy Coupling in Cellular Processes

3.3.4 Sequential Metabolic Pathways

3.3.5 Conserved Metabolic Pathways and Common Ancestry

3.4.1 Overview of Photosynthesis

3.4.2 Evolution and Significance of Photosynthesis

3.4.3 Chloroplast Structure: Stroma, Thylakoids, and Grana

3.4.4 Light Reactions and Photosystems I and II

3.4.5 Electron Transport and Proton Gradients in Chloroplasts

3.4.6 Chemiosmosis and Photophosphorylation

3.4.7 Calvin Cycle and Carbohydrate Production

3.5.1 Overview of Cellular Respiration and ATP Production

3.5.2 Mitochondrial Structure and Its Role in Respiration

3.5.3 Glycolysis: Splitting Glucose in the Cytosol

3.5.4 Pyruvate Oxidation and the Krebs Cycle

3.5.5 Electron Transport Chain and Proton Gradient

3.5.6 Oxidative Phosphorylation and Heat Production

3.5.7 Fermentation in the Absence of Oxygen

3.5.8 Respiration in Prokaryotes and Eukaryotes

4. Cell Communication and Cell Cycle

4.1.1 Modes of cell communication

4.1.2 Direct contact between neighboring cells

4.1.3 Short-distance signaling and local regulators

4.1.4 Long-distance hormonal signaling

4.2.1 Components of a signal transduction pathway

4.2.2 Ligands as chemical messengers

4.2.3 Receptors and ligand-binding domains

4.2.4 G protein–coupled receptors as examples

4.2.5 Phosphorylation cascades and protein modifications

4.2.6 Signal amplification and second messengers

4.2.7 Hormones and ligand-gated ion channels

4.3.1 Cellular responses to signaling pathways

4.3.2 Apoptosis as a signaling outcome

4.3.3 Effects of receptor mutations on signaling

4.3.4 Mutations in downstream pathway components

4.3.5 Chemical disruption of signal transduction pathways

4.3.6 Case studies of altered signaling and disease

4.4.1 Homeostasis and feedback mechanisms

4.4.2 Principles of negative feedback

4.4.3 Levels of negative feedback regulation

4.4.4 Principles of positive feedback

4.4.5 Biological examples of feedback loops

4.5.1 Overview of the eukaryotic cell cycle

4.5.2 Interphase: G1 phase and cell growth

4.5.3 Interphase: S phase and DNA replication

4.5.4 Interphase: G2 phase and preparation for mitosis

4.5.5 G0 phase and nondividing cells

4.5.6 Roles of mitosis in organisms

4.5.7 Prophase and metaphase in mitosis

4.5.8 Anaphase and telophase in mitosis

4.5.9 Cytokinesis and formation of daughter cells

4.6.1 Cell cycle checkpoints and regulation

4.6.2 Roles of cyclins and cyclin-dependent kinases

4.6.3 Checkpoint failure and uncontrolled cell division

4.6.4 Cell cycle disruptions and cancer

4.6.5 Cell cycle disruptions and apoptosis

4.1.1 Modes of cell communication

4.1.2 Direct contact between neighboring cells

4.1.3 Short-distance signaling and local regulators

4.1.4 Long-distance hormonal signaling

4.2.1 Components of a signal transduction pathway

4.2.2 Ligands as chemical messengers

4.2.3 Receptors and ligand-binding domains

4.2.4 G protein–coupled receptors as examples

4.2.5 Phosphorylation cascades and protein modifications

4.2.6 Signal amplification and second messengers

4.2.7 Hormones and ligand-gated ion channels

4.3.1 Cellular responses to signaling pathways

4.3.2 Apoptosis as a signaling outcome

4.3.3 Effects of receptor mutations on signaling

4.3.4 Mutations in downstream pathway components

4.3.5 Chemical disruption of signal transduction pathways

4.3.6 Case studies of altered signaling and disease

4.4.1 Homeostasis and feedback mechanisms

4.4.2 Principles of negative feedback

4.4.3 Levels of negative feedback regulation

4.4.4 Principles of positive feedback

4.4.5 Biological examples of feedback loops

4.5.1 Overview of the eukaryotic cell cycle

4.5.2 Interphase: G1 phase and cell growth

4.5.3 Interphase: S phase and DNA replication

4.5.4 Interphase: G2 phase and preparation for mitosis

4.5.5 G0 phase and nondividing cells

4.5.6 Roles of mitosis in organisms

4.5.7 Prophase and metaphase in mitosis

4.5.8 Anaphase and telophase in mitosis

4.5.9 Cytokinesis and formation of daughter cells

4.6.1 Cell cycle checkpoints and regulation

4.6.2 Roles of cyclins and cyclin-dependent kinases

4.6.3 Checkpoint failure and uncontrolled cell division

4.6.4 Cell cycle disruptions and cancer

4.6.5 Cell cycle disruptions and apoptosis

5. Heredity

5.1.1 Overview of meiosis and chromosome transmission

5.1.2 Prophase I: homologous chromosome pairing and synapsis

5.1.3 Metaphase I to telophase I and cytokinesis

5.1.4 Prophase II and metaphase II in meiosis

5.1.5 Anaphase II, telophase II, and formation of four gametes

5.1.6 Comparing mitosis and meiosis: phases and outcomes

5.2.1 How meiosis generates genetic diversity

5.2.2 Independent assortment of chromosomes in meiosis

5.2.3 Nondisjunction and errors in chromosome separation

5.2.4 Crossing over and recombination in prophase I

5.2.5 Sexual reproduction and sources of variation

5.3.1 Mendel’s laws of segregation and independent assortment

5.3.2 Fertilization and formation of new allele combinations

5.3.3 Probability rules in single-gene inheritance

5.3.4 Monohybrid crosses and predicting offspring ratios

5.3.5 Dihybrid crosses and independent assortment

5.3.6 Test crosses and determining unknown genotypes

5.3.7 Genotype versus phenotype

5.3.8 Patterns of autosomal and sex-linked inheritance

5.3.9 Using pedigrees and probability equations

5.4.1 When traits deviate from Mendelian ratios

5.4.2 Genetic linkage and gene mapping

5.4.3 Codominance and expression of both alleles

5.4.4 Incomplete dominance and blended phenotypes

5.4.5 Sex-linked traits and inheritance patterns

5.4.6 Pleiotropy: one gene, many effects

5.4.7 Organelle DNA and non-nuclear inheritance

5.4.8 Maternal inheritance in animals and plants

5.5.1 Phenotypic plasticity and environmental influence

5.5.2 Human traits influenced by environment

5.5.3 Environmental effects on plant and animal coloration

5.5.4 Temperature and environmental sex determination

5.1.1 Overview of meiosis and chromosome transmission

5.1.2 Prophase I: homologous chromosome pairing and synapsis

5.1.3 Metaphase I to telophase I and cytokinesis

5.1.4 Prophase II and metaphase II in meiosis

5.1.5 Anaphase II, telophase II, and formation of four gametes

5.1.6 Comparing mitosis and meiosis: phases and outcomes

5.2.1 How meiosis generates genetic diversity

5.2.2 Independent assortment of chromosomes in meiosis

5.2.3 Nondisjunction and errors in chromosome separation

5.2.4 Crossing over and recombination in prophase I

5.2.5 Sexual reproduction and sources of variation

5.3.1 Mendel’s laws of segregation and independent assortment

5.3.2 Fertilization and formation of new allele combinations

5.3.3 Probability rules in single-gene inheritance

5.3.4 Monohybrid crosses and predicting offspring ratios

5.3.5 Dihybrid crosses and independent assortment

5.3.6 Test crosses and determining unknown genotypes

5.3.7 Genotype versus phenotype

5.3.8 Patterns of autosomal and sex-linked inheritance

5.3.9 Using pedigrees and probability equations

5.4.1 When traits deviate from Mendelian ratios

5.4.2 Genetic linkage and gene mapping

5.4.3 Codominance and expression of both alleles

5.4.4 Incomplete dominance and blended phenotypes

5.4.5 Sex-linked traits and inheritance patterns

5.4.6 Pleiotropy: one gene, many effects

5.4.7 Organelle DNA and non-nuclear inheritance

5.4.8 Maternal inheritance in animals and plants

5.5.1 Phenotypic plasticity and environmental influence

5.5.2 Human traits influenced by environment

5.5.3 Environmental effects on plant and animal coloration

5.5.4 Temperature and environmental sex determination

6. Gene Expression and Regulation

6.1.1 Genetic information in DNA and RNA

6.1.2 Chromosomes in prokaryotes and eukaryotes

6.1.3 Plasmids in prokaryotes and eukaryotes

6.1.4 Base pairing and nucleotide categories

6.2.1 Overview and directionality of DNA replication

6.2.2 Roles of helicase and topoisomerase

6.2.3 RNA primers and DNA polymerase

6.2.4 Leading and lagging strand synthesis

6.2.5 Role of ligase in DNA replication

6.3.1 Types of RNA and overall functions

6.3.2 Messenger RNA and information flow

6.3.3 Transfer RNA and ribosomal RNA roles

6.3.4 Transcription initiation and elongation

6.3.5 Directionality of RNA synthesis

6.3.6 Eukaryotic mRNA processing and alternative splicing

6.4.1 Ribosomes and sites of translation

6.4.2 Coupling of transcription and translation in prokaryotes

6.4.3 Initiation of translation and the genetic code

6.4.4 Codons and universality of the genetic code

6.4.5 Role of tRNA during translation

6.4.6 Elongation and termination of translation

6.4.7 Retroviruses and reverse transcriptase

6.5.1 Regulatory DNA sequences and transcription factors

6.5.2 Epigenetic modifications and gene expression

6.5.3 Gene expression and cellular phenotype

6.5.4 Tissue-specific proteins and cell differentiation

6.5.5 Developmental gene regulation

6.5.6 Coordinated regulation of gene groups

6.6.1 Promoters, enhancers, and transcription initiation

6.6.2 Negative regulation of transcription

6.6.3 Differential gene expression and cell specialization

6.6.4 Small RNAs in gene regulation

6.7.1 Definition of mutations and their phenotypic effects

6.7.2 Beneficial, harmful, and neutral mutations

6.7.3 Types of gene-level mutations

6.7.4 Sources of random mutations

6.7.5 Mutations as a source of genetic variation

6.7.6 Chromosomal errors and aneuploidy

6.7.7 Horizontal gene transfer and recombination

6.8.1 Overview of genetic engineering techniques

6.8.2 Gel electrophoresis and DNA separation

6.8.3 Polymerase chain reaction (PCR)

6.8.4 Transformation and genetically modified organisms

6.8.5 DNA sequencing and DNA fingerprinting

6.1.1 Genetic information in DNA and RNA

6.1.2 Chromosomes in prokaryotes and eukaryotes

6.1.3 Plasmids in prokaryotes and eukaryotes

6.1.4 Base pairing and nucleotide categories

6.2.1 Overview and directionality of DNA replication

6.2.2 Roles of helicase and topoisomerase

6.2.3 RNA primers and DNA polymerase

6.2.4 Leading and lagging strand synthesis

6.2.5 Role of ligase in DNA replication

6.3.1 Types of RNA and overall functions

6.3.2 Messenger RNA and information flow

6.3.3 Transfer RNA and ribosomal RNA roles

6.3.4 Transcription initiation and elongation

6.3.5 Directionality of RNA synthesis

6.3.6 Eukaryotic mRNA processing and alternative splicing

6.4.1 Ribosomes and sites of translation

6.4.2 Coupling of transcription and translation in prokaryotes

6.4.3 Initiation of translation and the genetic code

6.4.4 Codons and universality of the genetic code

6.4.5 Role of tRNA during translation

6.4.6 Elongation and termination of translation

6.4.7 Retroviruses and reverse transcriptase

6.5.1 Regulatory DNA sequences and transcription factors

6.5.2 Epigenetic modifications and gene expression

6.5.3 Gene expression and cellular phenotype

6.5.4 Tissue-specific proteins and cell differentiation

6.5.5 Developmental gene regulation

6.5.6 Coordinated regulation of gene groups

6.6.1 Promoters, enhancers, and transcription initiation

6.6.2 Negative regulation of transcription

6.6.3 Differential gene expression and cell specialization

6.6.4 Small RNAs in gene regulation

6.7.1 Definition of mutations and their phenotypic effects

6.7.2 Beneficial, harmful, and neutral mutations

6.7.3 Types of gene-level mutations

6.7.4 Sources of random mutations

6.7.5 Mutations as a source of genetic variation

6.7.6 Chromosomal errors and aneuploidy

6.7.7 Horizontal gene transfer and recombination

6.8.1 Overview of genetic engineering techniques

6.8.2 Gel electrophoresis and DNA separation

6.8.3 Polymerase chain reaction (PCR)

6.8.4 Transformation and genetically modified organisms

6.8.5 DNA sequencing and DNA fingerprinting

7. Natural Selection

7.1.1 Natural selection as a mechanism of evolution

7.1.2 Darwin’s theory: competition and differential survival

7.1.3 Evolutionary fitness and reproductive success

7.1.4 Changing environments and shifting selection pressures

7.2.1 Phenotypic variation as raw material for natural selection

7.2.2 Environmental change and selective pressures

7.2.3 Phenotypic variation, fitness, and specific environments

7.2.4 Molecular variation inside cells and organism fitness

7.3.1 What is artificial selection?

7.3.2 Human-directed breeding in plants and animals

7.3.3 Comparing artificial selection with natural selection

7.4.1 Random processes and evolution

7.4.2 Mutation as a source of new variation

7.4.3 Genetic drift, bottlenecks, and founder effects

7.4.4 Gene flow and migration between populations

7.4.5 Random processes changing allele frequencies

7.4.6 Allele frequency changes as evidence for evolution

7.5.1 The Hardy–Weinberg model and assumptions

7.5.2 Large population size and no migration

7.5.3 No mutation and random mating

7.5.4 No natural selection and the null hypothesis

7.5.5 Calculating allele and genotype frequencies

7.6.1 Multiple scientific disciplines supporting evolution

7.6.2 Dating fossils and interpreting the fossil record

7.6.3 Geological and geographical patterns of evolution

7.6.4 Morphological homologies and vestigial structures

7.6.5 Molecular and genetic evidence from DNA and proteins

7.6.6 Extant and extinct species informing evolutionary relationships

7.7.1 Evidence for common ancestry among eukaryotes

7.7.2 Membrane-bound organelles as evidence of common ancestry

7.7.3 Linear chromosomes, introns, and evolutionary history

7.8.1 Evolution as an ongoing process

7.8.2 Genomic change and the fossil record

7.8.3 Evolution of resistance to drugs and chemicals

7.8.4 Pathogens, rapid evolution, and emerging diseases

7.9.1 Phylogenetic trees and cladograms as hypotheses

7.9.2 Time and change in trees versus cladograms

7.9.3 Gained and lost traits in constructing phylogenies

7.9.4 Outgroups and shared derived characters

7.9.5 Molecular data in phylogenetic analysis

7.9.6 Testing and revising phylogenetic hypotheses

7.10.1 The biological species concept

7.10.2 Reproductive isolation and new species formation

7.10.3 Sympatric and allopatric speciation

7.10.4 Prezygotic and postzygotic reproductive barriers

7.10.5 Gradualism and punctuated equilibrium

7.10.6 Divergent evolution and adaptive radiation

7.10.7 Convergent evolution and similar adaptations

7.11.1 Genetic variation and population dynamics

7.11.2 Genetic diversity and resilience to environmental change

7.11.3 Low genetic diversity, decline, and extinction risk

7.11.4 Context-dependent effects of adaptive alleles

7.12.1 Scientific models for the origin of life

7.12.2 Evidence supporting origin-of-life models

7.12.3 Evaluating evidence for the origin of life

7.12.4 Assumptions of the RNA world hypothesis

7.1.1 Natural selection as a mechanism of evolution

7.1.2 Darwin’s theory: competition and differential survival

7.1.3 Evolutionary fitness and reproductive success

7.1.4 Changing environments and shifting selection pressures

7.2.1 Phenotypic variation as raw material for natural selection

7.2.2 Environmental change and selective pressures

7.2.3 Phenotypic variation, fitness, and specific environments

7.2.4 Molecular variation inside cells and organism fitness

7.3.1 What is artificial selection?

7.3.2 Human-directed breeding in plants and animals

7.3.3 Comparing artificial selection with natural selection

7.4.1 Random processes and evolution

7.4.2 Mutation as a source of new variation

7.4.3 Genetic drift, bottlenecks, and founder effects

7.4.4 Gene flow and migration between populations

7.4.5 Random processes changing allele frequencies

7.4.6 Allele frequency changes as evidence for evolution

7.5.1 The Hardy–Weinberg model and assumptions

7.5.2 Large population size and no migration

7.5.3 No mutation and random mating

7.5.4 No natural selection and the null hypothesis

7.5.5 Calculating allele and genotype frequencies

7.6.1 Multiple scientific disciplines supporting evolution

7.6.2 Dating fossils and interpreting the fossil record

7.6.3 Geological and geographical patterns of evolution

7.6.4 Morphological homologies and vestigial structures

7.6.5 Molecular and genetic evidence from DNA and proteins

7.6.6 Extant and extinct species informing evolutionary relationships

7.7.1 Evidence for common ancestry among eukaryotes

7.7.2 Membrane-bound organelles as evidence of common ancestry

7.7.3 Linear chromosomes, introns, and evolutionary history

7.8.1 Evolution as an ongoing process

7.8.2 Genomic change and the fossil record

7.8.3 Evolution of resistance to drugs and chemicals

7.8.4 Pathogens, rapid evolution, and emerging diseases

7.9.1 Phylogenetic trees and cladograms as hypotheses

7.9.2 Time and change in trees versus cladograms

7.9.3 Gained and lost traits in constructing phylogenies

7.9.4 Outgroups and shared derived characters

7.9.5 Molecular data in phylogenetic analysis

7.9.6 Testing and revising phylogenetic hypotheses

7.10.1 The biological species concept

7.10.2 Reproductive isolation and new species formation

7.10.3 Sympatric and allopatric speciation

7.10.4 Prezygotic and postzygotic reproductive barriers

7.10.5 Gradualism and punctuated equilibrium

7.10.6 Divergent evolution and adaptive radiation

7.10.7 Convergent evolution and similar adaptations

7.11.1 Genetic variation and population dynamics

7.11.2 Genetic diversity and resilience to environmental change

7.11.3 Low genetic diversity, decline, and extinction risk

7.11.4 Context-dependent effects of adaptive alleles

7.12.1 Scientific models for the origin of life

7.12.2 Evidence supporting origin-of-life models

7.12.3 Evaluating evidence for the origin of life

7.12.4 Assumptions of the RNA world hypothesis

8. Ecology

8.1.1 Behavioral and physiological responses to environmental change

8.1.2 Information exchange and behavioral responses

8.1.3 Communication mechanisms between organisms

8.1.4 Signaling behavior and reproductive success

8.1.5 Behavioral responses, fitness, and natural selection

8.1.6 Cooperative behavior and population success

8.2.1 Energy use for organization, growth, and homeostasis

8.2.2 Endotherms, ectotherms, and thermoregulation strategies

8.2.3 Energy balance, growth, and survival

8.2.4 Reproductive strategies and energy availability

8.2.5 Energy flow and matter cycling through trophic levels

8.2.6 Phosphorus cycle and nutrient movement

8.2.7 Energy availability and population size

8.2.8 Energy changes and ecosystem disruption

8.2.9 Autotrophs, heterotrophs, and ecosystem energy flow

8.3.1 Defining populations and their interactions

8.3.2 Adaptations for obtaining energy and matter

8.3.3 Factors influencing population growth dynamics

8.3.4 Population growth equations and parameters

8.3.5 Exponential growth and rmax

8.3.6 Graphing and interpreting population growth data

8.4.1 Carrying capacity and resource limitation

8.4.2 Density-dependent and density-independent factors

8.4.3 Logistic growth model and carrying capacity

8.4.4 Comparing exponential and logistic population growth

8.5.1 Community structure, species composition, and diversity

8.5.2 Measuring diversity using Simpson’s Diversity Index

8.5.3 Communities as interacting populations over time

8.5.4 Species interactions and access to energy and matter

8.5.5 Modeling positive and negative species interactions

8.5.6 Competition, predation, and symbiosis

8.5.7 Trophic cascades and niche partitioning

8.6.1 Defining biodiversity and ecosystem diversity

8.6.2 Diversity and ecosystem resilience

8.6.3 Keystone species and ecosystem stability

8.6.4 Producers and abiotic–biotic factors in diversity

8.6.5 Adding or removing ecosystem components

8.6.6 Keystone species loss and ecosystem collapse

8.7.1 Adaptations, genetic variation, and environmental change

8.7.2 Heterozygote advantage and fitness

8.7.3 Random mutation and environmental pressures

8.7.4 Invasive species and ecosystem dynamics

8.7.5 Human activities and ecosystem change

8.7.6 Geological and meteorological events

8.1.1 Behavioral and physiological responses to environmental change

8.1.2 Information exchange and behavioral responses

8.1.3 Communication mechanisms between organisms

8.1.4 Signaling behavior and reproductive success

8.1.5 Behavioral responses, fitness, and natural selection

8.1.6 Cooperative behavior and population success

8.2.1 Energy use for organization, growth, and homeostasis

8.2.2 Endotherms, ectotherms, and thermoregulation strategies

8.2.3 Energy balance, growth, and survival

8.2.4 Reproductive strategies and energy availability

8.2.5 Energy flow and matter cycling through trophic levels

8.2.6 Phosphorus cycle and nutrient movement

8.2.7 Energy availability and population size

8.2.8 Energy changes and ecosystem disruption

8.2.9 Autotrophs, heterotrophs, and ecosystem energy flow

8.3.1 Defining populations and their interactions

8.3.2 Adaptations for obtaining energy and matter

8.3.3 Factors influencing population growth dynamics

8.3.4 Population growth equations and parameters

8.3.5 Exponential growth and rmax

8.3.6 Graphing and interpreting population growth data

8.4.1 Carrying capacity and resource limitation

8.4.2 Density-dependent and density-independent factors

8.4.3 Logistic growth model and carrying capacity

8.4.4 Comparing exponential and logistic population growth

8.5.1 Community structure, species composition, and diversity

8.5.2 Measuring diversity using Simpson’s Diversity Index

8.5.3 Communities as interacting populations over time

8.5.4 Species interactions and access to energy and matter

8.5.5 Modeling positive and negative species interactions

8.5.6 Competition, predation, and symbiosis

8.5.7 Trophic cascades and niche partitioning

8.6.1 Defining biodiversity and ecosystem diversity

8.6.2 Diversity and ecosystem resilience

8.6.3 Keystone species and ecosystem stability

8.6.4 Producers and abiotic–biotic factors in diversity

8.6.5 Adding or removing ecosystem components

8.6.6 Keystone species loss and ecosystem collapse

8.7.1 Adaptations, genetic variation, and environmental change

8.7.2 Heterozygote advantage and fitness

8.7.3 Random mutation and environmental pressures

8.7.4 Invasive species and ecosystem dynamics

8.7.5 Human activities and ecosystem change

8.7.6 Geological and meteorological events

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