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***Please
Sign the Sheet Provided in Class*** |
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Thinkwell
Table of Contents |
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Chapter 1
Introduction |
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1.1 |
Unity and Diversity of Life
on Earth |
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1.1.1 |
Properties of Life |
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1.2 |
Early Perspectives in
Science |
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1.2.1 |
An Introduction to Biology |
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1.2.2 |
The Nature of Science:
The Story of Darwin |
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1.2.3 |
Early Scientific Thought |
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1.2.4 |
The Emerging Science of
Geology |
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1.3 |
An Introduction of
Evolution |
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1.3.1 |
Linnaeus, Buffon, and Lamarck |
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1.3.2 |
Darwin: The Voyage
Continues |
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1.3.3 |
Darwin: More
Observations |
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1.4 |
Evolution: The Theory
of Natural Selection |
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1.4.1 |
Darwin: The Theory of
Natural Selection |
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1.4.2 |
The Theory of Natural
Selection |
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1.4.3 |
Contrasting Lamarck and Darwin |
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1.4.4 |
Contrasting Lamarck and
Darwin, Part 2 |
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1.5 |
Fossils and Evolution |
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1.5.1 |
Fossil Formation, Dating, and
Indexing |
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1.5.2 |
The Fossil Record |
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1.5.3 |
Some Fossil Surprises |
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1.5.4 |
The Coevolution of Horses and
Plants |
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1.5.5 |
Mass Extinctions: An
Asteroid Can Ruin Your Day |
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1.6 |
Human Evolution |
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1.6.1 |
Human Evolution: What is
a Primate? |
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1.6.2 |
Human Evolution: The
Family Tree |
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1.6.3 |
Human
Evolution: The Fossil Record |
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1.7 |
Evidence for Evolution |
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1.7.1 |
Evidence for Evolution:
Biochemical Similarities |
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1.7.2 |
Evidence for Evolution:
Vestigial Structures |
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1.7.3 |
Homologous Structures |
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1.8 |
Species Concepts |
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1.8.1 |
Species Concepts |
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1.8.2 |
Speciation |
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1.8.3 |
Prezygotic Reproductive
Isolation |
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1.8.4 |
Postzygotic Reproductive
Isolation |
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1.9 |
Examples of Artificial and
Natural Selection |
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1.9.1 |
Artificial Selection in Action |
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1.9.2 |
Natural Selection in Action |
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1.10 |
The Origin of Life |
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1.10.1 |
History of Life: The
Heterotroph Hypothesis: An Overview |
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1.10.2 |
The Heterotroph Hypothesis: An
Introduction |
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1.10.3 |
The Origin of Life: Life from
Nonlife |
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1.10.4 |
The Heterotroph Hypothesis:
Protobionts |
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1.10.5 |
The Heterotroph Hypothesis:
The First Genetic Material |
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1.10.6 |
The Origin of Life: The Rest
of the Story |
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1.11 |
Classifying Life |
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1.11.1 |
The Linnaean System |
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1.11.2 |
The Linnaean System: Still
Changing |
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Chapter 2 Inorganic and
Organic Chemistry |
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2.1 |
An Introduction to Atoms |
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2.1.1 |
Atomic Structure: SPONCH and
the Atom |
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2.1.2 |
Electrons, Orbitals, and
Electron Shells |
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2.1.3 |
Ions, Ionization, and Isotopes |
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2.1.4 |
Isotopes: Unraveling
Photosynthesis |
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2.2 |
Atoms and Bonding |
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2.2.1 |
Bonding and Electronegativity |
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2.2.2 |
Ionic and Covalent Bonds |
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2.2.3 |
Polar Covalent Bonds, Hydrogen
Bonds, and Van der Waals Inter. |
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2.3 |
Properties of Water |
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2.3.1 |
Water: Hydrogen Bonding,
Solubility, and Specific Heat |
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2.3.2 |
Water: Adhesion, Cohesion, and
a Solid That Floats |
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2.3.3 |
Water: Hydrophilic and
Hydrophobic Substances |
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2.3.4 |
Dissociation of Water and the
pH Scale |
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2.3.5 |
Hemoglobin as a Buffer |
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2.4 |
Carbon Chemistry |
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2.4.1 |
Carbon Chemistry and Isomers |
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2.4.2 |
Functional Side Groups |
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2.5 |
Carbohydrates |
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2.5.1 |
Carbohydrates: Monosaccharides |
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2.5.2 |
Dehydration Synthesis and
Hydrolysis: Disaccharides |
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2.5.3 |
Polysaccharides: Energy
Storage Molecules |
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2.5.4 |
Polysaccharides: Structural
Molecules |
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2.6 |
Lipids and Nucleic Acids |
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2.6.1 |
Lipids: An Introduction |
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2.6.2 |
Saturated vs. Unsaturated Fats |
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2.6.3 |
Phospholipids, Waxes, and
Steroids |
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2.6.4 |
Nucleic Acids: An Introduction
to Genetic Material |
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2.7 |
Proteins |
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2.7.1 |
Proteins: Amino Acids and
Peptide Bond |
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2.7.2 |
Amino Acids: The R Groups |
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2.7.3 |
Primary and Secondary
Structure |
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2.7.4 |
Tertiary Structure |
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2.7.5 |
Quaternary Structure |
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2.7.6 |
Protein Structure: A Summary |
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2.8 |
Enzymes |
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2.8.1 |
Bioenergetics: The Laws of
Thermodynamics |
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2.8.2 |
Activation Energy |
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2.8.3 |
Enzyme Characteristics |
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2.9 |
Enzyme Action |
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2.9.1 |
Enzyme Action: The
Induced-Fit Model |
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2.9.2 |
Enzyme Regulation: Allosteric
Regulation |
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2.9.3 |
Feedback Inhibition and
Cooperativity |
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Chapter 3 Cell Biology |
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3.1 |
An Introduction to Cell
Biology |
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3.1.1 |
The History of Cytology |
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3.1.2 |
Prokaryotes vs. Eukaryotes
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3.1.3 |
Plant and Animal Cell
Overview: The Basics |
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3.1.4 |
Membranes: Basic Structure |
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3.1.5 |
The Nuclear Envelope: The
initial Tour |
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3.1.6 |
Nuclear Function: Who's in
Charge? |
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3.2 |
Membrane-Bound Organelles |
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3.2.1 |
Cellular Function: Endoplasmic
Reticulum |
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3.2.2 |
Cell Function: Golgi Apparatus |
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3.2.3 |
Food Vacuole Formation: The
Role of the Lysosome |
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3.2.4 |
Still More Vacuoles and
Peroxisomes |
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3.2.5 |
Mitochondria: Welcome Guests |
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3.2.6 |
The Origin of Mitochondria and
Chloroplasts |
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3.3 |
The Cytoskeleton |
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3.3.1 |
The Cytoskeleton: Basic
Components |
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3.3.2 |
Centrioles, Flagella, and
Cilia |
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3.3.3 |
Cell Walls |
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3.4 |
The Plasma Membrane
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3.4.1 |
Plasma Membrane: The
Extracellular Matrix |
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3.4.2 |
The Plasma Membrane: The
Fluid-Mosaic Model |
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3.4.3 |
Proteins as the Mosaic of the
Cell Membrane |
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3.4.4 |
Animal Cell Junctions |
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3.5 |
Cell Transport |
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3.5.1 |
Simple and Facilitated
Diffusion |
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3.5.2 |
Passive Transport: Osmosis |
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3.5.3 |
Active Transport: Ion Pumps
and Cotransport |
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3.5.4 |
Active Transport: The
Sodium-Potassium Pump |
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3.5.5 |
Energy-Requiring Transport:
Endocytosis and Exocytosis |
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3.6 |
Tools for Cell Biology |
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3.6.1 |
Tools of the Cytologist: Light
and Fluorescent Microscopy |
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3.6.2 |
Scanning and Transmission
Electron Microscopes |
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3.6.3 |
Freeze Fractures and
Differential Centrifugation |
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3.7 |
The Evolution of Metabolic
Functions |
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3.7.1 |
Major Modes of Nutrition Among
Organisms |
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Chapter 4 Respiration |
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4.1 |
An Introduction to
Respiration |
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4.1.1 |
ATP Structure and Function |
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4.1.2 |
Phosphorylated Intermediates
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4.1.3 |
Respiration: An Overview |
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4.1.4 |
Redox: A Brief Review |
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4.1.5 |
Energy Release from Sugar: A
Demo |
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4.1.6 |
Coenzymes: The Role of NAD+ |
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4.2 |
Glycolysis and Fermentation |
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4.2.1 |
Glycolysis: The Initial Steps:
Energy Input |
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4.2.2 |
Glycolysis: The Energy Payoff |
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4.2.3 |
Anaerobic Respiration: The
Fermenation of Pyruvate |
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4.3 |
Aerobic Respiration |
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4.3.1 |
Aerobic Respiration: The
Acetyl CoA Step |
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4.3.2 |
Aerobic Respiration: The Krebs
Cycle |
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4.3.3 |
Glycolysis and the Krebs Cycle |
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4.4 |
The Electron Transport
Chain and Oxidative Phosphorylation |
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4.4.1 |
The Electron Transport Chain |
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4.4.2 |
Oxidative Phosphorylation |
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4.4.3 |
ATP Yield from Aerobic
Respiration |
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4.4.4 |
Other Fuels in
Respiration |
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4.4.5 |
The Evolution of Glycolysis |
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Chapter 5 Photosynthesis |
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5.1 |
Discovering Photosynthesis |
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5.1.1 |
The Unraveling of
Photosynthesis: A Historical Perspective |
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5.1.2 |
Photosynthesis:
Twentieth-Century Breakthroughs |
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5.1.3 |
Photosynthesis: The Final
Picture |
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5.2 |
Adaptations for
Photosynthesis |
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5.2.1 |
The Leaf: Adaptations for
Photosynthesis |
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5.2.2 |
The Structure of a Chloplast |
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5.2.3 |
Photosynthesis Pigments |
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5.2.4 |
The Nature of Light |
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5.2.5 |
Photoexcitation and Electron
Transfer |
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5.3. |
The Light Reactions |
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5.3.1 |
The Light Reactions: An
Introduction |
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5.3.2 |
Photosystem 1 |
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5.3.3 |
Photosystem 2 |
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5.3.4 |
The Light Reactions: A Summary |
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5.4 |
The Dark Reactions |
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5.4.1 |
The Calvin Cycle |
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5.4.2 |
The Calvin Cycle: RuBP
Regeneration |
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5.4.3 |
A Review of Photosynthesis
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5.5 |
Photorespiration
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5.5.1 |
Photorespiration |
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5.5.2 |
C4 Plants and CAM
Plants |
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5.5.3 |
The Evolution of
Photosynthetics |
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Chapter 6 Molecular
Genetics |
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6.1 |
Discovering DNA |
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6.1.1 |
Molecular Genetics: The
Protein vs. DNA Debate |
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6.1.2 |
Continuing to Link Genes to
Chemicals: Muller, Beadle, and Tatu |
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6.1.3 |
Griffith and Transformation |
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6.1.4 |
Avery, MacLeod and
McCarty/Hershey and Chase: DNA Wins! |
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6.1.5 |
Chargaff and Franklin and
Wilkins: The DNA Story Begins |
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6.2 |
DNA Structure Revealed |
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6.2.1 |
Watson and Crick: The Clues |
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6.2.2 |
Watson and Crick: The
Double Helix |
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6.3 |
Introduction to DNA
Replication |
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6.3.1 |
Replication: Meselson and
Stahl |
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6.3.2 |
DNA: Polymerization with
Triphospate Nucleotides |
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6.4 |
Events of DNA Replication |
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6.4.1 |
Events at the Replication
Fork: The Leading Strand |
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6.4.2 |
Events at the Leading Strand,
Part 2 |
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6.4.3 |
Events at the Replication
Fork: The Lagging Strand |
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6.4.4 |
Proofreading, End Replication,
and Telomeres |
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6.4.5 |
DNA Replication: A Summary |
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6.5 |
Translation |
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6.5.1 |
Transcription and Translation:
An Overview |
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6.5.2 |
Transcription: RNA Formation
from the DNA Template |
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6.5.3 |
Transcription: Termination and
RNA Protection |
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6.5.4 |
Posttranscriptional
Modification/RNA Splicing |
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6.6 |
Translation |
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6.6.1 |
Translation: Ribosomal and
Transfer RNA |
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6.6.2 |
The Role of Transfer RNA:
Charging a tRNA Molecule |
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6.6.3 |
Translation: Initiation Events |
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6.6.4 |
Translation/Elongation: The
Initiation of Elongation |
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6.6.5 |
Elongation Continued and
Termination |
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6.7 |
Protein Synthesis Review |
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6.7.1 |
Polypeptide Destinations:
Signal Peptides and ER Ribosomes |
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6.7.2 |
Protein Synthesis: An Overview |
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6.8 |
The lac Operon |
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6.8.1 |
Control Mechanisms: Lactose
Metabolism in E. coli |
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6.8.2 |
Jacob and Monod's Model: The
lac Operon |
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6.8.3 |
lac Operon: The Summary |
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6.9 |
Eukaryotic Genomic
Organization |
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6.9.1 |
The Eukaryotic Genome: DNA
Packing |
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6.9.2 |
Eukaryotic Genome
Organization: Repetitive DNA |
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6.9.3 |
Eukaryotic Genome
Organization: Gene Families |
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6.9.4 |
Eukaryotic Genome
Organization: Transposons and Amplified Gel |
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6.10 |
Controlling Protein
Synthesis in Eukaryotes |
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6.10.1 |
Eukaryotic Gene Control:
Transcriptional Controls |
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6.10.2 |
Eukaryotic Control Mechanisms:
Posttranscriptional and Posttranslational Controls |
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6.10.3 |
Prokaryotes vs. Eukaryotes:
Protein-Making Machinery |
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Chapter 7 Biotechnology
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7.1 |
Plasmids and Gene Cloning |
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7.1.1 |
Biotechnology: Plasmids in
Prokaryotes |
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7.1.2 |
Using a Restriction Enzyme to
Create a Vector |
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7.1.3 |
Biotechnology: Gene Cloning |
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7.1.4 |
Biotechnology: Detection of
Cell Clones |
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7.2 |
Techniques in Biotechnology |
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7.2.1 |
Biotechnology: Reverse
Transcriptase: A Tool Take from Viruses |
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7.2.2 |
Using Reverse Transcriptase to
Make cDNA |
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7.2.3 |
Electrophoresis: Separating
DNA |
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7.2.4 |
Sequencing DNA: The Sanger
Method |
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7.3 |
More Techniques in
Biotechnology |
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7.3.1 |
Restriction Fragment Length
Polymorphisms: Genetic Markers |
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7.3.2 |
Polymerase Chain Reaction: DNA
Amplification |
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7.3.3 |
DNA Fingerprinting |
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7.3.4 |
Southern Blotting |
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7.3.5 |
Detecting DNA Homology: A
Biotechnology Summary |
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7.4 |
A Human Genome Project |
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7.4.1 |
The Human Gene Pool |
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7.4.2 |
The Human Genome Project:
Recent Findings |
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Chapter 8 Cell Reproduction |
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8.1 |
An Introduction to the Cell
Cycle and Mitosis |
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8.1.1 |
The Eukaryotic Cell Cycle |
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8.1.2 |
Mitosis: An Overview |
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8.1.3 |
Mitosis: The Phases |
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8.1.4 |
Cytokinesis |
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8.2 |
Regulating Mitosis |
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8.2.1 |
Cell-Cycle Regulation: Protein
Kinases |
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8.2.2 |
Cell-Cycle Regulation: Other
Mechanics |
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8.2.3 |
Cancer: When Mitosis Goes
Unchecked |
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8.2.4 |
The ras gene and the
p53 Gene |
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8.3 |
Meiosis |
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8.3.1 |
Sexual Reproduction and the
Role of Meiosis |
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8.3.2 |
Homologous Chromosomes:
Thanks, Mom and Dad |
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8.3.3 |
Meiosis: Prophase I |
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8.3.4 |
Disjunction and Meiosis II |
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8.3.5 |
Mitosis vs. Meiosis |
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8.4 |
Understanding Meiosis |
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8.4.1 |
Independent Assortment |
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8.4.2 |
Spermatogenesis: Meiosis in
Males |
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8.4.3 |
Oogenesis: Meiosis in Females |
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Chapter 9 Mendelian
Genetics and Mutation |
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9.1 |
Gregor Mendel |
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9.1.1 |
Heredity: The Story of Gregor
Mendel |
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9.1.2 |
Mendel's Findings: A First
Look at Phenotypic Ratios |
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9.1.3 |
Mendel's Conclusions:
Alternate Alleles and Dominance |
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9.1.4 |
Mendel's Conclusions:
Segregation and Recombination |
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9.2 |
The Laws of Mendelian
Inheritance |
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9.2.1 |
Determining Heterozygosity:
Test Crosses and Back Crosses |
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9.2.2 |
Mendelian Inheritance |
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9.3 |
Segregation and Independent
Assortment |
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9.3.1 |
Segregation and Independent
Assortment |
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9.3.2 |
Independent Assortment: An
Explanation |
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9.4 |
Laws of Probability |
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9.4.1 |
Laws of Probability: Rule of
Multiplication |
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9.4.2 |
The Multiplicative Law: Some
Extensions |
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9.4.3 |
Laws of Probability: The
Additive Rule |
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9.4.4 |
Using the Laws of Probability
in Dihybrid Crosses |
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9.5 |
Genetic Dominance |
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9.5.1 |
What is a Dominate Gene?
Intermediate Inheritance |
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9.5.2 |
Codominance and Multiple
Alleles: ABO Blood Genes |
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9.5.3 |
ABO Blood Groups: Inheritance
Patterns and Pedigree Charts |
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9.6 |
Epistasis |
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9.6.1 |
Epistasis: One Gene Affecting
Another |
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9.6.2 |
The Bombay Phenotype:
Infidelity or Epistasis |
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9.7 |
Inheritance Patterns |
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9.7.1 |
Polygenic Inheritance |
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9.7.2 |
Pleiotropy: Multiple
Phenotypic Effects |
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9.7.3 |
Sickle Cell Anemia: The Case
Against Dominant and Recessive |
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9.8 |
Linked Genes and Genetic
Mapping |
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9.8.1 |
Linked Genes |
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9.8.2 |
Crossing Over and
Recombination: A Tool for Mapping Genes |
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9.8.3 |
Gene Mapping Using
Recombination Frequencies |
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9.8.4 |
Linking Genes to Chromosomes:
The Work of Morgan |
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9.8.5 |
Morgan's Conclusions |
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9.9 |
Sex Linkage and Pedigree
Charts |
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9.9.1 |
Sex-Linked Traits in Humans |
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9.9.2 |
X Inactivation in Humans |
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9.9.3 |
The Use of Pedigree Charts to
Determine Possible Genotypes |
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9.9.4 |
Pedigree Chart: Problem
Review |
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9.10 |
Problems in Heredity |
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9.10.1 |
Problems in Heredity |
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9.10.2 |
Problems in Heredity:
Chromosomal Aberrations |
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9.10.3 |
Translocations: 14/21 Downs |
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Chapter 10 Population
Genetics and Evolution |
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10.1 |
The Hardy-Weinberg Theory |
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10.1.1 |
Population Genetics: Darwin
Meets Mendel |
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10.1.2 |
An Introduction to
Hardy-Weinberg Theory |
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10.1.3 |
The Hardy-Weinberg Equation |
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10.1.4 |
Using the Hardy-Weinberg
Theory |
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10.1.5 |
Using the Hardy-Weinberg
Theory II |
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10.1.6 |
Hardy-Weinberg: What Does This
Have to Do With Evolution |
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10.2 |
Departing From
Hardy-Weinberg Equilibrium |
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10.2.1 |
Microevolution by Genetic
Drift |
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10.2.2 |
Microevolution: Continued |
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10.3 |
Variations in Populations
and Modes of Selection |
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10.3.1 |
Variations Within and Between
Populations |
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10.3.2 |
Modes of Selection |
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10.3.3 |
The Perfect Organism |
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10.4 |
Speciation |
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10.4.1 |
Speciation: What is a Species? |
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10.4.2 |
Allopatric Speciation |
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10.4.3 |
Sympatric Speciation |
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10.5 |
Evolution |
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10.5.1 |
Time Frame for Evolution:
Gradualism versus Punctuated Equilibrium |
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