Chapter 1 – Evolution and the Foundations of Biology

Hierarchy of Life

The biological world is organized into a hierarchy from the largest to the smallest levels, each with unique properties and functions.

• Biosphere: All life on Earth and all places where life exists.

• Ecosystem: All living things in a particular area, plus nonliving components.

• Community: Array of organisms inhabiting a particular ecosystem.

• Population: All individuals of a species within an area.

• Organism: Individual living thing.

• Organ/Organ System: Body parts that carry out specific functions.

• Tissue: Group of cells working together.

• Cell: Smallest unit of life.

• Organelle: Functional components within cells.

• Molecule: Chemical structure of two or more atoms.

Emergent properties arise at each level due to the arrangement and interactions of parts as complexity increases.

Cells: The Basic Unit of Life

• Cell: The smallest unit of life capable of performing all life’s activities.

• Prokaryotic cells: Lack a nucleus and membrane-bound organelles (e.g., Bacteria, Archaea).

• Eukaryotic cells: Have a nucleus and membrane-bound organelles (e.g., Plants, Animals, Fungi, Protists).

DNA and Gene Expression

• DNA (Deoxyribonucleic Acid): The molecule that stores genetic information. Composed of nucleotides (adenine, thymine, cytosine, guanine) with a sugar-phosphate backbone.

• Chromosome: DNA packaged with proteins.

• Gene: A segment of DNA that codes for a protein or RNA molecule.

• Gene expression: The process by which information from a gene is used to synthesize a functional product (protein or RNA).

Energy Flow and Nutrient Cycling

• Energy flows one-way through an ecosystem (usually entering as sunlight, exiting as heat).

• Nutrients cycle within an ecosystem (e.g., carbon, nitrogen cycles).

• Producers (autotrophs) convert energy from sunlight into chemical energy.

• Consumers (heterotrophs) obtain energy by eating other organisms.

Evolution and Diversity of Life

• Evolution: The process of change that has transformed life on Earth; explains both unity and diversity of life.

• Three Domains:

  • Bacteria: Prokaryotic, diverse, widespread.

  • Archaea: Prokaryotic, often in extreme environments.

  • Eukarya: Eukaryotic organisms (plants, animals, fungi, protists).

• Natural Selection: Mechanism of evolution proposed by Charles Darwin; individuals with advantageous traits survive and reproduce more.

The Scientific Process

• Inductive reasoning: Deriving generalizations from specific observations.

• Deductive reasoning: Making predictions from general premises.

• Scientific method steps: Observation, Question, Hypothesis, Prediction, Experiment, Analysis, Conclusion.

• Hypothesis: Testable explanation for an observation.

• Null hypothesis: States no effect or difference.

• Theory: Broader than a hypothesis; supported by a large body of evidence.

• Experimental group: Receives the treatment.

• Control group: Does not receive the treatment; used for comparison.

• Independent variable: Manipulated factor.

• Dependent variable: Measured outcome.

• Blind/double-blind: Prevents bias in experiments.

• Pseudoscience: Claims presented as scientific but lack supporting evidence.

• Anecdotal evidence: Based on personal accounts, not reliable.

Chapter 2 – The Chemical Context of Life

Elements and Atoms

• Element: Substance that cannot be broken down by chemical means.

• Atom: Smallest unit of an element, composed of protons, neutrons, and electrons.

• Proton: Positive charge; Neutron: No charge; Electron: Negative charge.

Electron Arrangement and Chemical Properties

• Electrons are arranged in shells around the nucleus.

• The valence shell (outermost shell) determines chemical reactivity.

• Electron distribution affects how atoms interact and bond.

Energy in Atoms

• Energy: Capacity to cause change.

• Potential energy: Stored energy due to position or structure.

• Kinetic energy: Energy of motion.

• Thermal energy: Kinetic energy associated with random movement of atoms.

Chemical Bonds

• Ionic bond: Transfer of electrons between atoms.

• Covalent bond: Sharing of electrons (can be polar or nonpolar).

• Polar covalent bond: Unequal sharing of electrons due to differences in electronegativity.

• Nonpolar covalent bond: Equal sharing of electrons.

• Hydrogen bond: Weak attraction between a hydrogen atom and an electronegative atom.

• van der Waals interactions: Weak attractions due to transient local charges.

Chemical Reactions and Equilibrium

• Chemical reaction: Making and breaking of chemical bonds.

• Reactants: Starting materials; Products: Resulting materials.

• Chemical equilibrium: Point at which forward and reverse reactions occur at the same rate.

Properties of Water

• Polarity: Water is a polar molecule due to unequal sharing of electrons.

• Hydrogen bonding: Leads to cohesion, adhesion, high specific heat, and surface tension.

• Specific heat: Amount of heat needed to change temperature; water has high specific heat.

• Evaporative cooling: As water evaporates, it removes heat, cooling surfaces.

• Ice floats: Solid water is less dense than liquid water due to hydrogen bonding.

• Solvent of life: Water dissolves many substances due to its polarity.

• Hydrophilic: Water-loving; Hydrophobic: Water-fearing.

Acids, Bases, and pH

• Acid: Increases H+ concentration in solution.

• Base: Reduces H+ concentration (often increases OH-).

• pH scale: Measures H+ concentration; ranges from 0 (acidic) to 14 (basic).

Chapter 3 – Carbon and the Molecular Diversity of Life

Organic Compounds and Carbon

• Organic compounds: Contain carbon and hydrogen.

• Hydrocarbons: Molecules with only carbon and hydrogen.

• Macromolecules: Large molecules (carbohydrates, lipids, proteins, nucleic acids).

• Carbon: Forms four covalent bonds, allowing for diverse structures.

Chemical Groups and ATP

• Seven important chemical groups: hydroxyl, carbonyl, carboxyl, amino, sulfhydryl, phosphate, methyl.

• ATP (Adenosine triphosphate): Main energy currency of the cell.

Macromolecules: Polymers and Monomers

• Polymer: Long molecule made of repeating units (monomers).

• Dehydration (condensation) reaction: Joins monomers by removing water.

• Hydrolysis: Breaks polymers by adding water.

Carbohydrates

• Monosaccharides: Simple sugars (e.g., glucose).

• Disaccharides: Two monosaccharides joined (e.g., sucrose).

• Polysaccharides: Many monosaccharides (e.g., starch, cellulose, glycogen).

• Functions: Energy storage, structural support.

Lipids

• Fats: Glycerol + fatty acids; energy storage.

• Phospholipids: Major component of cell membranes.

• Steroids: Four fused rings (e.g., cholesterol).

Proteins

• Amino acids: Building blocks of proteins; differ by side chains (R groups).

• Polypeptide: Polymer of amino acids linked by peptide bonds.

• Protein structure: Primary (sequence), secondary (alpha helix, beta sheet), tertiary (3D shape), quaternary (multiple polypeptides).

• Denaturation: Loss of protein structure and function due to environmental changes.

• Enzymes: Proteins that act as catalysts to speed up reactions.

Nucleic Acids

• DNA: Deoxyribonucleic acid; double helix; stores genetic information.

• RNA: Ribonucleic acid; single-stranded; involved in protein synthesis.

• Polynucleotide: Polymer of nucleotides.

• Pyrimidines: Cytosine, thymine, uracil; Purines: Adenine, guanine.

• Deoxyribose: Sugar in DNA; Ribose: Sugar in RNA.

• Antiparallel: Two strands run in opposite directions in DNA.

Chapter 4 – A Tour of the Cell

Cell Types and Organelles

• Cell: Basic unit of life; all cells share certain features but can differ greatly.

• Prokaryotic cells: No nucleus, no membrane-bound organelles; have cell wall, plasma membrane, cytoplasm, ribosomes.

• Eukaryotic cells: Nucleus, membrane-bound organelles (e.g., mitochondria, ER, Golgi apparatus, lysosomes, chloroplasts in plants).

• Organelles: Specialized structures within cells.

Microscopy and Cell Fractionation

• Light microscope: Uses light to view cells; lower resolution.

• Electron microscope: Uses electrons; higher resolution.

• Scanning electron microscope (SEM): Surface details.

• Cell fractionation: Separates cell components by size/density.

Cellular Structures and Functions

• Cytoplasm: Region between plasma membrane and nucleus.

• Surface area to volume ratio: Limits cell size; higher ratio allows efficient exchange.

• Plasma membrane: Phospholipid bilayer; controls entry/exit of substances.

• Endomembrane system: Includes nuclear envelope, ER, Golgi, lysosomes, vesicles, plasma membrane.

• Protein secretion: Synthesized in rough ER, modified in Golgi, transported via vesicles.

• Endosymbiosis hypothesis: Mitochondria and chloroplasts originated from engulfed prokaryotes.

Cytoskeleton and Cell Movement

• Cytoskeleton: Network of fibers (microtubules, microfilaments, intermediate filaments) for support and movement.

• Motor proteins: Move along cytoskeleton to transport materials.

• Centrosome: Microtubule organizing center; contains centrioles in animal cells.

• Basal body: Anchors cilia/flagella.

• Dyneins: Motor proteins in cilia/flagella.

• Microfilaments: Made of actin; involved in movement.

• Myosin: Motor protein interacting with actin.

Cell Walls and Extracellular Matrix

• Cell wall: Found in plants, fungi, some protists; provides support.

• Extracellular matrix (ECM): Outside animal cells; made of glycoproteins (e.g., collagen).

• Cell junctions: Connections between cells (e.g., plasmodesmata in plants, tight/gap/desmosomes in animals).

Chapter 5 – Membrane Transport & Cell Signaling

Membrane Structure and Function

• Fluid Mosaic Model: Membrane is a fluid structure with proteins embedded in a phospholipid bilayer.

• Phospholipids: Main component; hydrophilic heads, hydrophobic tails.

• Proteins: Serve as channels, carriers, receptors, enzymes.

Transport Across Membranes

• Selective permeability: Only certain substances can cross.

• Diffusion: Movement from high to low concentration.

• Osmosis: Diffusion of water across a membrane.

• Passive transport: No energy required (diffusion, facilitated diffusion).

• Active transport: Requires energy (ATP) to move substances against gradient.

• Aquaporin: Channel protein for water transport.

• Cotransport: Coupled transport of two substances; often uses a gradient created by active transport.

• Bulk transport: Movement of large molecules via vesicles (exocytosis, endocytosis, phagocytosis, pinocytosis, receptor-mediated endocytosis).

Cell Signaling

• Cell signaling: Cells communicate via chemical signals.

• Signal transduction pathway: Series of steps converting a signal to a response.

• Second messengers: Small molecules/ions that relay signals inside the cell (e.g., cAMP, Ca2+).

• G-protein coupled receptors (GPCRs): Membrane receptors that activate G-proteins, triggering signaling cascades.

• Phosphorylation: Addition of phosphate group to a protein; often activates or deactivates proteins.

• Phosphorylation cascade: Series of protein kinases activating each other.

Example: Testosterone Signaling

• Testosterone binds to intracellular receptor, forms a complex, enters nucleus, and regulates gene expression.

Additional info: These notes synthesize and expand upon the study guide prompts, providing definitions, examples, and context for foundational biology concepts relevant to a first-semester college course.