Chapter 1: Themes of Biology and Evolution

Five Themes of Biology

• Organization: Biological systems are structured in a hierarchy from molecules to the biosphere. Emergent properties arise at each level due to interactions among components.

• Information: Life processes depend on the transmission and expression of genetic information, primarily through DNA.

• Energy and Matter: Living organisms require energy to maintain order; energy flows through ecosystems while chemicals cycle within them.

• Interactions: Organisms interact with each other and their environment, affecting both their own survival and the ecosystem.

• Evolution: The process by which populations change over generations, explaining both the unity and diversity of life.

Cells and Genetic Information

• Eukaryotic cells have membrane-bound organelles, including a nucleus; prokaryotic cells lack a nucleus and most organelles.

• DNA stores genetic information and is transmitted during cell division.

Energy Flow and Chemical Cycling

• Producers (e.g., plants) convert energy from sunlight into chemical energy.

• Consumers obtain energy by eating other organisms.

• Energy flows through ecosystems; chemicals are recycled.

Regulation and Feedback

• Feedback regulation maintains homeostasis; negative feedback reduces the initial stimulus.

Evolution and Diversity

• Three domains of life: Bacteria, Archaea, Eukarya.

• Charles Darwin proposed natural selection as the mechanism of evolution.

Scientific Inquiry

• Inductive reasoning: Generalizations from specific observations.

• Deductive reasoning: Predictions from general premises.

• Hypothesis: Testable explanation for observations.

• Theory: Broad explanation supported by evidence.

• Variables: Independent variable is manipulated; dependent variable is measured.

Chapter 2: The Chemical Context of Life

Atoms, Elements, and Compounds

• Elements are substances that cannot be broken down chemically; compounds are combinations of elements.

• Essential elements are required for life (e.g., C, H, O, N).

• Atoms consist of protons, neutrons, and electrons.

• Atomic number = number of protons; atomic mass = protons + neutrons.

• Isotopes are atoms of the same element with different numbers of neutrons.

Electron Shells and Chemical Bonds

• Electrons occupy valence shells; chemical behavior depends on electron configuration.

• Covalent bonds: Atoms share electrons; can be nonpolar (equal sharing) or polar (unequal sharing).

• Ionic bonds: Transfer of electrons creates charged ions.

• Hydrogen bonds and Van der Waals interactions are weaker interactions important in biological molecules.

Chemical Reactions

• Rearrange matter; do not create or destroy atoms.

Chapter 3: Water and Life

Structure and Properties of Water

• Polar covalent bonds in water create partial charges; hydrogen bonds form between molecules.

• Four key properties:

  • Cohesion: Water molecules stick together (surface tension).

  • Moderation of temperature: High specific heat and evaporative cooling.

  • Floating of ice: Solid water is less dense than liquid.

  • Universal solvent: Dissolves many substances due to polarity.

Solutions, Acids, and Bases

• Solution: Homogeneous mixture; solvent dissolves solute.

• Hydrophilic substances interact with water; hydrophobic do not.

• pH measures hydrogen ion concentration; acids increase [H+], bases decrease [H+].

• Buffers minimize changes in pH.

Chapter 5: The Structure and Function of Large Biological Molecules

Macromolecules: Polymers and Monomers

• Polymers are long chains of monomers joined by dehydration reactions; broken by hydrolysis.

Carbohydrates

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

• Disaccharides: Two monosaccharides joined by glycosidic linkage.

• Polysaccharides: Storage (starch, glycogen) or structural (cellulose, chitin).

Lipids

• Fats and oils: Glycerol + fatty acids; saturated (no double bonds) vs. unsaturated (double bonds).

• Phospholipids: Major component of cell membranes.

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

Proteins

• Amino acids: Monomers; linked by peptide bonds.

• R groups determine properties.

• Four levels of structure: Primary, secondary, tertiary, quaternary.

• Denaturation disrupts structure; can cause diseases (e.g., sickle cell).

Nucleic Acids

• DNA vs. RNA: DNA is double-stranded, contains thymine; RNA is single-stranded, contains uracil.

• Nucleotides: Monomers (adenine, guanine, cytosine, thymine, uracil).

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

• Antiparallel double helix structure in DNA.

Chapter 6: A Tour of the Cell

Microscopy and Cell Types

• Light microscopes for living cells; electron microscopes for detailed structures.

• Prokaryotic cells: No nucleus, simple structure.

• Eukaryotic cells: Nucleus, membrane-bound organelles.

Cell Structures and Organelles

• Nucleus: Contains DNA, nucleolus (ribosome synthesis).

• Ribosomes: Protein synthesis.

• Endomembrane system: Nuclear envelope, ER (rough and smooth), Golgi apparatus, lysosomes, vacuoles.

• Mitochondria: Cellular respiration.

• Chloroplasts: Photosynthesis (plants/algae).

• Peroxisomes: Break down fatty acids, detoxification.

• Cytoskeleton: Microtubules, microfilaments, intermediate filaments.

• Cell wall: Structure in plants, fungi, some protists.

• Extracellular matrix: Animal cells; support and signaling.

• Cell junctions: Plasmodesmata (plants), tight junctions, desmosomes, gap junctions (animals).

Chapter 7: Membrane Structure and Function

Membrane Structure

• Fluid mosaic model: Membrane is a fluid bilayer of phospholipids with proteins embedded.

• Amphipathic: Molecules with both hydrophilic and hydrophobic regions (e.g., phospholipids).

• Cholesterol: Modulates membrane fluidity.

• Membrane proteins: Integral (span membrane), peripheral (surface); functions include transport, signaling, cell recognition.

• Membrane carbohydrates: Cell recognition.

Transport Across Membranes

• Selective permeability: Some substances cross easily (small, nonpolar); others require help.

• Transport proteins: Channel and carrier proteins facilitate movement.

• Passive transport: No energy required; includes diffusion and osmosis.

• Tonicity: Isotonic (no net water movement), hypertonic (water leaves cell), hypotonic (water enters cell).

• Osmoregulation: Control of water balance.

• Facilitated diffusion: Passive transport via proteins.

• Active transport: Moves substances against gradient; requires energy (e.g., sodium/potassium pump).

• Bulk transport: Endocytosis (phagocytosis, pinocytosis, receptor-mediated), exocytosis.

Chapter 8: Metabolism

Metabolic Pathways and Energy

• Catabolic pathways: Break down molecules, release energy.

• Anabolic pathways: Build molecules, consume energy.

• First law of thermodynamics: Energy cannot be created or destroyed.

• Second law: Every energy transfer increases entropy (disorder).

• Exergonic reactions: Release free energy; endergonic: require energy input.

• Free energy (G): Energy available to do work.

ATP and Enzymes

• ATP: Main energy currency; hydrolysis releases energy.

• Energy coupling: Using exergonic processes to drive endergonic ones.

• Enzymes: Biological catalysts; lower activation energy.

• Substrate: Reactant acted on by enzyme; binds at active site.

• Induced fit: Enzyme changes shape to fit substrate.

• Factors affecting enzymes: Temperature, pH, cofactors.

• Inhibitors: Competitive (bind active site), noncompetitive (bind elsewhere).

Chapter 9: Cellular Respiration and Fermentation

Overview and Formula

• Cellular respiration: Converts glucose to ATP.

• Overall equation:

• Redox reactions: Transfer electrons; oxidation (loss), reduction (gain).

Stages of Cellular Respiration

• Glycolysis: In cytosol; does not require oxygen; splits glucose into pyruvate; net gain of 2 ATP, 2 NADH.

• Citric Acid Cycle: In mitochondrial matrix; requires oxygen; pyruvate oxidized to acetyl-CoA; cycle turns twice per glucose; produces NADH, FADH2, ATP, CO2.

• Oxidative Phosphorylation: Inner mitochondrial membrane; includes electron transport chain (ETC) and chemiosmosis (ATP synthase); produces most ATP.

Fermentation

• Lactic acid fermentation: In animals; pyruvate reduced to lactate.

• Alcohol fermentation: In yeast; pyruvate converted to ethanol and CO2.

Chapter 10: Photosynthesis

Overview and Formula

• Photosynthesis: Converts light energy to chemical energy in plants, algae, some bacteria.

• Overall equation:

• Autotrophs: Produce their own food; heterotrophs: consume others.

Chloroplast Structure

• Mesophyll: Leaf cells where photosynthesis occurs.

• Stomata: Gas exchange pores.

• Thylakoids: Membranous sacs; stacked into grana.

• Chlorophyll: Light-absorbing pigment.

Stages of Photosynthesis

• Light reactions: In thylakoid membranes; convert light energy to ATP and NADPH; split water, release O2.

• Calvin cycle: In stroma; uses ATP and NADPH to fix CO2 into sugar.

Light Absorption and Electron Flow

• Electromagnetic spectrum: Range of light; visible light used in photosynthesis.

• Chlorophyll a and b: Absorb different wavelengths.

• Photosystems II & I: Protein complexes that capture light energy.

• Cyclic electron flow: Produces ATP only.

Calvin Cycle Phases

• Carbon fixation: CO2 attached to RuBP by rubisco.

• Reduction: ATP and NADPH reduce 3-PGA to G3P.

• Regeneration: RuBP regenerated for next cycle.

Photorespiration and Plant Adaptations

• Photorespiration: Rubisco adds O2 instead of CO2, reducing efficiency.

• C4 plants: Separate steps by space (mesophyll and bundle sheath cells).

• CAM plants: Separate steps by time (night and day).