Exploring Life and the Scientific Method

Properties and Organization of Life

Living organisms share several fundamental properties that distinguish them from nonliving matter. Understanding these properties and the hierarchical organization of life is essential for studying biology.

• Major Properties of Life: Organization, energy use, regulation (homeostasis), response to stimuli, growth and development, reproduction, and evolution.

• Homeostasis: The regulation of a relatively stable internal environment; internal conditions fluctuate within limits.

• Levels of Biological Organization (least to most inclusive): Molecule → Organelle → Cell → Tissue → Organ → Organ System → Organism → Population → Community → Ecosystem.

• Tissues: Composed of similar cells; Organs: Contain multiple tissues; Organ Systems: Groups of organs working together.

• Ecosystem: Includes organisms plus nonliving factors (soil, water, nutrients).

Ecosystems: Energy and Matter

Energy and matter move differently through ecosystems, affecting biological processes and environmental interactions.

• Energy Flow: Energy enters as sunlight, is captured by producers, transferred to consumers and decomposers, and exits as heat. Energy does not cycle.

• Matter Cycling: Chemical nutrients (e.g., carbon) cycle between organisms and the environment.

• Producers: Make organic molecules using energy sources (e.g., plants).

• Consumers: Obtain energy by eating other organisms.

• Decomposers: Break down dead organisms and wastes, returning nutrients to the environment.

The Scientific Method

The scientific method is a systematic approach to investigating natural phenomena.

• Observation: Information noticed or measured.

• Hypothesis: Proposed explanation; must be testable and falsifiable.

• Experiment: Tests the hypothesis; includes control and experimental groups.

• Control Group: Provides a basis for comparison; differs from the experimental group only in the variable being tested.

• Prediction: Expected outcome if the hypothesis is correct.

• Conclusion: Interpretation of results; evidence supports or refutes the hypothesis but does not prove it absolutely.

Evolution and Unity of Life

Evolution explains the diversity and unity of life, driven by natural selection and genetic inheritance.

• Evolution: Occurs in populations across generations; not due to individual changes or deliberate adaptation.

• Natural Selection: Increases frequency of traits that improve survival and reproduction.

• Artificial Selection: Human-driven selection (e.g., breeding, antibiotic use).

• Genetic Code: Universal among organisms; supports unity of life.

• Domains: Bacteria and Archaea are prokaryotic; Eukarya includes animals, plants, fungi, and protists.

The Chemical Basis of Life

Elements, Atoms, and Isotopes

Atoms are the basic units of matter, and their structure determines chemical properties.

• Most Abundant Elements: Carbon (C), Hydrogen (H), Oxygen (O), Nitrogen (N).

• Trace Elements: Required in small amounts (e.g., zinc, iodine).

• Atomic Number: Number of protons.

• Atomic Mass: Approximate sum of protons and neutrons.

• Isotopes: Same element, different number of neutrons; radioactive isotopes used in medical imaging.

• Compound: Two or more elements in a fixed ratio.

• Periodic Table: Elements in the same column have similar valence electron patterns.

Electrons, Ions, and Chemical Bonds

Chemical bonds form through interactions of electrons, resulting in molecules and compounds.

• Valence Electrons: Determine chemical behavior.

• Ionic Bond: Electron transfer creates charged ions (e.g., Na+ and Cl-).

• Covalent Bond: Electrons are shared; Nonpolar: Equal sharing; Polar: Unequal sharing.

• Electronegativity Order: O > N > C > H.

• Hydrogen Bond: Attraction between partial charges on different molecules or regions.

Chemical Reactions and pH

Chemical reactions rearrange atoms, and pH measures hydrogen ion concentration.

• Reactants: Starting substances; Products: Formed by reaction.

• pH Scale: Logarithmic; one-unit difference = tenfold change in [H+].

• Low pH: More H+, greater acidity; High pH: Less H+, greater basicity.

• Buffer: Minimizes pH changes by accepting or donating H+.

• Carbonic Acid: Formed from dissolved CO2, lowers ocean pH.

Formula:

Organic Molecules and Biomolecules

Carbon and Functional Groups

Organic molecules are based on carbon and contain functional groups that determine their properties.

• Organic Compounds: Contain carbon; not necessarily nitrogen or oxygen.

• Isomers: Same formula, different structure.

• Functional Groups: Hydroxyl (-OH), Amino (-NH2), Carboxyl (-COOH), Carbonyl (C=O).

• Hydroxyl: Alcohols; Amino and Carboxyl: Both in amino acids.

Building and Breaking Polymers

Polymers are built and broken down by dehydration and hydrolysis reactions.

• Dehydration Reaction: Joins monomers, releases water.

• Hydrolysis: Uses water to break bonds; important in digestion.

• Disaccharide: Formed by joining two monosaccharides.

• Peptide Bond: Joins amino acids; releases water.

Carbohydrates

Carbohydrates serve as energy sources, structural materials, and recognition molecules.

• Types: Monosaccharides, disaccharides, polysaccharides.

• Starch: Plant energy storage; digestible by humans.

• Cellulose: Plant cell wall; indigestible by most animals.

• Cows: Digest cellulose via microorganisms.

• Functions: Energy storage, structure, cell recognition, hereditary information.

• Lactose Intolerance: Due to low lactase activity.

Lipids and Health

Lipids include fats, phospholipids, and steroids, with important roles in membranes and health.

• Phospholipids: Major component of cell membranes.

• Saturated Fats: No C=C double bonds; solid at room temperature.

• Unsaturated Fats: One or more C=C double bonds; liquid at room temperature.

• Hydrogenation: Makes oils more solid; produces trans fats (linked to cardiovascular risk).

• Steroids: Four-ring structure; includes hormones and anabolic steroids.

Proteins, Enzymes, and Genetic Information

Proteins are polymers of amino acids, with diverse functions. Enzymes catalyze reactions, and genetic information flows from DNA to protein.

• Protein Structure: Amino acid sequence determines folding and function.

• Mutation: Substitution of similar amino acids may have minor effects; others can change function.

• Functions: Structure (keratin, collagen), transport, storage, signaling, defense, movement, catalysis.

• Enzymes: Proteins that lower activation energy and increase reaction rate.

• Information Flow: DNA gene → RNA message → Amino acid sequence → Protein.

Cell Structure and Function

Cell Theory, Cell Size, and Cell Types

Cells are the basic units of life, with structural and functional diversity.

• Cell Theory: All living things are composed of cells; all cells arise from preexisting cells.

• Cell Size: Surface-area-to-volume ratio limits cell size; exchange becomes less efficient as cells grow.

• Prokaryotic Cells: Lack membrane-bound nucleus and organelles; Bacteria and Archaea.

• Nucleoid: Region containing prokaryotic DNA; not membrane-bound.

• Bacterial Capsule: Attachment and protection.

• Eukaryotic Cells: Internal membranes create organelles and compartments.

Protein Production and the Endomembrane System

Eukaryotic cells use organelles to produce, modify, and transport proteins.

• Nucleus: Stores DNA; nucleolus produces ribosomal subunits.

• mRNA: Carries instructions from DNA to ribosomes.

• Ribosomes: Free in cytoplasm or attached to rough ER; site of protein synthesis.

• Rough ER: Produces proteins for secretion, membranes, or organelles.

• Smooth ER: Synthesizes lipids, detoxifies substances, stores calcium.

• Golgi Apparatus: Modifies, sorts, and packages proteins and lipids.

• Lysosomes: Digest macromolecules, bacteria, and damaged organelles.

• Pathway: DNA in nucleus → mRNA → Ribosome on rough ER → Transport vesicle → Golgi apparatus → Vesicle → Final destination.

Energy Organelles, Detoxification, and Cell Support

Cells contain specialized organelles for energy conversion, detoxification, and structural support.

• Mitochondria: Perform cellular respiration; inner membrane folds (cristae) increase surface area.

• Chloroplasts: Perform photosynthesis; thylakoids arranged in grana.

• Peroxisomes: Break down fatty acids and harmful substances.

• Central Vacuole (plants): Stores water, wastes, pigments, poisons; maintains pressure.

• Intermediate Filaments: Provide mechanical strength; anchor nucleus.

• Microtubules: Guide organelle and chromosome movement.

• Fluorescence Microscopy: Labels and visualizes cell structures.

• Cell Junctions: Anchoring (strength), tight (prevent leakage), gap (communication).

Membranes, Transport, ATP, and Enzymes

Plasma Membrane Structure and Signaling

The plasma membrane controls entry and exit of substances and mediates cell signaling.

• Fluid Mosaic Model: Phospholipid bilayer with embedded proteins; components move laterally.

• Selective Permeability: Some substances cross more easily than others.

• Membrane Proteins: Channels, carriers, enzymes, receptors, anchors, cell-identity markers.

• Cell Signaling: Signaling molecule binds receptor; receptor relays message inside cell.

• Receptor Regulation: Cells adjust sensitivity by changing receptor number.

Diffusion, Osmosis, and Tonicity

Transport across membranes occurs by diffusion, osmosis, and active transport, affecting cell volume and function.

• Diffusion: Net movement from high to low concentration due to random motion.

• Simple Diffusion: Crosses lipid bilayer without protein.

• Facilitated Diffusion: Uses channel or carrier protein; no energy required.

• Osmosis: Diffusion of water across membrane; water moves toward higher solute concentration.

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

• Aquaporins: Membrane channels for rapid water movement.

Active Transport, ATP, and Enzymes

Active transport moves substances against gradients, powered by ATP. Enzymes catalyze reactions by lowering activation energy.

• Active Transport: Requires energy (often ATP); moves substances against concentration/electrochemical gradients.

• ATP Hydrolysis: Terminal phosphate removed; produces ADP and inorganic phosphate.

• Enzymes: Lower activation energy; do not change reactant/product energy levels.

• Activation Energy Graph: Catalyzed pathway has lower peak; start and end at same energy levels.

Formula:

Cellular Respiration and Fermentation

Big Picture and Electron Transfer

Cellular respiration transfers energy from glucose to ATP through controlled steps involving electron carriers.

• Cellular Respiration: Transfers chemical energy from glucose to ATP; some energy lost as heat.

• Electron Carriers: NAD+ accepts electrons and hydrogen to become NADH.

• NADH: Donates electrons during respiration or biosynthesis.

• Oxygen: Final electron acceptor; reduced to water.

Stages and Locations

Cellular respiration consists of several stages, each occurring in specific cellular locations.

• Glycolysis: Cytoplasm; splits glucose into two pyruvate; produces ATP and NADH.

• Pyruvate Oxidation: Converts pyruvate to acetyl CoA; produces CO2 and NADH.

• Citric Acid Cycle: Mitochondrial matrix; completes oxidation; produces CO2, ATP, NADH, FADH2.

• Electron Transport Chain and ATP Synthase: Inner mitochondrial membrane; cristae increase surface area.

Order of Stages: Glycolysis → Pyruvate Oxidation → Citric Acid Cycle → Oxidative Phosphorylation

Fermentation and Thermogenesis

Fermentation allows glycolysis to continue without oxygen, and thermogenesis produces heat in specialized cells.

• Fermentation: Regenerates NAD+ in absence of oxygen; allows glycolysis to continue.

• Yeast: Produce ethanol anaerobically; favor aerobic respiration when oxygen is available.

• Anaerobic Metabolism: Produces less ATP per glucose; cells consume more glucose to compensate (Pasteur effect).

• Brown Fat: Contains many mitochondria; uncoupling proteins release energy as heat.

Application Practice and Review Checklist

Key Skills and Concepts

• Distinguish commonly confused terms (e.g., hypothesis vs. theory, energy flow vs. nutrient cycling, dehydration vs. hydrolysis, diffusion vs. active transport).

• Identify structures and processes from diagrams or graphs.

• Explain answers using biological reasoning.

• Review functions of major organelles and trace a secreted protein through the cell.

• Predict water movement and cell volume changes based on solute concentrations.

• Trace energy and electrons through cellular respiration stages.

Sample Application Questions

• Explain why energy flows through an ecosystem while matter cycles.

• Identify hypothesis, control group, independent variable, and dependent variable in an experiment.

• Explain the rise of antibiotic-resistant bacteria after exposure.

• Calculate protons, neutrons, and electrons for an atom given atomic number and mass number.

• Rank O, N, C, H by electronegativity; identify most polar bond.

• Compare polar covalent bonds within water and hydrogen bonds between water molecules.

• Compare dehydration and hydrolysis reactions.

• Explain why humans digest starch but not cellulose; why cows can digest cellulose.

• Trace a secreted protein from gene to release.

• Compare mitochondria and chloroplasts (structure and function).

• Predict effects of isotonic, hypotonic, and hypertonic solutions on animal cells.

• Compare simple diffusion, facilitated diffusion, osmosis, and active transport.

• Label ATP, ADP, and terminal phosphate; explain ATP energy release.

• Interpret activation-energy graphs with and without enzyme.

• Order glycolysis, pyruvate oxidation, citric acid cycle, oxidative phosphorylation; state locations.

• Explain necessity of fermentation without oxygen; why anaerobic cells consume more glucose per ATP.

Additional info: This guide covers foundational concepts for General Biology, including cell structure, biomolecules, membrane transport, and cellular respiration, suitable for exam preparation and review.