Biology: Exploring Life

1.1 Biology is the Scientific Study of Life

Biology is the branch of science concerned with the study of life and living organisms. It encompasses a wide range of topics, from molecular mechanisms to the interactions of organisms with their environment.

• Biology: The scientific study of life, including structure, function, growth, origin, evolution, and distribution of living organisms.

• Characteristics of Life: Order, regulation, energy processing, growth and development, reproduction, response to the environment, and evolutionary adaptation.

• Scientific Inquiry: The process of asking questions, making observations, forming hypotheses, conducting experiments, and drawing conclusions.

• Example: Studying how plants convert sunlight into energy through photosynthesis.

1.2 Biologists Arrange the Diversity of Life into Three Domains

All living organisms are classified into three major domains based on genetic and cellular differences.

• Three Domains of Life:

  • Bacteria: Prokaryotic, unicellular organisms with simple cell structure.

  • Archaea: Prokaryotic, often found in extreme environments, genetically distinct from bacteria.

  • Eukarya: Eukaryotic organisms, including protists, fungi, plants, and animals.

• Classification: Organisms are further classified into kingdoms, phyla, classes, orders, families, genera, and species.

1.3 Life’s Hierarchy of Organization

Biological systems are organized into a hierarchy, with each level exhibiting emergent properties not present at lower levels.

• Levels of Organization:

  1. Biosphere

  2. Ecosystem

  3. Community

  4. Population

  5. Organism

  6. Organ system

  7. Organ

  8. Tissue

  9. Cell

  10. Organelle

  11. Molecule

• Emergent Properties: New characteristics that arise at each level due to the arrangement and interactions of parts.

The Chemical Context of Life

2.1 Matter, Elements, Compounds, and Trace Elements

All living and nonliving things are composed of matter, which is made up of elements and compounds.

• Matter: Anything that occupies space and has mass.

• Element: A substance that cannot be broken down into other substances by chemical means (e.g., carbon, oxygen).

• Compound: A substance consisting of two or more elements in a fixed ratio (e.g., H2O).

• Trace Elements: Elements required by organisms in minute quantities (e.g., iron, iodine, fluoride).

• Example: Iodine is added to salt to prevent thyroid problems; fluoride is added to water to prevent tooth decay; iron is essential for oxygen transport in blood.

2.3 Structure of Atoms

Atoms are the smallest units of matter that retain the properties of an element.

• Protons: Positively charged particles in the nucleus.

• Neutrons: Neutral particles in the nucleus.

• Electrons: Negatively charged particles orbiting the nucleus.

• Atomic Number: Number of protons in an atom.

• Mass Number: Sum of protons and neutrons.

• Isotopes: Atoms of the same element with different numbers of neutrons.

• Radioactive Isotopes: Unstable isotopes that decay, emitting radiation.

2.4 Uses and Dangers of Radioactive Isotopes

• Uses: Medical imaging, cancer treatment, dating fossils.

• Dangers: Radiation can damage living tissue and DNA.

2.5 Electron Configuration and Chemical Behavior

The arrangement of electrons in shells determines how atoms interact and form bonds.

• Valence Electrons: Electrons in the outermost shell; determine chemical reactivity.

2.6–2.8 Types of Chemical Bonds

• Covalent Bonds: Atoms share electron pairs; strong bonds.

  • Nonpolar Covalent Bonds: Electrons shared equally.

  • Polar Covalent Bonds: Electrons shared unequally, creating partial charges.

• Ionic Bonds: Transfer of electrons from one atom to another, forming ions.

• Hydrogen Bonds: Weak attractions between a hydrogen atom and an electronegative atom (e.g., in water).

2.9 Chemical Reactions

• Chemical Reaction: The making and breaking of chemical bonds, leading to changes in the composition of matter.

• Reactants: Starting materials.

• Products: Resulting materials.

• Example: Photosynthesis:

2.10–2.13 Water’s Life-Supporting Properties

• Cohesion: Attraction between molecules of the same substance (e.g., water molecules stick together).

• Adhesion: Attraction between different substances (e.g., water to plant cell walls).

• Surface Tension: Measure of how difficult it is to stretch or break the surface of a liquid.

• Heat vs. Temperature: Heat is total energy; temperature is average kinetic energy.

• Evaporative Cooling: Sweating cools the body as water evaporates.

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

• Solution: Homogeneous mixture of two or more substances.

• Solvent: Dissolving agent (e.g., water).

• Solute: Substance dissolved.

2.14 Acids, Bases, pH, and Buffers

• Acid: Substance that increases H+ concentration in solution.

• Base: Substance that reduces H+ concentration.

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

• Buffers: Substances that minimize changes in pH by accepting or donating H+.

Carbon and the Molecular Diversity of Life

3.1 Carbon’s Versatility

Carbon atoms can form four covalent bonds, allowing for a diversity of stable, complex molecules essential for life.

• Organic Compounds: Molecules containing carbon and hydrogen.

• Hydrocarbons: Compounds composed only of carbon and hydrogen.

• Carbon Skeleton: The chain of carbon atoms in an organic molecule.

• Isomers: Compounds with the same formula but different structures.

3.2 Functional Groups

• Functional Groups: Specific groups of atoms attached to carbon skeletons that give molecules distinctive properties.

  • Hydroxyl (–OH)

  • Carbonyl (C=O)

  • Carboxyl (–COOH)

  • Amino (–NH2)

  • Phosphate (–PO4)

  • Methyl (–CH3)

3.3 Macromolecules: Monomers and Polymers

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

• Monomers: Small building blocks.

• Polymers: Chains of monomers.

• Dehydration Synthesis: Joins monomers by removing water.

• Hydrolysis: Breaks polymers by adding water.

3.4–3.7 Carbohydrates

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

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

• Polysaccharides: Long chains (e.g., starch, glycogen, cellulose, chitin).

• Functions: Energy storage, structural support.

• High-Fructose Corn Syrup: Produced by converting glucose to fructose; used as a sweetener.

3.8–3.10 Lipids

• Fats: Glycerol + fatty acids; energy storage.

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

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

• Trans Fats: Artificially hydrogenated; associated with health risks.

• Phospholipids: Major component of cell membranes; hydrophilic head, hydrophobic tails.

• Steroids: Four fused rings; e.g., cholesterol, hormones.

• Anabolic Steroids: Synthetic variants of testosterone; health risks include liver damage, hormonal imbalance.

3.12–3.14 Proteins

• Amino Acids: Building blocks of proteins; 20 types.

• Peptide Bonds: Link amino acids.

• Protein Structure:

  1. Primary: Sequence of amino acids.

  2. Secondary: Alpha helices and beta sheets.

  3. Tertiary: 3D folding.

  4. Quaternary: Multiple polypeptides.

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

• Function: Enzymes, transport, defense, structure, signaling.

3.15 Nucleic Acids

• DNA: Double helix; stores genetic information.

• RNA: Single-stranded; involved in protein synthesis.

• Nucleotides: Monomers of nucleic acids; consist of a sugar, phosphate, and nitrogenous base.

• Comparison Table:

A Tour of the Cell

4.1 Microscopy and Cell Theory

• Light Microscope: Uses light to view cells; lower magnification and resolution.

• Scanning Electron Microscope (SEM): Surface images; high resolution.

• Transmission Electron Microscope (TEM): Internal structures; highest resolution.

• Magnification: Increase in apparent size.

• Resolving Power: Ability to distinguish two close objects as separate.

• Cell Theory: All living things are composed of cells; cells are the basic unit of life.

4.2 Cell Size and Plasma Membrane

• Limits to Cell Size: Surface area-to-volume ratio limits efficiency of transport and metabolism.

• Plasma Membrane: Phospholipid bilayer with embedded proteins; controls entry and exit of substances.

4.3–4.4 Prokaryotic vs. Eukaryotic Cells

• Prokaryotic Cells: No nucleus, no membrane-bound organelles; e.g., bacteria, archaea.

• Eukaryotic Cells: Nucleus, membrane-bound organelles; e.g., plants, animals, fungi, protists.

• Compartmentalization: Eukaryotic cells have organelles that perform specialized functions.

• Plant vs. Animal Cells:

  • Plant cells: Cell wall, chloroplasts, large central vacuole.

  • Animal cells: Lysosomes, centrioles.

4.5–4.6 Nucleus and Ribosomes

• Nucleus: Contains DNA; surrounded by nuclear envelope.

• Nucleolus: Site of ribosome synthesis.

• DNA Packaging: DNA wraps around histone proteins to form chromatin.

• Ribosomes: Synthesize proteins; free in cytoplasm or bound to rough ER.

4.7–4.12 Endomembrane System

• Rough ER: Studded with ribosomes; protein synthesis.

• Smooth ER: Lipid synthesis, detoxification.

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

• Lysosomes: Digestive enzymes; break down waste.

• Vacuoles: Storage; large central vacuole in plants.

• Peroxisomes: Break down fatty acids, detoxify harmful substances.

4.13–4.15 Energy-Converting Organelles

• Mitochondria: Site of cellular respiration; produces ATP.

• Chloroplasts: Site of photosynthesis in plants and algae.

• Endosymbiosis Theory: Mitochondria and chloroplasts originated as free-living prokaryotes engulfed by ancestral eukaryotes.

4.16–4.18 Cytoskeleton and Motility

• Microfilaments: Actin filaments; cell shape and movement.

• Intermediate Filaments: Structural support.

• Microtubules: Tubulin; cell shape, organelle movement, cilia, and flagella.

• Cilia and Flagella: Motile structures; cilia are short and numerous, flagella are long and few.

4.19–4.22 Cell Surfaces and Junctions

• Extracellular Matrix (ECM): Network outside animal cells; support and signaling.

• Tight Junctions: Seal cells together.

• Anchoring Junctions: Attach cells to each other or ECM.

• Gap Junctions: Channels for communication between animal cells.

• Plant Cell Walls: Provide support; made of cellulose.

• Plasmodesmata: Channels between plant cells for transport and communication.

• Functional Categories of Organelles:

  1. Genetic control (nucleus, ribosomes)

  2. Manufacturing, distribution, breakdown (ER, Golgi, lysosomes, vacuoles, peroxisomes)

  3. Energy processing (mitochondria, chloroplasts)

  4. Structural support, movement, communication (cytoskeleton, plasma membrane, ECM, cell junctions)

Key Terms

• acid, adhesion, aqueous solution, atom, atomic mass, atomic number, base, buffers, chemical bond, chemical reactions, cohesion, compound, covalent bond, electron, electron shells, electronegativity, element, evaporative cooling, heat, hydrogen bond, ion, ionic bond, isotopes, mass number, matter, molecule, neutron, nonpolar covalent bonds, nucleus, ocean acidification, pH scale, polar covalent bond, polar molecule, products, proton, radioactive isotope, reactants, salt, solute, solution, solvent, surface tension, temperature, thermal energy, trace elements

• amino acids, amino group, anabolic steroids, carbohydrates, carbonyl group, carboxyl group, cellulose, chitin, cholesterol, dehydration reaction, denaturation, deoxyribonucleic acid (DNA), disaccharides, double helix, enzymes, fat, functional groups, gene, glycogen, hydrocarbons, hydrolysis, hydrophilic, hydrophobic, hydroxyl group, isomers, lipids, macromolecules, methyl group, monomers, monosaccharides, nucleic acids, nucleotides, organic compound, peptide bond, phosphate group, phospholipids, polymers, polypeptide, polysaccharides, primary structure, protein, quaternary structure, ribonucleic acid (RNA), saturated fatty acid, secondary structure, starch, steroids, tertiary structure, trans fat, unsaturated fatty acid