Life, Organization & Structure

The Cell: Basic Unit of Life

The cell is the fundamental unit of biological organization, capable of performing all activities required for life. Anything smaller than a cell is not considered alive independently.

• Definition: A cell is the smallest living unit.

• Levels of Complexity: Biological organization increases as follows: cell → tissue → organ → population → community.

• Population: A population consists of interacting individuals of a single species in a defined area.

• Emergence: Emergent properties arise when lower-level components combine, producing new characteristics ("the whole is greater than the sum of its parts").

• Reductionism: A scientific approach that breaks complex systems into simpler parts for study; not a property of living organisms.

DNA & Gene Expression

Genetic Material and Information Flow

DNA is the universal genetic material, organized into chromosomes, and is responsible for both the unity and diversity of life. Genes are inherited units, and gene expression is the process by which information in a gene is used to produce a functional product.

• Unity: All organisms use DNA to store genetic information.

• Diversity: Differences in DNA sequence create the diversity of life.

• Gene Expression: The process includes transcription (DNA to RNA), translation (RNA to protein), and protein folding.

• Sequence: Transcription → Translation → Protein Folding.

Core Themes: Evolution & Energy

Evolution and Biological Energy

Evolution is the central theme of biology, explaining adaptation and diversity. Energy flow and chemical cycling are essential for life.

• Evolution: All living things evolve and adapt.

• Descent with Modification: Shared traits indicate common ancestry; differences arise from adaptation via natural selection.

• Natural Selection: Acts at the population level.

• Domains of Life: Bacteria, Archaea, Eukarya.

• Ultimate Energy Source: The sun provides energy for most organisms.

• Chemical Cycling: Energy and matter are cycled through ecosystems via photosynthesis and decomposition.

• Feedback Regulation: Negative feedback shuts down pathways when enough product is made; positive feedback speeds up pathways.

Scientific Method & Reasoning

Hypotheses, Experiments, and Scientific Theory

The scientific method involves forming and testing hypotheses, using controls, and reasoning to draw conclusions.

• Hypothesis: Must be testable and falsifiable.

• Core Activity: Forming and testing hypotheses.

• Experimental Controls: Control groups provide a baseline for comparison.

• Controlled Experiments: Direct comparison of groups (e.g., plants with and without sodium).

• Inductive Reasoning: Generalizing from specific observations.

• Scientific Theory: A well-supported, widely accepted explanation with broad explanatory power.

Subatomic Particles & Atomic Structure

Atoms, Isotopes, and Radioactivity

Atoms are composed of protons, neutrons, and electrons. Isotopes differ in neutron number, and radioactive isotopes are used in dating and tracing.

• Electrons: Negligible mass; not counted in atomic mass.

• Neutrons: Mass ~1 dalton; neutral charge.

• Protons vs. Electrons: Equal in neutral atoms.

• Isotopes: Same protons, different neutrons; differ in atomic mass.

• Radioactive Isotopes: Decay spontaneously, releasing radiation.

• Radiometric Dating: Uses half-life to determine age of fossils/rocks.

• Radioactive Tracers: Used in biological research and medicine.

Chemical Reactivity & Electron Shells

Valence Electrons and Orbitals

Chemical properties depend on the number of unpaired electrons in the valence shell. Orbitals are regions where electrons are likely found.

• Valence Electrons: Determine chemical reactivity.

• Electron Orbitals: 3D spaces; each holds up to 2 electrons.

Elements of Life

Major and Trace Elements

Living organisms are composed mainly of four elements, with trace elements required in small amounts.

• Four Main Elements: Hydrogen, Oxygen, Nitrogen, Carbon (~96% of mass).

• Trace Elements: Needed in minute quantities.

• Essential Elements: Some (e.g., iron) are required by all life; others only by certain species.

Chemical Bonds & Electronegativity

Bond Types and Properties

Chemical bonds include covalent, ionic, and hydrogen bonds, each with distinct properties.

• Covalent Bonds: Atoms share valence electrons.

• Nonpolar Covalent Bonds: Equal sharing; atoms have similar electronegativity.

• Polar Covalent Bonds: Unequal sharing; one atom is more electronegative (e.g., oxygen).

• Ions: Formed when proton and electron numbers are unequal.

• Anions: Negatively charged ions (more electrons than protons).

• Ionic Bonds: Electrons are transferred; opposite charges attract.

• Hydrogen Bonds: Weak bonds between hydrogen and electronegative atoms (O, N).

Molecular Shape & Chemical Reactions

Shape and Function; Chemical Changes

The 3D shape of molecules determines their biological function. Chemical reactions involve making and breaking bonds.

• Molecular Shape: Determines recognition and response (lock and key analogy).

• Molecular Mimics: Similar shapes can bind the same receptors.

• Chemical Reactions: Reactants are transformed into products.

Water and Life

Polarity & Hydrogen Bonding

Water's polarity enables hydrogen bonding, making it an excellent solvent for charged and polar substances.

• Polarity: Oxygen and hydrogen share electrons unequally, creating partial charges.

• Hydrogen Bonds: Form between water molecules and with other polar substances.

Emergent Properties of Water

Water exhibits unique properties due to hydrogen bonding, crucial for life.

• Cohesion: Water molecules stick together, aiding transport in plants.

• Adhesion: Water clings to other substances.

• Surface Tension: Allows insects to walk on water.

• Density of Ice: Ice is less dense than liquid water; floats due to crystal structure.

• Hydrophilic vs. Hydrophobic: Hydrophilic substances are attracted to water; hydrophobic substances repel water.

Thermal Properties & Temperature Regulation

Water's high specific heat and heat of vaporization stabilize temperature and enable cooling mechanisms.

• High Specific Heat: Water absorbs/release heat slowly, stabilizing environments.

• High Heat of Vaporization: Evaporation cools organisms (e.g., sweating).

• Boiling Point: Water's boiling point is higher than similar-sized nonpolar molecules due to hydrogen bonding.

Acids, Bases & the pH Scale

Acids and bases affect hydrogen ion concentration; pH is a logarithmic scale.

• Acids: Donate ions.

• Bases: Accept or release ions.

• pH Scale: Each unit represents a 10-fold change in concentration.

• Examples: Moving from pH 8 to pH 10 is a 100x decrease in ; pH 3 to pH 7 is a 10,000x decrease.

• Buffers: Minimize changes in and to maintain pH stability.

Molar Solutions & Calculations

Solutions are prepared by dissolving a specific mass of solute in a given volume of solvent.

• 2 M Glucose Solution: Glucose molar mass = 180 g/mol. For 2 M in 1 L, dissolve 360 g glucose in water and bring volume to 1 L.

• 1 mM Methanol Solution: Methanol molar mass = 32 g/mol. For 1 mM in 1 L, dissolve 0.032 g methanol in water and bring volume to 1 L.

Carbon and the Molecular Diversity of Life

The Basics of Carbon & Organic Chemistry

Carbon is central to organic chemistry, forming diverse molecules due to its tetravalence.

• Organic Chemistry: Carbon always covalently bonded to hydrogen.

• Atomic Structure: Carbon has 4 valence electrons; forms 4 covalent bonds.

• Carbon Skeletons: Vary in length, branching, double bond position, and ring formation.

Hydrocarbons

Hydrocarbons are organic molecules composed only of carbon and hydrogen.

• Properties: Hydrophobic, nonpolar, energy-rich.

Abiotic Origin of Life & Miller's Experiment

Stanley Miller's experiment demonstrated abiotic synthesis of organic compounds from primitive atmospheric components.

• Application: Provided evidence for chemical origins of life.

Types of Isomers

Isomers have the same chemical formula but different structures.

Biologically Important Chemical Groups

Chemical groups confer unique properties to biological molecules.

• 6 Essential Elements: Carbon, Nitrogen, Oxygen, Hydrogen, Phosphate, Sulfur (CHONPS).

• Carboxyl Group (): Acts as an acid; can donate .

• Amino Group (): Acts as a base; can accept .

• Sulfhydryl Group (): Stabilizes protein structure via disulfide bridges.

• Methyl Group (): Regulates gene expression when bound to DNA/proteins.

• Phosphate Group (): Forms ATP; stores energy for cellular work.

The Structure and Function of Large Biological Molecules

Macromolecules & Synthesis/Breakdown Reactions

Macromolecules include carbohydrates, lipids, proteins, and nucleic acids. Monomers are joined into polymers via dehydration synthesis and broken down by hydrolysis.

• Dehydration Synthesis: Joins monomers; water is released.

• Hydrolysis: Breaks polymers; water is used to break bonds.

Carbohydrates

Carbohydrates are energy storage molecules with a general formula of in a 1:2:1 ratio.

• Monosaccharides: Simple sugars; form rings in water.

• Disaccharides: Sucrose, lactose, maltose.

• Polysaccharides: Starch (plants), glycogen (animals), cellulose (plant cell walls), chitin (insect exoskeletons).

• Cellulose: Animals cannot digest; cows rely on gut microorganisms.

Lipids

Lipids are hydrophobic molecules, including fats, phospholipids, and steroids.

• Phospholipids: Main component of cell membranes.

• Fats: Unsaturated fats have cis double bonds; liquid at room temperature.

• Steroids: Four fused rings; cholesterol is a precursor for sex hormones.

• Sex Hormones: Estrogen, progesterone, testosterone (lipid class).

Proteins

Proteins are polymers of amino acids, joined by peptide bonds, and have multiple structural levels.

• Primary Structure: Linear sequence of amino acids; single change can cause disease (e.g., sickle-cell anemia).

• Secondary Structure: Alpha helix and beta sheet; stabilized by hydrogen bonds.

• Tertiary Structure: 3D shape from R group interactions.

• Chaperonins: Assist in proper protein folding.

Nucleic Acids & DNA

Nucleic acids are polymers of nucleotides, which consist of a nitrogenous base, pentose sugar, and phosphate group.

• Nitrogenous Bases: Purines (A, G); Pyrimidines (C, T, U).

• DNA Structure: Double helix; strands run antiparallel.

• Phosphorus: Essential for DNA synthesis; forms backbone of nucleic acids.

Quick Recall Checklist

• Disaccharides: Sucrose, Lactose, Maltose

• Energy Storage Polysaccharides: Starch (Plants), Glycogen (Animals/Humans)

• Structural Polysaccharides: Cellulose (Plant walls), Chitin (Insect exoskeletons)

• Steroids (4 Fused Rings): Cholesterol, Estrogen, Testosterone, Progesterone

• Purines: Adenine (A) & Guanine (G)

• Protein Folding Assistant: Chaperonins