Foundations of Biology: Key Concepts and Processes

Introduction to Biology

Levels of Biological Organization

Biological systems are organized in a hierarchy from the smallest chemical units to the entire biosphere. Each level exhibits emergent properties that arise from interactions among components.

• Atom → Molecule → Organelle → Cell → Tissue → Organ → Organism → Population → Community → Ecosystem → Biosphere

• Emergent properties: New characteristics that appear at each level due to complex interactions (e.g., life emerges at the cellular level).

Genetic Information and Gene Expression

• DNA: The hereditary molecule storing genetic information.

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

• Gene expression: The process by which information from a gene is used to synthesize RNA and protein (includes transcription and translation).

Energy Flow and Matter Cycling

• Energy flow: Sunlight → Producers (plants) → Consumers (animals) → Heat loss.

• Matter cycles: Elements like carbon, nitrogen, and water cycle through ecosystems.

Feedback Regulation

• Negative feedback: Reduces the original stimulus (e.g., body temperature regulation).

• Positive feedback: Amplifies the original stimulus (e.g., blood clotting).

Evolution and Natural Selection

• Evolution: Change in the genetic composition of populations over generations.

• Natural selection: Individuals with advantageous traits reproduce more successfully, leading to adaptation.

Domains of Life

• Bacteria

• Archaea

• Eukarya

Scientific Inquiry

• Observation: Gathering information about phenomena.

• Hypothesis: Testable explanation for observations.

• Prediction: Expected outcome if hypothesis is correct.

• Variables: Independent (manipulated), Dependent (measured), Controlled (kept constant).

• Inductive reasoning: Specific observations to general conclusions.

• Deductive reasoning: General principles to specific predictions.

Chemistry of Cellular Components

Atoms, Molecules, and Bonds

• Atom: Smallest unit of matter.

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

• Compound: Substance formed from two or more elements.

• Molecule: Two or more atoms bonded together.

• Covalent bond: Atoms share electrons.

• Polar covalent bond: Unequal sharing of electrons.

• Nonpolar covalent bond: Equal sharing of electrons.

• Ionic bond: Electron transfer creates charged ions.

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

• Van der Waals interactions: Temporary weak attractions between molecules.

Properties of Water

• Cohesion: Water molecules stick to each other.

• Adhesion: Water molecules stick to other surfaces.

• Surface tension: Difficulty in breaking the surface of water.

• High specific heat: Water resists temperature changes.

• Ice floats: Hydrogen bonds form a lattice, making ice less dense than liquid water.

• Solvent: Water dissolves many substances ("universal solvent").

• Hydrophilic: Water-loving substances.

• Hydrophobic: Water-fearing substances.

Solutions and Acids/Bases

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

• Solute: Substance dissolved in solvent.

• Aqueous solution: Solution where water is the solvent.

• Acid: Increases H+ concentration.

• Base: Decreases H+ concentration.

• pH: Measure of H+ concentration.

Biological Molecules

• Functional groups: Hydroxyl, carbonyl, carboxyl, amino, sulfhydryl, phosphate, methyl.

• Isomers: Molecules with the same formula but different structures (structural, cis-trans, enantiomers).

• Monomer: Building block of polymers.

• Polymer: Chain of monomers.

• Dehydration reaction: Builds polymers by removing water.

• Hydrolysis: Breaks polymers by adding water.

Major Classes of Biomolecules

• Carbohydrates: Sugars and polysaccharides (energy storage and structure).

• Lipids: Fats, phospholipids, steroids (energy storage, membranes, signaling).

• Proteins: Made of amino acids; four levels of structure (primary, secondary, tertiary, quaternary).

• Nucleic acids: DNA and RNA (information storage and transfer).

• ATP: Main energy currency of the cell.

Quantitative Concepts

• Molecular mass: Sum of atomic masses in a molecule.

• Avogadro’s number: $6.02 \times 10^{23}$

• Molarity: Moles of solute per liter of solution.

• Redox reactions: Electron transfer; oxidation (loss of electrons), reduction (gain of electrons).

A Tour of the Cell

Microscopy and Cell Structure

• Light microscope: Uses light to view living cells.

• Electron microscope: High resolution; only dead samples.

• TEM (Transmission Electron Microscope): Views internal structures.

• SEM (Scanning Electron Microscope): Views surface structures.

• Cell fractionation: Separates organelles for study.

Cell Types

• Prokaryotic cells: No nucleus; generally smaller (e.g., bacteria, archaea).

• Eukaryotic cells: Have a nucleus and membrane-bound organelles (e.g., plants, animals, fungi, protists).

Major Organelles and Structures

• Nucleus: Stores DNA.

• Ribosomes: Site of protein synthesis.

• Rough ER: Synthesizes proteins.

• Smooth ER: Synthesizes lipids, detoxifies chemicals.

• Golgi apparatus: Modifies and ships proteins.

• Lysosomes: Digestion of macromolecules.

• Vacuoles: Storage (large in plants).

• Mitochondria: ATP production via cellular respiration.

• Chloroplasts: Photosynthesis in plants and algae.

• Microtubules: Cell shape, transport, spindle fibers.

• Microfilaments: Actin; cell movement.

• Intermediate filaments: Structural support.

Cell Junctions

• Tight junctions: Seal cells together.

• Desmosomes: Anchor cells.

• Gap junctions: Communication between animal cells.

• Plasmodesmata: Channels between plant cells.

Membrane Structure and Function

Membrane Composition

• Fluid mosaic model: Membrane is a mosaic of phospholipids, proteins, and carbohydrates.

• Phospholipids: Amphipathic molecules forming a bilayer.

• Integral proteins: Span the membrane.

• Peripheral proteins: Attached to membrane surface.

Transport Across Membranes

• Diffusion: Movement of molecules down their concentration gradient.

• Osmosis: Diffusion of water across a membrane.

• Facilitated diffusion: Transport via channels or carriers.

• Isotonic: No net water movement.

• Hypertonic: Cell loses water and shrinks.

• Hypotonic: Cell gains water and swells.

• Active transport: Movement against gradient; requires ATP.

• Na+/K+ pump: Maintains ion gradients in animal cells.

• Proton pump: Moves H+ ions across membranes.

Bulk Transport

• Endocytosis: Uptake of materials (includes phagocytosis, pinocytosis, receptor-mediated endocytosis).

• Exocytosis: Secretion of materials out of the cell.

DNA: Molecular Basis of Inheritance

DNA Structure and Replication

• DNA: Double helix, antiparallel strands, complementary base pairing (A-T, G-C).

• Griffith experiment: Demonstrated transformation in bacteria.

• Hershey & Chase: Showed DNA is the genetic material.

• Meselson & Stahl: Demonstrated semiconservative replication.

DNA Replication Enzymes

• Helicase: Unwinds DNA.

• Primase: Synthesizes RNA primer.

• DNA polymerase III: Adds nucleotides to new DNA strand.

• DNA polymerase I: Replaces RNA primers with DNA.

• Ligase: Seals Okazaki fragments.

• Topoisomerase: Relieves strain ahead of replication fork.

• Leading strand: Synthesized continuously.

• Lagging strand: Synthesized in Okazaki fragments.

Chromatin Structure

• Histones: Proteins that package DNA.

• Nucleosome: DNA wrapped around histones.

• Euchromatin: Loosely packed, active in transcription.

• Heterochromatin: Densely packed, inactive.

Gene Expression

Transcription and RNA Processing

• Transcription: DNA is transcribed to RNA.

• Initiation: RNA polymerase binds promoter (TATA box).

• Elongation: RNA strand is synthesized.

• Termination: RNA transcript is released.

• RNA processing: Addition of 5’ cap, poly-A tail, and splicing of introns.

Translation

• Translation: RNA is translated into protein.

• tRNA: Transfers amino acids to ribosome.

• Anticodon: tRNA sequence complementary to mRNA codon.

• Ribosome: Has A, P, E sites for translation.

Mutations

• Point mutations: Silent, missense, nonsense.

• Frameshift mutations: Insertion or deletion alters reading frame.

• Mutagens: Agents causing mutations (e.g., radiation, chemicals).

Mendelian Genetics

Basic Principles

• Character: Heritable feature (e.g., flower color).

• Trait: Variant of a character (e.g., purple or white).

• Gene: Heritable factor.

• Allele: Alternative version of a gene.

• Locus: Location of a gene on a chromosome.

• Homozygous: Two identical alleles.

• Heterozygous: Two different alleles.

• Phenotype: Observable traits.

• Genotype: Genetic makeup.

Mendel’s Laws

• Law of segregation: Alleles separate during gamete formation.

• Law of independent assortment: Genes on different chromosomes assort independently.

Extensions and Patterns

• Incomplete dominance: Heterozygote shows intermediate phenotype.

• Codominance: Both alleles expressed.

• Pleiotropy: One gene affects multiple traits.

• Epistasis: One gene affects expression of another.

• Polygenic inheritance: Multiple genes affect one trait.

• Pedigrees: Diagrams tracking inheritance in families.

Chromosomal Basis of Inheritance

Sex Chromosomes and Linkage

• X-linked genes: More common in males due to single X chromosome (hemizygous).

• Barr body: Inactive X chromosome in females.

• XIST gene: Inactivates one X chromosome.

Genetic Recombination

• Crossing over: Exchange of DNA between homologous chromosomes.

• Recombinants: Offspring with new combinations of traits.

• Map unit: 1% recombination frequency.

Chromosomal Alterations

• Nondisjunction: Failure of chromosomes to separate properly.

• Aneuploidy: Abnormal number of chromosomes (e.g., Trisomy 21, Turner syndrome, Klinefelter syndrome).

Cell Cycle

Phases of the Cell Cycle

• G1 phase: Cell growth.

• S phase: DNA replication.

• G2 phase: Preparation for division.

• Mitosis: Division of genetic material.

• Cytokinesis: Division of cytoplasm.

Regulation

• Cyclins: Regulatory proteins.

• Cyclin-dependent kinases (Cdks): Activated by cyclins.

• MPF (Maturation Promoting Factor): Triggers mitosis.

• Checkpoints: G1, G2, M; ensure proper progression.

• Cancer: Loss of cell cycle regulation; can metastasize.

Meiosis and Sexual Life Cycles

Meiosis Overview

• Meiosis: Two divisions produce four non-identical haploid cells.

• Meiosis I: Homologous chromosomes separate.

• Meiosis II: Sister chromatids separate.

Sources of Genetic Variation

• Crossing over

• Independent assortment

• Random fertilization

Metabolism

Energy Concepts

• Kinetic energy: Energy of motion.

• Potential energy: Stored energy.

• Chemical energy: Energy stored in chemical bonds.

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

• Second law of thermodynamics: Entropy (disorder) increases.

• Free energy equation:

$\Delta G = \Delta H - T\Delta S$

• Exergonic: Releases energy (spontaneous).

• Endergonic: Requires energy input (non-spontaneous).

Enzymes

• Enzymes: Biological catalysts; lower activation energy.

• Active site: Region where substrate binds.

• Induced fit: Enzyme changes shape to fit substrate.

• Competitive inhibition: Inhibitor blocks active site.

• Noncompetitive inhibition: Inhibitor binds elsewhere, changing enzyme shape.

• Allosteric regulation: Regulatory molecule binds at a site other than active site.

• Feedback inhibition: End product inhibits pathway.

Cellular Respiration

Stages of Cellular Respiration

• Glycolysis: Occurs in cytosol; produces 2 ATP, 2 NADH.

• Pyruvate oxidation: Converts pyruvate to acetyl-CoA.

• Citric acid cycle (Krebs cycle): Produces 2 ATP, 6 NADH, 2 FADH2.

• Oxidative phosphorylation: Produces ~26–28 ATP via electron transport chain and chemiosmosis.

Fermentation

• Alcohol fermentation: Produces ethanol.

• Lactic acid fermentation: Produces lactate.

Photosynthesis

Light Reactions

• Occur in thylakoid membranes.

• Photosystem II (PSII) and Photosystem I (PSI) involved.

• Produce ATP, NADPH, and O2.

Calvin Cycle

• Carbon fixation: CO2 attached to RuBP by rubisco.

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

• Regeneration: RuBP is regenerated for the cycle to continue.

Types of Plants

• C3 plants: Standard Calvin cycle.

• C4 plants: Spatial separation of steps to minimize photorespiration.

• CAM plants: Temporal separation; fix CO2 at night.

Example: In humans, sickle cell anemia is caused by a missense mutation in the hemoglobin gene, demonstrating the impact of gene mutations on phenotype.

Additional info: This guide summarizes foundational concepts in introductory biology, integrating key terms, processes, and examples relevant for college-level study.