Biology: Quick Reference Notes (Intro)

Introduction to Biology

• Biology: the scientific study of life.
• Systems biology: models the dynamic behavior of whole biological systems via interactions among parts.
• Five unifying themes (ways of thinking about life):
  • Organization
  • Information
  • Energy and matter
  • Interactions
  • Evolution

Goals and Core Topics

• After study: understand Introduction to biology, Scope of biology, Chemistry in biology.
• Core topics: Introduction to biology, Scope of biology, Chemistry in biology.

Properties of Life

• Seven characteristics shared by living systems:
  • Cellular organization: one or more cells; membranes separate from surroundings.
  • Ordered complexity: highly organized and complex.
  • Sensitivity (response to stimuli).
  • Growth, development, and reproduction; hereditary molecules passed to offspring.
• Additional life properties:
  • Energy utilization
  • Homeostasis
  • Evolutionary adaptation

Organization of Life (Hierarchy)

• Levels of organization (from small to large):
  • Atoms → Molecules → Macromolecules → Organelle → Cell
  • Tissue → Organ → Organ system → Organism
• Populational to ecosystem levels:
  • Population → Species → Community → Ecosystem → Biosphere

Scope of Biology

• CELL: Structure and Function
  • Cell is the smallest unit of life; all living activities arise from cellular activities.
  • Two main cell types: prokaryotic and eukaryotic.
  • Eukaryotic cells have membrane-enclosed organelles; prokaryotic cells do not.
• GENETIC MATERIALS
  • Genome: entire set of genetic instructions.
  • Chromosomes contain DNA; genes encode information for cell identity and function.
  • Gene expression: DNA -> RNA -> protein synthesis.
  • Proteins are major cellular workhorses.
• ENERGY TRANSFORMATION
  • Life requires energy input and transformation; plants (producers) pass energy to consumers.
  • Consumers feed on others or their remains.
• INTERACTION IN BIOLOGICAL SYSTEMS
  • Feedback regulation: negative vs positive feedback.
  • Interactions within ecosystems and with the environment.
• EVOLUTION AND DIVERSITY
  • Evolution: biological change with adaptation to environments.
  • Diversity: ~1.8 million identified species; three domains: Bacteria, Archaea, Eukarya.
  • Unity in life: universal DNA code; shared biochemistry.

Scientific Process

• Science is a way of knowing based on inquiry: observations, hypotheses, testing.
• Process is iterative: tests may revise hypotheses; repeat observations and tests; feedback and replication.
• Core cycle: Observing nature → Forming/testing hypotheses → Predicting results → Experiments/observations → Data analysis → Interpretation → Peer review/replication.

The Role of Chemistry in Biology

• Chemistry provides the context for life processes.
• Key concepts:
  • Elements and compounds; most life matter (~96%) composed of C, H, O, N.
  • Atoms: protons, neutrons, electrons; atomic number and mass; isotopes.
  • Electron shells and valence; reactivity linked to incomplete outer shells.
  • Orbitals determine molecular shape and recognition.
  • Bonds: covalent, ionic, hydrogen, Van der Waals; electronegativity drives polarity.
  • Reactions conserve matter; reversible to reach chemical equilibrium: $k<em>{forward}=k</em>{reverse} \quad \text{at equilibrium}$
  • Ions, acids and bases; pH and buffers.
  • Acid-base concept: $\text{pH}=-\log[\mathrm{H^+}]\,$
  • Carbon dioxide + water forms carbonic acid; buffers stabilize pH.
  • Hydration and hydrophobic effects influence molecular interactions.

Water and Life

• Emergent properties of water support life:
  • Cohesion and surface tension via hydrogen bonds.
  • Adhesion and capillary action.
  • High specific heat and heat of vaporization.
  • Ice less dense than liquid water; solvent properties.
  • Hydrophilic vs hydrophobic interactions.
• Acid-base and buffering in biology:
  • pH scale; buffers resist pH changes (e.g., carbonic acid/bicarbonate in blood).
  • Acids increase [H+]; bases decrease [H+].
  • For a unit pH change: $\Delta \mathrm{pH}=1 \Rightarrow \dfrac{[\mathrm{H^+}]<em>{new}}{[\mathrm{H^+}]</em>{old}}=10$

Macromolecules (Overview)

• Carbohydrates
  • Monosaccharides; disaccharides; polysaccharides (starch, glycogen, cellulose).
  • Functions: energy storage (starch, glycogen); structural support (cellulose).
• Lipids
  • Hydrophobic; include fats, phospholipids, steroids.
  • Fats: glycerol + 3 fatty acids; ester linkages; energy storage;
  • Phospholipids: two fatty acids + phosphate; form lipid bilayers.
  • Steroids: four fused rings (e.g., cholesterol).
• Proteins
  • Functions: enzymes, defense, storage, transport, signaling, movement, structure.
  • Made of amino acids; peptide bonds form polypeptides via dehydration reactions.
  • Protein structure: primary, secondary, tertiary, quaternary.
• Nucleic Acids
  • Polymers of nucleotides; DNA and RNA.
  • DNA: deoxyribose; bases A, T, C, G; double helix; base pairing (A with T, C with G).
  • RNA: ribose; bases A, U, C, G; single-stranded; mRNA directs protein synthesis.

Key Chemical Structures and Reactions (Condensed)

• Dehydration synthesis (protein):
  $\text{Amino acid} + \text{Amino acid} \rightarrow \text{Dipeptide} + \mathrm{H_2O}$
• Peptide bond formation yields polypeptides.
• Fats formation (triacylglycerol):
  $\text{Glycerol} + 3\,\text{Fatty acids} \rightarrow \text{Triacylglycerol} + 3\,\mathrm{H_2O}$
• Nucleic acids base pairing (DNA):
  $\text{A} \leftrightarrow \text{T}, \quad \text{C} \leftrightarrow \text{G}$
• RNA: A pairs with U in RNA.
• pH and buffers: $\text{pH}=-\log[\mathrm{H^+}]$

Quick Reference: Core Concepts for Recall

• Biology definition and five unifying themes: Organization, Information, Energy and matter, Interactions, Evolution.
• Seven life properties: cellular organization, ordered complexity, sensitivity, growth/development/reproduction, energy utilization, homeostasis, evolutionary adaptation.
• Hierarchy of life: atoms → molecules → macromolecules → organelles → cells → tissues → organs → organ systems → organisms → populations → species → communities → ecosystems → biosphere.
• Key macromolecules: carbohydrates (monosaccharides, starch/glycogen/cellulose), lipids (fats, phospholipids, steroids), proteins (amino acids, peptide bonds; structure levels), nucleic acids (DNA/RNA; bases; sugar-phosphate backbone).
• Chemistry in biology: bonds, electronegativity, hydrophilic/hydrophobic interactions, hydrolysis/dehydration, chemical equilibrium, buffers, pH.