General Biology: Foundations, Themes, and Scientific Inquiry

Five Unifying Themes in Biology

• Organization

• Information

• Energy and Matter

• Interactions

• Evolution (discussed in later sections)

Theme: Organization – New Properties Emerge at Successive Levels

Hierarchy of Biological Organization (From Largest to Smallest)

• Biosphere – All life on Earth

• Ecosystems – Living + nonliving in a region (e.g., soil, air, water)

• Communities – Different species living together

• Populations – Individuals of the same species in one area

• Organisms – Individual living beings

• Organs – Body parts with specific functions (e.g., leaf)

• Tissues – Groups of similar cells

• Cells – Basic unit of life

• Organelles – Structures within cells (e.g., chloroplasts)

• Molecules – Chemical structures made of atoms

Key Concepts

• Reductionism: Studying smaller parts to understand the whole (e.g., DNA structure).

• Emergent Properties: New functions arise at higher levels due to arrangement and interaction (e.g., photosynthesis occurs only in an intact chloroplast).

• Systems Biology: Studies complex interactions within biological systems.

Structure and Function

• Form fits function at every level.

• Leaf shape = efficient sunlight capture

• Hummingbird wings = unique hovering and backward flight

• Understanding structure helps predict function.

Theme: Information – Expression and Transmission of Genetic Information

DNA: The Genetic Blueprint

• DNA found in chromosomes: made of nucleotides (A, T, C, G).

• Genes are units of inheritance → code for proteins or RNAs.

Gene Expression Process

• Genes are the units of inheritance that transmit info from parents to offspring.

• DNA is made of two long chains arranged in a double helix.

• Transcription: DNA → mRNA

• Translation: mRNA → amino acid chain → protein

• Protein Folding: Functional 3D structure is formed

Universality of Genetic Code

• All organisms use the same basic genetic code → evidence for common ancestry.

• Genetic similarities between organisms can be traced through ancestry.

Genomics and Proteomics

• Genome: All genetic material in an organism

• Proteome: Full set of proteins a cell/organism expresses

• Technological Advances:

  • High-throughput sequencing

  • Bioinformatics: Computational biology

  • Interdisciplinary teams (biology + tech)

• Bioinformatics: Using computers to analyze DNA

Theme: Energy and Matter – Life Requires Energy Transfer and Transformation

Key Concepts

• Life processes require work, which needs energy.

• Energy mainly enters as sunlight → converted to chemical energy via photosynthesis.

• Producers (plants) → Consumers (animals)

Chemical Cycling

• Chemicals are recycled: Air/soil → organisms → decomposers → back to environment

Theme: Interactions – Life Involves Interacting Systems

Organism Interactions

• Biotic: With other organisms (e.g., pollinators, predators, mutualism)

• Abiotic: With environment (e.g., air, sunlight, soil)

Types of Species Interactions

• Mutualism: Both benefit (e.g., fish remove parasites from sea turtle)

• Predation: One benefits, one harmed (e.g., lion eats zebra)

• Competition: Both may be harmed (e.g., plants compete for limited resources)

Human Impact & Climate Change

• Fossil fuel use ↑ CO2 → global warming

• Climate change effects:

  • Habitat loss (e.g., polar bears, lizards)

  • Shifting species ranges

  • Population declines and extinctions

What Is Evolution?

Definition

• Evolution is the process by which species accumulate differences from their ancestors as they adapt to different environments over time.

Key Ideas

• Evolution explains both the unity (shared traits) and diversity (differences) of life.

• Example: Seals, bats, whales, and humans all have similar skeletal structures due to common ancestry.

Unity and Diversity of Life

• Unity: Results from heritable changes and adaptation to different environments.

• Diversity: Shows life has evolved for billions of years, creating vast diversity.

• Fossil Record: Shows life has evolved for billions of years, creating vast diversity.

Classification of Life

• Purpose: To organize species based on similarities and relationships.

• Hierarchy of Classification:

  • Species → Genus → Family → Order → Class → Phylum → Kingdom → Domain

• Example: Leopard (Panthera pardus) is in:

  • Genus: Panthera

  • Family: Felidae

  • Order: Carnivora

  • Class: Mammalia

  • Phylum: Chordata

  • Kingdom: Animalia

Three Domains of Life

• Bacteria: Most diverse and widespread prokaryotes. No nucleus.

• Archaea: Prokaryotes living in extreme environments (e.g., hot springs, salty lakes).

• Eukarya: All eukaryotes. All have a nucleus, DNA in nucleus.

  • Kingdom Plantae – Photosynthesis

  • Kingdom Animalia – Ingest food

  • Kingdom Fungi – Absorb nutrients

  • Protists – Mostly unicellular and simple multicellular eukaryotes

Charles Darwin & Natural Selection

• Key Work: On the Origin of Species (1859)

• Two Main Ideas:

  • Descent with modification – All species are related and have diverged over time.

  • Natural selection – Main mechanism of evolution.

• Darwin's Observations:

  • Variation in traits (heritable)

  • Overproduction of offspring → competition

  • Adaptation: Traits that enhance survival become more common.

Natural Selection Example

• Scenario: Beetles on darkened soil after a fire.

  • Light-colored beetles are eaten more often.

  • Over time, darker beetles become more common.

Tree of Life

• Shared Structures: Similar limb structures in mammals (e.g., bats, whales, humans) reflect shared ancestry.

• Speciation: Populations split → adapt → form new species.

• Example: Galapagos Finches – Descended from one ancestral species. Beaks adapted to different food sources.

• Tree Diagrams: Show relationships through common ancestors.

Big Takeaways

• All life is connected through evolutionary history.

• Evolutionary explanations differ (adaptation, speciation).

• The universal genetic code and homologous structures are strong evidence for evolution.

Concept 1.3: In Studying Nature, Scientists Form and Test Hypotheses

Science as Inquiry

• Science: Way of knowing about the natural world.

• Driven by curiosity, it involves observation, explanation, and testing.

• No rigid "scientific method" – it's dynamic, with trial and error, creativity, and persistence.

Data: Gathering and Analysis

• Data: Recorded observations

• Qualitative: Descriptions (e.g., Jane Goodall's field notes on chimp behavior)

• Quantitative: Numerical data (e.g., frequency/duration of behaviors)

• Data are analyzed using statistics to determine significance.

• Generalizations based on many observations = inductive reasoning (e.g., all organisms are made of cells).

Forming and Testing Hypotheses

• Hypothesis: Testable, logical explanation based on prior data and reasoning.

• Example: If a lamp doesn't work → hypothesis: bulb is burnt out. Leads to predictions: If X, then Y.

Types of Reasoning

• Inductive reasoning: Specific → General (e.g., many cells = all life made of cells)

• Deductive reasoning: General → Specific (e.g., If the bulb is out, then replacing it should fix the lamp)

Limits of Science

• Hypotheses must be testable and falsifiable.

• Science cannot test supernatural or unobservable phenomena (e.g., ghosts, religious claims).

Scientific Process is Flexible

• Not a strict step-by-step method.

• Often involves backtracking, feedback, and revisions.

Case Study: Camouflage in Mice

• Observation: Beach and inland mice have different coat colors.

• Hypothesis: Coat color evolved for camouflage to reduce predation.

• Experiment: Painted model mice with light/dark fur → placed in both environments.

• Result: Non-camouflaged mice were attacked more often. Supports hypothesis.

Variables and Controls

• Controlled experiment: Compares experimental (non-camouflaged) and control (camouflaged) groups.

• Independent variable: Manipulated – model coat color

• Dependent variable: Measured – predation rate

• Control unwanted variables by keeping them constant or canceling out their effect.

Theories in Science

• Theory ≠ Hypothesis

• Theory: Broad, supported by extensive evidence, can generate testable hypotheses.

• Example: Theory of Natural Selection explains camouflage in mice.

• Theories can be modified or rejected if new evidence contradicts them.

Science as a Social Process

• Collaborative: Scientists work in teams, publish, review each other's work.

• Peer review ensures quality and repeatability.

• Self-correcting: Claims not reproducible must be revised.

Concept 2.1: Matter Consists of Chemical Elements in Pure Form and in Compounds

Definition of Matter

• Matter: Anything that takes up space and has mass.

• Examples: Rocks, water, metals, organisms, air.

Elements and Compounds

• Element: A substance that cannot be broken down by chemical reactions. Each element has a unique symbol (e.g., O = oxygen, Na = sodium).

• Compound: A substance made of two or more elements combined in a fixed ratio. Emergent properties: Compounds have properties different from the elements they are made of.

The Elements of Life

• About 20–25% of natural elements are essential for life.

• Humans require 25 elements; plants need 17.

• 4 major elements in living organisms:

  • Oxygen (O), Carbon (C), Hydrogen (H), Nitrogen (N) – make up ~96% of body mass

• Other important elements (4%):

  • Calcium (Ca), Phosphorus (P), Potassium (K), Sulfur (S), Sodium (Na), Chlorine (Cl), Magnesium (Mg)

• Trace elements: Needed in very small amounts (e.g., Iron (Fe), Iodine (I))

Evolution of Tolerance to Toxic Elements

• Some organisms adapt to toxic environments.

• Example: Sunflowers absorb heavy metals (like lead and zinc) – used for soil detox after Hurricane Katrina.

• Shows natural selection and evolutionary adaptation.

Concept 2.2: An Element’s Properties Depend on the Structure of Its Atoms

Atoms and Subatomic Particles

• Atom: Smallest unit of an element that retains its properties.

• Subatomic particles:

  • Proton: Positive charge, ~1 dalton

  • Neutron: No charge, ~1 dalton

  • Electron: Negative charge, ~1/2000 of a dalton

• Nucleus: Contains protons & neutrons (dense center)

• Electron cloud: Electrons orbit the nucleus, held by attraction to protons.

Atomic Number and Mass

• Atomic number: Number of protons

• Mass number: Protons + Neutrons

• Example: Sodium (Na) – Atomic number = 11, Mass number = 23

  • Neutrons = 23 – 11 = 12

• Atomic mass: Actual mass (in daltons); close to mass number