KA

Introduction to AP BIOLOGY II: Evolution and Foundations (Chapter 1) - Comprehensive Notes

The Study of Life: Unifying Themes

  • Big ideas to organize and make sense of biology: Organization, Information, Energy and matter, Interactions, Evolution
    • Organization: life is studied at multiple levels, from molecules to the biosphere
    • Information: genetic information stored in DNA; how information is transmitted and used
    • Energy and matter: life requires energy input and matter transformed and conserved in cycles
    • Interactions: organisms interact with other organisms and their physical environment
    • Evolution: all life is related through descent with modification and diversification over time
  • Purpose: to provide a framework for understanding biological information and phenomena through these unifying themes

Theme: New Properties Emerge at Successive Levels of Biological Organization

  • Life can be studied at different levels, from molecules to the entire living planet (hierarchy of organization)
  • Emergent properties arise from the arrangement and interaction of parts within a system
  • In reductionism, complex systems are reduced to simpler components to make them more manageable to study
  • Levels of biological organization (from small to large):
    • Molecules → Organelles → Cells → Tissues → Organs → Organ systems → Organisms → Populations → Communities → Ecosystems → The biosphere
  • The study of life often uses a reductionist approach, but systems biology complements this by analyzing interactions among parts to understand whole-system behavior

Emergent Properties (1 of 2)

  • Emergent properties are features that arise from the organization and interaction of parts, not present in any single part
  • Example: photosynthesis requires an intact chloroplast; chlorophyll molecules alone do not perform photosynthesis
  • Emergent properties can characterize nonbiological systems as well

Emergent Properties (2 of 2)

  • Systems biology asks questions like:
    • How do networks of molecular interactions in the body coordinate to generate a 24-hour wake-sleep cycle? ext{24-hour cycle}
    • How does increasing network complexity alter the biosphere? ext{Complexity}
      ightarrow ext{Biosphere-level consequences}
  • The approach emphasizes interactions and network dynamics over isolated parts

Structure and Function

  • At each level of organization, there is a correlation between structure and function
  • Analyzing a biological structure can provide clues about its role and how it works

The Cell: An Organism’s Basic Unit of Structure and Function (1 of 2)

  • The cell is the smallest unit of life capable of performing all life-sustaining activities
  • All cells are bounded by a membrane
  • Two main cell types: prokaryotic and eukaryotic

The Cell: An Organism’s Basic Unit of Structure and Function (2 of 2)

  • A eukaryotic cell contains membrane-bound organelles, including a DNA-containing nucleus
  • Some organelles, such as chloroplasts, are limited to certain cell types (photosynthetic cells)
  • Prokaryotic cells lack a nucleus and other membrane-bound organelles and are generally smaller

Figure 1.3 Contrasting Eukaryotic and Prokaryotic Cells in Size and Complexity

  • Visual comparison of cell types and their organelles; highlights structural differences and size

Theme: Life’s Processes Involve the Expression and Transmission of Genetic Information

  • Chromosomes contain a cell’s genetic material in the form of DNA (deoxyribonucleic acid)
  • DNA encodes genes and directs development through gene expression

Figure 1.4 A Lung Cell from a Newt Divides into Two Smaller Cells That Will Grow and Divide Again

  • Demonstrates cell division and cellular replication as part of growth and development

DNA, the Genetic Material (1 of 4)

  • A DNA molecule holds hundreds or thousands of genes
  • Genes are units of inheritance that transmit information from parents to offspring
  • As cells grow and divide, the genetic information encoded by DNA directs their development

Figure 1.5 Inherited DNA Directs the Development of an Organism

  • Visualizes how DNA information guides the formation and growth of an organism

DNA, the Genetic Material (2 of 4)

  • A DNA molecule is made of two long chains (strands) arranged in a double helix
  • Each link in a chain is one of four nucleotide building blocks: A, T, C, G

Figure 1.6

  • DNA: The Genetic Material (illustrations of DNA structure and nucleotides)

DNA, the Genetic Material (3 of 4)

  • For many genes, the DNA sequence provides blueprints for making proteins
  • Proteins are major players in building and maintaining a cell
  • Genes influence protein production indirectly via RNA as an intermediary
  • Gene expression is the process by which the information in a gene directs production of a cellular product

DNA, the Genetic Material (4 of 4)

  • All life uses essentially the same genetic code
  • The universality of the genetic code supports a common ancestry
  • Molecules of mRNA are translated to produce proteins; other RNAs regulate gene expression or form the cellular machinery that manufactures proteins

Figure 1.7 Gene Expression: Cells Use Information Encoded in a Gene to Synthesize a Functional Protein

Genomics: Large-Scale Analysis of DNA Sequences (1 of 2)

  • An organism’s genome is its entire library of genetic instructions
  • Genomics studies sets of genes in one or more species
  • Proteomics studies sets of proteins and their properties
  • The proteome is the entire set of proteins expressed by a cell, tissue, or organism

Genomics: Large-Scale Analysis of DNA Sequences (2 of 2)

  • High-throughput technology enables rapid analysis of many biological samples
  • Bioinformatics uses computational tools to store, organize, and analyze large data sets
  • Interdisciplinary teams aim to understand how activities of all proteins and RNAs encoded in DNA are coordinated in cells and whole organisms

Theme: Life Requires the Transfer and Transformation of Energy and Matter (1 of 2)

  • Life depends on energy input, primarily from the sun, and the transformation of energy from one form to another
  • Producers (photosynthetic organisms) convert sunlight into chemical energy in sugars
  • This chemical energy is transferred to consumers through consumption of other organisms or their remains

Theme: Life Requires the Transfer and Transformation of Energy and Matter (2 of 2)

  • Energy flows through ecosystems: energy enters as light and exits as heat
  • Matter cycles within ecosystems: elements are used and recycled
  • Elements move from plants to animals and back to the environment via decomposers

Figure 1.8 Energy Flow and Chemical Cycling

  • Diagram showing energy flow from sunlight to plants (chemical energy), through organisms, with heat loss, and chemical elements cycling via soils, plants, and decomposers

Theme: Organisms Interact with Other Organisms and the Physical Environment (1 of 3)

  • Every organism interacts with other organisms and with physical factors in its environment
  • Interactions can benefit one organism and harm the other, or benefit both, or harm both

Figure 1.9 A Mutually Beneficial Interaction Between Species

Theme: Organisms Interact with Other Organisms and the Physical Environment (2 of 3)

  • Interactions affect both organisms and their environments
    • Plants take up CO2 from the air and release O2
    • Plants take up water and minerals from soil through roots
    • Roots break up rocks, contributing to soil formation

Theme: Organisms Interact with Other Organisms and the Physical Environment (3 of 3)

  • Humans' impact on the atmosphere has increased the planet’s average temperature since 1900; climate change is a directional change lasting three decades or more
  • Climate change has already affected organisms and habitats globally; populations of many species are shrinking or disappearing

Figure 1.10 Threatened by Global Warming

Concept 1.2: The Core Theme: Evolution Accounts for the Unity and Diversity of Life

  • The diversity of life on Earth arose through evolutionary processes
  • Evolution is a process of biological change in which species accumulate differences from their ancestors
  • Differences between two species reflect heritable changes after divergence from a common ancestor
  • Similar traits in two species explainable by descent from a common ancestor

Classifying the Diversity of Life (1 of 3)

  • Diversity is a hallmark of life; humans classify by similarities and relationships
  • Careful comparisons of form and function are used to classify life forms
  • New methods, especially DNA sequence comparisons, have led to reevaluation of larger groupings

Classifying the Diversity of Life (2 of 3)

  • Biologists currently divide life into three domains: Bacteria, Archaea, and Eukarya
  • Domains Bacteria and Archaea are prokaryotes

Classifying the Diversity of Life (3 of 3)

  • Domain Eukarya includes all eukaryotic organisms
  • Eukarya contains three multicellular kingdoms: Plantae, Fungi, and Animalia
    • Plantae: photosynthesis to produce food
    • Fungi: absorb nutrients from surroundings
    • Animalia: obtain food by eating and digesting other organisms

Figure 1.11 The Three Domains of Life

  • Visuals show representative members from Bacteria, Archaea, and Eukarya with typical sizes (e.g., 2 μm, 100 μm)

Unity in the Diversity of Life

  • A remarkable unity underlies diversity; DNA is a universal genetic language across all organisms
  • Similarities appear at all levels of the biological hierarchy
  • Fossils and other evidence document the evolution of life on Earth over billions of years

Figure 1.12 Studying the History of Life

Charles Darwin and the Theory of Natural Selection (1 of 4)

  • Darwin published On the Origin of Species by Means of Natural Selection in 1859
  • Two main points: descent with modification from common ancestors and natural selection as the primary mechanism
  • Darwin’s theory captures the duality of life’s unity and diversity

Figure 1.13 Charles Darwin

Figure 1.14 Unity and Diversity among Birds

  • Examples: red-tailed hawk, American flamingo, Gentoo penguin, and other birds illustrating diversity within a lineage

Charles Darwin and the Theory of Natural Selection (2 of 4)

  • Observations: individuals in a population vary in traits, many of which are heritable
  • More offspring are produced than survive; competition is inevitable
  • Species are generally suited to their environment

Charles Darwin and the Theory of Natural Selection (3 of 4)

  • Reasoning: individuals best suited to their environment are more likely to survive and reproduce
  • Over many generations, advantageous traits become more common in a population

Charles Darwin and the Theory of Natural Selection (4 of 4)

  • Mechanism: natural selection — the environment acts as a selective force for advantageous traits

Figure 1.15 Natural Selection

  • Diagram shows a population with varied inherited traits; selection removes some variants, enhances others, and shifts trait frequencies over generations

The Tree of Life (1 of 2)

  • Shared skeletal architecture among limbs (e.g., human arm, horse foreleg, whale flipper, bat wing) reflects inheritance from a common ancestor
  • Diversity of limbs results from modification by natural selection over millions of years

The Tree of Life (2 of 2)

  • Darwin proposed that natural selection can cause ancestral species to give rise to two or more descendant species (radiation)
  • Evolutionary relationships are often shown with treelike diagrams

Figure 1.16 Descent with Modification: Finches on the Islands

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

  • Science is an approach to understanding the natural world
  • Inquiry is the search for information and explanation of natural phenomena
  • Science involves challenge, adventure, and luck, along with planning, reasoning, creativity, patience, and persistence
  • The scientific process includes making observations, forming logical hypotheses, and testing them

Exploration and Discovery

  • Biology begins with careful observations
  • Biologists rely on the scientific literature; past studies provide foundations for new work

Gathering and Analyzing Data (1 of 2)

  • Recorded observations are data
  • Data types:
    • Qualitative data: descriptions rather than measurements; e.g., behavioral observations
    • Quantitative data: numerical measurements, often organized into tables and graphs

Figure 1.17 Jane Goodall Collecting Qualitative Data on Chimpanzee Behavior

Gathering and Analyzing Data (2 of 2)

  • Inductive reasoning draws generalizations from many observations
  • Example: all organisms are made of cells, a generalization built from centuries of microscopic observations

Forming and Testing Hypotheses (1 of 2)

  • A hypothesis is an explanation based on observations and assumptions that leads to a testable prediction
  • A hypothesis is an explanation on trial and must lead to predictions testable by observations or experiments
  • An experiment tests the hypothesis under controlled conditions

Forming and Testing Hypotheses (2 of 2)

  • A single observation can lead to multiple hypotheses
  • Example: desk lamp that does not work could be due to a burnt-out bulb or a broken lamp; both are testable hypotheses

Deductive Reasoning (1 of 2)

  • Deductive reasoning extrapolates from general premises to specific predictions; testing follows in an experimental framework
  • The form is often if-then logic: If A and B, then C

Deductive Reasoning (2 of 2)

  • A hypothesis can never be conclusively proven true because not all alternatives can be tested
  • Scientific confidence grows when a hypothesis withstands multiple tests
  • Scientific consensus is the shared conclusion among scientists that a particular hypothesis explains known data well and stands up to testing

Questions That Can and Cannot Be Addressed by Science

  • A hypothesis must be testable and falsifiable
  • Supernatural explanations lie outside the realm of testable science

The Flexibility of the Scientific Process

  • Few studies follow a strict, linear sequence of steps; science is often iterative and nonlinear

Figure 1.18 The Process of Science: A Realistic Model

A Case Study in Scientific Inquiry: Investigating Coat Coloration in Mouse Populations (1 of 3)

  • Coat color variation exists in nature; two mouse populations in different habitats show different coat colors
  • Beach environment: light, dappled fur; inland environment: darker fur

Figure 1.19 Different Coloration in Beach and Inland Populations of Peromyscus polionotus

A Case Study in Scientific Inquiry: Investigating Coat Coloration in Mouse Populations (2 of 3)

  • Francis B. Sumner hypothesized that coat patterns evolved as camouflage to protect against predation
  • Hopi Hoekstra and students tested this hypothesis through predictions and experiments

A Case Study in Scientific Inquiry: Investigating Coat Coloration in Mouse Populations (3 of 3)

  • Prediction: mismatched coloration should experience higher predation than well-matched coloration
  • Methods: created many models resembling beach or inland mice; distributed equal numbers in both habitats
  • Results: camouflaged models suffered lower predation than mismatched models

Figure 1.20 Inquiry: Does Camouflage Affect Predation Rates on Two Populations of Mice?

Experimental Variables and Controls (1 of 2)

  • A controlled experiment compares an experimental group to a control group
  • Independent variable: color (the factor manipulated by researchers)
  • Dependent variable: predation (the effect measured)

Experimental Variables and Controls (2 of 2)

  • A controlled experiment does not require eliminating every variable
  • Unwanted variables are managed by using control groups to cancel out their effects

Theories in Science

  • A theory is broader in scope than a hypothesis and can generate many testable hypotheses
  • Theories are supported by a large body of evidence relative to a single hypothesis
  • If there is truth in science, it is conditional on the weight of available evidence

Science as a Social Process (1 of 2)

  • Scientists benefit from the discoveries of others and often work in teams
  • Replication: scientists test others' claims by attempting to confirm observations or repeat experiments

Science as a Social Process (2 of 2)

  • Science and society are intertwined when considering technology
  • The goal of technology is to apply scientific knowledge for practical purposes
  • Science and technology are interdependent

Note: Figures and captions referenced in this summary (e.g., Figures 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9, 1.10, 1.11, 1.12, 1.13, 1.14, 1.15, 1.16, 1.17, 1.18, 1.19, 1.20) are described to illustrate concepts; access to the original figures is recommended for visual context.

Key Equations and Notable Expressions

  • Energy flow through an ecosystem (conceptual):
    \text{Light energy} \rightarrow \text{Chemical energy in sugars} \rightarrow \text{Work} \rightarrow \text{Heat (lost)}
  • Matter cycling in ecosystems (conceptual): elements are taken up, transformed, used, and returned by decomposers
  • Gene expression overview: \text{DNA} \rightarrow \text{RNA} \rightarrow \text{Protein}
  • DNA structure: two long chains arranged in a double helix; nucleotides A, T, C, G
  • Universal genetic code: nearly universal across organisms; supports common ancestry
  • Natural selection (conceptual):\text{Variation} \Rightarrow \text{Differential survival and reproduction} \Rightarrow \text{Descent with modification}

Note on numbers and units used in this transcript:

  • Levels of organization example: Molecules, Organelles, Cells, Tissues, Organs, Organ systems, Organisms, Populations, Communities, Ecosystems, Biosphere
  • Dimensions mentioned in figures: 2\ \mu\text{m} and 100\ \mu\text{m} for cell sizes
  • Evolution and taxonomy references: three domains (Bacteria, Archaea, Eukarya); Eukarya includes Plantae, Fungi, Animalia
  • Time scales and history references: Darwin's publication year 1859; evolution working over timescales of millions of years; climate change discussed in decades to centuries timescales
  • Energetic/time reference: the 24-hour wake-sleep cycle; climate change timelines of decades or more
  • Genomics and proteomics terms: high-throughput, proteome; genome size not numerically specified in the transcript