General Biology: Study Guide for Test 1 (Chapters 1–2)

Chapter 1: Biology — The Study of Life

1.1 Fundamental Characteristics of Life

Biology is the study of living organisms, all of which share five fundamental characteristics that distinguish them from non-living matter.

• Cells: All organisms are made up of membrane-bound cells.

• Replication: All organisms are capable of reproduction.

• Information: All organisms process hereditary information encoded in genes as well as information from the environment.

• Energy: All organisms acquire and use energy to stay alive.

• Evolution: Populations of organisms are continually evolving.

1.1.1 Three Theories Form the Framework for Modern Biological Science

• Cell Theory: All organisms are made of cells; all cells come from preexisting cells.

• Theory of Evolution by Natural Selection: Explains how organisms are related and change over time.

• Chromosome Theory of Inheritance: Hereditary information is transmitted from one generation to the next via chromosomes.

1.2 Life is Cellular and Replicates through Cell Division

• Historical Experiments:

  • 1665 — Robert Hooke: Made microscope with 30x magnification and found cells.

  • Anton van Leeuwenhoek: Created microscope with 300x magnification and saw single-celled organisms (“animalcules”).

  • 1800s: German biologists claim all organisms consist of cells.

• Cell Theory: Cells are highly organized compartments separated from their environment by membrane barriers.

• Testing Cell Theory: Spontaneous Generation

  • All-cells-from-cells hypothesis: Cells are produced when pre-existing cells grow and divide (Virchow).

  • Spontaneous generation hypothesis: Life can arise spontaneously under certain conditions.

  • Louis Pasteur’s experiment: Supported the all-cells-from-cells hypothesis.

• Cell Division: All cells in multicellular organisms descend from preexisting cells; life arose from non-living matter via chemical evolution.

1.3 Life Processes Information and Requires Energy

• Hereditary Information: Encoded in genes, located on chromosomes.

• DNA Structure: Double-helix (Watson and Crick); DNA is the hereditary material, and genes are segments of DNA that code for cell products.

• Central Dogma: Flow of information in cells: $\text{DNA} \rightarrow \text{RNA} \rightarrow \text{Proteins}$

• DNA Replication: DNA is copied (highly accurate) to pass genetic information from cell to cell or from one organism to its offspring.

• Mutations: Cause changes in proteins and genetic variation.

• Energy Requirements:

  • Organisms acquire chemical energy in the form of adenosine triphosphate (ATP).

  • Plants and bacteria: Can produce sugar using energy from sunlight.

  • Other organisms: Use molecules absorbed from the environment as food.

1.4 The Evolution of Life

1.4.1 Darwin and Wallace’s Claims

• Species are related by common ancestry.

• Characteristics of species can be modified from generation to generation (“descent with modification”).

Evolution: Change in characteristics of populations over time; species are related to one another and can change through time. Population: Group of individuals of same species living in the same area at the same time. Speciation: Natural selection causes one species to diverge and form new species.

1.4.2 Natural Selection

• Individuals must vary in heritable characteristics.

• Certain heritable traits lead to increased success in producing offspring.

• Traits become more common in population over time.

• Natural selection acts on individuals; evolutionary change occurs in populations.

• Speciation occurs when populations diverge to form new species.

1.4.3 Fitness and Adaptation

• Fitness: The ability of an individual to produce offspring. Individuals with high fitness produce more surviving offspring than others.

• Adaptation: A trait that increases fitness of an individual in a particular environment.

1.5 The Tree of Life Depicts Evolutionary History

1.5.1 Phylogeny and Genetic Analysis

• Phylogeny: Actual genealogical relationships among all organisms.

• Methods:

  • Biologists study RNA and DNA from different organisms.

  • Compare sequences of building blocks (A, T, C, G).

  • Fewer sequence variations between two species indicate closer relationship.

1.5.2 Phylogenetic Trees

• Branches that share recent common ancestor represent species closely related.

• Branches that do not share recent common ancestors represent species that are more distantly related.

1.5.3 Domains of Life

• Eukarya (Eukaryotes): Have nucleus (about 10x the size of a prokaryote).

• Bacteria (Prokaryotes): Lack nucleus.

• Archaea (Prokaryotes): Lack nucleus.

1.5.4 Taxonomy

• Taxon: A named group.

• Domain: Most inclusive taxonomic level: Bacteria, Archaea, Eukarya.

• Phylum: Major lineage within domain.

1.5.5 Linnaeus’ Taxonomic System

• Each organism given unique two-part scientific name: genus and species.

• Genus: Made up of closely related group of species.

• Species: Individuals that regularly breed together or whose characteristics are distinct from those of other species.

Chapter 2: Water and Carbon — The Chemical Basis of Life

1.1 Molecular Structure

Water (H2O) has unique features that make it essential for life.

• Small size

• Highly polar covalent bonds (O-H)

• Bent geometry (not linear)

• Overall polarity: Partial negative charge ($\delta^-$) on oxygen; partial positive charges ($\delta^+$) on hydrogens

1.2 Hydrogen Bonding

Hydrogen bonds are weak electrical attractions between a hydrogen atom with partial positive charge and another atom (usually O or N) with partial negative charge.

• Each water molecule can form up to 4 hydrogen bonds

• Oxygen forms 2 hydrogen bonds (as acceptor)

• Each hydrogen forms 1 hydrogen bond (as donor)

• Weaker than covalent or ionic bonds, but very important due to sheer number

2.1 Hydrophilic Substances

Substances that interact with water through hydrogen bonding or electrostatic interactions:

• Polar molecules (e.g., glucose): Water forms hydrogen bonds with polar regions; molecules stay in solution.

• Ionic compounds (e.g., NaCl): Water molecules surround ions; partial negative (O) orients toward cations (Na+), partial positive (H) orients toward anions (Cl-).

2.2 Hydrophobic Substances

• Nonpolar molecules (e.g., octane, oils): Do not readily dissolve; minimal/no interaction with water.

• Water molecules form organized "cages" around nonpolar molecules.

• Nonpolar molecules cluster together to minimize disruption of water’s hydrogen bonding.

• Hydrophobic interactions: Association of nonpolar molecules in aqueous solution.

2.3 Van der Waals Interactions

Weak electrical attractions between molecules due to London dispersion forces:

• Constant electron motion creates temporary charge asymmetry.

• Induces opposite charge in nearby molecule.

• Very weak relative to covalent or hydrogen bonds.

• Large numbers can stabilize clustered hydrophobic molecules.

3 Cohesion, Adhesion, and Surface Tension

• Cohesion: Attraction between like molecules (water-water).

• Adhesion: Attraction between unlike molecules (water-solid surface).

3.1 Cohesion in Water

• Water stays together due to hydrogen bonds.

• Important for water movement in plants (roots to leaves against gravity).

3.2 Surface Tension

• Surface molecules have no molecules above for hydrogen bonding.

• Form hydrogen bonds with neighbors beside and below.

• Creates tension that minimizes surface area.

• Water surface acts like elastic membrane; resists forces that increase surface area.

3.4 Structural Explanation

Property	Ice	Liquid Water
Hydrogen bonding	Each molecule forms 4 H-bonds simultaneously	H-bonds constantly forming and breaking
Structure	Regular, repeating crystal lattice	No fixed lattice structure
Molecular spacing	Open, attractive with large spaces between molecules	Molecules packed more closely together
Extent of H-bonding	Maximum (4 per molecule)	Less extensive than ice
Density	Less dense	More dense

4 Energy Absorption Properties

4.1 Specific Heat

• Definition: Energy required to raise temperature of 1 g of substance by 1°C.

• Water has high specific heat (4.18 J/g°C): Hydrogen bonds must be broken before heat transfer occurs; more polar molecules = more hydrogen bonding = higher specific heat.

• $q = m c \Delta T$

4.2 Heat of Vaporization

• Definition: Energy required to change 1 g of liquid to gas.

• Water has high heat of vaporization: Must break many hydrogen bonds for phase change.

• Cooling mechanism: Sweating is effective because water absorbs heat from body before evaporating.

4.3 Table: Water Properties and Biological Consequences

Property	Cause	Biological Consequences
Solvent for charged/polar compounds	Electrostatic attractions between partial charges on water and opposite charges on solute	Most reactions important for life occur in aqueous solution
Denser as liquid than solid	Each molecule maintains 4 H-bonds in ice, forming low-density crystal lattice	Ice floats, insulating bodies of water and preventing them from freezing solid
High specific heat	Water molecules must absorb lots of energy to break H-bonds and increase movement (temperature)	Temperature of aqueous solutions changes slowly; occurs moderate coastal climates
High heat of vaporization	Water molecules must absorb lots of energy to break H-bonds and change from liquid to gas	Evaporation of water cools organisms (sweating)

5 Acid-Base Chemistry

5.1 Water Dissociation

• Water molecules undergo chemical reaction with themselves:

$\mathrm{H_2O} + \mathrm{H_2O} \rightleftharpoons \mathrm{H_3O^+} + \mathrm{OH^-}$

Or simply:

$\mathrm{H_2O} \rightleftharpoons \mathrm{H^+} + \mathrm{OH^-}$

• Products:

  • $\mathrm{H^+}$: Hydrogen ion (proton) — actually exists as hydronium ion ($\mathrm{H_3O^+}$)

  • $\mathrm{OH^-}$: Hydroxide ion

• Equilibrium: Forward and reverse reactions proceed at same rate; concentrations remain constant.

• In pure water: $[\mathrm{H^+}] = [\mathrm{OH^-}]$

5.2 Definitions

• Acid: Substance that gives up protons ($\mathrm{H^+}$) during reactions; raises hydronium ion concentration.

• Base: Substance that acquires protons ($\mathrm{H^+}$) during reactions; lowers hydronium ion concentration.