Foundations of Biology: Elements, Molecules, Cells, and Scientific Inquiry

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Elements and Atomic Structure

Essential Elements of Life

Living organisms require a subset of the naturally occurring elements for survival and function. These elements are categorized based on their abundance and necessity in biological systems.

Essential elements: About 20–25% of the 92 natural elements are required for life.
Major elements: Carbon, hydrogen, oxygen, and nitrogen make up approximately 96% of living matter.
Secondary elements: Calcium, phosphorus, potassium, and sulfur comprise most of the remaining 4%.
Trace elements: Required by organisms in only minute quantities, but are vital for proper physiological function.

Atoms and Subatomic Particles

Atoms are the fundamental units of matter, composed of subatomic particles that determine their chemical properties.

Atom: The smallest unit of matter that retains the properties of an element.
Matter: Anything that occupies space and has mass; all matter is composed of atoms.
Nucleus: Central core containing protons (positive charge) and neutrons (neutral).
Electrons: Negatively charged particles forming a "cloud" around the nucleus.
Mass units: Neutron and proton masses are nearly identical, measured in daltons.
Electrically neutral atoms: Number of protons equals number of electrons.

Atomic Number, Isotopes, and Atomic Mass

Atomic number: Number of protons in an atom; defines the element.
Isotopes: Atoms of the same element with different numbers of neutrons.
Radioactive isotopes: Unstable isotopes that decay, emitting energy and/or particles.
Half-life: Time required for half the atoms in a sample to decay.
Atomic mass: Sum of protons and neutrons in the nucleus.
Mass vs. Weight: Mass is the amount of substance; weight is the force exerted by gravity on that mass.

Electrons and Ions

Ions: Atoms with unequal numbers of protons and electrons.
Cation: More protons than electrons; carries a positive charge.
Anion: Fewer protons than electrons; carries a negative charge.

Molecular Structure and Chemical Bonds

Molecules and Compounds

Molecule: Group of atoms held together by chemical bonds in a stable association.
Compound: Substance composed of two or more different types of atoms with unique properties.
Chemical bonds: Forces that hold atoms together in molecules.

Covalent Bonds and Hydrogen Bonds

Covalent bond: Sharing of electron pairs between atoms (not explicitly listed but implied).
Hydrogen bond: Weak attraction between a hydrogen atom covalently bonded to one electronegative atom and another electronegative atom (usually oxygen or nitrogen).
Hydrogen bonding in water: Responsible for many of water's unique properties.

Carbon and Organic Chemistry

Organic Molecules and Carbon Properties

Organic chemistry: Study of carbon-containing compounds.
Organic molecules: Molecules containing carbon, often with hydrogen, oxygen, and nitrogen.
Carbon atom: Atomic number 6; 4 valence electrons; forms up to four covalent bonds.
Importance: Carbon's versatility allows for a diversity of molecular structures and functional groups.

Functional Groups

Functional groups are specific groups of atoms attached to carbon skeletons that confer distinct chemical properties.

Hydroxyl (—OH): Alcohols (e.g., ethanol)
Carbonyl (C═O): Ketones and aldehydes (e.g., acetone, propanal)
Carboxyl (—COOH): Carboxylic acids (e.g., acetic acid)
Amino (—NH₂): Amines (e.g., glycine)
Sulfhydryl (—SH): Thiols (e.g., cysteine)
Phosphate (—OPO₃²⁻): Organic phosphates (e.g., glycerol phosphate)
Methyl (—CH₃): Methylated compounds (e.g., 5-methylcytosine)

Hydrocarbons

Hydrocarbons: Molecules consisting only of carbon and hydrogen.
Properties: Hydrophobic due to nonpolar C—C and C—H bonds; major components of fossil fuels and fats.
Energy: Release large amounts of energy when oxidized.

Isomers

Isomers: Compounds with the same molecular formula but different structures and properties.
Structural isomers: Differ in covalent arrangement of atoms.
Cis-trans isomers: Same covalent bonds, different spatial arrangements; cis double bonds cause molecular bending.
Enantiomers: Mirror-image isomers; often only one is biologically active (e.g., S-Ibuprofen vs. R-Ibuprofen).

Polymer Synthesis and Breakdown

Macromolecules and Monomers

Macromolecules: Large molecules (polymers) made of repeating subunits (monomers).
Dehydration synthesis: Joins monomers by removing water (—OH from one, —H from another).
Hydrolysis: Breaks covalent bonds by adding water; important in digestion.

Water Chemistry and Properties

Water as a Solvent

Solution: Homogeneous mixture of substances.
Solvent: Dissolving agent (water in aqueous solutions).
Solute: Substance dissolved in the solvent.
Water: Effective solvent due to polarity and hydrogen bonding; dissolves polar and ionic substances.

Hydrophilic and Hydrophobic Substances

Hydrophilic: Affinity for water (e.g., salts, sugars).
Hydrophobic: Repel water (e.g., oils, fats); major components of cell membranes.

Cohesion, Adhesion, and Surface Tension

Cohesion: Attraction between water molecules; responsible for surface tension.
Adhesion: Attraction between water and other substances.
Surface tension: Difficulty of breaking the surface of a liquid; high in water due to hydrogen bonding.

Temperature Moderation Properties

Specific heat: Amount of heat to change 1g of a substance by 1°C.
Water's high specific heat moderates Earth's climate and stabilizes temperatures in organisms.
Heat is absorbed when hydrogen bonds break; released when they form.

Heat of Vaporization

Heat of vaporization: Energy required to convert 1g of liquid water to gas (586 calories).
High due to extensive hydrogen bonding.

Expansion Upon Freezing

Ice is less dense than liquid water due to ordered hydrogen bonds.
Water is densest at 4°C; floating ice insulates aquatic life.

pH and Hydrogen Ions

Acids: Increase H⁺ concentration; pH < 7.
Bases: Decrease H⁺ concentration; pH > 7.
Buffers: Minimize changes in pH; contain weak acid and conjugate base.
Water can dissociate:

Emergent Properties of Water

Cohesive behavior
Ability to moderate temperature
Expansion upon freezing
Versatility as a solvent

Biological Molecules

Carbohydrates

General formula: (CH₂O)n
Monosaccharides: Simple sugars (e.g., glucose).
Disaccharides: Two monosaccharides joined by a covalent bond (e.g., sucrose).
Polysaccharides: Long chains of monosaccharides (e.g., starch, cellulose).

Type	Example	Function
Monosaccharide	Glucose	Energy source
Disaccharide	Sucrose	Transport in plants
Polysaccharide	Starch	Energy storage in plants

Lipids

Properties: Hydrophobic, insoluble in water; include fats, oils, phospholipids, and steroids.
Function: Energy storage, insulation, cushioning of organs.

Fats and Fatty Acids

Triglyceride: Glycerol + 3 fatty acids.
Saturated fatty acids: No double bonds; solid at room temperature.
Unsaturated fatty acids: One or more double bonds; liquid at room temperature.
Cis double bonds: Cause bending in the molecule.

Phospholipids

Structure: Two fatty acids (hydrophobic tails) + phosphate group (hydrophilic head) attached to glycerol.
Form bilayers in water, fundamental to cell membranes.

Steroids

Four fused carbon rings.
Cholesterol: Component of animal cell membranes; precursor for steroid hormones.

Proteins

Polymers of amino acids linked by peptide bonds.
Twenty common amino acids; each has a central carbon, amino group, carboxyl group, hydrogen, and variable R group.

Level of Structure	Description
Primary	Sequence of amino acids
Secondary	Alpha helix or beta pleated sheet (hydrogen bonds)

Functions: Enzyme catalysis, defense, transport, support, motion, regulation, storage.

Nucleic Acids

Polymers of nucleotides (sugar, phosphate, nitrogenous base).
DNA: Double helix, deoxyribose sugar, bases A, T, C, G.
RNA: Single strand, ribose sugar, bases A, U, C, G.
Central Dogma:

Type	Sugar	Bases	Strands
DNA	Deoxyribose	A, T, C, G	Double
RNA	Ribose	A, U, C, G	Single

Cells and Cellular Organization

Prokaryotic vs. Eukaryotic Cells

Prokaryotic cells: No nucleus or membrane-bound organelles; DNA in nucleoid region; examples: Bacteria, Archaea.
Eukaryotic cells: Membrane-bound organelles, including nucleus; examples: Plants, animals, fungi, protists.

Cellular Components

All cells have a plasma membrane, cytoplasm, and genetic material (DNA).
Eukaryotic cells have additional organelles (e.g., mitochondria, endoplasmic reticulum).

Cell Theory

The cell is the lowest level of organization capable of all life functions.
All organisms are composed of cells.
All cells arise from pre-existing cells.

Genetic Information and Inheritance

Chromosomes: Structures containing DNA, the genetic material.
Genes: Units of inheritance; segments of DNA encoding information for traits.
Continuity of life is based on heritable information in DNA.

Biological Organization Hierarchy

Levels of Organization

Atoms
Molecules
Organelles
Cells
Tissues
Organs and Organ Systems
Organisms
Populations
Communities
Ecosystems
Biosphere

Emergent properties: New properties arise at each level due to the arrangement and interactions of parts.

Evolution and Natural Selection

The Tree of Life and Unity in Diversity

Unity in diversity results from descent with modification from common ancestors.
Homologous structures (e.g., vertebrate forelimbs) and fossils provide evidence for evolution.

Darwin's Theory of Evolution

Species show evidence of descent with modification.
Natural selection is the mechanism for evolution.
Individuals with advantageous traits are more likely to survive and reproduce.

Darwin's Observations and Natural Selection Mechanism

Variation exists in populations; many traits are heritable.
More offspring are produced than survive; competition is inevitable.
Individuals best suited to their environment leave more offspring.

Organism-Environment Interaction

Organisms interact with both living and nonliving components of their environment.
These interactions affect both the organism and the environment (e.g., trees cycling water, minerals, and gases).

Taxonomy and Classification of Life

The Three-Domain System

Domain Bacteria: Prokaryotes
Domain Archaea: Prokaryotes
Domain Eukarya: Eukaryotes (plants, animals, fungi, protists)

Eukaryotic Kingdoms

Plantae (plants)
Fungi (fungi)
Animalia (animals)
Other eukaryotes (formerly Protista) are now classified based on DNA analysis.

Taxonomy

Branch of biology that names and classifies organisms.
Classification hierarchy: Domain > Kingdom > Phylum > Class > Order > Family > Genus > Species

Rank	Example (Ursus americanus)
Domain	Eukarya
Kingdom	Animalia
Phylum	Chordata
Class	Mammalia
Order	Carnivora
Family	Ursidae
Genus	Ursus
Species	americanus

Scientific Method and Experimental Design

The Scientific Method

Idealized process of inquiry: Observation → Question → Hypothesis → Prediction → Experiment → Results → Conclusion
Scientific investigations may involve backtracking and revision.

Hypotheses

Explanation based on observations and assumptions; must be testable and falsifiable.
Supernatural explanations are outside the scope of science.

Forming and Testing Hypotheses

Experiments are controlled tests of hypotheses.
Example: Desk lamp not working—testable hypotheses include bulb not screwed in or bulb burnt out.

Experimental Variables and Controls

Controlled experiments compare experimental and control groups.
Independent variable: Manipulated by the researcher.
Dependent variable: Predicted to change in response.
Control groups help account for unwanted variables.

Experimental Example: Redi's Maggot Experiment

Tested whether maggots arise spontaneously or from flies.
Covered meat (experimental group) vs. uncovered meat (control group).
Result: Only uncovered meat developed maggots, supporting the hypothesis that flies produce maggots.

Theories in Science

Theory: Broader than a hypothesis; supported by substantial evidence; can generate new hypotheses.
Examples: Cell theory, Germ Theory of Disease.

Questions Addressed by Science

Scientific questions must be testable and falsifiable.
Supernatural and religious explanations are not scientific.

Systems Biology

Studies complex interactions within biological systems.
Uses models to predict system behavior (e.g., drug effects, climate change).

Characteristics and Themes of Life

Seven Characteristics of Life

Order
Regulation (homeostasis)
Evolutionary adaptation
Reproduction
Energy processing
Growth and development
Response to the environment