Foundations of Biology: Themes, Chemistry, Water, Carbon, and Biological Molecules

Themes in the Study of Life (Chapter 1)

Eukaryotes vs. Prokaryotes

The distinction between eukaryotic and prokaryotic cells is fundamental to understanding biological diversity and cellular organization.

• Eukaryotes: Organisms whose cells contain a nucleus and membrane-bound organelles (e.g., plants, animals, fungi, protists).

• Prokaryotes: Organisms whose cells lack a nucleus and most organelles (e.g., Bacteria and Archaea).

• Key Difference: Presence or absence of a membrane-bound nucleus.

Order of Organization (Hierarchy) in Systems

Biological systems are organized in a hierarchical manner, from the smallest chemical units to the entire biosphere.

• Hierarchy: Atom → Molecule → Organelle → Cell → Tissue → Organ → Organ System → Organism → Population → Community → Ecosystem → Biosphere

Evolution, Natural Selection, Adaptive Radiation

Evolution is the process by which species change over time, primarily through natural selection and adaptive radiation.

• Evolution: Descent with modification; the change in genetic composition of a population over generations.

• Natural Selection: The process where organisms better adapted to their environment tend to survive and produce more offspring.

• Adaptive Radiation: The diversification of a group of organisms into forms filling different ecological niches.

Unity Among Organisms (Structure and Function of DNA)

All living organisms share a universal genetic code based on DNA, reflecting their evolutionary unity.

• DNA: Deoxyribonucleic acid, the molecule that stores genetic information in all living things.

• Structure: Double helix composed of nucleotides (adenine, thymine, cytosine, guanine).

Steps in the Scientific Method

The scientific method is a systematic approach to inquiry in biology.

• Observation

• Question

• Hypothesis

• Experiment

• Analysis

• Conclusion

The Chemical Context of Life (Chapter 2)

Essential Elements of Life

Living organisms are primarily composed of a few essential elements.

• Four Essential Elements: Carbon (C), Hydrogen (H), Oxygen (O), Nitrogen (N) — make up about 96% of living matter.

Atomic Structure

Atoms are the basic units of matter, composed of subatomic particles.

• Proton: Positively charged particle in the nucleus.

• Neutron: Neutral particle in the nucleus.

• Electron: Negatively charged particle orbiting the nucleus.

• Atomic Number (Z): Number of protons in the nucleus.

• Mass Number (A): Number of protons plus neutrons.

• Atomic Mass: Weighted average mass of an atom's isotopes.

Chemical Bonds

Atoms interact through chemical bonds to form molecules.

• Covalent Bond: Sharing of electron pairs between atoms.

• Polar Covalent Bond: Unequal sharing of electrons, leading to partial charges.

• Hydrogen Bond: Weak attraction between a hydrogen atom and an electronegative atom (e.g., O or N).

• Ionic Bond: Transfer of electrons from one atom to another, resulting in oppositely charged ions.

Water and the Fitness of the Environment (Chapter 3)

Structure and Charges of Water Molecule

Water's unique properties arise from its molecular structure and polarity.

• Water Molecule (H2O): Two hydrogen atoms covalently bonded to one oxygen atom.

• Polarity: Oxygen is more electronegative, creating a partial negative charge near O and partial positive charges near H atoms.

Properties of Water

Water exhibits several emergent properties essential for life.

• Cohesion: Attraction between water molecules due to hydrogen bonding.

• Adhesion: Attraction between water molecules and other substances.

• Surface Tension: Measure of how difficult it is to stretch or break the surface of a liquid.

pH and Bonding

pH measures the concentration of hydrogen ions in a solution, reflecting its acidity or basicity.

• pH Scale: Ranges from 0 (acidic) to 14 (basic), with 7 as neutral.

• Formula: $\mathrm{pH} = -\log_{10}[\mathrm{H}^+]$

Carbon and the Molecular Diversity of Life (Chapter 4)

pH, Carbon Dioxide, Acidification, and Seawater

Carbon dioxide dissolves in seawater, affecting pH and leading to ocean acidification.

• Ocean Acidification: CO2 + H2O → H2CO3 (carbonic acid), which lowers pH.

Importance of Carbon

Carbon is the backbone of all major biological molecules due to its ability to form four covalent bonds.

• Versatility: Forms chains, rings, and complex structures.

Isomers

Isomers are compounds with the same molecular formula but different structures.

• Structural Isomers: Differ in covalent arrangement of atoms.

• Cis-Trans Isomers: Differ in spatial arrangement around double bonds.

• Enantiomers: Mirror images of each other, often with different biological activity.

Functional Groups

Functional groups are specific groups of atoms within molecules that confer characteristic chemical properties.

• Examples: Carbonyl group (C=O), Carboxyl group (COOH), Hydroxyl group (OH), Amino group (NH2), etc.

• Role: Determine the reactivity and interactions of organic molecules.

Monomers and Polymers

Biological macromolecules are polymers built from monomer subunits.

• Monomer: Small building block molecule (e.g., glucose, amino acid).

• Polymer: Long molecule consisting of many similar or identical monomers linked by covalent bonds.

The Structure and Function of Large Biological Molecules (Chapter 5)

Overview of Biological Macromolecules

There are four major classes of biological macromolecules, each with distinct structures and functions.

• Carbohydrates: Serve as fuel and building material; monomer is the monosaccharide (e.g., glucose).

• Proteins: Perform a wide range of functions including catalysis, structure, and transport; monomer is the amino acid.

• Lipids: Hydrophobic molecules important for energy storage, membranes, and signaling; not true polymers but built from fatty acids and glycerol.

• Nucleic Acids: Store and transmit genetic information; monomer is the nucleotide (e.g., DNA, RNA).

Macromolecule	Monomer	Function
Carbohydrates	Monosaccharide	Energy, structure
Proteins	Amino acid	Catalysis, structure, transport
Lipids	Fatty acid, glycerol	Energy storage, membranes
Nucleic Acids	Nucleotide	Genetic information

Example: Starch (a carbohydrate polymer) is made of glucose monomers; hemoglobin (a protein) is made of amino acids.