General Biology: Core Themes, Chemistry of Life, and Macromolecules

Chapter 1: Themes of Biology

Unifying Themes

Biology is organized around several unifying themes that help explain the complexity and diversity of life.

• Organization: Life is structured hierarchically (atoms → molecules → cells → organisms → ecosystems). Each level builds on the previous one, with emergent properties appearing at higher levels.

• Information: DNA stores and transmits genetic information, guiding the development and functioning of organisms.

• Energy & Matter: Life requires energy input and recycling of matter. Organisms transform energy (e.g., sunlight to chemical energy) and cycle matter (e.g., water, carbon, nitrogen).

• Interactions: Organisms interact with each other and their environment, affecting survival and evolution.

• Evolution: Explains both the unity and diversity of life through descent with modification and natural selection.

Emergent Properties

New functions arise when parts interact at higher levels of organization.

• Example: Photosynthesis requires intact chloroplasts, not just chlorophyll.

• Reductionism simplifies systems by studying components, but systems biology studies interactions among system parts.

Structure & Function

Form fits function at all levels of biology.

• Example: Wings for flight, enzyme shape for catalysis.

Cells

• Prokaryotes: No nucleus, smaller, simpler (e.g., Bacteria, Archaea).

• Eukaryotes: Nucleus, organelles, larger, more complex (e.g., Eukarya).

• Three Domains: Bacteria, Archaea, Eukarya.

• Cell is the smallest unit of life.

Genetic Information

• DNA is the genetic material; genes are units of inheritance.

• Gene expression: DNA → RNA → Protein.

• Genetic code is universal, supporting common ancestry.

Energy & Matter

• Energy flows (e.g., sunlight → chemical → heat).

• Matter cycles (e.g., C, N, water).

Interactions

• Examples: Mutualism, parasitism, competition.

• Human impacts: Climate change, resource use, global warming, ecosystem impacts.

Evolution

• Descent with modification, natural selection.

• Variation in traits + competition = survival of best-suited.

• Darwin: CO2 rise, global warming, ecosystem impacts.

Chapter 2: Matter, Atoms & Water

Matter & Elements

Matter occupies space and has mass. Elements are substances that cannot be broken down further and are defined by their number of protons.

• Four essential elements: C, H, O, N (~96% of life).

• Compounds are fixed ratios of ≥2 elements; emergent properties arise from combinations.

• ~25 elements are essential to life; deficiencies cause illness.

Atoms

• Protons (+), Neutrons (0), Electrons (–)

• Atomic number: Number of protons.

• Atomic mass: Protons + neutrons.

• Isotopes: Same element, different neutrons (radioactive isotopes used in medicine, dating fossils, imaging).

Electron Shells

• Electrons fill lowest shells first; outer shell (valence) determines chemical behavior.

• Atoms form bonds (ionic, covalent) to fill valence shells.

Chemical Reactions

• Reactants → products.

• Reversible vs. irreversible reactions.

Chemical Bonds

• Ionic: Electron transfer, attraction between ions.

• Covalent: Electron sharing, strong bonds.

• Nonpolar covalent: Equal sharing.

• Polar covalent: Unequal sharing (e.g., water).

• Hydrogen bonds: Weak attractions (e.g., between water molecules, DNA base pairs).

• Van der Waals: Weak, temporary interactions.

Water Properties

Water's unique properties are essential for life.

• Polarity: Water is a polar molecule, forms hydrogen bonds.

• Cohesion: Molecules stick to each other (surface tension).

• Adhesion: Molecules stick to other surfaces.

• Solvent of life: Dissolves polar/ionic solutes.

• High specific heat: Resists temperature change.

• Ice floats: Less dense than liquid water.

pH & Buffers

• pH < 7 = acidic, 7 = neutral, > 7 = basic.

• Buffers resist pH changes (e.g., blood bicarbonate buffer).

Chapter 3: Carbon & Macromolecules

Carbon

Carbon's four valence electrons allow it to form four covalent bonds, enabling a diversity of organic molecules.

• Forms chains, rings, branches; bonds with H, O, N, S, P.

• Isomers: Same formula, different structures (structural, cis-trans, enantiomers).

ATP

• Adenosine + 3 phosphates.

• Energy currency of the cell.

Macromolecules Overview

• Organic molecules: Contain carbon.

• Monomers → Polymers: Monomers are building blocks; polymers are long chains.

• Dehydration synthesis: Builds polymers by removing water.

• Hydrolysis: Breaks polymers by adding water.

Carbohydrates

• General formula: (CH2O)n, ratio C:H:O = 1:2:1.

• Monosaccharides: Glucose, fructose (energy).

• Disaccharides: Sucrose, lactose (short-term energy).

• Polysaccharides: Starch (plants), glycogen (animals) = storage; cellulose (plants), chitin (arthropods) = structure.

Lipids

• Hydrophobic, nonpolar.

• Fats (triglycerides): Energy storage, insulation.

• Saturated: Solid, unhealthy; Unsaturated: Liquid, healthier.

• Trans fats: Hydrogenated, very unhealthy.

• Waxes: Waterproofing.

• Steroids: 4-ring structure (cholesterol, hormones).

• Phospholipids: Cell membranes (hydrophilic head, hydrophobic tails).

Proteins

• Monomers = amino acids (20 types).

• Functions: Enzymes, structure, transport, hormones, defense.

• Structure levels:

  • Primary: Amino acid sequence.

  • Secondary: α-helix, β-sheet.

  • Tertiary: 3D folding, functional.

  • Quaternary: Multiple polypeptides.

• Denaturation: Loss of structure = loss of function.

• Essential amino acids are those the body cannot synthesize.

Nucleic Acids

• Monomers = nucleotides (sugar, phosphate, base).

• DNA: Double helix, A-T, G-C.

• RNA: Single-stranded, A-U, G-C.

• Function: Store & transmit genetic info, protein synthesis.

Genomics & Proteomics

• Genomics: Study of whole genomes.

• Proteomics: Study of protein expression.

• Bioinformatics: Computational analysis of biological data.

• DNA & proteins act as "tape measures" of evolution.

Table: Comparison of Macromolecules

Macromolecule	Monomer	Function	Example
Carbohydrates	Monosaccharide	Energy, structure	Glucose, starch, cellulose
Lipids	Fatty acids, glycerol	Energy storage, membranes	Triglycerides, phospholipids
Proteins	Amino acids	Enzymes, structure, transport	Hemoglobin, enzymes
Nucleic Acids	Nucleotides	Genetic information	DNA, RNA