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

Chapter 1: Themes of Biology

Unifying Themes

Biology is organized around several core themes that help explain the complexity and diversity of life. Understanding these themes provides a framework for studying biological systems.

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

• Information: DNA stores and transmits genetic information, guiding cellular processes and inheritance.

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

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

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

Example: Photosynthesis in plants converts solar energy to chemical energy, supporting life on Earth.

Emergent Properties

Emergent properties arise when components interact to produce new functions not present in individual parts.

• Photosynthesis requires intact chloroplasts, not just chlorophyll.

• Reductionism simplifies systems by studying components, but systems biology integrates across levels.

Structure & Function

The structure of biological molecules and organisms determines their function.

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

Cells

Cells are the fundamental units of life, classified as prokaryotic or eukaryotic.

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

• Eukaryotes: Nucleus, organelles, larger, more complex (e.g., plants, animals, fungi).

• Three Domains: Bacteria, Archaea, Eukarya.

Genetic Information

Genetic information is encoded in DNA and expressed through gene products.

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

• Gene expression: DNA → RNA → Protein.

• Genetic code is universal, supporting evidence of common ancestry.

Energy & Matter

Life depends on energy transformations and matter cycling.

• Energy flows: sunlight → chemical energy → heat.

• Matter cycles: carbon (C), nitrogen (N), water (H2O).

Interactions

Organisms interact through various ecological relationships.

• Mutualism, parasitism, competition.

• Climate change and ecosystem impacts.

Evolution

Evolution explains the diversity of life through natural selection and adaptation.

• Descent with modification.

• Variation in traits, competition, survival of the fittest.

Chapter 2: Matter, Atoms & Water

Matter & Elements

Matter occupies space and has mass. Elements are pure substances defined by their atomic number.

• Elements: Cannot be broken down further; defined by number of protons.

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

• Compounds: Fixed ratios of ≥2 elements; emergent properties.

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

Atoms

Atoms are the basic units of matter, composed of protons, neutrons, and electrons.

• 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).

Electron Shells

Electrons fill lowest shells first; atoms form bonds to fill outer shells.

• Stable when outer shell is full.

• Atoms form bonds (ionic, covalent).

• Outer shell electrons are valence electrons.

Chemical Reactions

Chemical reactions rearrange atoms to form new products.

• Reactants → products.

• Reversible vs. irreversible reactions.

Chemical Bonds

Bonds hold atoms together in molecules.

• Ionic: Electron transfer, attraction between ions.

• Covalent: Electron sharing.

• Polar covalent: Unequal sharing.

• Hydrogen bonds: Weak attractions (water, DNA base pairs).

• Van der Waals: Weak, temporary interactions.

Water Properties

Water is essential for life due to its unique properties.

• Polar molecule: Forms hydrogen bonds.

• Cohesion: Molecules stick to each other.

• Adhesion: Molecules stick to other surfaces.

• Surface tension: Water resists breaking.

• Solvent of life: Dissolves polar/ionic solutes.

• High heat capacity: Moderates temperature.

• Ice floats: Less dense than liquid water.

pH & Buffers

pH measures hydrogen ion concentration; buffers stabilize pH in biological systems.

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

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

Chapter 3: Carbon & Macromolecules

Carbon

Carbon forms the backbone of organic molecules due to its ability to make four covalent bonds.

• Valence electrons = 4 covalent bonds.

• Small, versatile—chains, rings, branches.

• Forms diverse molecules with H, O, N, S, P.

• Isomers: Molecules with same formula, different structure (structural, cis-trans, enantiomers).

ATP

ATP (adenosine triphosphate) is the energy currency of the cell.

• Adenosine + 3 phosphates.

• Provides energy for cellular processes.

Macromolecules Overview

Macromolecules are large organic molecules essential for life, built from smaller monomers.

• Organic molecules: Carbon-based.

• Monomers → polymers: Dehydration synthesis builds polymers (removes water); hydrolysis breaks polymers (adds water).

• Enzymes catalyze both reactions.

Carbohydrates

Carbohydrates are energy sources and structural components.

• 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

Lipids are hydrophobic molecules used for energy storage, insulation, and cell membranes.

• Fats (triglycerides): energy, 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

Proteins are polymers of amino acids with diverse functions.

• Monomers = amino acids (20 types).

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

• 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 not synthesized by the body.

Nucleic Acids

Nucleic acids store and transmit genetic information.

• 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 and proteomics are modern fields that analyze whole genomes and protein sets.

• Genomics: Study of whole genomes.

• Proteomics: Study of protein expression.

• Bioinformatics: Computational analysis of biological data.

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

Key Table: Comparison of Macromolecules

Macromolecule	Monomer	Function	Example
Carbohydrate	Monosaccharide	Energy, structure	Glucose, starch, cellulose
Lipid	Fatty acid, glycerol	Energy storage, membranes	Triglyceride, phospholipid
Protein	Amino acid	Structure, enzymes, transport	Hemoglobin, enzyme
Nucleic Acid	Nucleotide	Genetic information	DNA, RNA

Key Equations & Concepts

• Dehydration Synthesis: Monomer + Monomer → Polymer + Water

• Hydrolysis: Polymer + Water → Monomer + Monomer

• pH Calculation: $pH = -\log[H^+]$

• General Formula for Carbohydrates: $(CH_2O)_n$

• Central Dogma: $\text{DNA} \rightarrow \text{RNA} \rightarrow \text{Protein}$