Three Domains of Life: Archaea, Bacteria, Eukarya Explained (Biology Lecture)

Biological classification organizes organisms into hierarchical categories. Taxon is singular while taxa is plural. Binomial nomenclature, developed by Carolus Linnaeus (father of taxonomy), assigns each organism a two-part scientific name: genus (generic name) and species (specific epithet). Scientific names are always written in Latin. The seven main taxonomic categories are Kingdom, Phylum, Class, Order, Family, Genus, and Species, with Species being the smallest unit and Kingdom the largest. In ascending order (Species to Kingdom), common characteristics decrease; in descending order, they increase. Dogs and cats belong to the same family (Felidae) but different genera. Tiger, lion, leopard, and jaguar all belong to the same genus (Panthera) but different species. Potato, tomato, and brinjal all belong to the same genus (Solanum).

Species is the fundamental unit of biological classification, defined as a dynamic group of genetically similar and potentially inter-breeding natural populations that share a common gene pool and are reproductively isolated from other groups. There are four main species concepts: the typological concept (species as static ideal types), the nominalistic concept (species as human-made abstractions), the biological concept (species as reproductively isolated inter-breeding populations), and the evolutionary/phylogenetic concept (species as monophyletic groups with common ancestry). Genus is a taxonomic category consisting of one or more species of monophyletic origin, requiring constituent species to be monophyletic and sufficiently different from other genera. Family is a higher taxonomic category consisting of one or more genera of monophyletic origin, positioned above genus in the taxonomic hierarchy.

Taxonomy is the systematic classification of species into hierarchical categories called taxa. The hierarchy progresses from broad to specific: species (most commonly used), genus, family, and higher ranks. Students must master the lower three ranks (family, genus, species) as they form the foundation for all biological discussion. Examples include Homo sapiens (genus Homo, species sapiens) and Canis lupus (genus Canis, species lupus). Each level contains the previous one—species compose genera, genera compose families. Understanding this hierarchy is essential as it underlies all biological organization and will be referenced throughout the course without repeated explanation.

Taxon vs category: category is the rank name, taxon is the organism holding that rank. Species is the basic unit of classification - group of morphologically and genetically similar organisms sharing a common gene pool. Biological species concept (Mayr): members of same species can interbreed, different species show reproductive isolation. Genus groups similar species (Panthera: tiger, lion, leopard). Family groups related genera (Solanaceae, Felidae). Order groups related families (Carnivora, Polymoniales). Class groups related orders (Mammalia, Dicotyledonae). Phylum (animals) or Division (plants) groups related classes. Five kingdoms: Monera, Protista, Fungi, Plantae, Animalia.

Species is defined as a group of individual organisms with fundamental similarities. Three species concepts exist: (1) Morphological species concept - based on external physical features, (2) Ecological species concept - based on geographic distribution, (3) Biological species concept (proposed by Ernst Mayr) - based on reproductive isolation, where organisms that can interbreed and produce fertile offspring belong to the same species. Taxonomic categories from lowest to highest: Species, Genus, Family, Order, Class, Phylum/Division, Kingdom. Only species actually exist in nature; all higher categories are human-made groupings for convenience. Examples: Solanum (genus) for potato, brinjal, nightshade; Solanaceae (family) for Solanum; Felidae (family) for Panthera and Felis; Polymoniales (order) for Convolvulaceae and Solanaceae; Mammalia (class) for Carnivora and Primates; Chordata (phylum) for fish, amphibians, reptiles, birds, mammals.

Two key concepts from evolutionary thinking are ancestral common and phylogenetic tree. Ancestral common refers to the shared ancestor from which different species evolved. Phylogenetic tree is a diagram that shows the evolutionary relationships among organisms, similar to how family trees show relationships among family members. These concepts help explain why organisms share some characteristics while also having differences.

Phylogenetics is a branch of biology that analyzes and produces diagrams representing the proximity or relatedness between living organisms. The term 'phylo' indicates proximity or friendship, based on evolutionary history. Organisms are related because they share a common ancestor, and the closeness of the relationship is determined by how recent that common ancestor is. For example, siblings share a more recent common ancestor (their parents) than they do with cousins (who share grandparents). Phylogenetic trees can be simplified by removing ancestor names and keeping only descendant names, with branching points representing where lineages diverged.

Cladistics and phylogenetics are systems for grouping organisms by common evolutionary descent. Phylogenetic trees show evolutionary relationships where branches originate from common ancestors. Humans and chimpanzees share a recent common ancestor but did not evolve from each other—both share an ancestor that lived in the past. Different tree orientations represent identical relationships. Family trees provide an analogy: nodes represent ancestors (parents, grandparents), and branches represent descendants. The most ancestral part of a tree is at one end, with all species branching from shared common ancestors.

Phylogeny is the name given to evolutionary relationships between organisms and forms the basis of classification. When organisms are grouped into the same taxonomic groups (such as genus), they must share a common ancestor. Phylogenetic trees represent these evolutionary relationships, with the bottom of the tree representing the common ancestor to all organisms. Branching points represent the last known common ancestor of the descendants within those branches.

Phylogeny represents the evolutionary history of organisms. Phylogenetic trees diagram lines of descent, with branching points (nodes) representing common ancestors. Trees use common characters (present in all group members and ancestors) and derived characters (new traits evolving in some members). Polytomies show uncertainty when multiple branches emerge from a single node. Sister taxa share immediate common ancestors and are each other's closest relatives. The root species represents the most recent common ancestor of all included species. Trees are hypotheses that can be supported or rejected as new evidence emerges. Molecular data comparing DNA sequences provides reliable evidence for evolutionary relationships.

Living organisms are organized hierarchically from cells to organ systems (digestive, circulatory, respiratory, nervous, skeletal, muscular, endocrine). Cells contain organelles like the nucleus (containing DNA) and mitochondria (producing energy). The four major biological macromolecules are carbohydrates, lipids, proteins, and nucleic acids. Carbohydrates are polymers with carbon, hydrogen, and oxygen in a 1:2:1 ratio (C(H2O)n), classified as simple (monosaccharides like glucose, fructose, galactose; disaccharides like sucrose, maltose, lactose) or complex (starch, cellulose, glycogen). Lipids are non-homogeneous compounds made of fatty acids and alcohols (glycerol with three hydroxyl groups), classified as simple (fats, oils, waxes) or complex (phospholipids, steroids). Proteins are polymers of amino acids, each containing a central carbon bonded to hydrogen, carboxyl group, amino group, and variable R group. Peptide bonds form through condensation reactions, creating polypeptide chains. Nucleic acids (DNA and RNA) are polymers of nucleotides, each consisting of a five-carbon sugar, nitrogenous base, and phosphate group. DNA contains deoxyribose and bases adenine, guanine, cytosine, and thymine, forming a double helix. RNA contains ribose and bases adenine, guanine, cytosine, and uracil, typically single-stranded.

DNA (Deoxyribonucleic acid) is double-stranded and contains genetic information. RNA (Ribonucleic acid) is single-stranded and involved in protein synthesis. Prokaryotic cells (like bacteria) are smaller (1-10 micrometers) and lack a proper nucleus and membrane-bound organelles. Eukaryotic cells (like plant and animal cells) are larger (10-100 micrometers) and have a proper nucleus and membrane-bound organelles. Prokaryotic cells have their genetic material in a region called the nucleoid, while eukaryotic cells have it enclosed in a nucleus. Eukaryotic cells contain membrane-bound organelles like mitochondria, endoplasmic reticulum, Golgi apparatus, and lysosomes.

Life is classified into three domains: Bacteria, Archaea, and Eukarya. Bacteria and Archaea are prokaryotic domains, while Eukarya represents eukaryotic organisms. Key cellular differences include: (1) Nucleus is present only in Eukarya; (2) Membrane-bound organelles exist only in Eukarya; (3) Peptidoglycan is found in bacterial cell walls; (4) Ribosomes are 70S in Bacteria and Archaea, 80S in Eukarya; (5) Operon system is present in Bacteria and Archaea; (6) Plasmids are found only in Bacteria. Membrane lipids consist of glycerol, phosphate, and fatty acids. In Bacteria, ester bonds form with branched fatty acid chains. In Archaea, ether bonds form with unbranched fatty acid chains. In Eukarya, ester bonds form with unbranched fatty acid chains. Histone proteins are present only in Eukarya for DNA condensation. Chromosomes are circular in Bacteria and Archaea, but linear in Eukarya. Photosynthesis occurs in Bacteria and Eukarya, but not in Archaea.

Biomacromolecules have molecular weight >1000 Daltons (proteins, polysaccharides, nucleic acids). Lipids are not strictly biomacromolecules (MW <800 Daltons) but are classified under acid-insoluble fraction due to their structural role in cell membranes. Cell composition: Water (70-90%), Proteins (10-15%), Nucleic Acids (5-7%), Carbohydrates (3%), Lipids (2%), Ions (1%).

Biological macromolecules are categorized into four major classes based on their structure and function: (1) Lipids are nonpolar/hydrophobic molecules that form cell membranes, provide insulation, and store energy; they may be amphipathic with both polar and nonpolar regions; (2) Carbohydrates follow the CH2O formula and serve as energy sources, structural components (cell walls, exoskeletons), and DNA constituents; they polymerize through glycosidic bonds into starch, glycogen, or cellulose; (3) Nucleic acids (DNA and RNA) carry hereditary information and are composed of nucleotides containing a sugar (ribose/deoxyribose), phosphate, and nitrogenous bases (adenine, guanine, cytosine, thymine/uracil); (4) Proteins are polymers of amino acids, with each amino acid containing an alpha carbon bonded to an amino group, carboxyl group, hydrogen, and a variable R side group that determines its properties. Each class can be recognized by specific characteristics: lipids show nonpolar hydrocarbon chains, carbohydrates display the CH2O formula with polar oxygen/hydroxyl groups, proteins feature the alpha carbon with amino and carboxyl groups plus an R group, and nucleic acids contain phosphate groups attached to sugars with nitrogenous bases.