Chapter 35. Biodiversity
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2. Domain
1. Biological Classification
⑴ Purpose : A classification of organisms to reveal their relationships with each other.
⑵ Methods
① Natural Classification : Classifying organisms according to their evolutionary processes or relationships.
② Artificial Classification : Classifying organisms based on arbitrary criteria.
○ Example : Terrestrial animals, aquatic plants, medicinal plants, edible fungi, herbivores, etc.
⑶ Phylogenetic Classification Methods
① Method 1: Structural similarity
○ Mainly used to classify extinct species; based on geological age.
○ Used for subdividing the history of extinct organisms, determining geological epochs.
② Method 2: Modern phylogenetic classification
○ DNA sequences of closely related organisms are more similar in evolution.
○ Comparison using small subunit rRNA genes (ribosomal RNA), cytochrome c amino acid sequences, etc.
○ These encode important proteins, thus evolutionarily conserved.
③ Modern species are divided into domains and their subdomains based on structural similarity and phylogenetic history.
⑷ Biological Classification System
① Comprehensive Taxonomic Ranks : Implying recent shared ancestry within the same rank.
② Taxonomic Ranks : Domain – Kingdom – Phylum – Class – Order – Family – Genus – Species, total of 8 levels.
○ Domain : Bacteria domain, Archaea domain, Eukarya domain
○ Kingdom : Eukarya domain subdivided into Protista, Plantae, Fungi, Animalia
○ Current classification system : 3 domains, 6 kingdoms
③ History of Classification
○ Aristotle : Classified 540 animal species.
○ 2-kingdom classification : Divided into non-motile plants and motile animals.
○ 3-kingdom classification : Classified unicellular organisms as Protista.
○ 4-kingdom classification : Divided non-nucleated organisms into Prokaryota.
○ 5-kingdom classification : Separated non-photosynthetic bacteria from Plantae.
○ 3-domain, 6-kingdom classification : Archaea found to be more similar to Eukarya than Bacteria.
④ When finer classification is needed, terms like Domain, Division, Phylum, Class, Order, Family, Genus, and Subspecies are added between each rank.
○ Subspecies : Geographically or morphologically distinct group, no reproductive barriers.
○ Variety : Group with 2-3 differing traits or distributions due to natural mutations.
○ Cultivar : Cultivated group of a species with artificial selection.
⑸ Scientific Nomenclature
① Necessity : For the uniformity of academic research.
○ Latin remains unchanged over time and location.
② Binomial Nomenclature : Genus and species names combined in Latin.
○ Invented by Linnaeus in the 18th century.
○ Genus - Species - Namer
③ Trinomial Nomenclature
○ Used for subspecies, varieties, and cultivars.
○ Genus - Species - (Subspecies, Variety, Cultivar) - Namer
④ Writing scientific names
○ Genus : Capitalized, italicized
○ Species : Lowercase, italicized
○ Subspecies, Variety, Cultivar : Lowercase, italicized
○ Variety indicated by “var.”
○ Cultivar indicated by “for.”
○ Namer : Capitalized, regular font; can be omitted or only the first letter of the namer’s name can be used.
○ Example, Tiger : Felis tiger Linne
○ Example, Korean Tiger (Subspecies) : Felis tiger coreansis Brass
2. Domain
⑴ Prokaryotes (Bacteria Domain + Archaea Domain) vs. Eukaryotes
① Nucleus, Mitochondria, Chloroplasts : Absent vs. Present
② Unicellular vs. Unicellular, Multicellular
⑵ Archaea Domain
① Most archaea are harmless, but familiar ones are often pathogens.
② Many archaea decompose organic matter as decomposers.
③ Characteristics of Pure Archaea
○ Cell structure : Peptidoglycan (cell wall composition), LPS, Teichoic acid
④ RNA Polymerase : α2ββ’
⑤ Useful Compounds from Archaea
○ Antibiotics : Over 50% of antibiotics are derived from archaea.
○ Restriction enzymes : Proteins cutting DNA at specific sequences, used in biotechnology.
⑥ Initiator Amino Acid : fMet (formyl methionine), unique to archaea, faster translation than Eukarya
○ fMet leads to faster translation
⑶ Archaea Domain
① Types
○ Thermophilic Archaea : Inhabit high-temperature environments like hot springs, deep-sea hydrothermal vents.
○ Halophilic Archaea : Thrive in high salinity environments like salt pans, salt flats. Maintain high intracellular K+ concentration for osmotic balance.
○ Acidophilic Archaea : Live in highly acidic environments.
○ Methanogenic Archaea : Inhabit oxygen-depleted environments like swamps, marshes.
② Archaea-Specific Characteristics : Related to cell structure, such as lipids, cell wall, S-layer.
○ Ether binding in archaeal lipids: for extreme environmental adaptation
○ Archaeal lipids of Crenarchaeota = Phosphate head + Ether linkage of fatty acids + Fatty acid × 2 + Ether linkage of fatty acids + Phosphate head
○ Lipids of Euryarchaeota and Thaumarchaeota = Phosphate head + Ester linkage of fatty acids + Fatty acid × 2
Figure. 1. Difference between lipids of Crenarchaeota and lipids of Euryarchaeota and Thaumarchaeota
○ Note that the difference in lipids of Euryarchaeota and Thaumarchaeota lies in the hydrophilic end (e.g., ethanolamine).
○ Monolayer of lipids: Organized by tetraether
○ Isoprene frequently observed in fatty acids: Attached hydrocarbon (polyisoprenoid alcohol)
○ Cell wall : Pseudopeptidoglycan (similar to murein), β 1→3 linkage
○ Peptidoglycan: Absence of branches
○ Pseudopeptidoglycan: Presence of branches. Beta 1,3 linkage
○ Peptidoglycan has muramic acid, while N-Acetyltalosaminuronic acid is present in pseudopeptidoglycan.
○ S-layer (Surface layer): Similar to the LPS of Gram-negative bacteria or teichoic acid of Gram-positive bacteria in Euryarchaeota.
○ Archaea with unique shapes such as rectangles also exist.
③ Similarities between Archaea and Eukarya
○ Transcription regulation
○ RNA Polymerase only one type in Archaea, recently corrected
○ Lack of nuclear envelope, lack of membrane-bound organelles, unicellular
○ Circular DNA, plasmids (transferred by conjugation), operons, 70S ribosome
○ Presence of restriction enzymes
○ Eukaryotes have three types of RNA Polymerase: RNA pol Ⅰ, Ⅱ, Ⅲ
○ Eukaryotic organism Trypanosoma has operons
④ Similarities between Archaea and Eukarya : Pertaining to genome composition and regulation
○ Transcription mechanism
○ Initiation amino acid is Met
○ Histone proteins and introns present
○ TATA box sequence present
○ HU : Similar to eukaryotic histone proteins
○ Presence of branches in isoprene chains of membrane lipids
○ Resistant to penicillin, ampicillin, lysosome : These enzymes degrade peptidoglycan
○ Resistant to streptomycin, chloramphenicol, tetracycline : Only target prokaryotic ribosomes
⑤ Histone proteins are absent in eukaryotic cells too.
⑥ Archaea thrive in extreme conditions (high temperature, pressure, salinity).
○ Less competitive compared to mesophiles, so they inhabit environments where typical organisms cannot survive.
○ Taq polymerase is derived from the thermophilic archaeon Thermus aquaticus.
⑦ rRNA sequences are more similar between Archaea and Eukarya than between Archaea and Bacteria → Eukarya and Archaea have a closer relationship.
⑷ Density and Total Amount of Prokaryotes
Table. 1. Density and Total Amount of Prokaryotes
⑸ Domain Eukarya : Divided into 4 kingdoms
① RNA Polymerase : RNA pol Ⅰ, Ⅱ, Ⅲ
② Presence of nuclear envelope and membrane-bound organelles
3. Eukarya Domain
⑴ Monera Kingdom : Archaea, Bacteria
⑵ Protista Kingdom : Mostly unknown, estimated 8-80 phyla
① Animal-like Protists : Parasites, pathogens
○ Examples : Malaria parasite, sleeping sickness parasite, vaginal trichomonad
② Algae-like Protists
○ Examples : Plant pests (potato blight pathogen)
③ Plant-like Protists : Photosynthetic autotrophic organisms, primary producers
○ Examples : Diatoms, green algae, brown algae
⑶ Animal Kingdom : 25 phyla
① Multicellular, heterotrophic, motile
② Emerged around 530 million years ago in the Cambrian Explosion
③ Development of intercellular communication, organ systems, and organizations
④ Invertebrates (6-30 million species) comprise around 96% of the animal kingdom
⑤ Humans belong to the Chordata phylum
⑷ Fungi Kingdom
① Dependent nutrition organisms, obtaining nutrition through mycorrhizae, capable of spreading over wide areas.
② DNA sequence analysis shows that algae are more closely related to animals than to plants.
③ Algae are decomposers, competing with bacteria and producing antibiotics (1/3 of antibiotics).
○ Example: Penicillin
⑸ Plant Kingdom
① Characteristics
○ Autotrophic nutrition: Chlorophyll a, b, carotenoids
○ Multicellular eukaryotes with differentiated cells and tissues
○ Main component of cell walls: Cellulose
○ Rosette-forming cellulose synthesis enzymes: Shared only with brown algae (Phaeophyceae) and land plants
○ Non-motile
○ Adapted to terrestrial life
○ Adapted to dry environments: Thick cuticle layer with high water repellency on the surface
○ Differentiation from roots, stems, and leaves
○ Development of water-conducting and vascular tissues (exception: bryophytes)
② Evolution
○ Exist on land for over 400 million years
○ First land plants: Small size, no vascular tissue
○ Evolution of vascular tissue allowed the emergence of large trees and growth in dry areas
○ Seeds: Adaptation to dry terrestrial environments
○ Evolution of flowers: Most modern plants evolved around 140 million years ago
○ Diversification of angiosperms led to 150 families, over 90% of modern plants: Duplicated modifications
○ Double fertilization: Two sperm cells, one fertilizes the egg to form a diploid embryo (2n), the other fuses with two polar nuclei to form a triploid endosperm (3n)
○ Lack of nutrient provisioning until egg is fertilized
○ Assisted by animals, wind, water for fertilization
④ Uses
○ Chemical defense: Secondary metabolites produce toxins as byproducts of primary metabolic processes → Examples: morphine in poppies, caffeine in coffee
○ Primary source of natural medicine: Bacteria as secondary source, algae as tertiary source
4. Prokaryota Domain
⑴ Characteristics
① Eukaryotes; nuclear membrane and membrane-bound organelles present
② Unicellular or multicellular
③ In multicellular forms, organs not fully differentiated compared to other eukaryotes
⑵ Classification 1. Protozoa : Heterotrophic, classified based on types of locomotion
① Type 1. Flagellates (e.g., Trypanosoma): Locomotion via flagella
② Type 2. Ciliates (e.g., Paramecium): Locomotion via cilia
③ Type 3. Amoebas (e.g., Amoeba): Amoeboid movement
④ Type 4. Sporozoans (e.g., Plasmodium): Non-motile
⑶ Classification 2. Algae : Perform photosynthesis, classified based on photosynthetic pigments
① Chlorophyta (Green algae): Tissue-level organization, chlorophyll a, b
○ Closest relationship with terrestrial plants
○ Shared chlorophyll a, b, carotenoids (e.g., chlorophytes, carotenes)
○ Similar cell wall composition: Cellulose
○ Examples: Ulva, kelp
② Rhodophyta (Red algae): Unicellular stage, chlorophyll a, c
③ Phaeophyceae (Brown algae): Tissue-level organization, chlorophyll a, c
○ Contains iodine
○ Examples: Kelp, wakame
④ Rhodophyta (Red algae): Tissue-level organization, chlorophyll a, d
○ Closest relationship with cyanobacteria
○ Both possess phycobilins
○ Examples: Nori, dulse
⑤ Euglenids: Unicellular stage, chlorophyll a, b
○ Flagella: Mode of movement
○ Eyespot: Light reception
○ Contractile vacuole: Maintains osmotic pressure
○ Chloroplasts: Photosynthesis, can be both autotrophic and heterotrophic, but prefer heterotrophy
⑷ Classification 3. Protozoa
① Depend on organic matter from dead organisms for nutrition
② Form spores
③ Multinucleate stage
⑸ Summary of Protista Kingdom
① Tissue-level organization: Red algae, green algae, brown algae
② Multinucleate stage: Ciliates, sporozoans
③ Unicellular stage: Euglenids, dinoflagellates, diatoms, ciliates, flagellates, amoebas
④ Chlorophyll a + d: Red algae
⑤ Chlorophyll a + b: Green algae, euglenids
⑥ Chlorophyll a + c: Brown algae, ciliates, diatoms
⑦ Spore formation: Sporozoans, dinoflagellates
⑧ No spore formation: Ciliates, flagellates, amoebas
5. Evolution of Animals
⑴ Overview
① Homology analysis: Shared traits exist
② Convergence analysis (convergent evolution): Example is body shape
⑵ 1st. Choanoflagellates are the oldest animal form
⑶ 2nd. From choanoflagellates, branching to sponges and cnidarians
① Cnidarians: Animals with only a gastrovascular cavity
○ Examples: Bathypelagic animals (e.g., bathysal, volcanoan)
② Ctenophores: Animals with tentacles
○ Examples: Excluding ①
⑷ 3rd. From cnidarians, branching to bilaterians and triploblasts
① Cnidarians: No distinction between body layers
○ Example: Sponges
② Bilaterians: Bilateral symmetry animal group
○ Examples: Bilateria (= coelomate animals), Ecdysozoa, Lophotrochozoa
○ Bilateria (e.g., tapeworm, hydra): Nervous system, digestion in coelom
③ Triploblasts: Radial symmetry animal group, excluding ① and ②
⑸ 4th. From triploblasts, branching to protostomes and deuterostomes
① Protostomes: Embryonic blastopore becomes mouth, excluding ②
○ Additional feature: Tough mesodermal blocks form muscles between the gut and nerve cords
○ Examples: Platyhelminthes, Rotifera, Annelida, Mollusca, Arthropoda, Echinodermata
② Deuterostomes: Embryonic blastopore becomes anus, radial cleavage occurs
○ Additional feature: Hollow dorsal nerve cord → develops into brain or spinal cord
○ Additional feature: Gill slits
○ Additional feature: Muscular tail posterior to anus
⑹ Protostomes: Embryonic blastopore becomes mouth
① 5th - 1st. Branching to molting animals and lophotrochozoans
② Lophotrochozoans: Larvae pass through trochophore stage
○ Trochophore: Free-swimming larva
○ Type 1: Flatworms (e.g., planarians): First excretory system (flame cells), flat and bilaterally symmetrical body
○ Type 2: Rotifers (e.g., rotifers)
○ Type 3: Trochozoa, Bilateria, Brachiopoda: Presence of lophophore
○ Type 4: Annelida, Mollusca, Echiura: Presence of spiral cleavage
○ Annelida (e.g., snails, squids, clams): Presence of trochophore larva, segmentation reduction
○ Mollusca (e.g., snails, squids, clams): Presence of trochophore larva, development of foot
○ Echiura (e.g., spoonworms): Presence of trochophore larva, development of segmented body
○ Echiura: Presence of segmented body
③ Ecdysozoans
○ Type 1: Ecdysozoans
○ Examples: C. elegans, nematodes
○ Type 2: Arthropods
○ Defining trait 1: Ecdysis: Flexible, chitinous exoskeleton between digestive tract and body wall
○ Arthropods (e.g., insects, spiders): Ecdysis throughout life
○ Type 3: Lophophorates: Possess lophophore within mesodermally derived cells
○ Defining trait 1: Lophophore: Circular, ciliated or tentacled structure between digestive tract and body wall
○ Lophophorates (e.g., brachiopods, phoronids, bryozoans): Unique feeding structure
⑺ Deuterostomes: Embryonic blastopore becomes anus
① 5th - 2nd. Branching to chordates
② Echinoderms: Bilaterally symmetrical in larval stage, radial in adult
○ Examples: Jellyfish, sea urchins, sea cucumbers
③ Chordates
○ Defining trait 1: Notochord: A flexible rod located between the digestive tube and nerve cord
○ Defining trait 2: Hollow dorsal nerve cord: Develops into the brain and spinal cord
○ Defining trait 3: Pharyngeal slits: Develop into gills or other respiratory structures
○ Defining trait 4: Muscular, post-anal tail
④ Classification of Chordates
○ Urochordates (e.g., tunicates): Retain notochord only in larval stage
○ Cephalochordates (e.g., amphioxus): Retain notochord throughout life
○ Vertebrates: Notochord replaced by vertebral column, closed circulatory system, kidneys, cranium
Table 2. Classification of Vertebrates
⑻ 6th. Evolution of Coelom: Coelom evolved independently through convergent evolution, shared trait
① Coelom: Cavity between animal body wall and inner organs (e.g., human thoracic and abdominal cavities)
② Acoelomates: No space between digestive tract and body wall
○ Examples: Bathypelagic animals, flatworms
③ Pseudocoelomates: Coelom enclosed by mesoderm and endoderm during development
○ Examples: Rotifers, Ctenophores
④ Eucoelomates: Coelom fully enclosed by mesoderm-derived tissues, excluding ② and ③
○ Examples: Annelida, Mollusca, Brachiopoda, Cnidaria, Echinodermata
○ Deuterostome eucoelom: Annelida, Echinodermata
Input: 2015.07.09 15:50
Modified: 2019.02.05 12:57