BIOB 170N 1st EditionExam # 1 Study Guide Chapters: 1-2 1. Kingdoms and domains2. Taxonomy and classification a. Hierarchical Classification and binomial nomenclature3. PhylogeneticsChapters 1&2 will be useful throughout the semester 10-12 &29-100I. Kingdoms and Domainsa. Earliest biologists recognized 2 kingdomsi. Plantsii. Animalsb. 1960’s – agreed upon 5 kingdom systemi. Plantae, Fungi, Animalia, Protista (Eukaryotes), Monera (Prokaryotes)ii. Pro vs Eukaryotes1. Pro- always single celled, lack of internal organelles (ribosomes are not organelles but a cluster of molecules not membrane bound), lack nuclei2. Euk- c. Rise of idea of Protista, Monera, and Plantae kingdomsd. 2 ptsi. Kingdom level approach to classification doesn’t completely represent biological realityii. Kingdom-level approach supplemented by domainse. 3 Domain system of classificationi. Bacteria, Archaea, Eukaryaii. These three ^ have a universal ancestoriii. 3 of the former karyote kingdoms are with us still**f. 5 Kingdom systemII. Taxonomy and Classificationa. Hierarchical Classification and binomial nomenclature introduced by Carolus Linneaus 1735i. Proposed Hierarchical Classification1. Hierchy- Classification based on size or other details2. Kingdom, phylum, class, order, family, genus, species3. ^Most Inclusive   Least inclusive ^ii. Binomeal Nemenclature1. Each species identified by 2 terms2. Genus + Specific epithet3. Both italicized or underlined4. Ex: Leopard as species- Panthera pardusIII. PhylogeneticsThese notes represent a detailed interpretation of the professor’s lecture. GradeBuddy is best used as a supplement to your own notes, not as a substitute.1. Domain Archaea (oldest of something)a. General characteristicsb. Eukaryote affinities2. Domain Bacteriaa. Distinguishing featuresI. Prokaryotesa. Earliest forms in lifeb. Appear > 3.5 billion years agoi. Earth is 4.5/4.6 billion years oldc. Early divergence into 2 lineagesi. Each prokaryote domain consists of several “subgroups”ii. Know prokaryotes, Bacteria, and Archaea not the subgroupsd. Phylogenitics unclear??e. Little Consensus at phylum/class levels (a lot of debate the farther down the trees you look on what organism is what)f. Standard phylogenetic concepts may not applyi. Mutations arise giving diversity…II. 3 Domains of Lifea. Bacteriai. First living things found themselves in a protein, carbohydrate lithic stew (ocean,fed off organic molecules)ii. Virus vs Bacteria1. Cause bacteria to “blow up”. Sharing its information with other bacteria and changing/warping?iii. Most widespread forms of life on earthiv. Numerous ecological nichesv. Great metabolic diversity (many different ways in which bacteria get their energy)vi. Distinguishing traits of bacteria1. Flagella apparatusa. Allow to swim, adhere to surfacesb. Can have many flagella or flagella on both endsc. Consists of distinctive protein microtubule array: axonemed. Microtubials?e. Membrane-bound, rooted in cytoplasm (Ch 2) f. Consists of stiff tubular protein: filament (Stiff and just turns like a corkscrew for propultion)i. Has rotary motion powered by basal apparatusii. Not membrane boundiii. The sub parts of the motor have no function until they are put together in the motor?2. Cell wall/ extra-cellular features3. Genome organization4. Mechonisms of reproduction5. Reproduction (no sex though)6. Metabolic diversityb. Archaeai. Initially though most archaic of prokaryotes (not though)ii. Exhibit features of both bacteria and eukaryotesiii. Sometimes termed “extremophiles”1. Typical of extreme environments (Ex: hotsprings 90-113 C and low pH)iv. Hyper-saline environments (halophiles)v. Anaerobic aquatic sediments (methanogens)vi. 3 Destinctive traits (all 3 are Eukaryote-like)1. Lack peptidoglycan (Molecule that makes up the cell wall in bacteria only) in cell wall2. Some w/Histones ( molecular spools that DNA wraps around)3. Antibiotic response negative4. NOTE TABLE 6.2 (Peptidoglycan in cell wall, Response to the antibiotics streptomycin and chloramphenicol, Histones associated with DNA) 3 bitsof evidence to why archaeas are more like usc. Eukaryai. Plants, Animals, Fungi1. Bacteriaa. Cellular featuresb. Reprocution/persistencec. MetabolismI. Bacteriaa. Characteristicsi. Flagellar apparatusii. Cell wall/ extra-cellular featuresiii. Genome organizationiv. Reproductionv. Cell membrane surrounded by cell wall (as in plants)1. Humans don’t have a cell wallvi. Peptidoglycan (carbohydrate) primary wall matrix1. can analyze this to see if bacteria is presentvii. Mucilaginous (sticky) capsule commonly present1. Bacterial capsules ^ think when your slipping on rocks algae have the same capsuleb. 2 major groups of bacteria i. Gram-positive1. Easily treated with antibiotic2. Gram stain binds w/peptidoglycan3. Dark violet after stainingii. Gram-negative1. Antibiotic resistanta. b/c the wall structureb. very thin peptidoglycan and extra membrane layerc. outer shield interferes with antibiotic uptake2. pink-light red after stainingiii. general antibiotics (penicillin) action is to interfere with peptidoglycan formationiv. Both distinguished by simple chemical procedurec. Extra cellular features (outside)i. Fimbriae1. Not moving like flagella2. Protein-tubes (similar to filament of flagellum)3. Facilitate substrate adhesionii. Bacteria don’t have appendages but have 2 important ways of sticking to things. Fimbriae and Mucilaginous capsules (sicky outside)d. Inside Bacteriai. Region of concentrated DNA: nucleoidii. Consists of single, large circular DNA moleculeiii. Small, independent circular DNA molecules may be present: plasmids1. Plasmids can be transferred between bacteria (in a process of gene exchange; generally a one way exchange)a. Kinda sexb. But its not because sex involves the recombination of TWO individuals into onec. Called horizontal gene transfere. Bacteria Reproduction / persistencei. In some bacteria fimbriae may be modified to form sex pilus1. Sex pilus (not true sex/tubish thing connecting bacteria):2. Permits conjugation, gene (plasmid) transferii. Rapid “cell cycle”1. Simple cell division: binary fission2. <60 min under good conditionsiii. under unfavorable conditions endospores are formed1. endospores- bacterial cell 2. the bacteria then has a hard housing to protect the endospore3. a lot of bacteria is transferred as endospores (inactive form/endobollically shut down)iv. mytosis refers to “dance cells do before leading