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Midterm Study Notes - Winter 2013

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BIOL 165
Kirsten Muller

BIOL 165 BIOL 165 Study Notes - Midterm #1 - primitive fern Ophioglossum reticulatum has the highest known chromosome number of any plant, 2n = ca. 630 - Hierarchy - Kingdom, Phylum, Subphylum, Class, Subclass, Order, Family, Genus, Species. The Species Concept - Morphological or Typological - a species is a “different thing” or looks different - species are real - practical, simplest - Nominal Species Concept - species not real, nature made up of individuals (not used) - Non-dimensional - concept based on relationship of two co-existing natural populations at a single locality (sympatric, synchronous - growing/living in same place, same time, but don’t interbreed). No hybrids present. - Interbreeding concept - considers a species as a group of populations that actually or potentially interbreed with each other - Mayr or Biological - involves any species concept or definition that stresses reproductive isolation and a community gene pool - 3 main aspects - species defined by distinctiveness (shared traits) rather than by relative differences - species consist of populations rather than unconnected individuals - species are defined by their reproduction isolation - Bicameral Genome - species is a population or group that has a unique “closed” genome component as well as a potentially non unique “open” genome component - derived from the Carson/Templeton Founder-Flush Speciation Hypothesis Phylogenetic Terminology Cladogenesis - the branching or splitting of lineages (phylads) Anagenesis - evolution of lineages between branching points Phylogenesis - evolutionary processes of cladogenesis and anagenesis Phylogenetics - study of phylogenesis Phylogeny - particular phylogenetic sequence; an evolutionary history Monophyly - condition that a taxon or group of organisms contain the most recent common ancestor of its group and all its descendants Paraphyly - condition that a taxon or group of organisms contains the most recent common ancestor but excludes some descendants of the ancestor Polyphyly - condition that a taxon or group of organisms does not contain the most recent common ancestor of the group (The group is of multiple origins) Polyploidy - whole genome duplication Cladistics and Cladograms Cladistics - system of arranging taxa by analysis of evolutionarily derived characteristics so that the arrangement will reflect phylogenetic relationships Cladogram - branching diagram showing pattern of sharing of evolutionarily derived characters among species or higher taxa Parsimony - rule that the solution with the fewest number of steps is searched for and reported Synapomorphy - shared derived character (e.g. mammary glands b/n mammals) Plesiomorphy - primitive character Example: Vertebrae - synapomorphy that defines the vertebrates, but a plesiomorphy within the vertebrates Universal Phylogenetic Tree BIOL 165 - based on comparative sequencing of 16S and 18S ribosomal RNA Triangle of Life - cell fusion = plasmogamy, nuclear fusion = karyogamy, meiosis = reduction division - sexually reproducing organsims have a brief dikaryotic phase after gamete cell fusion; some fungi have a distinct dikaryon phase Endosumbiosis of Chloroplast - Evidence: 1. DNA of Cyanobacteria and Purple proteobacterua, 2. Ribosomes - bacteria - secondary: Chryptophyta - has 4 membranes around chloroplast - only only ever see 2-4 membranes around chloroplast - tertiary: host call that has eaten a crytophyte which at a read algae which ate a bacteria Domain Bacteria - prokaryote - all known disease causing pathogens, most prokaryotes in soil, water, animal digestive tracts, and many other environments - shapes: coccus (round), rod, spirillum (smooth worm-like), spirochete (rigged worm-like), budding or appendaged (round with point), filamentous. - Cell division - simple binary fission. Duplicated chromosomes are attached to the cell membrane on opposite sides of division plane. New cell wall synthesized along a central zone b/n wall bands. New wall then pinched off to form 2 daughter cells. - Some bacteria divide by budding, the formation of a daughter cell. Some bacteria form a bud at the end of a thin stalk projecting from the cells - chromosome coiling - genes can be transcribed in diff. directions - lateral gene transfer - can receive genes from plasmids - ex. open circle, supercoiled, star-like (supercoiled domain attached together by protein) - conjugation in bacteria - cell w/ plasmid and cell w/o meet - cells form pilus (connects them together), pilus retracts, drawing cells together - cell pairs stabilized, plasmid nicked in one strand - transfer of one strand from cell w/ plasmid to cell w/o. Plasmid simultaneously replicated in plasmid cell - synthesis of complimentary strand begins in recipient cell, cells seperate - Gram staining of bacteria - gram-positive - have cell wall consisting mostly of petidogylcan and lacking the outer membrane of gram- negative bacteria. Gram-positive bacteria turn purple when stained. - gram-positive - synapomorphy - gram-negative - not synapomorphy = paraphyletic Phyla Traits Examples Proteobacteria - distinctive life cycle most complex of all - purple sulfur bacteria, uses (Myxobacteria) prokaryotes hydrogen sulfide as an electron - gliding bacteria that can aggregate (chemotaxis) donor for CO2 reduction in into large mounds that form “fruiting-bodies” photosynthesis. Sulfur is oxidized to when nutrients are rare elemental sulfur S that is stored into - these produce resting spores called myxospores globules inside the periplasm of the which can be enclosed in a walled structure gram-negative cell. called a cyst, which is resistant to environment BIOL 165 Phyla Traits Examples Actinomycetes - large group of filamentous, gram-positive - Streptomyces bacteria that form fungal mycelial-like masses of - Actinomyces filaments - spores produced on sometimes elaborated branching structures - produce a number of substances that are used to produce antibiotics Cyanobacteria - “blue-green algae”, chlorophyll a - Gloecapsa - accesory pigments: carotenoids, phycocyanin - Merismopedia (blue, phycoerthrin (red) - Lyngbya - cyanophyte starch - Anabaena - no flagella - Nostic - cellulose and pectin in cell wall; often w/ sheath- Rivularia sometimes calcified - Stromatolites - mostly fresh water - specialized cells: Akinetes - resting spore cells (thick-waled, rich in stored organics), Heterocysts - aneaerobic cells specializing in nitrogen fixation (lacks chlorophyll) - chemolithotrophs - use inorganic chemicals as energy sources and electron donors and CO2 as carbon source - chemoorganotrophs - use organic chemicals as energy sources and electron donors and as the carbon source (heterotrophs) - mixotrophs - used inorganic chemicals as electron donors and organic chemicals as the carbon source Domain Archaea - most occupy extreme habitats - unusual biochemistry - eg/ some produce methane - Kingdoms, Euryachaeota, Crenarchaeota, and Korarchaeota Phyla Traits Examples Extremely Halophilic Archaea - inhabit highly saline habitats, such as solar salt evaporation ponds - obligates of extreme (2-4M NaCl, 12-23%) Cernarchaeota - able to survive in sulfur hot springSulfolobus - chemoautotroph found on the sides of a volcano + in mud pots of Yellowstone Methanococcus - produce or live in methane Domain Eukaryota - includes four kingdoms: Protoctista, Plantae, Fungi (Eumycota) and Animalia - Organelles of Eukaryote Cells - Nucleus - bounded by double membrane (nuclear envelope) - Endoplasmic Reticulum - network of interconnecting membranes. Rough ER=ribosomes, smooth ER=lipid synthesis - Golgi Complex - flattened membranes, mediate the modification, sorting and transport of proteins within the cell. Proteins produced on rough ER transported via vesicles to Golgi. BIOL 165 - Cytoskeleton -array of protein filaments, anchors organelles, consists of microtubules and microfilaments - Mitochondria - surrounded by double membrane - Chloroplasts - sites of photosynthesis, double membrane, stacks (granna) of inner membranes called thylakoid membranes - Undulipodia - (flagella and cilia), both have 9+2 tubule structure. Basal apparatus (kinetid) consists of the kinetisome(s) and associated tubules and fibres. - Origins of Eukaryotes - began as distinct third prokaryote group, evolution of nucleus yielded eukaryotic cells 1.5-2 billion years ago - Mitochondria and chloroplasts acquired in a process called serial endosymbiosis, originated as bacteria that were engulfed by host and enclosed in a membrane. Instead of being consumed, they became endosymbionts. Kingdom Protoctista Supergroup Phyla Traits Examples Ammoebbozoa Myxostelida --pasmoodialslme moods (akaacelluarslmee molds)) --enormous sngge celswiih housaandsoffnuceiiormeedby Ammeobbas usionoffnumeeouus ndvidualflagelate celslls --amoebbod occomotonniiiio --pasmoodium can ook lke a ungalmyycelum,,someebrrghtylly moovemeentcauseddby cooured enxenndng porrons offffio --gantcellcan ooze outtofind new food sources he cytopasm ccaledllllle --wih rghtstmuullgiantcellorms spore podducng ““uiingiin pseudopodia)))) bodes”” --durng movvementttt,,,, --when sporesgeemiinae,,hey give se toamooeboid celslls cyoskeleton sbroken whichmaay deveoppflagela in he pessenceoffwaterr heseth down and reassembbedlle mottecels functo
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