BIOL 112 1st EditionExam # 2 Study Guide Lectures: 8 - 14Lecture 8 (February 11)Documented (Therio) example of speciation with intermediate types in fossil record•S. yellowstonensis descendent from S. niagarae•Centric diatom (alga) found only in Lake Yellowstone•Diatom species defined by details of silica cell wall structuresUses for systematics:•Aids understanding of structures and functions of components and organs•Aids understanding of evolution and "family tree" of organisms: good systematics should reflect evolutionary history•Aids rapid identification of relatives of previously unknown organisms•Provides a framework to learn (and remember) different types of organismsTaxonomy -- science of naming organisms and groups of organisms, one part of the larger activity which is systematicsSystematics -- science of developing and evaluating classification schemesLinnaean InnovationsLinnaean system of classification (what we see today as systematics)Brevity of writing styleDevelopment of, and focus upon, concept of species as fundamental biological unityFormal rules of binominals:•Two words, always Latin or Classical Greek•Why?•It is impartial to certain countries since they are dead languages•Most education systems makes it essential to become fluent in these•Always italicized or underlined•Always used as a pair of words•First word: Genus name•Second word: specific epithet, or specific descriptorDomain, Kingdom, Phylum, Class, Order, Family, Genus, SpeciesLecture 9 (February 13) Develop a scheme of organization which reflects the phylogeny (evolu-tionary "family tree") of organisms:•Create monophyletic categories:All organisms in category (taxon) have immediate common evo-lutionary ancestry, including ancestors•Avoid polyphyletic or paraphyletic taxaParaphyletic: leave creatures out of the taxa that make the data invalidPolyphyletic: include other taxa that isn't homologous with the data, has a different lineageDomains reflect major structural, biochemical and molecular (DNA se-quences) categories of life:•D. Bacteria -- Prokaryotic, familiar biochemistry•D. Archaea -- Prokaryotic, less familiar biochemistry•D. Eukarya -- Eukaryotic formsArchaeans closer in many features to eukaryans than than they are to bacteriaLUCA = "last universal common ancestor”Lecture 10 (February 18)Cell Wall present in most prokaryotic forms. Cell wall prevents osmotic swelling; bacteria usually live in hypotonic environment for this reason.Complicated polymer of amino sugar and short amino acid chainsComponents:•N-acetyl glucosamine•N-acetyl muramic acid (bacteria-specific)•PeptidesAll components are covalently cross linked into a giant polymer so that the cell wall is one large macromolecule called a peptidoglycan.Two basic arrangements of cell wall components:•Gram Positive: Thicker cell wall ~20 nm; wall is 90% peptidoglycan, lipid content low (0-2%). Highly resistant to ethanol extraction, so gram stain will remain in cell and leave darkly stained cell. Purple/Blue.•Gram Negative: Thinner cell wall ~10-15 nm; contains only 20% peptidoglycan, higher lipid content (10-20%). High lipid content makes wall sensitive to ethanol extraction, so most of the gram stain will be removed and leave weakly stained cell. Pink.Gram positive cells are especially sensitive to penicillin (Penicillin in-hibits enzymes that synthesize cross links in wall.)Gram negative cells are less sensitive to penicillinLecture 11 (February 20)Heterotrophy•Symbionts: Some prokaryotes livein association with other organ-isms, derive carbon nutrients fromliving organic matter (host)•Mutualism: relationship is ben-eficial to both partners•Commensalism: one symbiontbenefits while the host is nei-ther harmed nor helped•Parasitism: Symbiont benefits, host is harmed Prokaryotic para-sites are also known as pathogens (disease causers)Domain Archaea•Very ancient-like forms, have a number of fundamental differences from true bacteria which distinguish them•Cell Walls — variable content•Many use proteins in cell wall•No peptidoglycan•Cell Membrane: Lipid content differs, some lipid moieties are branched.•Ribosomes and RNA polymerase more like eukaryotic forms than other prokaryotes, drug sensitivity also eukaryote-likeLecture 12 (February 25)Molecular homologies link most chloroplast genomes most closely to cyanobacteria (blue-green algae)This could mean that most modern chloroplasts arose from one origi-nal cyanobacterial-like ancestor, or that several times with closely-re-lated cyanobacteria.Eukaryotic Life Cycle:•Alternation between haploid and diploid phases of life cycle, with sexual events (meiosis and fertilization) between phases. The X scheme.•Diploid Phase -- 2n -- "sporophyte": phase of meiosis and spore for-mation•Haploid Phase -- n -- "gametophyte": phase of gamete formation for fertilizationBody Plan•Bilateral Symmetry implies several axes:•Anterior/Posterior (A/P)•Dorsal/Ventral (D/V)•What are the molecular bases of these axes as they develop dur-ing embryogenesis?•How did these control systems evolve?•Important Features•Body axes: A/P, d/v, L/R•What are the genetic bases of development of this body plan?•Cephalization: Making a head•Genetic basis of collection of sensory organs and brain in head?Lecture 13 (February 27)Beginning about 550 x 10^6 years ago, appearance of most modern animal phyla over 10x10^6 year period•At Cambrian Explosion, fossil animals become common because we now see shells and skeletons; things more easily preservedAncestral Bilateral•General agreement that common ancestor to modern bilaterian phyla is most likely something like a flatworm•Has bilateral symmetry: A/P and d/v axes•Bilateral symmetry implies cephalization — development of a head (brain, cluster of sensory organs) on anterior•Three tissue layers formed by gastrulationPhylum Chordata•Vertebrates are sub-phylum within this phylum•Very old: early chordates seen in Burgess Shale•Distinguishing Characteristics of this Phylum:•Presence of a notochord at some time in life cycle•Dorsal, hollow nerve cord (nervous system - spinal cord)•Presence of pharyngeal slits at some time in development•Presence of post-anal tailLecture 14 (March 4)Kingdom Plantae•Multicellular, mostly macroscopic, mostly autotrophic•Cell walls made up of cellulose•Multiple tissue/cell types organized into stereotyped structures: stems, leaves, &