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General Biology 2

by: George Dahdouh

General Biology 2 01:119:116

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George Dahdouh

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General Biology
Dr. Keeting
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Date Created: 08/11/16
Lecture 1: Classification Review/Virology Tuesday, January 20, 2015 10:26 PM Classification I. Species A. Base Unit B. Taxonomy - giving names C. Binomial nomenclature (Linnaeus) 1. 2 part name 2. genus & specific epithet 3. rules a. Latin b. italics c. genus - Uppercase - Abbreviate - Unique d. specific epithet - Lowercase - Not unique II. Classification A. evolutionary relationships can be understood B. species is basic unit of classification C. phylogeny - history of species D. systematics - process of classifying E. hierarchal classification III. Phylogenetic Trees A. Branching diagrams 1. shows patterns of descent 2. not phenotypic similarities B. Hypothesis C. Dichotomies C. Dichotomies D. Components 1. nodes - branch points - Divergence from common ancestor (CA) 2. sister taxa - Groups of organisms that share a common ancestor (CA) 3. rooted tree - Has 1 branch point that represents the most recent common ancestor of all taxa on tree 4. basal taxon - Diverged early in history of group 5. polytomy - Multibranch 6. extant species - Species that are alive, current - Fig. 26.4 - Fig. 26.5 7. homologous - Shared ancestry 8. analogous - Similar as a result of convergent evolution IV. Evolution A. Accumulation of genetic change over time B. Natural selection - Variation - Mechanism by which evolution occurs - Acts on individuals but population is what evolves V. Biological diversity VI. Tree of life A. 3 domains 1. bacteria (prokaryotes) 1. bacteria (prokaryotes) 2. archaea (prokaryotes) 3. eukarya Fig. 26.21 Virology I. Characteristics A. non-living particles 1. not cells 2. no metabolic activities on their own 3. cannot reproduce on their own B. has genetic material - Either DNA or RNA, never both C. 20-300nm in size, can't use light microscope D. obligate intracellular parasite II. Discovery A. TMV - tobacco mosaic virus B. Adolph Mayer - 1883 - Transmitted disease from infected plant to healthy one C. Martinus Beijerinck - late 19th century 1. Experiment Fig. 19.2 2. Conclusions a. smaller than bacteria b. replicates in plants c. could not cultivate in nutrient media such as petri dish or test tubes III. Components of viruses A. Nucleic acids 1. either DNA or RNA 2. single or double strand 3. linear genetic or circular or segmented 4. 3-100 genes - Info to replicate within host cell B. capsid 1. protein coat surrounds genetic material 2. subunits called capsomere 3. determines shape of virus 4. in some viruses capsid plays role in attachment C. envelope - some viruses 1. acquired from moving through host plasma 2. lipid bilayer - Host phospholipids and proteins - Viral proteins and glycoproteins Fig. 19.3 Fig. 19.3 IV. Viral replication A. intro 1. obligate intracellular parasites - Only replicate inside host cell 2. host range - Species that can be infected by particular viruses ▫ Ex. Measles - only humans (narrow) ▫ Ex. West Nile virus - humans, birds, etc. (broad) 3. viruses of multicellular eukaryotes - Limited to a particular tissue 4. why specificity - Due to interaction between viral surface proteins & specific receptor molecules on the outside of host cell B. basic features of viral replication 1. virus binds to host cell 2. viral genome enters host cell 3. viral genome directs production of proteins --> take over host cell 4. host cell copies viral genome & produce viral proteins 5. viral nucleic acids & capsomeres in cell come together spontaneously --> new viruses 6. exit cell Fig. 19.4 Fig. 19.4 Bacteriaphages C. lytic cycle 1. death of host cell --> virulent phages Fig. 19.5 2. bacterial defenses a. natural selection favors bacterial mutants that don't have surface receptors recognized by virus b. restriction enzymes - Reorganize foreign DNA and cut up - Reorganize foreign DNA and cut up - Bacterial DNA - protected by methylation D. lysosomic cycle 1. replication of phage genome without destroying host cell 2. temperate phages - Capable of lytic and lysosomic replication 3. ex. Phage (lambda?) a. phage attaches to host cell and injects DNA b. phage DNA forms a circle c. either: 1. viral genes convert host cell into factory --> lytic cycle 2. viral DNA incorporated into host chromosome prophage - integrated virus - Genes which code for protein that prevents transcription of most other viral genes --> virus does not enter the lytic cycle - Replicates along with host chromosome indefinitely d. certain environmental conditions --> trigger entry into lytic cycle Fig. 19.6 V. Evolution of viruses A. cellular origin hypothesis 1. viruses are derived from bits of nucleic acids that "escape" from cellular organisms 2. ex. Plasmids 3. species specific - virus originated from a host 4. genetic similarity between viruses and host cells B. coevolution hypothesis 1. viruses - evolved early in history of life 2. before 3 domains diverged Lecture 2: Prokaryotes Tuesday, January 20, 2015 11:12 PM I. Intro A. prokaryotes ~ 3.5 bill years ago B. Origin of life (Ch. 25.1 & 25.3) Chemical evolution hypothesis - life developed from non-living matter -->Heterotrophs --> photosynthetic autotrophs --> aerobes C. Domains bacteria and archaea D. dominant Ex. Human body - 70 mill cells E. pervasive F. size 0.5-5 microns II. Cell surface structures A. cell wall 1. Functions i. Protects cell ii. Shape 1) Cocci - balls/spheres O a) Diplococcus 2 b) Steptococcus - chain c) Staplycoccus - clump 2) Bacilli - rods 3) Spirals a) Spirillum - rigid b) Spirochete - flexible iii. Prevents bursting in a hypotonic environment Does not prevent plasmolysis in a hypertonic environment Fig. 7.12 2. Peptidoglycan a. only domain bacteria b. polymer Sugars crosslinked by short polypeptides c. not in eukaryotic cell walls Plants - cellulose Fungi - chitin d. Gram stain 1. 2 stains are used 1) 1st crystal violet - purple 2) 2nd safranin - pink 2. Gram positive 1) Thick wall of peptidoglycan 2) Retain crystal violet stain - only see purple Penicillin - interferes with peptidoglycan synthesis (most effective against gram positive) Bio II Page 8 Penicillin - interferes with peptidoglycan synthesis (most effective against gram positive) 3. Gram negative 1) Cell wall - thin layer of peptidoglycan 2) Do not retain crystal violet - see pink 3) Outer membrane of lipopolysaccharides (LPS) a) Toxic, induces fever 4. Correct antibiotics Fig. 27.3 A. Capsules & slime layers 1. Surround cell wall 2. Comprised of polysaccharides or proteins 3. Provide protection against phagocytosis Fig 27.4 B. Fimbriae & pili Fig 27.6 1. Hair-like appendages 2. Fimbriae - shorter and more numerous than pili 3. Used for attachment C. Endospore 1. Dormant stage Fig 27.5 Bio II Page 9 III. Motility A. Taxis 1. Directed movement in response to a stimulus 2. Positive taxis - organism moving toward stimulus 3. Negative taxis - move away from stimulus 4. Ex. Chemotaxis - response to chemical B. Flagella 1. Common motility structure 2. Found in bacteria and archaea and eukarya 1) A comparison of prokaryotic and eukaryotic flagella a) Prok - 1/10 wide as euk - Not covered by plasma membrane b) Prok and euk have different molecular composition of flagella & diff mech. of propulsion 2) A comparison of bacteria and archaea a) Similar size b) Similar propulsion mech. c) Different composition 3) Bac., arch, and euk a) Perform similar functions b) Arose independently --> analogous structures 3. Prokaryotic flagella 1) 3 parts a) Motor - rings embedded in the cell wall and in plasma membrane b) Hook - curved c) Filament - rotates --> propels cell through environment 2) Function a) H+ pumped across plasma membrane of cell --> produces gradient b) H+ diffuses though motor, turns hook, turns filament IV. Internal A. Simpler than euk B. Lack membrane bound organelles 1. No nucleus 2. No mitochondria 3. No chloroplasts C. Nucleoid 1. Region of cytoplasm 2. Chromosome located - DNA Single --> haploid (n) D. Plasmid 1. smaller rings of DNA 2. Replicate independently 3. Few genes Non-essential E. Cytoplasm 1. Ribosomes 2. Storage granules 3. Enzymes F. Plasma membrane 1. Extensively folded (increase surface area) Bio II Page 10 1. Extensively folded (increase surface area) 2. Enzymes embedded in membrane Cellular respiration Photosynthesis V. Reproduction Binary fission Optimal conditions - temp, nutrients, etc. Divide every 1-3 hours Fig. 12.12 Genetic recombination is the combining of DNA from two sources and occurs via horizontal gene transfer: Prokaryotic DNA (genes) from different individuals are brought together by transformation, transduction, and conjugation 1. Transformation occurs when prokaryotic cell takes up and incorporates foreign DNA (e.g. plasmid DNA) from the surrounding environment 2. Transduction: viral phages carry pieces of bacterial chromosome from donor to recipient Lytic phages:  Phage injects DNA  Enzymes destroy host (recipient) DNA  Host DNA segment is accidently incorporated into phage DNA  Recombinant phage progeny formed Lysogenic (prophage):  Phage injects recombinant DNA into new host  Recombinant DNA incorporates into host DNA  Produces new recombinant bacteria 3. Conjugation is the process where genetic material is transferred between two prokaryotic cells  A piece of DNA (F factor) is required for production of pili  A donor cell (F+) attaches to a recipient (F-) by the pilus  Pulls it closer, and transfers the F-factor VI. Genetic diversity 1) Mutations are rare on a per gene basis but: genetic variation increases quickly in large pops that have short generation times VII. Nutrition and metabolic A. Energy sources 1. Phototrophs 2. Chemotrophs B. Carbon sources 1. Autotrophs - CO2 Bio II Page 11 1. Autotrophs - CO2 2. Heterotrophs - organic (ex. Glucose) Table 27.1 C. Oxygen needs and tolerances 1. Obligate aerobes - must have oxygen 2. Obligate anaerobes - cannot tolerate oxygen Ex. NO3-, SO4- --> e- acceptors rather than oxygen 3. Facultative anaerobes - flexible D. Nitrogen metabolism 1. Nitrogen cycle Fig 55.14 Ex. Nitrogen fixation - N2 --> NH3 Nitrification NH3 --> NO3- VIII. Prokaryotic diversity A. Molecular evidence - rRNA sequences 2 domains Bio II Page 12 2 domains Horizontal gene transfer - movement of genetic material between species --> key role in prok evolution Archaea are more closely related to eukarya than bacteria B. Bacteria Fig 27.16 1. Proteobacteria Ex. a) Alpha i) Rhizobium - nodules on roots of legumes - nitrogen fixation b) Beta i) Nitrosomonas - soil bacteria - NH4+ --> NO2- c) Gamma i) Salmonella d) Delta i) Bdellovibrio - predatory bacteria e) Epsilon i) Helicobacter pylori - stomach ulcers 2. Chlamydias 1) Parasites 2) Trachamatis - blindness, US most common transferred STD 3. Spirochetes 1) Treponema pallidum - syphilis 2) Borrelia burgdorferi 4. Cyanobacteria 1) Gram-negative 2) Photoautotrophs 3) Chloroplasts 5. Gram-positive 1) Bacillus - anthrax C. Archaea 1. Extremophiles 2. Extreme halophiles 3. Extreme thermophiles 4. Methanogens - release methane byproduct, strict anaerobes Ex. Swamps, marshes Table 27.2 Bio II Page 13 Bio II Page 14 Lecture 3: Protists Tuesday, January 20, 2015 11:12 PM I. Eukaryotic Evolution A. Endosymbiosis in Eukaryotic Evolution - Endosymbiosis: relationship between 2 species in which 1 organism lives inside another - throughout evolutionary history one organism has engulfs another to mutually benefit both - Serial endosymbiosis: proposes key eukaryotic organelles evolved through sequence of endosymbiotic events 1. Primary endosymbiosis - phagocytosis of a bacterium by another cell: 2 key eukaryotic organelles: a. Mitochondria - was aerobic bacterium engulfed by anaerobic cell - studies show engulfed bacterium was - alpha proteobacteria—> endosybiont - mitochondria of all eukaryotes descend from one common ancestor - mitochondria arose only once over course of evolution b. Plastids - group of closely related organelles of photosynthetic eukaryotes including: - chloroplasts - chromoplasts - amyloplasts - found in cells host was heterotrophic eukaryote - endosymbiont was a photosynthetic cyanobacterium - evidences—> plastids arose after mitochondria - lineage gave rise to 2 lineages of photosynthetic protists: red algae and green algae 2. Secondary Symbiosis (Figure 28.3) - host cell from primary endosymbiosis engulfed by another cell - red and green algae underwent secondary symbiosis—> occurred frequently B. Diversity in Eukaryotes: Most are single-celled - Protists are eukaryotic cells—> have organelles and are more complex than prokaryotic cells 1. Eukaryotic cellular structure: - nucleus and membrane-bound organelles - well-developed cytoskeleton - extends throughout cell - provides structural support - change shape as move, feed, and grow 2. Eukaryotic Phylogeny - huge eukaryotic diversity: new date and rapidly changing hypotheses - root of eukaryotic tree not know: 4 main supergroups diverging simultaneously from one ancestor - this is a polytomy: because we don’t know which diverged first - 4 Subgroups: Excavata; “SAR” Clade; Archaeplastida; Unikonta - most eukaryotes are protists; only others are land plants, animals, and fungi II. Protists Introduction - name means “the very first”—> thought to be first euk. cell - evolved 1.5-1.6 by a —> one billion years before plants, fungi and animals - evolved 1.5-1.6 by a —> one billion years before plants, fungi and animals - enormous structural and functional diversity: - most are unicellular, some colonial or multicellular - extremely complex cell organization - Variety of nutritional strategies - Photoautothrophs: have chloroplasts - Heterotrophs: ingest organic molecules - Mixotrophs: both photosynthetic and heterotrophic nutrition - reproduction and life cycles vary A. Clades: Excavates - includes protists with modified mitochondria and protists with unique flagella - characterized by its cytoskeleton - excavated (deep) feeding groove on one side of cell body - group includes: 1. Diplomonads 1. no plastids and modified mitochondria and live in anaerobic environment - have mitosomes: are reduced mitochondria - no functional electron transport chains - can’t use O 2o get energy from organic molecules - get energy from anaerobic pathways - have two equal-sized nuclei and multiple flagella - many are parasites—> ex. giardia intestinal is - live in small intestine—> backpacker’s diarrhea - major cause of diarrhea throughout the world 2. Parabasalids - no plastids and modified mitochondria and live in anaerobic environment - have hydrogenosomes: are reduced mitochondria - generate some energy anaerobically - release H 2s a by-product - many are parasites—> ex. Trichomonas vaginalis - causes STD trichomoniasis 3. Euglenozoans - main feature distinguishing them as a class is a spiral or crystalline rod inside their flagella - very diverse clade - clade includes a. Kinetoplastids - single, large mitochondrion contains kinetoplast (organized mass of DNA) - found free-living and as parasites - ex. Trypanosoma brucei—> African sleeping sickness b. Euglenids - one or two flagella emerge from pocket at one end of cell - some are mixotrophs: photosynthesis when light available and heterotrophs when none - ex. Euglena (should be able to identify structures) B. Clade: “SAR” - doesn’t have a formal name—> known by first letters of its 3 major clades 1. Stramenopiles - most have “hairy” flagellum paired with a “smooth” flagellum - 3 main groups: a. Diatoms - Photosynthetic unicellular algae - unique two-part glass=like wall of silicon dioxide - provides protection from crushing - provides protection from crushing - diatomaceous earth—> massive accumulations of fossilized diatom walls (sediments) - mined for wide range of use. ex. filters, absorbent b. Golden Algae - most are unicellular; extremely minute (2-10 um) - cells covered ith tiny scales of silica or calcium carbonate - named for their color—> yellow and brown carotenoids - photosynthetic - Habitat: freshwater and marine—> significant portion of the nanoplankton - the cells of golden algae are typically biflagellated, with both flagella near one end - plankton—> diverse group of organisms that live in water column and are incapable of swimming against the current c. Brown Algae - called “seaweeds”—> largest and most complex algae - all multicellular and most are marine - Photosynthetic: contain chlorophyll and carotenoids (pigments) - Habitat: marine, in cold northern waters - commercial importance: - some edible - algin in cell wall: use as thickener (in pudding, hand lotion,…) - ex. Kelp—> live deep in ocean: 3 parts: - blade: leaf-like - stipe: stem-like - holdfast: anchor to rock 2. Alveolates - characterized by alveoli: membrane-enclosed sacs just user the plasma membrane (support) - include: a. Dinoflagellates - most are unicellular and have 2 flagella and each cell reinforced by cellulose plates - abundant components in phytoplankton - bloom (pop explosions) cause toxic “red tides” - hypothesized that coastal pollution such as animal waste may trigger blooms - some make neurotoxins that attack fish nervous system - fish can die and birds can die if they eat contaminated fish b. Apicomplexans - almost all are parasites of animals - complex life cycles - their apical complex—> specialized for penetrating host cells - ex. Plasmodium—> cause malaria - one of the most serious parasitic diseases in world - each year 1-3 million people die of it mainly in tropics c. Ciliates - use of cilia to move and feed - large macronuclei and small micronuclei - asexual reproduction by binary fission - conjugation—> sexual process= exchange haploid micronuclei—> is separate from reproduction by binary fission 3. Rhizarians - Many are amoebas—> move and feed by threadlike pseudopodia—> extensions - Many are amoebas—> move and feed by threadlike pseudopodia—> extensions of cell surface - include: a. Radiolarians - internal skeletons made of silica - pseudopodia—> reinforced by bundles of microtubules b. Foraminiferans = forams - tests—> porous multi chambered shells made of valium carbonate - dies and form thick marine sediments - from shells of billions of forms c. Cecozoans - threadlike pseudopodia C. Clade: Archaeplastida - red algae and green algae are photosynthetic descendants of ancient heterotrophic protist that acquired a cyanobacterial endosymbiont - land plants are descended from green algae - monophyletic group includes: 1. Red Algae - photosynthetic: red color due to phycoerythrin (red pigment) - many pigments allow them to live very deep (100 feet down) - usually multicellular, highly branched - habitat: most in warm tropical ocean water, attach to rocks and other substrates - ex. Porphyra: one of red algae: used to wrap sushi 2. Green Algae - closely related to land plants—> chloroplast are very similar - green algae are paraphyletic group - includes: a. Chlorophytes - most live in fresh water - simple, unicellular b. Charophytes - closely related to plants c. Land Plants D. Clade: Unikonts - includes animals, fungi, and some protists - 2 major protist clades: 1. Amoebozoans - amoeba that have lobe- or tube-shaped, rather than threadlike pseudopodia - include: a. Slime molds (not fungi) b. Tubulinids - consume bacteria and proteins c. Entamoebas - most are free-living parasites - ex. Entamoeba histolytica: lives in intestines 2. Opisthokonts - includes animals, fungi, and several groups of protists - highly variable a. Nucleariids - more closely related to fungi than other protists b. Choanoflagellates - more closely related to animals than to other protists Lecture 4: Unikont Diversity I - Fungi Tuesday, January 20, 2015 11:12 PM I. Evolution of fungi A. Review Fig 31.8 Fungi and their close relatives B. Origin of fungi Fig 31.8 1. Evolved from a unicellular, flagellated ancestor 2. Animals, fungi, and related protists form opisthokont clade 3. Animals and fungi may have diverged into separate lineages 1-1.5 bill years ago 4. Nucleariids - heterotrophic amoebas (protists) - ancestors of fungi C. Colonization of land 1. Fungi colonized land before plants (~470 mill years ago) 2. Before there were plans on land a. Green slime  Cyanobacteri  Algae  Small heterotrophs - fungi D. Diverse lineages 1. ~100k species idenified 2. ~1.5x10^6 species 3. 5 major groups II. General characteristics A. Nearly all are multicellular B. Not photosynthetic 1. No chlorophyll 2. No chloroplasts 3. Not plants C. All fungi are absorptive heterotrophs 1. Heterotroph a. Do not ingest food and digest food inside body b. Not animals 2. Resources a. Secrete hydrolases into environment  Hydrolytic enzymes b. Break down polymers into monomers c. Predigested food is absorbed d. Grows best in moist environments 3. Main types a. Decomposers  Absorb their nutrients from non-living material b. Parasites  Absorb their nutrients from the cells of living hosts - Athlete's foot c. Mutualists  Absorbs nutrients from some host organism, but reciprocates with actions that benefit host D. Cell wall - chitin 1. Nitrogen containing polysaccharide a. Strong, flexible, durable a. Strong, flexible, durable 2. In contrast a. Prokaryotes  Gram positive - peptidoglycan  Gram negative - peptidoglycan, lipopolysaccharide (LPS) b. Plants - cellulose III. Body structure A. Types 1. Multicellular - most 2. Unicellular - yeasts B. Multicellular 1. Hypha(e) - building block a. Long branched threadlike filaments b. Tubular cell walls c. Grow and secrete hydrolases --> expand into new food resources 2. Types of hyphae a. Septate  Septa (septum) - cross walls  Pores - perforate - Organelles & cytoplasm move between cells b. Coenocytic  Not divided into individual cells  One big cell - many nuclei Fig 31.3 3. Mycelium (mycelia) a. Tangled mass of hyphae b. Feeding network 4. Reproductive structures a. Spores b. Spore production  Aerial hyphae  Fruiting body - mushroom - Complex multicellular reproductive structure Fig 31.2 5. Some fungi have specialized hyphae for feeding on living animals Fig 31.4a 6. Haustoria a. Specialized hyphae that penetrate host tissues b. Used to extract nutrients from, or exchange nutrients with, plant hosts 7. Mycorrhizae a. Mutually beneficial relationships between fungi and plant roots b. Mycorrhizal fungi more efficient than plant roots at getting soil nutrients. c. Deliver phosphate ions and minerals to plants d. Plans supply fungi with organic nutrients such as carbs e. Most vascular plants have mycorrhizae f. Two main types  Ectomycorrhizal fungi - form sheaths of hyphae over a root and also grow into extracellular spaces of the root  Arbuscular mycorrhizal fungi - extend hyphae through cell walls of root cells and into tubes formed by invagination of the root cell membrane Fig. 31.4b IV. Reproduction A. Spore 1. Haploid (n) 1. Haploid (n) 2. Produced either at the tip of hypha or in a fruiting body 3. Sexually or asexually 4. Not motile (no flagella) - cannot move a. Must be dispersed  Wind, water, animals 5. Moist environment - food a. Germinate --> mycelium produced B. Sexual reproduction 1. Mating types (not male/female) a. Result of genes that encode enzymes responsible for the production of pheromones and pheromone receptors  Pheromones - sexual signaling molecules b. Sexual reproduction depends on pheromones that are produced from variant alleles of same gene 2. Hyphae from 2 mycelia produce pheromones 3. If mycelia are of different mating types, pheromones of each will bind to receptors of the other --> passed compatibility test --> genetic variation 4. Hyphae extend toward source of pheromones 5. Meet and fuse a. Haploid nuclei do not fuse at this point  Plasmogamy (cytoplasm fuse) b. Heterokaryon - fused mycelium  Coexisting genetically different nuclei c. Dikaryotic mycelium  n+n 6. Mycelium grows a. Nuclei divide without fusing 7. Karyogamy a. Nuclei fuse --> diploid zygote 8. Meiosis --> haploid a. Spores ultimately formed --> sexual spores C. Asexual reproduction 1. ~20k species that only undergo asexual reproduction 2. 2 main types a. Grow as filamentous fungi (haploid)  Produce spores by mitosis  Molds b. Yeasts - unicellular  Cell division  Small bud cells Fig 31.7 Fig 31.5 V. Chytrids A. Terrestrial, freshwater, marine B. Flagellated spores --> zoospores 1. Primitive characteristic Fig 31.11 C. Diverged early in fungal evolution VI. Zygomycetes A. Most are decomposers in soil B. Ex: Rhizopus stolonifer - black bread mold VII. Glomeromycetes A. Arbuscular mycorrhizae VIII. Ascomycetes A. Intro 1. ~65k species 2. Single-celled and filamentous 3. Examples: a. Penicillium b. Morels and truffles Fig 31.15 c. Baker's yeast d. Lichens 4. Septate, perforate hyphae 5. AKA sac fungi a. Sexual spores are formed in microscopic sacs called asci B. Life cycle - asexual 1. Conditions favorable - reproduce fast 2. Conidia - haploid a. Spores produced in structures called conidiophores b. Conidia break off --> germinate --> undergo mitosis C. Life cycle - sexual 1. Conidia (n) fuse to specialized hypha (n) of opposite mating type --> Plasmogamy occurs --> dikaryotic hyphae (n+n) 2. Ascocarp = fruiting body a. Intertwining of monokaryotic hyphae (n) and dikaryotic hyphae (n+n) 3. Cells at tips of dukaryotic hyphae --> asci 4. Within each ascus a. Karyogamy - 2n 5. Meiosis - within each ascus --> 4 different nuclei (n) --> undergo mitosis --> 8 ascospores 6. Ascospores - discharged from asci 7. Dispersed Fig 31.16 IX. Basidiomycetes A. Ex. Bracket fungi, puff balls, wheat rust and corn smut, agaricus bisporus - edible X. Ecological importance A. Decomposers 1. Break down organic material 2. Releases inorganic nutrients into ecosystems B. Mutualists 1. Absorb their nutrients from host a. Benefit host 2. Fungus-plant mutualism a. Micorrhizal fungi b. Endophytes  Live inside leaves or other plant parts  No harm  Ex. In grasses fungi produce toxins - deter herbivores  Presence increase plant tolerance of environmental stress Fig 31.20 3. Fungus-animal mutualism a. Ex. Guts of cattle - fungi break down plant material 4. Lichens a. Fungus - ascomycete  Provides habitat  Photosynthetic microorganism - Algae - Cyanobacteria --> Provide carbon compounds b. Rocks, trees, roofs C. Parasites 1. Absorb from living hosts 2. Plants a. Ex. Chestnut blight 3. Mycosis a. Fungal infection in animal b. Ex. Ringworm - ascomycete  Athlete's foot is ringworm c. Systemic mycosis  Spores inhaled  Spread through body  Serious D. Practical uses 1. Consumption - morels, truffles 1. Consumption - morels, truffles 2. Ripen blue cheeses 3. Yeasts a. Anaerobic conditions - fermentation --> sugars --> alcohols & CO 2 4. Research a. Sacchromyces cerevisae  Molecular genetics - euk 5. Medical - antibiotics Lecture 5: Unikont Diversity II Tuesday, January 20, 2015 11:12 PM I. Characteristics of animals A. Heterotrophs 1. Ingest food and digest in body B. Cell structure 1. Eukaryotic 2. Multicellular 3. Do not have cell walls 4. Proteins external to plasma membrane a. Connect cells to each other b. Provide structural support c. Collagen is most abundant C. Organization 1. All animals have differentiated cells (specialized) a. Perform specific functions 2. Most have differentiated tissues a. Groups of cells  Common structure  Act as functional unit 3. Higher forms have differentiated organs a. Made up of tissues b. Adapted to perform specific function or group of functions 4. Muscle and nerve tissue a. Defining characteristic D. Reproduction - sexual, 2n (diploid) stage dominant 1. Meiosis 2. Fertilization a. Small flagellated sperm b. Fertilized larger, nonmotile egg --> zygote (2n) E. Development Fig 32.2 1. Cleavage - series of mitotic cell divisions without cell growth between divisions 2. Blastula - typically a hollow ball of cells that surround a cavity called blastocoel (blastoseal) 2. Blastula - typically a hollow ball of cells that surround a cavity called blastocoel (blastoseal) 3. Gastrulation - process in which the embryo folds inward, expands, and fills blastocoel. Produces a gastrula. 4. Gastrula a. Endoderm - inner layer of embryonic tissue b. Ectoderm - outer layer of embryonic tissue c. Archenteron - pouch, opens to outside via blastopore 5. Some animals will develop directly into adults (ex. Humans) 6. Other animals have at least 1 larval stage a. Larva - sexually immature form, morphologically different from adult b. May eat different foods, inhabit different habitats c. Metamorphosis --> juvenile - sexually immature --> adult 7. Development is regulated by gene expression a. Homeobox genes  Code for proteins that regulate expression of developmental genes b. Ex. Hox genes - role in development of animal embryos F. Evolution Fig 32.3 II. Body plans Fig pg. 679 A. Particular set of morphological and developmental traits 1. Compare key animal features 2. Key steps in animal evolution B. Differentiation of cells, tissues, and organs 1. All animals have specialized cells 2. 1st major step in animal evolution 2. 1st major step in animal evolution a. Porifera (sponges)  Do not have clearly defined tissues and organes b. Eumetazoa ("true animals")  Do have clearly defined tissues and organs C. Symmetry Arrangement of body structures in relation to a particular axis of the body Fig 32.8 1. Radial a. Wheel or cylinder b. Multiple planes that can divide the animal into mirror images c. Many radial are sessile (don't move around) live attached to substrate d. Others are planktonic 2. Bilateral - 2 sided a. Body can be divided only by one plane through the midline b. Cephalization  Development of a head region ◊ Central nervous system ◊ Coordinate complex movements c. Dorsal - back/top Ventral - underside Anterior - toward head Posterior - toward tail Right and left d. Bilateria 3. Asymmetry - no plant will produce mirror images --> porifera (sponges) D. Embryonic tissue development Embryos of all eumetazoans because layered 1. Germ layers - concentric layers of eukaryotic tissue a. Ectoderm - outer  Gives rise to outer covering  Nervous system in some phyla b. Endoderm - inner  Lines archenteron  Gives rise to lining of digestive tract of other digestive organs c. Mesoderm - middle  Gives rise to most other body structures 2. Diploblastic organisms Only ectoderm and endoderm layers 3. Triploblastic organisms Develop all 3 layers Bilateria Bilateria E. Body cavities 1. Coelom - body cavity a. Fluid-filled space b. Between body wall and digestive tube c. Only in triploblastic organisms 2. 3 types a. Acoelomate (NO SPACE)  Lack coelom  Are triploblasts  Body is solid ◊ No fluid, just tissue b. Pseudocoelomate (SPACE ENDO NOT COVERED BY MESO)  Have fluid-filled coelom  Body cavity is formed from endoderm and mesoderm  Not completely lined with mesoderm c. Coelomate (SOME SPACE BUT MESO COVERS ENDO)  True coelom  Body cavity completely lined with mesoderm Fig 32.9 3. Advantages of coelom/pseudocoelom a. Hydrostatic skeleton  Fluid under pressure --> movement b. Circulating materials  Do not need to be flat  Do not need to be flat  Surface area:volume c. Internal organs grow and move independently of outer body wall III. Developmental modes ○ Separate Bilateria into protostomes and deuterostomes A. Cleavage Mitotic cell divisions in zygote not accompanied by cell growth 1. Protostomes a. Spiral cleavage  Plants of cell division are diagonal to vertical axis of embryo b. Determinant cleavage  Development fate of each embryonic cell rigidly set very early  If a cell is removed --> adult lack parts 2. Deuterostomes a. Radial cleavage  Planes are parallel or perpendicular to vertical axis of embryo b. Indeterminate cleavage  Each cell produced during early cleavage retains capacity to develop into a complete embryo B. Coelom formation 1. During gastrulation a. Embryos developing digestive tube initially forms as a blind pouch --> archenteron (becomes gut) 2. Protostomes a. As archenteron forms, solid masses of mesoderm split and form coelom 3. Deuterostomes a. Mesoderm buds from the wall of archenteron and its cavity becomes coelom C. Fate of blastopore 1. During early development Embryo consists of a ball of cells --> blastula a. Group of cells in blastula moves inward --> forms blastopore 2. Protostomes (1st mouth) Blastopore --> mouth. 3. Deuterostomes (2nd mouth) Blastopore --> anus 2nd opening forms later --> mouth Fig 32.10 IV. Diversification A. Cambrian explosion (535 - 525 mill years ago - MYA) 1. Rapid appearance of many different animal body plans 2. 1st fossils of large animals with hard mineralized skeletons B. Most of current phyla of animals established around 500 MYA 1. ~36 different phyla are extant 2. Kingdom animalia ~ 1.3 x 10^6 species, est. 10-20 x 10^6 species C. Animal phylogeny Fig 32.11 1. All animals share a common ancestor a. Monophyletic --> clade metazoa 2. Sponges - basal animals a. Branches from base of tree (branches off earliest) b. Phylum Porifera --> monophyletic 3. Eumetazoa a. True tissue b. Phyla Ctenophora and Cnidaria a) Basal eumetazoans b) Diploblasts c) Radial symm 4. Clade Bilateria a. Most animal phyla b. Bilateral symm c. 3 germ layers 5. 3 major clades/linages of bilaterians a. Deuterostomes/Deuterostomia  Some organisms with deuterostom devel. patterms are not in this clade  Phylum chordata - only phylum with vertibrates also invert b. Lophotrochozoa  Only invert  Some develop lophophore feeding structure  Trochopore larval stage Fig 32.12 c. Ecdysozoa  Only invertebrates  Ecdysis - molting - exoskeleton - cuticle Lecture 6: Unikont Diversity III Tuesday, January 20, 2015 11:12 PM I. Invertebrates - Chapter 33 A. Animals that lack a backbone B. > 95% of known animal species C. Throughout animal phylogenic tree Pg. 710 figure II. Phylum Porifera - sponges A. Structure 1. Least complex of all animals 2. Multicellular a. Specialized cells b. No true tissue or organs 3. Asymmetric 3. Asymmetric B. Typical simple sponge 1. Simple saclike body 2. Opening called osculum 3. Spongocoel a. Central cavity b. Passage cavity for water c. Not digestive cavity d. Filter feeder - filters food particles out of water e. Water goes through spongocoel and comes out of osculum 4. Choanocytes - collar cells Fig 32.3 a. Flagellated cells b. Collar of microvilli c. Line spongocoel d. Ingest bacteria and tiny food Fig 33.4 III. Phylum Cnidaria A. Mostly marine 1. Jellies, coral, sea anemone B. Characteristics 1. Radial symmetry 2. Diploblastic C. Body structure 1. Hollow sac 2. Mouth and tentacles at one end 3. Mouth - only opening 4. Gastrovascular cavity a. Digestive D. Cnidocytes Fig 33.5 1. Cells in tentacles 2. Defense 3. Capturing prey IV. Lophotrochozoa A. Intro 1. Most bilaterians 2. Bilaterally symmetrical a. Triploblastic 3. Molecular data defines 4. Common features a. Lophophore - Crown of ciliated tentacles that are found around the mouth b. Trochophore larva - Stage of development Fig 32.12 B. Phylum Platyhelminthes 1. All dorsoventrally flattened 2. Acoelomates 3. Exist in a variety of habitats Free living ex. Planarians Fig 33.10 Parasitic ex. Tapeworms Fig 33.12 C. Phylum Rotifera Fig 33.13 1. Found in freshwater, marine, damp soil 2. Very small 50um - 2mm 3. Pseudocoelomates 4. Possess alimentary canal - complete digestive tract 5. Have crown of cilia at head end - Beats and create a vortex of water to draw it into the mouth 6. Trophi - jaws grind up food 7. Feed on microorganisms in water D. Lophophorates Fig 33.14 1. Lophophore 2. Coelomates 3. Found in fresh water and marine habitats E. Phylum Mollusca 1. Snails, slugs, oysters, clams, squid, octopus 2. Soft body a. Most are covered by a dorsal shell - Comprised of CaCO 3 3. Coelomates - has 3 main parts Fig 33.15 a. Foot - Muscular used to move around - Tentacles b. Visceral mass - Contains viscera (organs) c. Mantle - Thin sheet of tissue - Covers visceral mass - Glands - secrete shell 1. Radula a. Belt of teeth found in mouth area b. Scrape up food b. Scrape up food c. Most have but not all - Not in bivalves 2. 3 of major clades a. Gastropods Fig 33.17 - Mostly marine, freshwater, and terrestrial - Snails - shell - Slugs and sea slugs - no shell a. Bivalvia - Marine and freshwater - Clams, mussels, oysters, scallops - Shell has 2 parts ◊ Hinged ◊ Secreted by mantle - No radula - Trap particles of food in water - suspension feeders b. Cephalopodia - Marine - Squid, octopus - Predators - hunt down prey - Mantle - radula - 2 strong beaks - Foot - tentacles A. Phylum Annelida 1. Segmentation a. Body wall, coelom, and many internal organs → divided into segments Digestive tract NOT segmented 2. Marine species, freshwater, damp soil 3. Ex. Earthworms Fig 33.25 V. Ecdysozoa A. There are very many species - more than animals and plant species 1. Ecdysis = molting 2. Organism will shed external covering during growth B. Phylum Nematoda 1. Roundworms - cylindrical tapered ends 2. Aquatic, soil, parasitic 3. Covering called cuticle - covers body a. Gets shed as grows 4. Pseudocoelomates a. No circulatory system 5. Do have alimentary canal 6. Ex. Heartworm C. Phylum Arthropoda 1. Largest phylum - most species of all animals 2. Coelomates 3. Structure a. Have a segmented body - Specialized to perform certain functions - Head - Thorax - legs and wings - Abdomen b. Jointed appendages - Adapted for variety of functions such as: ◊ Swimming ◊ Walking ◊ Sensory ◊ Sensory c. Exoskeleton - jointed - Comprised of chitin and protein - Covers entire body - Advantages ◊ Offers protection ◊ Reduces water loss ◊ Solid substrate so provides points of attachment for muscle - Disadvantages ◊ Limits growth → molts - sheds exoskeleton - and grows new larger one 4. Ex. Centipedes, spiders, ticks, horseshoe crabs, etc. VI. Deuterostomes A. Characteristics 1. Radial and indeterminate cleavage (during development) 2. Blastopore becomes anus, mouth forms second B. Phylum Echinodermata (spiny skin) 1. Larvae a. Exhibit bilateral symmetry 2. Adult stage - five-part body symmetry 3. Characterized by endoskeleton - internal skeleton a. Comprised of - CaCO 3 b. Spines project out through epidermis (outer covering) 4. Water vascular system a. Fluid-filled canals and chambers - complex network b. Functions in feeding and gas exchange 5. Ex. Sea star Fig 33.42 A. Phylum Chordata - are invertebrates and vertebrates VII. Chordate Phylogeny - Chapter 34 VII. Chordate Phylogeny - Chapter 34 Figure 34.2 Pg. 749 Figure A. Echinodermata - sister group to chordates B. Chordates 1. All share a set of derived characteristics (at some point in their life cycle, does not need to be at same time) a. Notochord - Firm, flexible longitudinal supporting rod - Located between gut and nerve cord - Functions as internal skeleton - Found in all chordate embryos and in some adults - Forerunner of backbone b. Dorsal, hollow nerve cord - Other animals have solid nerve cords - usually ventrally located, not dorsal - Develops into central nervous system - Develops into central nervous system c. Pharyngeal gill slits (throat area) - Ancestor porbably suspension feeder d. Muscular post-anal tail - Extends posterior beyond anus 2. Basal clades a. Lancelets - Most basal group out of all chordates - Invertebrates - Marine suspension feeders b. Tunicates - Invertebrates - Marine suspension feeders - Characterized by having one set of Hox genes (responsible for coding proteins that determine development) C. Vertebrates 1. Characteristics a. Chordate characteristics most evident during embryonic stage b. Adult stage possesses backbone - Bone, cartilage c. Two or more sets of Hox genes - More genetic complexity - Potentially explanation for many features and structures that evolve 2. Basal clades - hagfishes and lampreys a. Only lineages of living vertebrates that lack jaws b. Rudimentary vertebrae - comprised of cartilage, not bone D. Gnathostomes (-stomes = mouth, "jaw-mouth") 1. Characteristics a. Hinged jaws b. 4 sets of Hox genes 2. Basal clade - Chondrichthyes a. Aquatic organisms b. Skeleton comprised of cartilage, flexible c. Cartilagenous fishes - Sharks, rays, skates E. Osteichthyans 1. Characteristics a. Bony skeleton - hard matrix - Calcium phosphate b. Lungs - Supplement gas exchange by gills 2. Basal clade - Actinopterygii a. Aquatic b. Ray-finned fishes - Fins supported by rays c. Ex. Trout, tuna, salmon, perch F. Lobe-fins 1. Characteristics a. Muscular fins or limbs used for locomotion 2. Basal clades a. Actinistia - coelocanths b. Dipnoi - lungfishes (lungs and gills) - Sister group of tetrapods G. Tetrapods G. Tetrapods 1. Characteristics a. Four limbs b. Neck c. Fused pelvic girdle - bones fused together, more efficient in transferring forces throughout body 2. Basal clade - Amphibia a. First tetrapods b. Eggs - water, damp - Larvae -aquatic c. Thin, moist skin - need damp environments 3. Ex. Frogs, salamanders H. Amniotes 1. Characteristics a. Amniotic egg - Amnion - membrane that forms fluid-filled sac around embryo - Can be on land b. Ribcage ventilation - allow breathing 2. Reptilia a. Hard, dry scales - contain keratin - Help provide protection against drying out b. Shelled eggs - laid on land c. Lizards, snakes - ectothermic (temp fluctuates with environment) d. Birds - Anterior limbs → wings - Feathers - Light skeleton - Endothermic (use metabolic energy to maintain constant body temp) 3. Mammalia a. Key characteristics - Mammary glands - produce milk - Birth to live young - Have hair and fat (layer under skin) ◊ Help retain heat - Endothermic - High metabolic rate ◊ Have very efficient respiratory and circulatory system b. Monotremes - Lay eggs - ancestral characteristic - Have hair - Produce milk (no nipples - collects and young lap up) - Australia - Platypus and echidna c. Marsupials - Nipples - Live young - Placenta - allow nutrient and waste exchange between embryo and mother - Born early in development ◊ Complete during nursing ◊ Marsupium - pouch - Opossums, kangaroos, koala d. Eutherians - Placental mammals ◊ Complex placenta ◊ Complex placenta - Have long pregnancies (all embryonic development completes inside) Fig 34.2 Pg. 749 Figure Lecture 7: Plant Diversity I Tuesday, January 20, 2015 11:12 PM I. Introduction A. Charophytes - green algae (closest relative of land plants) B. Characteristics of charophytes 1. Inhabit shallow waters around edges of bodies of waters like ponds or lakes → possibility of drying out a. Natural selection favors individuals that can withstand those conditions 2. Sporopollenin a. Polymer layer b. Prevents exposed zygotes from drying out C. Land plants share a number of traits with only charophytes 1. Rings of cellulose synthesizing proteins a. Found in plasma membrane b. Synthesize cellulose microfibrils → cell wall 2. Flagellated sperm - similar in both groups 3. Share formation of phragmoplast a. Group of microtubules - Form between daughter nuclei during cell division b. Cell plate - Forms in middle of phragmoplast - Gives rise to cell wall of new daughter cells D. Derived traits of plants Fig 29.3  Key traits which are found in land plants but not in charophytes 1. Alternation of generations a. Plant will alternate between two multicellular stages a. Plant will alternate between two multicellular stages b. Gametophyte (gametes are haploid) - Haploid multicell stage - Produces gametes (n) by mitosis c. Sporophyte - Produced by the fusion of gametes → diploid - Produces haploid (2n) spores by meiosis 2. Multicellular, dependent embryos a. 2n embryo (sporophyte) - Is retained within tissue of female gametophyte (n) b. Nutrients transferred from parent to embryo via placental transfer cells - Getting nutrients from gametophyte c. Land plant - Embryophytes 3. Walled spores produced in sporangia a. Sporangia - Multicellular organs in sporophytes - Produce spores b. Sporocytes - actual 2n cells in sporangia that will produce haploid cells - Undergoes meiosis → haploid spores produced c. Spores - haploid reproductive cells - Grow (mitosis) → multicellular gametophyte d. Spore wall - Sporopollelin - Makes resistant to harsh environments 4. Multicellular gametangia a. Gametangia - Produced by gametophyte - Produces gametes - Mitosis b. Can be female = archegonium - Produces eggs - Site of fertilization c. Can be male = antheridium - Produce and release sperm 5. Apical meristems a. Roots (nutrients in soil) and shoots (light above ground) can elongate → increase access to resources b. Localized regions of cell division - At tips of roots and shoots c. Cells → differentiate into various tissues 6. Cuticle a. Waxy covering - Over all above ground parts b. Prevents drying out c. Provides some protection against microbes d. Does not allow gas exchange to occur 7. Stomata a. Tiny openings found in surfaces of leaves and stems b. Can open and close c. Sites of gas exchange d. Main route for water evaporation E. Origin and diversification of


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