BIOL 1030- EXAM 1 NOTES
BIOL 1030- EXAM 1 NOTES BIOL 1030 - 002
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This 20 page Study Guide was uploaded by Brooke Polinsky on Thursday February 11, 2016. The Study Guide belongs to BIOL 1030 - 002 at Auburn University taught by Debbie R. Folkerts in Summer 2015. Since its upload, it has received 62 views. For similar materials see Organismal Biology in Biology at Auburn University.
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Date Created: 02/11/16
Organismal Biology Exam One Notes: • Phylogeny= evolutionary history of a group or species ◦ reconstruct and interpret phylogenies using systematics ◦ also use classiﬁcations ◦ Taxonomy- naming and classifying diverse forms of life ‣ Binomial Nomenclature- two part format of the scientiﬁc name; invented by Carl Linnaeus • Genus- 1st part of the name, capitalized • Speciﬁc Epithet/Species- 2nd part of the name and is unique for each species within the genus ◦ Hierarchical Classiﬁcation- grouping of organisms into a hierarchy of increasing inclusiveness ‣ ﬁrst grouping is built into the binomial: species that appear to be closely related are grouped into the same genus ‣ Taxonomic system is also called the Linnaean System ‣ This system places organisms into: Domain--> Kingdom--> Phylum--> Class--> Order--> Family--> Genus--> Species ‣ Preﬁxes: infra (less than an order)--> Sub (part of an order)--> Super (more than an order) ‣ Taxon- taxonomic unit at any level of the hierarchy ◦ Phylogenetic Trees- represents how taxonomists classify organisms ‣ branch point- represents the common ancestor of two branches ‣ sister taxa- groups of organisms that share an immediate common ancestor and are the most closely related ◦ Phylogenies are inferred from morphological (shape), physiological (physical), and molecular data ‣ make sure that characteristics in a certain species are homologous ‣ Homology- shared ancestry ‣ Analogy- convergent evolution, which occurs when similar environmental pressures and natural selection produce similar adaptations in organisms from diﬀerent evolutionary lineages. • don't want to look for analogous features ◦ Cladistics philosophy- common ancestry is the primary criterion used to classify organisms ‣ clades- includes an ancestral species and all of its descendants • like the Linnaean system are grouped into larger clades ‣ Taxon is only equivalent to a clade if its monophyletic • Monophyletic- consists of an ancestral species and all of its descendants • Paraphyletic- consists of an ancestral species and some, but not all of its descendants • Polyphyletic- includes distantly related species but does not include their most common ancestor ◦ these are both in contrast to monophyletic ◦ biologists DO NOT want groups classiﬁed using polyphyletic ‣ Organisms have characteristics they share with their ancestors and ones that diﬀer • Shared ancestral character (Symplesiomorphic)- a character that originated in an ancestor of the taxon. • Shared derived character (Synapormorphic)- an evolutionary novelty unique to the clade • Autapomorphic- one deﬁning characteristic in a group • Three Diﬀerent Domains: Archea, Bacteria, and Eukarya ◦ Eukarya- membrane bound organelles (eukaryotic) ◦ Prokaryotic- Archea and Bacteria; single-celled organisms without membrane bound nucleus ◦ Archea and Bacteria are distinguished through molecular properties • Six diﬀerent Kingdoms: Archeabacteria, Eubacteria, Fungi, Animalia, Protista, Plantae ◦ 1 kingdom of Archea and Bacteria ◦ 4 kingdoms of Eukaryotes • Domain Prokaryotes ◦ most are unicellular and small: most are 1-5 micro meters ◦ Shapes ‣ Coccus- round ‣ Bacillus- rod shaped; usually solitary but sometimes arranged in chains ‣ Spirillus- spiral ◦ Coloniality ‣ solitary- single-celled, unattached ‣ colonial- most grouped; can take a chain shape and form something like strepobaccilli ‣ Straphylo- clusters ◦ Cell Wall- maintains cells shape, protects the cell, and prevents it from bursting in a hypotonic environment ‣ diﬀer from cell walls of eukaryotes ‣ most bacterial cell walls are composed of peptidoglycan- a polymer composed of modiﬁed sugars cross-linked by short polypeptides • encloses the entire bacterium and anchors it to other molecules that extend from its surface • Archaeal cell walls lack peptidoglycan ‣ Gram Stain- scientists can categorize bacterial species according to the diﬀerences in their cell wall • Samples are ﬁrst stained with crystal violet dye and iodine and then rinsed in alcohol and ﬁnally stained with a red dye. • The structure of the cell wall determines the staining response • Gram Positive- bacteria have simpler cell walls with a large amount of peptidoglycan ◦ The response is violet • Gram Negative- the bacteria have less peptidoglycan and are structurally more complex with an outer membrane that contains lipopolysaccharides ◦ response is pink or red because the crystal dye can easily pass through the thin cell wall and is removed by the alcohol rinse unlike the gram positive results ‣ Capsules- sticky layer of polysaccharides or proteins; nonliving • allows prokaryotes to stick to other members of their colony • some protect against dehydration and other shield pathogenic prokaryotes from attacks by their host's immune system ‣ Some prokaryotes stick to their substrate by hair like appendages called ﬁmbriae • Others use pili- shorter and more numerous than ﬁmbriae and are appendages that pull two cells together prior to DNA transfer ◦ sex pili- tube structure that extends from a cell to allow the exchange of DNA ◦ Motility ‣ about half of the prokaryotes are capable of taxis ‣ Taxis- directed movement toward or away from a stimulus • chemotaxis- change their movement pattern in response to chemicals • phototaxis ‣ Flagella- most common • may be scattered over the entire surface of the cell or concentrated at one or both ends. ◦ Internal Organization and DNA ‣ Genome- have circular chromosomes and are associated with fewer proteins than eukaryotes; also they lack a nucleus • nucleoid- a region of the cytoplasm that is not enclosed by the membrane; ring-shaped DNA • plasmids- smaller rings of independently replicating DNA molecules only carrying a few genes ◦ Reproduction ‣ Asexually ‣ Binary Fission- single prokaryotic cell splitting into 2 cells; many can divide every 1-3 hours ‣ they are small, they reproduce by binary ﬁssion, and they often have short generation times. • this means that their populations can consist of trillions of individuals, far more than the eukaryotic populations ‣ Budding- if a cell produces a smaller cell ‣ Congugation- cells donate plasma to other cells • use sex pilus ◦ Genetic Recombination- the combining of DNA from two or more sources ‣ Transformation- the genotype and phenotype of a prokaryotic cell are altered by the uptake of foreign DNA from its surroundings; plasmids being picked up • cell surface proteins that recognizes DNA from closely related species and transport it into the cell, once inside the foreign DNA can be incorporated into the genome by homologous DNA exchange ‣ Transduction- phages, carry prokaryotic genes from one host cell to another • most of the time it results from an accident that occur during the phage replicative cycle; viral transfers of plasmids and cross species ‣ Conjugation- DNA is transferred between two prokaryotic cells that are temporarily joined • DNA transfer is always one way= one cell donates and one cell receives the DNA • uses a pilus • the ability to form pili and donate DNA comes from the F factor ◦ Endospores- spores that are produced inside the cell with thick walls that are resistant to many things ‣ can be format during bad conditions ‣ used for dispersal, resistance, and dormancy ◦ Nutritional modes for prokaryotic cells ‣ heterotrophic= don't make their own food; require at least one organic nutrient such as glucose to make other organic compounds • free-living= decomposers • symbiotic= mutualistic, pathogenic ◦ pathogenic- feeds on living organisms and causes diseases ‣ Photoheterotrophic- use light energy but get thuer carbon from a diﬀerent source; in-between a heterotroph and an autotroph ‣ Autotrophs- organisms that need only CO2 or related compounds as a carbon source • photoautotrophs • chemoautotrophs- use chemicals to make organic food ◦ Oxygen Relationships for Prokaryotes ‣ Obligate aerobes- must use O2 for cellular respiration and can't grow without it ‣ Obligate anaerobes- poisoned by O2 • some live exclusively by fermentation others extract chemical energy by anaerobic respiration • anaerobic respiration- substances other than O2, such as nitrate ions or sulfate ions, accept electrons at the downhill end of the electron transport chain • Facultative anaerobes- use O2 if present but can also carry out fermentation or anaerobic respiration ◦ Nitrogen Metabolism ‣ Nitrogen ﬁxation- process of converting atmospheric N2 into NH3 or ammonia ‣ Cells can incorporate this "ﬁxed nitrogen" into amino acids and other organic molecules ◦ Ecological Relationships/Metabolic Cooperation for Prokaroytics ‣ Heterocysts- specialized cells that carry out only nitrogen ﬁxation • surrounded by a thick cell wall that restricts entry of O2 produced by neighboring photosynthetic cells • intercellular connections allow heterocysts to transport died nitrogen to neighboring cells and to receive carbs ‣ Bioﬁlms- the waste of one is the food of the other; metabolic cooperation between diﬀerent prokaryotic species often occurs in these surface-coating colonies • secrete signaling molecules that recruit nearby cells, causing the colony to grow polysaccharides and proteins form the capsule • channels in the bioﬁlms allow nutrients to reach cells in the interior and wastes to be expelled ‣ mutualists- live with other organisms in a beneﬁcial way ‣ pathogens- live with other organisms in a harmful way ‣ decomposers- feed on dead material • Domain: Archea- "old bacteria" ◦ Kingdom: Archeabacteria (really 1-4 kingdoms) ◦ Extremophiles- organism that live in very extreme environments ‣ extreme halophiles- live in highly saline environments such as the great lakes ‣ extreme thermophiles- thrive in very hot environments • their protein doesn't de-fold because they have adaptations that make their DNA and proteins stable at high temperatures • hydrothermal vents ◦ Methanogens- release methane as a by-product of their unique ways of obtaining energy ‣ many use CO2 to oxidize H2, a process that produces methane waste and energy ‣ some of the strictest anaerobes, poisoned by O2 ◦ Non extreme Archea- has a common ancestry with methanogens and extremophiles ‣ live in farm soils to lake sediments • Domain: Bacteria ◦ Single Kingdom: Eubacteria ◦ Phylum: Cyanobacteria ‣ blue-green algae ‣ gram negative photoautotrophs ‣ only prokaryotes with plantlike, oxygen-generating photosynthesis ‣ nitrogen ﬁxation( above) ‣ similar to chloroplasts because of folding of inner membrane- Serial Endosymbiosis ◦ Phylum: Proteobacteria ‣ large and diverse clade that includes autotrophs, chemoautotrophs, and heterotrophs ‣ some are aerobic and some are anaerobic ‣ ﬁve subgroups: alpha, beta, gamma, delta, epsilon ‣ Alpha Proteobacteria • closely associated with eukaryotic hosts • Rhizobiums species lives in nodules of roots of legumes where bacteria converts atmospheric N2 to compounds the host plant can use to make proteins • Agrobacterium- produce tumors in plants ◦ genetic engineers use this to carry foreign DNA into the genomes of crop plants • Serial Endosymbiosis- scientists believe that mitochondria evolved from aerobic from this bacteria ( purple-green bacteria) ◦ Spirochetes ‣ gram negative heterotrophs spiral through the environment ‣ some are free-living and some are pathogenic parasites ‣ cause diseases like Lyme Disease ◦ Chlamydias ‣ can only survive within animals cells ‣ gram negative walls lack peptidoglycan ‣ STDS, causes blindness, urethritis ◦ Mycoplasmas ‣ gram positive bacteria but because of no cell wall, they are considered gram negative ‣ smallest of all bacteria ‣ only bacteria known to lack cell walls ‣ many are free-living soil bacteria, but others are pathogens • Domain: Eukarya ◦ 4 kingdoms ◦ General Characteristics of Eukaryotes: ‣ true nucleus= a nucleus that is a membrane-bound organelle with DNA • Mitochondria also carries DNA ‣ Other membrane-bound organelles ‣ Cytoskeleton ‣ Sexual and A-sexual Reproduction • Meiosis= produces 4 haploids half of the parental and half of the maternal ◦ replication with 2 divisions ◦ 2n--> n with variation ◦ gamete is produced which is a cell involved in reproduction that fuses into a haploid cell ‣ syngamy ◦ zygote= diploid cell produced from syngamy • Mitosis= cell division into 2 cells (cloning) ◦ replication and 1 division ◦ 2n-->2n produce more diploids • Spores= can be diploid or haploid ◦ single-celled usually ◦ asexual or sexual ◦ dormancy or dispersal • Illustration of Syngamy: ◦ n------>2n • Illustration of Meiosis: ◦ 2n------>n • Three sexual reproductive life cycles: Zygotic Meiosis, Gametic Meiosis, and Sporic Meiosis ◦ Zygotic Meiosis=In kingdom Fungi and some protists ‣ "zygote undergoes Meiosis" to form haploid oﬀspring ‣ illustration in notes ◦ Gametic Meiosis= Animalia and Protista ‣ life cycle in which syngamy immediately follows meiosis, thus giving rise to diploid cells ‣ illustration in notes ◦ Sporic Meiosis= Plantae and Protista ‣ life cycle in which both syngamy and meiosis are followed by a period of extended development ‣ alternation of generation= haploid and diploid ‣ illustration in notes ‣ spores are produced by meiosis- sporophyte ‣ also can be a gametophyte produced • Kingdom Protista ◦ most are unicellular ◦ heterotrophic, autotrophic, and mixotrophic ‣ mixotroph= combine photosynthesis and heterotrophic nutrition ◦ 4 or 5 major ◦ evolutionary trends ‣ single celled--> multi celled ‣ asexual--> sexual ‣ zygotic-->gametic-->sporic meiosis ‣ sporic meiosis • isomorphic-->heterophoric= when u can't distinguish between gametophytes and sporophytes • dominant gametophyte-->dominant sporophyte • isogamy-->anisogamy (diﬀ) • Oogamy= is a version of anisogamy where there is one egg and one sperm ◦ Phylum Diplomonadida ‣ have a reduced mitochondria that lacks functional electron transport chains and cannot use oxygen to help extract energy ‣ instead they get their energy from anaerobic biochemical pathways ‣ have a paired nuclei and numerous ﬂagella ‣ symbiotic relationships= parasitic and mutalists ‣ Example: Giardia Intestinalis • usually live in the guts of vertebraes • parasitic and anaerobic ◦ Phylum Parabasala ‣ parabasal organ= large and modiﬁed Golgi Apparatus; associated with a nuclei and attached to the basal body of ﬂagella ‣ reduced mitochondria called hydrogenosomes • generate energy anaerobically by releasing hydrogen gas as by-product ‣ Most famous one: Trichomonas Vaginalis • a sexually transmitted parasite that infects 5 million people each year • mucus coated lining of the human reproductive system and urinary tracts by moving its ﬂagella and undulating part of its ﬂagella • has a gene that feeds on the vaginal lining promoting infection • parasite ◦ Phylum Euglenozoa= euglena like animals ‣ have rods with either a spiral or a crystalline structure inside each of their ﬂagella ‣ a mixture of photosynthetic, mixotrophic, and parasitic organisms ‣ two best groups of this are: Kinetoplastida and Euglenids ‣ phototaxis= positive; moves organisms towards the light and is very adaptive ‣ stigma= red spot that acts like an eye and controls their movement toward the light ◦ Phylum Kinetoplastida • have a single large mitochondrion that contains an organized mass of DNA called a kinetoplast • Bodo= free living and heterotrophic • more parasitic then free-living ◦ Example: Trypanosoma brucei ‣ infects humans and causes the African Sleeping Sickness ‣ the infection occurs via bite of a vector organism, a ﬂy called the African Tsetse ‣ also can cause Chagas' disease which is transmitted by bloodsucking and can lead to congestive heart failure ‣ evade immune responses with an eﬀective "bait and switch" defense ◦ Phylum Dinoﬂagellata ‣ two types of ﬂagella: longitudinal and encircling • located in the grooves in this "armor" that make dinoﬂagellates • longitudinal= directs the ﬂagella • encircling= makes the ﬂagella spin ‣ over half of these organisms are heterotrophic ‣ others are important species of phytoplankton; many of these photosynthetic organisms are mixotrohpic ‣ Example: Gymnodinia • lives in water and sometimes experiences explosive population growth • this causes algae blooms that are referred to as red tides ◦ red tides produce toxins that kill ﬁsh ◦ also produces bioluminescence ◦ Phylum Apicomplexa ‣ nearly all are parasites of animals ‣ parasites spread through their host as tiny infections called sporozoites ‣ most have intricate life cycles with both asexual and sexual stages • most life cycles require 2 or more host species for completion • Example: Plasmodium Life Cycle ◦ parasite that causes malaria that lives in both mosquitos and humans ◦ Step 1: Mosquito injects sporoziote ◦ Step 2: enters bloodstream travels to liver but then returns to bloodstream to reproduce cells ◦ Step 3: enter red blood cells and enter the trophoziote stage ‣ trophoziote=a growing stage in the life cycle of some sporozoan parasites, when they are absorbing nutrients from the host. ◦ Step 4: Schizogamy (asexual reproduction by multiple fission)--> merozoite --> reenter RBC and convert back to trophozoite ◦ Step 5: Gametophyte which is picked up by mosquito ◦ Step 6: Gametes ◦ Step 7: Syngamy--> Oocyst (fertilized egg) ◦ Step 8: Meiosis--> sporozoite ◦ this life cycle is an example of zygotic meiosis ◦ Phylum Ciliophora ‣ ciliates that have cilium ‣ most are predators, typically bacteria or small protists ‣ contain oral grooves ‣ cytosome= food particles can cross through membrane ‣ Cytopharynx and food vacuole= changes color with digestion system ‣ Cytoproct= anus; reverse of exocytosis ‣ Example: Paracium mulitmicronucleatom ‣ Pellicle- cell membrane with alveoli ‣ Oral groove, cytosine, cytopharynx, food vacuole, and cytoproct are used for digestion ‣ contractile vacuole for osmosis ‣ some ciliates have reduced ciliature and/or modified cilia ‣ Example: Euplotes ‣ cirrus- are tufts of cilia fused to form leg-like structures ‣ membranelles are rows of cilia fused to form sheet-like structures ‣ Cilia and flagella have similar internal structures • 9+2 arrangement of microtubules • 9 fused pairs of microtubules on the outside of the cylinder, plus 2 unfused microtubules in the center ‣ Dynein "arms" attached to microtubules serve as the molecular motors • Flagella (longer and less numerous ) undulate, while cilia (shorter and usually more numerous) move in an oar-like fashion. ◦ Phylum Bacillariophyta - diatoms ‣ The cell wall is a 2-part, silicious frustule. • One valve fits inside the other. When cells divide, each daughter cell forms a new valve to fit inside the old one, so some cells are smaller. They get smaller and smaller until, at 1/3 original size • they reproduce sexually and return to full size. ‣ These unusual algae (photosynthetic) occurred in large numbers in the past (blooms) in places where their remnant frustules formed layers of diatomaceous earth (now used as water filters and polishing compounds, including tooth paste.) ◦ Phylum Phaeophyta – brown algae ‣ these marine algae are often very large, like kelp and sargassus ‣ have a simple, multicellular form ‣ They have zones of growth, called meristems. ◦ Phylum Rhodophyta- red algae ‣ red algae are deep-water,marine macroalgae ‣ pigments are suitable for deep water. ‣ Some are edible and provide useful products, like carrageenan (used in ice cream), nori, and agar. ◦ Ameboid protozoa ‣ Amebas – with and without tests (shell-like structures) ‣ Pseudopods are used for movement and phagocytosis • Pseudopod movement involves a thick ectoplasm and a thin flowing endoplasm. ‣ Cytoskeletons break down and rebuild as one converts to the other. ◦ Phylum Gymnamoeba ‣ “naked” amoebae, without tests. Some are parasitic and some are free-living. ◦ Phylum Radiolaria ‣ axopodia and silicious tests with perforations. ‣ Axopodia are pseudopods reinforced with microtubules – stiff and needle-like. ◦ Phylum Foraminifera ‣ reticulopodia and chambered, calcareous tests. ‣ Reticulopodia are threadlike and branching pseudopods. Ancient ‣ oozes of foraminifera formed the White Cliffs of Dover and pink sands of Bermuda. Some of them are the largest protists ever lived. ◦ Phylum Myxomycota – plasmodial slime molds ‣ The body form is a plasmodium – a multi-nucleate mass of protoplasm ‣ complex life cycles include spore formation ◦ Phylum Chlorophyta – green algae ‣ cell walls and chloroplasts ‣ solitary or colonial ◦ Phylum Choanoflagellata ‣ collar cells adapted for filter-feeding ‣ a collar of microvilli and a single flagellum ‣ These protists are more closely related to Animalia than any other group. They are considered to be a sister • Kingdom Plantae ◦ plants differ in how much time and growth is spent in one generation versus the other ◦ the first plant had a gametophyte dominated life cycle ◦ first group of plants is Bryophytes ‣ there are three phyla ‣ superphylum ‣ three things that the group has in common: • a gametophyte dominated life cycle • no vascular tissue (therefore, no true organs) • small size • sperm that must be dispersed in water • restricted to moist habitats • three phyla in this group are: Brophyta (true mosses), Hepatophyta (liverworts), and Anthocerophyta (hornworts) • Phylum Brophyta= true mosses ◦ Life Cycle: ‣ the haploid generation starts with a meiospore that sprouts into protonema (first stage of gametophyte). It soon develops a left shoot and forms a mature gametophyte ‣ gametophytes produce gametes by mitosis ‣ gametes are produced in a gamete container called: gametangium ‣ Male gametangia are called antheridia • male shoots with antheridia in splash cups= encourages sperm to come out and swim over to egg • significant because its disperses water • also aids in sperm dispersal • non vascular ‣ Female gametangia are called archegonia • female shoots with archegonia at the tips • each vase-shaped archegonium contains a single egg or ovum ‣ from the fertilized egg (zygote) within archegonium, grows the diploid sporophyte and is still attached to the gametophyte ‣ "amphibians" of plant world ‣ It consists of a seta and a capsule • capsule has spores inside formed by meiosis • The spores are aided int heir dispersal by the peristome which are hygroscopic (move in response to change in humidity) • An operculum and calyptra cover the opening of the capsule ◦ calyptra= actually a remnant of the archegonium and is the only haploid part of this whole ◦ once it is removed by the wind or something else the operculum can open to release the spores ◦ the peristome teeth move up and down, helping to disperse the spores ◦ Phylum Hepatophyta= liverworts ‣ the gametophyte of liverworts is a simple sheet like structure called a thallus • thallus is a lobed like a liver and dichotomously (2- way branched). ‣ liverworts have gemma in gemma cups for asexual reproduction; produced by mitosis and produce little gemma • each gemma can disperse and grow into a new thallus ‣ liverwort atheridia/gamteangium/sperm are born on structures called antheridiophores • archegonia are born on archegoniophores ‣ sporophytes develop from the fertilized egg within the archegonium, are short, and hang upside down ‣ spores are aided in dispersal by hygroscopic elaters (the corkscrew-like structures seen with the spores on the right) ◦ Phylum Anthocerophyta- hornworts ‣ the gametophyte is a simple thallus and the sporophyte, attached and dependent on the gametophyte is a horn-shaped structure ‣ spores are produced by meiosis within the sporophyte ‣ when mature, the sporophytes simply dehisces (splits) to release the spores ‣ hornwort sporophytes release through simple dehiscence ‣ anthoceros???
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