Bio 2 Final Exam Study Guide PDF

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Diversity of Prokaryotes    

Microbiome – wellbeing driven by the microorganisms that live inside us. Physical and mental. Protective or neutral bacteria that live in and on us LUCA – basal architecture; bacteria form Archaea – vastly growing and better understanding over diversity. Color of hot springs determined by the community of microorganisms that live in the water. o Hotsprings; completely dominated by archaea due to high temperatures o Extremophile – liking extreme conditions; “Phile” = like o Hypersaline lakes – only organisms that are super tolerant to salt such as archaea commonly found o Live also in the same places as bacteria o Interesting mix of prokaryotic features; no membrane enclosed organelles, circular chromosome, etc. Interesting properties such as introns and ability to reproduce at high temperatures > 100C. no peptidoglycan cell wall, rnA POLYMERASE, METHIONINE, HISTONES ASSOCIATED WITH DNA o Branch of LUCA diversifies into bacteria and some branch off to form archaea. o Alpha proteobacteria formed an association with a large heterotrophic archaea (Crenarcheota lineage)and evolved into the eukaryote (LECA)

Functional Diversity of Protists     

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Eukaryote (Eu = True), (Karyote = Nucleus), chromosomes are linear and bounded by a nuclear envelope into the cell Many transitions; unicellularity to multicellularity , symbioses (produce organelles/plastids), Sex -> meiosis Groups of focus – fungi, plants and animals Protist – any eukaryotes that isn’t a plant, animal or fungus***. Protists are core group and everything else is diverged from it Symbiosis – long term close association between two different species (can be positive or negative, ex: parasitism, commensalism) o Both benefit – mutualism (Ex: Termites and ciliates) o One benefit and other harmed – exploitation; predation, parasitism, competition o Both lose – competition, Spite, Primary Endosymbiosis – a cell forms a partnership with another cell o *Be able to describe the difference and similarities between primary and secondary emndosymbiosis and what organsisms they create** Multicellularity – easy to eat, harder to be eaten. Multicellularity has evolved independently in several key groups Protists – term very broad

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Excavates – single celled protists that are parasitic or commensalitic. Include the euglanozaos o Giardia -found in stagnant water (fresh) through ingestion contaminated by feces o Trichomonas vaginalis – parasite of the urogenital tract in humans. Most are asymptomatic. o Trypanosoma – blood parasite. Many different species. Neurological disorder and casues fevers and exhaustion. Death of fatigue;  “sleeping sickness” ; crupside species goes into muscle of heart and cause heart attacks in young people. Big problem in texas, south and central america  Chagas – SW united states, o Euglena – formed secondary endosymbiosis with green alagea and led to the formation of PLASTIDS. Single cell organism that consumes organic matter and turns it into ATP and sugars. o Most bacterial contamination comes from water (unsafe v. safe drinking water) Stramenophiles – very diverse, o Diatoms – amoeba type organisms, photosynthetic (secondary endosymbiosis with red alagae) , live in shells made of silicone dioxide (glass); very attainable in oceans, inorganic, o Brown Alagae – NOT PLANTS, only disatnly realted to other algae, only look like plants because of convergent evolution Dinoflagellates – free living alagea species, protist, very abundant, primary produces, single celled, primarily marine habitats, free living form in surface waters, photosynthesis, base of food web. Sensitive or make use of same fertilizer as terrestrial plants; fertilizer in water causes them to be too abundant and create red tides. Not naturaly negative, only in human conditions. Breathe out carbon dioxide creating an anoxic organism at night. Also produce neurotoxin that can hurt humans through the consumption of fish, and even swimming through can cause problems. Big problem in the indian n river of florida. o Form partenerships with corals; feed of dinoflagellates and the rest from photosynthesis. Not permananet yet, corals can reject causing bleaching. ( aicidfication and warming) o Zooxanthellae o Red algol cell that has a modified chloroplast, forms partnership with larger cell, and created a plastid and tertiary creates a symbiont with coral o *Symbiosis – VERY COMMON IN NATURE*** o Apicoomplexans – intracellular parasites, symbiotic with another organism and cause harm,  Plasmodium – RBC’s , no nucleus, grows inside rbsc, burst, infects another cell, creates fever, malaria, transmitted by mosquitos = malaria  Taxoplasma – taxoplasmosis, carried by cats to feces to mice= causes mice to be sexually attracted to cats . humans get it from not wearing

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gloves when cleaning litter box. Common killer of people with AIDS, and pregnant women, low immune systems, receiving transplant. Zoonotic disease  Kryptospirillium = very common Ciliates – thousands of cilia for locomotion. Paramecium Rhizarians – radiolara, foraminifera, Cercozoa, ameoby organisms living in shells. Very diverse (some silicon, some calcium carbonate) Archaeplastida – single celled and multicellular  Red Algae- single celled form partnerships with dinoglalletes  Charophyta- ancestors of land plants  Green Algae – single celled from partnerships with, 1st to move on to land  Land plants – all descendants of green algae  Color of organisms reflects fundamental aspect of their biology; wavelengths for photsynthesis Unikonta – humans, amoeba like organisms  Entamoebas – found in digestive tract, can also be pathogenic  Slime molds- amoeba that live in multicellular aggregates,  Amoeba Proteus – deformations of cell membrane for locomotion and digestion  Opisthokonts – fungi and Choanoflagellate  Choanoflagelletes – single cells, ring of cilia with one flagella that attracts food sources ; nearest relative without being animals. Most realted to sponge cells

Functional Biology of Plants   

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Archaeplastida (Algaes; red, green -> Charophytes-> plants) fromed through primary endosymbiosis with cyanobacteria Plants are lineage of green alagea that have moved onto land (highly modified green alagea) Challenges/ oppurtunities for moving onto land o Benefits – unfiltered sunlight (full light spectrum), High levels of CO2, nutrients, fewer hebivores (at first) o Challenges – structural support (water very buoyant), lots of water (limited amount on land Plants are green algae that have adapted to life in terrestrial habitats o Multicellular and Photosynthetic (although some have lost their chloroplasts and have become parasitic; brazillian pepper plant, love vine) o Cell walls made of cellulose (glucose polymer; beta linkages orientation) o Alternation of generations (gametophyte generation, sporophyte generation); switches back and forth o Provide significant maternal care to multicellular, dependent embryos*

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Alternation of generations o Gametophyte – produces gametes (haploid) o Plants spend most time as haploid organism o Gametophye produces eggs and sperm through mitosis o Sporophyte produces haploid spores through meiosis o Picture a plant: sporophyte o Picture a moss: Gametophyte o Gametes only there for reproduction, spores responsible for dispersal Plants divide labor o Roots for taking up water and minerals o Leaves for absorbing CO2 and expelling water and oxygen o Leaves also responsible for photosynthesis Parts of plant o Body; shoot system, stem with shoots that extend out and form leaves o Leaves flattened shoots to maximize surface area with the sun o Root; Anchor system, strategies vary but goal is the same Modifications of the plant o Root come in various shapes and occupy various roles o Prop roots – push plant above substrate, good if substrate becomes anoxic at times (muddy, etc.) o Pneumatophores – cypress ‘knobby bits” respiratory structures o Root for strangling, grow very large and store carbohydrates (turnips) o Rhizomes – tuber with root extensions o Tuber – swelling of the roots at distinct points for energy storage o Stolon’s – root that colonize adjacent habitats Leaves o Simple leaf – one leaf ex: Oak o Compound leaf – many leaflets Ex: Acacia o Structure  Cuticle – waxy outerlayer to retain water  Upper layer – chloroplasts perpendicular to maximize sunlight  Palisades layer; Support cells – transport of sugar  Humid air flows through the leaf and exits/ enters through stomata  Plants lose moisture through gas exchange because of stomata and periodically close the stomata when they don’t need them to prevent loss of moisture o Modifications o Spines – leaves that have adoptd to provide protections o Onion – stem protected by lots of modified leaf o Tendrils – long, narrow tendrils for anchorage or feeding in parasitic plants

o Agave – leaves have capacity to drop off and anchor and form new plant (reprodictive structure) o General trends in plant evolution o Vascular tissue, allowing plant to grow taller and transport fluids more efficiently in their bodies o Increasing ability to colonize dry habitats o Decreased size and independence of the gametophyte generation o Package sperm into pollen o Increased parental investment in their embryos  Use seeds instead of spores  Flowers for efficient pollination v. wind  Fruits to improve seed dispersal o Microscopic gametophytes in flowers and fruits o Vascular Tissue in Plant o Xylum – water and nutrients transport o Phloem – sugars o *Parallel systems made of different cells (X: non living interconnected tubes of cellulose with pores) o Cohesion and adhesion and osmosis draws water up through plant. That way plants don’t have to use energy to pump water up through the plant o Floem is made of live cells to actively transport sugar (think of a bucket brigade) o Modern day plants o Vascualr tissue in ancestors scattered evenly; monocot o Modern day more ring like bundles; eudicot o Plants really tiny before moving on land and vscualr system evolved; fossil record plants grow quickly after this: creates arms race as plants compete for resources o Evolution of sperm – flagellated v. pollen. Pollen protects sperms and makes it aerodynamic so it can spread over a wide area o Spores v. Seeds ; a spore is a single cell = covered in protein that helps them prevent dessication and survive (little package of hope). Seeds better for dispersal (require lost of energy) o Flowers and fruits: fruit derive from flowers, flowers attract pollinators to spread seeds and pollinate adjacent plants. Male parts die off, females stay and develop and turn into fruit o Major Plant groups o Plants without vascular tissues (mosses) o Palnts with ascular tissues (ferns) o Vascualr plants with seeds (gymnosperms) o Vascualr plants with seeds + fruit (angiosperms) Trends in plant diversity

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Green alagea that have developed from secondary endosymbiance Multicellular Photosynthetic Cell walls made of cellulose Alternation of generations Provide significant maternal care to multicellular, dependent embryos (except spores)  Placental tissues – serves same purpose as in humans (blood, nutruents, food to embryo)  Embryophyta Origin of land plants occur 475 million years ago  Thready like scum earliest plants  410 million years ago you get the first plants with height  30 million; seeds and pollen – plants move fully on land  Angiosperms come last Mosses; the plants without vascular tissue  Moses grow on side facing away from dominant sun (cold,damp)  Like damp habitats and don’t grow very tall  Sporophyte; short lived  Gametophyte dominant in early plants  *think of a cattail plant**  Antheridia – sperm , Archegonia-egg  Antheridia must have aquatic environment to reproduce  Spores produced through meiosis Plants with vascular tissue: ferns  Produce spores that germinate and form gametophyte (hermaphrodite)  Sporophyte rapidly becomes depedent from gametophyte; roots of its own. As a result Is very little and new sporophyte  Sporophyte produces sports  Sporophyte gets biger, gametphyte gets smaller Earth evolving – first forests, swampy, first land animals (amphibian tye tettrapods, amphibian ancestros, insects, first tetrapods) Death becomes large carbon deposits (coal) Lots of fossils found in coal beds as a result Plants with vascular tissue and naked seeds: gymnosperms  Ex: Palm trees (cycads)  Gymno (Naked) and sperm(seed)  “Naked seed” plants  Sporophyte houses the gametophyte which produces the egg  Gametophyte divides and produces starch to form seed and then basically dies off once the seed forms

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Seed; 3 parts  Embryo: 50% male, 50% gametophyte  Coating: 100% sprophyte  Food: 100% female gametphyte o Angiosperms  Angio “Vessel” sperm (seed)  “The flowering plants”  Embryo housed in ovary; better for dispersal  Plant insect Coevolution : sex via insects  Many of the insects have evolved at the same time as the plant  Adaptation in plant, mirrored by insect; flowers rely on insects  Like security updates for computer  In fruit “form follows function”  Coevolution with digestive system of animals  Branch of eucot and dicot o Plant insect coevolution II: Secondary chemical defenses  Animals that actually kill plant; not just pollinate. Plants creatge these compounds to increase and lengthen survival The Fungi: Key Role Players 

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What are Fungi o All Heterotrophs o Eukaryotic (LECA) o Feed by secreting digestive enzymes inti (and directly absorbing nutrients from) their environment o Some are unicellular (yeast) but most are multicellular Animals are multicellular descendants of fungi; relatives Humans closest relatives are Fungi What do they have in common with humans o Heterotrophic o Cellular structure Specilize to digest different things Ex: Tinea – Athletes foot Structure: really tiny threads (mushroom is only a sex accessory like flowers) o Once cell thick, made of network of cells forming threads o Hyphae – individual threads o Mycelim – all the threads together Fungi evolved towards multicellularity on their own; indepedently evolved o Two different ways of being multicellular  Cell wall with hole that allows diffusion and osmosis (compartments): Septate Hypha (cell wall made of chitin)

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One continuous cytoplasm with hundred and hundreds of nuclei: Coenocytic Hypha (Like Human Muscle cells)

Reproduction o Alternate between asexual and sexual reproduction  Asexual to create genetically clones o Mycelium (haploid) throws up some spores that germinate and create new mycelium o Sexual reproduction  Growing mycelium from one mating type touches another mating type and cytoplasms fuse (plasmogamy) and exist in a heterokaryotic stage  Heterokaryotic: N + N (two copies of each chromosome but haven’t made it to diploid yet; haven’t united)  Karyogamy: fusion of nuclei = diploid  Zygote goes through meisos and produces spores that germinate and then the new fungus can either go through asexual and sexual reproduction  Rhizopus (bread mold) posterchild  Plasmogamy fstage forms threads creating umbrella and meiosis occurs underneath mushroom cap (mushroom is only temporary since its only part of sexual cycle) o Ecological role: decomposer  Convert sgar from cellulose into readily available nutrients o Ecological role: Mutualist  Symbiosis – mutualism  Mutualism between a plant and a fungus*  Roots interdigit with fungi mycelium to break down organic molecules in soil so they can be taken up to the plant so the plant can conduct photosynthesis. The plant transfers sugars to the roots for storage which are used by the fungi  Mycorrhizae – relationship between plants and fungi  Some can go south; parasitic fungi  Mustualism with cyanobaceteria or green alagae  Fungus extracts difficult to extract nutrients and transfer to alagea which uses them for photosynthesis and shres them with the fungi. Rather new symbiosis – Lichen  Lichen – symbiosis between a fungus and cyanobacteria or green alagea  Ecological Role: Parasite  Pray on insects  Tinea – athletes foot Animal Body Plans: Overview o Evolutionary relationships o Unicellular, flagellated ancestor

o Multicellularity evolved independently in animals and other fungi o Choanoflagellates – human offshoots of them; unicellular or loosely multicellular (colonial). Spongelike and hetertrophic. ROOT OF ANIMAL TREE (live in protein clumps) o What is an animal? o Multicellular o Eukaryotic o Heterotrophic opisthokonts o No cell walls o Supported by matrix of collagen and glycoprotein fibers o Unique cell types: nerves, muscles o Sexuall reproduction dominant o Zygote goes through characteristic steps during development (same in basically all animals) o Multicellularity has evolved independently in many different taxa o Start off as one cell (fertilization) and then develop into multiple cells o *there must be some disadvantage to being unicellular*  Problem with multicellularity only some cells are allowed to reproduce and larger size requires more energy to operate. Cancer (requires lots of coordination)  Advantage: Size (survey environment, less predation), specialized cells o How did the animals get there  Ancestors of chanoflagellates; most likely followed the same gradual process (stalks, colonial, protein matrix…) o Most basic animals: Sponges (Porifera)  Cell specialization, symmetry separate other animals from the sponges o Figure 32.4* o Stages of Multicellularity  Happens gradually  Cells stick together  Cells recognize each other  Communicate/coordinate with each other  Cells develop mechanisms to deal with cheaters  “Alignments of fitness” the zygote bottleneck  “Export of fitness” germ cells vs. somatic cells o * last two: how your body makes sure that cell division and coordination are in every cells best interest; make sure specialize cells don’t despecialize and try to reproduce on their own, only a subset of cells are responsible for reproduction (germ cells) = align simultaneously with each other o Sponges will rebuild themselves and reorganize o Tissue – a group of cells that contain the same function in an organism  Clear internal anatomies

 Found even the simplest animals such as the corals and jellies  Layers o Organs – tissue(s)that group together to perform a specific functions o Anus – rate of energy constant because energy absorption constant  No anus  incomplete digestive system  Yes anus  complete digestive system o Specialized cell types  Muscle cells – specialized cells that are made up of proteins that in the presence of ATP can move against each other. More cells = more strength  *unique to only the animals! *  Nerve cells – can conduct electrical impulses  All cells are capable of generating current  Potassium sodium pump causes negative charge on the inside and positive on the outside that creates possibility for current to flow o Sexual reproduction  Two parents that donate 50% of genes each to child  Mitochondria have given some of their DNA to parent genome; keeps mitochondria playing nice where they don’t fight  Mitochondria come from mother (female produce larger gametes) o Animal early development o Zygote  cleavage  eight cell stage  cleavage  blastula (sphere)  blastocoel (cavity within the blastula)  gastrulation (formation of digestive system) o Cell are already specializing themselves o Skin , muscle , nerve outer layer of gastrula – ectoderm o Innermost layer of gastrula – endoderm o Bottom opening – blastopore o In more complex animals; two openings = mouth and anus (mollusks, analids) o Symmetry o Radial – numerous number of planes you can divide an animal into two equal halves as long as the cut passes through the central axis o Bilateral – singals an animal wih a purpose to move in given direction; only a single cut you can make t...