Biology II Syllabus See attached  Doesn't copy/paste well at all....... Lab Notes Lab 12 Exam 1 - Notes Chapter 26 Overview Taxonomy and Systematics Phylogenetic Trees Horizontal Gene Transfer Taxonomy The Science of describing, naming, and classifying living an extinct organisms and viruses. Systematics Study of biological diversity and the evolutionary  relationships among organisms, both extinct and modern. Taxonomic groups are based on hypothesis regarding evolutionary relationships from systematics  Hierarchical system involving successive levels Each group at any level is called a taxon Highest level is Domain All life belongs to 3 domains Bacteria, Archaea, and Eukarya The Eukarya Domain is often divided into Kingdoms in the next level This is typically called the 4 Kingdom concept Four Kingdoms Domains Bacteria and Archaea Prokaryotic cells Lack nucleus Kingdom Protista, Fungi, Plantae, Animilia Eukaryotic cells True nucleus Types of cells Prokaryotic  Lack Nucleus Lacks membrane-bound organelles Typically singled celled Eukaryotic  Well defined nucleus Membrane-bound organelles internal membrane system (compartments) Binomial Nomenclature Genus name + Specific epithet ex. Homo sapiens ('wise humans') Genus name is always capitalized Specific epithet is never capitalized Both names are either italicized or underlined   Phylogenetic Trees Phylogeny Evolutionary history of a species or group of species To propose a phylogeny,  biologist must use the tools of systematics Trees are usually based in morphological and genetic data Subjective vs. Objective data Diagram that describes the phylogeny A hypothesis of evolutionary relationships among various species Based on available information Monophyletic Group or Clade Group of species (taxon) consisting of the most recent ancestor and all of its descendants Smaller and more recent clades are nested within larger clades that have a common ancestor Paraphyletic group Contains a common ancestor and some, but not all of its descendants Over time, taxonomic groups will be reorganized so that only monophyletic are recognized Reptiles were a paraphyletic group because birds were excluded In the class and lab, we are going to separate birds and reptiles Systematics Morphological Analysis First systematic studies focused on morphological features of extinct and modern species Most of early classifications were based upon morphological features Molecular Analysis Analysis of genetic data (DNA, Amino Acids, rRNA) to identify and study genetic similarities and propose phylogentic trees DNA and Amino Acid sequences from closely related species are more similar to each other than sequences from more distantly related species Horizontal Gene Transfer any process in which an organism incorporates genetic material from another organism without being the offspring of that organism (by means of asexual reproduction) Vertical Evolution Changes in groups due to descent form a common ancestor (sexual reproduction)   Chapter 27-31 Prokaryotic Diversity Prokaryotes dated at 3.5 billion years old Modern Prokaryotes  are most abundant, lacking sexual reproduction Domain Bacteria Proteobacteria "true bacteria" Cyanobacteria "Blue-Green bacteria" Domain Archaea Have and "almost" nucleus specialized membranes surrounded by a cell wall old, can live in extreme conditions Eukaryotic Diversity (Ch 28) Kingdom Protista Earliest eukaryotes in fossil record most are microscopic and found in moist environments DNA many separate groups Most artificial category "catch-all" category Subgroups Algae Plant-like organisms 10 groups autotrophic (self-feeding) most are photosynthetic few ingest food cell wall with Protozoans Animal-like mostly netraothrophic (food-eating) Slime Molds Fungal-like Protist Mostly saprothrophic (absorb-feeding) mostly multicellular Kingdom Fungi (Ch 31) Conspicuous portion of the organism in the mushroom/yeast/mold/etc Saprothrophic (some are heterotrophic) Natures recyclers Composed of: Mycelium compacted mass of tubular filaments called hyphae Fruiting body site of spore production Cell wall composed of muramic acid/chitin Kingdom Plantae (Ch 29 & 30) >330,000 species eukaryotic and multicellular autotrophic (mostly) self-feeding capture sunlight to produce energy by photosynthesis Food storage copound starch cell wall cellulose Are referred to as "land plants" fossils dated to ~400mybp (million years before present) Ancestor stock probably a group of algae (green) Life on land requires special innovation Must be able to get water ROOTS! Phyla (divisions) 10 phyla  Typically combine these into 4 broad categories for convenience  Bryophytes Phylum Hepatophyta Liverworts ~6500 species Phylum Anthocerophyta Hornwarts ~100 species Phylum Bryophyta Mosses ~12,000 species Referred to as "mosses and their friends" Characteristics Reproduce by spores (not seeds) non-vascular plants lack conducting tissues xlem and phloem Small plants Require external H2O for reproduction Pteridophytes Phylum Lycopodiophyta lychophytes 1000 species Phylum Pteridophyts Ferns and allies 12,000 species Characteristics Sporangia Where the spores are produce Reproduce by spores no seeds vascular plants xylem water and minerals phloem food and solutes true roots, stem, and leaves due to being vascular vascular allows for larger size Require external H2O for reproduction Gymnosperms Phylum Cycadophyta cycads 300 species Phylum Ginkophyta Ginko 1 species Phylum Gnetophyta gnetophytes 300 species Phylum Coniferophytes conifers 500 species Means "Naked seeds" Seeds are not enclosed Biggest group are the conifers (Cone bearing trees) Oldest Bristle cone pine Over 4600 years Biggest Giant Sequoia estimated 600 tons Tallest Coastal Redwood 180 meters in height Characteristics Vascular more advanced that Pteridophytes Advance seed It has more survival value Contains: Embryo Offspring Stored food Integument Seed coating Does not require external H2O for reproduction Pollen tubes deliver sperm to egg location Angiosperms Phylum Anthophyta 300,000 species Characteristics Enclosed seed produces flowers and fruits most advance vascular tissues Seeds advance Enclosed in a vesses (fruit) no survival value Embryo Stored food 2 integuments Seed coats Does not require external H2O for reproduction Flowers Attract pollinators Fruit Enclose and protect the seed assist with seed dispersal Chapter 32 & 33 Kingdom Animilia Over 1.5 million species Estimated 73 million 35 Phylums Over half are insects More similarities within animal genomes than other kingdoms Characteristics  Multicellular Lack of cell wall Sexual reproduction mobile sperm larger non-motile egg Nervous Tissue Complexity Responsiveness Hox Genes Special clusters of genes associated with the planning of the body Metazoans All animals Multicellular animals Paratoans Sponges Eumetazoans "true" multicellular animals Classification/Systematics Old Morphology Embryonic Development Recent Molecular genetics Body Plans Morphological and Developmental Features Body Symmetry Number of tissue Layers Patterns of Embryonic development  Symmetry Eumetazoa Divided by symmetry Radiata Radial symmetry Often Circular or tubular Bilateria Bilateral symmetry Dorsal Back Ventral Front Anterior Posterior cephalization enlarged head Tissues Metazoa all animals divided on weather or not they have specialized tissues Parazoa Porfera sponges may have distinct cell types Enmetazoa more than one type of tissue organs all other animals Germ Layers Radial 2 layers Diploblastic endoderm ectoderm Bilateral 3 layers Triploblastic endoderm ectoderm mesoderm Embryonic Development Protostome Blastopore becomes mouth cleavage is determinate fate of embryonic cells are determined early Deuterostome (second opening) Blastopore becomes anus cleavage is indeterminate each cell produced by early cleavage can develop into a complete embryo  Other Morphological Characteristics Used in classification Presence or absence or coelom Body segmentation Molecular data suggest these features are unreliable in terms of understanding evolutionary history Body Cavity Coelom a fluid-filled body cavity Coelomate or eucolemate true coelom coelom completely lined with mesoderm Pseudocoelom coelom only partially lined with mesoderm rotifers and roundworms Acoelomate lack of a body cavity and instead have mesenchyme flatworms Flatworm has no mesoderm Functions of the Coelom Cushions internal organs Enables movements and growth of internal organs independent of the body wall Fluid acts as a simple circulatory system Segmentation Body may be divided into regions called segments occurs in annelid worms, arthropods, and chordates allows specialization of body region DO NOT worry about the number of species Molecular views of Animal Diversity Scientist now use molecular techniques to classify animals Compare similarities in DNA, rRNA, and Amino Acids Closely related organisms have fewer differences than those more distantly related Advantages over morphological data in that genetic sequences are easier to quantify and compare Example: A,T,G, and C in DNA Genes used in Molecular Systematics Studies often focus on ribosomal RNA (rRNA) Universal in all organisms changes slowly over time Hox genes also studied often Found in all animals duplications in these genes may have led to evolution of body form Phylogenies constructed using rRNA and Hox genes are similar and often agree with those based on morphology Invertebrates "without backbone" +95% of all species Phylum Porifera Sponges lack tissues (organs) multicellular pores filter H2O and food Invertebrates Phylum Cnidaria Jelly fish, corals, anemones  Diploblastic development Two tissue layers Mesoclea gelatinous covering Nerve net interconnected nerve cells  no brain One opening with gastrovascular cavity Protostomes Invertebrates Radial symmetry Salt and fresh water Stingers Phylum Ctenophora Comb jellies Same characteristics as Cnidaria Strictly salt water No Stingers Phylum Platyhelminthes Flatworms, tapeworms, flukes Triploblastic Organs and organ systems Enhanced nerve net 2 cerebral ganglia One opening with gastrovascular cavity Protostomes invertebrates bilateral symmetry Acoelomate Phylum Rotifera rotifers pseudocoelomate Triploblastic Two openings complete gut tract alimentary canal Protostomes  Corona simple brain invertebrates Phylum Mollusea Snails, slugs, oysters, octopus, squid, clams, muscles Triploblastic Eucoelomate Complete gut tract Protostomes Invertebrates Three part Body Foot Visceral mass Mantle Many have outer shells Phylum Annelida Segmented ring worms Triploblastic Eucoelomate Complete gut tract Protostomes Enhanced nervous system Invertebrates Phylum Nematoda Roundworms Triploblastic Pseudocoelomate Complete gut tract Protostomes Invertebrates Phylum Anthropoda Insects, crustaceans, spiders, ticks Highest diversity of animals >1.5 million species Hardened Exoskeleton Protostomes Invertebrates Eucoelomate Triploblastic Complete gut tract Enhanced nervous system Insects, in particular, have an enhanced brain segmented appendages Phylum Echinodermata sea stars, urchins, sea cucumbers, sand dollars Triploblastic Eucoelomate Complete gut tract Deuterostomes Simple nervous system Endoskeleton series of plates Phylum Chordata Deuterstomes Complete gut tract Endoskeleton Few invertebrates Mostly vertebrates Eucloemates Triploblastic Four Critical Innovations of Chordate Body Design Notochord Dorsal, hollow nerve cord Pharyngeal gill pouches Post-anal tail These four features are exhibited at some point of life history/development Only some Fishes exhibit all four Notochord Cartilaginous supporting rod along the dorsal axis Replaced by jointed "backbone" Vertebral column of hardened cartilage or bone Dorsal, hollow nerve cord Expanded at the anterior end Brian Enclosed/supported/protected by the Notochord Pharyngeal gill pouches Gill slits pharynx back of mouth cavity Post-anal Tail Tail extends posterior of the anus Humans Notochord replaced by vertebrae only pieces left are the inter-vertebral discs between vertebrae  Nerve cord Dorsal, hollow with largest brain capacity (compared to body size) Pharyngeal Pouches Embryonic Development 1 pair retained as Eustachian tubes Post-anal Tail One vertebra as a tail bone (coccyx) Subphylum Urochordata tunicates invertebrates ~3000 species Marine Filter feeders   Subphylum Cephalochordata Lancelets Invertebrates 25 species marine Filter feeders   Chapter 34 Subphylum Vertebrata Vertebrates Chordates with a backbone Chordate features as well as: Vertebral column Series of cartilaginous or bony elements Cranium Endoskeleton or cartilage or bone Hox genes (lots of them) Neural crest Cyclostomes Jawless Fishes Class Myxini Hagfishes lack jaws, eyes, fins vertebrae skeleton comprised of notochord and cartilaginous skull covered in slime Class Cephalospidomorphi Lampreys Has notochord, and cartilaginous vertebral column lacks jaws and appendages (fins) Oldest fossil records 510 mybp Class Chondrichthyes Cartilaginous fishes Sharks, skates, rays Cartilaginous skeleton and notochord as adults jawed fishes paired appendages (fins) < 900 species Class Osteichthyes Bony fishes Most diverse vertebrate group with  < 26,000 species Bony skeleton (most do have this) Jawed paired appendages (fins) Tertapod: Gnathastomes Four limbs with jawed mouth Transition to land involved adaptions for locomotion, reproduction, desiccation (drying out) prevention, and gas exchange Sturdy lobe-finned fishes became animals with four limbs Vertebral column strengthened, ship and shoulder bones braced against backbone relatively simple changes in gene expression, especially Hox genes Class Amphibia >4000 species Amphibios greek - "living double life" split their life between aquatic and terrestrial stages Successfully invaded land but reproduce in water Lunges are and adaption to semi-terrestrial lifestyle Three chambered heart Fishes only have a two chambered heart External Fertilization Larval stages are aquatic Undergo metamorphosis Not completely separated from water Order Anura Frogs and toads Nearly 90% of amphibians Carnivorous adults Herbivorous tadpoles Order Apoda Caecilians Nearly blind tropical burrowers Secondarily legless Order Urodela Salamanders Often have colorful skin patterns Most have four limbs Amniotes Tetrapods with a desiccation resistant egg Critical innovation Development of a shelled egg Amniotic egg Broke the tie to water Three internal membranes Shell is permeable to Oxygen and CO2 Birds Hard and Calcareous Reptiles Soft and Leathery Most Mammals Embryo embeds in uterine wall Only three species lay eggs These eggs are soft and leathery Other Key Innovations of the Amniotes Desiccation resistant skin contains keratin Thoracic breathing Negative pressure sucks air in  Water conserving Kidneys Concentrate waste prior to elimination Internal fertilization Class Reptilia >8000 living species turtles, crocodilians, lizards, snakes Can live away from water thicker skin and scales larger brain larger limbs with muscles enhanced kidneys Amniotic egg "indoor pond" Vertebrate Reproductive Modes Oviparous Egg laying outside of the body Ovoviviparous live baring wuth retention of eggs No maternal connection Viviparous live bearing with egg retained Maternal connection Class Aves Birds Evolved form small dinosaurs Fossils 150mybp Adaptions for flight Feathers Modified front limbs Lightweight skeleton Organ reduction Lungs and air sacs more gas exchange Oviparous all leg layers Bill beak Encloses mouth and nasal cavity Adapted for environment Endothermic "Internal temperature" Body temperature is primarily controlled by trapped metabolic heat. Birds and mammals Ectothermic "External temperature" Body temperature is primarily related to external temperature Metabolic heat is generated but difficult to capture/maintain the heat Fishes, amphibious, reptiles Class Mammalia Milk producing Amniotes Evolved from amniote ancestors (reptiles) earlier than birds >6000 species Appeared ~ 225mybp Evolved from small mammal-like reptiles After dinosaur extinction, mammals flourished Range of sizes, body forms, and complexity unmatched Fish-like mammals Marine mammals Bird-like mammals Bats Reptile-like mammals Three egg layers Distinguishing Characteristics Mammary Glands Secrete milk All have hair In varying amounts Only vertebrate with multiple dentitions Heterodont Different types of teeth  incisors, canines, molars, premolars Thecodont Teeth with long roots embedded in sockets of jawbone Diphyodont Milk teeth that are mostly replaced by "adult" teeth later in life Pinna Flap of cartilage and lose connective tissue to channel and funnel sound The "outer ear" Three middle ear ossicles (bones) Enlarged Skull Brain enlarged in large skull Larger Cerebrum Single lower Jawbone (Dentary) Anucleate red blood cells Order Primates Primarily tree dwelling species grasping hands with  opposable thumbs Large brain Some digits with flat nails Not claws Binocular vision Complex social behavior and well-developed parental care  Enhanced sense of touch Taxonomy of Humans Kingdom Animalia Phylum Chordata Subphylum Vertebrata Class Mammalia Order Primates Suborder Anthropoidea Superfamily Hominoidae Family Hominidae Subfamily Homininae Tribe Hominini Genus Homo Species Homo s apiens Exam 2 - Notes Chapter 35 Introduction to Plants Kingdom Plantae We will primarily be discussing the angiosperms Phylum Anthophyta Flowers and fruits Only group that does/has these things Advanced traits Seeds Advanced vascular tissues From seed to seed The life of a flowering plant Seeds reproductive structures produced by angiosperms and other seed plants usually the result of sexual reproduction contains embryos that develop into seedlings upon germination has survival value Alternation of Generations Exhibited by all plants (and plant-like organisms) that have sexual reproduction There is an alternation between a diploid (2N) form [sporophyte] and a haploid (1N) form [gametophyte] Gametophyte (haploid) Gamete-producing plant fomr multicellular microscopic in flowering plants female embryo sac with egg male pollen grain grow and develop within flowers of angiosperms produces gametes by mitosis/cytokineses Sporophyte (diploid) multicellular large "plant" in flowring plant produces haploid spores by meiosis (reduction) called meiospores The plant embryo Fertilization (syngamy) results in the formation of a diploid zygote, which undergoes mitosis to form an embryo (multicellular) the embryo is a sporophyte that lies dormant in the seed with a supply of stored food and a seed coat may lay dormant for long periods until conditions are favorable  The plant body Composed of three organ types stems leaves roots Shoot system stem produce leaves and branches and bear the reproductive structures leaves flattened structure specialized for photosynthesis Root system roots Provide anchorage in the soil and foster efficient uptake of water and minerals can store food Growth Indeterminate growth increasing in size as long as the plant is alive grows into a seedling and then a mature plant Plant growth occurs by 3 means Increase in number of cells cellular reproduction (mitosis/cytokineses) increase in cell size elongation increase in weight/mass Development Mature plants produce reproductive structures flowers seeds fruits flowers and floral buds are reproductive shoots that develop when shoot apical (tip) meristems produce flower parts instead of new tissues and leaves flowers are produced by determinate growth Seed coats Flower tissues enclose and protect tiny male and female gametophytes sperm in pollen fertilizes the egg, triggering ovules to develop into seed and flower parts to develop into fruit fruits enclose  seeds and function in seed dispersal Angiosperms   Meristems Seedlings and mature plants produce new tissue from meristems cell factories meristem is a region of undifferentiated cells that produce new tissue by cell division A dormant meristem occurs at the shoot and root of seed embryos activate in seedlings mature plants have shoot apical meristems (SAM) and root apical meristems (RAM) Mature sporophyte develop from seedlings photosynthesis powers the transformation of seedlings into mature plants provides the ability to produce organic food plants undergo both vegetative growth and reproductive development Hierarchy of structures in a mature plant Specialized cells tissues organs organ systems branches, buds, flowers, seeds, fruits root and shoot systems plant (the organism itself) Primary Growth Elongation of plant organs roots, stems, and leaves Occurs in ALL plants Produces primary tissues from apical meristems (SAM  and RAM) Primary Tissues Primary xylem vascular/conducting tissue water and minerals Primary  phloem vascular/conducting tissue food and solutes Epidermis dermal Outter-most tissue protection holds water in plant Support ground tissues Parenchyma most abundant type storage water and food part of cortex/pith Collenchyma Protection/support of growing plant organs cortex Sclerenchyma protection/support of non-elongating organs cortex Secondary Growth Expansion of plant organs lateral meristems roots and stems only does not occur in leaves noes not occur in all plants Produces secondary tissues woody tissues Major groups of Angiosperms Eudicots >240,000 species all have primary growth most have secondary growth for this class we are saying they all have secondary growth Monocots >60,000 species all have primary growth very few have secondary growth for this class we are saying that non have secondary growth grasses, corn, tulips, lilies Root system adaptations Major functions absorbing water and minerals anchoring the plant in the soil storing nutrients and water Eudicots Taproots Monocots fibrous roots Three zones of root growth Region of cell division RAM and root cap RAM contains cells that ar dividing Quiescent center keeps nearby cells undifferentiated Root cap embedded in mucigel Mucigel is a slimy substance that covers the root cap of the roots of plants. Region of elongation cells extend by uptake of water Region of maturation root cell differentiation  and tissue specialization identified by presence of root hair water and mineral uptake Root Internal Structure Epidermis of mature roots encloses a cylinder of parenchyma called the root cortex One cell thick often rich in starch functions as food storage many contain inter-cellular air spaces Endodermis selective absorption of minerals one cell thick Meristematic pericycle encloses root in vascular tissues provides lateral branches woody roots produce primary vascular tissues followed by secondary vascular tissues Eudicot root Monocot Root The shoot system Stem and leaf adaptations Shoots are modular with 4 parts Stem node leaves or branches emerge Internode stem between adjacent nodes elongation Leaf Axillary Meristem generate axillary buds can produce flowers or branches Lateral shoots New branches bear SAM at their tips Shoot Tip Terminal bud at the end of each shoot includes the SAM and other parts scales Leaf anatomy Leaf adaptation Leaf venation Eudicot Pinate (feathery) Palmate (palm) Netted provides more support for the leaves Monocot Parallel  Stem Primary growth mostly above ground organs,but some modified stems are blow ground Irish potato underground stem Eudicot Stem ALC Primary (elongation) and secondary (expansion) growth vascular bundles (xylem and phloem) form a ring pattern  exhibit both a pith and a cortex cambium ring produce cells provide secondary growth Lateral Meristems Produces secondary growth 2 lateral merstems both are rings that retain cell division properties and produce secondary tissues to the inside and outside of the cambium ring Vascular cambium produces ring of secondary xylem (wood) to the inside and a ring of secondary phloem (inner bark) to the outside Cork cambium Produces ring of periderm (outter bark) that replaces the epidermis and cortex for external protection Secondary vascular tissue woody plants begin life with only primary vascular systems produces secondary tissues and bark as they mature secondary xylem wood Secondary phloem inner part bark has both outer bark (mostly dead cork cells) and inner bark (secondary phloem) Secondary growth begins late in first year of growth eudicot stem after 3 years of growth Monocot stem Primary growth (elongation) vascular bundles (xylem and phloem) are scattered lacks both pith and cortex Comparison between Plant types Leaves Eudicot net venation Monocot parallel venation Roots Eudicot primary and secondary growth (mostly) cortex no pith core of xylem in the root Monocot Primary growth only both cortex and pith Stems Eudicot primary and secondary growth (mostly) vascular bundles in a ring pattern around cortex Monocot Primary growth only vascular bundles scattered around no pith or cortex Primary Growth Due to activities of Apical Meristems RAM and SAM Results in production of primary growth Secondary Growth Due to activities of lateral maristems vascular and cork cambiums Results in production of secondary tissues   Chapter 36 Overview of plant behavioral responses Behavior is a response of an organism to an internal or external stimulus types of plant behavior movement bending,twisting, or rotating nutation rapid movement as in sensitive plants response to touch growth seed germination seasonal production of reproductive structures defensive responses to attacks thorns, spines, chemicals Responses to internal and external stimuli Internal Internal biological clock circadium rhythms chemical signals transcriptions factors and other proteins or hormones often interact with each other and external signals External light atmospheric gases (CO2 and water vapor) temperature, touch, wind, gravity, water, rocks, and soil minerals Herbivors, pathogens, organic chemicals from neighboring plants, and beneficial or harmful organisms Plant Behavior Involves internal and external stimuli tropism growth response that is dependent on a stimuli that occurs in a particular direction Reception molecules located in plant cells sense stimuli and cause response Phototropism Growth response to light light causes movement of hormone auxin away from said light result in unequal distribution of auxin causing unequal cell elongation positive tropism Gravitropism growth response to gravity positive tropism roots negative tropism shoots columella cells in root cap/tip region sense gravity  Thigmotropism  Growth response to touch roots columella cells cause roots to grow around obstacles Regulation of plant growth Hormones chemical messengers that regulate plant growth most transported in phloem tissue all require an expenditure of energy on part of the plant (ATP) for transport interact with external environmental stimuli Hormones control growth seed germination flowering fruiting shedding of leaves color change of leaves Hormones of two broad categories growth inhibiting mostly fall/winter certain times of the year growth is not good growth promoting mostly spring/summer Auxins first group of plants hormones to be described growth promoting produced in shoot tips, seeds, fruits, leaves, stem NOT in the roots Effects of auxin Promotes cell elongation shoot elongation production of wood fruit development Inhibits lateral bud development absission (falling off) of leaves, flowers, fruits Cytokinins Originally detected in coconut "milk" growth promoting prodiced in seed, fruits, roots Effects of Cytokinins Promotes cellular division named derived from Cytokenesis Inhibits senesence change of color due to breakdown of pigments Gibberellins (giberellic acids) many types >200 more than any other group growth promoting found throughout the plant but concentrated in seeds Effects of Gibberellins Promotes stem elongation by cell division and cell elongation intake of water causes swelling and embryo hydration embryo secretes gibberellins gibberellins transported to cells of aleurone layer to secrete enzyme (alpha-amaylase) for breakdown of endosperm (starchy stored food) to glucose embryo will respire glucose to produce ATP embryo is directing the timing of plant germination Advantage seed plants Brassinosteriods growth promoting Effects of Brassinosteriods Promotes cell expansion shoot elongation xylem tissue development stress response Inhibits leaf abscission Abscisic Acids (ABA) Growth inhibiting found in large quantities in seeds. mature leaves, and dormant buds Effects of ABA Promotes senesence production of storage molecules in seeds Inhibits cell elongation alpha-amaylase production Ethylene growth inhibiting actually a gas produced by incomplete metabolism interacts with the 4 growth promoting hormones to determine cell size and shape Effects of Ethylene Promotes fruit ripening abscission of leaves, fruits, flowers Seed germination requires breaking of dormancy combination of internal and external factors Internal hormones stored food H2O absorption embryo swelling External sunlight temperature longer day light soil moisture Generalized Seed Seed coat(s) as seed coat cracks Radical comes out first then then shoot Seedling result of cellular reproduction and increase size internal development cells>tissues>organs>organism Chapter 37 Nutritional resources of plants Essential elements Play many roles in plant metabolism often function as enzyme factors Macronutrients required in amounts of atleast 1g per 1kg of dry plant mass Micronutrients trace elements required in amounts at or less than 0.1g per 1kg of dry plant mass Limiting factors resources that can limit plant growth too little or too much carbon dioxide water other mineral nutrients   Chapter 38 Transport of materials in plants Root system absorbs water and dissolved minerals from the soil Shoot system takes CO2 from the atmosphere via stomata Photosynthetic cells use these materials to produce organic compounds needed for growth and reproduction long-distance transportation occurs withing the plant body using a continuous system of conducting materials Xylem transport water and dissolved minerals Only goes up Phloem transports food and other solutes (hormones) Goes up and down Importance of water Photosynthesis support of plant organs conduction cell elongation most chemical reactions Average plant is 90% water Solvent for most substances Solution Solvent Solute Properties of water Polar molecule neutral Hydrogen bonding Cohesiveness Adhesiveness Temperature Stabilizer Transport medium Best biological solvent Occurs in all 3 forms of matter within earth's temperature range Principles of movement Bulk\Mass flow Mass movement of liquid cause by pressure and\or gravity Ex: leaching movement of ion though soil to plant roots Faster than diffusion Diffusion high concentration > low concentration Simple diffusion Movement of molecules through a phospholipid bilayer down a concentration gradient Facilitated  Diffusion transport of molecules across a plasma membrane down a concentration gradient with the aid of membrane protiens Osmosis"gatekeeper" Diffusion across a selectively permeable membrane in response differences in solute concentration simple diffusion of water does not occur rapidly enough for rapid expansion of plant cells Aquaporins protein channels that allow facilitated diffusion of water Tissue-level transport trans-membrane transport export of material via membrane proteins, followed by import of the same substance by an adjacent cell Ex. Auxin transport aided by carrier protiens Symplastic Transport Movement from cytosol of one cell to cytosol of another cell via plasmodesmata Cytosol Everything inside the cell wall Apoplastic transport  movement along cell walls and inter-cellular spaces Ex: water and disolved minerals Cellular water content water content of plant cells depends on osmosis, which depends on: Solute concentration Turgor preassure hydrostatic pressure that increases as water enters plant cells cell walls restrict the extent to which the cells can swell Turgid plant cell has cytosol full of water and plasma membrane pushes up against the cell wall Plasmolyzed cell has lost so much water that turgor pressure is lost and the plasma membrane no longer presses on the cell wall Water potential Potential energy of water Water moves from highest to lowest water potential affected by pressure solute concentration other factors (damage, temperature) Concept used in 2 ways to understand the movement of water into and out of cells (cellular water potential) to understand the movement of water between entire plants and their enviroments Water (and soil mineral) movement through the plant Transpiration Evaporation of water from plant surfaces "cost" for the plant to live on land capable of pulling water up by bulk flow primary form of long distance water transportation in plants Stomata Opening has 2 guard cells control balance of CO2, O2, and H2O inside leaf Xylem Flowering plant xylem consists of 4 types of cells Xylem parenchyma cells Thick-walled supportive fibers may be alive or dead at maturity  vessel elements Speacilized water conducting cells and are always dead and empty of cytosol when mature Wide tubes Tracheids tracheory elements Rich in lignin which offers strength, durability, and water proofing Narrow tubes Stomata Plants produce a waxy cuticle to prevent water loss stomata facilitate gas exchange  90% of water that evaporates from plants is lost through stomata when stomata are open, O2 and water vapor are released and CO2 is taken up controlled by guard cell pairs Mechanisms of Guard cells Daytime/sunlight CO2 is low in leaf Guard cells "pump" in K (potassium) Changes solute concentration H2O from xylem moves by osmosis onto guard cells cells become turgid Guard cells swell and open stomata CO2 diffusion into leaf "Pump" out K (potassium) H2O moves out by osmosis out of guard cells causing shrinking   Pumping Expenditure of ATP energy Causes of water loss Sunlight energy heats up leaf causing evaporating of H2O from mesophyll cells Causes a decrease in H2O concentration causing a "pull" of H2O This "pull" moves H2O though the "Transpiration stream" Transpiration Stream Soil H2O (and nutrients) root epidermis root cortex endodermis root xylem stem xylem leaf xylem mesophyll Vapor into atmosphere Unidirectional movement Only goes UP! C-A-T Mechanism Occurs once the stomata are open Purely a physical process "pull" of H2O one molecule at a time unidirectional movement C ohesion H2O molecules stick together   A dhesion H2O adheres to cellulose in cell walls T ension "pull" due to H2O loss from mesophyll NO ENERGY expended Only energy is sunlight heating leaf Solute movement in plants Translocation movement of solutes in plants food dissolved in H2O Moved in form of Sucrose Goes form Source to Sink Site with excess of carbohydrate Site where the carbohydrate is stored or immediately needed Bidirectional Long-distance transport in phloem Phloem transports sugars from where they are produced and\or stored to other sites where they are stored and/or needed Source > Sink Primary Phloem Occurs in the vascular bundles of herbaceous plants Secondary Phloem Occurs as the inner bark of woody plants  Phloem Structure Phloem of flowering plants in composed of supporting fibers , parenchyma cells , sieve-tube elements , and adjacent companion cells (members) Sieve-tube members (STM) are arranged end-to-end , and together with companion cells, form a system to transport soluble organic substances Sieve-tube members lose their nucleus and most of the cytoplasm to reduce obstruction to bulk flow phloem sap passes through sieve plate pores   Pressure Flow Hypothesis At source Companion cells "pump" sucrose into STM (STP expended) As sucrose concentration increases in STM, water potential (concentration) decreases within STM Adjacent Xylem has higher water potential than STM, H2O moves into STM by osmosis Bulk flow of Sucrose Higher Pressure > lower Pressure At sink Companion cells unload sucrose (ATP expended) Sucrose converted into starch for storage in root cortex Without sucrose, higher H2O potential in STM H2O moves from STM to adjacent Xylem by osmosis ATP spent only by companion cells at source (loading) and sink (unloading) Bulk flow (pressure/potential differences) and osmosis (H2O potential\concentration differences) No energy Expended Similarities Between Translocation and Transpiration Both involve conduction both involve physical properties of H2O Translocation Transpiration Phloem Bidirectional Must expend ATP energy by plant Xylem Unidirectional Sunlight energy (no expenditure by plant) Chapter 39 Reproduction in plants Most flowering plants display sexual reproduction Two gametes fuse to produce offspring with a unique combination of genes They undergo  Alternation of Generations Two multicellular life cycle stages diploid Spore producing sporophyte produces spores by meiosis a type of cell division that results in four daughter cells each with half the number of chromosomes of the parent cell, as in the production of gametes and plant spores. haploid Gamete producing gametophyte produces gametes by mitosis a type of cell division that results in two daughter cells each having the same number and kind of chromosomes as the parent nucleus, typical of ordinary tissue growth. Egg is Female Sperm is Male Evolutionary Trends in the Plant Kingdom Sporophyte has become larger, more complex Flowering plants Sporophyte independent  Dependent gametophyte is only a few cells contained within flowers Gametophyte has become smaller, less complex Moss Sporophytes small and dependent on gametohyte (Dominant form) Female 7 cells Male 2-3 cells Flower and Sexual Cycle Flowers ONLY in angiosperms All sizes, shapes, colors, and aromas Essential process of Sexual reproduction occurs within flowers Meiosis/cytokenesis reduces chromosome number Syngamy (fertilization) restores chromosome number "Ideal" Flower Uses highly modified leaves arranged in whorls (circular) at the tip of a highly modified stem A flower is a highly modified determinate (short term) shoot system Pedical, receptical, 4 sets of highly modified leaves are all 2N and part of the sporophyte generation Pollen (sperm) and eggs of embryo sac are part of the 1N generation Pedical flower stalk Recepticle tip of modified stem with 4 whorls attached Sexual Cycle Male Pollen formation occurs within the anther of stamen Anther Bilobed with 2 pollen chambers per lobe 2N microspore mother cell meiosis/cytokenesis 4 1N microspores Each: mitosis/cytokenesis unequal and incomplete 1N Generating cell 1N Tubecell Male Gametophyte Pollination Transfer of pollen from the anther to the stigma Self-pollination Transfer with the same flower or between flowers on the same plant   Cross-Pollination Transfer between  flowers of other plants Pollinating Agents Mechanisms utilized for transfer of pollen Wind small/lightweight pollen Water Transfer with a few aquatic plants Animals Majority of plants Utilized as a "trick and reward" system nectar, colors, and aromas to attract animals Female Ovule Development Ovule future seed Enclosed within the ovary of pistol  (carpel) One to many ovules per ovary ovary will become fruit Ovule attached to central axis or to wall of hollow fruit always enclosed angiosperms within ovule is 1 large 2N cell megaspore mother cell 2N megaspore mother cell meisos/sytokenesis 4 1N Megaspores 3 degrade 2N Functional megaspore Series of 3 mitosis/cytokenesis cycles Incomplete and unqueal 7-celled embryo sac 8 nuclei Female gametophyte   1N Functional megaspore 3 mitosis/cytokenesis divisions One cell with 1 nucleus becomes 8 nuclei but only 7 cells Embryo sac 8 nuclei, 7 cell structure female gametophyte 3 antipodal cells (1N) opposite end from micropyle 1 central cell with 2 large 1N polar nuclei 2 Synergids (1N) Micropyle end on outside 1 egg (1N) Middle at micropyle end Syngamy (fused gametes) 1N egg + 1N sperm = 2N zygote (single fertilized egg) Pollen grain germination tube cells form pollen tube (delivers sperm) generative cell divides by mitosis/cytokenesis to produce 2 sperm Pollen tube enters micropyle digests tube cell nucleus Pollen tube enters one synergid releases it's content (sperm) synergid ruptures mycropyle closes   "Double fertilization" (double fusion) 1N egg +1N sperm = 2N zygote 1N sperm +2 1N polar nuclei = 3N primary endosperm cell   Post fertilization with ovule 2N zygote grows by mitosis/cytokenesis into 2N multicellular embryo 3N primary endosperm cell grows by mitosis/cytokenesis into 3N multicellular endosperm nutrient tissue for embryo   Ovule/ovary with 2N zygote  mature/enlarges with sugars/H2O into a fruit (mature ovary) with enclosed seeds (mature ovules) Seed dispersal (seeds enclosed withing a fruit) agents wind water animals - majority Seed germination Seed with 2N embryo enters period of dormancy dormancy broken by a combination of internal (hormones) and external factors (environmental) radical (first root) emerges and grows down shoot emerges and grows up Exam 3 - Notes Chapter 40 Intro to Animal Structure(Form) & Function Key concepts organization of animal bodies the relationship between structure and function homeostasis All Animals: Share similarities in the ways in which they: Exchange materials with their surroundings Obtain energy from organic molecules synthesize complex molecules reproduce themselves detect and respond to signals in their immediate surroundings Levels of Animal Organization Cellular Phylum Porifera Tissue Phylum Cnidaria  Phylum Ctehotophora Organ System All advanced animal groups Internal Organization of Animals Cells with similar properties group together to form tissues Tissues combine together to form organs Organs are linked together to form organ systems Organ Systems form an organism Tissues Tissue An association of many cells that have a similar structure and function Types Epithelial tissue Connective tissue Muscle tissue Nervous tissue Epithelial Sheets of densely-packed cells that: cover the body or enclose organs line the walls of the body cavity and organs Specialized to protect and secrete/absorb ions and organic molecules cells have a variety of shapes   cuboidal squamous columnar arranged to form different types of tissues simple one layer stratified multi layer pseudo-stratified one layer, but appears stratified All are asymmetrical or polarized One side rests on the basal lamina (basement membrane) the other faces the environment Types of Epithelial Tissue Simple squamous one layer of flat cells Simple cuboidal one layer of square cells Simple columnar single layer of rectangular cells Pseudo-stratified columnar 1 cell thick with all at basement barrier Stratified squamous multi-layered flattened cells Transitional stretchable tissue All may be involved with secretions/absorption/protection Connective tissues Connect, surround, anchor, bind, & support For extracellular matrix (ECM) around cells provides scaffolds for attachment protects and cushions mechanical strength transmit information transport Types of Connective tissue Blood transport and protection adipose (fat) insulation, protection, support, and storage bone support, protections, and movement cartilage support and flexibility loose connective tissue holds internal organs in place dense connective tissue strength and support Muscle Tissues Cells specialized to contract, generating mechanical force Types of muscle tissue Skeleton muscle attached to bone(via connective tissue) or exoskeleton for locomotion elongated fibers voluntary control striated Smooth muscle surrounds tubes and body cavities for propulsion of contents flattened cells involuntary control cardiac muscle only in the heart elongated fibers involuntary control striated branched Nervous tissue complex networks of neurons (nerve cells) initiate and conduct electrical signals from one part of the body to another electrical signals produced in one neuron may stimulate or inhibit other neurons initiate new electrical signals stimulate muscle cells to contract stimulate glandular cells to release chemicals also contains neuro-glial cells more numerous than neurons provide metabolic support, maintenance, ion balance, and cleaning for the neurons Organ Systems 10 organ systems that we will cover (not in this order) Structure and function organization of structure(form) can predict the function of a structure we will concentrate of the increasing complexity of structural(form), and thus the increasing complexity of organismal function most emphasis on vertebrates Homeostasis changing variables in environmental: air temperature water temperature food supply water supply pH O 2  Concentration Process of adjusting to the external environment and maintaining a stable internal environment Integumentary System Apparently there is no chapter/section for this in the book? Integument the skin and all accessory structure (hair, feathers, scales) Skin The largest vertebrate organ major part of the integument system Vertebrate integument and derivatives Functions Protection form abrasion protects against water loss barrier to disease causing pathogens protection from UV light temperature regulation contains sensory receptors excretion (limited) Vertebrate Integument skin and all other accessories skin is the largest organ o vertebrates skin consists of 2 layers epidermis dermis Epidermis outer layer nutrients diffuse into the epidermis form the dermis stratified squamous epithelial cells Cell types langerhans cells defensive cells Melanocytes produce pigment melanin skin coloration protect form UV light Merkel cells touch receptors Keratinocytes primary cell type produce insoluble protein Keratin amount of keratin increases from the inside to outside keratin fill cytoplasm and impairs nutrient diffusion, cell dies Dermis Inner layer of skin thinner than dermis highly vascularized contains: sensory structures vessels nerves glands Origin of hair/scales/feathers in vertebrates Sensory structures Meissner's corpuscles light touch Pacinian corpuscles deep vibrations Sweat Glands temperature regulation produce sweat (primarily water) evaporating cooling release of waste ions 2.5 million on the body release of heat Sebaceous Glands all over body, except palms and soles large on face, neck, and upper chest produce sebum lubricates and soften hair and skin water proofing in aquatic mammals Hypodermis subcutaneous layer below the dermis not a layer of the skin contains much adipose (fat) tissue females have thicker layer of adipose tissue than males Function body contour insulation support the skin Chapter 45 & 46 Digestive System Key Concepts Animal nutrition general principles of digestion and absorption of food overview of vertebrate digestive systems mechanisms of digestion and absorption in vertebrates Intro to nutrition nutrient any substance taken in by an organism that is needed for: survival growth development tissue repair or reproduction nutrition process of consuming and using food for nutrients animals receive nutrients by consuming food Dietary categories basic similarities in organ system function lead to similarities in nutritional requirements different animal physiologies can have different nutrient demands   Herbivores eat only plants digestive system contains micro-organisms that help digest cellulose Carnivores eat only animal flesh or fluid  Omnivores eat both Animals are heterotrophic Heterotrophs ingest feeders cannot manufacture more food require already synthesized organic compounds of plants of other animals to supply materials survival maintenance growth reproduction Gut Tracts Two types Blind Gut no cavity between gut and body wall one opening primitive form tube-within-a-tube flow through digestive tube body cavity between git and body wall separate opening (mostly) Digestion the breakdown of large molecules into smaller ones Digestive enzymes (hydrolases) carbohydrases proteases lipases nucleases Food processing in animals Occurs in Five phases Ingestion food is taken into the body and moves into a digestive digestion food is broken down into smaller molecules chemical and mechanical transport absorption ions, water, and small molecules are transported into the circulatory system egestion undigested materials and other waste are passed from the body elimination or exceretion Alimentary canal digestive tract or tube Gastrointestinal tract Five regions of food processing Single tube with opening at each end contains smooth muscles in walls lined with epithelial cells synthesize and secrete digestive enzymes secrete hormones transport digestive materials several specialized regions different structures for different processes storage area Structure of GI Tract some general structure from midpoint of esophagus, to the anus or cloaca lumen lined by epithelial and glandular cells  secretory cells release a protective layer of mucus other cells release hormones glands release enzymes, acids, water, and ions Epithelial cells linked by tight junctions and surrounded by layers of tissue made of smooth muscle, neurons, connective tissues, and blood vessels neurons activated by sight and smell of food and presence of food in tract Region of Reception Buccal cavity mouth and accessory structures ingestion site and digestion site chemical and mechanical jaws, teeth, cheek muscles, tongue, and salivary glands (saliva) Pharynx back of mouth cavity point that respiratory and digestive system cross paths Region of Conduction Esophagus tube carrying materials from mouth cavity to the rest of the alimentary canal forces/pushes good down conducts food from pharynx to stomach Peristalsis rhythmic wave-like contractions which propel food forward in the GI tract No new digestion here only chemical continuation from buccal cavity Region of digestion and storage Stomach (mostly) saclike organ evolved for storing food muscular nature helps break up food partial protein digestion regulates rate of emptying into small intestine Secretions hydrochloric acid kills microbes dissolves particulate matter secreted by parietal cells Pepsinogen converted to pepsin to begin protein digestion secreted by Chief cells Epithelium coated with an alkaline mucus carbohydrate digestion continues from mouth little lipid digestion happens lumen (cavity) stomach pepsinogen + HCL -> pepsin (for protein breakdown) Region of terminal digestion and absorption Small intestine near Chapter 41 - 43 (mostly 41) Nervous System Chapter 44 Musculoskeletal system