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Bio 2217 lecture notes Midterm 1

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Biology 2217B
Richard Gardiner

Lecture 1: - botanist: study of plant structure physiology photosynthesis, mycology/ fungi, bacteriology, phycology/algae, plant genetics, plant pathology, ecology, biotechnology, forestry, agriculture - Economically important: grasses, beans, starch plants, fibre plants (cotton), oil plants, wood producers, medicinal - Plants can move in response to stimuli, ex: vines, leafs on plants - Resurrections plants: dry up into tight ball, add water and it will grow very fast - Predators: Venus fly trap (leafs are lined with special hairs, traps snaps shut and captures insect and digests it), sundew (hairs with mucus where insects get stuck, hairs hold it there), pitcher plant (insects fall inside and drown, like a well) live in areas low in phosphorus and nitrogen (bogs) - Stranglers: bind weed, kudzu, grow fast and around other plants and choke them out - Poisonous: hydrangea (vomiting, weakness, sweating, coma), lily of the valley (nausea, vomiting, heart palpitations), chrysanthemum (keep rabbits away), Narcissus (don’t eat the bulbs) - Vampires: mistletoe (stem parasite, phloem of plant and gets its nutrients from plants, stem parasite, hemi parasite, poisonous) - Lichens and fungi are not plants- lichens have symbiosis of fungi, indicator of sulfur dioxide sign of pollution, can eat fungi - Scifi plants: triffids, killer tomatoes, the thing, pod people, trouble with lichens - For Tuesday: textbook chapters 1,8 (118-128), 9 (134-136) Textbook: Chapter 1: - green plants, especially flowering plants, are more than just landscaping for the planet, since they supply humanity with all the essentials of a life: food and oxygen as well as other products that have shaped modern society - The algae are an extremely diverse group of photosynthetic organisms that are key producers in aquatic food chains, a valuable source of human food, and the base for a number of commercial and industrial products - Fungi are also an economically important group of organisms affecting society in numerous ways, from fermentation in the brewing process to the use of antibiotics in medicine to their role as decomposers in the environment and as the cause of many plant and animal diseases - All living organisms share certain characteristics: growth and reproductions, ability tom respond, ability to evolve and adapt, metabolism, organized structure and organic composition - The processes of life are based on the chemical nature and interactions of carbohydrates, lipids, proteins and nucleic acids - Food is made through photosynthesis by producers in the food chain, and consume d by primary or secondary consumers - Flowering plants (angiosperms): consists of sepals, petals, stamens and one or more carpels, the latter two are involved in sexual reproduction, monocots (lilies, grasses, palms, orchids), dicots (geraniums, roses, tomatoes, dandelions, most broad leaved trees) - Non flowering plants: seed-bearing but do not form fruit, gymnosperms (cones, conifers), - algae: photosynthetic organisms, base of food chain, algal blooms- sudden population explosions are related to nutrient pollution and produce toxins - Fungi: molds, mildew, yeast, mushrooms, cause plant diseases as well as benefits to society, threadlike body (mycelium), reproduce by spores, nonphotosynthetic, get nutrient from decomposing matter (saprobes, parasites), decomposers - Scientific method: observation, hypothesis, hypothesis testing - Fundamental properties of life: 1. Growth and reproduction: growth is an irreversible increase in size, reproduction (production of new individuals) can occur sexually or asexually 2. Ability to respond: environment is always changing and organisms must be able to respond 3. Ability to evolve and adapt: evolve or adapt to the environment in a way that promotes survival 4. Metabolism: sum of all chemical reactions, cellular respiration and photosynthesis 5. Organized structure: unicellular or multicellular, prokaryotic or eukaryotic 6. Organic composition: carbohydrates, proteins, lipids, nucleic acids - Carbohydrates: sugars, starches, cellulose, monosaccharide (glucose, fructose), disaccharide (sucrose, maltose), polysaccharides (starch, glycogen, cellulose), composed of hydrogen, carbon and oxygen - Proteins: large, complex macromolecules composed of amino acids (20 of them with N-C-C backbone) which bind together to form polypeptides, enzymes, structural molecules, regulatory molecules, transport molecules, etc - Lipids: composed of carbon and hydrogen, insoluble in water, triglycerides (sources or energy, fats, oils), phospholipids (structural components of cell membranes) waxes, steroids (hormones), cholesterol (structural components of cell membranes) - Nucleic acids: contain carbon, hydrogen, oxygen, nitrogen and phosphorus, composed of nucleotides (ribose or deoxyribose, phosphate group, nitrogenous base- purine (adenine/guanine) and pyramidine (thymine, cytosine, uracil)), ex: DNA, RNA Chapter 8: - Scientific names are two word named. Called binomials that are internationally recognized by the scientific community - Carolus Linnaeus, an eighteenth century Swedish botanist, started the binomial system and is therefore known as the father of taxonomy - With the publication in 1859 of On the Origin of Species, Charles Darwin proposed that species are not static entities but are works in progress that evolve in response to environmental pressures - Natural selection favours the survival and reproduction of those individuals in a species that possess traits that better adapt them to a particular environment Lecture 2: - split into three large groups: bacteria, eukaryotes, archaea - Plants: develop from an embryo, indeterminate growth, no nervous system, sedentary, alternation of generations - What is a plant: - Aquatic environments: in water, sperm swims, not dry, supported by Bianca, absorb nutrients, float near surface for light - Land environment: need to absorb minerals, fight gravity, grow higher for more light, adaptations for dry environments, reproduction differs (different strategies to exchange gametes), roots to anchor and absorb nutrients, water transport system, water loss systems, pollen and seeds - Alternation of generation: plants can exist as a diploid or haploid, - Evolutionary trend from haploid to diploid: sporophyte is living off gametophyte, easy for one or the other to get destroyed then reproduction gets messed up, gametophyte in flowering plants (ovum and pollen) is protected by sporophyte (plant) - What is in a name: genus species, convolvulus arvensis (bindweed, field bindweed, common bindweed, small bindweed, morning glory, liseron des champs) - Latin names are not obtuse, same everywhere in the world, always written in Latin, we can know a specific plant name written anywhere on earth, don't worry if you can't pronounce it, as long as you can read it ( not italics) - International code of botanical nomenclature: uniqueness (only one correct name for any group), type principal (specimen deposited in herbarium), priority (first name counts), authorities (certain letters follow a name, first time you mention a species you have to put the authority after, oryxopsis exhua Thurber, etc, name in brackets mean a change has been made since original naming) - Domain (eukarya)- Kingdom (plantae) - division (-phyta) - class (-opsida)- subclass (-ae), order (-ales) - family (-aceae) - genus- species - Tables 8.1,8.2,8.3 can be names for person, shape, colour, use, characteristics, location, season, etc - Classification systems: magnoliophyta (angiosperms or flowering plants), magnoliopsida (dicot), Linux (flax), liliopsida (monocot). APG system (Clade monocots), APG II, APG III, bessey system, cronquist system (flowering plants, class liliopsida), Melchior system (class monocotyledoneae), etc - Retention of embryo: fertilized egg develops into multicellular embryo in female gametagium, the embryo is protected during development, in algae the fertilized egg develops away from gametagniuim - Stomata: allow for gas exchange and control of water loss, needed for larger multicellular structures that leaves became - Vascular tissue: specialized vascular tissue for support and conduction to all parts of the plant, xylem conducts water, phloem conducts carbohydrates, allows for larger growth - True leaves: thallus not differentiated into leaves, stems or roots, arose as fusion of small branch stems, specialized organs of photosynthesis, designed to collect light efficiently under varied conditions - Spores not seeds: germinate to produce thallus, very limited capacity to store nutrients so doesn't help germinated plants - Seeds: spores (haploid reproductive untie that give rise to gametophytes), seeds (an important adaptation for life on land, embryonic sporophyte plants, nutritive tissue and protective coat, superior to spores (seed has well developed young plant, seed contains abundant food supply, multicellular seed coat allow seeds to survive extended periods - Gymnosperm: naked seed (not in fruit), seeds are totally exposed or borne on scales, no ovary wall surrounds them - Angiosperms: seed is enclosed in a vessel or case, seed produced in a fruit, ovules enclosed within an ovary, interdependence on insects, birds and bats to pollinate, better developed vascular system - Mosses and liverworts (Bryophyta and others): mosses, liverworts, homeostasis, non vascular, typically small, river edges (shaded moist areas), swimming spermatozoa, dominate stage is gametophyte, reproduce via spores, peat moss, not as economically important but still unknown, 15000 species - Ferns and fern allies (pteridoohyta and others): club mosses, ferns, horsetails, vascular, reproduce via spores, swimming sperm, separate gametophyte (n) and sporophyte (2n) in ferns, 13000 species - Gymnosperms (coniferophyta): vascular, male And female gametophytes, reproduce via naked seeds, pollen allows for not needing water for reproduction, conifers, cycads, ginko, gnetophytes, 980 species - Flowering plants (magnoliophyta): vascular, male and female gametophytes, repduce via seeds, seeds are enclosed within an ovary (fruit), the flowering plants, earth's dominant form, 200000 species - Read chapter 8 Lecture 3: - cell walls with cellulose, main vacuole, Plasmodesmata (passage through the wall), chloroplast - Plasma membrane: fluid mosaic model, lipid bilayer, inner and outer surfaces differ. System boundaries that mediate transport, synthesis and assembly of cell wall microfibrils, plasma membrane decides what goes in and out, synthesis and assembly of cell wall microfibrils - Cells have polarity - Cytoplasm: material surrounding nucleus, bordered by plasma men, always in motion (cytoplasmic streaming- can be seen moving of chloroplasts, actin and myosin and microtubules, facilitates exacted of materials, - Nucleus: controls ongoing activities of the cell, repository if the cells genetic information, porous double membrane (complexes), filled with nucleoplasm (enforced with skeleton), continuous with ER at several functions, haploid (n), diploid (2n), polyploid (3n, 4n, 5n, etc), plants accept higher ploidy better, chromosomes with chromatin (DNA + proteins), nucleolus (RNA + proteins) - Plastids: organelles (chloroplasts, Chromoplasts, leucoplasts), characteristic of plant cells, double membrane,p (storms, thylakoids used in photosynthesis), Semiautonomous organelles (endosymbiosis), nuceloids, small genome, 70s ribosomes, mesophyll cells, not in xylem or phloem - Chloroplasts: photosynthesis (chlorophyll, carotenoids), variable number (3-300), broad surface parallel to cell wall, starch granules active tint photosynthesis, not in dark plants, thin structure loaded with chloroplasts, numerous copies of DNA (100 proteins encoded) - Leaf: upper and lower epidermis, spongy mesophyll with air space for gas exchange, veins contain xylem and phloem to carry things in and out, stoma on bottom control gas exchange and water loss - chloroplast has thylakoids that stack and increase surface area for photosynthesis, ribosomes and copies of DNA, amount of grana and thylakoids can change as well - Other plastids: proplastids or eoplasts (small, colourless and undifferentiated), all plastids in adult plant derived from a single parent (identical genome, binary fission, asexual) - When not exposed to light it loses it's pigment and is called an etioplast, petal of plasma has pigment (no photosynthesis) it is luekoplast, proreinoplast store protein, amyloplast have starch and elaioplast stores lipids, statolith move down towards gravity and are sensed by the cytoskeleton and tells the roots where to grow - Chromoplasts: carotenoids pigments (yellow, orange, red), flower colour, autumn leaves, fruit, loses thylakoids, chlorophyll, rRNAs, ribosomes, storage - Leucoplasts: uniform, colourless stroma, roots and other non-photosynthetic tissues (starch storage- amyloplasts, proteins- proteinoplasts, fats- elaioplasts), potatoes have a dingle starch grain - Mitochondria: cell respiration (ATP), smaller than plastids (0.5um in diameter), double membrane, inner convoluted (cristae for maximum surface area), matrix, in constant motion, one or more circular chromosomes, semiautonomous, maternally inherited - Be able to recognize mitochondria and chloroplast on a EMG - Vacuoles: unique to plants (May have more than one type, storage, lyric compartmented, multifunctional organelles, diverse in size, content and function), tonoplast, can be used to store metals/ waste, meristematic cells contain small vacuoles that later fuse, 90% volume in mature cell, consists of cell sap (water), storage compartments, likely form ER (endomembrane) - Ribosomes: 17-23 nm in size, protein and RNA synthesis, small and large subunits (polysomes), most numerous cellular structures - Endomembrane system: all cellular membranes, continuous 3D membrane system (permeates cytosol), internal space (lumen) - Cytoskeleton: 3D network, microtubules (structural integrity), actin/myosin - Cell wall: distinguishes plant from animal cells, characterizes plants, determines size and shape of cell, cell types identified by their walls, plays a role in defence, cellulose in microfibrils (4-10nm, wind together to macrofibrils, tensile strength approaches that of steel), embedded in a matrix of polysaccharides (ex: pectin), walls vary in thickness - Solute transport: apoplastic (through cell walls and intercellular spaces, doesn't cord the plasma membrane, faster due to less resistance) or symplastic (travels through cytoplasm through Plasmodesmata, doesn't cross plasma membrane after entering root) - Plasmodesmata: cytoplasm strand connecting cells, cell to cell passage, analogous to gap junctions in animal cells, cell wall creates symplastic and apoplastic (interconnected protoplasts form continuum), need for connections between cells but diseases can be passed through them - Cell cycle: ordered sequence of events from dormancy to division, most plant cells uninucleate - Mitosis in plants: similar to animal cells, most higher plant cells do not contain visible centrioles, an analogous region of hype plant cell acts as the microtubule organizing centre (MTOC) - Know differences between types of organelles Lecture 4: the plant body • Root system: normally underground, dark, moist, woody, gathering water and nutrients • Shoot system: aerial position, illuminated, relatively dry, herbaceous (does not develop woody parts), leaves, stems, petiole, etc • Annuals: herbaceous, grow reproduce and die in one year, many flowers • Biennials: 2 years to complete life style, carrot, potatoes • Perennials: woody or herbaceous that live more than 2 year, tree • Meristems produce three types of tissues: dermal, ground and vascular tissues, found in apical tips, cambium is found in woody growth (secondary xylem) • Epidermis: outer layer of cells covering entire plant body, roots, SMS, leaves, flowers, fruits, seeds, not on root cap, different on apical meristem, usually just one layer of cells, on aerial parts of plant (reduction if water loss, mechanical protection, gaseous exchange/ stomata, complex composed of many cell types, photosynthesis does not occur in these cells • Can peel leaf in half (epidermal peel) to stain it and view under microscope • Leaf hairs tricombs? Predation, break up wind, secretory • Ground tissues: parenchyma, collenchyma, sclerenchyma, bulk of herbaceous plants, distinguished by cell wall structure, growing cells secrete a primary cell wall. Some cells later secrete a secondary cell wall between primary wall and plasma membrane • Parenchyma: undifferentiated precursors of all cells, involved in photosynthesis, respiration, storage and secretion, able to resume meristematic activity (wound healing) • Cell shapes vary, space between parenchyma cells, meristematic may differentiate into phloem, companion cell, fibre cell, • Collenchyma: elongated cells with thickened primary walls, may contain chloroplasts, thick walked type of parenchyma cells specialized for support, may become meristematic • Sclerenchyma: cells with secondary walls, mechanical support, dead when mature, May for singly or in groups, May retain protoplasts at maturity, Divided into two categories, Fibres and sclereids • Fibres: long cells, usually in strands, tensile but elastic • Sclereids: short cells, strongly lignified, maybe clustered or isolated, stems, leaves, fruits, seeds • Vascular tissue: embedded in ground tissue (parenchyma, etc.), transport materials throughout plant • Xylem: water and nutrients from roots to stems and leaves, no pump operates on system that relies on osmosis and transpiration, air bubble-cavitation will never clear • Xylem cell types: tracheids (in all woods, the only conducting cells in gymnosperms, long tapering, with spiral thickening, simple or bordered pits), vessel elements (in most angiosperms, shorter, wider than tracheids, stacked to for a conduction tube, end walls are perforated or lacking a maturity), fibres (in all woods, slender, tapering, with thickened/ lignified walls for strength and support), parenchyma (In all woods. Thin-walled, undifferentiated in living cells. Storage, or radial transport (in rays)) • Phloem: food nutrients throughout the plant (source to sink) • Phloem cell types: sieve tube members (living but with degenerate nucleus, cylindrical, somewhat thick walled with porous and oblique end walls/ sieve plates, stacked to form a conduction tube), companion cells (thin yelled with enlarged nucleus that runs the adjacent sieve tube element) • Picture of vascular tissue • Root system: fibrous (many separate roots from plant, grasses and taproot (central root) • Root structures: Pericles is tissue, between the endodermis and the phloem can be meristematic, root picture • Leaves: most variable plant organ, leaf characteristic of species on which is grows, composed of blade (broad flat portion) and petiole (stalk that attaches stem to blade), may have stipules (small, leaf-like structures at base), sessile leaf lacks a petiole (grasses), simple, compound, different arrangements • Simple or compound, alternate, opposite or whirl • Leaves vary in size cm to m Lecture 5: wood and forest - Wood: secondary xylem (formed by herbaceous perennials and some annuals), wood is related to how lands grow in girth, accomplished by special meristems called Cambia (cambium), vascular cambium (vascular tissue) and cork cambium (tissues to replace epidermis) - Trees in the plant kingdom image - Coniferophyta are used for economical reasons, other ones are not - New growth occurs as a sheath covering the main stem, branches and twigs - Wood formation image, from apical meristem - Around pith are areas of xylem, around edge we have formation of new xylem and phloem , triangular because of phloem rays get pulled a bit on the outside, old phloem is crushed into bark so it isn't seen as much as xylem - Heart wood (can be stained colour, empty xylem, very feel living cells), sapwood (has the xylem, activity growing, has flowing of movement) - hardwood, sapwood (xylem), cambium, phloem, outer bark - Wood is useful because it is make out of cellulose which is impermeable to breakdown, microorganisms are the only ones that can break it down, - Cell wall has cross hatching of cellulose microfibrils, amorphous regions are spun into fibre - Cellulose microfibrils synthesized at plasma membrane - Cell wall polysaccharides by dictyosome - Polysaccharides are secreted to wall by fusion of membrane vesicles to plasma membrane - Secondary wall is on the inside of cell - Secondary walls: many plants synthesize secondary walls after the cell has reached maturity (elongated), Bulk of woody plants, tracheary elements develop reinforced cell walls that can form a variety of patterns - Bark: cork cambium (dead, impermeable layer, cork, phelloderm/ epidermis, periderm, complex layers), also contains the secondary phloem, vascular cambium (secondary phloem and xylem) - Xylem does not carry dissolved gases (oxygen), tree is not green with stomata to dissolve gases so we use - Lenticel: area that allows gases to be exchanged, area looks like its burst, between pieces of bark - Can tell the environmental conditions based on rings- rings that are close together means that there is a dry spell, wider rings show good growth, fired are super close together, read in textbook - Cross sections: radial. Transverse, longitudinal - Cutting it different ways can see the grains for different purposes, - Wood use: strip bark, rounded sides/ slabs are sent to chipper, outer portions/ clear lumber are made into boards or planks, centre of log as more knots, this is made into heavier planks and beams - Pick the wood for the purpose: • White pine: soft, uniform wood, home and boar construction, easy to work with • White oak: hard, dense, waterproof wood, in barrels and some flooring • Hard maple: hard, uniform wood, bowling pins and alleys, croquet mallets • Bed cypress: softer, weather-resistant wood, used in railroad ties and water tanks • Black walnut: very hard wood, used in fine furniture • White ash: hard, straight grained wood, used in baseball bats, tennis racquets, oars and tool handles - Hardwood and softwood: forestry terms, hardwood comes from braodleaved deciduous tress (angiosperms, dicots, maple, birch, oak, aspen), softwood comes from coniferous tress (pines, Douglas fir, western red cedar, hemlock are all mostly used in construction; spruces and fir as pulp (some spruce in construction) - Hardwood: angiosperms with vessels, May form in prominent rings, ring porous (oaks and ashes, form larger vessels in sporting wood and much smaller ones in summer) or ring diffuse (maples and birches, form rings of approximately even size throughout the growth cycle), Some rings (e.g. poplars and willows) are so small you must look for them with a hand lens, In rare cases, vessels may be lacking (e.g. Drimys) - Softwood: gymnosperms that lack vessels, wood (self day xylem, contains tracheids-90% fibres and parenchyma), May contain resin ducts which are flowing Sao or pitch that helps prevent fungal decay and defends against woodeating arthropods) - Plywood: a multi layered wood sandwich, each layer with its longitudinal grain running at right angles to the last grain for increased strength, cheap woods may be used I'm the interior while better ones are used for outside, particle board (chip boards, glued together, inexpensive furniture), Medium density fiberboard (MDF, Often covered in veneer with multiple coats of tough paint for cabinetry), Oriented strand board (OSB, Used in subflooring or roofing) - Aspen poplar is used for matches, disposable chopsticks and paper pulp - World land use: industrial timber and unprocessed logs account for about half of worldwide wood consumption, developed countries produce less than half of all industrial wood, but account for about 80% of consumption, Fuelwood accounts for the other half of worldwide wood consumption - Tropical rainforests: despite occupying less than 10% of earth’s land surface, tropical rainforests are thought to contain: More than two-thirds of all higher plant biomass, At least one-half of all plant, animal, and microbial species in the world, High productivity (NPP) means they are globally important in removing CO2 from air - Deforestation: global deforestation is approx 13M ha/y, estimate 0.8% of remaining tropical forests is cleared yearly, Brazil has largest rainforests, and highest rate of deforestation, Deforestation of African rainforests also a great concern for conservation biologists, Even our (and Russia’s) huge boreal forests, are shrinking fast, with wildlife consequences - Oak:Quercus sp., Approx. 400 species worldwide, white and red, Spiral arranged leaves, fruit is a nut (acorn), deciduous and evergreen species, found in northern hemisphere northern hemisphere, heavy, strong (great strength and hardness), light coloured hardwood, national tree of England, Estonia, France, Germany, Moldova, Latvia, Lithuania, Poland, the United States, Basque Country, Wales, Bulgaria, and Serbia. - Maple: Acer sp., 125 species of maple, Latin word meaning "sharp", referring to the characteristic points on maple leaves, Most native to Asia, So hard and resistant to shock, that it is often used for bowling alley floors. - Mahogany: Meliaceae, or the Mahogany family, Native American wood, tropical hardwood indigenous to Central and South America and Africa, Boat production, instruments, furniture - Cherry: Genus Prunus, Genus of trees and shrubs, which includes the plums, cherries, peaches, apricots and almonds, 430 species spread throughout the northern temperate regions of the globe, Eastern half of the U.S.. It is sometimes called fruitwood, A moderately hard, strong, closed grain, light to red-brown wood brown wood - Walnut (genus juglans): 21 species in the Genus, one of the most versatile and popular cabinet making woods, Grows in Europe, America and Asia. Strong, hard and durable, without being excessively heavy, - Pine (genus pinus): Between 105 to 125 species worldwide. Softwood which grows in most areas of the Northern Hemisphere, soft, light, white or pale yellow. Straight grained and lacks figure. Resists shrinking and swelling. - Cedar (genus cedrus): 4 species, native to western Himalaya mountains and the Mediterranean region, several species grow in the southern US, central and South America,. Knotty softwood with a light streaked red-brown colour, its aromatic and moth repellent qualities make it a popular wood for lining drawers, chests and boxes - Spruce (genus picea): 35 species, Strong and hard. Low resistance to decay. Moderate shrinkage and light in weight. Used for masts, spars for ships, aircraft crates, boxes, general millwork and ladders Plant fibres: • many economically important products, such as paper, rope and textiles, are derived form plant fibers • Long cells with tapering ends and very Long cells with tapering ends and very thick, heavily lignified cell walls. •
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