concept of plant blindness

plants carry importance via

• agriculture/consumption
  • basis of all food chains → primary producers
  • primary producers photosynthesize solar heat/energy into chemical energy as sugar
  • primary producers include many algae and bacteria
• sheltering (material culture)
  • shelter via wood
  • generally things are made out of materials derived from wood or other plants
• medicinal
  • plant-based medicines (aspirin originated from willow plants)
  • different chemicals used than those in food/consumption (sugar, starch, proteins vs.)
  • consumption chemicals are primary chemicals
  • medicine, toxins, and flavors are secondary chemicals and not part of major biosynthetic pathways
    • cinnamons, basil compounds
• ecosystem services: purification, water estuaries, erosion prevention, etc.
  • services which provide a monetary/chargeable value
  • global warming and prevention of global warming
    • use of carbon dioxide in photosynthesis and removing it from the overall ecosystem

phylogenetic review

• plants and algae are primary producers; fungi are decomposers
• monophyletic groups/clades
• biological classification system:
  1. domain
  2. kingdom
  3. phylum
  4. class
  5. order
  6. family
  7. genus
  8. species
• maintained due to some reasons such as endangered species act (unable to remove the species definition)
• species: an evolutionary lineage/line
  • biological species definition: a species is reproductively isolated and only is able to reproduce with its species and not other groups/species
  • plants falter under the biological species definition; plants can often produce fertile hybrid offspring (vs. sterile hybrid offspring in animals)
    • hybrid swarms can occur
    • hybrids can back-breed
  • bacteria cannot breed sexually
  • main definition is on an evolutionary line; vaguer definition here

land plants

• four informal groups of land plants
• overarching plant groups: nonvascular and vascular plants
  • non-vascular: bryophytes
    • liverworts, mosses, hornworts
  • vascular has two subgroups
    • seedless vascular plants
      • lycophtes (club mosses, spikemosses, quillworts)
      • monilophytes (ferns, horsetails, whisk ferns)
    • seeded plants
      • gymnosperms and angiosperms
      • angiosperms are flowering plants and the most familiar often
• non-vascular plants are tiny and lack vascular tissues (“plumbing systems”, veins, water/sugar/mineral transport systems)
  • limited and small
  • live in wet areas; sperm must flow through water and moist areas (flagella)
• seedless vascular plants have a water transport system but do not reproduce via seeds
  • reproduce using spores
  • live in wet areas; sperm must flow through water and moist areas (flagella)
• seed plants do not need to be restricted to moist/wet areas
  • seeds have embryos and sperm + food package and covering
  • seeds lack flagella and do not need to swim
  • often evolutionary advantageous
• gymnosperms: “naked seed plants”
  • gymno- refers to “being naked”
  • seeds are not enclosed in fruit or larger coverings; seeds are exposed
• angiosperms: flowering plants
  • angio- refers to “container”
  • fruit is the vessel/container
  • both flowers and seeds are present in fruits

angiosperm morphology

• flowering plant form
• morphology is the study of form

non-reproductive morphology

• composed of 3 primary plant organs
• roots usually grounded/underground
  • forms a root system to absorb water and minerals
    • including common nutrients such as nitrogen, phosphorus, calcium
  • anchors the plant and keeps it in place
• above-ground organs include leaves and stems
• leaves have two specific components
  • blade: flat, expansive section
  • petiole: thin, skinny “stem”
  • primarily used in photosynthesis
• stems
  • hold up leaves and often make leaves or part of what we think makes up leaves
  • several regions
    • leaves attach at the stem nodes
    • internodes are sections between nodes/leaf nodes
• leaves and stems make up the shoot system
  • the end of the plant opposite of the roots: “shoot tip” or “terminal bud”
  • axil: the angle of the region between a leaf and the stem
  • axillary/apical bud: the bud structure present at the axil
    • growing points with a specific arrangement
• simple vs compound leaves
  • depends on the subdivision of the blade into leaflets
  • in both there is not the presence of multiple axillary buds; only at the base of the leaf
• phenotypic/developmental plasticity
  • leaves may differ in form due to their environment, temperature, function, amount of sunlight received, etc. even though they have the same genes
  • organs may be modified (onion leaves/stems)
• stems are necessary organs for the plant
  • stems can be green, photosynthetic, underground, etc.
  • not the normal function, but is possible

meristems

• a group of cells usually undifferentiated (or deemed separate types of cells) that can perform cell division
• equivalent of stem cells; no stem cells in plants
• growing regions of plants
• two kinds of meristems
  • apical meristems are always present; must exist for a plant to exist
    • exists in all buds, root tips
    • lengthen plants; increase height/depth
    • tissue formed is primary tissue or the primary plant body
  • lateral meristem are not always present, but optional; two subtypes
    • cylindrical, not pointed
    • occur on the sides of the plant
    • create secondary tissues or a secondary plant body
    • widen the plant; diameter
    • found in large trees
    • many types of plants, such as wood, cork, etc.
    • woody plants are hard due to wood tissue
• dome of undifferentiated cells underneath horns

common terms

• herb: any non-woody plant
• wood: tissue that transports water and minerals up and down plant
  • xylem tissue
  • secondary
• woody plants include trees and shrubs
  • trees have one main stem (the trunk) and are usually larger than shrubs
  • shrubs have several main stems rather than one big stem; shrub stems branch out from one group/point

growth in plants vs. animals

• meristems cause indeterminate growth
• indeterminate: no fixed size; infinite growth only limited by resources/supplies
• animal growth is determinate; fixed by number of stem cells
• differences in growth form
  • animals have fixed amounts of growth; unitary body plans (some exceptions)
  • plants have modulary body plans; indeterminate

reproductive physiology

flowers

• modified determinate shoot stems and leaves
• modified via evolution
• four flower parts: sepals, petals, stamen, pistil
• sepal: lowest node, usually multiple (3+) on one node
  • protects flower whilst in the bud
• petal: usually colored to attract pollinators, but not always; also usually large
  • exist in wind pollination plants, but less showy
• stamen: produces pollen grains which carry sperm
  • the top part usually produces → ??? ; lower stem is filament
• pistil: sexual organs
  • carpels are modified leaves which make up the pistil; fused together
  • ovary on top of the carpels; produces ovules which carry eggs
  • long connecting part called the style
  • stigma is sticky/feathery; catches pollen grains
    • pollen grains grow a long tube through the style into the ovary in attempt to cause fertilization
• fertilized zygotes develop into embryos; ovules grow into seeds

monocot/eudicot

• eu- → “true”; revision of dicot polyphyletic clade
• primary classes
• named by the number of cotyledons (seed leaves)
  • cotyledon: a leaf on the embryo of the seed
  • monocots have one cotyledon, eudicots have two
• can also be differentiated by veins
  • monocot veins are parallel, eudicots are netted; very small, usually noticed more under light
• different organizations of stem/shoot vascular tissue
  • complex arrangement of monocots
  • eudicot tissue arranged in a ring
• different root systems
  • monocots have a fibrous root system
  • eudicots have a taproot system; one tap root and lateral roots
• different numbers of flower parts; standardize across clades
  • monocots: in threes
  • eudicots: in fours or fives

plant cells

• plastids: bound by 2 membranes outside
  • chloroplasts: 4-6 um in diameter
    • perform photosynthesis
    • disc-shaped, but are able to change shapes and orientation with regard to the cell membrane
    • thylakoid membrane sacs interconnected and stacked
    • granum/grana stack in thylakoid
    • stroma fluid
    • semi-autonomous; able to divide via binary fission, have nucleoid with several copies of chromosome, and regulated via dual control
  • chromoplast: a colored, but non-green plastid
    • usually yellow, orange, or red → carotenoids
    • carotenoids are fat soluble, not water soluble; stored in the thylakoids
    • found in fruits mostly, also flowers
  • leukoplasts: white/clear plastids
    • store starch or oil
  • amyloplasts: clear plastids
    • store starch
  • all plastids are developmentally related to each other
    • all plastids start out as proplastids then differentiate
    • chloroplasts aboveground, chromoplast belowground, etc.
    • mature chloroplasts can convert to chromoplasts and vice versa
• central vacuole
  • bound by one membrane: tonoplast
  • large; small vacuoles merge into one central vacuole which occupies up to 95% cell volume
  • contains cell sap made of water, sugars, ions, salts, water-soluble pigments, toxins, enzymes, etc.; many solutes
  • many functions; perform enzymatic/digestive role instead of lysosomes (subsume in central vacuole and digest)
    • store pigments as long as they are water-soluble; anthocyanins (red, blue, “nice flower colors”)
    • store toxins; avoids keeping it in cytosol and damaging organelles
    • stores crystals; sometimes toxins crystallize due to volume
    • facilitate growth; maintain turgor/water pressure
      • keeps erect/rigidity of cell walls

cell walls

• cell walls: in the apoplast
  • protoplast: the cell membrane and structures inside the membrane
    • aka symplast
  • apoplast: all sections outside the cell membrane: cell walls, spaces between the cells, and spaces inside dead cells
  • share an extracellular matrix like animal cells; may be more rigid/supportive
  • different functions: helps maintain shape and turgor pressure
    • protects from predators and viruses
    • many allow transport through the cell wall
    • enzymes are embedded in cell wall
  • several layers of the cell wall
• a minimum of two layers
  • middle lamella: a glue-like more outermost layer
    • lamella → “layer”
    • hydrophilic
    • made from pectins
      • causes the structure of jams/jellies
      • pectin makes cells stick together
      • hydrophilic
    • made of polysaccharides; no cellulose
  • primary cell wall: a layer within the middle lamella
    • not rigid, but contains cellulose
    • specific arrangement of cellulose
    • composed in a matrix which includes other materials; cellulose is embedded in the matrix
      • cellulose: beta glucose subunits (the hydroxyl on the first unit of the ring is parallel to the ch2oh unit)
        • beta glucose subunits are attached together while hydroxyl-ch2oh parallels are opposite of the adjacent units
        • linear repeating chain; not coiled; strong; composed of 1000s of beta glucose units
        • glucose molecule
        • not the basis of the cell wall alone; large amounts exist in parallel and form hydrogen bonds between themselves creating a cellulose molecule “cable”
          • cables form cellulose microfibrils; basis of the cell wall
      • matrix has two main components: pectins (polysaccharides) and hemicellulose
        • both are polysaccharides
        • both are hydrophilic
        • water will go through the primary cell wall and the middle lamella without transport channel usage
        • pectins form a mesh/net; some but irregular hydrogen bonding between pectins
        • hemicellulose crosslinks; tethers together cellulose microfibrils by forming hydrogen bonds across one length of a microfibril then traveling across to form bonds to the other microfibril
          • always runs parallel to the cellulose microfibrils
        • proposed correct layout
        • glycoproteins, waterproofing materials, lignin can all also be in the matrix, but are not necessary
  • additional cell walls are further in
  • secondary cell wall is within the primary cell wall
    • can be much thicker than previous two layers
    • often when a cell has deposited this, it will die
    • rigid, hydrophobic wall; needs channels for transport
    • cellulose microfibrils; several parallel layers arranged in different orientations; cross-netting
    • matrix made of many materials: hemicellulose, lignin
      • lignin is a phenolic polymer which reinforces the rigidity/hydrophobic properties of the secondary cell wall
        • aromatic ring with a hydroxyl; no repeated linkage between lignin
    • secondary cell wall prevents growth
• cellulose microfibrils are particularly arranged in order to facilitate cell expansion
  • microfibrils cannot be stretched; hemicellulose crosslinks must be broken and turgor pressure will expand microfibrils and cells within
  • elongation; more microfibrils can be created afterwards
  • in random arrangement, cells expand in all random directions

plasmodesmata

• plasmodesma: a cytoplasmatic connection between two cells that facilitates communication
• lumen: the inside of the cell
• cell membrane between neighboring cells is continuous
• endoplasmic reticulum has a portion of the reticulum form a membrane channel and connect into and through the neighboring cell
  • inner tubule is the desmotubule
• channels are very small
• grouped into a primary pit field: group of plasmodesmata

pits

• areas that lack the secondary cell wall after it has been deposited; a hole in the secondary cell wall
• pits occupy a primary pit field; avoids blocking off primary pit fields immediately
• created after a cell membrane has usually died off

cell types, tissues, and tissue systems

• cell: basic unit of life
• tissue: a group of cells which forms a structural unit
• simple tissue: 1 cell type; complex: 2+
• tissue system: a group of tissues which form a structural unit
• three tissue systems in vascular plants
  • dermal tissue system: the external outer covering
    • epidermis tissue in primary growth
    • in herbs, one single continuous tissue represents the epidermis tissue
    • covers everything except meristems
  • vascular tissue system
    • xylem transport system (for water and minerals)
    • phloem transport system (for sugars produced by photosynthesis)
    • veins in stem and root
  • ground tissue system
    • a tissue system between the vascular and dermal tissue
    • everything else not in the dermal and vascular tissue system

dermal tissue system

epidermis tissue in primary growth

• represented as a continuous layer on both above and underground growth
• does not represent the meristems
• functions vary on location of epidermis tissue
  • common function: protection against viruses and bacterial infection
  • protects against water loss above ground (waxes)
  • allows permeability for water underground
  • photosynthesis is not a function of epidermis (production of sugars)
• complex tissue with differences between monocots and eudicots
  • monocot stem: cells are arranged in linear, staggered rows; normal epidermal cells
    • these resemble typical ones drawn from an elodea leaf
    • no air space between monocot cells
  • eudicot stem: puzzle piece, freeform
    • no air space between eudicot cells
    • normal epidermal cells
  • both of the above cells are aboveground normal epidermal cells; only one type
    • both are covered by cuticle layer made from cutin and wax
    • ridged cuticle which prevents water loss
  • another type: guard cells
    • always occur in pairs
    • may be covered with pores
    • 2 guard cells and a pore form a stoma
      • pore allows for gas exchange
    • if no pore exists between guard cells, gas exchange is prohibited
    • guard cells are more elongated in monocots than eudicots, but they perform the same functions
    • guard cells are surrounded by normal epidermal cells
    • only epidermal tissue cell which has chloroplasts
      • make sugars, but are used to control stomata openings
    • much smaller than normal cells
  • another type: trichomes
    • a type of hair for plant cells
    • various appearances and various functions
      • water vessels, hairs, branched hairs, scales, etc.
      • unicellular – papillae, water vesicles, hairs
      • multicellular – hairs, branches, pelltate scales, glands
    • may be much larger than guard and normal, especially if protective
  • another type: glandular cells
    • secrete material, usually a protective material (insect repellent)
    • typically a type of trichome, so these are actually often glandular trichomes
    • flatter, sac-like trichomes
  • another type: subsidiary cells
    • adjacent to guard cells and aid function of guard cells
• single layer of cells

vascular tissue system

• vascular bundles surrounded by the ground tissues
• ring shape around the stem center

xylem

• complex tissue which transports water and minerals
• three cell types: water-conducting cells, parenchyma, sclerenchyma fibers
• xylem water-conducting cells last for many years due to secondary cell walls
• water conducting cells: dead, hollowed-out, elongate cells; thick walls (2* cw), with easy flow through cell for water
  • two types of wcc found in angiosperms, and can be found either in any angiosperms
    • most gymnosperms and non-vascular plants only have tracheids
  • tracheids and vessel elements
  • water mostly moves up the plant (sometimes lateral)
  • begin as live cells; end walls are degraded, removing organelles and primary cell wall
• tracheids: long, thin cells which taper at the ends
  • several pits across the elongate
  • in tracheids, water zig-zags through the pits of each cell; pit pairs line up to connect between tracheids
  • “pit membrane” between the pit pairs: actually the primary cell wall and middle lamella sandwiched and thinned down between the tracheids
  • pit membranes prevent embolisms from traveling through conduits/pits and destroying tracheids like vessels
• vessel elements
  • stacks form a vessel; a pipe that carries the water; 30-50 stacked, sometimes as small as 2 stacked
  • shorter and wider than tracheids
  • pits found on the lateral walls, the side walls, and the end walls; no tapering
  • end walls have openings/perforations: perforation plate
    • large, flat or slanted opening that goes through all of the wall layers; water enters through the middle
    • perforation plate may have several smaller openings surrounded by wall material, creating possible resistance; grate-like
    • one large hole: simple perforation plate
    • grate: compound perforation plate
  • simple perforation plates are more efficient than compound perforation plate; both are more efficient than tracheids
  • possible to have massive embolisms: vessels are wholly destroyed
• above found in secondary xylem: lateral meristems and non-elongate, fully mature primary xylem; full complete rigid secondary walls

primary xylem

• protoxylem and metaxylem
• both are for immature, elongate cells
• protoxylem is the earliest xylem found in maturing plants/xylem
  • very stretchable
  • will have rings of secondary cell wall or helices (helix/spiral)
  • when protoxylem stretches, more space between cell wall, but does not rupture
• metaxylem occurs later
  • network/reticulum of intersecting cell wall as added
  • or complete 2 cell wall with pits and possibly perforations
  • less stretchable; still alive

phloem

• “information highway”; transfers sugars, rna, and some hormones in any direction across the plant
• contents are placed under positive pressure; rupture would emit materials
• complex tissue
  • sieve-tube elements
    • only one sugar-conducting cell type is seen in angiosperms
  • companion cells
  • parenchyma
  • sclerenchyma fibers
• sieve tube elements
  • alive when functioning even though they have protoplasts
  • no secondary walls; soft, only primary and middle lamella
  • can be damaged; last only 1 year on average
  • have pores: enlarged plasmodesmata
    • used as connections between cells
    • connected/clustered in sieve areas
    • sides of walls/cells
  • very small cells
  • end walls → sieve plates
    • have sieve walls on the end plates
    • flat walls contain simple sieve-plates with a single sieve area
    • slanted walls contain compound sieve-plates with multiple sieve areas
  • 30-40 stacked
  • may look like vessel elements in diagrams
  • stack on top of each other

callose

• polysaccharide made from glucose (beta 1-3 linkages vs. cellulose and starch)
• lines the top and bottom of pores; doesnt overlap
• stains blue, recognizable
• definitive callose appears at the end of the cell’s life to block off full sieve plate preventing sugar from falling out
• wound callose eventually becomes definitive

p-proteins

• only in eudicots
• p-protein bodies; distinctive bodies in the cytoplasm
• hydrate to become slime; gooey, hydrated
• lines side of elements
• quick response for cell wounds/damage
• slime plug

modified protoplasm

• no tonoplast; no central vacuole to impede movement
  • no cytoskeleton, no nucleus, no ribosomes
  • contents of sieve tube elements can go through room in center easily
  • remaining tonoplast lines edges of cells, such as er
  • some mitochondria in cell

companion cells

• developmentally related to sieve tube elements; elements are paired with companion cells
• mother cell unequally divides into sieve tube element and a small companion cell sliver cut off from mother cell
• aids in metabolism; many more mitochondria and ribosomes in companion cells to aid
• especially helps put sugars into sieve tube elements: “phloem loading”
• soft tissue, easily damaged

ground tissue system

• everything inside and around the vascular tissue system
• center region of stem: “pith” region
• outer region between epidermis and vascular ring: “cortex” region
• intervals in vascular region: “pith ray” region
• ground tissue system is in these regions and others
• involves 3 simple tissues

parenchyma tissue

• singular cell type: parenchyma cells
• ubiquitous with the exception of the epidermis
• most common tissue in a plant
• all cells in parenchyma are alive
• majority of parenchyma cells are isodiametric: cubical in nature, but not necessarily square
  • some are elongated/long and thin, but not all
• only the primary cell wall and the middle lamella are present in parenchyma tissues
  • thin cell wall
• primarily functions for photosynthesis (found in leaves) or metabolism ie cell respiration (roots), storage, contributing to growth, reversion to meristematic state
  • meristematic state: begins dividing again in order to repair wounds
• air space between parenchyma cells; 25 um
  • necessary for gas exchange
• no chloroplasts; too deep within the leaf to pick up light

collenchyma

• found at the edges/periphery of organs; closer to but not necessarily next to the epidermis
• found in bundles and layers
• all cells in collenchyma are alive
• collenchyma cells elongate over maturity
• only the primary cell wall and the middle lamella are present in collenchyma tissues
  • lots of pectin in the cell wall; may make it look glossy
  • some regions of the cell wall are thick, and some are thin; irregularly thickened
  • distinctive irregularity
    • thick cell walls support the collenchyma
• functions primarily to support growing regions; elongates/stretches as the organ grows and stretches
  • not a lot of support, but is some support
• known as the collenchyma strands found in celery strings

sclerenchyma

• found in many locations; its main locations vary
• all cells in sclerenchyma are dead at maturity
• 2 different cell shapes with specific names
  • fibers: long and thin; very small, empty lumen surrounded by a thick cell wall; like a very bad straw/tube
    • majority is secondary cell wall filled in, with a thin primary cell wall
  • sclereids: various shapes as long as not long and thin; star-shaped, spherical, etc.
    • also have a small lumen and thick cell walls
    • shapes may be for protection (hurt to bite down on star-shaped)
  • cells have secondary cell walls, primary cell walls, and middle lamella
    - lignin present; makes cells rigid and adds support
    - regular, even thickness of cell walls

other notes

• transfer cells: a variation of parenchyma
  • cell walls protrude in projections; cell membrane increases, so ability to transport increases
• stone cells: a variation of sclereid schlerenchyma cells
  • roughly spherical; sclerified secondary cell walls feel stone-like, gritty (seen in pears)
  • 5 um

development

• totipotency: all well; one cell, if treated via tissue culture, would be able to divide and form a full organism
  • with parenchyma; could be done with collenchyma but would have to remove wall
  • vs. stem cells
  • genes for all different plant cells are present in the parenchyma cell
• three overlapping processes; hard to distinguish
  • growth: an increase in size
    • cell division: mitosis → more cells → enlarge
    • cell enlargement: huge process in plants vs animals; plants have a central vacuole that makes it easier to enlarge by absorbing water vs. making large amounts of cytoplasm
  • morphogenesis
    • generating a form
    • used to believe was mostly due to the plane of cell division’ anticlinal (perpendicular) cell division or periclinal (parallel)
      • is important specifically when an uneven/asymmetrical division occurs
      • is important when generating plant polarity
      • is important in first zygotic cell division (plant polarity)
    • cell enlargement; enlarge parallel to organ
  • cell differentiation
    • specialization
    • compare to animal cells; animal cells have cell lineages and develop into specific cells based on their precursor; plants develop based on relative position to the rest of the plant (and thus the hormones adjacent to it in the plant)
    • “pattern formation”
    • differential gene expression
• meristem cells are known as initials
  • in first division, the plane matters; it forms an initial and derivative
  • in second division, plane is hopefully the same; one initial, three derivatives
  • meristems are not fully meristematic; as derivative cells divide, they lose the ability to divide and become progressively more differentiated; vs. the initial cell
    • some cells may divide longer than others; gradual process
  • three primary meristems for each tissue system
    • protoderm: surface level meristem; used for dermal tissue system
    • procambium: strands found inside the stem; vascular tissue system
    • ground meristem: ground tissue system
• phase change: juvenile leaves differ from adult leaves
  • flowers: flowers are modified determinate leaves
• current hypothesis of flower phase change; switching from vegetative growth to flowering growth
  • the meristem must change from a vegetative meristem to a floral meristem
    • meristem identity genes produce transcription factors which change identity of meristem
  • abc hypothesis
    • sepal > petal > stamen > carpel
    • three sets of genes: a, b, c genes
    • each set of genes is active in two roles/worlds
      • a: sepal and petal
      • b: petal and stamen
      • c: stamen and carpel
    • the activity of genes and mutations in these genes affects what parts of the flowers are produced
      • cultivated vs wild rose gene activity

leaves

photorespiratory processes

• standard photosynthesis occurs in C3 plants: first product of carbon fixation is a 3 carbon molecule
• in xeric environments, first product of carbon fixation is a 4 carbon molecule, disrupting calvin cycle
  • c4 plants
  • cam plants
• both c4 and cam have pep carboxylase (phophoenolpyruvate) which can only add co2 to pep; forms oxaloacetate (4c)
• in non-hot temperatures, c3 plant does better
• in darker/less intense light intensities, c3 plant does better
• photorespiration occurs due to buildup of o2 while stomata is closed to prevent dehydration/death from remaining open in xeric environments
  • rubp will catalyze with both co2 and o2; o2 will create one 3-phophoglycerate and one 2-phosphoglycolate which is broken down and released as co2

calvin cycle

• 400 to 500g h2o per gram of co2 for c3
  • poor efficiency; tend to be in areas where water is abundant
  • high use of co2
• light reaction: absorbs light, and water is split for electrons in electron transport chain; photosystems produce oxygen (o2) and atp and nadph in stroma
• calvin cycle
  • RuBisco catalyzes carbon fixation
    • ribulose bisphosphate carboxylase oxygenase
    • slow and large enzyme; common; huge amount of protein
  • 3Rubp → (3CO2) → 6PGA
    • 3 rubp: ribulose bisphosphate
    • 3 co2 is fixated to 3rubp; forms unstable carbon molecules which form 6 3cs (3-phosphoglycerate/3pga)
    • fixation: adding inorganic carbon to organic molecule
    • PGA: 3C with a COOH, OH, CH2OP group
  • 6PGA → (6ATP) (6NADPH) → 6G3P
    • G3P: Glyceraldehyde 3-Phosphate
      • COH group instead of COOH
    • reduction; energy from sunlight added; G3P is the sugar createed
    • 1 g3p siphoned off for sugar production, starch, etc.
  • 5G3P → (3ATP) → 3RuBP
    • regenerate RuBP

c4 plants

• sugarcane, bermuda grass, zea mays, amaranthus, purslane
• evolved at least 45 times and in 19 different families (3 monocot, 16 eudicot)
• kranz anatomy: “wreath”; enlarged bundle sheath cells around the vein; puffy looking; altered chloroplast; and mesophyll cells are wrapped around bundle sheath
  • initial carbon fixation occurs in the mesophyll cells
  • calvin cycle occurs in the bundle sheath cells
  • the processes are separated across location/spatially separate
• mesophyll chloroplasts have large amounts of thylakoids (light reactions) and linear + cyclic electric flow → high oxygen flow; no rubisco
• bundle sheath cell chloroplasts have low oxygen/airspace, have rubisco, and don’t have many thylakoids; thylakoids only have cyclic electric flow, so no rubisco made
• in mesophyll: co2 is picked up with pep carboxylase enzyme → catalyzes addition to produce oxaloacetate 4c → converts into other 4cs (aspartate, malate)
• in bundle: move to bundle, break off co2, and produce carbon cycle; co2 breakage forms pyruvate
• move back to mesophyll: pyruvate is converted with atp to form phosphoenol pyruvate
• uses more atp via this process
• uses 250-300g h2o per gram of co2

cam plants

• initial carbon fixation occurs at night; calvin cycle occurs at day
• agave, orchids, pineapples cacti and succulents; stonecrop, crassulaceae, kalanchoe
  • orchids and agaves — monocots
  • very hot and dry environments; xeric
    • opening stomata would dehydrate/kill
• Crassulacean Acid Metabolism
  • named after crassulaceae family (stonecrop/kalanchoe lilies)
  • stomata only open at night to collect co2; gas exchange
  • pep carboxylase in cytosol catalyzes co2 to pep forming 4c oxaloacetate
  • converts to malic acid and stored in central vacuole; accumulated overnight
    • sour in morning; high acidity
  • stomata close in day
  • malic acid is taken out of vacuole, co2 broken off and produces calvin cycle sugars
    • light rxns only in day
  • pyruvate forms; use atp to convert into phosphoenol pyruvate
• uses 50-100g h2o per gram of co2

sun vs. shade leaves in c3

• phenotypic plasticity
• how much sun is in location where leaf develops
• thicker leaf is in sun, thinner in shade; even if they have same volume

roots

• primarily for anchoring and absorbing minerals
  • modified sometimes
    • storage (carrot taproots, manioc, sweet potato)
    • prop roots (corn) hold plant up
    • buttress roots
    • strangler fig roots; dispersed roots growing and sending roots down, surround main tree
    • pneumatophores: living cells, gas exchange (black mangroves)
    • aerial roots/epiphytic: epiphytic orchids; upwards/canopy roots
• anatomy of primary growth
  • root cap protecting the apical meristem; produced by the apical meristem
    • sheds over time/sloughs off
    • makes mucigel: hydrated polysaccharide; slimy; secretes into soil; creates a region of soil next to the root different from that further away — rhizosphere (rhizome)
      • different bacteria, microbes
    • cell division zone
      • quiescent zone in apical meristem
      • generates pattern; contributes cells to rest of root, but very slowly (~15 days)
    • cell elongation zone
    • cell maturation zone
      • root hair: extension of one epidermal cell
        • increases surface area for absorption
        • 70-90% of actual absorption
        • temporary; only lasts ~1 week and more root hairs are produced
        • root hairs necessary for specialization, but also because only place for root hair safely; avoids elongating cells destroying root; higher up is at branch roots
• root has primary structures/tissues
  • epidermis with a thin or no cuticle, root hairs, and no stomata
  • large, thick cortex
    • standard normal parenchyma cells but also endodermis length
    • both part of cortex
    • ground meristems
  • vascular cinder/stele
    • procambium
    • vascular tissue
• endodermis
  • screens what passes into the vascular cylinder/tissue
  • thickened/transverse/stained walls:
  • no air space between endodermis
  • casparian strip
    • suberin: waterproof, lipid, fat
    • could also be lignin (phenolic)
    • anticlinal walls (perpendicular) fully permeated by casparian strip
    • binds to cell membrane
    • forces solutions to cross cell membrane to regulate vascular tissue
  • passage cells
• different routes through endodermis
  • apoplastic route: materials enter through cell wall and spaces in cell wall
  • symplastic: materials travel across membrane early and go through cytosol through cells
  • transmembrane: across cytosol and membrane of cells
• vascular cylinder in eudicots
  • pericycle: one layer of cells; parenchyma cells
    • lateral roots originate in pericycle while meristematic and bridging out
    • secondary growth
  • move into primary phloem (outside) and primary xylem (inside)
    • has protoxylem and metaxylem
      • protoxylem: poles that radiate outward
      • metaxylem: everything else inside
      • number of protoxylem poles varies; 2 minimum; 2–~6
        • can change over time/developmentally
  • single layer of residual procambium between phloem and xylem if secondary growth is possible
• vascular cylinder in monocots
  • central pith; monocot stems don’t have a pith but roots do, vice versa on eudicots; pith instead of central metaxylem
  • primary xylem surrounds pith in uneven rows/poles
  • many protoxylem poles
  • metaxylem around pith
  • patches of primary phloem outside
  • one layer of pericycle
• basic function diagram
  • vertical transport, storage, connection to lateral roots
  • absorption
  • growth
  • tip of root
• fungi mutualism and bacteria nodules