Plant Biology

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What are photoreceptors?: Proteins that respond to light and regulate aspects of development.
What mediates hormone response and photoreceptor action?: Signal transduction pathways

signal -> reception -> transduction -> cellular response
What are some environmental cues that trigger photoreceptors?: - Length of night (winter dormancy),
- light color, intensity, duration
- temperature
What do phytochromes do?: Mediate the effects of red (660) and far-red (730) light.

- seeds listen to last light exposed to
What are cryptochromes and where are they found?: yellow photorecptor pigments (absorb blue and UV light)

found in plant nuclei
What is the photoreceptor for phototropism (grow to light)?: phototropin, upon absorbing blue light activates signal transduction leading to phototropic curvature
What does the phototropin gene encode?: one PK and two lov domains
What do the lov domains do?: Bind FMN (flavin chromophore) which is embedded in beta-sheet to absorb light, make conformation more alpha-helical, activate PK domain (lov 1 and 2 have similar absorbtion spectra)
Where do chloroplasts move and under what light conditions?: weak blue light - accumulate at surface, distribute evenly

strong blue light - go to edge of cell
Discribe the phytochrome proteins:: - bluish receptor proteins

P_r absorbs red -> P_fr
P_fr absorbs far red -> P_r

P_fr does the crazy shit
What are some effects of phytochrome action on the plant?: controls processes of non-photosynthetic seedling, initiates seed germination, greening of seedling
Describe the phytochrome receptor:: - dimer, each w/ 2 domains
- one domain has photorecptor activity, cov. bonded to chromophore pigment
- one domain kinase activity
- some activate G proteins
Name the three flowering plant life cycles and how long they are:: annuals - complete life cycle in less than one year
biennials - live almost 2 yrs
prennials - live a few to many years
What do some plants require to flower?: photoperiodic signals
(certain day or night length)
Discribe short, long and day-neutral plants:: short day plants - flower only when day lenght shorter than critical max
long day plants - flower when day longer than critical min
day neutral - flowering independant of day lenght, most common
What factor is measured by plants to determine day lenght?: The lenght of the night. Interuptions during dark period reset teh dark time period. Phytochromes are involved in this, but mech not understood.
Describe circadian rythms:: - maintained by biological clock
- in all eukaryotes
- highly persistant, although can be moved from 24 hr clock
What is an example of a circadian rythm.: Flowers open in day and close at night. Amplitude affected by temp. Occurs even in all light or all dark.

Turgor pressure causes beans to raise (day) or lower leaves (night). Cycle continues in all dark or all light.
What is florigen?: An as of yet uncharacterized flowering hormone. Same in short and long day plants.
What is vernalization?: Induce flowering by low temperatures. (ex. winter wheat needs cold to later flower)
What is gravitropism?: The process by which plants sense and respond to gravity. Orient stem, leaves to grow up and roots down even in darkness of soil.
What is etiolation?: Growth of plant in dark, when gravitropism controls direction of growth.
What is photomorphogenesis?: Process that once shoot is exposed to light, leaves develope and become green.
Describe the statolith hypothesis for root gravitropism:: statoliths - specialized plastids containing dense startch grains which settle to the lower portion of cells orient up and down in roots

aggregation of statoliths triggers redistribution of Ca, causes lateral transport of auxin in root. Ca and auxin accumulate in the lower side of zone of elongation. Ausin inhibits cell elongation, causing other side to elongate and root curves down as it grows.
Do mutants without statoliths still respond to gravitropism?: Yes, only slower.
What are nastic plant movements?: Response to environmental stimuli but direction of response does not depend on direction of stimulus. (unlike tropic movements)
What is thigmotropism?: Directional growth in response to touch.
What is thigmonasty?: Touch induced movement. In mimosa movement depends on strength of stimulus.
Explain how thigmonasty occurs:: Mechanical or heat signal -> electrical signal -> moves from cell to cell -> electrical potential reaches motor cells in pulvini at leaflet base -> rapid efflux of K -> rapid water transport out of motor cells

(can propogate to rest of leaf, causing folding in several places
Heliotropism: involves movements in pulvini at the bases of leaves or leaflets, track sun
diaheliotropism: keeps leaves perpendicular to sun all day to maximize photosynthesis
paraheliotropism: plants actively avoid direct sunlight, min photosynth
What is the source of hydrogen for plants?: water
What two things fix nitrogen?: bacteria and lightening
How do plants take up most nutrients?: As dissolved solutes in the soil.
Define autotroph (whiich plants are): make their own organic molecules from co2, water and minerals, most photosynthesize
How do stationary organisms find nutrients?: Roots mine soil for minerals, stems and leaves grow to get solar energy
Where are all mineral nutrients except N derived from?: rock
What is an essential nutrient?: - necessary for normal growth and reproduction
- not replaceable by another element
- requirement direct
What amounts of macro and micro nutrients are required by plants?: macro - 1 g/ kg
micro - 100 mg/ kg or less
What is the most common symptom of N deficiency?: slow growth, yellowing of older leaves (chlorosis)
What are symptoms of Fe deficiency?: chlorosis of younger leaves
Why is chlorosis seen in old leaves in N deficiency and young leaves in Fe deficiency.: N is easier to translocate than Fe, move it to new leaves where it is needed most
What is Mg essential for?: chlorophyl
enzyme cofactor
What is Phosphate essential for?: energy metabolism (ATP)
nucleic acids
switching the activities of enzymes
What is Ca needed for?: cytoskeleton
processing of hormonal and environmental cues (sig trans)
What are the components of soil?: bacteria, fungi, earthworms, aminals, rock, clay, water, mineral, air spaces, dead things
How do minerals move in soil?: Minerals are leached by water and sink to deeper soil horizons.
Describe soil horizon A: topsoil
most organic matter and living stuff here
sand makes air space
clay holds minerals and water
What is the best type of topsoil?: loam - mixture of clay, sand and silt
Describe soil horizon B: subsoil
has leached material for A, but little to no organic matter
Describe soil horizon C: parent rock from which soil is derived, roots rarely grow this deep
What determines the type of soil in a given area?: rock from which it comes
climate
landscape features
organizms in it
time
How are rocks broken down?: mechanical weathering
chemical weathering - required to form clay
What minerals does clay trap and how?: Clay anionic, traps cations (Ca, Mg, etc)
How do plants uptake cations stuck to clay?: Release H+ and H2CO3 (carbonic acid) from respiration, ion exchng with clay
What happens to anions.: Not held by clay, leach out of soil more readily.
What is the optimal pH for most crops? Why is this important?: 6.5, affects availability of nutrients
What forms humus.: Dead plant matter is broken down by fungus and bacteria to humus. It is thus rich in minerals esp N, and texture provides roots w/O2.
Why is K important?: - osmoticum for cellular growth and stomatal function
- balances charges of anions
- in more than 50 enzymes
- translocates btw tissues and organs in plant
Describe the long distance K transport pathway:: absorbed across root cell plasma membrane -> transported to nonliving thick-walled xylem vessels by efflux across cylem parenchyma plasma membrane -> apoplast surrounding leaf cells -> leaf parenchyma cells -> loaded into phloem of fully expanded source leaf -> goes to seive tube companion cell by combo of apoplastic and symplastic routes -> moves through phloem to shoot and root apices -> unloaded for use
Where is most mineral N?: igneous rocks
What do nitrogen fixing bacteria do?: Fix N2 to ammonia.
Where does most of the N taken up by organisms come from?: A recycled pool of N compounds previously used by other organisms.
What 5 non-bacteria factors put N into this pool?: lightening, fire (forest), volcanic eruption, internal combustion engines, application of chemical fertilizers
What is the main input to this pool?: N fixation
What carries out N fixation.: Only prokaryotes
What do nitrifying bacteria do?: Make ammonia into nitrates.

NH3 -> NO2 and NO3
How do losses from the N pool occur?: leaching, denitrification makes N2 again
How are N products distributed?: rain or snow
What fixes N in oceans and fresh water?: cyanobacteria
How much N does a bacteria fix?: sometimes just what they need to live and they release it when they die, some release up to 90% of the N they fix
Talk about rhizobiums: - Fix N only in close association with plants
- infect plant roots in root nodules
How do rhizobiums enter into mutualistic relationships with plants?: - legume roots secrete flavinoids
- activates gene regulator Nod D
- binds nod box
- nod genes transcribed
- enzymes for pathway making nod factor
- nod factors cause infection thread and nodule to form
- rhizobiums enter root and become surrounded by membranous vessicles
- leghemoglobin controls level of free oxygen there for bacteria
What do we know about nitrogenase?: - enzyme fixes N
- energy supplies by ATP
- inhibited by O2
- legume nodules provide just enough O2 for respiration, but not inactivate nitrogenase
What form of S so plants uptake?: sulfate (oxidized)
What is it used for?: Mainly synthesis of methionine and cysteine
How does S enter plants?: roots through active uptake,
gaseous S enters leaves
How do plants use S?: Uptake sulfate then reduce to sulfide
What is dissimilation?: Bacteria use sulfate as terminal e acceptor, generates H2S
How is H2S then oxidized to sulfate?: - aerobic catabolism by aminals, microorganisms and plants
- bacteria that use reduced S compoundsas e donors for chemosynthetic and photosynthetic reactions
- geochemical mechanisms where organic sulfur is volitilized into the air
How does P availability affect plants?: major constraint on growth
In what form does it exist in plants?: Inorganic P, or organic phosphates
- it is not reduced by plants during assimilation but remains in oxidized state
What is Pi needed for?: Nucleic acids
phospholipids
signal transduction
energetic bond formation
phosphorylation and dephosphorylation
Why is phosphate relatively unavailable to plants?: Low solubility
high sorption capacity in soil
rapidly depleted from soil by roots
What puts P in rocks?: P goes into shells -> sedimentary rocks, which then gets turned up on land and gives P back
also precipitates out of water
Describe mycrorrhizal associations:: between fungi and roots to give plants P
What are other root responses to low P?: - branching to explore soil more (alterations in root architecture)
- increases in root hair density and lenght to increase surface area and reduce lenght of diffusive pathway for P to reach root surface
- release H+ to solubilize Pi
- exude phosphatases to release organically bound P from soil
- up-regulate high affinity P transporters in root cell plasma membrane
What is the predominant type of mycorrhizal association?: endomycorrhizae
Talk about endomycorrhizae.: - infect wide array of plants
- in almost all types of soil
- associate w/ plasma membrane in hyphal networks but do not penetrate cell
- from branched haustoria within tissues of the root cortex for solute exchange
What are the benefits of hyphal growth?: decrease distance Pi must diffuse to reach site of absorbtion
What does the plant provide fungus for P?: fixed carbon
What is phytoremediation?: using plants to rid soil of toxic heavy metals, Zn Cu Ni
Bioremediation: detoxify metal-contaminated soil by means of biological activity
phytoextraction: removal of toxins from soil
phytostabilization: complexation and immobilization of toxins within the soil
phytodegradation: degradation by microorganisms in soil
Where do carniverous plants live?: acidic, N poor places
aminals supply N
As plants develop what 3 fundamental processes do environmental cues, photoreceptors and hormones affect.: cell division
cell expansion
cell differentiaion
What occurs when a seed germinates? simple: imbibe water
digest stored polymers into monomers
When do plants flower?: during a specific time of year
or
when they reach a certain size or age
What do plants that flower based on hours of daylight need?: Photoreceptors in leaves
What hormone helps maintain dormancy in perennials that are dormant for part of the year?: abscicic acid
What hormones regulate leave senescence?: auxin and ethylene
How long can seed dormancy last?: week to centuries
What are the 3 principle strategies of dormancy?: - exclusion of water and/ or O2 from seed coat
- mechanical restraint of embryo
- chemcial inhibition of embryo developent
What can end dormancy?: - breaking seed coat
- microorganisms in soil softening seed coat
- fire releasing mechanical restraint
- leaching away of chemical inhibitors
What adaptive advantages are conferred by seed dormancy?: - survive dry/ cold better than plants
- access to areas cleared by fire
- not germinating in light ensure seed is in soil
- wait until envrironmental conditions favorable
How does imbibing water activate germination?: - neg water potential causes swelling
- activates enzymes, allowing synthesis of proteins
- cells expand (dont usually divide yet)
What provides energy before photosynthesis begins?: reserves in endosperm and cotelydon
What are the energy storage molecules?: starch, fat, oils

proteins provide amino acids
starch yields glucose
oils yield fatty acids
What do gibberelins secreted by the embryo do?: trigger changes in aleurone layer in seed coat
How do plant kinases differ from those in aminals?: phosporylate mostly serine and threonine, as opposed to tyrosine
Please review list of hormone functions page 130.: did you do it?
How does a plant respond to environmental cues?: adjusting pattern of growth and development

causes much more variation of body plan within species
tropism: any growth response that results in curvature of the whole plant towards or away from stimulus
phototropism: growth in response to light

positive - towards light
neg - away from light
What affect on plant growth does pinching off the apical bud have?: increases lateral bud growth
What hormone mediates apical or lateral bud growth, and growth towards light?: auxin
How does auxin move?: only from apex to base
What establishes the auxin gradient?: carrier proteins transport auxin transport auxin unidirectionally
How does auxin pass through the cell wall?: diffusion
What occurs when auxin encounters the acidic environment of the cell wall?: pick up H+ to become neutral

the small, neutral molecule can pass through the plasma membrane
What happens in the cytoplasm, which is pH 7?: auxin ionizes
How does auxin exit cell?: only where transport proteins can carry charged molecule accros membrane, carrier proteins are embedded in membrane at bottom only (basal end)
How is this favorable?: Proton pumps generate membrane potential across membrane, which favors transport of anions out
What two growth processes are aided by the redistribution of auxin?: phototropism and gravitropism
How does auxin cause phototropism?: - light strikes coleoptile of one side of plant
- the side of the plant far from light gets more auxin
- auxin side grows more
- plant bends towards light
In what ways does auxin affect vegetative growth?: - initiates root growth in cuttings
- inhibits detachment of old leaves
- maintains apical dominance
- promotes stem elongation
- inhibits root elongation
From what does abscission result?: the breakdown of a specific part of the petiole
What is apical dominance?: the tendency for lateral buds to remain dormant
How does auxin affect fruit growth?: stimulates fruit growth, can be used to make seedless fruit from unfertilized ovaries
Describe plant cell walls:: - cullulose and other components
- cellulose molecules join in parallel
- 250 cellulose molecules form one micorfibril
- networked microfibrils give cell wall rigidity
How does auxin affect cell wall?: - causes release of cytoplasmic cell loosening factor
- proteins "expansins" modify H boding between polysaccharides in wall
What is auxin-binding protein 1?: a receptor for auxin
What good work to cytokinins do?: - aid germination
- inhibit stem elongation
- stimulate lateral bud growth
- lateral swelling of stems
- delay leaf senescence
Where is the main site of cytokinin production?: roots
auxin = cytokinin: vegetative growth
auxin > cytokinin: root growth
Why are axillary buds near shoot tip less likely to grow than those closer to the roots?: auxin goes down inhibits
cytokinin comes up promotes
What are the uber many effects of gibberelins? How many are there?: about 80
- role in fruit production (size)
- plant size
- induce bolting
- promote seed germination
- bring plants out of winter dormancy
What are the affects of abscisic acid?: - promotes storage in seeds
- high conc in dormant buds
- inhibits stem elongation
- accumulates when plants low on water
How does abscisic acid aid reduce water loss?: - causes release of Ca ions from vacoules in gaurd cells
- K channels are opened
- water leaves the cell
- gaurd cells sag
- stomata close
What are the effects of ethylene?: - promotes leaf abscission
- ripens fruit
- maintains apical hook of eudicot
How does ethylene aid fruit ripening?: promotes loss of chlorophyl and cell wall breakdown
Mechanical stress stimulates ethylene. How does this effect the apical hook?: - slows stem elongation
- thickens stem
- increases horizontal growth
Describe the signal transduction pathway for ethylene:: - binds to EIN2 receptor
- activates messenger
- activates CTR1
- allowed to enter nucleus
- stimulates gene transcription
How do oligosaccharins aid in plant defense from bacteria and fungi?: - bacteria and fungus eat cell wall
- oligosaccharins (part of wall) are released
- signal plant to stimulate other defenses
What other hormones serve as important signals for plant defense?: jasmonates, salicylic acid, systemin
What is systemic aquired resistance (SAR)?: A local attack triggers mobile signal warning rest of plant, triggering defense mechanisms.
What is transpiration?: loss of water vapor by plant parts - mostly stomata
Why do plants loose water?: CO2 uptake coupled to water loss
What are the three levels of transport in plants?: - water loss and uptake by individual cells
- short dist cell to cell transport
- long dist whole plant transport
What are the 4 essential function of water?: - transports solutes
- supports plant body
- cools plant body
- photosynthesis
How does water enter the plant?: osmosis
In osmos which way does water flow in a concentration gradient?: from low solute conc to high solute conc
Water potential:: tendency for a solution to take up pure water from across a membrane
What is required for osmosis?: membrane permeable to water, but impermeable to solutes
Wilting:: loss of pressure potential
bulk flow:: movements of fluids in plants due to differences in pressure potential
How do ions pass through membranes?: active transport, gates

- facilitated diffusion when more ions in soil than plant
How do plants uptake Na and K: No pump for active transport.
Use ATP driven proton pump to pump H out, ions come in to the neg charged interior
symport protein: couple H+ in to Cl- in
What estrablishes the membrane potential?: intracellular negativity
Aquaporins:: - membrane channels for water to pass through
- control rate but not direction of water movement
What does bulk water flow carry?: dissolved minerals
How do minerals move across certain membranes?: active transport
What are the steps water takes as it enters the plant?: - ions transported in by root hair cells
- water follows
- enter APOPLAST, cell walls and intercellular spaces or SYMPLAST
apoplast: cell walls and intercellular spaces

water and minerals can flow w/o crossing membranes

allows ungregulated movement
symplast: portion of the plant body enclosed by membranes - continuous network
plasmodesmata: connect cytoplasm of cells
Where does water in the apoplast move to?: the endodermis - the innermost layer of the cortex
casparian strip: waxy, suberin containing structures that prevents movement around cells of the endodermis into the stele
What must water and ions pass through to enter the steele?: endodermal cytoplasm
parenchyma cells: aid minerals in returning to the apoplast
transfer cells: use ATP pumps to move ions from cytoplasm (symplast) to cell walls (apoplast)
What does the active tranport of ions by transfer cells cause?: water to move from the symplast to the apoplast
guttation: forcing of water through openings in leaves by root pressure
By what mechanism moves water in the xylem?: transpiration-cohesion-tension
Describe the transpirational pull:: - neg pressure lowers water potential
- water moves from high to low potential
- mesophylly cells loose water to the surface film liningn air spaces
- water lost via stomata is replaced by water pulled out of teh xylem
cohesion: H bonding allows pulling of sap through the column w/o water separating

(makes water stick together)
adhesion: water H bonding with hydrophilic wall of xylem overcome gravity

(water sticks to other things)
transpiration: evaporation of water from leaves, this pulls new water up
What causes the tension in this model of water transport?: the diffusion of water vapor via the stomata
How does tension pull water upwards?: - as water vapor leaves leaf, more water evaporates from cell walls of mesophyll cells
- film of water surrounding these cells begins to curve where the water retreats into the pores
- surface tension here creates a neg pressure potential
- this force pulls water from roots
What provides the energy for pulling water up the plant?: the sun drives it
Briefly, how do guard cells regulate stomata opening and closing?: guard cells turgid - stomata open
guard cells flacid - stomata closed
Now describe the mechanism by which guard cells open stomata.: - blue light absorbed by guard cell plasma membrane
- protons tranported out
- K ions come into cell
- water comes into cell
- turgor pressur high, open
How do gurad cells close stomata?: - abscisic acid causes stomata to close
- protons stop being pumped out
- K and water diffuse out of cell
- low turgor pressure, closed
What factors stimulate stomata opening at dawn?: - light (blue) activates H pump
- low CO2 levels
- circadian rythms
What factors can stimulate stomata closing?: - water deficiency
- high temp
xerophytes: plants adapted to arrid climates
How have xerophytes adapted to arrid climates?: - small thick leaves lower surface to volume ratio
- thick, leathery cuticl
- stomata on lower shaded portionof leaf
- in pits protected from wind
- trichomes
- shed leaves in driest months
trichomes: hairs that minimize transpiration by breaking up air flow
How does substances move in the phloem?: source to sink
What is a source?: leaf that photosynthesizes
What is a sink?: root or flower
What are the steps in seive tube flow that require energy?: - loading of solutes into sieve tubes at sources
- unloading solutes from sieve tubes at sinks
How does this aid water movement?: water flows from low solute concentration in xylem to high solute conc in phloem near source cell

water then flows to sink cell, solutes are removed and water returns to xylem

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