Plan A Standard lecture course Plan B Standard

Plan A Standard lecture course Plan B Standard lecture course, except: 1. Last lectures will be chosen by you -> electives 2. Last 4 labs will be an independent research project 3. 20% of grade will be “elective” • Paper • Talk • Research proposal • Poster • Exam

Plan C 1. 2. 3. 4. 5. 6. 7. 8. 9. 10. 11. 12. 13. 14. 15. 16. 17. 18. 19. Phytoremediation Plant products Biofuels Effects of nutrient deprivation Effects of stresses Climate/CO 2 change Hormones Non-coding RNAs Plant movements: flytraps, mimosa, soybeans Carnivorous plants Plant tropisms and nastic movements Root growth responses Circadian rhythms Plant signaling (including neurobiology) Flowering Biotechnology magnetic fields Different colors of light Something else?

Plan C 1. Pick a problem 2. Pick some plants to study 3. Design some experiments 4. See where they lead us

• • • Plant Development Cell division = growth Determination = what cell can become Differentiation = cells become specific types Pattern formation Morphogenesis: organization into tissues & organs

Plant Development umbrella term for many processes • Embryogenesis • Seed dormancy and germination • Seedling Morphogenesis • Transition to flowering, fruit and seed formation Many responses to environment

Unique features of plant development Meristems: plants have perpetually embryonic regions, and can form new ones • No germ line! Cells at apical meristem become flowers: allows Lamarckian evolution! • Different parts of the same 2000 year old tree have different DNA & form different gametes

Endomembrane system Organelles derived from the ER 1) ER 2) Golgi 3) Vacuoles 4) Plasma Membrane 5) Nuclear Envelope 6) Endosome 7) Oleosomes

VACUOLES Vacuoles are subdivided: lytic vacuoles are distinct from storage vacuoles!

Endomembrane System Oleosomes: oil storage bodies derived from SER Surrounded by lipid monolayer! • filled with lipids: no internal hydrophobic effect!

Peroxisomes Fn: 1. destroy H 2 O 2, other O 2 -related poisons 2. change fat to CH 2 O (glyoxysomes) 3. Detoxify & recycle photorespiration products 4. Destroy Et. OH (made in anaerobic roots)

endosymbionts 1) Peroxisomes (microbodies) 2) Mitochondria

Mitochondria Bounded by 2 membranes

Mitochondria 2 membranes Smooth OM

Mitochondria 2 membranes Smooth OM IM folds into cristae

Mitochondria -> 4 compartments 1) OM 2) intermembrane space 3) IM 4) matrix

Mitochondria matrix contains DNA, RNA and ribosomes

Mitochondria matrix contains DNA, RNA and ribosomes Genomes vary from 100, 000 to 2, 500, 000 bp, but only 40 -43 genes

Mitochondria matrix contains DNA, RNA and ribosomes Genomes vary from 100, 000 to 2, 500, 000 bp, but only 40 -43 genes • Sometimes mutate to cause cytoplasmic male sterility

Mitochondria matrix contains DNA, RNA and ribosomes Genomes vary from 100, 000 to 2, 500, 000 bp, but only 40 -43 genes • Sometimes mutate to cause cytoplasmic male sterility Reproduce by fission

Mitochondria Reproduce by fission IM is 25% cardiolipin, a bacterial phospholipid Genes most related to Rickettsidae

Mitochondria Fn : cellular respiration -> oxidizing food & supplying energy to cell Also make many important biochemicals

Mitochondria Fn : cellular respiration -> oxidizing food & supplying energy to cell Also make important biochemicals & help recycle PR products

Mitochondria Fn : cellular respiration -> oxidizing food & supplying energy to cell Also make important biochems & help recycle PR prods • Have extra oxidases: burn off excess NADH or NADPH? • Can’t kill plants with cyanide because of alternative oxidase!

Mitochondria Fn : cellular respiration -> oxidizing food & supplying energy to cell Also make important biochems & help recycle PR prods • Have extra oxidases • Do lots of extra biochemistry

endosymbionts 1) Peroxisomes 2) Mitochondria 3) Plastids

Plastids Present in all plant cells, but take many forms • Chloroplasts do photosynthesis • Amyloplasts store starch • Chromoplasts store pigments • Leucoplasts are found in roots

Chloroplasts Bounded by 2 membranes 1) outer envelope 2) inner envelope

Chloroplasts Interior = stroma Contains thylakoids • membranes where light rxns of photosynthesis occur • mainly galactolipids

Chloroplasts Interior = stroma Contains thylakoids • membranes where light rxns of photosynthesis occur • mainly galactolipids Contain DNA, RNA, ribosomes

Chloroplasts Contain DNA, RNA, ribosomes 120, 000 -160, 000 bp, ~ 100 genes

Chloroplasts Contain DNA, RNA, ribosomes 120, 000 -160, 000 bp, ~ 100 genes Closest relatives = cyanobacteria

Chloroplasts Contain DNA, RNA, ribosomes 120, 000 -160, 000 bp, ~ 100 genes Closest relatives = cyanobacteria Divide by fission

Chloroplasts Contain DNA, RNA, ribosomes 120, 000 -160, 000 bp, ~ 100 genes Closest relatives = cyanobacteria Divide by fission Fns: Photosynthesis

Chloroplasts Fns: Photosynthesis & starch synth Photoassimilation of N & S

Chloroplasts Fns: Photosynthesis & starch synth Photoassimilation of N & S Fatty acid & some lipid synth

Chloroplasts Fns: Photosynthesis & starch synth Photoassimilation of N & S Fatty acid & some lipid synth Synth of ABA, GA, many other biochem

Chloroplasts & Mitochondria Contain eubacterial DNA, RNA, ribosomes Inner membranes have bacterial lipids Divide by fission Provide best support for endosymbiosis theory

Endosymbiosis theory (Margulis) Archaebacteria ate eubacteria & converted them to symbionts

cytoskeleton network of proteins which give cells their shape also responsible for shape of plant cells because guide cell wall formation left intact by detergents that extract rest of cell

Cytoskeleton Actin fibers (microfilaments) ~7 nm diameter Form 2 chains of polar actin subunits arranged in a double helix

Actin fibers polar subunits arranged in a double helix • Add to + end • Fall off - end • Fn = movement

Actin fibers Very conserved in evolution

Actin fibers Very conserved in evolution Fn = motility Often with myosin

Actin fibers Very conserved in evolution Fn = motility Often with myosin: responsible for cytoplasmic streaming

Actin fibers Very conserved in evolution Fn = motility Often with myosin: responsible for cytoplasmic streaming, Pollen tube growth & movement through plasmodesmata

Actin fibers Often with myosin: responsible for cytoplasmic streaming, Pollen tube growth & movement through plasmodesmata

Intermediate filaments Protein fibers 8 -12 nm dia (between MFs & MTs) form similar looking filaments Conserved central, rod-shaped alpha-helical domain

Intermediate filaments 2 monomers form dimers with parallel subunits Dimers form tetramers aligned in opposite orientations & staggered

Intermediate filaments 2 monomers form dimers with parallel subunits Dimers form tetramers Tetramers form IF

Intermediate filaments 2 monomers form dimers with parallel subunits Dimers form tetramers Tetramers form IF Plants have several keratins: fn unclear

Intermediate filaments 2 monomers form dimers with parallel subunits Dimers form tetramers Tetramers form IF Plants have several keratins: fn unclear No nuclear lamins! Have analogs that form similar structures

Microtubules Hollow, cylindrical; found in most eukaryotes outer diameter - 24 nm wall thickness - ~ 5 nm Made of 13 longitudinal rows of protofilaments

Microtubules Made of tubulin subunits polymerize to form protofilaments (PF) PF form sheets Sheets form microtubules

Microtubules Protofilaments are polar -tubulin @ - end -tubulin @ + end all in single MT have same polarity

Microtubules In constant flux polymerizing & depolymerizing Add to (+) Fall off (-)

Microtubules Control growth by controlling rates of assembly & disassembly because these are distinct processes can be controlled independently! Colchicine makes MTs disassemble Taxol prevents disassembly

Microtubules Control growth by controlling rates of assembly & disassembly Are constantly rearranging inside plant cells!

Microtubules Control growth by controlling rates of assembly & disassembly Are constantly rearranging inside plant cells! • during mitosis & cytokinesis

Microtubules Control growth by controlling rates of assembly & disassembly Are constantly rearranging inside plant cells! • during mitosis & cytokinesis • Guide formation of cell plate & of walls in interphase

µT Assembly µTs always emerge from Microtubule-Organizing Centers (MTOC)

µT Assembly µTs always emerge from Microtubule-Organizing Centers (MTOC) patches of material at outer nuclear envelope

Microtubules MAPs (Microtubule Associated Proteins) may: • stabilize tubules • alter rates of assembly/disassembly • crosslink adjacent tubules • link cargo

2 classes of molecular motors 1) Kinesins move cargo to µT plus end 2) Dyneins move cargo to minus end “Walk” hand-over-hand towards chosen end

µT functions 1) Give cells shape by guiding cellulose synth

µT functions 1) Give cells shape by guiding cellulose synth 2) Anchor organelles

µT functions 1) Give cells shape by guiding cellulose synth 2) Anchor organelles 3) Intracellular motility

WATER Plants' most important chemical • most often limits productivity

Climate change will alter rainfall Overall prediction is that crops will suffer in many parts of world

WATER Plants' most important chemical • most often limits productivity Often >90% of a plant cell’s weight

WATER Plants' most important chemical • most often limits productivity Often >90% of a plant cell’s weight Gives cells shape

WATER Plants' most important chemical • most often limits productivity Often >90% of a plant cell’s weight Gives cells shape Dissolves many chem

WATER • Dissolves many chem • most biochem occurs in water • Source of e- for PS

WATER • most biochem occurs in water • Source of e- for PS • Constantly lose water due to PS (1000 H 2 O/CO 2)

WATER • most biochem occurs in water • Source of e- for PS • Constantly lose water due to PS • Water transport is crucial!

WATER Water transport is crucial! SPAC= Soil Plant Air Continuum • moves from soil->plant->air

Water is drawn through plants along the SPAC, using its special props to draw it from the soil into the air Plant Water Uptake

WATER Formula = H 2 O Formula weight = 18 daltons Structure = tetrahedron, bond angle 104. 5˚

WATER Structure = tetrahedron, bond angle 104. 5˚ polar: O is more attractive to electrons than H + on H - on O

Water Polarity is reason for water’s properties water forms H-bonds with polar molecules

Water Polarity is reason for water’s properties water forms H-bonds with polar molecules Hydrophilic = polar molecules Hydrophobic = non-polar molecules

Properties of water 1) Cohesion = water H-bonded to water

Properties of water 1) Cohesion = water H-bonded to water -> reason for surface tension

Properties of water 1) Cohesion = water H-bonded to water -> reason for surface tension -> why water can be drawn from roots to leaves

Properties of water 1) Cohesion = water H-bonded to water 2) Adhesion = water H-bonded to something else

Properties of water 1) Cohesion = water H-bonded to water 2) Adhesion = water H-bonded to something else • capillary action

Properties of water 1) Cohesion = water H-bonded to water 2) Adhesion = water H-bonded to something else • capillary action • why things dissolve in water

Properties of water 1) Cohesion = water H-bonded to water 2) Adhesion = water H-bonded to something else • Cohesion and adhesion are crucial for water movement in plants!

Properties of water 1) Cohesion = water H-bonded to water 2) Adhesion = water H-bonded to something else • Cohesion and adhesion are crucial for water movement in plants! • Surface tension & adhesion in mesophyll creates force that draws water through the plant!

Properties of water 1) Cohesion = water H-bonded to water 2) Adhesion = water H-bonded to something else 3) high specific heat • absorb heat when break H-bonds: cools leaves

Properties of water 1) Cohesion = water H-bonded to water 2) Adhesion = water H-bonded to something else 3) high specific heat • absorb heat when break H-bonds • Release heat when form H-bonds

Properties of water 1) Cohesion = water H-bonded to water 2) Adhesion = water H-bonded to something else 3) high specific heat 4) Ice floats

Properties of water 1) Cohesion = water H-bonded to water 2) Adhesion = water H-bonded to something else 3) high specific heat 4) Ice floats 5) Universal solvent

Properties of water 1) Cohesion = water H-bonded to water 2) Adhesion = water H-bonded to something else 3) high specific heat 4) Ice floats 5) Universal solvent • Take up & transport nutrients dissolved in water

Properties of water 5) “Universal” solvent • Take up & transport nutrients dissolved in water • Transport organics dissolved in water

Properties of water 1) Cohesion = water H-bonded to water 2) Adhesion = water H-bonded to something else 3) high specific heat 4) Ice floats 5) Universal solvent 6) Hydrophobic interactions

Properties of water 1) Cohesion = water H-bonded to water 2) Adhesion = water H-bonded to something else 3) high specific heat 4) Ice floats 5) Universal solvent 6) Hydrophobic interactions 7) Water ionizes

p. H [H+] = acidity of a solution p. H = convenient way to measure acidity p. H = - log 10 [H+] p. H 7 is neutral: [H+] = [OH-] -> at p. H 7 [H+] = 10 -7 moles/l p. H of cytoplasm = 7. 2 p. H of stroma & matrix =8 p. H of apoplast = 5. 5 p. H of lumen = 4. 5

p. H Plants vary p. H to control many processes!

p. H Plants vary p. H to control many processes! • Plants alter p. H @ roots to aid uptake

Water movement Diffusion: movement of single molecules down ∆[ ] due to random motion until [ ] is even Driving force?

Water movement Diffusion: movement of single molecules down ∆[ ] due to random motion until [ ] is even Driving force: lowers free energy ∆G = ∆H- T∆S

Water movement Diffusion: movement of single molecules down ∆[ ] due to random motion until [ ] is even Bulk Flow: movement of groups of molecules down a pressure gradient

Water movement Diffusion: movement of single molecules down ∆[ ] due to random motion until [ ] is even Bulk Flow: movement of groups of molecules down a pressure gradient • Independent of ∆ [ ] !

Water movement Diffusion: movement of single molecules down ∆[] due to random motion until [ ] is even Bulk Flow: movement of groups of molecules down a pressure gradient • Independent of ∆[ ] ! • How water moves through xylem

Water movement Diffusion: movement of single molecules down [] due to random motion until [ ] is even Bulk Flow: movement of groups of molecules down a pressure gradient • Independent of ∆ [ ] ! • How water moves through xylem • How water moves through soil and apoplast

Water movement Bulk Flow: movement of groups of molecules down a pressure gradient • Independent of ∆ [ ] ! • How water moves through xylem • Main way water moves through soil and apoplast • Very sensitive to radius of vessel: increases as r 4

Water movement Diffusion: movement of single molecules down ∆[] due to random motion until [ ] is even Bulk Flow: movement of groups of molecules down a pressure gradient • Independent of ∆[ ] ! • How water moves through xylem • Main way water moves through soil and apoplast • Very sensitive to radius of vessel: increases as r 4 Osmosis: depends on bulk flow and diffusion!

Water movement Osmosis: depends on bulk flow and diffusion! water crosses membranes but other solutes do not water tries to even its [ ] on each side

Water movement Osmosis: depends on bulk flow and diffusion! water crosses membranes but other solutes do not water tries to even its [ ] on each side other solutes can’t: result is net influx of water

Water movement Osmosis: depends on bulk flow and diffusion! • Moves through aquaporins, so rate depends on pressure and [ ] gradients!

Water movement Osmosis: depends on bulk flow and diffusion! • Moves through aquaporins, so rate depends on pressure and [ ] gradients! • Driving force = water's free energy (J/m 3 = MPa)