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Photosynthesis - Coggle Diagram

- - - - photon (particle nature)
        
        each photon carries a discrete amount of energy that acts as a function of its wave properties (frequency and wavelength)
        
        1 Einstein = 1 mole photons
      - Electromagnetic wave properties
        
        defined by wavelength and amplitude
        
        speed of light constant: 3 x 10^8 m s-1; related to wavelength and frequency
    - - Red region has longest wavelengths and least energy
      - Blue region has shortest wavelengths and most energy
      - Photosynthetically active radiation: abbr = PAR, wavelengths = 400-700 nm
  - - - wide range of wavelengths
      - not all wavelengths reach earth's surface
      - plant pigments
        
        unique, overlapping absorption spectra
        
        small fraction of solar output absorbed
        
        Chl a has only 2 major absorption peaks: 400 nm and 700 nm
        
        harvest specific light wavelengths reaching earth's surface
  - - - 400-700 nm wavelengths
      - 85%-90% absorbed by plant
      - green: 500-600 nm not absorbed as well, therefore green plants
      - far-red/infrared wavelengths (>700) not absorbed well
  - - - MEMORIZE: PHOT INDUCING CHANGES IN BLUE LIGHT
  - - - moderate excess of light energy
      - quantum efficiency decreased
      - maximum photosynthesis unchanged
      - overload of protective mechanisms
      - occurs at mid-day
    - - quantum efficiency decreased
      - maximum photosynthesis decreased
      - overload of protective mechanism and photochemical reactions
  - - - MEMORIZE PATHWAY AND CONVERSIONS P110-111
      - carotenoid system dissipates excess light energy via conversion among epoxidation states
      - Epoxidation occurs when NADPH transfers e- to xanthophylls
      - de-epoxidation occurs when xanthophylls transfer e- to H2O via ascorbate
  - - - C3 Photosynthesis
      - Calvin-Benson-Bassham cycle
      - Reductive pentose phosphate (RPP) cycle
      - Photosynthetic carbon reduction (PCR) cycle
    - - Includes:
        
        C4 photosynthesis in angioperms in hot environments
        
        C4 Photosynthesis
        
        C4 Leaf Anatomy
        
        plasmodesmata connect mesophyll and bundle sheath cnells
        
        mesophyll cells only 2-3 cells from bundle sheath cell
        
        Bundle Sheath Cells
        
        Overall Pathway:
        
        C4 acid are first detectable intermediates (malate, aspartate)
        
        PEPCase carries out CO2 fixation
        
        Energetics: one additional ATP required per CO2 fixed
        
        reduces PR loss:
        
        PEPCase has high affinity for HCO3-
        
        O2 does not compete with HCO3-
        
        Permits reduced stomatal aperature, reducing H2O loss and permitting growth at higher temperatures
        
        MEMORIZE OVERALL PATHWAY 165
        
        Three flavors of C4 metabolism:
        
        NADP-ME pathway
        
        regulated by PEP carboxylase, which is activated by protein phosphorylation
        
        regulated by pyruvate-Pi dikinase, which is controlled by adenylate energy charge
        
        regulated by malate dehydrogenase, which is activated by thioredoxin system (light)
        
        PEP Carboxykinase pathway
        
        regulated by PEP carboxylase, which is activated by protein phosphorylation
        
        regulated by pyruvate-Pi dikinase, which is controlled by adenylate energy charge and whose regulation is mitigated by PEP transport
        
        MEMORIZE REGULATION AND REDUCING AGENT FOR EACH
        
        NAD-ME pathway
        
        regulated by pyruvate-Pi dikinase, which is controlled by adenylate energy charge
        
        regulated by PEP carboxylase, which is activated by protein phosphorylation
        
        no taxonomic relationship between types of C4 photosynthesis; has arisen via convergent evolution 62 times
        
        C4 plants are more efficient than C3 plants
        
        respiration increases with temperature, rather than decreasing like in C3 plants
        
        C4 mechanism traps and recaptures respired CO2, so quantum yield is stable with increasing temperature
        
        found in maize, sugar cane, sorghum, etc
        
        CO2 pumps in aquatic plants
        
        algae adapted to low CO2 do not photorespire
        
        inorganic C actively transported into cell, driven by ATP derived from light reactions
        
        effectively increases CO2 around Rubis
        
        CAM photosynthesis in angiosperms in deserts
        
        improves water-use efficiency
        
        CO2 fixation occurs at night and end of day to reduce water loss while fixing CO2 and allow stomates to close during high temperature
        
        CAM idling recycles respired CO2 for months at a time with little H2O loss and slow growth
        
        Pathway:
        
        In the dark. open stomata permit CO2 entry and H2O loss; CO2 uptake and fixation; leaf acidification
        
        In light, closed stomata prevent H2O loss and CO2 uptake; decarboxytlation of stored malate and refixation of internal CO2; deacidification of leaf
        
        carbon partitioning acts as the metabolic fate of photosynthetic products, with TP as a decision point
        
        sucrose is synthesized directly from photosynthesis during light or synthesized from starch at night
        
        starch is accumulated during the day and converted to sucrose during the night
        
        starch is main storage carbohydrate, second only to cellulose in abundance; long linear chains of glucose units; packs into regular semi-crystalline arrays leading to insoluble granules
        
        two main types
        
        2 more items...
        
        Starch synthesis occurs in three steps:
        
        3 more items...
        
        Starch degradation requires phosphorylation of starch granules
        
        3 more items...
        
        use of triose-phosphates and triose-phosphate translocators
        
        cytosolic F-1,6-P2 phosphatase (F-2,6-P2); cytosolic PP-F6P kinase (F-2,6-P2); F-1,6-P2; F-2,6-P2
        
        FAMILIARIZE WITH P198-201
        
        sucrose-phosphate synthase
        
        allosterically regulated--activated by G6P and inhibited by Pi
        
        protein phosphorylation--activated in light and inactivated in dark
        
        chloroplastic F-1,6-P phosphatase interacts with thioredoxin system
        
        ADP-Glucose pyrophosphorylase activated by thioredoxin
        
        Trehalose-6-phosphate links leaf carbon metabolism in cytoplasm to starch synthesis, with positive correlation; trehalose synthesis controlled by levels of UDP-glucose and glucose-6-phosphate
        
        C4 mechanism both spatially and temporally separate from C3 photosynthesis
        
        malate stored in vacuole at night
        
        utilize C3 pathway during day
      - some plants exhibit little to no PR
      - works as add on to C3 photosynthesis
    - - 200B tons of CO2 fixed per year
      - 40% fixed by phytoplankton
    - - is rising
      - C3 plants grow better at elevated CO2 due to lower photorespiration
      - CO2 enrichment used in greenhouses, with nutrients and light optimized
    - - photosynthesis requires diffusion of CO2 into leaf to rubisco, with cuticle preventing CO2 diffusion and stomata regulating CO2 diffusion
      - water and CO2 move in opposite directions in same pathway
    - - infrared gas analyzer
      - net photosynthesis
      - net CO2 fixation
      - net CO2 assimilation
    - - FAMILIARIZE P121
      - CO2 compensation point where net photosynthesis = 0, with photosynthesis = respiration
    - - most stable carbon isotope: 12C, followed by 13C
        
        12CO2 diffuses faster than 13CO2
        
        Rubisco discriminates against 13CO2
        
        PEPCase discriminates against 13CO2 to a small degree
- - - - PET generates negative change in proton motive force across thylakoid membrane
        
        H+ translocated from stroma to thylakoid lumen
        
        water-splitting reaction in thylakoid lumen
      - Dissipation of electrochemical gradient occurs through ATP synthase
  - - - derived from primitive cyanobacterium
      - dual membrane system
      - maternal inheritance pattern
    - - circular DNA chromosome that may be linear but branched
      - divides by fission
      - replicates independently of nucleus, with the number within a cell type remaining constant and with some coordination with the nucleus
      - 70S ribosomes for protein synthesis, inhibited by CAP
  - - - tRNAs
      - ribosome components (rRNAs, ribosomal proteins)
      - some PET components
    - - ctDNA + mtDNA = 1/3 Nuclear DNA
      - Chloroplast genome increases polyploidy with maturity
        
        immature leaf: mtDNA > ctDNA
        
        mature leaf: ctDNA > mtDNA
  - - - inherited maternally via egg cell
      - Proplastid phenotype:
        
        few (if any) internal membranes
        
        no chlorophyll
        
        incomplete complement of photosynthetic enzymes
        
        found in meristematic cells
      - Conversion to chloroplasts:
        
        requires light
        
        rapid enzyme formation from chloroplast and nucleus genes
        
        Formation of light-absorbing pigments (chlorophylls, carotenoids)
        
        Rapid membrane proliferation (stromal lamellae, grana stacks)
      - Conversion to etioplasts:
        
        occurs in seedlings maintained in dark
        
        prolamellar bodies formed (semicrystalline tubular arrays)
        
        accumulation of protochlorophyllide (pale yellow-green pigment, precursor of chlorophyll)
        
        Etioplast conversion to Chloroplast
        
        occurs within minutes in light
        
        prolamellar bodies become thyllakoid and stroma lamellae
        
        protochlorophyllide becomes chlorophyll
    - - morphogenesis
      - chlorophyll biosynthesis
- - - - lost e- replaced with e- from plastocyanin
      - a proton-pigment complex including chl a
      - very strong reducing agent; very unstable
      - light absorption by PSI initiates e- transfer
      - transfers e-to ferredoxin (Fd)
        
        Fd transfers e- to multiple molecules
        
        most e- used to produce NADPH for C3 carbon reactions
        
        some e- used to reduce thioredoxin to regulate various enzyme activities in chloroplast
        
        some e- used to convert NO2 to NH4 for incorporation into organic molecules
      - can operate in cyclic mode
        
        MEMORIZE PATHWAY
        
        Found in bundle sheath of C4 plants
        
        heterocysts of cyanobacteria
      - transforms far-red light into charge separation
      - absorbs maximally at 700 nm (far-red)
      - was experimentally isolated first, hence its name, but occurs second in pathway
      - genes that make up complex designated psaX
    - - absorbs maximally at 680 nm (red light)
      - was isolated experimentally second but occurs first in pathway
      - Genes that make up complex designated psbX
  - - - process determined by Jagendorf experiment: generation of electrochemical gradient in the dark without PET activity
      - Proton Motive Force
        
        MEMORIZE EQNS
        
        MEMORIZE PROCESS
        
        Change in pH is main component of change in proton motive force in chloroplasts
      - Chloroplast ATP Synthase
        
        CFo-CF1 ATP Synthase is a multimeric enzyme complex
        
        CFo: hydrophobic core
        
        forms channel that H+ pass through
        
        CF1 subunit: hydrophilic catalytic subunits
        
        peripheral membrane protein complex on stromal side of thylakoid with several protein subunits and regulatory units
        
        MEMORIZE MECHANISM P101
      - Chemiosmosis
        
        MEMORIZE MECHANISM P102
  - - - oxygenic photosynthesis
      - series of redox reactions
      - isolated chloroplasts oxidize and reduce many compounds inc. electron donors and electron acceptors and this is used to dissect PET
        
        use O2 electrode to monitor oxygen evolution
        
        use spectroscopy to monitor redox state of electron donors/acceptors
- - - - holoenzyme assembled in chloroplast, folded by chaperonins
      - 40% soluble protein in leaves
      - rbcS encoded in nucleus
      - rbcL encoded in chloroplast
      - Variations: L2 in non-sulfer bacteria and dinoflagellates; some brown, red, and green algae encode both rbcL and rbcS
    - - rubisco catalyzes CO2 fixation with product being 3-PGA in C3 photosynthetic pathway
      - CO2 concentration in solution relative to O2 is important
        
        increased temp leads to decreased CO2/O2
        
        rubsico active sites about 4 mM in stroma
        
        carboxylation favored, but O2 competes and reduces net photosynthesis
        
        CO2 concentrating mechanism deals with O2 problem
  - - - CO2 fixation yields two 3-PGAs
      - Initial fixation product is C3 acid
      - catalyzed by rubisco
    - - reduce 3-PGA to triose phosphate (TP)
      - C3 acid becomes C3 carbohydrate
      - Main site of NADPH and ATP use
    - - regenerate RuBP from TP
      - synthesis of C5 sugar-P
      - utilizes ATP
  - - - sucrose in cytoplasm
      - starch in chloroplast
      - regenerates RuBP
  - - - MEMORIZE ALL
      - MEMORIZE DIAGRAM P145
      - Ionic movements
        
        light induces H+ pumps (stromal pH goes from 7 to 8)
        
        pH alters Mg2+ distribution
      - Enzymes that require Mg2+ for catalysis more active at alkaline pH, including rubisco and others
    - - Rubsico Activase
        
        removes bound substrate before carbamylation
        
        carbamylation
        
        removes carboxyarabinitol-1-P (natural inhibitor that binds in dark and is removed in light)
        
        activation step requiring CO2 binding
        
        uses non-catalytic CO2
      - Ionic regulation
        
        final activation state requires Mg2+ complex
        
        optimum activity at alkaline pH
    - - thioredoxin coordinates PET activity with other pathways or processes
      - mechanism of action:
        
        PSI reduces Fd via PET
        
        Fd-thioredoxin reductase
        
        transfers electrons and reduces disulfide bridge to dithiols
        
        Thioredoxin reduces target enzyme by altering enzyme activyt or sensitivity to allosteric effectors
        
        dithiols on enzyme oxidized by O2
      - Light-regulated C3 Enzymes
        
        MEMORIZE, MEMORIZE, MEMORIZE FOUR ENZYMES REGULATED P150
        
        glyceraldehyde-3-phosphate dehydrogenase
        
        Phospho-ribulokinase
        
        Fructose-1,6-Bisphosphatase
        
        Sedoheptulose-1,7-Bisphosphatase
      - Thioredoxin-Inactivated Enzymes
        
        inhibits enzyme G6PDH, thereby inhibiting the oxidative pentose phosphate pathway
        
        oxidative pentose phosphate pathway changes NADP+ to NADPH in chloroplast
      - Supercomplex Formation
        
        complex formation regulated by ratio of oxidized and reduced thioredoxin
        
        the more light there is, the more reduced thioredoxin is present
        
        increased oxidized thioredoxin results in oxidization of CP12 and creation of complexes that bind the enzymes PRK and G3PDH to inactivate them
        
        increased reduced thioredoxin dissociates CP12 complex to allow PRK and G3PDH to become active
- - - - epidermal cells
      - guard cells/stomata
  - - - epidermis
        
        transparent cells without pigments
        
        convex shape focus light like lens
        
        increases internal light intensity several fold
        
        important in shade species
      - Palisade mesophyll (paranchyma)
        
        columns of closely packed cells
        
        sieve effect
        
        only chloroplasts absorb light
        
        chloroplasts not uniformly distributed
        
        gaps in light absorption
        
        more light absorbed by equal concentration of chlorophyll in solution than by chloroplasts
        
        light channeling
        
        light transmitted via intracellular spaces, cell walls, and central vacuole to cells below
        
        no chloroplasts in these structures
      - Spongy mesophyll cells
        
        irregular shaped cells around large air spaces
        
        reflects light within leaf, resulting in light scattering and a path of light 4x leaf thickness
        
        results in more uniform light absorption across entire leaf
    - - high light environments such as deserts
        
        potentially dangerous light levels
        
        modifications to reflect light such as hairs, salt glands, and epicuticular wax
        
        decrease light absorption by 40%
    - - low light
        
        chloroplasts align along cell surface parallel to plane of leaf lamina
        
        perpendicular to incident light
      - High light
        
        chloroplasts align along sides of cell
        
        chloroplasts shade each other
        
        reduces light absorption about 15%
      - Move along cytoskeleton
        
        usually respond to blue light
        
        phototropins (PHOT) are blue light receptors
        
        PHOT activates protein kinase and induces a rapid change in cytoskeleton
        
        some species respond to red light using phytochromes
  - - - heliotropism
        
        diaheliotropic
        
        paraheliotropic
      - maintains maximal light harvesting throughout day, maximizes photosynthesis when water loss is lower
      - nyctinasty
        
        MEMORIZE MECHANISM
- - - - MEMORIZE MECHANISM
    - - blue: shorter wavelength, high energy, high excited state
      - red: long wavelength, low energy, low excited state
  - - - Light Harvesting complex II (LHCII)
        
        associated primarily with PSII
        
        trimeric transmembrane complex, with each monomer containing three alpha helices spanning the thylakoid membrane and 14 chl a and chl b molecules plus four carotenoid molecules
      - Light harvesting complex I (LHCI)
        
        associated primarily with PSI and structurally similar to LHCII
      - chlorophyll a/b antenna proteins are members of a large family of structurally related proteins
    - - energy of excited RC used for phytochemistry
    - - FAMILIARIZE P62 DIAGRAM
- - - - long-wave radiation
      - sensible heat loss via conduction/convection of heat to cool air
      - evaporative heat loss (latent) via evaporative cooling and transpiration
      - isoprene emissions related to heat dissipation
        
        gives forest odor and blue haze
        
        transgenic plants without isoprene emission more heat sensitive
    - - Bowen Ratio = sensible heat loss / evaporative heat loss
        
        MEMORIZE
      - in well-watered plants, increased transpiration = decreased Bowen ratio
      - on a still day, decreased sensible heat loss means decreased bowen ratio
      - approaches infinity in desert plants
      - may be negative--cotton leaves cooled below air temp by evaporation, resulting in sensible heat flow into leaf
    - - high CO2: rubisco saturated; limited by light reactions
      - ambient CO2: rubisco limits
- - - - Chlorophylls
        
        FAMILIARIZE WITH TRAITS AND VARIATIONS
      - Carotenoids
        
        FAMILIARIZE WITH TRAITS
      - Phycobiliproteins
        
        FAMILIARIZE WITH TRAITS
    - - Each pigment has a unique absorption spectrum that overlaps with that of other pigments