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    Glossary - Botany Plant Physiology

    Hi,

    I thought this would make a good sticky, as one member, at least, has expressed frustration at the terms often used in plant physiology. I hope this helps some folks, it's not perfect, but it a good resource.

    Glossary - Botany Plant Physiology
    http://web.archive.org/web/200610012.../plant-phy.pdf



    #2
    Outstanding resource spurr.
    I'm in it for the tomatoes. I been growing tomatoes for a long long time. Sometimes I get to thinking I know everything about tomatoes.
    My tomatoes make me completely delusional.

    Comment


      #3
      tnx, I thought you would dig it

      Comment


        #4
        Welcome back Spurr.
        RIP Moth - A brother never met always known! Peace be upon you now and forever!

        How do you leave this world? Better or worse than you enter it? This is the measure of success, not money in the bank or stuff in your house but the measure of impact whether positive or negative that you make in the world in which you live.

        Comment


          #5
          tnx

          Comment


            #6
            Nice to see you back senor spurr. Don't know you, but your contributions have definitely provided (and still provide) me much novel and useful reading material. great link. bookmarked
            breath...

            Comment


              #7
              thanks spurr this would be a good sticky.
              My contributions to this website in no way imply support for any political or cultural views promoted here.
              -----
              To the large and singular furniture of this noble island i have added from foreign places all the variety of herbs and flowers that i might any way obtain. I've laboured with the soil to make it fit for plants, and with the plants that they might delight in the soil - so they might live and prosper under our climate as in their native and proper country.
              Gerard's Herbal (1636)

              Comment


                #8
                thank you spurr ... great resource, as most of your posts too

                Comment


                  #9
                  Thank you for the link! I would also like to recommend Hartmann and Kester's Plant Propagation: Principles and Practices (7th Edition). I'm using it in my Plant Propagation class right now.

                  Comment


                    #10
                    here is the glossary cut and pasted (except for the diagrams on the last page) i'll edit in the bold script for the words at some point!

                    Glossary - Botany Plant Physiology
                    Abscission: The dropping off of leaves, flowers, fruits, or other plant parts, usually following the formation of an abscission zone.
                    A. Zone: The area at the base of a leaf, flower, fruit or other plant part containing tissues that play a role in the
                    separation of a plant part from the main plant body. ATP (adenosine triphosphate): A nucleotide consisting of adenine, ribose sugar, and three phosphate groups; the
                    major source of usable chemical energy in metabolism. On hydrolysis, ATP loses one phosphate to become adenosine diphosphate (ADP), releasing usable energy. ATP Synthase: An enzyme complex that forms ATP from ADP and phosphate during oxidative phos- phorylation in the inner mitochondrial membrane. During photosynthesis formed in the PS I photo-reaction: ADP+Pi →ATP
                    Allelophathy: (Gk. allelon, of each + pathos, suffering) The inhibition of one species of plant by chemicals produced of another plant.
                    Bacterium: An auto- or hetero-trophic prokaryotic organism. Cyanobacterium: Autotrophic organism capable of fixing nitrogen from air (heterocyst) and utilizing light energy to accomplish its energetical requirements. • Chloroplast: The thylakoids within the chloroplasts of cyanobateria are not stacked together in grana, but
                    randomly distributed (lack PS II, cyclic photo-phosphorylation).
                    Oxygenic photosynthetic reaction: CO2 + 2H2O → (Elight = h⋅f) → CH2O≈P → (CH2O)n + H2O + O2 • Heterocyst: Site of N2 fixation; a specially differentiated cells, working under anoxic onditions (H2 would
                    combine with O2 to form water). Ferrodoxin taking part in the nitrogenase reaction, is reduced via a strongly exergonic reaction which is fueled by energy from photosynthesis of neighboring cells, probably maltose, which is broken down in the heterocyst (see also cycle N2-fixation): N2 + 8e- + 10H+ → (nitrogenase) → H2 + 2NH4+(strongly exergonic, ammonium, used in amino acids)
                    Halobacterium: A color-sensing chemo-autotrophic bacterium (contains rhodopsin) capable of phototaxis (move to/fro a light gradient with a H+ powered flagellar motor); the purple pigment changes the absorptive spectrum under the influence of light 570 nm to 412 nm) yielding H+ protons. The externally generated pH gradient drives phosphorylation of ADP to ATP via passive back diffusion. C-fixation is achieved by using H2S; since this process results in a solid product, sulfur will be deposited in the soil. Anoxygic photosynthesis does not require two photosystems since the energy level to split H2S is lower than that one of water (H2O). Anoxygic photosynthesic reaction: CO2 + 2H2S → (Elight = h⋅f) → (CH2O) + H2O + 2S
                    Rhizobium: Flagellated, free-living heterotrophic soil bacteria. Approach chemotactically the rhizosphere of a susceptible root-hair, proliferating into it, causing curling growth. Rhizobia fuses with the plasma membrane of the root hair cell (without infecting them, separated by a peribacteroid membrane), tunnel through the cytosol of the cortex, force cortical- and pericycle cells to divide until in touch with the vascular tissues. Once there, bacterial colony stops dividing, enlarges, and differentiate into N2-fixing endosymbiotic organelles (nodules). In exchange from fixed nitrogen (NH4+), the host provides C-compounds and a highly regulated watery O2 environment. Since O2 is a potent inhibitor of nitrogenase, “infected“ cells produce large quantities of the O2 binding leghemoglobin to keep its partial pressure at 21% but that of N2 below 78%; see cycle, nitrate fixation.
                    Calvin Cycle: see CO2-pathway, or plant types. CO2 Pathways: The conversion of CO2 to basic sugars during photo- or chemosynthesis can be fixed in plants in
                    various ways based on their carbon-fixing metabolism; see plants, types of. Carnivorous Plants: A semi-autotrophic plant, feeding upon animals; see motility. Chemosynthesis: Chemosynthetic organisms derive their energy requirements from the oxidation of inorganic
                    material; as performed by hydrogen bacteria etc.; see carbon cycle.
                    6CO2 + 12H2S → C6H12O6 + 6H2O + 12S Chlorophyll: see photosynthetic pigments. Chloroplast: A two-membranous plastid containing pigments (chlorophyll and carotenoids); see photosynthesis. Circadian Rhythm: The biological clock; see motility.
                    plants) • Respiration: Consumption of oxygen to obtain energy (light independent!)
                    2NADP+ + 2H+ → (Elight = h⋅f) → 2NADPH
                    2
                    Coenzymes: An organic molecule, or nonprotein organic cofactor, that plays an accessory role in enzyme-catalyzed processes, often by acting as a donor or acceptor of electrons. NAD+ (nicotinamide adenine dinucleotide): A coenzyme that functions as an electron acceptor in many of theoxidation reactions of respiration.
                    NADP+ (nicotinamide adenine dinucleotide phosphate): A coenzyme that functions as an electron acceptor in many reduction reactions of biosynthesis; similar in structure to NAD+ except that it contains an extra phosphate group. During photosynthesis in the PS II photoreaction, NADP+ is converted to NADPH: 4NADP+ + 4H+ → (Elight = h⋅f) → 4NADPH (is 7 times more efficient as an energy carrier than ATP)
                    Cycle: Bio-geochemical cycles on a global and local scale. Carbon C.: Is in equilibrium between the photo autotrophic plant kingdom, the heterotrophic animal kingdom and microorganisms. The final breakdown (mineralization) of organic matter bound in living systems is executed by bacteria and fungi by aerobic breakdown, and frequency by anaerobic degradation (fermentation). Besides the CO2 which returns to the atmosphere, there is also carbon which is deposited in the form of carbonates in the oceans. • Photosynthesis: Conversion of light energy to chemical energy; see there
                    CO2 Fixation: CO2 can be fixed via a photosynthetic pathway or a chemosynthetic pathway:
                    Light dependent reaction Photosyn.: 2H2O → (Elight = h⋅f) → O2 + 4H+ + 4e-
                    (algae, and ADP + Pi → (Elight = h⋅f) → ATP
                    Light independent reaction CO2 + H2O → CH2O≈P → (CH2O)n 2NADPH → 2CH2O≈P → 2NADP+ + 2H+
                    Chemosyn.: 2H2 + O2 → 2H2O CO2 + H2O → CH2O≈P → (CH2O)n
                    (H-bacteria) ADP + Pi → ATP 2NADPH → 2CH2O≈P → 2NADP+ + 2H+ • Fermentation: Catabolic reactions producing ATP; see microbiology. Nitrogen C.: Organic (NH3-) and inorganic (NO3-) linked via denitrification and atmospheric N2 fixation: • N2 Fixation.: The incorporation of atmospheric dinitrogen into nitrogen-compounds (usually ammonium
                    NH4+); carried out by certain free-living and symbiotic bacteria; see also bacterium: N2 + 8e- + 10H+ → (nitrogenase) → H2 + 2NH4+(ammonium, used in amino acids); exergonic NH4+ is assimilated by beans and other nearby plants, which itself are consumed by herbivores; the released feces (nitrate) is converted back to ammonium ions in a process known as ammonification.
                    • Ammonification: Decomposition of amino acids and other nitrogen containing organic compounds, resulting in the production of ammonia (NH3) and ammonium ions (NH4+) ready to be taken up again. Nitrate Fixation: The conversion of nitrate (NO3-) into amino nitrogen by heterotrophoc organs (roots) or by symbiotic organisms (Nostoc sp.) and takes place in leucoplasts. Although this process is light- independent, ATP used in these steps are generated during light-dependent carbon fixation:
                    NO3-(cytoplasma) + NADPH + H+ → (nitrogen reductase) → NO2- + NADP + H2O NO2-(chloroplast) + 6ferredoxin (e-donor) + 8H+ → (nitrite reductase) → NH4+ + 2H2O NH4+ + 2-oxoglutarate + 2H+ + ATP* → glutamate + H2O + H+ + ADP + Pi
                    *) Conversion of the ammonium ion (NH4+) into organic compounds happens in chloroplasts (in tough competition with CO2 reduction for ATP and free “e-“) predominately through a 2-step reaction in which glutamine serves as intermediary product. The successor glautamate is then used as an amino group donor for various 2-oxo acids, e.g. oxaloacetate, within and outside the chloroplast (transamination).
                    • Denitrification: Conversion of nitrate to gaseous nitrogen in which ammonia is oxidized, summarized in four enzymatic reactions yielding nitrogen; carried out by a few genera of free-living soil bacteria.
                    NO3-(nitrate) → NO2-(nitrite) → NO(nitric oxide) → N2O(dinitric oxide) → N2 (dinitrogen) Oxygen C.: It is complementary to the carbon cycle; in contrast to CO2 in photosynthesis, O2 is due to its high concentration in the atmosphere, no longer a globally limiting factor. In water, however, it is often not possible to supply enough O2 for the complete mineralization of dead organisms, leading to the deposition of organic materials; respiration and photosynthesis are elementary steps within the oxygen cycle. Water C.: Evaporation from the oceans precipitates on land; runoffs (rivers and streams) close the loop.
                    Defense Mechanism of plants: Effective protection is often achieved by physical means (thorns,. Leaf hairs, sticky sap) but also chemically (cyanides, camphor, tannins, cocaine, caffeine, nicotine, morphine, salycilic acid, etc.). Injured areas are usually walled off (compartmentalization) with resins.
                    Growth of Plants: Growth proceeds in an irreversible sigmoidal increase in size (slow, fast, slow, adult plant). The roots are the first structure to emerge (rhizoid pole) anchoring the germinating seed. Light controls elongation of hypocothyl (HC), the thallus pole; see also photosynthetic pigments - phytochrome: • Germinated, darkness promotes a huge increase in length of the HC, otherwise remain dormant.
                    • Blue light triggers germination, orientation toward light source, lateral branching and greening of HC.
                    • Red-light causes the HC to remain short (slow vertical cell elongation) but green (photosynthetic active); Heat: Many plants, (e.g.: aroids) when inflorescence is ready for pollination, generate heat by oxidizing large
                    amounts of stored food, manly fats (up to 1/4 of their total weight a day). The heat (up to 30°C above ambient temp.) causes bad smelling amines to emanate attracting pollinating insects (flies, etc.). A common fuel is known to be salicylic acid (similar to aspirin). Since many of these plants flower in late fall, trapped pollinating insects are kept warm during the night to be released, loaded with pollen, the morning after.
                    Hormones of Plants: (Gk. hormaein, to excite) Chemical-organic substances that regulate growth, flowering, etc. released by the action of light (phytochromes), water, temperature, or other influences. Some hormones act locally while others are transported to distant tissues, where they produce specific physiological responses; others act within the same tissue where they are produced.
                    • ABA (abscisic acid): (L. abscissus, to cut off) Growth inhibitor; brings about dormancy in buds, maintains dormancy in seeds (until washed out), and brings about stomatal closure, promotes yellowing of leaf; ABA levels increase during early seed development preventing premature germination; opposes growth hormones, among other effects. Travels short distances in leaves and fruits.
                    • Cytokinins: Promote growth; Stimulates cell division; kindle growth in lateral buds, and block leaf senescence. Chemically related to adenine. Transported from roots upward in vascular system.
                    • IAA (indoleacetic acid) or Auxin: (Gk. auxein, to increase) Promotes growth; controls cell elongation (increases number of H+-pump in tonoplast - extension of vacuole), inhibit growth of lateral buds (apical dominance), orient root/shoot growth, promotes cell division, root growth, at low concentration prevents abscission of leaves and fruits, among other effects. Excess auxin-dosage causes death due to growth beyond sustainability. Tryptophan is the precursor of IAA; IAA occurs in the tips of shoots, leaf premordia, young leafs and is transported down to the root tips of the vascular cylinder.
                    • Ethylene: Promotes maturation; a simple hydrocarbon involved in the ripening of fruit (transported via air-currents), leaf/flower abscission, and senescence (collapse of lytic compartment); (H2C = CH2). Plays a major role as a perhormone by communicating to neighboring plants attacks of herbivores, triggering the production of defensive chemicals.
                    • Gibberellines: Promote growth; stimulate both cell division and cell elongation, causes bolting (without the need to expose plant to cold or long days), new leaves, branches, flowering, larger and looser fruits, among other effects. Seeds need higher levels to germinate (conversion of starch to sugars); low levels in young plants cause dwarfism, high levels the opposite; is transported up-/downward in vascular system.
                    Auxin and gibberelline stimulate plant growth by increasing the extensibility of cell walls. • Jasmonate or jasmonic acid: Growth inhibitor; a methylester occurring in the oil of jasmine. It inhibits
                    growth of certain plants and promotes leaf senescence (deterioration and aging). Law of the Minimum: The growth of a plant is dependent upon the amount of “foodstuff“ (trace elements) presented
                    to it in minimum quantities (J. Liebig). Light Compensation Point: CO2 fixation balanced by mitochondrial respiration; see photosynthetic response. Light Dependent Reaction: Photosynthetic reaction in the photosystems I & II that require light and cannot occur in
                    dark; see photosynthetic proteins and photosynthesis. Light Independent Reaction: The enzymatic reaction (calvin cycle) in photosynthetic cells concerned with the
                    synthesis of glucose (more stable and compact than ATP and NADPH) from CO2, ATP, and NADPH; see
                    plants- types of and photosynthesis. Light Shielding: Absorption (conversion into heat) of excessive light; see tropism (cytoplasmic streaming) and
                    photosynthetic pigments (xanthophyllic carotenoids). Malate (malic acid): A C4 compound and the end-product of the C4-pathway. Used as a counter ion for K+ uptake,
                    and to supply H+ for the proton pump (intercellular pH regulation) and is the product of the C4 pathway of the CO2 fixation; see there. During stomatal opening, starch in the guard cells is broken down via glycolysis to phosphoenolpyruvate, which is used with CO2 uptake to form malate, therefore the level of malate increases;
                    My contributions to this website in no way imply support for any political or cultural views promoted here.
                    -----
                    To the large and singular furniture of this noble island i have added from foreign places all the variety of herbs and flowers that i might any way obtain. I've laboured with the soil to make it fit for plants, and with the plants that they might delight in the soil - so they might live and prosper under our climate as in their native and proper country.
                    Gerard's Herbal (1636)

                    Comment


                      #11
                      Mesophyll: The ground tissue (parenchyma) of a leaf, located between the layers of epidermis; it is structured into pallisade- and spongy parenchyma, housing chloroplasts which contain chlorophyll (site of photosynthesis).
                      Motility of Plants: Even though plants cannot move actively across a given area (except adventitious root development) it possesses various ways of motion, which requires ATP: Insectivory: Feeding upon animals; plants that are able to utilize proteins obtained from trapped animals, chiefly insects; e.g. venus fly trap, in which inward-lying cells are elongated by virtue of the high vacuole- turgor-pressure; once an insect touches the trigger-hairs the flaps snap shut rapidly (deflation of stretched cells consumes ATP), pressing the insect against digestive glands on the inner surface of the trap. The trapping mechanism is so specialized that it can distinguish between living prey and inanimate objects.
                      Tropism: (Gk. tropes, turning) A growth response involving bending, curving of a plant part towards (positive) or away (negative) from an external stimulus that determines the direction of movements. • Gravitropism: (L. gravis, heavy; also geotropism) Response of a shoot or root to the pull of the earth’s
                      gravity. Roots grow downwards, positive gravitropism (high levels of auxin inhibit growth in roots), whereas shoot grows upwards, negative gravitropism. Roots are more sensitive to the response of auxin than stems (high auxin concentration, inhibits root growth). Perception of gravity is correlated with sedimentation of amyloplasts (starch containing statolithic plastids) w/n specific cells of shoot and root.
                      • Heliotropism: (Gk. helios, the sun) Ability of the leaves and flowers of many plants to move diurnally, orienting themselves either perpendicular or parallel to the sun’s direct rays; also called heliotropism. Diaheliotropism: the movement of the leaves is such that the broad surfaces of the blades remain perpendicular to the sun’s direct rays, resulting in a higher photosynthetic rate.
                      Paraheliotropism: Avoiding direct sunlight during periods of drought by orienting leaf blades parallel to
                      the sun’s rays. Minimizes absorption of solar radiation, lowers leaf temp., and transpirative water loss. • Phototropism: (Gk. photos, light) Growth movement of cells or organs in which light plays a decisive
                      role, and is related to the direction of light as the controlling external factor; e.g.: growth of a plant toward a light source by the influence of auxin; the cells of the shaded side of the tip migrates from the light-side to the dark-side, resulting in a turn or bend (compare photoperiodism). Cytoplasmic streaming: The plasma in the cell rotates and circulates actively under the influence of light. Particles in the protoplast such as nucleus, mitochondria, and plastids are often carried passively. Chloroplastic Orientation: Active repositioning of chloroplasts in the cytoplast of the mesophyll cells.
                      i) Diastrophic: Dark-light position, with max. light absorption i.e.: perpendicular to incoming light.
                      i) Parastrophic: Bright-light position; reduced light absorption; i.e.: almost parallel to incoming light. • Thigmotropism: (Gk. thigma, to touch) Response to contact with a solid object as seen in tendrils. They
                      wrap around any object with which they come in contact, and so enable the plant to cling and climb. NADx: see coenzymes.
                      Oxaloacetate: ): The C4-molecule formed in C4- plants, i.e.: the krebs cycle; the product when Pi is split off from PEP. Depending on the species, oxaloacetate is either reduced to malate or converted to asparate (additional amino group NH2), both C4 -compounds. Malate or asparate is a mediator transporting CO2 used in the calvin cycle.
                      Pathogen: (Gk. pathos, suffering + genesis, beginning) An organism that causes disease. PEP or Phosohophenolpyruvate: The compound to which CO2 binds in C4-plants. PEP converts under the influence
                      of CO2 to oxaloacetate, which is either reduced to malate (malic acid) or asparate (extra amino group NH2). Peroxisome: A microbody that plays an important role in glycolic acid metabolism associated with photorespiration. PGA (3-phoshoglycocerate): The C3-sugar formed in C3- plants, i.e.: the calvin cycle. Phosphoryltation: (Gk. phosphorous, bringing light) A reaction in which phosphate is added to a compound; e.g.:
                      the formation of ATP from ADP (PSI), NADPH from NADP+ (PSII) and inorganic phosphate; see photosystem. Photo-P.: (Gk. photos, light) The formation of ATP in the chloroplast during photosynthesis. Cyclic Photo-Phosphorylation: A photosystem lacking PSII, yielding only small amounts of ATP an no NADPH; a very ancient type of photosynthesis.
                      Noncyclic Photo-Phosphorylation: The modern type of plant having both PS I & II - the zigzag scheme providing both ATP, and the more efficient energy carrier NADPH.
                      Light dependent reaction: Light is required to generate ATP and NADPH.
                      PSII: 2H2O → (Elight = h⋅f) → O2 + 4H+ + 4e- ADP+Pi →(Elight =h⋅f)→ATP
                      5
                      Photoperiodism: Response to duration and timing of day and night; a mechanism evolved by organisms for measuring seasonal time. Plants that flower only under certain day-length conditions; and is a biological response to a change in the proportions of light and dark in a 24 hour daily cycle. • Short Day Plants: Flower in early spring or fall when days are shorter with less intense light.
                      • Long Day Plants: Flower in the summer, when the light periods are longer than the critical length.
                      • Day Neutral Plants: Flower without respect to length of the day. Photorespiration: see plants, types of - C3-plant. Photosynthesis: (Gk. photos, light + syn, together + tithenai, to place) Conversion of light energy to chemical energy;
                      PLANTS: Solar radiation is used by plants to oxidize water, reduce CO2, and release of O2. Plants use <5% of the radiant energy, the majority is reflected or lost as heat; see also cycle-carbon. Chloroplast: A two-membranous plastid containing pigments (chlorophyll and carotenoids); most active photosynthetic tissue in higher plants is found in the pallisade parenchyma of leaves (mesophyll).
                      • Granum: Stacks of thylakoids seen with electron microscopes, and as green granules with light microscopes; grana contain chlorophylls and carotenoids; see also photosynthetic pigments.
                      • Stroma: (Gk. stroma, to spread out) Ground substance, aqueous region of plastids; the site of reactions by which photochemical energy is used to synthesize carbon containing compounds (site of dark reaction). • Thylakoid: (Gk. thylakos, sac + oides, like) A saclike membranous structure in cyanobacteria and grana in
                      eukaryotic autotrophic organisms (stacks of thylakoids form grana); chlorophyll pigments are found within
                      the thylakoid membranes (site of light dependent reaction). Intense photosynthesis, causes some of the photosynthate to be stored temporarily in chloroplast as starch- grains; sugars are transported via phloem to target cells (root) for nourishment and to produce cellulose.
                      Light independent reaction (dark reaction in the stroma of photosynthetic cells), the enzymatic reactions resulting in the synthesis of glucose from CO2, ATP; and NADPH;
                      CO2 +H2O→CH2O≈P→(CH2O)n
                      PSI: 2NADP+ + 2H+ → (Elight = h⋅f) → 2NADPH Nitrate (NO2-) conversion to ammonium (NH4+) occurs in chloroplasts as well, hence, in stark competition for ATP and free electrons with the carbon fixing process! Allover oxygenic photosynthesic reaction: CO2 + 12H2O → (Elight = h⋅f) → C6H12O6 + 6H2O + 6O2 An/oxic autotrophic organisms use light energy to satisfy their energetical requirements; anoxic bacteria derive their H+ protons from chemical compounds other than H2O requiring less energy to be split); see bacterium. Phototrophic anoxic reaction: CO2 + H2S → (Elight = h⋅f) → CH2O + H2O + S
                      2NADPH → 2CH2O≈P → 2NADP+ + 2H+
                      6
                      Photosynthetic Pigments: A substance that absorbs light, often selectively. P. Spectrum: The spectrum of light waves absorbed by a particular pigment eliciting a certain reaction; gamma rays (short wavelength) are too energetic (destroy biological molecules), radio waves don’t excite them at all. Carotenoids: A class of fat-soluble pigments (yellow and orange pigments); found in chloro- and chromo- plasts of plants. Carotenoids act as accessory pigments in photosynthesis. • β-C.: A yellow to red carotenoid with the empirical formula C40H56, found in fruits e.g.: pericarp of
                      tomatoes. • Fucoxanthin: (Gk. phykos, seaweed + xanthos, ye/br) Brownish pigment of brown algae and
                      chrysophytes. • Xanthophyll: (Gk. xanthos, yellowish-brown + phyllon, leaf) A yellow fat-soluble light shielding pigment.
                      Light Shielding: Besides cytoplasmic streaming, xanthophyllic carotenoid absorb excessive light (electromagnetic radiation) to protect the photosynthetic complex from overexposure by converting EMR it into heat; light converts violaxanthin into zeaxanthin which deactivates the antenna complex of the photosystem, preventing photodistruction of chlorophyll by overexposition to pure O2.
                      Chlorophyll: (Gk. chloros, green + phyllon, leaf) The green pigment of plant cells, which is the receptor of light energy in photosynthesis; a tetrapyrrole ring structure on top with 4 internally placed N-atom, itself facing towards the centrally located Mg-atom; the entire complex is attached to a hydrophobic C20H39 phytol tail, which anchors the molecule into the photosynthetic thylakoid membrane; see table and scan below.
                      • C. a: blue-green; with an extra CH3 molecule attached at the opposite end of the tetrapyrrole. • C. b: yellow-green; aldehyde (CHO) instead of CH3 attached at the opposite end of the tetrapyrrole. Phycobilins: A group of water-soluble accessory pigments, which occur in the red algae and cyanobacteria. Phytochrome: A phycobilin-like pigment (photoreceptor for red and far-red light) found in the cytoplasm of plants and a few green algae; phytochromes do not participate in photosynthetic reactions. Plants contain phytochrome in two different inter-convertible forms: • Pr absorbs red light (660 nm), the biological inactive form of the protein (inhibits reactions, but allows
                      plant to grow pale and spindly, changes to Pfr (pigment fully reactive) when exposed to (red) light.
                      Phytochrome is continuously synthesized as Pr from its amino acid precursors. • Pfr absorbs far-red light (730 nm), the biological active form triggering reactions, e.g.: induces germination
                      flowering, dormancy, leaf formation, seed germination, shade detection, etc. by triggering the release of plant hormones via a cis-trans isomerisation (cascade amplification). Pfr is converted back to Pr when exposed to far-red light (darkness, dark reversion) or lost through hydrolysis by proteases.
                      My contributions to this website in no way imply support for any political or cultural views promoted here.
                      -----
                      To the large and singular furniture of this noble island i have added from foreign places all the variety of herbs and flowers that i might any way obtain. I've laboured with the soil to make it fit for plants, and with the plants that they might delight in the soil - so they might live and prosper under our climate as in their native and proper country.
                      Gerard's Herbal (1636)

                      Comment


                        #12
                        Photosynthetic Proteins: The protein complexes of PSI and PSII spatially separated within the thylakoid membrane indicating a one to one stoichiometric ratio between those two systems. Antenna: Large numbers of light collecting pigment serve as antenna, where the excitation transfer process in the antenna is a purely physical phenomenon and does not involve an chemical change. Chemical reactions first take place in the reaction center of PSII and PSI; subsequent reactions stabilize the unstable products of the initial chemical reactions.
                        Cytochrome: (cyt b6-f) Four different integral proteins, three of which contain iron that undergoes reduction to Fe2+ and then oxidation back to Fe3+ during electron flow. It mediates electrons generated by PSII towards the PSI reaction center. Cyclic Electron Flow: In chloroplasts, the light induced flow of electrons originating from and returning to photosystem I.
                        Noncyclic Electron Flow: The light-induced flow of electrons from water to NADP+ in oxygen-evolving photosynthesis; it involves both photosystem I and II. Photosystem: A discrete unit of organization of chlorophyll and other pigment molecules embedded in the stroma thylakoids of chloroplasts and involved with the light-requiring reactions of photosynthesis. Oxygenic photosynthesis requires two photosystems since the energy level to split H2O is very high. P680 and P700 refer to the wavelength of maximum absorption of the reactions center chlorophylls in PSII and PSI.
                        • PS II: A series of noncovalently bondend complex intrinsic polypeptides; associated with three peripheral (extrinsic) polypeptides, thought to aid in binding of Ca2+ and Cl-, both of which are essential for photolysis of water. The P680 core complex (LIGHT HARVESTING COMPLEX-II) receives red light energy by inductive resonance from a total of about 250 chlorophyll a and b molecules (associated with few integral chlorophylls + xanthophylls proteins which act as an antenna system), producing a strong oxidant (oxidizes water) and a weak reductant: f, frequency [s-1] [Hz]
                        2H2O → (Elight = h⋅f) → O2 + 4H+ + 4e- h, plank’s c. 6.63⋅10-34 [J⋅s] more precise: 2H2O + 4 photons + 2 oxidized plastoquinone (2PQ) → O2 + 4H+ + 2 reduced plastoquinone (2PQH2) 2PQH2 + 4 plastocyanin (4PC-Cu2+) → 2PQ + 4PC(Cu+) + 4H+ (lumen)
                        The increasing H+ concentration (low pH causes an electrochemical proton gradient) within the lumen of the thylakoid is used to synthesize ATP, when H+ tunnels back out to the stroma through the integral coupling factors (CF’s): ADP + Pi → ( H+) → ATP PS I: Even though it uses (far) red light independently, PSII recruits electrons originally released by the PSII H2O-lysis mediated via the cytochrome complex. This reaction causes cytochrome to transport H+ ions across the membrane from the stroma into the thylakoid membrane (further decrease of internal pH). Two large polypeptides bind the reaction center P700, some chlorophyll a molecules and three electron carriers (NADP+) called phylloquinone and a Fe-S group. The PSI core complex receives light by inductive resonance from about 100 chlorophyll a and b molecules formed to an other antenna system (LIGHT HARVESTING COMPLEX-I). The strong reductant produced by PSI reduces NADP+, to NADPH, which is released into the stroma: f, frequency [s-1] [Hz
                        2NADP+ + 2H+ → (Elight = h⋅f) → 2NADPH] h, plank’s c. 6.63⋅10-34 [J⋅s] more precise: 4PC(Cu+) + 4Fd(Fe3+) → (Elight = h⋅f) → 4PC(Cu+) + 4Fe(Fd2+) 4Fe(Fd2+) + 2NADP+ + 2H+ → 4Fd(Fe3+) + 2NADPH
                        Photosynthetic Products: Most of the fixed carbon is converted either to sucrose, the major transport sugar, or to starch, the major storage carbohydrate in amyloplasts and in the stroma (temporarily) of plants. Sucrose (disaccharide) is favored over glucose (monosaccharide), to avoid digestion of monosaccharides during transportation down the phloem by those cells. Once arrived at target tissues, disaccarides are cleaved into glucose and fructose.
                        Photosynthetic Response: The dose-response of photosynthetic C-fixation as a function of photon flux. A C4 (sun loving) plant has a higher light compensation point, a higher maximal photosynthetic rate, than a C3 (shade) plant. Maximal saturation is determined by the slow-working carboxylase - see rubisco and plants, types of. Light Compensation Point: At this point, the amount CO2 evolved by mitochondrial respiration is balanced by the amount of CO2 fixed by photosynthesis.
                        Phytochrom: see photosynthetic pigments.
                        8
                        Plants, Types of : According to the light-independent reaction, CO2 fixation is achieved by the following: C3 P.: (Calvin cycle) Enzymatically mediated photosynthetic reactions of shade-plants during which CO2 is attached to ribulose, a C5-sugar (RuBP, a CO2 acceptor), yielding a C6-sugar which spontaneously breaks into 2 C3-sugars (3-PGA). Rubisco is resynthesized out of 5C3-sugars giving 3C5-sugars. Sugar-compounds can temporarily be converted to starch, stored in amyloplasts, and reconverted into sugars via ATP and NADPH to ADP and NADP+ (glucose is more stable and compact than ATP, NADPH) - see scan below:
                        6CO2 + 12NADPH + 12H+ + 18ATP → 1glucose + 12NADP+ + 18ADP + 18Pi + 6H2O • Photorespiration (PR): In C3 plants only; photosynthesis in C3 plants is always accompanied by PR, a
                        process that consumes O2 and releases CO2 in the presence of light. Since no ATP is yielded by PR, it diverts some of the light-depending reactions from biosynthesis of glucose into reduction of O2. Up to 50% of CO2 fixed in C3 plants may be again reoxidized to CO2.
                        C4 P.: Sun-loving plants; CO2 is fixed to a compound known as PEP (by the enzyme PEP carboxylase in mesophyll cells) to oxaloacetate (a C4 compound), which is rapidly converted to malic acid. This malate is then transported to bundle sheath cells (spatial separation), where the CO2 is released (turbo charger) converting back to pyruvate. The CO2 thus enters the calvin cycle, ultimately yielding sugars and starch. Pyruvate returns to the mesophyll cells for regeneration of phosphoenolpyruvate (PEP); requires more energy than in C3 plants.
                        • Spatial separation: Photosynthesis in chloroplasts of mesophyll cells, synthesis of sugars and starch in the bundle sheath; due to spatial separation no competition between O2 and CO2, hence no photorespiration.
                        CAM P.: (Crassulacean Acid Metabolism) Variant of the C4 pathway; phosphoenolpyruvate fixes CO2 in C4 compounds (PEP carboxylase) at night. The malic acid so formed is stored in the vacuole. During daytime, fixed CO2 (malic acid) will be decarboxylated and transferred to the ribulose biphosphate (RuBP) of the calvin cycle within the same cell. Characteristic of most succulent, slow-growing, desert-plants; e.g.: cacti.
                        • Temporal separation: CO2 fixation at night (dark reaction), photosynthesis at day (light reaction). RuBP (ribulose 1.5-biphosphate): A C5-sugar with two attached phosphate groups; the precursor of Rubisco and
                        PGA (calvin cycle); rubisco is later regenerated by the synthesis of 5C3-sugars to yield 3C5-sugars. Rubisco or RuBP carboxylase: A very abundant enzyme in chloroplasts that catalyzes initial reaction of the calvin
                        cycle (C3 plants), involving the fixation of CO2 to ribulose 1.5-biphosphate (RuBP); plants need a large
                        amount of this slow-working enzyme; up to 50% of leaf matter consists of carboxylase. Senescence: Aging of a plant by dissolving cell walls; see hormones - ethylene. Stomata: (Gk. stoma, mouth) Minute openings, bordered by guard cells in the epidermis of leaves and stems through
                        which gases pass (CO2, O2, H2O-vapor); the entire stomatal apparatus (guard cells plus pores). Guard Cell: Pairs of specialized epidermal cells surrounding a pore, or stoma; changes in turgor pressure of a pair of guard cells cause opening and closing of the pore. Stomatal Regulation: Stomatal movements results from changes in turgor pressure with in the guard cells. The major solute responsible for this gradient is potassium (K+); higher K+ and Cl- concentration causes stomata to open (water rushes in due to osmosis), whereas closure when it drops. Opening occurs when solutes are actively accumulated in these cells. Stomatal closure is brought about by the reverse process (a declining guard cell solute); water moves out of the guard cells lowering turgor pressure. Guard cells chloroplasts fix CO2 photosynthetically to form sugar, which contribute to the solute buildup required for stomatal opening. Environmental factors that effect stomatal movement: 1. Increase in CO2 concentration (sensors in guard cells, PEP & Rubisco) cause stomata to close. 2. Water shortage increases concentration of abcidic acid (ABA, originating from mesophyll) which causes
                        K+ to leave the guard cells resulting closed stomata. 3. Temperatures > 30 to 35°C causes stomatal closure. 4. Circadian rhythm (L. circa, approx. + dies, day) contribute to stomatal opening and closure. Stomata open
                        with light (blue light stimulate stomatal opening, independent of CO2 due to K+ uptake by the guard cells)
                        and close in darkness (red light stimulate stomatal closing). 5. Dryer air and wind accelerates dehydration of plant; water loss can be retarded by epidermal hairs or
                        stomatal openings lowered into the mesophyll. 6. Glycolytic breakdown of starch (in guard cells of C4-plants only) to PEP is used to form malate (along with
                        CO2), an increase level of malate, cause stomata to open. Tropism: A growth response involving bending, curving of a plant; see motility of plants.
                        My contributions to this website in no way imply support for any political or cultural views promoted here.
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                        To the large and singular furniture of this noble island i have added from foreign places all the variety of herbs and flowers that i might any way obtain. I've laboured with the soil to make it fit for plants, and with the plants that they might delight in the soil - so they might live and prosper under our climate as in their native and proper country.
                        Gerard's Herbal (1636)

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                          #13
                          Great resource spurr, thanks!

                          Comment


                            #14
                            @ all,

                            It appears the link I posted is now broken, so here is the same glossary from 2006, thanks to WayBackMachine:
                            http://web.archive.org/web/200610012.../plant-phy.pdf

                            I am also going to upload that glossary here.

                            Attached Files

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                              #15
                              Great resource, thanks

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