Hydrogen bacteria

A chemolithoautotroph which uses H₂ as its energy source.

Alveolates

A superphylum of Chromista photoautotrophs. Chlorolasts have three membranes: secondary or tertiary endosymbiosis. Unique xanthophylls, such as peridinin. Starch is stored in the cytosol. Membrane sacs are called alveoli. Includes dinoflagellates.

Anaerobic  ammonium oxidation bacteria

A type of chemolithotrophic bacteria. Anaerobic chemolithotrophs. Contribute 50 - 60% of global denitrification. Carbon fixation pathway is the reductive acetyl-CoA pathway. Perform denitrification; electron donor is NH₄⁺ and electron acceptors are NO₂^- and CO₂. Oxidized product is N₂. No photochemistry. First identified in 1999. Contain three intermemrbane compartments, and the centre one is the anammoxosome. Slow-growing; extracts electrons very slowly. Produces hydrazine as an intermediary metabolite. Can be used to purify nitrates from water.

NH₄⁺ + NO₂^- → N₂ + H₂O

"Receptacle seed"

A group of land plants. Consist of fifteen lineages, including monocots and dicots. Have flowers which enhance pollination. Seed is protected in an ovary. There is fruit dispersal. Have a dimorphic life cycle with diploid sporophyte and haploid gametophyte components.

Spirulina

Cyanobacteria that are grown commercially to make Spirulina food supplement. Does not contain active vitamin B₁₂.

Vitamin C

It has roles in plants as well as animals. Plants do not produce it for animals' needs.

ATPase

A protein complex found in the thylakoid membrane. Occurs only in exposed thyalkoid membrane, allowing for exposure to the stroma and pH gradient between lumen and stroma. Dimers of this complex interact with specific lipids to cause curving at the edges of grana where the thylakoid membranes fold over. Uses the proton gradient between the thylakoid lumen and stroma to generate ATP, according to the chemiosmotic model proposed by Peter Mitchell in 1961. Experiments by Jagendorf using chloroplasts thylakoids provided first evidence for this theory. Structure was first proposed by Boyer. Consists of a CF₁, soluble stromal subunits, and CF₀, membrane-bound subunits. Can hydrolyze or synthesize ATP, depending on conditions in the cell. Hydrolyzation is unlikely to occur in vivo. Light-activated by a ferredoxin-thioredoxin system. Protons cause the c₁₄ ring to rotate as they move from lumen to stroma, causing γ and ε subunits to rotate. The γ subunit turns off centre in a hydrophobic chamber inside the α₃β₃ hexamer, which is held in place by subunits a, b, b', and δ. Acts like a nanoscale motor with rotor and stator. The number of ATP produced per proton depends on the number of c subunits: yeast and mitochondria have 10, producing 3.3 ATP (actually 2.9), and chloroplasts have 14, producing 4.6 (actually 3.9). Difference between predicted and actual yield may be due to protons moving the c ring less than one c unit, or needing different amounts of protons. A rotation of 120º in the γ subunit causes synthesis or hydrolysis of one ATP. Rotates up to 12,00 rpm in an experiment where a gold bead was attached to the c ring. The γ subunit acts like a camshaft, changing conformation of α and β subunits as it turns, with five conformational changes:

1. C: High-affinity state where ATP forms reversibly. Sometimes called T.

2. D: Binds ADP preferentially.

3. D': Readily binds ADP and P_i.

4. T: Binds ATP preferentially.

5. O: Low-affinity site between D and T.

"Self-nourishing"

The utilization of light or reduced minerals as a source of energy to establish a flow of electrons and an electrochemical gradient to allow for the synthesis of ATP and NAD(P)H, which are usable forms of enegy and reducing power for the synthesis of complex, reduced organic biomolecules from inorganic carbon.

Phaephyceae

A class of Heterokontophyta in Chromista. Oxygenic photoautotrophs. Use chlorophyll a and c, and carotenoids. Mostly marine. Multicellular, filamentous to a thallus. Harvested for seedweed and alginate. Around 2,000 species. The most energy-efficient phototrophs.

Chemoorganotraophy

Light is used to sense surroundings. Rhodopsin pigment is used. Carbon source is organic compounds. Consumes O₂. In bacteria, archaea, and protists.

Chemoautotroph

All autotrophs which use inorganic reduced minerals as a source of energy. Chemolithotrophs which are autotrophic. Includes bacteria and archaea. Includes some that live in extreme environments, such as hyperthermophiles. Light is not an energy source for establishing electron flow and electrochemical gradient; not photoautotrophic. Electron flow is established through oxidation of reduced inorganic compounds. Electrons enter an electron transport chain, allowing for either forward or reverse electron transport, both of which are required to reduce CO₂ to organic carbon. Insignificant in terms of global CO₂ fixation. Important in certain environments. Have roles in the ecosystem such as global biogeochemical N, S, and Fe cycles, and sediment recycling. Includes nitrifying bacteria, colourless sulphur bacteria, iron bacteria, and hydrogen bacteria. Inorganic sources of energy have low amounts of free enregy, so large amounts of substrate must be used; typically these are found in specific environments, not ubiquitious to Earth.

A pigment found in all oxygenic photoautotrophs, except some cyanobacteria. Has a very high molar extinction, for high efficiency in absorbing light. Found in the light harvesting complex. Have energy and electron fransfer between each other. Can associate non-covalently at high conentration with other Chl molecules, the thylakoid membrane, and light harvesting complex proteins to allow fast energy transfer. Have a relatively slow rate of fluorescence, essential for energy transfer to the reaction centre. Has a resonating structure with resonating double bonds, and phytol tail (C₂₀) for membrane insertion. Absorbs light and transfers energy to the reaction centre. Has two main absorptioin maxima: red and blue. Reflects green, giving green colour to plants. Peripheral groups affect absorption peak. Includes Chl a, b, c1, c2, c3, d, and f; names are based on order of discovery. There are two excited singlet states, the first and second state, corresponding with red and blue light, respectively. There is also a third energy state. In organic solvent its concentration flatlines at 0.1 M, but in vivo it can reach 0.3 M, due to positioning with proteins. Absorbs 3% of light through one membrane. Chlorophyll mutants don't produce LHC IIb because chlorophyll regulates its synthesis. It is derivd from an N compound. When chlorophyll absorbs a photon, six things can happen:

1. An electron falls back from second to first to ground state. The second state is unstable, lasting less than 10^-12 s. Occurs when blue light hits the chlorophyll. Energy is lost; there is not enough time for the energy to be captured.

2. The energy is transferred to another pigment. This energy transfer is non-enzymatic, and involves quantum superposition, lasting 10^-13 s, and requires chromophores be positioned very exactly and closely. Occurs when red light hits the chlorophyll. Excitation moves through the light harvesting complex.

3. The energy causes photochemistry.

4. The energy is lost as a photon of longer wavelength (fluorescence). The first singlet state lasts 4 x 10^-9 s. Occurs when red light hits the chlorophyll. There is enough energy to get to the reaction centre.

5. The energy is lost as heat. The first singlet state lasts 4 x 10^-9 s.

6. A triplet excitation state forms emitting a photon by phosphorescence, losing energy, and possibly forming an ROS. The third triplet state lasts an "eternity": 10^-4 - 10^-2 s.

"Green one who forms"

A type of plastid. The only plastid that contains chlorophyll and has the capacity for light reactions of photosynthesis. Can develop from or into a proplastid, etioplast, chromoplast, or amyloplast, and can develop into a tannosome-forming chloroplast. Most arise from pre-existing chloroplasts, but in young cells they arise from proplastids. There are 5 - 200 chloroplasts per cell, 10⁵ - 10⁶ per leaf. They self-divide and are semi-autonomous. They create a "sieve effect" in the leaf, for better light distribution. Have a high membrane surface to volume ratio, enhancing light capture and metabolite transport. Has 3 membrane system: outer membrane, inner membrane, and thylakoid membrane. Each contains 20 - 40 cDNA plasmids, 89 - 400 kb each, encoding around 100 proteins, mostly photosynthetic. Associate with the plasma membrane with KAC protein, cp-actin filaments, and CHUP1 protein. Gather along periclinal walls during low light, and along anticlinal walls during high light. Move to become adjacent to air spaces in mesophyll tissues, for less resistance to gas exchange. Most of its membranes are synthesized by itself, but some can come from the endomembrane system. Associate with peroxisomes and mitochondria, to deal with toxins of photorespiration. Store starch.

Chloroplast Unusual Positioning 1

Helps chloroplasts associate with the plasma membrane.

Non-purple sulphur bacteria

A diverse group of chemolithoautotrophic bacteria and archaea. Grouped according to the location of the S depositioin: intra- or extra-cellular. Do not use light for energy. They can have colour; the term in the name indicates that there are no pigments used for light capture. They are often red in actual colour. Many are found in microaerophilic environments such as the gut of animals, including Thiothrix. Some species oxidize sulphur anaerobically, some are acidophiles, and some are thermophiles. Includes Thioploca, Thiosphaera, Thermothrix, Sulfolobus, and Acidianus. Obligate chemolithotrophs.

HS^- + 2 O₂ → SO₄^2- + H⁺ + 8 e^-

Flavoparmelia caperata

A type of lichen.

Bluegreen algae

Eubacteria, prokaryotic. Oxygenic photoautotrophs. A photoautotrophic bacteria with an inner membrane compartment (unusual for a prokaryote). Use chlorophyll a, and carotenoids and phycobilins. Includes UCYN-A. The first photoautotrophs, and progenitors to the first eukaryotic photoautotrophs. Probably the ancestors of chloroplasts; have similarities to chloroplasts including membrane network and lumen. Responsible for 25% of marine photosynthesis. Around 3,000 species, possibly many more to be discovered. Two major genera include Prochlorococcus and Synechococcus. Contain chlorophyll a, β-carotene, store glycogen, and contain carboxysomes. Some are N₂ fixers. Most genera have phycobilisomes except prochlorophytes which have chlorophyll b instead. Up to 40% of protein may be phycobilisomes.

Bacillariophyceae

A class of Heterokontophyta in Chromista. Oxygenic photoautotrophs. Eukaryotic phytoplankton. Use chlorophyll a and c, and carotenoids. The chloroplast originated from red algae, with secondary endosymbiosis. The silica cell wall is in two halves. Calcium concentration microdomains are located in pyrenoids. Mostly unicellular, but some are colonial. Account for 40 - 45% of marine photosynthesis. Around 100,000 species. The major phototroph in spring phytoplankton blooms in lakes and coastal waters, owing to high efficiency in using high N and P levels, fast growth rate at low temperatures, and adaptability to changes in irradiance typical of spring. One of the most successful groups of organisms, in terms of adaptability, distribution, biomass, and relative age. Dominate the phytoplankton population, and primary productivity rate exceeds that of the rainforests. Includes Thalassiasira and Asterionella. Reasons for success:

1. Silica cell wall. Relative abundance of silicon, strong and protective, less energy to synthesize compared to organic cell walls. Silica depositing machinery is very flexible morphologically. The cell produces proteins for silicon nucleation, forming many different patterns. Masters of morphogenesis at the cellular level. About 70 genes control wall shape. Ecological diversity.

2. Metabolic flexibility afforded by secondary symbiotic origin, including adaptability to low and high light. Mixotrophs.

3. Large central vacuoles for nutrient storage, advanced biochemical defences, and CO₂ concentration mechanism.

4. Ability to change depth in water through cell conglomeration and production of heavy spores under unfavourable conditions.

5. Formation of mutualistic associations with bacteria that provide reduced N, vitamin B₁₂, and iron.

Inorganic carbon species predominantly found in solution an earth. There are four total: cabonic acid (H₂CO₃), bicarbonate (HCO₃^-), carbonate (CO₃^2-), and carbon dioxide (CO₂). Proportion of each depends on pH and rate of constants.

CO₂ + H₂O ↔ H₂CO₃ ↔ HCO₃^- + H⁺ ↔ CO₃^2- + H⁺

Megagametophyte

The female gametophyte. A seven-celled, eight-nuclei structure. Cells include the egg cell two synergids (egg apparatus at the micropylar end), three antipodals at the chalazal end, and the binucleate central cell. Produced from megasporogenesis and megagametogenesis.

CO dehydrogenase/acetyl-CoA synthase

An enzyme in the reductive aceytl-CoA pathway. Highly sensitive to O₂.

The number of electrons transferred, in moles. Gives the answer in Jules. If it is negative, the reaction is spontaneous. Where F is the Faraday constant, equal to 96,500 J/V*mol, and ΔE₀' is the difference in standard reduction potential.

ΔG₀' = -nF(ΔE₀')

Two half reactions: a reduction (gain electrons), and an oxidation (lose electrons). If ΔE₀' is positive, the reaction can occur spontaneously, but if it is negative, net energy input is needed.

ΔE₀' = (E₀' reduced substance) - (E₀' oxidized substance)

Riftia pachyptila

An animal in the phylum Anelida. Colourless sulphur bacteria live in a symbiotic relationship with this organism near hydrothermal vents. Live in deep oceanic volcanic vents in the Pacific. The plume is positioned in an H₂S - O₂ mixing zone. It lacks a digestive system. Grows very fast, 1 m per year, but has a short lifespan, less than two years. The fastest growing invertebrate.

An ecological role of chemolithoautotrophs. Colourless sluphur bacteria fix CO₂ using mostly the CBB cycle (some archaea use the rTCA or 3-OH propionate cycles).

2 HS^- + 2 H⁺ + O₂ → 2 S + 2 H₂O

2 S + 2 H₂O + 3 O₂ → 2 SO₄^2- + 2 H⁺

SH + NO₃ → S + NO₂^- + H₂O

UV + PAR + infrared radiation

Maximal irradiance is 2,000 μmol photons/m²*s, much greater than the irradiance required by PSII.

Crysophyceae

A class of Heterokontophyta. Mostly freshwater. Unicellular, but some are colonial. Around 1,000 species.

Viridoplantae

Oxygenic photoautotrophs. Viridophytes which lack the ability to live on land. Use chlorophyll a and b, and carotenoids. Uncellular reproductive structures. Around 8,000 species. Require water medium to survive. Many live in colonies. Some cells may contain only one chloroplast. Cells may have characteristic shapes used for identification.

Chloroflexi

A type of photoorganoautotrophic bacteria. Anoxygenic photoautotrophs that contain chlorosomes.

Chlorobi

Anoxygenic photoautotrophs that contain chlorosomes. Absorb very low light levels which emanate from volcano lava. Bacteriochlorophyll associates with a protein-containing baseplate that interacts with FMO light harvesting complexes that transfer energy to the reaction centre.

Heterokonts

Stramenopiles

A division/phylum of Chromista photoautotrophs. Chloroplasts have three membranes: secondary endosymbiosis. Xanthophyll is fucoxanthin, with a brown colour. Laminarin is stored in vacuoles. Motile stage has two dissimilar flagella with tripartite tubular hairs. The anterior flagellum has tripartite mastigonemes. Classes include diatoms (Bacillariophyceae), golden algae (Chrysophyceae), and brown algae (Phaephyceae).

Chemolithoautotrophs which use H₂ as an electron donor. Live in microaerophilic and anaerobic environments, with the aid of hydrogenase. Live in the rhizosphere, marine sediments, and hydrothermal vents. Found in hyperthermophilic environments, where a number of electron acceptors are possible.

H₂ + (oxidized electron carrier) → (reduced electron carrier) + 2 H⁺

Comes from hydrogenases at high temperatures and low oxygen. Anaerobic prokaryotes including methanotrophs produce hydrogen gas. It can be used as a fuel; it is more effective, and gives off water when you burn it.

2 H⁺ + 2 e^- → H₂

A free radical, reactive oxyen species, which can be formed during non-photochemical quenching, and is scavenged in the second line of defence. May be produced from •O₂^- by superoxide dismutase. May be converted into H₂O by ascorbate peroxidase, or into H₂O and O₂ by catalase. Can attack double carbon bonds, leading to oxidative destruction of pigments, unsaturated fatty acids, proteins, and nucleic acids.

•O₂^- + e^- + 2 H⁺ → H₂O₂

A free radical, reactive oxygen species, which can be formed during non-photochemical quenching, and is scavenged in the second line of defence. Very reactive. Can attack double carbon bonds, leading to oxidative destruction of pigments, unsaturated fatty acids, proteins, and nucleic acids.

H₂O₂ + •O₂^- → •OH + OH^- + O₂

"Superheat-loving"

Bacteria and archaea which grow optimally at 80 - 113º C in primarily anaerobic environments. In these environments, H₂, H₂S, S, and Fe²⁺ are important elecron donors. Carbon source is CO₂. The first autotrophs were anaerobic hyperthermophilic chemolithotrophs.

Monotropa uniflora

An epiparasitic plant species that parasitizes ectomycorrhizal fungi which are connected to an autotrophic plant. It has white vegetative tissue.

Kinesin-like protein for Actin-based Chloroplast movement

Helps chloroplasts associate with the plasma membrane. Mutants, kac1-1 and kac-2, have a different mutation in the same gene, both causing loss of function, producing chloroplasts that cannot move.

The major light harvesting complex protein found in PSII and PSI of plants. Exists as a trimer on the thylakoid membrane, surrounding PSI like an antenna network. There are approximately 8 trimers per PSII complex: four tightly bound near the PSII core, and four that are bound more loosely. Accounts for 50% of protein in the thylakoid membrane of plants. There are M trimers and S trimers. Phosphorylation affects in the proportion of energy shunted between PSI and PSII, affecting relative rates of cyclic and non-cyclic electron flow. PSII can repulse away phosphorylated LHC-II, and spatially displaced LHC II complexes can tansfer energy to PSI. Has a chlorophyll b:a ratio of 0.8, and increases in low light. One thylakoid membrane absorbs 3% of light: ε = 10,000 L/mol*cm for chlorophyll at 625 nm, c = 0.25 M chlorophyll in LCH-II, 1 - 5 thickness of one LHC-II timer.

A = εcl = log l₀ / l

Electromagnetic radiation (EMR)

Its energy is inversely proportional to its wavelength. 50% of all photons from the sun can be used by photosystems of land plants, but only 74% of total energy can be chemically utilized, so only 37% is used, without considering energy efficiency in converting light energy into chemical energy of ATP and NADPH. Light energy excites electrons in pigments. Electrical and magnetic waves at 90º to each other. Has properties of waves and particles: wave-particle duality. Can be quantified by its energy content (Watts), or its particle nature (PPFD).

E = hv = hv/λ = pc

E = energy of one photon in Jules.

h = Plank's constant = 6.626 x 10^-36 Js.

v = frequency in s^-1 = c/λ.

c = speed of light = 299,792,458 ms/.

λ = wavelength in m.

p = momentum in J/c = h/λ.

Plasmodium

It is related to dinoflagellates. It has plastids. It is a huge problem worldwide: 300 - 60 million people suffer from malaria every year, and 1.2 million people die from it. Has apicoplasts. Some medicine inhibitors are directed at its apicoplasts, because humans lack them.

Water splitting complex

A component of photosystem II. Splits two H₂O into four electrons, four protons, and one O₂. Electrons replace those lost in the special chlorophyll pair in the reaction centre. Has an oxygen-evolving complex. The O₂ is released only after 4 photons hit the MSP.

Prokaryotes an algae make up over 90% of marine photoautotroph biomass, and are responsible for about 50% of global carbon fixation. The earth has 361.0 x 10⁶ km² of ocean, producing 55.0 Pg of dry matter and 51 Pg of carbon every year. Subsurface prokaryotes, including chemoautotrophpic and heterotrophic prokaryotes have 303 Pg of carbon, more than in terrestrial ecosystems. Turnover rate is faster than terrestrial ecosystems due to being mostly unicellular autotrophs which are productive even with low biomass. Most autotrophs are chromista, with not a lot of green algae. There is a limit to cell size due to osmosis in the salty environment. As depth of water increases, longer wavelengths of light and UV are preferentially lost due to absorption by the water; habitat is enriched with green and blue light. Absorption spectra of photoautotrophic organisms corresponds to the available light spectrum.

Turnover = (4 Pg C) / (51 Pg C/y) = 0.08 y

A deviation (δ) in the O₂/N₂ mole ratio. 4.8 meg^-1 is equivalent to 1 ppmv O₂, since O₂ is 20.95% of air by volume (209,500 ppmv).

δ(O₂/N₂) = ((O₂/N₂)sample / ((O₂/N₂)reference - 1)) x 10⁶

Facultative heterotroph

An organism which may be autotrophic or heterotrophic at different times. Light is used to produce ATP and NADPH. Chlorophyll a is used. Carbon source is CO₂ or organic compounds. Produces and consumes O₂. Includes some bacteria and protists.

Molar extinction coefficient (ε)

An aerobic chemolithotrophic process found in the slow-growing soil bacteria Nitrobacter and Nitrosomonas. The electron donors are NO₂^- and NH₄⁺, and the oxidized product is NO₃^- and NO₂^-. Electrons are extracted to produce an electrochemical gradient. Part of the biogeochemical N cycle. Most species are Proteobacteria (α, β, γ, or δ). Includes nitrosifyers and nitrifiers. No bacterial species alone can oxidize ammonium to nitrate due to energetics requirements, instead there is syntrophy. If you add ammonium fertilizers to the soil, it will be converted into nitrate.

NH₄⁺ + 2 O₂ → NO₂^- + 2 H₂O

NO₂^- + ½ O₂ → NO₃^-

A nitrosifyer bacteria, an obligate chemolithoautotroph. Has AMO and HAO. Its 2.8 Mpb genome was sequenced, and has 2,460 bp of protein-coding genes. The sequence was used to derive the nitrosifying reaction. Protons move in reverse and forward electron transport, and the citric acid cycle is anabolic in nature. 11.5% of the genome is in transport systems. There is evidence for fructose uptake, so it is possibly mixotrophic under anoxia, however it is best designed for autotrophy. A model organism for nitrifying bacteria. Carbon fixation cycle is the CBB cycle.

NH₄⁺ + O₂ + H⁺ → NH₂OH + H₂O

First line of defence

A line of defence against excess photons. A regulatory process involved in controlling the delivery of excitation energy to the reaction centre of PSII. Some toxic photoproducts may be formd (³Chl, •O₂^-, H₂O₂, •OH, and ¹O₂), which are scavenged for in the second line of defence. Quenches excess energy in the form of heat. Three mechanisms including high energy state quenching (qE) and xanthophyll cycle. The last mechanism involves state of aggregation of antenna complexes in the membrane, including migration of PSII through phosphorylation-dephosphorylation: mechanisms are uncertain, but there is a decrease in electron transport. Metabolic, occurring very quickly in vivo. It is measured with a fluorometer because some energy is lost as fluorescence.

Mn₄O₅Ca

A component of the manganese stabilizing protein, a component of PSII. Interacts with amino acid residues from CP₄₂ and D1 of the reaction centre and core antenna, determined by X-ray crystallographic analysis. The tetranuclear cluster of Mn atoms allows 4 electrons to be sequentially released from water to P₆₈₀, according to the Kok S state model. For every water split, 4 protons are released into the lumen, one O₂ is evolved, and 4 electrons are shunted to the electron transport chain. Electrons move from the OEC to an aa side chain (Y161) on D1, oxidizing the reaction centre to P₆₈₀⁺. Manganese is a transitional metal, which has many stable oxidation states, including +2 and +7. Has a chair-shaped molecular structure that changes sequentially through a series of five conformations, S₀ - S₄, each with progressively higher oxidation states from the manganese atom. S₁ is a dark, stable state. Four water molecules interact with the complex, and through the sequental steps, two H₂O are split into one O₂, 4 electrons, and 4 protons. The electrons are donated to PSII before the O₂ is released. It is unknown which water molecules form the O₂. The protons are released into the thylakoid lumen, contributing to the proton gradient. Researchers have tried to mimic the OEC catalyst, for efficient H₂ production from H₂O.

Light is used to produce ATP and NADPH. Chlorophyll a is used. Carbon source is CO₂. Originated as early as 3.2 billion years ago. It allowed oxidative respiration to evolve, and also formed reactive oxygen species (ROS). The source of protons and electrons is H₂O, and O₂ is released as a byproduct of autotrophy. Includes plants, green algae, diatoms, dinoflagellates, brown and yellow algae, red algae, and cyanobacteria. Require light-absorbing pigments to allow interception and transfer of light energy. All have chlorophyll a and carotenoids. All require two photosystems. Some don't have phycobilins. Wavelength absorption is typically below 700 nm. Includes linear electron flow only. Up to 75% of absorbed energy can be dissipated within 1 second if the photon supply exceeds the ability to utilize the energy for photosynthetic reactions. Transfer of a single electron from water to NADP⁺ involves around 29 metal ions (19 iron, 5 magnesium, 4 manganese, 1 copper), and 7 aromatic groups (quinones, pheophytin, NADPH, tyrosine, flavoprotein).

8 photons + 2 H₂O → O₂ + 2 NADPH₂ + 3 ATP

One of the thing which could happen when chlorophyll absorbs a photon. Loss of an electron from a pigment to an electron acceptor, causing a charge separation. Occurs at special chlorophyll molecules in the centre of PSI and PSII. 100 - 300 photochemical events occur each second, per photosystem. Takes 3.5 x 10^-12 s. An electron is released at the reaction centre, initiating electron transport. The electron comes from water.

Pigment (ground) + acceptor → pigment (excited) + acceptor → pigment (oxidized + acceptor

CO₂ is consumed and O₂ is evolved. Inverse O₂ and CO₂ fluctuations reflect is chemical equation, however inverse rates are not equal because CO² is converted to dissolved inorganic carbon in the oceans. Overall it is an inefficient process, considering the amount of light energy that is available in the environment.

2 H₂O → O₂ + 4 H⁺ + 4 e^-

Viridoplantae

Oxygenic photoautotrophs. Use chlorophyll a and b, and carotenoids. Most carbohydrates produced become part of the cell wall. All use the CBB cycle, and have similar electron transport chains, but there is diversity in light-harvesting machinery. All plants on Earth have 560 Pg of carbon, 472 of which are found in forests and woodlands. Have primary endosymbiosis. Have mitochondrial respiration. Designed for autotrophy, with an extensive above-ground foliage system for light interception and CO₂ uptake, and subterranean root system for access to water and mineral salts, rendering plants non-motile. Must deal with their constantly changing abiotic and biotic environment. Have tremendous anabolic capability. Have enormous versatility in synthesizing complex and unique compounds including secondary compounds. Autotrophy allows for simple body system with only three vegetative organs: roots, stems, and leaves, as well reproductive floral organs. Each oragn is a local variation of the three tissue systems: dermal, vascular, and ground. Have metabolic machinery, enabled by semi-autonomous plastids. Use simple oxidized materials to synthesize all food requirements and reduced organic biomolecules. Cell wall acts as mechanical support, and defines the shape of plant cells. Cells have large vacuoles, allowing for large cells so that solar light collectors may be produced cheaply. At the cellular level, more complex than animals. There are many genes and processes which animals lack. Grow more at night than in the day.

Microgametophyte

The male gametophyte. A two- or tree-celled structure surrounded by a tough outer wall, the exine, and a cellulosic inner wall, the intine. Has starch or oil, depending on species, which acts as the energy source. Produced from microsporogenesis and microgametogenesis.

Efficiency of the photosystem

Photochemical quantum efficiency

Quantum efficiency of photochemistry

The portion of excited state decays shunted to photochemical reactions. Efficiency of light harvesting and energy transfer. Typically it is high, around 0.95 in low light, with an average at 0.85; optimized in low irradiance. It is not the overall energy-conversion efficiency of photosynthesis: represents one of several steps where energy loss can occur. 8 photons are sufficient when quantum efficiency is 1.0, so around 9.5 photons are actually needed per O₂ evolved. Total overall efficiency of photosystems in using absorbed sunlight, for ATP and NADPH synthesis is 13%. Actual efficiency of plants, taking in all energy-losing steps, is 0.2 - 4.0%.

Φ (# photochemical products) / (# products absorbed)

Wood-Ljundahl pathway

The carbon fixation pathway found in aceticlastic methanogens, acetogens, and anammox bacteria. Has high energy efficiency, but is restricted to anaerobic niches. Includes enzyme 11. Has a high demand for metals such as Mo, Co, Ni, and Fe. Extensive use of coenzymes. It is a pathway, not a cycle. Produces methane; important for the carbon cycle. It is the oldest carbon fixation pathway. The terminal electron acceptor is CO₂, producing methane.

Red algae

Around 4,000 species. Chloroplasts contain chlorophyll a and phycobilins, and β-carotene. Store Floridean starch in the cytosol. Mostly unicellular. Lack flagella. Some have two separate sporophytic stages and gametophytes. Taxonomic classification is still in flux.

Ribulose bisphosphate carboxylase/oxygenase

The CO₂ fixing enzyme in the CBB cycle. The most abundant enzyme on earth. It is affected by O₂, causing photorespiration.

Affects light intensity, light quality, leaf temperature, and humidity of the air. It is difficult to separate what environmental parameters influence what shade responses, and what interactions occur. Causes total irradiance to decrease significantly, and far red to red light ratio increases significantly. Plants respond developmentally to the R;FR ratio through phytochrome photoreceptor. This acclimation event is at biochemical and whole plant level, affecting many genes. Effects in the whole plant include thinner leaves, reduced branching, longer and thinner stems, sometimes increased leaf area, and decreased leaf cuticle and trichomes (cannot be reversed). Effects on leaf cell structure include reduction in cell volume, fewer palisade layers, fewer mesophyll cells, smaller chloroplasts, and greater amount of appressed thylakoid membranes (can be reversed). Biochemical effects include increased PSII:PSI ratio (accommodated by increased appressed thylakoid membrane), lower chlorophyll and protein levels, and increased chlorophyll b:a ratio in some plants. Effects on source activity in the leaf are decreased light compensation point, decrease in maximal rate of net carbon fixation, and similar quantum yield of net carbon fixation, 0.05.

R:FR = [photon fluence rate in 10 nm band, centred on 660 nm] / [photon fluence rate in 10 nm band, centred on 730 nm]

The tendency of a compound to become reduced, in units over volts (V). Helps explain the structure and function of chemoautotrophic and photoautotrophic organisms. The higher the value, the more likely a substance is reduced, more able to gain electrons, and is a stronger oxidizer. Important for understanding photosynthesis and how autotrophic organisms function. When ΔE₀' is positive, the reaction is spontaneous.

ΔE0' = E₀'_{electron acceptor} - E₀'_{electron donor}

Absorption spectroscopy

Spectrophotometry

Used to measure the timing of events in electron transfer with the reaction centre. A light is on the sample continuously. Uses the Beer-Lambert law to identify and quantify compounds with medium sensitivity.

Witchweed

A hemiparasitic plant species that causes losses to major staple crops. A big problem in sub-Saharan Africa, causing $1 billion in losses. Infects grass species and cowpea, causing drought-like symptoms and twisted appearance. Requires a living host for germination, and initial development underground. Host roots produce strigolactones and ethylene that promote seed germination (thios is where it gets its name). An obligate parasite; it needs a host in order to produce an above-ground green shoot which flowers and can produce up to half a million small seeds. Flowers are blue-purple. A problem in low-N soils, especially in developing countries. It is beginning to spread to the USA.