3-phosphoglyceric acid

A metabolite of the Calvin cycle. Produced by Rubisco when carbon dioxide binds to RuBP. Reduced into PGAL in two reversible reactions using NADPH.

Hormogonia

Specialized cells in cyanobacteria that are thick-walled for dormancy. Common structures to all cyanobacteria. Motile spore-like cells.

A Nobel laureate. Discovered vitamin C.

"What drives life is a little current kept up by the sunshine"

Occurs in yeast and plant cells. An anaerobic process that produces 2 ATP. Pyruvate is converted into ethanol. 93% of the energy is preserved as ethanol. Used in the brewing of alcoholic beverages, and in bread making. The CO₂ produced causes bread to rise.

Glucose + 2 ADP + 2 P_i → 3 ethanol + 2 CO₂ + 2 ATP + 2 H₂O

"Other-shape"

An enzyme with an active site and an effector site. It reversibly changes form when a regulatory substance binds to the effector site.

Destroying angel

A member of hymenomycetes, and agaricomycotina basidiomycetes. The most poisonous mushroom. A few bites can be fatal.

Nitrogen mineralization

Release of ammonium ions by soil bacteria or fungi. Plants can take up ammonium ions. If the soil is alkaline, it is often converted into ammonia gas.

Specialized hyphae of lichen mycobionts that penetrate photobiont cells with pegs. Transfer carbohydrates and nutrients between the photobiont and mycobiont.

A swelling of the hyphae as it forms a haustorium on the surface of a plant cell.

"Ancient ones"

A domain of life. Prokaryotic, no nuclear envelope, one circular chromosome, no organelles, no cytoskeleton, and no chlorophyll-based photosynthesis. Resemble bacteria, but are distinct. Half of them are methanogenic bacterai.

384 - 322 BC

Observed that animals were dependent on the food they ate, and that animals ultimatley derived all food from plants. Thought that plants derived all their food from the soil.

Formerly known as Armillaria ostoyae.

The largest living organism on Earth. A fungus which covers 900 ha of forest in eastern Oregon, and is estimated to be 2400 years old.

Singular: ascus

A sac-like structure that forms from crozier at the end of ascogenous hyphae on the hymenial surface of an ascoma in sexual reproduction in ascomycetes. Karyogamy between nuclei occurs, immediately followed by meiosis and one round of mitosis. Eight haploid nuclei are formed in a row, cell walls form between them to form ascospores. Sometimes the ascus has turgid pressure which explodes ascospores outward, as far as 30 cm.

Ascocarp

A complex structure of tightly woven ascogenous hyphae which form for sexual reproduction in ascomycetes. May be macroscopic. Asci form on the hymenial layer. Three types: apothecium, cleistothecium, and perithecium. 

Sac fungus

A group of fungus. The phyla Ascomycota. 32,300 species, including Neurospora, Morchella, Aspergillus sp. Peniclilin, and Trichoderma as well as powdery mildews, ergots, Athlete's foot, ringworm, sclerotium, and blue-green, red, and brown food moulds. The oldest known ascomycetes species are 438 million years old. Three major sub-phyla: Taphrinomycotina, Saccharomycotina, and Pezizomycotina. Perforated hyphae. Multi- or uni-nucleate cells. Filamentous or unicellular growth. Reproduce asxually by budding, fragmentation, or conidia. Homothallic or heterothallic sexual reproduction: antheridia and ascogonia form, which come together to form an ascus which produces ascospores.

Coenocytic

"Contained in a common cytoplasm"

Hyphae that lack septa. Multinucleate cells.

Nitrogen gas

Nearly 80% of the atmosphere is nitrogen gas. It has a very stable triple bond that requires a lot of energy to break. Can be fixed by nitrogenase or the Haber-Bosch process.

Adenosine triphosphate

An adenine, a ribose sugar, and three negatively charged phosphate groups each linked by a phosphoanhydride bond, then to the ribose by a phosphodiester bond. The intermediate energy carrier between endergonic and exergonic reactions. Energy is released when a phosphate group is removed by hydrolysis, producing ADP. Performing this reaction a second time to remove the second phosphate group releases the same amount of energy, producing AMP. ATPases and kinases use ATP.

Composed of many subunits. Uses energy of chemiosmotic coupling to produce ATP.

Found on the thyalkoid membrane of chloroplasts. Provides a channel for protons to flow down their gradient from the thylakoid membrane into the stroma. Uses the energy to perform photophosphorylation.

Found on the inner membrane of the mitochondria. Allows protons to flow from the intermembrane space into the matrix, and uses the energy to synthetize ATP from ADP and phosphate.

Saltbush

A halophyte. Salt is concentrated in salt bladders on trichomes which expand and burst. Rain or passing tides wash salt away, and leaves are regularly shed.

"Self-feeder"

Organisms which can create their own food. Evolved about 3.5 billion years ago from heterotrophs due to pressures for self-generation of energy supplies as organic compounds dimished on the earth.

Singular: basidium

Club-shaped structures on basidiomata for sexual reproduction in basidiomycetes. Have karyogamy followed by meiosis and four or eight (zero or one round of mitosis) haploid nuclei which segregate into basidiospores.

Singular: basidioma

Fleshy bodies that form billions of basidiospores for sexual reproduction in basidiomycetes. Form from tertiary mycelium; formation may require light or low CO₂ levels, signalling that the mycelium is above the substrate. Form basidia which produce basidiospores.

Nacrosis

N₂ gas is absorbed into tissues. Occurs during scuba diving accidents where the diver is exposed to high concentrations of N₂.

Elements that are essentially only for a small group of plants, or plants grown in certain conditions.

Al, Co, Na, Se, Si

Methemoglobinemia

Caused by leaching of nitrites and nitrates into water sources. Causes reduced O₂ carrying capacity of the blood.

Hatch-Slack pathway

Named after M.D. Hatch and C.R. Slack. Occurs alongsied the Calvin cycle. Occurs in C₄ plants. Bicarbonite ion (HCO₃^-, the hydrated form of carbon dioxide) is fixed to PEP by PEP carboxylase in the mesophyll, producing malate or aspartate, which moves to the bundle-sheath cells where it is decarboxylated to form carbon dioxide and pyruvate. There, carbon dioxide is used for the Calvin cycle, and pyruvate returns to the mesophyll where it reacts with ATP to form PEP. Oxaloacetate is produced. Reduces photorespiration by concentrating carbon dioxide around Rubisco in the bundle sheaths.

C₃ pathway

Named after Melvin Calvin. Occurs in the stroma of the chloroplast. Carbon dioxide binds to RuBP, and rapidly hydrolyzed to form 2 PGA, catalyzed by Rubisco. PGA is reduced to PGAL in two reversible reactions, using NADPH. Some PGAL is converted into RuBP using ATP, repeating the cycle, and some is used to produce sucrose or starch. More ATP is needed than NADPH. One PGAL is produced for every 3 CO₂, 9 ATP, 6 NADPH, 6 H+, and 3 turns of the cycle.

A protein-encapsulated organelle found in cyanobacteria. Components are hexamers and pentamers. They could be incorporated into the chloroplasts of C₃ plants to increase efficiency of photosynthesis. There are two types:

α: Deep sea cyanobacteria, loosely packed Rubisco, 150 nm in diameter.

β: Tightly packed Rubisco, 200 - 400 nm in diameter.

Krebs cycle

Tricarboxylic acid (TCA) cycle

Named after Sir Hans Krebs. Part of respiration. Acetyl CoA molecules are completely oxidized to form carbon dioxide, and electrons are transferred to the electron transport chain. Occurs in the matrix of the mitochondria. Acetyl CoA is combined with oxaloacetate to produce citrate, releasing CoA. One cycle produces 2 CO₂, 1 ATP, 3 NADH, and 1 FADH₂. ATP formation is by substrate-level phosphorylation.

Oxaloacetate + acetyl CoA + 3 H₂O + ADP + P_i + 3 NAD⁺ + FAD → oxaolacetate + 2 CO₂ + CoA + ATP + 3 NADH + 3 H⁺ + FADH₂

Proteoid roots

A cluster of roots with many closely spaced, hairy rootlets, used to increase phosphorus uptake. Ephemeral and must be continuously replaced. Have exudative bursts. Formed in plants which do not often form mycorrhizal associations, such as Proteaceae, Betulaeceae, Casuiarinaeceae, Cyperaceae, and Fabaceae.

Cohesion-adhesion-tension theory

Transpiration-pull theory

Postulated by Dixon and Joly. Transpiration creates pull of water in the xylem. Cohesion and adhesion of water molecules pulls water from the roots through the xylem. In theory, a stand of xylem 300 m tall can maintain cohesive forces.

"Conidia bearers"

Modified hyphae that form from conidia for asexual reproduction. Produce conidia, which are the primary propagators of ascomycetes.

Shepherd's crook

A hooked tip at the ends of ascogenous hyphae on the hymenial layer of the ascoma in sexual reproduction of ascomycetes. Allows nuclei to divide simultaneously for the formation of asci.

White-egg bird's nest fungus

A basidiomycota. The "eggs" contain basidiospores which are splashed out by raindrops.

Chestnut blight

An ascomycetes. Accidentally introduced to North America from Japan.

2,6-dichlorophenol-indolphenol

A dye used to analyze NADP⁺. Blue when oxidized. As electrons reduce, it becomes colourless.

DCPIP(ox) + 2e^- → DCPIP(red)

Diuron

3-(3,4-dichlorophyll)-1,1-dimethylurea

One electron flows from plastoquinone if PSII is inhibited by it.

Veiled stinkhorn

Netted stinkhorn

A basidiomycotina that releases basidiospores in a foul-smelling, sticky mass which attracts flies that pick up and distribute the spores.

"Two nuclei"

Dikaryotic mycelia that form after plasmogamy and before karyogamy. Nuclei divide in tandem.

Palmer's grass

A halophyte. Salt exudes through specialized cells onto the surface of the leaf.

"Energy-in"

A process where potential energy of the system increases. Cannot take place without input of energy. ΔG is positive. Endergonic reactions in cells are driven by coupling them to exergonic reactions.

Arbuscular mycorrhizae (AM)

The more common type of mycorrhiza: accounts for 80% of species. Species are 400 million years old, and probably played a role in evolution of early land plants by allowing colonization of nutrient-poor soils. Hyphae penetrate root cells. Most have vesicular-arbuscular mycorrhizae structure (arbuscules and vesicles) with aseptate hyphae. Obligate biotrophs. Includes Glomermycota.

"Energy-out"

A process where potential energy of the system decreases. Can take place spontaneously. In many cases it is also exothermic (gives off heat). ΔG is negative.

Legumes

A family of plants which form root nodules.

Flavin adnin dinucleotide

Produced in the citric acid cycle. One FADH₂ produces about 2 ATP from oxidative phosphorylation.

Singular: gametangium

Gamete-producing structures. Fuse to form a zygospores. May form gametes, or have nuclei that function as gametes.

"Stomach fungi"

A group of agaricomycetes. No hymenium is visible on the basidiometa when basidiospores are released. Basidiomata have a periderm. Includes stinkhorns, earthstars, false puffballs, bird's nest fungi, and puffballs. Stinkhorns have gleba.

3-phosphoglyceraldehyde

A metabolite of the Calvin cycle. Produced when PGA is reduced using NADPH. The end product of the Calvin cycle. Some is converted into RuBP, using ATP. Some is converted into sucrose or starch.

"Sugar splitting"

Part of respiration. Glucose, 6 carbons, is broken into two 3 carbon pyruvate molecules, which are oxidized into two molecules of acetyl CoA. A ten-step process wich occurs in the cytoplasm of virtually all living cells. There is a preparatory phase and a payoff phase. An anaerobic process that produces ATP and NADH. Net ATP formation is 2, by substrate-level phosphorylation. Evolved before the Earth's atmosphere contained oxygen. In anaerobic conditions, glycolysis is followed by fermentation

Glucose + 2NAD⁺ + 2ADP + 2P_i → 2 pyruvate + 2NADH + 2H⁺ +2ATP + 2H₂O

Stacked thylakoids

The stacking regulates distribution of radiant energy between photosystems.

The industrial process for fixing nitrogen. First developed in 1914 by Frizt Haber and Cal Bosh. N₂ is reacted with H₂ at high temperatures (450 - 600ºC) and pressures (1000 atm) with a metal catalyst, forming ammonia. High energy requirements, met by fossil fuels. Current use produces 50 million MT/year, almost half of the earth's biological fixation. Mostly used to produce agriculture fertizers, but can be used to make explosives.

3H₂ + N₂ → 2NH₃ + heat

Singular: haustorium

Modified arbuscules. Specialized feeding structures found in symbiotic mycorrhizae or parasitic fungi. Increase surface area for absorption of nourishment from the cells of other organisms, while keeping host cells alive.

"Other-feeder"

Organisms which cannot produce their own food. Evolved into autotrophs.

Hops

Used in beer making, as a preservative, and to add flavour to beer.

Tooth fungi

A group of agaricomycotina that include edible and poisonous mushrooms, coral fungi, tooth fungi, and shelf fungi. Produce basidiospres on the hymenium. Includes Agaricus campestris, Agaricus bisporus, Letinula edodes, and Amanita virosa.

Anamorphs

Asexually reproducing state of a fungi.

Monotropa uniflora

A parasitic flowering plant which is non-photosynthetic.

Discovered the lac operon in bacteria.

"The first scientific postulate is the objectivity of nature: nature does not have any intention or goal"

1831 - 1879

Demonstrated that visible light is a small part of the electromagnetic spectrum.

1577 - 1644

A Belgian physican. Had a willow tree in a pot. After five years, the tree increased 74.4kg in weight, but the soil decreased in weight by 0.057kg. Concluded that plants obtain most of their mass from water, not the soil, which is partially true.

1730 - 1799

A Dutch physician. Repeated Joseph Priestley's experiment in 1796, and found that air could only be restoed in the presence of sunlight, and only using green parts of plants. Suggested that carbon dioxide is split b the plant, sequestering carbon, and releasing oxygen gas.

1733 - 1804

In 1744 he found that he could "regenerate" air with a sprig of mint, enabling a candle to burn. Concluded that plants restore the air. Was presented with a medal for this discovery.

1839 - 1903

First integrated free-energy change.

"Wreath"

Two concentric layers of cells around the vascular bundle in C₄ plants. The cells may have poorly developed grana in their chloroplasts. Provides spatial separation between the carbon sequestering and the Calvin cycle.

Occurs in bacteria, fungi, protists, and animal cells. Occurs in animals undergoing heavy exercise. An anaerobic process that produces 2 ATP.

Glucose + 2ADP + 2P_i → 2 Lactate + 2ATP + 2H₂O

Shiitake mushroom

A member of hymenomycetes, an agaricomycotina basidiomycetes. A commercially grown edible mushroom.

Energy-transduction reactions

The first process of photosynthesis. Requires light energy. Produces ATP and NADPH. A water molecule is split, producing O₂ waste, electrons which are used to produce NADPH, and protons which contribute to the pH gradient for ATP production.

Elements required in large amounts, over 100 mg/kg of dry weight.

H, C, O, N, K, Ca, Mg, P, S

Sheath

A structure of hyphae of ectomycorrhizae that covers the root surface. Mycelial strands extend from the mantle into the surrounding soil. Root hairs do not develop: roots are often short and branched.

1628 - 1694

An Italian scientist who in 1675, showed that photosynthates move through the phloem. Girdled a tree (removed the outer phloem), and observed that swelling occurred above the girdle in the summer, but not in the winter. Swelling is caused by accumulation of sugars above the girdle. Girdling causes the tree to die because the roots become starved of photosynthates.

Biochemical pathway

A series of chemical reactions, each catalyzed by an enzyme. Serve different functions in cells. Intermediate products do not build up in the cell. If one reaction is highly exergonic, it will drive the other reactions. Some reactions are common to more than one metabolic pathway.

Methane-producing Archaebacteria. The first organisms. Obligate anaerobes, killed by O₂. Produce methane from hydrogen and CO₂, and use amminium as an N source. Found in sewage treatment plants, bogs and swamps, deep in the ocean, animal digestive tracts, and landfills. Produce the natural gas found in the earth. The population of one cow's gut produces 50 L of methane a day. They thrived 3.5 billion years ago in the anaerobic atmosphere, and produced a lot of methane which altered the atmosphere.

CO₂ + 4H₂O + ADP + P_i → ATP + CH₄ + 2H₂O

Trace elements

Elements required in small amounts less than 100 mg/kg of dry weight.

Cl, Fe, B, Mn, Zn, Cu, Ni, Mo

E = c/λ

c = the speed of light = 30,000 km/s

"Fungus-life"

The fungal component of a lichen. 98% are ascomycetes, and the rest are basidiomycetes. Reproduce normally, but spores can only germinate if they come into contact with cells of an appropriate photobiont. The mycobiont controls the growth rate of the photobiont, and provides it with nutrients.

"Fungus"

The study of fungi.

"Fungus roots"

The most important relationship between fungi and plants. Glomeromycetes fungi form associations with plants, and cannot be grown independently. Occur in about 80% of vascular plants, wild and cultivated. Families that lack mycorrhizae are mustards, sedges, and Chenopodieaceae (beets and quinoa). Increases the plant's ability to uptake water and essential elements, especially P, Zn, Mn, and Cu. Defends the plant from pathogneic fungi and nematodes. Some plants cannot survive if they lack mycorrhizae, including orchids. The fungus receives carbohydrates and vitmins. Roots of neighboring plants may be connected to the same mycelium, allowing transfer of nutrients from one plant to another. Colonization of the soil is inhibited by P fertilizers. Important to forest ecosystems. A modified relationship of a parasitic relationship. Includes endomycorrhizae and ectomycorrhizae.