yana-notes

Botany

2022-08-23: !Biology reference:

Botany #

  • Structure
    • Cells & Tissues
    • Roots
    • Stems
    • Leaves
  • Physiology & Regulation
    • Photosynthesis & Respiration
      • Chemoautotrophs extract energy from inorganic chemical compounds to synthesize sugars.
    • Environmental Responses
    • Nutrition and Soils
    • Hormones
    • Transport
    • Development

Biodiversity #

  • Horizontal gene transfer is the introduction of genetic material from one spcies to another by mechanisms other than parent->offspring “vertical” gene transmission.
    • Many prokaryotes siomply uptake DNA. Bacteria uptake a bacteriophage. Rice and millet plants use transposons (“jumping genes” discovered in 1983)
      • Aphids obtain the ability to synthesize carotenoids (desaturase enzyme) and become red by some kind of fungal infection,
    • Agrobacterium insert part of their owngenome into a plant, and make it produce a gall thing.
  • In the Endosymbiotic Theory, mitochondria, plastids, etc. were once prokaryotes that incorporated themselves into the eukaryotic cell and differentiated its DNA into the nucleus. This is why Mitochondrial DNA is a separate thing (it’s also only inherited from the mother since it degrades in the sperm in the fertilized egg).
  • There are fibrous roots, like trees, and taproots that is a mtain root with little branching - this is seen in Carrots, turnips, beets, which are just food-storing roots. Some plants have root nodules with nitrogen-fixing bacteria, includng legumes.
  • Structures that produce or release sugars for the growing plant are referred to as sources. Their storage point, i.e. fruits, seeds, roots, are sinks.

Taxonomy/Phylogeny #

  • Phylogeny is the evolutionary history of a specific group of a species.
  • So the clades on wikipeida are in a top-down order. It’s just that there are tons of subclaseses - for some reason all this variety happens mostly between order and phylum.*
  • So like, Phylae have multiple clades.
  • 600
    • These affixes are only for plants btw.
  • 770
    • DNA sequencing revolutionized the construction of phylogenies. I’m excited that our dear VEGF is so different between species!

Big Tree #

  • Life (2 empires: prokaryote and eukaryote), then (3 Domains)

    • Archaea (Unicellular; prokaryotes) (became accepted in 1990)
      • Psuedopeptidoglycan cell walls
      • Their DNA structure differs from that of bacteria
    • (‘Eu’)Bacteria (Usually unicellular; prokaryotes)
      • Peptidoglycan + sometimes LPS cell walls.
    • Eukarya (Usually multicellular)
      • (3 main Kingdoms): Animalia, Fungi, and Plantae:
      • Kingdom Protista is unicellular.
        • Protazoa
    • Parallel to these domains are the 5 ‘dominiums’ which adds viruses/viroids and prions (part of the controversial ‘superdomain’ of non-cellular life)

  • Archaea and Prokarya coevolved during the early stages of life. Apparently archaea were the first. Eukarya they split off from Archaea.

  • Clade: Tracheophyta (vascular)

    • C.: Spermatophytes (seed-bearing)
      • C.: Angiospermae (Flowering/fruiting plants) - All flowers become fruits. ‘Angio’ = vessel (for the seed) - that is to say, fruit. 80 Auxins are hormones (all have carboxyls; usually indoles) that stimulate the wall of the ovary to develop into the fruit; it can be supplemented for commercial use.
        • C.: Eudicots (two seed leaves upon germination): 80 (left: monocot)
          • C.: Rosids
            • Order: Fabales
              • Family: Fabacaea (legumes)
                • Subfamily: Faboidae
                  • Genus: Lens
                    • L. Culinaris: Lentil
                  • Pisum
                    • P. sativum: Pea
                      • (L. Sativus: cultivated, planted)
                  • Phaseolus (Bean)
                    • P. vulgaris: kidney, pinto, navy beans (AKA white bean or pea bean)
                  • Vigna
                    • V. radiata (Mung bean)
            • Brassicales
              • Brassicaceae
                • Brassica
                  • B. oleracea : also includes broccoli, cauliflower, brussel sprouts, collards. Low in proGoitrin

                    • B. oleracea Acephala: kale #

                    • B. oleracea Capitata: cabbage
                  • B. Rapa: bok choy, mustard greens, turnip, russian kale (purple stem). High proGoitrin content. L. for rapa = turnip.
            • Sapindales
              • Rutaceae
                • Aurantioideae
                  • Citrus: 100
              • Anacardiaceae: these fruits are “dupes” that have a fruit surrounding a big kernel.
                • Mangifera
                  • M. indica Mango. Indica = L. Indicate, uncover, etc.
            • Vitales
              • Vitaceae
                • Vitis:
                  • V. labrusca, etc.: Grape
          • Caryophyllales: many are succulent, i.e. cactuses, beets, as well as carnivorous plants.
            • Amaranthaceae
            • Aizoaceae
              • Mesembryanthemum
          • Malvales
            • Malvaceae
              • Helicteroideae
                • Tribe: Durioneae
                  • Durio (9 different species: Durian)
              • Theobroma
          • Rosales
            • Rosaceae
              • Fragaria: Strawberry
                • F. ananassa: Common garden Strawberry
            • Moraceae
              • Ficus
                • F. carica: Fig. Apparently one of the first plants cultivated by humans: before 9000 BC.
              • Artocarpus
                • A. heterophyllus: Jackfruit, the largest fruit of all trees
            • Cannabaceae
          • Myrtales
          • Asterids
            • Ericales
              • Ericaceae
                • Vaccinium
                  • Vaccinium sect. Cyanococcus: Blueberry
                  • Vaccinium Oxycoccus: Cranberry
            • Solanales
              • Solanaceae: Nightshades. Its 4 most famous alkaloids are Solanine, Tropanes (yeah like Tropisetron), Nicotine, and Capsaicin.
                • Solanum (where the Glycoalkaloid action gets real)
                  • S. lycopersicum: Tomato
                  • S. melongena: Eggplant
                  • S. tuberosumL Potato
                • Nicotianeae
                • Capsiceae
                  • Capiscum: chili peppers.
              • Convolvulaceae
                • Ipomoea
                  • I. batatas: Sweet potato
                  • I. tricolor: Motrning Glory
                    • This as well as some others contain ergine AKA d-lysergamide for LSD. (I think Hoffman used fungi)
            • Lamiales
              • Lamiaceae: Quite Estrogenic. Includes mint, oregano, basil, rosemary, sage, thyme, lavender, catnip, salvia, etc.
            • Gentianales
              • Rubiacaea
                • Coffea
                  • C. arabica
        • Monocots (Seeds contain only one embryonic leaf)
          • Commelinids
            • Arecales
              • Arecaceae
                • Cocoseae
                • Phoenix
                  • P. dactylifera: Date palm
            • Zingiberales
              • Musaceae
                • Musa: Banana
                • True plantains are a “cultivar” group. Something like Musa balbisiana
            • Poales
          • Dioscoreales
            • Dioscoreaceae
              • Dioscorea: Yam
      • Gymnospermae: Seed-producing plant (γθμνός = naked, i.e. without a fruit/ovary covering it). Includes Ginkgo and other boring stuff

Fungi #

  • Biodiversity All 1.5 million+ are eukaryotes. Yeast is the only single-celled fungus. They do not photosynthesize. They aerobically respirate, but yeast of course ferments.
  • White button mushrom = Agaricus bisporus
  • Kingdom: Eucomycota
  • Can be sexual, asexual. or both.
  • A fungus’ role in a plant’s rhizosphere - the roots that connect fungi with a plant’s - are mycorrhizae. Fungi receive glucose, while exchanging minerals and water with the plant.
  • WTF. Leaf cutter ants feed leaves to Leucoagaricus gongylophorus to digest cellulose and feed them “gongylidia”. They guard it and tend to the fungi.,

Viruses #

  • Not even included in the tree of life, since they have no cells, but they do have a DNA or RNA genome, which is surrounded by a protein capsid or a phospholipid membrane.
  • They work by entering a host cell and changes the genome accordingly in order to replicate form new virus particles (virions).
  • Bacteria-infecting viruses = bacteriophages/phages.

Protists #

Eukaryotes. Neither animals, fungi, nor plants. Included are amoeba, algae, invertebrates, slime molds, protozoans, etc.

Algae #
  • Molecular evidence supports that all Archaeplastida are descendants of an endosymbiotic relationship between a heterotrophic protist and a cyanobacterium

Plant Cells #

  • It seems the main differences are as follows:
    • Cell wall. Consists of cellulose 150 pectin, and hemicelluloses, and other polymers like lignin, suberin, cutin.
      • Algae have cell walls made of glycoproteins and polysaccharides like agar and even carrageenan! Fungi have cell walls made of chitin.
    • Plastids: 440 R
      • Amyloplasts store Starch.
      • They are actually considered endosymbiotic cyanobacteria.
      • Chloroplasts store their pigments in interconnected sacs called thylakoids. Chloroplasts contains its own DNA+ribosomes and is double membraned - just like the Mitochondria.
    • A large permanent vacuole - which are usually absent in animal cells. It’s a sap that contains enzymes and stuff in solution. They’re basically just big vesicles. It controls the water concentration.
      • When a plant wilts, its vacuoles are emptying and becomes hypertonic.
    • Photosynthesis makes their own food; animal cells do not do this
    • No movement; square. It will bend and has strong tensile strength.
    • Usually no lysosomes.

Growing/Harvest #

  • Knowing the last frost date of the year is important - when the air is <= 32°F/O°C which is when the more tender plants are killed. 24°F and under is damaging to most everything.
  • Or, you plant in late summer before the first frost. In Michigan, the first fall frost is on the end of October. The last spring frost is the end of April.
  • Containerized plants need to be two zones hardier than your winter since the roots lack protection.

Permaculture Tips #

Hydroponics #

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