DOMAINS AND KINGDOMS – Chapter 1 and 27-31 Archaea, Bacteria, Eukarya – Protista, including Algae, and Fungi

Carl Woese based on studies of r-RNA of smaller ribosomal subunit in various groups of living things suggested 3-Domain classification of living things. The arrangement of nucleotides is highly conserved because the mutation rate in r-RNA is very slow.

# BACTERIA ARCHAEA EUKARYA 1 Prokaryotic cells Prokaryotic cells Eukaryotic cells 2 Circular chromosome present Present Absent. Linear DNA in chromosomes 3 Peptidoglycan in cell wall present absent absent 4 No Histones associate with DNA Histones + DNA Histones + DNA 5 RNA polymerases: 1 type several types several types 6 Introns (non-coding part of gene) rare Sometimes present present 7 Membrane bound organelles absent absent Present Table 27.2

BACTERIA: multiple kingdoms Cell Wall: contains Peptidoglycan. It can get stained with crystal violet-Iodine. If the bacteria retain the stain on washing-these are called Gram+. If the stain is washed, the bacteria are stained with Safranin. These are called Gram- bacteria and have a second membrane outside cell wall.

Forms: 3 main forms exist. 1 Bacillus - rod shaped bacteria 2 Coccus - spherical bacteria 3 Spiral or Curved bacteria

Cell Structure: Bacteria lack all membrane bound organelles including nucleus. There are no histones associated with DNA. Ribosomes are smaller than ribosomes of eukaryotes. Flagella lack 9+2 arrangement.

Metabolism: Bacteria are both autotrophs and heterotrophs. Most require organic molecules for source of energy and carbon source (chemoheterotrophs). These are saprobes and release enzymes to absorb food from outside. Besides fungi these are the main decomposers.

Cyanobacteria have Chlorophyll a for photosynthesis like algae and plants (photoautotrophs). Others use hydrogen sulfide instead of water and release sulfur instead of oxygen. Still others can gain electrons from inorganic chemicals to reduce CO2 (Chemoautotrophs).

Reproduction: All prokaryotes reproduce by Fission. DNA is replicated and 2 daughter chromosomes move apart followed by division of cell by plate method. Some bacteria produce Endospores which can tolerate extreme harsh conditions. Examples are Anthrax and Tetanus bacteria.

ARCHAEA: multiple kingdoms These prokaryotic organisms of ancient origin discovered first living in extreme environments. They lack peptidoglycan in cell wall. They have like Eukarya histones associated with DNA, many kinds of RNA polymerases and their growth is not slowed by antibiotics. Like bacteria archaea divide by fission and have circular DNA. These include: Extremophiles: Many archaea can tolerate extreme conditions. Picrophilus oshimae can live at pH 0.03 enough to dissolve metals. Dienococcus radiodurans can tolerate 3x106 rads (3000x fatal dose for humans). 1 Other extremophiles are: Halophiles – these can tolerate very high concentrations of salts. Halobacterium a unicellular archaea turns the color of Lake Owen in CA to pink/red color. Salt content reaches 32% in summer (9X sea water). Single Celled Halobacterium has red membrane pigment Bacteriorhodopsin. It enables to produce ATP by using sunlight. Thermophiles – these can tolerate very high temperatures >100⁰C. Their DNA and proteins are stable at very high temperatures. Sulfolobus grows in sulfur springs up to 90⁰C. Geogemma barossi lives near hydrothermal vents in Pacific ocean and lives at 121⁰C. Moderate Archaea: Methanogens – these produce methane, the marsh gas as bye-product and live in anaerobic marshes or digestive tracts of mammals including cows. These are most strict obligate anaerobes. Even small amount of O2 kills them.

Protists: multiple kingdoms Protists were first eukaryotes to evolve. Protists include unicellular eukaryotes and their simple multicellular relatives. The latter are filamentous or colonial. Mitosis, Meiosis and sexual reproduction arose for the first time in this kingdom. All the organelles of plants, fungi and animals arose in this kingdom. Protists also possess many unique organelles not found anywhere else in the 3 domains. Like the 3 higher kingdoms the Protists are photosynthetic (like plants) or heterotrophic absorptive (like fungi) or heterotrophic Ingestive (like animals).

Algae are now part of kingdom protista. All have Cholorophyl a, and some additional pigments. The chloroplasts in Algae have special organelle, Pyrenoid, to store and metabolize starch. Asexual reproduction can be by flagellated spores called zoospores or spores without flagella. Sexual reproduction is by flagellated gametes. Many algae, like plants, form a non-flagellated egg and a flagellated sperm. This sexual reproduction is called Oogamy. Algae lack multicellular sex organs.

Green Algae are most common in fresh water. These have Chlorophyll a and b, store food as starch and have cellulose in cell walls. All characteristics are common with plants. But lack multicellular sex organs covered with sterile jackets and embryos. They have various forms: unicellular-Chlamydomonas; filamentous-Spirogyra; leafy - Ulva or colonial - Volvox with daughter colonies inside.

Diatoms are most abundant unicellular forms in oceans. The body is covered with an intricately designed 2-half silica shell. Adults are Diploid and lack cilia or flagella. Main reproduction is by binary fission. Sexual reproduction is by flagellated gametes. The remains of shells produce Diatomaceous earth mined for filtering and abrasive materials. Diatoms are most important producers in biosphere.

Dinoflagellates – Pyrrophyta are unicellular covered with cellulose plates. They have 2 flagella placed at right angle to each other. These are important phytoplanktons in oceans. They are also responsible for causing Red Tides, example Gonyaulax. The red tide is caused due to sudden growth due to availability of Nitrogen or Phosphorus brought by rivers.

Red Algae - Rhodophyta are important sources of gelling agents Agar and Carageenan. Porphyra is edible red alga used as a sushi-wrap. These are mainly filamentous or leafy. Besides Chlorophyll a, these have red and blue pigments to give various colors. Red algae are delicate sea weeds.

Brown Algae - Phaeophyta are usually the large sea weeds called Kelps. In addition to Chl a, these have fucoxanthin a brown pigment. Coastal areas have Laminaria and giant marine kelp Macrocystis. Sargasso Sea has floating brown alga, Sargassum. Algin a gelatinous material added to ice creams and cream cheese is extracted from brown algae.

2 Euglenophyta are unicellular freshwater forms. Many have choloroplasts others lack them. The chloroplasts are surrounded by 3 membranes than the normal 2. The anterior end has vase-like invagination. Out of which emerges a long flagellum, the other is small. Eye-spot is sensitive to detect light. The body is covered by Pellicle formed of protein strips. They can change body shape. A contractile vacuole lies near the anterior end. Reproduction is by longitudinal cell division. Sexual rep is absent. Euglenozoa = Euglena (euglenophyta) + Trypanosoma (Zoomastigophora)

Protozoan Protists These are animal-like-protists. They are motile and heterotrophic ingestive portists. There are 4 main types: Ciliates include Protist moving with cilia and covered with pellicle. Common example is Paramecium species. It has a Meganucleus and a Micronucleus. These reproduce asexually by transverse cell division. Sexual rep is by Conjugation for which 2 paramecia join temporarily and exchange nuclei and separate. 2 nuclei from different paramecia fuse to result in fertilization. They have 2 contractile vacuoles surrounded by feeding canals. They lack sexual rep.

Amoeboids are covered with cell membrane only and locomote by pseudopodia which are formed by flowing cytoplasm. They change, all the time, their body-shape. They feed by phagocytosis. Freshwater forms have contractile vacuoles to expel excess water. Common example is Amoeba proteus. Entamoeba causes dysentery-blood in stools and gingiva-soft bleeding gums. Forams are amoeba like organisms covered with lime-shells called tests with many pores. Radiolarians have internal silica test. The shells of the 2 groups deposit as sedimentary rocks at sea bottom.

Zooflagellates locomote with flagella and body is covered by plasma membrane. Most are symbionts and help in digestion of cellulose (stomach of ruminant mammals). Others are parasites and cause diseases. Common example is Trypanosoma which lives in blood plasma of humans and causes sleeping sickness in Africa. It is transmitted by Tse-tse fly. Sporozoans are without any locomotory organelle. At one end of the cell is apical complex. It helps in entry into host. Common example is Plasmodium species which causes Malaria. It is transmitted by females of mosquito, Anopheles species. Malarial parasite completes sexual phase in Anopheles and asexual reproduction in human liver and red blood cells.

Molds as Protists: These are fungus-like-protists. They have flagellated cells. 2 types:

Water Molds - Oomycota are filamentous and their cell walls are mainly formed from cellulose. Asexual reproduction is by flagellated spores. Sexual rep is by oogamy- an egg and sperm. Common example is Phytophthora which causes potato blight. It caused the Irish famine in 1940. Slime Molds are naked protists which feed by phagocytosis. Plasmodial Slime Molds have multinucleate protoplasmic masses called plasmodium. These reproduce asexually by spores formed in walled sporangia in a cluster called fruiting body. Spores develop into amoeboid or flagellated gametes. Common example is Physarum species. Cellular Slime Molds live as solitary amoeboid cells. Under unfavorable conditions these can form aggregations called pseudoplasmodium. When favorable conditions return sporangia in a fruiting body produce spores. The spores give rise to single cells to complete the cycle.

FUNGI These are multicellular, heterotrophic-absorptive eukaryotes. The fungus body is called Mycelium, formed of many thread like Hyphae (singular is hypha). Chytridiomycota are oldest fungi; only group to possess flagellated spores, zoospores. They have both cellulose and chitin in their cell walls. These are predominantly aquatic. Example is Chytridium.

3 Zygospore Fungi-Zygomycota are molds with non-septate hyphae. These reproduce asexually by spores. The gametes formed at the tips of special hyphae, fuse to form zygospore, a thick walled zygote. Under favorable conditions zygospore undergoes meiosis and forms spores which produce the mold again. Common example is Rhizopus the black bread mold.

Sac fungi - Ascomycota have septate hyphae. Most of them reproduce asexually by conidia. Conidia are formed in chains by budding. Two hyphae of + and – strains fuse. The resulting hyphae have 2 nuclei in each cell. Fusion takes place in a special structure called Asci (singular ascus) which are enclosed in a fruiting body called Ascocarp. Common examples are Yeasts, Morels and Truffles.

Club Fungi- Basidiomycota has special bodies called basidia. Fusion of nuclei take place in it and 4 sexual spores are formed externally from each basidium. Spores germinate to form monokaryotic mycelium. The tips of + and – strains of hyphae fuse to form dikaryotic hyphae which form the fruiting body called basidiocarp. Basidiocarp bears gills on its under surface. Gills have basidia. Common examples are Mushrooms, puff-balls. Fungi Imperfecti are mostly ascomycotes that have either lost sexual reproduction or it has not been observed so far. Most reproduce asexually by Conidia. Common examples are Aspergillus and Penicillium. Penicillium was the source of 1st commercial antibiotic drug Pencillin to cure bacterial diseases.

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