Archaea and Bacteria Chapter 27 DOMAINS AND KINGDOMS Archaea, Bacteria, and Eukarya 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 First organisms were most probably prokaryotes. Bacteria and Archaea domains have prokaryotic cells. 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, Hay bacteria - Bacillus subtilis, Anthrax 2. Coccus - spherical bacteria, Diplococcus pneumoni, Streptococcus and Staphylococcus 3. Spiral or Curved bacteria, Treponema pallidum – causes Syphilis, Heliobacter pylori – causes peptic ulcers, and Vibrio cholera causes cholera. Cell Structure: 1. DNA lies in cytoplasm. No nucleus. 2. Cell membrane surrounded by cell wall of peptidoglycan. 3. Bacteria lack all membrane bound organelles including nucleus. 4. There are no histones associated with DNA. 5. Ribosomes are smaller than ribosomes of eukaryotes. 6. Flagella lack 9+2 arrangement. Fimbriae, Pili and Flagella 1. Fimbriae: Some prokaryotes have fimbriae, which allow them to stick to their substrate or other individuals in a colony. 1 2. Pili (or sex pili) are longer than fimbriae and allow prokaryotes to exchange DNA 3. Flagella help to locomote bacteria. Bacterial flagellum is hollow cylinder of spirally arranged Flagellin proteins. Each flagellum has a motor at base , a hook and a filament. Motor rotates clockwise or anticlockwise. 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). Cyanobacteria use water as source of Hydrogen to reduce CO2 and release O2. Some cyanobacteria have specialized cells heterocysts to fix N2 into ammonia and produce amino acids from it. 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). Role of Oxygen in metabolism 1. Prokaryotic metabolism varies with respect to O2 2. Obligate aerobes require O2 for cellular respiration 3. Obligate anaerobes are poisoned by O2 and use fermentation or anaerobic respiration 4. Facultative anaerobes can survive with or without O2 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. Five Groups in Bacteria 1. Prtoeobacteria is large diverse clade of gram negative bacteria and has 5 subgroups: a. Alpha Prtoeobacteria includes many species of bacteria living inside eukaryotic organisms. Rhizobium is N-fixing bacteria in root nodules of legumes. Agrobacterium makes tumors in plant cells. Scientists use it to deliver foreign genes in cells of crop plants. Mitochondria evolved from alpha Prtoeobacteria. + - b. Beta proteobacteria is diverse group. Nitrosomonas lives in soil and converts NH4 to NO3 c. Gamma proteobacteria is another diverse group. Autotrophic sulfur bacteria Thiomargaria namibiensis, Salmonella causes food poisoning, Vibrio cholerae causes cholera and Escherichia coli lives in colon. d. Delta proteobacteria includes slime secreting myxobacteria. When soil gets dry these bacteria aggregate into fruiting body and release myxospores. Bdellobacteria attack other bacteria and bore into at great speed. e. Epsilon proteobacteria include pathogenic bacteria. Campylobacter causes blood poisoning and intestinal inflammation. Heliobacter pylori causes stomach ulcers. 2. Chlamydias are parasites and can only survive in animal cells. Chlamydia trachomatis is most common cause of blindness in world and also causes STD, nongonococcal urethritis. 2 3. Spirochetes are helical heterotrophs. These use internal flagellum to rotate and locomote. Many are free living but others cause serious diseases; Treponema pallidum causes syphilis and Borrelia sps causes Lyme disease spread by ticks. 4. Cyanobacteria are unicellular or multicellular photoautotrophs. Cyanobacteria have Chlorophyll a for photosynthesis like algae and plants. Oscillatoria has a trichome of photosynthetic cells. Nostoc has mostly photosynthetic cells but also Heterocysts, swollen cells that fix atmospheric N2 to NH3. In Anabena photosynthetic cells and Heterocysts undergo metabolic cooperation by exchanging materials produced by them. Cyanobacteria are among most nutritionally independent organisms and are pioneers (first colonizers) to colonize bare places like rocks. 5. Gram Positive Bacteria rival the proteobacteria in diversity. a. Actinomycetes form colonies having branched fungus like bodies and like them form chains of spores. Most of them are free living decomposers in soil and are responsible for earthy odor of rich soil. Pharmaceutical companies cultivate Streptomycetes to procure many antibiotics (bactericidal drugs). Two species of actinomycetes cause tuberculosis and leprosy. b. Gram positive bacteria include solitary species like Bacillus anthracis which causes Anthrax and Clostridium botulinum which causes food poisoning. Streptococcus and Staphylococcus are gram +. c. Mycoplasmas have the smallest cells (0.1μm diameter). Mycoplasmas are only known bacteria without cell walls. These have very small genomes (517 genes in Mycoplasma genitalium). Many are free living soil bacteria but others are pathogens. ARCHAEA: multiple kingdoms a. These prokaryotic organisms of ancient origin discovered first living in extreme environments. b. Archaea lack peptidoglycan in cell wall. c. Like bacteria archaea are prokaryotes, divide by fission and have circular DNA. d. Like Eukarya, some Archaea have histones associated with DNA e. Introns in genes and many kinds of RNA polymerases f. Their growth is not slowed by antibiotics like streptomycin or chloramphenicol. 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). Other example are: Halophiles – these can tolerate very high concentrations of salts (Greek halo means salt) and live in places like the Great Salt Lake and the Dead Sea. 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. 6. Halobacterium dies below 9% salinity. These have special proteins and cell wall to tolerate high salinity. 7. Thermophiles – these can tolerate very high temperatures >90⁰C. These have branched hydrocarbons in cell membrane. Sulfolobus archaea live in sulfur rich volcanic springs at 90⁰C. Geogemma barossi lives at 121⁰C around hydrothermal vents. Ordinary organisms die at high 3 temperatures because their DNA loses its double helical structure and proteins get denatured and lose their important functions. DNA polymerase from archaea is used in PCR technology to magnify concentration of desired DNA. Moderate Archaea: are archaea living at normal conditions of temperature or salinity. Methanogens – These use CO2 as source of oxygen to oxidize H2 and produce methane, CH4, the marsh gas as bye-product in marshes. Other species live in gut of cattle, termites or other herbivores. Methanogens are strict anaerobes and very little amount of O2 kills them. 8. Euryarchaeota (Eury = wide range) include most extreme halophiles and methanogens and also some extreme thermophiles. 9. Crenarchaeota (Cren = spring) include most extreme thermophiles. 10. Recently many species of both euryarchaeota and crenarchaeota have been discovered in ordinary habitats like farm soil, lake sediments or surface waters in open seas. 11. New clades discovered recently include Nanoarchaeota, very tiny archaea in hydrothermal vents and other habitats. Korarchaeota discovered in hot springs in yellow stone national park do not seem to belong to either euryarchaeota or crenarchaeota. Important questions: 12. Study the wall structure of gram positive and gram negative bacteria. 13. Understand the functions and differences between fimbrae, pili and flagella in bacteria. 14. Study the structure and action of bacterial flagellum. 15. Study the organization of DNA in chromosome (nucleoid) and plasmid. 16. Describe role of endospore and binary fission in bacteria. 17. Study the phylogenetic tree of 3 domains and table registering characters of 3 domains. Table 27.1 18. Study the table registering Major Nutritional Modes. Table 27.2 4 .