MCB 100 1st EditionFinal Exam Study Guide Lectures: 27- 41Lecture 27 (April 3)What are the classical traits and genetic traits used to identify and group microorganisms? Howdo you classify microrganisms based on microscopic morphology? Describe bacteria, archaea, and eukaryotes. I. Classical traits used to identify and group microorganismsa. Presence of a thick vs. thin cell wall- Gram stainb. Presence of endosporesc. Cell morphology (shape)d. Cell arrangements (group structure)e. Biochemical tests (metabolic pathways, enzymes) II. Classification based on microscopic morphology (old approach)a. Common cell shapes:i. Coccus- round berry shapeii. Bacillus- rod shapediii. Vibrio- bent rodiv. Spirillum- thick helical shapev. Spirochete- very skinny helical shapevi. Coccobacillus- difficult to explainb. Common cell arrangementsi. Strepto- chainsii. Staphylo- a bunchiii. Tetrads- groups of 4iv. Sarcina- groups of 8v. Diplo- twovi. Palisades- V-shapedII. Genetic traits used to classify microorganismsa. Conserved gene sequences such as the 16S rRNA b. All cellular organisms have ribosomesc. 16S rRNA's are about 1542 bases in lengthd. Each base in the sequence can be considered as a traite. The more closely related two organisms are, the fewer changes will be seen in the rRNA sequences f. Analysis of rRNA sequence data is useful for determining relationships between organisms having ribosomes (everything except viruses, viroids, and prions) g. Based on genotypic data rather than phenotypesh. Data is analyzed by a computer using mathematical algorithms that remove human biasi. Pioneering work was done by Carl WoeseII. Bacteria, archaea, eukaryotesa. Tree of Life- based on 16S rRNA sequence analysisb. Archae and bacteriai. Similarities1. Prokaryotic cell- no nuclear membrane, one circular chromosome2. 70S ribosomes3. Most have cell walls4. Some species stain purple and others end up red in gram stain ii. Differences1. Ribosomal RNA sequence data2. Archaeal cell walls lack peptidoglycan (no N-acetyl muramic acid) 3. Archael cytoplasmic membrane lipids have branched chain fatty acids thatmay extend through the membrane4. The initial amino acid in protein synthesis in archaea is methionine rather than formyl-methionine, which is used in bacteria5. Archaeal RNA polymerase is similar to eukaryotic RNA pol. II6. Archaeal flagella are simple protein threads that rotate like those of bacteria, but they are very different. Archaea flagella are not hollow tubes, they are solid. Assembly differs from bacterial flagella toob. Traits of archaeai. Archaeal cell walls are chemically different from bacterial cell walls 1. Resistant to lysozyme, penicillin, and vancomycin2. Vary among taxa (in gram stain, some are purple and others red)3. Composed of a variety of compounds (proteins, glycoproteins, lipoproteins, and polysaccharides but not peptidoglycan, they don’t use N-acetyl muramic acid)4. Pseudomureina. Cell wall polymer found in some species of archaea that is similar to peptidoglycan in that it consists of sugar chains that are cross linked by amino acid chains; contains N-acetyl-L-talosaminuronic acid 2. Currently no archaea known to be human or animal pathogens3. Archaea include methanogens and extremophiles/thermophiles (grow at temperatures over 45 degrees C)4. (Hyperthermophiles grow at temperatures over 80 degrees C5. Not all thermophiles are archaea, not all archaea are thermophilesII. Methanogens a. Obligate anaerobes that produce methane -CH4 b. Substrates for methanogenesis include: CO2 + H2, methanol and various organic acidsc. Some methanogens are thermophilesd. Convert organic wastes in pond, lake, and ocean sediments into methane and CO2e. Make gas in the gut of cows and grass eating animals f. Play an important role in anaerobic digestion of organic wastes in sewage treatmentII. Extremophiles- halophiles a. Halophiles grow in extremely salty environmentsb. Their habitats are more than 9% NaCl (sea water is 0.9%); some survive in 35% NaClc. Many make red-orange pigments that absorb light energy and protect from UVd. Use sunlight to produce a PMF that is used to make ATPe. Lack chlorophylls or bacteriochlorophylls f. Make bacteriorhodopsins (purple-red pigments)g. Rhodopsinprotein helps protect Halococcus from the extreme salinity of their naturalenvironments II. Bacteriaa. Currently grouped into more than 23 phyla based on 16S rRNA sequence datab. Deeply branching bacteria (thought to be similar to very earliest life forms!) c. Phototrophic bacteria i. Blue-green bacteriaii. Green sulfur bacteriaiii. Green non-sulfur bacteriaiv. Purple sulfur bacteriav. Purple non-sulfur bacteriad. Gram positive bacteriai. Thick cell wall composed of peptidogycan with teichoic acids and no outermembrane or periplasmic spaceii. Low G + C gram positive bacteria 1. DNA contains more A=T base pairs than G=C basepairs iii. High G + C gram-positive bacteria1. DNA contains more G=C basepairs than A=T basepairs e. Clostridiumi. Club-shapedii. Anaerobes (many are obligate anaerobes that die in the presence of O2)iii. Produce heat resistant endosporesiv. They have a wide variety of fermentative pathways such as acetone-butanol productionv. Many produce and excrete potent toxins vi. Botulism- severe form of food poisoning vii. Improperly canned non-acidic foodviii. Neurotoxinix. Headache, double vision, flaccid paralysis x. Natural habitat is anaerobic sediments in ponds and soilxi. Produces a potent neurotoxin that causes flaccid paralysis xii. Involved in large duck die offsxiii. Most cases of botulism are due to ingestion of toxinxiv. Botulism toxin is denatured by cookingxv. May infect stomachs of infants and produce toxin in vivoxvi. Spores are common in honeyf. Tetanusi. Clostridium tetaniii. Gram positive rod, spore former, anaerobiciii. Predilection for deep, soil contaminated, woundsiv. Tetanospasmin1. Prolonged contraction of muscles2. Voluntary muscles do not relaxv. Incubation period: 3 days- 3 weeksvi. Lock jaw: prolonged contraction of massitervii. Vaccine is a toxoid (inactive tetanospasmin)viii. Antitoxin availableix. Protect patient from stimulix. Untreated mortality rate of 40-80%Lecture 28 (April 6)What are some factors that affect the development of wound infections? What is the difference between topical infection and systematic infection? List and describe the microorganisms that cause infections. I. Factors affecting the development of wound infectionsa. Virulence of contaminating