MMG 301 Study Guide for Exam 1 Lecture 1. Vocabulary: 1. Prokaryote: Lack of nucleus & membrane enclosed organelle.

Circular DNA Member of Archae &

Bacteria.

2. Eukaryote: Membrane enclosed organelle & nucleus. Member of Eukarya 3. Spontaneous Generation: Aristotle idea Life arose from inanimate objects 4. Kochs Postulate: Microorganism cause specific disease His Hypothesis & Proves Germ Theory 1. Pathogenic present on diseased but not on healthy 2. Pathogenic org. grown on pure culture 3. When injected w/pathogen, healthy Diseased 4. Now, healthy one get infected & show pathogen. 5. Phytopathogenic: Microorganism that cause plant disease. 6. Turberculin: Case of tuberculosis. What Koch isolated & used as vaccine. 7. PCR: Artificial amplication of DNA sequence by repeated cycles of strand separation & replication. 8. Winogradsky column: Glass column packed w/mud & overlayed w/water to mimic aquatic environment in which various bacteria develop over period of month. 9. Pathogen: Disease causing microorganism. 10. Phenol: Carboxylic acid. Used to clean surgical sites and instrument. (Lister) Concepts: 1. Swan Neck Flask Exp. By Pasteur: -Heated food will not putrify w/microbial growth even while exposed to fresh air. -Pasteurs exp. Put on end to spontaneous generation theory 2. Contributions: a. Aristotle: Spontaneous Generation b. Hooke: Used early microscope to describe structure of fruiting mold. c. Cohn: Used early microscope to study photosynthetic algae & heat resistant bacteria (Lay foundation for bacterial classification system). -Discovered role of nutrient cycling and Bacterial endospores. d. Spallazani: Boiled medium in sealed flask & did not putrify. Thus, fresh air necessary for Spontaneous Generation. e. Beijernick: Est. central role of microbes in Nitrogen cycle needed to sustain life. -Enrichment Culture Technique: Use selective culture media & incubation conditions to isolate specific microorganism from natural samples. f. Winogradsky: Discovered autotrophic bacteria (Use CO2 as carbon source) & importance of chmolithotropy in biogeochemical cycles. g. Leewnhoek: Made 300X stronger microscope. Discovery of bacteria and challenged Spontaneous Generation 3. Contribution and Disease investigation: a. Pasteur: First used rabies vaccine on human. - Injected child w/15 day old spinal cord from rabies infected rabbit & continued w/ fresher ones. -Also developed vaccines for antrax & cholera b. Koch: Found causative agent of tuberculosis. -Used Semisolid media which is used to isolate & grow pure cultures.

-Growed turberculin and used it as vaccines. -Also found cause of anthrax. 4. Contribution in sanitation and infection a. Lister: British physician -Carbolic acid (Phenol) killed bacteria so treating surgical sites, instrument, and dressing with it result in lower infection rates. b. Semmelweis: Ran two birthing unit - hand washing and sanitation reduced infection of sepsis 5. Contribution of Marshall & Warren -Cured patients using antibiotics -Causative is Helicobacter Pylori -Received Nobel prize for medicine. 6. Best studied Bacteria properties: 1. Grow rapidly 2. Exhibit planktonic growth (Single cell) 3. Studied in pure cultures 4. Utilize sugars as carbon source 5. Appear as rods or cocci 6. Not potent pathogens 7. ex.) E. Coli, Salmonella, Lactococcus, Bacillus Lecture 2: Microscopy & Morphologies 1. Resolution: Ability to distinguish two adjacent obj. as distict & separate. Resolution cant be increased w/o limit. Dictated by light prop. 2. Magnification: Inc. apparent size, Inc. w/o limit. 3. Total Mag.: Mag. Of obj. X Ocular lenses 4. Empty Mag.: Mag. That exceeds limits of resolution. 5. Resolving Power: short wavelength, better R.P 6. Simple Stains: Use only 1 stains, hence all are same color -Spread culture Heat fix Flood slide in stain 7. Differential Stains: Use multiple to distinguish different type of organisms (ex. Gram Stains & Acid Fast). 8. Counter Stain: Staining so the other one have different color (Gram (-) and Non Acid) 9. Fluorescent Microscopy: Visualize specimen that fluoresce, that is, emit light of one color when light of another color shines upon them 10. Auto fluorescent: Cell that contain naturally fluorescent substances such as chlorophyll or other cpds. 11. Atomic Force Microscopy: Probe, laser, & deflector used to obtain surface image samples. No staining or coating needed. Also fixating. Concepts: 1. Light vs. Electron Microscopes: Light uses refractive lenses and Electron uses electromagnets 2. Simple vs. Compounds: Simple has 1 lenses (early microscope) and Compound has at least 2 (Ocular lenses & Objective). 3. Benefit of Oil Immersion: Used to inc. resolution b/c of inc. amt. of light passing through specimen 4. Numerical Aperture & Wavelength: Smaller Wavelength=Better resolution. N.A is a measure of light gathering ability used to estimate smallest observable obj. As Mag. Inc., N.A Inc.

5. Gram Staining Steps: Differential stain [ Distinguish Gram (+) & (-)] 1. Flood heat fixed smear w/ crystal All cells purple 2. Add Iodine for 1 min. All cells remain purple 3. Decolorize w/alcohol Gram (+) purple & (-) are colorless 4. Counter stain w/safranin for 1-2 min. Gram (+) purple & (-) pink 6. Acid Fast Steps: Differential stain 1. Small amt. of org. suspended in Salin is fixed on slide Acid & Non colorless 2. Slide flooded w/Carbonol Fuchsin & Phenol for 3 min & Rinse Acid: Pink Non: Pink 3. Slide decolorized w/3% HCl in 70% Alcohol until color removed & rinse Acid: Pink Non: Colorless 4. Counter stain w/methylene blue for 30sec. Acid: Pink Non: Blue. 1. Usefulness of Phase and Contrast: a. Phase: Can look at live, unstained cells. Provide improved contrast btwn unstained bacteria and surrounding medium. b. Dark Field: Utilize cardiod vs. dark background. Ideal for examining thin cells. 2. Transmission & Scanning: a. Transmission: Method of choice to resolve internal cell structures and very thin external appendages on bacteria. Can visualize down to molecular level. -Limitations: Must preserve & dehydrate and view in vacuum. Require cooking and thin sectioning to view interior. -Must inc. contrast using electron dense stains Methods: 1. Embed in plastic, thin section, stain w/metal salts, show external coats, cell envelop and internal structures 2. Negatively stain whole cells, shoes cell surface texture and very thin external appendages. b. Scanning: Coat specimen w/gold. - Advantages: High depth of field, wide range of mag., ideal for viewing surfaces colonized by bacteria in 3D 3. Usefulness of Laser Scanning Confocal & Differential interference contrast microscopes: a. Laser Scanning: Use laser beam illumination, narrow range of wavelength that inc. resolution. -Eliminated out of focus light that interferes w/obj. image. -Diminishes background fluorescent cells (live/dead) on/ beneath the surface of specimen w/minimal manipulation/damage to it. b. Differential Interference: A variation of phase contrast. Utilize pairs of matched prisms & polarizers. Light passing through sample is retarded to varying degrees base upon localized differences in reactivity. - Produce high contrast 3-D like images, adds details of internal structures w/in unstained cells due to difference in their refractive index. Lecture 3: Classification: 1. Phenotype: Observable characteristic traits of organism. Expression of genetic info. 2. Genotype: Complete genetic makeup; complete description of cells genetic info. 3. Endosymbiosis: relationship that occurs when one organism lives w/in the body/cells of another organism. In many cases, one cant survive w/o the other. (Mitochondria & Chloroplast originated from descendent of Bacteria) 4. Blovars: Varieties w/in species

5. 6. 7. 8. 9. 10. 11. 12. 13.

14.

a. Serovar: Serological varieties (det. By testing w/ antibodies) b. Pathovar: Pathogenic varieties Evolutionary distance: Sum of physical distance on a tree separating organisms; distance is inversely proportional to evolutionary relatedness (ex. For A B 3 diff. out of 12 3/12=0.25) Clade: Descendent from single ancestor. Corrected Evolutionary distance: Correction for two step mutation & back mutation. Stromatolites: Fossilized microbial communities Autotroph: Produce complex cpds. From simple inorg. Mol. Using energy from light (Photosynthesis) or inorg. Chem. Rxn (Chemosynthesis). Use CO2 as sole C source (Self feeders) Hetrotroph: Use several preformed org. carbon molecules (like glucose) as C source this is used by majority of microorganisms Phototropth: Organisms that carry out phothosynthesis to get energy. Use energy from light to convert CO2 and water into org. materials to be utilized in cellular f(x). Chemotroph: Organism that obtain energy by oxidation of e- donors in their environments. Can be organic (Organotroph) or inorganic (lithotrophs). List of Bacterial names w/ standing nomenclature: Each species has unique name. Names are Latinized binomial. The International Journal of Systemetic and Evolutionary Microbiology makes the Approved lists. Around 10,000 named species. Ribosomal database project: Database at MSU which provides ribosome related data and services to the scientific communities. Including online data analysis and aligned and annotated bacterial and archael 16S rRNA sequences.

Concepts: 1. Phylogenic tree construction from 16S rRNA seq.: The accped method of linkage species evolutionary past. -Obtaining DNA seq of 16S rRNA (PCR): 1. Amplify by PCR 2. Det. DNA seq. of fragment 3. Align seq. 4. Generate Tree 2. Evidence of Endosymbiotic theory: Many organelle in eukaryotic cells originated from gradual incorporation of symbiotic bacteria. a. Mitochondrion-Aerobic bacterium that supplied energy to the cell b. Chloroplast-Oxygenic Phototroph uses light to produce sugars. 3. DNA-DNA Hybridization, Ribotyping, Multilocus sequence typing, and FAME analysis: a. DNA-DNA Hybridization: Take DNA Heat to denature Mix DNA from 2 organisms (this make HYBRIDIZED DNA) Remove unhybridized DNA if 70% has hybridized=the 2 organisms are same species b. Ribotyping: Restriction enzyme fragments probe w/16S rRNA genes, no DNA sequencing involved. [Steps: Isolate genomic DNA from organism Cut w/restricted enzymeSeparate w/gel electrophorisis Hybridize w/radioactive 16S rRNA Analyze resulting pattern c. Multilocous sequence typing: Compares the DNA sequences of 5-7 housekeeping genes most microbes are known to have (housekeeping genes=basic encoding genes that are essential for cell survival). Can distinguish very closely related strains. Often used in clinical microbio. Or epidemiology. d. FAME Analysis: Fatty Acid Methyl Ester Analysis-Each species has a unique fatty acid composition. Used for: microbial ID, microbial testing.

4. FISH and its uses for ID: Fluorescent in situ hybridization-Oligoneucliotide probe has sequence complementary & specific to a particular bacteria, as well as fluorescent flag Steps: Cells treated to become permeableOligonucleotide added & allowed to base-pair (if seq. match)Cells then viewed by microscopy. -Basically: Different colors=different species 5. RNAs Involvement in Primitive Life: -Dilemma: DNA provide genetic info for proteins BUT DNA requires proteins for replication. -Solution: Primitive RNA world-RNA has the ability to act as both genes and enzymes, they can self-replicate and also synthesize nucleotides. Lecture 4: Fermentation: 1. Catabolism: Break down molecules into smaller units & release Energy 2. Anabolism: Involved in synthesis of cell constituent from simpler molecule; usually require Energy 3. Fermentation: Organic cpds. (substrate) serves as e- donor and another org. cpds. Serve as eacceptor. ATP produced by Substrate Level Phosphorylation. Doesnt consume oxygen. 4. Homofermentive: Lactic Acid fermentation=Glucose2 Pyruvate+2e- latic Acid (yields 2 ATP) 5. Hetrofermentive: Lactic Acid Fermentation=Glucose 2 Pyruvate+2e- Lactic Acid, ethanol, CO2 (Yields 1 ATP) 6. Gibbs Free Energy: Thermodynamic potential that measures the useful work obtainable from chemical rxns. (Endergonic and Exergonic) 7. Redox Couple: One reactant becomes oxidized and one becomes reduced (ex. NO3-/NO2oxidized on left, reduced on right) 8. Redox potential: A measure of the tendency to give up an e9. Electron tower: Determines whether overall redox rxns are energetically favorable. E- want to go DOWN the tower. E- are donated from redox couples above and accepted by redox couples below. Concepts: 1. Fermentation vs. Respiration Fermentation Respiration Purpose Oxidation of cpds. ATP Substance Oxidized Organic Org./Inorg. Oxidation/Reduction No external terminal eRequires external terminal eacceptor acceptor Method of ATP production Substrate level Electron transport(Proton phosphorylation motive force) 2. Electron carriers that transport 2e- + 2H+: NAD &NADPD, flavins (3rings), quinomes(1 ring w/long hydrocarbon chain) 3. Carriers that transport only e-: Heme-containing proteins called cytochrome. Also non-Heme Iron proteins like 2Fe, 2S, and 4Fe, 4S 4. Types of high Energy Chem. Bonds: High energy Phosphate bonds used for energy storage. 2 basic strategies for producing ATP. 1. Substrate level: Used in fermentation. Yields ATP. High energy phosphorylated intermediates are used to add phosphate to ADP, forming ATP. Other intermediates include acetyl phosphateAcetate. 2. Oxidative Phosphorylation: Used in respiration. Involve proton translocation and the proton motive force to generate ATP using ATP synthase. 5. Main Features of Fermentation: Anaerobic (no O2) process. Involves no membranes, and has LOW energy yield.

=Steps: Org. Cpds. Is the e- donorE- flow goes from oxidized intermediate to reduced org. cpds. ATP produced from fermentation. ATP consumed for cell synthesis. 6. Glycolysis: Fermentation of Glucose in which glucose (6C) is split into 2 pyruvate (3C). Produces 2 ATP &NADPH (1NADPH=3ATP). It is anaerobic pathway founf in many different organisms, has LOW energy yield compared to respiration 7. Mixed Acid fermentation: Anaerobic fermentation where the products are three acids [Lactate, Acetate, and formate] as well as ethanol and equal amounts of H2 and CO2. 8. Butanediol Fermentation: Anaerobic fermentation of glucose w/2,3-butanediol. The stoichiometry of the reaction is: 2 Pyruvate + NADH2CO2+2,3-butanediol. It is typical for Enterobacter and is tested for using Voges-Proskauer test. 9. Bacterium used for solvent production last century: Clostridium bacteria can produce solvents. 10. Strickland Fermentation: The name for a chem. Rxn, that involves the coupled oxidation and reduction of amino acids to org. acids. The e- donor amino acids is oxidized to a volatile carboxylic acid one carbon atom shorter than the original amino acids. Lecture 5: Respiration:

1. Terminal e- acceptor: Found at the last step in the sequence of rxns. For eukaryotes, O2 is the 2. 3.
terminal e- acceptor. Electron transport Phosphorylation: The synthesis of ATP involving a membrane associated electron transport chain and the creation of proton motive force. Electron Transport Chain: Couples electron transfer between an e- donor (NADH) and electron acceptor (O2) with the transfer of protons across membrane an energized membrane. Yields 38 ATP, 2 in glycolysis, 2 from citric acid cycle, rest via electron transport chain. Is more efficient and has higher ATP yield than fermentation. ATP synthase: enzyme that moves protons back across the membrane through Adenosine 5-phosphosulfate: the enzyme that catalyses the formation of active sulfate fromadenosine 5-phophosulfate and ATP

4. Oxidative phosphorylation: transport of the protons to the outside of the membrane results in 5. 6.

7. Oxygenic photosynthesis: Oxygen producing when light energy drives electrons flow. Electron
transport chain to make ATP. Has Photosystem I and II. 8. Anoxygenic photosynthesis: light energy drives a cyclic electron flow. Protons are pumped out through membrane and proton gradient used to drive ATP. Usually in purple bacteria, some NADH is made using electrons from donors like H2S 9. Accessory pigments: act as photoprotetants (carotenes) and increase efficiency of light harvesting. 10. Carotenes: membrane bound, alternating double bonds of long hydrocarbon chains. They are red, yellow, green, brown. Also photoprotection. 11. Phycobilins: Phycocyanin (blue) and phucoerythrin (red). Nontoxic, non-carcinogenic colorants. Function in light harvesting. Attached to proteins in phycobillisome. Concepts: 1. Membranes required for respiration: It involves electron transfer between electron carriers and proteins anchored in membranes 2. 2 Substrates required for respiration: a. Substrate: Oxidized, either org. or inorg. b. Electron acceptor: Reduced, wither org. or inorg.

12. Heterocyst: nitrogen fixing cells formed by some cyanobacteria.

3. Anaerobic uses electron acceptors other than O2: Some examples are Nitrate, Sulfate, Methanogenesis. 4. General scheme of electron transport pathways: 1. Substrate is oxidized 2. E- reduce NADNADH 3. ETP moved NADH through a series of membranes to final e- acceptor 5. Chmoorganotrophic & Chmolithotrophic respiration: a. Chemoorganotrophic: Organic cpds. Is oxidized (CO2) and e- transferred to oxygen or another acceptor b. Chemolithotrophic: Inorganic Compound is oxidized (H2) and the electrons are transferred to oxygen or another acceptor 6. Usuage of microbial respiratory reactions be for production of electricity: Amount of energy production from aerobic respiration of glucose compared to fermentation: - 10 fold, 38 ATP respiration, fermentation only 2 ATP 8. Efficient method of Pseudomonas stutzeri carrying out anaerobic respiration of nitrate: - Transforms nitrate to N2, uses ETP to pump protons outside of cell to make ATP 9. Utilizationof carbon dioxide by methanogens and acetogens: a) Methanogens: use proton motive force b) Avetogenesis: use proton or sodium motive force plus substrate-lvl-phosphorylation 10. 4 groups of photosynthetic bacteria, their type of photosynthesis and membranes: a) Cyanobacteria: oxygenic and use thyalkoid membranes b) Purple bacteria: anoxygenic, Photosynthetic components localized to lamellar of cytoplasmic membrane or as vesicles. c) Green bacteria: anoxygenic, use non-unit membranes. Two phylogenetically distinct groups (sulfur and non sulfur, with the green sulfur bacteria often having granules of sulfur w/in or attatched to the cell). Most possess chlorosomes. d) Heliobacteria: anoxygenic, components localized in cytoplasmic membrane 11. How can organisms using bacteriochlorophyll a co-exist with organisms that use chlorophyll a without significant competition for light energy - Different organisms contain different chlorophylls ot bacteriochlorophylls and various accessory pigments. They absorb different wavelengths to avoid competition 12. Oxygenic (Z scheme with 2 photosynthetic reaction centers) and anoxygenic (one photosynthetic reaction center) photosynthesis; how is ATP generated a) Anoxygenic: light energy drives cyclic electron flow. Protons are pumped out of the membrane creating a gradient which drives ATP synthesis. [yields oxidized sulfur, but some also oxidized H2/org. cpds.] b) Oxygenic: Photosystem I: chlorophyll P700; excited electrons transport through carriers to drive ATP synthesis to make NADPH. Photosystem II P680 electrons resulting from splitting water aretransported back to photosystem I. [Yields O2]. Lecture 6. Archae 1. Crenarchaeota: contains hypertermophilic (above 80) and cold dwelling organisims 2. Euryarchaeota: extreme halophiles and methanogens 3. Halophile: salt loving 4. Methanogen: methane producing 5. Bacteriorhodopsin: in the membrane of halophiles and use light to make ATP when moving proteins out the cell. 7.

6. Retinal: attached to the bacteriorhodopsin 7. Coenzyme M: a coenzyme required for methyl-transfer reactions in the metabolism of methogens 8. Coenzyme F420: a coenzyme involved in redox reactions iin methogens 9. Coenzyme F430: catalyzes the final step of methagonosis 10. Osmosis: the diffusion of water across a semipermitable membrane 11. Tetraether lipids: chains of isoprene units form long bi-leaflet hydrocarbon chains that are essential for survival in extreme environments 12. Isoprene: units that form the hydrocarbon chains 13. Volta experiment: showed that bubbles eminating from agitated lake bottoms was flammable because of methane producing organisms 14. Photoautotroph: use light energy to make ATP 15. Chemoorganotroph: use organic compounds to make ATP 16. Chaperonins: Help proteins fold 17. Reverse DNA gyrase: type I DNA topoisomerase able to positively supercoil DNA and is found in thermophilic archaebacteria and eubacteria. Concepts: 1. ARMAN: (Archaeal Richmond Mine Acidophilic Nanoorganism): Newest member of Archaea, Discovered in acid mine, smaller than any other known cellular life form, Lives in pH 0.5-1.5 [Small cells=high Surface/Volume ratio]. 2. Lipids in Archaea: Ether lipids chain a. Tetrahedral lipids: Essential for survival in extreme environments b. Phytanyl & Biphytanyl lipids: contain chains of isoprene units=These can form bilayered or monolayered. c. Ether lipids that contains rings. 3. Halophile survival: a. Some have unique pathway of Energy productions b. Maintaining water balance: -Ion Pumps: K pumped in-K inside cell balances Na outside the cell -Production of compatible solutes=synthesized in cell, balance H20 concentration c. Cell wall stability: Ba ions essential for stability of glycoproteins on outer surface d. stabilization of components inside the cell: K stabilizes proteins, ribosomes. 4. Why do some salt lakes appear pink under certain conditions; how do some halophilic Archaea generate energy from light - They use Bacteriorhodopsin to pump protons out of the cell to make ATP 5. How do proteins and DNA survive high temperatures encountered by thermophilic Archaea - Hydrophobic cores, more salt bridges, protein folding by histones and chaperonins, Thermosome (protein) 6. Examples of Euryarchaeota (Thermoplasma, Archaeoglobus) and Crenarchaeota (Sulfolobus, Pyrodictium) a) Thermoplasma: found in hot coal refuse piles (high temp low pH). No cell wall, tetaether lipids, small genome, chemoorganotroph b) Archaeoglobus: hydrothermal marine vents, energy from SO4-> H2S, lacks methyl-CoM reductase c) Sulfolobus: forms lobes on sulfur granules in hot springs, 90 degrees and 1-5 pH, aerobe d) Pyrodictium: hypothermal vents, grows at 105 degrees, strict anaerobe, chemolithotrophic Lecture 7: Eukaryotes: 1. Achlorophyllous: Not having chlorophyll hence unable to engage in photosynthesis.

2. Euglena: Unicellular protest. Some Euglena are considered both plant and animal features. Has single flagella 3. Merozoites: Parasitic. Infect and reproduce in red blood cells. (Malaria) 4. Chitin: long-chain polymer of a N-acetylglucosamine. It is the main component of the cell walls of fungi. In terms of structure, chitin may be compared to the polysaccharide cellulose and, in terms of function, to the protein keratin. 5. Mycoses: Fungal disease in human. a. Superficial: Only surface layers (Hair, skin), Trichophyton (Athletes foot), Mycrosporium (Ringworm). b. Subcutaneous or Invasive: Deep layer of skin and a different group of organisms. Sporothrix schenckii (from soil, woods c. Systemetic: Affect internal organs. Histoplasma capsulatum (histoplasmosis; Lungs) and coccidioidomycosis and also Candida albicans (Oral infection). 6. Plasmodium: Masses of multinucleated protoplasm (Slim molds) . Actively motile by amoeboid movement, engulfing food particles. Genetically diploid. 7. Pseudoplasmodium: a slug from which a fruiting body form. 8. Hydrogenosome: Metabolically simpler than mitochondria, but lack TCA cycle enzymes and cristae (Folded internal membrane) -provide energy through fermentation pathways. [trichomonas and various ciliated protists have this]. 9. Dunalielia: Most common green algae in salt lakes 10. Penecillium: Produce Penicillin antibiotics. 11. Ostreococcus: Member of algae. Member of plankton community. Smallest eukaryotic organism. Major producers of organic matter in biosphere. 12. Endolithic: (Endo=inside, Lithic=Rocks). Algae are major components of endolithic microbial communities w/in rocks in dry environments. Concepts: 1. Features of Eukaryotic cell: a. Dual Membrane enclosed nucleus: defining organelle of eukaryotes. b. Ribosomes on rough ER connected to nucleus c. Nucleolus: Site of rRNA synthesis and ribosome assembly d. Mitochondria: O2 consuming respiratory organelle in most eukaryotes; is replaced by hydogenosome in some anaerobic eukaryotes e. Chloroplast: Photosynthetic organelle in photosynthetic eukaryotes f. Golgi: Secretion g. Cytoskeleton of microtubules & microfilaments: Sytoplasmic motility h. Cytoplasmic Membrane: Nutrient Transport, hormone receptors, various biosynthetic rxns, not respirationMitochondria and bacteria i. ER: Membrane site of lipid &CHO metabolism(Smooth), and site of attatched ribosomes(rough). j. Some have ridged cell walls of cellulose, chitin, silicon, CaCO3, etc. k. Some have eukaryotic-type sheathed flagella 2. Disease causing eukaryotes that are members of Aveolates: a. Plasmodium falciparum: Malaria b. Pfiesteria piscicida: cell from hell that cause hrmorrhagic lesions in fish, shellfish poisoning (Neurotoxin). c. Gonyaulax: Produce toxins and red pigments

d. Harmful Blooms-photosynthetic dinoflagellates w/red pigments, marine bloo ms cause red tide fish kills and shellfishhuman poisoning due to neurotoxins 3. Life cycle of Plasmodium falciparum: a. In Mosquito, sporozoites develops and when bites human, it is released into blood stream b. Sporozoites removed from blood to liver and enters liver cell. c. Exoerythrocytic stage: Formation of schizont and merozoites Infection of red blood cell. d. Erythrocytic stage: Merozoites infect & reproduce in red blood cells [Due to synchronous multiplication of merozoites in blood cells and their rupture, fever/chill symptoms of malaria occurs]. e. Production of gametes and cycle continues. 4. Features of Fungi, role in nature, 5 major groups of fungi; major impact to humans. a. Features: -Contain cell walls of chitin & other glucans -Achlorophyllous chemoorganotrophs -Commonly filamentous(molds; branched filaments, hyphae mycelia), some unicellular(yeast). b. Major role in nature: Major players in decomposition and mineralization of organic carbon -Dominates microbial biomass in soil, esp. acidic soil -Various lifecycle. c. 5 Major groups: 1. Chytridiomycetes: Most primitive fungi; exist as single cells or in colonies 2. Zygomycetes: Resulting from fusion of hyphal gametes; bread mold 3. Glomeromycetes: Small group w/major ecological importance; form symbiosis w/most terrestrial plant roots. 4. Ascomycetes: Spores in sac (Ascucs) 5. Basidiomycetes: Spores in a club-like basidium/large fruiting bodies(mushrooms) d. Major impact on humans (health and ecology): -Penicilin production -Disease causing pathogens (Mycoses) -enhance nutrient intake 5. Candids albicans: Cause oral infection in infants and Histoplasmosis is respiratory infection. 6. What disease associated with Trypanosoma brucei: Causes African sleeping sickness-parasite grow in blood stream. 7. Two types of slime molds: a. Cellular slime molds: individual cells w/amoeboid motility. When starved, the cellular slime mold cells aggregate in response to a cellular chemical signal (cAMP) producing a pseudoplasmodium slug that differentiates into a stalk and head fruiting body which sporulates. Mature spores are dispersed by wind, land on new terrain, and germinate into vegetative amoeba. b. Acellular: produce masses of multinucleated protoplasm called plasmodia. 8. Cell from Hell: Pfiesteria piscicida cause hemorrhagic lesions in fish and shellfish poisoning(neurotoxins). Cause diarrheic, neurotic, paralytic, memory loss, and blurred vision. 9. Algae habitate: Commonly found in aquatic habitats also in moist soils and beneath surface of translucent rocks in dry desserts (endolithic). 10. Division of protozoa: Major activity in nature: predators of bacterial prey, inc. carbon cycling, and animal parasites. 6 subdivision:

Diplomonads(Have 2 neucli of equal size) & Parabasalids (Contain Parabasal body, lack mitochondria, but have hydrogenosomes for anaerobic metabolism) -Giardia cause Giardiasis, a waterborne intestinal disease (Diplomonads) -Trichomonas-Cause STD (Parabasalids) 2. Euglenozoans: Trypanosoma brucei 3. Alveolates 4. Stramenopiles 5. Cercozoans & Radiolarians 6. Amoebozoa Lecture 8: Cell envelope: 1. Peptidoglycan: Polymer consisting of sugars and amino acids that forms mesh-like layer outside plasma membrane of bacteria forming cell wall. Composed of N-acetylglucosamin, Nacetylmuramic acid, and certain Amino acids. 2. Periplasm: Between cytoplasmic and outer membrane of Gram (-) cell. 3. Lipopolysaccharide: Large molecules consisting of lipid and polysaccharide joined by covalent bond; they are found in outer membrane of Gram (-) bacteria. Act as endo toxins and elicit strong immune responses in animals. 4. Membrane leaflet: (Gram(-))-Outer leaflet contain lipopolysaccharide and inner contain phospholipids. 5. Murein Sacculus: One massive covalently-linked supramolecule sheet of peptidoglycan completely enclosing the cell protoplast. 6. Braun lipoprotein: Connects the outer membrane to the peptidoglycan sheet in the periplasm. Its very abundant protein, stabilizes OM-Peptidoglycan complex, and contributes to formation of periplasm. 7. Endotoxins: toxin associated w/Gram(-) bacteria. Structural molecule of bacteria that is recognized by the immune system. 8. Porins: Proteins that cross membrane and act as a pore through which molecules can diffuse. Large enough to aloe passive transport. Act as channels. They are present in outer membrane of Gram(-) and some (+). 9. Transmembrane: Protein that goes from one side through other side. F(x) as gateway/loading docks to deny/permit transport of specific substances across membrane, get in/out of cell. Concepts: 1. Phospholipid structure:

1.

2. Gram(-) vs. Gram (+): a. Gram (+): -Have very thick crosslinked peptidoglycan layer wall external to the cell membrane(No outer membrane) -During Gram stain, when dehydrated by alcohol, the thicker/more cross linked wall retains the crystal violet iodine complex during alcohol extraction -Surface texture is smooth b. Gram(-):

-Have Thin peptidoglycan layer w/periplasm created by unique outer membrane and the cytoplasmic membrane. -During Gram stain, the greated porosity of the thin wall in the lipid-rich envelop allows the crystal violet-iodine complex to be extracted -Surface texture is uniquely convoluted. 3. Molecular architecture of Gram(-) cell envelop Outer membrane is asymmetric (outer and inner leaflets differ) Outer leaflet uniquely contains lipopolysaccharide Inner leaflet uniquely contains phospholipids Outer membrane proteins: some outer leaflet only, some inner leaflet only, some traverse the outer membrane, e.g., porins Periplasm between outer and inner membrane, contains cross -linked peptidoglycan supramolecular structure (= murein sacculus), connected to inner leaflet of the outer membrane by a special (Braun) lipoprotein, will also contain special proteins (certain enzymes, transport proteins, etc). Inner (cytoplasmic) membrane contains bi-leaflet of phospholipids, some glycolipids, and various proteins. 4. Difference between starch, glycogen, and cellulose a. Starch: Glucose units joined together by glycosidic bonds. This polysaccharide is produced by all green plants as energy source. b. Glycogen: Molecule that serves as the 2ndary long-term energy storage in animal and fungal cells. Made by liver and muscles. c. Cellulose: Structural component of primary cell wall of green plants, many forms of algae. Most common organic cpds. On Earth. 5. Types of proteins & Enzymes found on periplasm: -20-40% of total cell volume of Gram negative cell Functions at crossroads of biosynthetic and degradative processes in cell Contains peptidoglycan matrix (=murein sacculus), a variety of proteins, and some oligosaccharides (for osmotic balance) Functions of periplasmic proteins include: Nutrient binding proteins for nutrient uptake Chemoreceptor proteins involved in chemotaxis Catabolic scavenging enzymes that degrade complex substrates Biosynthetic enzymes involved in biogenesis of cell envelope Detoxifying enzymes (e.g., enzymes that degrade and inactivate certain antibiotics) 6. How does O-specific polysaccharide, Core polysaccharides, and Lipid A form the LPS: a. O-specific polysaccharide: -Also called O-antegen polysaccharide varies significantly among species (Can even be strain specific) b. Core Polysaccharide: -KDO, Hep(Heptpse), Glu(Glocose), Gal(Galactose), GluNac, GluN(Glucosamin) c. Lipid A: this portion can be toxic to animals: this component of LPS is endotoxin. Lecture 9: Cell Envelop II 1. Tetrapeptide: peptide consisting of 4 amino acids joined by peptide bonds. 2. Repeat unit: Part of polymer chain whose repetition would produce complete polymer by linkage.

3. Teichoic acid: Found in cell wall of Gram (+) bacteria. Polymer with side chain of amino acids or sugars attatched. Some terminate in fatty acids which are inserted into cell membrane. 4. FtsZ Protein: Essential for cell division and is the most important(Involved in peptidoglycan growth) 5. MreB Protein: Important for cell shape 6. Bactoprenol: Carries Peptidoglycan precursors to the site of synthesis. It is the carrier Molecule 7. Protoplast: Cell w/no wall 8. Lysis: Rupture of cell wall 9. Lysozyme: This enzyme digestion of the wall in isotonic solution releases an intact protoplast or spheroplast. 10. Polar vs. Non Polar: Polar region, Hydrophilic, Non-Polar, Hydrophobic 11. Carrier-mediated transport: Used when there is low concentration on external. 12. Semi-Permeable: Allow certain molecules/ions to pass through it by diffusion & facilitated diffusion. 13. Proton-Motive Force: Generation of ATP by movement of Hydrogen ions across membrane during cellular respiration 14. Pleomorphism: two or more structures form can occur during lifecycle esp. in plants and marine animals. 15. Hopanoids: Primary f(x) is to improve plasma membrane strength and rigidity in Bacteria. Concepts: 1. Major components of peptidoglycan and tetrapeptide unit of E.Coli:

2. Sequence events for growth of murein sacculus:

3. Peptidoglycan in Gram(-) vs. Gram(+):

4. Major f(x) of cytoplasmic membrane & bacterial cell wall:

5. Involvement of autolysins in growth of peptidoglycan:

6. 3 Types of simple membrane transport; group translocation; features of ATP-type transport. Examples presented of each type: