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MIBO test 1
Microbio test 1
| Question | Answer |
|---|---|
| What are the super domains | Prokara and Eukarya |
| two domains in prokarya | bacteria and archaea |
| What is the difference between the old kingdoms and the new domains | The old kingdoms are based on phenetic observations: membrane size, cell size and cell organization the domains are based on phylogenetic sequences: rRNA, DNA and protein |
| rRNA sizes | eukaryotes have 18S and prokaryotes have 16S |
| finction is identical in all organisms | rRNA function |
| three distinctions about prokaryotes | 1. only unicellular organisms 2. lacks membrane bound organelles 3. DNA is not bound by a membrane thus known as a nucleoid |
| three distinictions about eukaryotes | 1. orgainisms are uniclellular and muti-cellular 2. have membrane bound organelles 3. DNA is bound by a membrane thus called a nucleus |
| Bacteria contain what | peptidoglycan |
| bateria reproduce how | binary fission |
| Bacter is motile how | flagella or flagellum |
| Domain archaea lacks what | peptidoglycan |
| archaea reproduce how | binary fission |
| archaea is motile how | flagellum or flagella |
| what is the domain that is saprophytic | domain eukarya |
| domain eukarya include | mushrooms, molds and yeast |
| Algae explain | aquatic, contains pigments for photosynthesis (autotrophic) |
| explain protists | some are autotrophic and some are heterotrophic, terrestrial and aquatic, some have CaCO3 and some have silica cytoskeletons, motile by flagella, cillia or psuedopodia |
| RNA world hypothesis | chemicals interact with one another creating enzymes, proteins and DNA |
| what are ribozymes | RNA with catalytic activity like enzymes |
| what is LUCA | last universal common ancestor bacteria is the root of all three domains lacks fossil evidence |
| endosymbiotic hypothesis | mitocondria, chloroplast, hydrogenosomes likely evolved from prokaryotic symbiotes of eukaryotic partners |
| Survival of the fittest Eukaryotes vs Prokaryotes | eukaryotes: vertical sexual reproduction prokaryotes: horizontal asexual reproduction |
| binomial nominclature is invented by | linnaeus |
| species vs genus | there can be many species within a genus |
| Lucretius and francastoro | diseases were because of invisible living creatures |
| van leeuwenhoek | men's haberdasher that discovered animalcules by means of the first microscope 300x magnification |
| Redi | disproves spontaneous generation by three experiments 1. meat open to the air--maggots and flies 2. meat covered with paper--no maggots or flies 3. meat covered with gauze--maggots on the gauze but not the meat |
| spallazani | sealed glass flask and boiled contents said air either carries the organisms OR air is required for germs to grow |
| schwann | flasks with boiled broths are left open and air passes through red-hot glass tubes concludes air carries germs |
| schroder | flask with boiled broth is stopped with serilized cotton/wool germs are stopped by serilized wool/cotton |
| Pasteur | created swan-neck flask to catch the germs results:spontanteous generation is solidly disproved--he was a wine maker and his wine was turning into vinegar before he did this |
| tyndall | Hypothesizes that some forms of germs may be more resistant to heat |
| Cohn | demonstrates the existance of heat-resistant germs (endospores) |
| bassi | showed that disease affecting silk worm production was caused by fungal infection--only worms without infection could produce silk |
| Lister | found an antiseptic for infection--carbolic acid and heat serilized his instruments |
| Koch | Germ theory of disease 1. microbe must be present in every disease and absent in healthy 2. microbe must be isolated and grown in pure culture 3. same disease must result when inoculated into a healthy host 4. same micro must be reisolated and grown |
| Germ Theory | 1. microbe must be present in every disease and absent in healthy 2. microbe must be isolated and grown in pure culture 3. same disease must result when inoculated into a healthy host 4. same micro must be reisolated and grown |
| Koch and pure cultures | used agar because it could withstand high temps and most bacteria didnt use it |
| vaccine against anthrax and rabies using what and developed by who | using attentuation which is weakening of germs (successive passage through hosts and heat) pastuer |
| what do microbes do | make me sick, make and preserve foods, fertilize soils, bioremediation |
| bioremediation | GEM– genetically engineered microbes like for the oil spill |
| types of microscopes | light and electron |
| how electron microscopes work | use electron radiation to capture and reproduce images |
| light microscope magnification | 1000x |
| four types of light microscopes | 1. brightfield 2. dark field 3. phase contrast 4. flouresence |
| Brightfield | Light microscope: specimen appear dark and background is white specimen need either natural color or to be stained--not good for live specimen |
| Dark field | Light microscope: Specimen are light and background is dark no need for stain or pigment--good for live specimen light is scattered by a disc (patch stop) |
| Phase Contrast | Light microscope: Image is bright background is dark good for live material Produces images in which the dense structures appear darker than the background and a glow around their edges |
| Fluorescence | Light microscope: use dyes or natural pigments that produce light some work for live specimen pigments and dyes create a different wavelength and see them glow |
| two types of electron microscopes | scanning and transmission 1000x better magnification than light microscopes can be expenseive because materials are often coated with gold or platinum |
| transmission | electron microscope: electron beam penetrates specimen and scatters intracellular details are studied this way |
| scanning | electron microscope: beams hit surface of coated specimen surface structure studied this way 100x better than light microscopes |
| oil for microscopes | almost no refraction and increases resolution like mineral oil at work |
| fixation | kills and adheres microbes to slides toughen cell walls and perserves the cell structure |
| methods of fixation | heat and chemical |
| explain the methods of fixation | heat: air-dried and passed through flame preserves the morphology of cell but not the internal structures if not dired completely then cell can lyse Chemical: keeps internal structures in tacked some chemicals are toxic |
| types of dyes and explain | basic and acidic basic: Carry a positively charged chromophore group is attracted to negatively charged components of cells, Most common dyes in lab acidic: carry negative charge chromophore group is attracted to positively charged parts of the cell |
| four staining techniques | positive negative simple differential |
| positive stain | cell is stained and background remains the same |
| negative stain | cell stays the same and background is stained |
| simple stain | positive or negative only one dye is used |
| differential stain | two or more dyes are used positve or negative |
| examples of differential stains | gram stain and acid fast stain |
| differences of acid-fast stain and gram stain | acid fast: based on presence of waxy mycolic acids end result is fushia or blue gram stain: most widely used method based on peptidoglycan content is purple or red end result is |
| how does a gram stain work | primary stain: crystal violet all cells are purple Mordant: Gram's iodide decolorizer: ethanol Dissolves lipopolysaccharide layers in cell walls counterstain: safranin turns vacant cells pink |
| gram stains--what each color is | Pink--lipopolysaccarides purple--peptidoglycan |
| gram stain important factors | Lipopolysaccharides are easily dissolved by ethanol, Peptidoglycan is not easily deteriorated by ethanol,After decolorization, Gram - cells take up counterstain |
| how does acid-fast stain work | Primary stain: Carbol fuchsin heat is used to soften the mycolic acid Mordant: Cooling Decolorization: Acid alcohol Dissolve the walls of non-acid fast bacteria Counterstain: Methylene blue Blue cells--non acid fast Pink cells--acid fast |
| capsules | Capsules are layers of polysaccharides which are slimy and starchy Nigrosin or India ink is used The visibility of cells can be increased by counterstaining |
| endospores | it's the dormant stage of bacteria and is nonreproductive and difficult to stain resistant to heat and chemicals, when conditions are favorable, the spore germinates to produce a vegitative cell |
| how does an endospore stain work | Primary stain: Malachite green Mordant (physical): Cooling Decolorizer: Water Counterstain: Safranin Turns vegetative cells pink/red |
| Flagella | use electron microscopes to see |
| monotrichous | one flagellum at one pole |
| bitrichous | two flagellum at one pole |
| lophotrichous | a tuft of flagellum at one pole |
| amphitrichous | one flagellum at each pole |
| peritrichous | flagellum around the perimeter |
| amphilotrichous | a tuft of flagellum at each pole |
| bacterial morphologies | coccus, bacillus, vibrio, spirilla, pleomorphic and appendages (have tubes or stalks) |
| bacterial arrangements | strepto--chain staphylo-cluster diplo--two tetrads--squares of four sarcina--packets of eight |
| bacterial cell sizes | nanobacteria giant bacteria |
| bacterial cytoplasm | 70 to 80% water mix of amino acids, sugars and salts |
| bacterial cytoskeleton | microtubules (tublin in E), microfilaments (actin in E), and intermediate filaments (laminin in E) **look at notes** |
| bacterial intracytoplasmic membrane | observed in photosynthetic and nitrifying bacteria similar to endoplasmic reticulum and golgi apparatus, derived from invagination of plasma membrane and is part of complex structures in Eukaryotes (mitochondria and chloroplast) |
| bacterial nucleoid | usually a single cellular chromosome contains genes that are essential for survival |
| bacterial plasmids | genes that are nice to have but not neccesary for survival are double stranded DNA circular replicate seperately from chromosomes genetic recombination (episome) |
| plasmid types | conjugative--horizontal gene transfer (carry antibiotic resistant genes) virulence--carry virulence genes metabolic--carry genes for alternate metabolic substratescol--carry genes for colicin production |
| bacterial inclusions | granuoles or gas "vacuoles" primarily formed for storage purposes membranes may be phospholipid bilayers or proteins |
| oligotrophic | inclusions store low or scarce nutrients |
| examples of inclusions | PHB Glycogen volutin sulfur granuoles/globuoles cyanophycin granules carboxysomes magnetosomes gas vacuoles ribosomes |
| PHB | lipid-like, carbon and energy source found in purple photosynthetic bacterial surrounded by single layer of protein and phospholipids |
| glycogen | starch like, carbon and energy source in many bacteria |
| volutin | stores phosphate used to be called metachromatic granules |
| sulfur granules | energy and electron source found in purple photosynthetic bacteria |
| cyanophycin graules | used to be called blue/green algae polymer of arginine and aspartic acid stored nitrogen source |
| carboxysome | contain Rubisco and CO2 for carbon fixation reactions surrounded by protein coat |
| magnetosomes | orientation for navigation toward nutrients found in magnetic bacteria |
| gas vacuoles | aggregates of many gas vesicles impermeable to water but permeable to gas provides buoyancy for aquatic bacteria each is composed of a single protein repeating |
| ribosomes | site of translation made of two separate components |
| Bacteria and Archaea ribosomes subunits | 30+50S = 70S total |
| Eukarya ribosomes subunits | 40+60S = 80S total |
| endospores (Sporulation) | develope in unfavorable conditions most are gram + clostridium--tetnus, botulism and gangrene bacillus--anthrax and food poisoning |
| endospore (water content) | water content is VERY low |
| how to eliminate endospores | sterilization |
| what contains dipicolinic acid | endospores |
| endospores: seven stages | 1.axial filament of DNA formed 2.cell membrane forms septum 3.double layered membrane=protection 4.cortex forms around forespore 5.spore coat synthesis starts 6.spore coat complete--true endospore 7.released endospore |
| dormant endospores transform to vegetative cells in three stages | activation--usually heat germination--spore swells and coat ruptures outgrowth--cell returns to vegetative state |
| bacteria cytoplasmic membrane | boundary between cell and environment flexible phospholipid bilayer contain hoponoids to stabilize structure (are steroid like) |
| peripheral and intergral proteins | peripheral--loosly connected to cytoplasmic membrane, hydrophilic intergral--amphipathic, extend from the inside of the cell to the outside |
| cytoplasmic membrane analogous to eukarya | site for enzyme interactions regulates transport for sugars and salts houses components for etc |
| cell wall--bacteria | prevents cell from lysis and holds shape gram + and gram - |
| Peptidoglycan for gram + and gram - | gram + has lots of peptidoglycan gram - has little peptidoglycan |
| peptidoglycan backbone | alternating amino sugars NAM and NAG (chain of a metal fence) |
| chain between NAM and NAG | tetrapeptide chains composed of peptide bonds (chain link fence) |
| gram - peptidoglycan backbone | DAP linked to D-alanine DAP is unique to bacteria |
| gram + peptidoglycan backbone | interpeptide bridge formed (5 glycines) from D-alanine to L-lysine |
| gram + cell walls | teichoic acid aids in stability lipoteichoic acid connect peptidoglycan to cytoplasmic membrane lipids |
| gram - cell walls | outermost edge is lipopolysaccharides contains porins--channels for small molecules large periplasmic space |
| gram - antibiotics | cells recognize antibiotics and pump them out by porins |
| lysozyme | weakens existing peptidoglycan found in tears and saliva forms protoplasts (gram +) and spheroplast (gram -) more effective on gram + |
| glycocalyx | expolysaccharide (EPS) is used for energy storage and protection not all bacteria examples are capsules and slime layers |
| S-layers | primarily on archaea (usually the only form of protection) like bubble wrap pattern like floor tiles protection |
| bacterial flagella | swimming may aid in attachment threadlike propellars protein made of flagellin |
| prokarya flagella | hollow |
| axial filaments | in spirochetes flagella in periplasmic space |
| bacterial flagella structure | filament, hook, basal body |
| tumble pattern of flagella | counterclockwise--run clockwise-- tumble and direction change proton motive force produces energy |
| flagella motors | Rotor: turns in a cylindrical ring of electromagnets Stator: electromagnetic ring made of MotA and MotB that anchor to peptidoglycan and form channel in plasma membrane |
| fimbriae and pili | hair like appendages thinner and horter than flagella |
| fimbriae | Velcro attach bacteria to solid surfaces (dental plaque) |
| Pili | allows transfer of plasmids from one cell to another |
| Nutritional requirements | microelements (trace elements), macroelements, and growth factors (organic compounds that cannot be synthesized like amino acids, vitamins and purines and pyrymidines) |
| autotrophs | carbon source make own organic compound |
| heterotrophs | carbon source must get organic compound from somewhere else (us) |
| phototroph | energy source light |
| chemotroph | energy source break down chemicals |
| lithotroph | elcetron source inorganic |
| organotroph | electron source organic |
| flexability of purple nonsulfur bacteria | O2 at normal levels: follow chemoorganoheterotrophy O2 absent: follow photoorganoheterotrophy O2 at low levels: follow a mix of both pathways |
| diffusion | high to low concentration to reach homeostasis (equilibrium) |
| four nutrient transport mechanisms | passive diffusion facilitated diffusion active transport group translocation |
| passive diffusion | concentration high to low for O2 and CO2 |
| facilitated diffusion | carrier proteins concentration high to low (50000 fans through 12 gates) |
| facilitated diffusion carrier proteins | permeases intergral proteins change conformational shape when it binds saturable gradient must be maintained |
| facilitated diffusion waste | waste is exported through reverse mechanism |
| faciliated diffision prokaryotes | not the primary mechanism of nutrients |
| active transport | energy is required primary is ATP secondary is energy from gradients (proton and sodium pumps) low to high saturable most common uptake of microbes energy comes from breaking the phosphate bond |
| active transporter paths three types | uniport antiport (two molecules different direction) symport (two molecules same direction) |
| ABC transporters | requires a solute binding protein permease has two domains spans the phospholipid bilayer (transport domain) one in cytoplasm (nucleotide binding) binds to ATP cleaves to ADP so solute can pass through |
| Proton and Na pumps | coupled anti and symport antiport: Proton-motive force drives expulsion of Na+ from the cell as H+ enters symport: Conformational change in carrier occurs to release Na+ and solute inside the cytoplasm |
| group translocation | molecule is being transported into the cell while being chemically altered break a phosphate bond, make a phosphate bond |
| group translocation example | PEP or PTS transport PEP becomes pyruvate (substrate for kreb cycle) May also play a role in chemotaxis Mechanism widely distributed in prokaryotes |
| agars | complex polysaccharide but bacteria dont eat it extracted from seaweed remains stable at human pathogen incubation 37 degrees C |
| chemical types of media | complex chemically defined |
| chemical types of media explain | complex: contains material that we do not know the exact ingredients to and varies from batch to batch such as meat extract chemically defined: we know the exact formula for it |
| special purpose media: selective | allows growth of some organisms but inhibits others example: Thayer-Martin agar used for STD screening with antibiotics in it |
| special purpose media: differential | everyone can grow growth is differentiated |
| special purpose media: sel/dif | Example: MacConkey Agar does not grow gram + differentiation is based on fermentation of lactose fermenters (break down lactose)--pink non fermenters--off white |
| bacterial colonies | all cells arise from single parent cell all protegy are identical binary fission |
| three ways to isolate pure cultures | streak plate doesnt enumerate spread plate enumerates pour plate enumerates |
| what is microbial growth | increase in number achieved by binary fission (bacteria) and budding |
| budding | two unique cells mother and daughter |
| bacterial cell cycle | c phase: replication d phase: delayed phase getting pulled to either side of the cell cytokinesis: septation complete |
| chromosome replication | begins at origin bidirectional replication makes two copies |
| chromosome partitioning | MreBmodel in rod shape bacteria (actin in E) form spiral complex inside the cell chromosome separate to either pole as they move down the MreB helix |
| steps in cytokenisis in E. coli | 1. select site where septum will form 2. assemble of Z ring 3. link Z ring to plasma membrane 4. assemble cell wall machinary 5.constict cell and form septum |
| batch culture growth phases | lag log stationary death |
| lag phase | cells are metabolically active but no increase in number adaption: chromosome replication and synthesis increase in cell size length of phase varies with environment and species |
| log phase (exponential) | population doubles with each generation average is 20 minutes asynchronous--not all at once growth rate is saturated |
| stationary phase | curve becomes horizontal population stays the same--new cells gorm as old cells die very common |
| reasons for stationary phase | nutrition or O2 limitations accumulation of toxic waste cell density |
| death phase | viable cells decrease exponentially inability to grow may experience a new lag and log phase because it relieves cell o2/space/nutritional limitations |
| what causes cell death | build up of toxin survival of the fittest current theories: Viable but not Culturable (VNBC) programmed cell death |
| VNBC | viable but not culturable "bacterial coma" dormant without change in morphology inability to grow unless environment changes public health threat |
| Programmed cell death | suicide of cells to provide more space and nutrients to surviving cells it triggers an enzyme to break down it's own cell wall and die |
| cell number calculation | Nt = N0 x 2^n Nt--the number in the population at time t No--the originial population number n--the number of generations in time t |
| two ways to measure microbial growth | by cell number and by cell mass |
| microbial growth--cell number | viable vs total direct microscope counts |
| microbial growth--cell mass | calculations and conversions total cell weight and turbidity |
| direct microscope counts | Petroff-Hauser Counting Chamber counts number of cells per 0.1ml but cant distinguish between viable and dead cells |
| cell counters | automated counting device ex. coulter counter cant distinguish live and dead and cant distiguish between a cell and small debris |
| flow cytometry | automated counting device cant distinguish live and dead and cant distiguish between a cell and small debris |
| viable counts | measures colony forming units |
| turbidity (cell mass) | measures the amount of light scattered by cells more mass=more scatter uses spectrophotometer to measure optical density of the cell |
| six chemical and physical factors determining growth | solutes and water activity pH temperature o2 availability pressure radiation |
| osmotic pressure four types | moderate halophile:marine bacteria extreme halophiles:found in hypersaline places osmotolerant: growth over wide range (skin bacteria) saccharophile: yeast and mold |
| effects of osmotic pressure | osmotic pressure and water activity are inverse low water activity causes metabolic limitaions high water activity may lyse cells because too much water in them--cell wall helps with protection |
| pH requirements | acidophiles-- 1-5.5pH neutrophiles (most)-- 5.5-8pH alkalophiles-- 8.5 - 11.5pH |
| keeping the cytoplasmic pH neutral | neutrophiles exchange of K for h alkalophiles exchange of na for h synithesize special proteins in acidic conditions acid shock proteins use ATP to export H out of cell export waste out of cell fermentation pruduces acids putrefication-ammonia |
| temp requirements (4) | psychrophile 0-20 degrees mesophile 15-45 thermophile 45-70 hyperthermophile 70-120 degrees c |
| psychrophile | causes soilage of food in the fridge |
| mesophile | include most human pathogens 37 degrees |
| thermophile | found in compost heaps |
| hyperthermophile | hot springs |
| major groups based on o2 availability | obligate areobe facilitative anaerobe obligate anaerobe areotolerant anaerobe microareophiles |
| abligate aerobes | o2 required so live at top of test tube |
| facilitative anaerobe | in a test tube dense at top but growth everywhere in presence of o2 more atp=more growth lack of o2 less atp=less growth |
| obligate anaerobe | test tube they are mostly at the bottom with some alittle above the bottom oxygen is toxic to them |
| obligate anaerobes catalase | breaks down hydrogen peroxide to h2o and o2 |
| obligate anaerobe peroxidase | converts peroxides to water and NAD+ |
| aerotolerant anaerobes | no toxic affect of O2 to to SOD in test tube they can live everywhere |
| microaerophiles | too high of o2 is damaging require 2-10% o2 and atmosphere has 20% many are respiratory pathogens Grow with other organisms to float through the atmosphere test tube--all near the top but not at the top |
| hydrostatic pressure | land or surface water: 1 atm deep sea bacteria: 600 to 1100 atm |
| barotolerant | adaptable to pressure |
| barophiles | grow better with higher pressure than the atmosphere ones that grow in high temps are archaea and one that grow in cold temps are bacteria |
| radiation | damages DNA mutations indrectly lead to cell death Thymine dimers are easy to break individually but together it’s much harder to break all of the covalent bonds |
| radiation ultraviolet rays | uv light DNA damage can be repaired photoreactivation dark reactivation read slide 46 chapter 7 |
| ionizing radiation | atoms lose electrons x-rays and gamma rays low levels cause mutation high levels are lethal often used as a sterilizing treatment |
Created by:
dmr18
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