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| the science of classifying organisms using binomial nomenclature system |
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| the study of evolutionary relatedness among groups of organisms. expanded taxonomy. |
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| grouping organisms according to common properties. implies that a group of organisms evolved from a common ancestor. |
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| used to construct ancestor trees |
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| used because universal nucleic acid and means it arose very early in life and passed to every organism: evolutionary reasons |
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| bacteria, archaea, eukarya. always changing with new technology and knowledge gained. |
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| artificial system that is man made. similar things are grouped together |
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| eukaryotic definition of a species |
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| a group of organisms that has the potential to breed. based on sexual reproduction. |
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| prokaryotic definition of a species |
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| populations that have similar characteristics. |
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| grown in laboratory media |
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| population of cells derived from a single cell. think streaking for isolation. |
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| genetically different cells within a clone. still considered same species. identified with numbers, letters, or names. |
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| all closely related strains constitute |
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| multicellular, no cell walls, chemoheterotrophic |
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| multicellular, cellulose cell walls, usually photoautotrophic |
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| chemoheterotrophic, unicellular or multicellular, cell walls of chitin, develop from spores or hyphal fragments |
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| a catchall kingdom for eukaryotic organisms that do not fit other kingdoms. grouped into clades based on rRNA. |
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| animalia, plantae, fungi, protista |
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| population of viruses with similar characteristics that occupies a particular ecological niche. |
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| cells to complete their life cycles. |
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| viral species classified by |
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| similarities of infecting same type of organisms |
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| putting organisms into groups that have closely related species. lists of characteristics of known organisms. |
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| matching characteristics of an "unknown" organism to lists of known organisms. can identify without knowing classification. |
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ID: Bergey's Manual of Determinative Bacteriology (what we use)
Classify: Bergey's Manual of Systematic Bacteriology (5 volume, expensive) |
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| morphological characteristics |
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Definition
| useful for identifying eukaryotes. only get you so far with prokaryotes. |
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| gram staining, acid-fast staining |
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| determines presence or absence of bacterial enyzmes. ex: use lactose? metabolize citrate? |
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| start with general questions then follow arrow/answer to the question until you reach the bottom |
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| rapid ID method, results 4-24 hours, easy to read, ID card/matrix. 15 different tests at one time. |
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| the reactions of microorganisms with specific antibodies. Western blot, Southern blot, Northern blot, etc. |
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| only can tell using serology test |
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| uses differences in electrical conductivity between species. ID method. At end of flow has laser, electrode, etc. with a charge. |
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| DNA base composition, DNA fingerprinting, rRNA sequencing, polymerase chain reaction (PMR) |
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| guanine and cytosine content percentage |
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| electrophoresis of restriction enzyme digests. chop up DNA> |
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| polymerase chain reaction (PCR) |
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| nucleic acid hybridization |
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Definition
| based on complimentary based pairing. DNA's ability to hybridize with itself or another organism. |
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| complete nucleic acid hybridization |
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Definition
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| partial nucleic acid hybridization |
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| organisms are related, but not the exact same |
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| none nucleic acid hybridization |
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| organisms not related at all |
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aka microarray, spots have single stranded DNA. 6 squares with 100 spots in each square.
hybridizing dna colors (in hybridization %): red=no green=100% |
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| eat things, don't produce their own food |
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| hijack cell "pirates", have protein coat and can be surrounded by envelope |
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| have few or none of their own |
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| scientific idea of viruses |
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| extremely complex aggregates |
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| very small, can't see with light microscope, 20-1,000 nanometers in length |
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| can be proteins, lipids, carbs |
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| completely assembeled viral particle |
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| describes/distinguishes the virus from others |
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| virion structure possibilities |
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| polyhedral, helical, enveloped, complex |
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| geometric shape that forms icosahedron (20-sided) common in cold and polio |
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| long rod with hollow capsids. ebola virus and rabies |
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| helical or polyhedral in nature, highly pleomorphic, spikes |
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| polyhedral head and helical tail, bacteriophages, recognize bacteria by leg/tail fibers |
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| classification of viruses is based on |
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| type of nucleic acid, strategy for replication, morphology |
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Definition
| a group of viruses sharing the same genetic information and ecological niche (host) |
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| virus type of nucleic acid |
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Definition
1. single stranded DNA
2. double stranded DNA
3. single stranded RNA (sense or missense)
4. double stranded RNA
5. reverse stranscript RNA |
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| virus strategy for replication |
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| how to infect and replicate host |
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| difficult because need host. bacteriophages are easiest to grow. |
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| immortalized cells. reproduce over and over and don't die out because has tolamerase which repairs telomeres. |
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| cells were taken out of her without her knowledge at Johns Hopkins Hospital in 1940's. Now HeLa cells. Ethical issues. |
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| soooo many medical advances. polio, genome mapping, etc. |
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| two mechanisms for viral multiplication |
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Definition
| lytic cycle and lysogenic cycle |
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| phage causes lysis and death of host cell |
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| prophage DNA incorporated in host DNA. phase conversion. specialized transduction. |
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Definition
1. attachment
2. penetration
3. biosynthesis
4. maturation
5. release |
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| phage attaches to the cell |
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| sheath contracts and injects intertube of sheath into the cell wall. cell membrane and cytoplasm-nucleic acid released into the cell |
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Definition
| genetic material is beginning to be transcribed, translated, and replicated to make more particles |
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Definition
| produced components assemble-DNA and capsids come together |
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| cell is producing lysosyme-bursts open-goes and infects other cells |
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| reasons for lysogenic cycle |
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| genes are selfish maybe?? provides genetic diversity, makes more hosts/not killing host so still surviving. |
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| results of lysogenic cycle |
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Definition
| cells immune to further infection, phage conersion, makes specialized transduction possible |
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| bacteria replication during lysogenic cycle |
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Definition
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| prophage incorporated in chromosome and can change behavior of that bacteria. changes with prophage DNA incorporated in chromosome. |
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| consequences of lysogenic cycle |
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| normally harmless bacteria turns harmful. diphtheria, cholera, dysentery, scarlet fever. |
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Definition
| specific bacterial genes are transferred from one bacteria to another. use to manipulate genome of cells. |
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| specializied transduction seen in |
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Definition
| right after infection ex: influenza |
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| remains dormany days, months, years ex: herpes, cold sores, etc. |
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| persistent viral infections |
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| progresses slowly over a long period of time, can be fatal ex: HIV |
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| acute and persistent viral infections |
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Definition
| can have ex: mono, chicken pox to shingles |
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Definition
| proteinaceous infectious particle. infectious proteins. proteins that are misfolded |
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| prions inherited and transmissible by |
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| ingestion, transplant, and surgical instruments |
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| directly to humans from water |
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| microbial water pollution |
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| some pathogens are transmitted to humans in drinking and recreational water. fecal-oral route in poor countries. |
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| filters out pathogens from water |
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| people who are infected by water pollution |
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| in US 900,000. worldwide 1.6-2 million. mostly in children due to lack of immune system. |
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| fever, neuropsychological. spaced out, feverish |
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| watery diarrhea and vomiting=dehydration, electrolyte imbalance |
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| fever, vomitting, cramps, diarrhea, 4-7 days |
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| bloody, mucousy diarrhea, fever, pain 2-4 weeks |
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| streams, from animal feces, cysts in digestive tracts, environmentally resistant. |
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| turns into methylmercury which goes into plankton and goes through the food chain |
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| fish due to the plankton they eat then we eat the fish |
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| get rid of chemical pollutants |
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| NO! there are no biological mechanisms to do so |
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| found in birds that eat fish. makes birds shells become brittle |
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| nutrients enter into bodies of waters to help plants grow better, but do it excessively. Causes algal blooms. |
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| eutrophication in the ocean. eat shellfish in red tide you will get sick |
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| block out sunlight to plants on bottom of body of water and plants die. water is turbid and produce toxins |
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| feedback system in eutrophication |
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| large amounts of organic matter put in system causing this |
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| get water from where it is available. same watering hole that cows use |
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| water in industrialized countries |
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| have actual water treatment system. water treatment plants, water towers, etc. |
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| just to maintain pressure in the system |
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| municipal water purification treatment |
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| how water is purified in industrialized countries. flocculant tank, particulate, chlorine, etc. |
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| chemicals added (ex: allum) has coagulation effect so more particulate matter falls out |
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| rocks on top of sand to simulate natural cycle. water drawn out of bottom |
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| primary treatment sewage treatment |
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Definition
| removal of solids, disinfection. physical way, sediment falls out about 25-35% of solid matter (sludge) |
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| secondary treatment sewage treatment |
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| removal of much of the BOD, disinfection, water can be used for irrigation. biological, trickling filter (sand) or activated sludge system (organic digested out) |
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| removal of remaining BOD, N, and P, disinfection, water is drinkable |
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| sent to anaerobic sludge digester to pay for part of the power bill at the plant |
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| tertiary sewage treatment |
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| very expensive, not really used. uses filtration through sand and activated charcoal and chemical precipitation. |
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| secondary effluent contains |
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| residual BOD, 50% of the original nitrogen, 70% of the original phosphorus. |
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| phosphorus gets into system |
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| through detergents and can lead to eutrophication |
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| works more like a natural system similar to a marsh. leaches out into the grass and sludge most be removed occasionally. |
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| historically food storage was |
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| drying out, osmotic pressure (salt, sugar, smoke), fermentation (increase acid level of certain foods) |
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| modern world food storage |
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| put hot food into can and put into retort to seal can. don't store in high temps |
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| pressure cooker/autoclave around 121 degrees with 15 psi. to destroy c. botulinum |
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| if can isn't sealed perfectly |
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| when the vacuum effect takes place, it will suck in bacteria before getting sealed up |
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| usually safe because of the acid |
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| presterilized materials assembled into packages and aseptically filled with heat-sterilized liquid foods. |
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| xray, cesium/cobalt source. misconceptions by public, does not radiate food. |
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| dangerous way. takes a long time and exposed to source for a couple hours. |
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| uses high energy beam. deep penetration so can stack and send crates through |
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| use bacteria to produce lactic acid and proteins coagulate causing cheese. does not need to be sterilized. |
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| from stomach of animals to help coagulate cheese |
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| BACTERIA!!! helps to flavor and ripen |
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| other food made by bacteria |
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| butter milk, yogurt, sour cream |
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| use of microorganisms, cells, or cell components to make a product. classical: fermentation. recombinant dna. bloomed over past 20 years. |
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Definition
| amino acids, citric acid, vitamins, antibiotics, steroid |
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Definition
| inflow of fresh culture and outflow of bacteria |
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Definition
| used for large fermentatino DNA |
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| organic mass turned into biofuel |
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Definition
| collect methane from land fill to microturbines to burned and produce energy |
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| bacteria creates. cellulose digested by cellulase. sugars fermented to ethanol or higher alcohols or hydrogen. |
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| algae produces own oil which is turned into biodiesel |
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