Chapters 10,11,12,13,8
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| Taxonomy | The science of the classification of organisms. It's goal is to show the relationships among organisms. Also provides a means to identifying organisms.
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| Classification | Provides a list of characteristics and a means for comparison to aid in the identification of an organism.
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| Identification | Microorganisms are identified for practical purposes for example to determine an appropriate treatment for an infection.
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| Phylogeny (Systemics) | The study of evolutionary history of organisms.
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| What are the 3 domains living organisms are classified into? | Eukarya (plants, animals. fungi, and protists), Bacteria, and Archea.
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| Eukaryotic species | A group of closely related organisms that breed among themselves.
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| Prokaryotic species | A population of cells with similar characteristics. (Clone: population of cells derived from a single cell) (Strain: genetically different cells with in a clone).
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| Viral species | A population of viruses with similar characteristics that occupies a particular ecological niche.
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| Animalia (Eukarya) | Multicellular; NO cell walls; ingestive chemoheterotrophs.
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| Plantae (Eukarya) | Multicellular; Cellulose cell walls; usually photoautotrophic.
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| Fungi (Eukarya) | Unicellular OR multicellular; Cell WALLS with chitin; develop from spores of hyphal fragments, are absorptive chemoheterotrophs.
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| Protista (Eukarya) | Are mostly unicellular organisms;
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| Bergey's Manual of Determinative Bacteriology | Provides identification schemes for identifying bacteria and archea (morphology, differential staining, biochemical tests).
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| Bergey's Manual of Systemic Bacteriology | Provides phylogenetic information on bacteria and archea.
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| Biochemical tests | With the presence of various enzymes, as determined by this test, it is used to identify bacteria and yeasts.
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| Seroligical testing | Involves the reactions of microorganisms with specific antibodies, are useful in determining the identity of strains and species. (examples in ELISA and Western blotting)
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| Dichotomus Keys | Are used for the identification of organisms.
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| Cladograms | Show phylogenetic relationships among microorganisms.
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| Phage typing | Is the identification of bacterial species and strains by determining their susceptibility to various phages (it's what the bacteria are susceptible to).
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| Prokaryotes | One circular chromosome, no tin a membrane, NO organelles, peptidoglycan cell walls, binary fission. (Classified into two domains Archea and Bacteria).
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| What is the correct order for most species? | Kingdom, Phylum, Class, Order, Family, Genus, Species.
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| Bacteria | Are essential to life on earth, relatively few species of bacteria cause disease in humans, animals, plants, or any other organisms. Without bacteria much of life as we know it would not be possible.
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| Proteobacteria | Includes most of the gram negative, chemoheterotrophic bacteria. Largest taxonomic group of bacteria. Separated into 5 classes by Greek letters: alphaproteobacteria, betaproteobacteria, gammaproteobacteria, deltaproteobacteria, and epsilonproteobacteria.
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| Alphaproteobacteria (Include nitrogen fixing bacteria, chemoautotrophs, & chempheterotrophs) | Includes most of the proteobacteria that are capable of growth at very low levels of nutrients. Some have unusual morphology such as stalks or buds. Also include bacteria capable of inducing nitrogen fixation in symbiosis with plants,&plant/human pathogen
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| Betaproteobacteria (Includes chemoautotrophs, & chemoheterotrophs) | Considerable overlap between the betaproteobacteria & these. Often use nutrient substances that diffuse away from areas of anaerobic decomposition of organic matter, such as hydrogen gas, ammonia,& methane. Pathogenic bacteria are found in this group.
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| Gammaproteobacteria (Examples; Pseudemonadales, Legionellales, Enterobacteriales, and Pasteurellales) | Constitute the largest subgroup of the proteobacteria and include a great variety of physiological types. they are aerobic mostly.
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| Deltaproteobacteria | Are instinctive in that they include some of the bacteria that prey on other bacteria. Examples are Bdellovibro, and Myxococcales. Some important contributors to sulfur cycle ex. Beggiatoa.
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| Epsilonproteobacteria | Are slender gram-negative rods that are helical or curved. Examples; Campylobacter are microaerophilic (each cell has 1 flagellum),& Helicobacter microaerophilic curved rods w/ multiple flagella.
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| obligate intracellular parasites | They can only reproduce within a mammalian cell.
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| Chemoautotroph | An organism that uses on organic chemicals as an energy source and CO2 as a carbon source.
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| Chemoheterotrophs | an organism that uses organic molecules as a source of carbon and energy.
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| Photoautotroph | An organism that uses light as it's energy source and carbon dioxide (CO2) as it's carbon source.
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| Photoheterotroph | An organism that uses light as it's energy source and an organic carbon source.
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| Aerotolerant anaerobe | An organism that does not use molecular O2 but is not effected by it's presence.
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| Obligate anaerobe | An organism that does not use molecular oxygen (O2) and is killed in the presence of O2.
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| Obligate aerobe | An organism that requires molecular oxygen (o2) to live.
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| Facultative anaerobe | An organism that can grow with or without molecular oxygen (O2).
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| Nosocomial infection | Infection that develops during the course of a hospital stay that was not present when patient was admitted.
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| Opportunistic pathogen | A microorganism that does not ordinarily cause a disease but can become pathogenic under certain circumstances.
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| What bacteria produce acetic acid from ethyl alcohol? | Acetobacter & Gluconobacter
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| Oxygenic | Producing oxygen, as a plant and cyanobacterial photosynthesis.
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| Anaoxygenic | Not producing molecular oxygen; typical of photophosphorylation.
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| Cyanobacteria | Oxygen-producing photoautotrophic prokaryotes, fix nitrogen and gliding motility.
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| Hyperthermophiles | An organism whose optimum growth temperature is at least 80 degrees Celsius; also called extreme halophiles. (Example of archea;Pyrodictium & Sulfolobus)
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| Methanogens | Example of archea: Methanobacterium
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| You have isolated a bacterium that grows in a medium containing inorganic nutrients. Ammonia oxidized to nitrate for energy, bacterium is? | A Chemoautotroph
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| Thibaccilus oxidizes inorganic sulfur compounds for energy and fixes CO2. This bacterium is? | A Chemoautotroph
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| All of the following are motile, which does not have an external flagella but has an internal axil filament? | Spirochetes
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| Fungi | Eukaryotic, aerobic or facultatively anaerobic, chemoheterotrophic, most are decomposers (Classified according to rRNA). Can grow in acidic, low-moisture, aerobic environments.
Are able to metabolize complex carbohydrates.
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| Mycology | The study of fungi
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| Fungi molds | The fungal thallus consists of hyphae; a mass of hyphae is mycelium.
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| Fungi yeast | Unicellular fungi, Fission yeast divide symmetrically & Budding yeast divide asymmetrically.
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| Pathogenic dimorphic fungi | Are yeast-like at 37 degrees Celsius and mold-like at 25 degrees Celsius.
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| Teleomorphic fungi | Produce sexual and asexual spores
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| Anamorphic fungi | Produce asexual spores only (include; Penicillium, Candida albbicans (thrush)).
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| Asexual spores | Sporangiospores and conidiospores
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| Sexual spores | Are usually produced in response to special circumstances, often changes in the environment.
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| Systemic mycoses | Deep within body
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| Subcutaneous mycoses | Beneath the skin
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| Cutaneous mycoses | Affects hair, skin and nails
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| Superficial mycoses | Localized, e.g., hair shafts
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| Opportunistic mycoses | Caused by normal microbiota of fungi that are normal not harmful.
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| Ascospore | Formed in a sac (ascus)
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| Basidiospore | Formed externally on a pedestal (basidium)
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| Zygospore | Fusion of haploid cells produces one zygospore.
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| Positive effects of fungi are? | Bread, wine, beer (Saccharomyces), Cellulose used for juice & fabric (Trichoderma), Taxol production (Taxomyces), & Gypsy moth control (Entomorphaga).
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| Negative effects of fungi are? | Food spoilage (Saccharomyces), Cryphonectria parasitica- chesnut blight (Trichoderma), Ceratocystis ulm -dutch elm disease (Tsxomyces).
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| Linchen | A mutualistic combination of an alga (or cyanobacterium) and a fungus. The alga photsynthesizes, provideng carbs; the fungus provides a holdfast. May be classified on basis of morphology as crutose, foliose, or fruticose.
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| Algae | Eukaryotic, unicellular, filamentous, OR multicellular (thallic), most are photoautotrophs. Many reproduce sexually, but can produce asexually by cell division and fragmentation.
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| Brown algae- kelp (Phaeophyta) | Cellulose + alginic acid cell walls, mulicellular, stores carbohydrates, harvested for algin.
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| Red algae (Rhodophyta) | Cellulose cell walls, MOST are multicellular, store glucose polymer, harvested for agar carrageenan & grow deeper in the ocean than other algae.
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| Green algae (Chlorophyta) | Cellulose cell walls, unicellular OR multicellular, stores glucose ploymer, gave rise to plants in evolutionary times.
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| Diatoms (Bacillariophyta) | Pectin and silica cell walls, unicellular, produce domoic acid, some produce a neurotoxin.
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| Dinoflagellates | Produce neurotoxins that cause paralytic shellfish poising and ciguatera. Cellulose in plasma membrane, unicellular, & store starch.
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| "Water molds" (Oomycota) | Cellulose cell walls, multicellular, chemoheterotrophic, decomposers and plant parasites (responsible for Irish potato blight).
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| Protozoa | Eukaryotic, unicellular, chemoheterotrophs, can be either motile or non-motile, asexual or sexual reproduction, some intracellular parasites, & have complex life cycles. Found in soil & water & as normal microbiota in animals.
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| Amoebas (Rhizopoda) | Move by pseudopods, include; Entamoeba & Acanthamoeba.
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| Cilliates (Ciliophora) | Move by cilia, are complex cells, Balantidium coli is the only human parasitic ciliate.
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| Euglena (Euglozoa) | Move by flagella and lack sexual rproduction include photoautotrophs such as Euglenoids & chemoheterotrophs suach as Trypanosoma (transmitted by vector) and Leishmania (form in a vertebrate host).
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| Cellular slime molds | Resemble amoebas and ingest bacteria by phagocytosis.
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| Plasmodial slime molds | Consists of a multinucleated mass of protoplasm that engulfs organic debris and bacteria as it moves.
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| Helminths (parasitic "worms") | Eukaryotic, multicellular animals, chemoheterotrophic Kingdom: animalia, Phylum: Platyhelminthes (flatworms), Class: Trematodes (flukes), Class: Cestodes (tapeworms), Phylum: Nematodes (roundworms).
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| What is the anatomy and life cycle of a parasitic helminths? | They are modified for parasitism, the adult stage of a parasitic helminth is found in the definitive host, each larval stage of a parasitic helminth requires an intermediate host, helminths can be monoecious or dioecious.
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| Arthropods as Vectors | Kingdom: Animalia, Phylum: Arthropoda (exoskeleton, jointed legs), Class: Insecta (6 legs) include lice, fleas and mosquitoes, Class: Arachnida (8 legs) include mites, and ticks and may transmit diseases (vectors).
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| Viruses (obligatory intracellular parasites) | Contain DNA or RNA, a protein coat, some are enclosed by an envelope composed of lipids, protiens and carbs, most infect only specific types of cells in 1 host, host range is determined by specific host attachment sites and cellular factors.
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| What are viruses size and structure? | Viral size is ascertained by electron microscopy, range form 20 to 100 nm in length. A viron is a complete fully developed viral particle composed of nucleic acid surrounded by a coat.
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| Capsid (head) | The protein coat surrounding the nucleic acid of the virus. composed of subunits, capsomers, which can be a single type of protein or several.
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| Viral taxonomy | Family names end in - Virdae. Genus names end in - virus.
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| Viral species | A group of viruses sharing the same genetic information and ecological niche (host). Common names are used for species. Subspecies are designated by numbers.
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| Growing viruses | Must be grown in living cells. Animal viruses may be grown in living animals or embryonated eggs. Animal and plant viruses may be grown in a cell culture.
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| Growing bacteriophages in Lab | The plaque method mixes bacteriophages with host bacteria and nutrient agar. After several viral multiplication cycles, the bacteria in the area surrounding the original virus are destroyed; the area of lysis is called plaque.
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| Virus identification | Serological tests are used most often to identify viruses, they detect antibodies against viruses in patients. Viruses may also be identified by nucleic acids such as RFLPs and PCR.
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| Multiplication of Bacteriophages (Lytic Cycle) | Attachment-Phage attaches by tail fibers to host cell, Penetration-Phage lysozyme opens cell wall, tail sheath contracts to force tail core & DNA into cell, Biosynthesis-Production of phage DNA & proteins, Maturation- Assembly of phage particles.
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| Multiplication of Bactriophage (Release stage) | Release- Phage lysozyme breaks cell wall.
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| Lytic cycle | Phage causes lysis and death of host cell.
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| Lysogenic cycle | Prophage DNA incorporated in host DNA.
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| Multiplication of Animal viruses | Attachment-viruses attaches to cell membrane, Penetration-By endocytosis of fusion, Uncoating-By viral of host enzymes, Biosynthesis-Production of nucleic acid & proteins, Maturation-Nucleic acid & capsid proteins assemble, Release- By budding or rupture.
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| Cancer | Activated oncogenes transform normal cells into cancerous cells. Mutagenic chemicals, radiation & some viruses can activate oncogenes & lead to cancer, transformed cells have increased growth, loss of contact inhibition.
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| Oncogenic viruses | The genetic material of oncgenic viruses becomes integrated into host cell's DNA.
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| Latent Viral infections | Virus remains in asymptomatic host cell for long periods. Examples; Cold sores & shingles.
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| Persistent Viral infections | Disease process occurs over long period, generally fatal. Examples: Subacute sclerosing panencephalitis (measles virus).
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| Prions (discovered in the 1980's) | Infectious proteins. Inherited and transmissible by ingestion, transplant, & surgical instruments. Diseases: Spongiform encephalopathies, CJD,& mad cow disease all involve degeneration of brain tissue. Are a result of an altered protein; a mutated gene.
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| Plant viruses | Must enter plant host through wounds or with invasive parasites such as insects (via insects).
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| Viroids | Are infectious pieces of RNA that cause some plant diseases, such as potato spindle disease.
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| Genetic changes in a bacterium (by horizontal gen flow) can be brought about by? | Transduction, Mutation, Conjugation, and Transformation.
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| In double-stranded DNA if the base strand is Thymine, what is the base of matching strand? | Adenine (DNA: T-A, C-G) (RNA: A-U, C-G)
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| The damage to DNA caused by ultraviolet radiation is? | Cut out and replaced by special enzymes (Light repair).
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| An enzyme that copies DNA to make a molecule or RNA is? | RNA Polymerase
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| In Transcription | DNA is copied to RNA
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| Transcription | Begins when RNA polymerase binds to the DNA at a site called the promoter (starting site on a DNA strand for transcription of RNA by RNA polymerase).
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| Messenger RNA (mRNA) | Carries coded information for making specific proteins from DNA to ribosomes, where proteins are synthesized.
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| Ribosomal RNA (rRNA) | Forms an integral part of ribosomes, the cellular machinery for protein synthesis.
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| Transfer RNA (tRNA) | Also involved in protein synthesis, without tRNA proteins cannot be made.
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| Translation | Protein synthesis; involves decoding the "language" of nucleic acids and converting that information into the "language" of proteins.
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