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MICR 2420 (17)
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Microbiology Reading1.docx

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Department
Microbiology
Course
MICR 2420
Professor
Emma Allen- Vercoe
Semester
Fall

Description
Microbiology Readings Lecture 1-2 (1.1-1.3) Definitions: Microbe: living organism that requires a microscope to be seen Viruses: a non-cellular particle containing genetic material that takes over a cell in order to create more viruses Prokaryotic: lacking a nucleus (archaea and bacteria) Eukaryotic: membrane bound DNA (in a nucleus) (algae, fungi and protists) Genome: total genetic info contained in a organisms chromosomes Metagenome: the environmental collection of sequences (all the genomes in an environment) Spontaneous Generation: the theory that living creatures could arise spontaneously Fermentation: a process by which microbes gain energy by converting sugars into alcohol Autoclave: steam pressure device used to kill endospores Endospores: a heat resistant form of bacteria (must use pressure) Germ theory of disease: theory that most diseases are caused by microbes Epidemiology: a chain off infection or transmission of a disease Pure culture: a culture grown from a single parental cell Colonies: distinct populations of bacteria, all grown from a single cell Koch’s postulates: four criteria used to determine the causative link between an infectious agent and disease Attenuated: to lose some of the required molecular structure Immunity: the resistance to a specific disease by stimulating the immune system Immunization: the stimulation of an immune response by deliberate inoculation with an attenuated pathogen Antiseptic agent: a chemical that kills microbes Antibiotics: molecule that kills microbes alone and not their host Notes:  Microbes range in size from millimeters to fractions of micrometers o Viruses can be even smaller  Some microbes are only a single cell, but all contain a genome and the capacity to reproduce  Common contradictions in the definition of microbe o Some cells are supersized and are able to be seen by the naked eye o Many microbes form complex multicellular assemblages (mushrooms, biofilms and kelps)which are differentiated into distinct types but complement each other  Yet some multicellular worms that can only be seen by a microscope are not considered microbes o Viruses are considered microbes yet they are not a living organism  Definition is derived from tradition as well as genetic considerations o Microbes can be both prokaryotic and eukaryotic  By comparing genomes we can measure the degree of relatedness between 2 organisms  Virus genomes were the first to be sequenced o Determined by Fred Sanger in 1977 o Had only 5000 base pairs  Microbial disease has had a profound impact on human demographics and cultural practices o Fate of human cities is usually determined by microbes  Florence Nightingale (1820-1910)- discovered and showed that microbial disease was the top cause of death in the Crimean war o Convinced British governments to upgrade standards of living for soldiers  Hooke and Van Leeuwenhoek – first to see and record observations of microbes using simple microscopes  Spallanzani- showed microbes come from pre-existing microbes using chicken broth o Also demonstrated that sterilization using heat will prevent microbial growth  Pasteur- discovered microbial basis of fermentation o Built swan neck flask in order to demonstrate importance of oxygen (providing oxygen does not enable spontaneous generation  Tyndall- showed that repeated cycles of heat are necessary in eliminating spores from certain bacteria  Some microbes are unable to grow in pure culture o Viruses must be in the presence of a host cell Koch’s Postulates 1. The microbe is found in all cases of the diseased but is absent in healthy people 2. The microbe is isolated from the diseased host and grown in pure culture 3. When the microbe is introduced into a new host the disease occurs 4. The same strain of microbe is obtained from the newly diseased host  During a period outside of the body the viruses attenuate and are therefore safe for inoculation  Cowpox amongst milkmaids in England prevented smallpox, patients were inoculated with matter from the cowpox and then were unable to contract smallpox, this was called vaccination  The knowledge of microbes and diseases caused surgical rooms to become antiseptic environments o If antiseptics were ingested it would kill a patient too  Bacteria can become resistant to antibiotics Lecture 3-4 (1.4- 1.5, 21.1) Definitions: Chemotrophs or Lithotrophs: organisms that feed solely on inorganic materials Enrichment culture: the use of specific growth media that support certain classes of microbial metabolism but exclude others Geochemical cycling: the global interconversion of inorganic and organic forms of minerals Endosymbionts: organisms living symbiotically inside larger organisms Biofilms: organized multispecies communities upon a surface Monera: kingdom that is neither plant nor animal Polyphyletic: multiple ancestries of living species Monophyletic: all diverge from a single common ancestor Archaea: seeming to be bacterial but grow in the most extreme of environments Assimilation: the processes by which organisms acquire an element to build into cells (put together- fixation) Primary producers: produce biomass from inorganic carbon Dissimilation: the process of breaking down organic compounds into inorganic minerals (take apart) Biomass: the bodies of living organisms Food web: the way in which various organisms live off each other Trophic levels: levels of consumption Consumers: acquire nutrients from producers and immediately dissimilate it (several levels) Grazers: directly feed on producers (convert 90% of nutrients) Predators: feed on grazers (convert the leftover 10%) Extremophiles: species that can live in extreme environments (by human standards) Acidophile: acidic environments (pH at or below 3) Alkaliphile: basic environments (pH 9-14) Barophile: high pressure Endolith: within rocks or minerals Halophile: high salt Hyperthermophile: extreme high temperature (<80 C) (use sulfur instead of oxygen) Oligotroph: low carbon concentration Psychrophile: low temperature (>15 C) Thermophile: moderately high temperatures (50 C- 80 C Xerophile: extremely low water activity Notes:  Microbes cycle many minerals essential to all life  Earths ecology IS microbial ecology  First things tested for microbes were things humans needed o Then discovered that other things (like soil) cycle minerals but will not if treated with heat or acid (hinting that there were microbes)  Chemotrophs are unable to grow in organic culture (some are actually poisoned by it)  All microbes and forms of life work together to preform geochemical cycling  Microbes nitrogen fix, and plants need fixed nitrogen to function and animals need plants to function  Nitrogen fixing bacteria (rhizobia) live endosymbiotically with plants inside nodules  Endosymbionts usually have a positive contribution to the host animal  Microbes include eukaryotes and prokaryotes  Microbes could not be basically classified as just animals or just plants  Eukaryotes evolved through endosymbiosis (mitochondria)  Archaea are different from prokarya and eukarya  All microbes exist within ecosystems  Each microbe fills a niche in their environment ( one mans waste is another mans food)  Van Niels postulates o Every molecule existing in nature can be used as a source of nutrients for a microbe o Microbes can be found in every environment on earth  What a microbe gives and takes depends on : o Microbial genome (can they produce the enzymes and proteins to do it) o Environmental factors (if an environment needs or has too much of something the the microbes will adapt  Major interactions between organisms in a biosphere are dominated by the production and transformation of biomass  At each trophic level the energy dissipates more and more  Food webs depend on primary producers for absorbing energy from outside sources and assimilating minerals into the biomass  When an organism dies at each trophic level decomposers return minerals back to the producers  Who the producers and consumers are is decided by the environment Lecture 5-6 (3.1, 3.4, 3.7, 19.1) Definitions: Cell membrane: also called inner membrane; contains cytoplasm Cell wall: rigid structure that forms a sort of cage around the bacterium Envelope: cell wall and outer membrane Flagellum: helical protein filament whose rotary motor propels the cell in search of a more favourable environment Nucleoid: genetic material which is not membrane bound Glycan: parallel polymers of disaccharides Cross bridges: connect parallel strands of glycan Gram positive: thick cell wall with many layers of peptidoglycan Gram negative: thin cell wall with 1-3 layers of peptidoglycan Contractile vacuole: pump wa
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