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146 Cards in this Set
- Front
- Back
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Microbe
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any organism that cannot be visualized by the naked eye. All members of three domains (bacteria, archaea, eukaryotes) - Viruses. Prokaryotic microbes included virtually all bacteria and archaea. Eurkaryotic microbes include yeast, many fungi, protozoa, and some higher.
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Contradictions in microbe definition, 3
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1. supersize microbial cells (ex. thiomargarita namibiensis), 2. microbial communities (ex. biofilms), 3. viruses
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Robert Hooke
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drew first microscopic being
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Anton Van Leeuwenhoek
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"first microbiologist". Saw first bacteria using a microscope of his own making. Discovered existence of microbes, calling them "wee animals". Observed heat killed microbes upon drinking coffee and swabbing mouth
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Ferdinand Cohn
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described life cycle of endospore forming bacteria Bacillus
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The Golden Age of Microbiology
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1850-1920. 1) Spontaneous generation debunked, 2) role of microbes in disease recognized, 3) development of septic technique, 4) role of microbes in transformation of organic matter (ex. mold)
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Lazzaro Spallanzani
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helped debunk spontaneous generation with sealed flask experiments
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Louis Pasteur
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helped debunk spontaneous generation using swan neck flask experiments. After boiling the contents remain free of microbial growth despite access to air (since S curve in flask excludes dust and microbes from growth medium). Also contributed to germ theory of disease, that infectious diseases result from germs (led to rabies vaccine, pasteurization, yeast for production)
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Robert Koch
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father of microbiology. certain microbes cause certain diseases. Created Kochs postulates, criteria for establishing a causative link between an infectious agent and a disease. Used this technique to identify M. Tuberculosis as the cause of Tuberculosis (difficult staining because of high lipids, solid media had bacteria grow slow and fastidious, sacrifice of guinea pigs). Also responsible for pure culture techniques still used today.
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Kochs Postulates
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Demonstrated with Anthrax in mice. 1) Microbe always present in diseased host and absent in healthy, 2) When microbe grown in pure culture, no other microbes present, 3) when introduce microbe into a healthy host the individual becomes sick/infected, 4) microbe isolated from sick individual matches the original microbe.
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Lady Mary Montague
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In 18th century smallpox infected large percentage of Europe. She introduced smallpox inoculation in 1717.
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Edward Jenner
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Deliberately infected patients with matter from cowpox lesions as form of inoculation - first vaccine (vacca latin for cow)
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Ignaz Semmelweis
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1847 ordered doctors to wash their hands with chlorine, an antiseptic agent
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Joseph Lister
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Developed carbolic acid to treat wounds and clean surgical instruments in 1865. In 20th century aseptic surgery was developed to create microbe free environments.
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Alexander Fleming
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1929 discovered Penicillium mold generated a substance that kills bacteria (no bacteria surrounding the mold on slides)
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Howard Florey and Ernst Chain
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1941 purified penicillin. First commercial antibiotic to save human lives.
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Martinus Beijerinck
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1898. Found agent of Tobacco Mosaic Disease is not a bacterium because passed through a filter that retains bacteria, but was a Virus
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Wendell Stanley
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1935. Purified and crystallized agent of Tocabbo Mosaic Disease found by Beijerinck, Tocabbo Mosaic Virus (TMV)
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Sergel Winogradsky
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Among first to study bacteria in natural habitats. Discovered lithotrophs. Developed enrichment cultures and built Winogradsky column, a wetland model ecosystem. Showed importance of bacteria in geochemical cycling (soil bacteria fix ammonia, bacteria symbionts of legumes, and fix nitrogen)
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Ernst Ruska
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developed electron microscope, which revealed internal structure of cells
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Theodor Svedberg
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developed centrifuge, which enabled separation of subcellular parts
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Frederick Griffith
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Discovered transformation in bacteria. Helped in development of microbial genetics
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Oswald Avery et. al
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Showed that the substance undergoing transformation in bacteria (that Griffith discovered) is DNA
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Rosalind Franklin
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1953 used x-ray crystallography to determine DNA is double helix
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James Watson and Francis Crick
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discovered complementary bases and antiparallel nature of DNA
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How DNA revolution began with bacteria?
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Many advances seen for the first time in bacteria and bacteriophages. Restriction endonucleases (signifies where to cut DNA at restriction site) led to recombinant DNA, DNA polymerase used for amplifying DNA via polymerase chain reaction, and gene regulation provided models
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Ernst Haeckel
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Microbes are neither plant nor animal, but a third type of life called Monera.
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Herbert Copeland
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Divided Monera (Haeckel) into two groups, eukaryotic protists (protozoa and algae) and prokaryotes
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Robert Whittaker
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added fungi as a fifth kingdom of eukaryotic microbes
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Lynn Margulis
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modified 5 kingdom system. Proposed eukaryotic organelles evolved by endosymbiosis from prokaryotic cells engulfed by proto-eukkaryotes (organelles were free living bacteria taken inside another cell).
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Carl Woese
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Developed a molecular clock to build a new tree of life. Old tree was hierarchial and implied certain organisms had evolved more than others.
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Taxonomy
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classification of organisms by distinguishable characteristics. Develop a method for predicting what group a given organisms belongs to. Traditionally based on phenotypic characteristics (growth requirements, aerobic/anaerobic, stain, lytic properties - breakdown blood cells). But majority of prokaryotes can be described as small and beige
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Phylogeny
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Full description of branching divergence of a species. Evolutionary development and history of a species or higher taxonomic group of organisms. Classification schemes based on evolutionary relationships.
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clade
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branching groups of related organisms. Each clade is a monophyletic group (a group of species that share a common ancestor). Each monophyletic group then branches into small groups, then ultimately species.
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3 mechanisms of evolution
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1) random mutations as chromosome replicates, 2) natural selection favors organisms that produce more offspring, 3) reductive (degenerative) evolution- loss or mutation of DNA encoding unselected traits
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Molecular clock/ Evolutionary Clock and requirements for reliability
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temporal information contained in a macromolecular sequence. Based on the acquisition of new random mutations in each round of DNA replication. Used to gain information on when two species diverged. 1) Must be universally distributed, 2) functionally homologous (orthologous), 3) easily aligned base pair for base pair, 4) must change at a rate commensurate with evolutionary distance
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Small subunit rRNA (SSUrRNA)
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Genes that show most consistent measures of evolutionary time encode components of the transcription and translation apparatus. Gene encoding SSUrRNA is 16S in bacteria or 18S in eukaryotes. Study of 16S rRNA in hot spring led Carl Woese to discover Archaea.
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16S rRNA
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Idea clock for phylogeny of life on Earth. Part of the ribosome, thus high conserved throughout all forms of life. Encodes both variable loop regions and invariant stem regions, making alignment straight forward.
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The Woesian Revolution
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using 16S rRNA Carl Woese and colleagues proposed 3 domains instead of 5 kingdoms: eukaryotes, bacteria, archaea (had previously been classified with bacteria, but found archaea were actually distant form of life after 16S comparison)
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What is a species for bacteria, eukaryotes, and prokaryotes? What is most widely accepted criteria for microbiologists?
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Bacteria- anything >90% similar, eukaryotes- group of individuals capable of interbreeding, prokaryotes- phylogeny and ecology (shared traits and niche) important because reproduce asexually. Criteria (all > or equal): 1) DNA hybridization >70%, 2) SSUrRNA >97%, avg nucleotide identity (ANI) of orthologs >95%
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Phylogenetic Trees
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Can be generated using frequency of differences between homologous sequences. Estimates when species diverged and length of divergence. Assumes mutation rate is same. PCR or hybridization techniques used for non-culturable organisms.
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Signature sequence
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Short DNA sequences unique to certain groups of organisms
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Phylogenetic probes
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oligonucleotides (short DNA or RNA strands with broad use) made from signature sequences used to identify organisms or groups of organisms in a mixed sample.
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Maximum parsimony
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"best fit" phylogenetic tree is the one requiring the fewest mutations to fit data
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Maximum likelihood
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probability that such a tree would have produced observed DNA sequences
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Rooted vs. Unrooted phylogenetic trees
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Rooted indicate the position of the ancestor, unrooted do not
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Phylum/ bacterial phyla
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A group of bacteria sharing a common ancestor that diverged early from other bacteria. Well studied phyla include deep-branching thermophiles, cyanobacteria, gram postiive and negative, bacterioidetes, and chlorobi, spirochetes, chlamydiae and pianctomycetes
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Taxonomy
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description of distinct life forms and their organization into different categories with shared traits
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Classification
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Recognition of different classes of life. Generates a hierarchy of taxa (group of one or more populations that make a unit), with long studied organisms having many ranks, and recent isolates having few
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Nomenclature
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Naming of different classes
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Identification
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Recognition of the class of a given microbe isolated in pure culture
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Dichotomous Key
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Series of yes/no decisions that narrow down possible categories of species. Most traits phenotypic. DIsadvantage is that there are many steps so it's time consuming.
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Probabilistic Indiator
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Means of identification. Battery of biochemical test performed in enterotube simultaneously on an isolated strain, results are multiplied to generate a probability score, and score is compared to computed score for each species in the database and matched to most probable species.
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Epulopiscium
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Bacterium that illustrates why phenotype is a poor means of determining which group an organism belongs to. Up to one million x larger than E.Coli. Thought to be protists due to size. Esther Angert collected organism from fish gut, sequenced SSUrRNA and revealed epulopiscium are bacteria and close relatives of Clostridia (anaerobic, spore forming gram + bacteria)
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Nucleoid
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contain and protect cells genome. Eukaryotes have membrane-bound nucleus, prokaryotes have nucleoid region that extends through cytoplasm. Prokaryotic nucleoid forms about 50 loops or domains, within which the DNA is supercoiled by DNA-binding proteins.
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Bacterial chromosome
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Circular and usually haploid. Advantages are cell division is more simple, no shortening telomeres/cap on division, and facilitate horizontal gene transfer.
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Bacterial cytoskeleton and eukaryotic homologs
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Tubulin (cell division)- FtsZ, Actin (shape)- MreB, Intermediate Filament (shape)- Crescentin, WACA (Walker A cytoskeletal ATPase)- MinD. Also bactofilins (cytoskeletal proteins), CTP synthase (UTP to CTP), ESCRT (endosomal sorting complex for transport into vesicles) proteins.
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Nucleoid occlusion negative regulators
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Negative regulators prevent transcription or translation to inhibit FtsZ and bind to nucleoid to prevent division of nucleoid. Dictate where and when FtsZ will assemble since center only free of nucleoid after DNA replication and segregation. SlmA and MinD both inhibit FtsZ. Both proteins more present next to origin of replication, and least present in mid section where FtsZ forms.
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WACA
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Walker A Cytoskeletal ATPases. Variant Walker A motif within nucleoid binding P-loop/ Crystal structures of monomers and dimers, EM of filament bundles. Involved in cell division, DNA segregation, replication control, positioning of chemotaxis proteins
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Cell Membrane
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8nm thick, lipid bilayer, envelopes cell, highly selective. Archaea have partially monolayer and ether linkages, bacteria bilayer and ester linkages. Establishes and maintains electrochemical gradient of ions (H+ and Na+), protein secretion, motility and chemotaxis, selectively import/export, point of cell wall synthesis, location of ETC for energy generation.
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Cell Membrane constituents
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Approximately equal parts of phospholipids and proteins. A phospholipid is a glycerol with ester links to two fatty acids and a phosphoryl head group. Vary with phosphoryl head group and fatty acid side chains.
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Hopanoids/Hopanes
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Planar molecules that fill gaps between hydrocarbon chains in cell membrane. In eukaryotes, reinforcing agent is sterols such as cholesterol.
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Cell Wall
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confers shape and rigidity to the cell and helps withstand turgor pressure. Bacterial cell wall called the sacculus, a single interlinked molecule, and peptidoglycan wall is the major structural feature. Gram + cell wall has several layers of peptidoglycan, and teichoic acids running perpendicular. Lipotechoic acids anchored to plasma membrane. In Gram - the cell wall is composed of a single layer of peptidoglycan, surrounded by an outer membrane, and lipopolysaccharides.
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Peptidoglycan
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long polymers of disaccharides N-acetylglucosamine (NAG) and N-acetylmuramic acid (NAM) bound to a peptide of 4-6 amino acids (gram -) or 5 glycine molecules (gram + Strapohylococcus)
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Gram - Peptidoglycan Synthesis
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Alternating molecules of N-acetylglucosamine and N-acetylmuramic acid. NAM has ether connected to peptide side chain of L-alanine, D-glutamate, Diaminopimelic acid, and D-alanine. (L-ala, D-glu, DAP, D-ala). Chains can link by interpeptide bond between DAP and D-ala on nearby strand, releasing a D-ala. Antibiotics such as penicillin block enzymes from releasing this D-alanine, thereby blocking cell wall synthesis in the bacteria.
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Gram + Peptidoglycan synthesis
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Some variation, best studied example staphylococcus aureus. In place of DAP is L-lysine, and instead of interpeptide bond is an interpeptide bridge. Connects Lysine to D-alanine by 5 glycine moelcules.
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Bactoprenol
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hydrophobic cloack that transports the peptidoglycan subunits through the cell membrane and to the site of peptidoglycan synthesis (between cytoplasmic membrane and outer membrane)
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Mycobacterial cell envelopes
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Very complex. Include unusual membrane lipids (mycolic acids) and unusual sugars (arabinogalactans)
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Periplasm
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Gel-like material between the cytoplasmic membrane and the outer membrane in gram negative bacteria. Contains hydrolytic enzymes, binding proteins, chemoreceptors, etc.
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FtsZ
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Bacterial homolog to Tubulin. Involved in cell division. Forms an entire complex to bind to and bring down all layers - peptidoglcan, plasma membrane, outer membrane - during septum formation.
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MreB
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Actin homolog, involved in maintaining shape. Old model depicted MreB in spiral shape around cell, however current model shows MreB in patches linked to peptidoglycan elongation synthesis machinery to maintain rod shape.
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Crescentin
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Intermediate filament homolog. Involved in maintaining cell shape, when removed cells lose their shape.
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Lysozome
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Enzyme that can cleave the glycan backbone of the peptidoglycan molecule and is present in animal serums and tissues. Lysozymes lyse bacterial cells as a defense against bacterial pathogens. Cleaves between NAM and NAG bond. Gram + more vulnerable because no outer membrane.
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Lipopolysaccharide structure
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O-polysaccharide head with repeat of 40 units attached to core polysaccharide. Core attached to glycosamine phosphate dimer, which has fatty acid tails.
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Flagella
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Filamentous protein structures attached to the cell surface that provide swimming movement for motile prokaryotes. The flagellar filament is rotated by a motor apparatus in the plasma membrane which is powered by PMF.
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Flagellar structure
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Gram - have four rings - C ring, S-M ring (plasma membrane), P-ring (peptidoglycan) and L-ring (lipopolysaccarides), gram + only have two. The rings make up the basal body in the cell envelope, the hook comes out of the membrane, and the flagellar filament is inside. The P and L rings function as bushings to support the rod. The Mot complex is the rotary engine anchored in the plasma membrane. The M and S rings comprise the motor apparatus, as the M ring turns the rotary is transferred to the filament, and this is powered by the influx of H+. Fli and Mot proteins make up the Mot complex.
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Rotary Flagella
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enable motility. Peritrichous = flagella randomly around cell, lophotrichous= flagella at ends, monotrichous= single flagellum.
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Pili or Fimbriae
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Straight filaments of protein monomers called pilin. Sex pili are used in conjugation. Stalks are membrane embedded extensions of the cytoplasm. During conjuation the pilus will retract and pull the two cells together, allowing for exchange of DNA via plasmid or transposon. Twitching motion is when extension and retraction of pili generate movement. Important in formation of certain types of biofilms.
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Holdfasts
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Adhesion factors excreted by the tips of pili.
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Inclusions
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Structures within the cell that are metabolic reserves, organelles or positioners. Glycogen and polyphosphate are for energy storage. Elemental sulfure stored by photo or lithotrophs for energy or electron source. pHB (polyhydroxybutyrate) are lipid like polymers used for energy. Gas vesicles provide buoyancy.
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Thylakoids
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Specialized for phototrophs. Folded intracellular membranes where light reaction for photosynthesis takes place.
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Carboxysomes
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Polyhedral bodies packed with enzyme Rubisco for CO2 fixation.
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Magnetosomes
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Membrane-embedded crystals of magnetite Fe2O4 aligned by actin-like MamK. Allow orientation along geomagnetic field lines possibly as a means of reaching favorable microaerophilic habitats.
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Bacterial Endospores
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Clostridium and Bacillus species produce dormant spores that are heat-resistant, initiated by starvation of nutrients. Asymmetrical cell division creating a forespore and ultimately an endospore.
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Chromosome partitioning and asymmetric division enzymes for endospore formation
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RacA- DNA binding, collapses chromosomes, helps axial filament , DivIVA- RacA attaches so extended collapsed chromosome, Translocase- helps chromosome be moved to spore, SporeIIIE- DNA translocase, draws separated chromosome to spore , FtsZ- tubulin homolog, forms septum
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Transcription factors
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proteins that sit on certain regions of DNA to turn gene on/off. Sigma factors found in bacteria and associated with RNA polymerase. During sporulation a number of these are present to regulate transcription (H, F, K, G). Limited to certain regions because inactive.
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Regulated Intra-membrane Proteolysis (RIP)
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Ex. Sigma G in forespore relays signal that releases inhibitors on protease (on the septal membrane) to cleave the N terminal 20 AA tail on Pro-SigmaK to form active Sigma-K.
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Spore Crust
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Fourth layer of endospore made up of glycoprotein
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Heterocysts
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Anabaena differentiates into heterocysts which allow it to fix nitrogen anaerobically while maintaining oxygenic photosynthesis. Every 10th cell made into a heterocyst. Nitrogenase does not function in presence of oxygen so must block from O2.
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Fruiting bodies
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Myxococcus xanthus uses fliding motility. Starvation triggers aggregation of thousands of cells which form fruiting body. Filled with spores that can release and sporulate
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Mycelia and Sporangia
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Formed by Streptomyces. As nutrients decline, aerial hyphae release spores which are resistant to drying. Hyphae formed during favorable conditions.
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Biofilms
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Formed by many bacteria by one or more species on organic or inorganic surfaces. 1-attachment of monolayer (pili), 2-microcolonies (divide and more join) 3- exopolysaccaride (EPS), 4- mature biofilm, 5- dissolution and dispersal.
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Bacterial Growth Curve
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Based on growth of populations and how changing conditions affect their physiology. Most easily demonstrated in batch culture (liquid medium in closed system). 4 phases- lag, exponential, stationary, death
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Lag Phase
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Synthesis of RNA, enzymes, not yet ready to divide. If fresh culture innoculated with cells from older or stationary phase, need time to resynthesize. If cells from exponential phase there is generally no lag.
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Exponential phase
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Population doubles in mass per time unit until growth limited. Measured by optical density and plotted on a log scale. Exponential curve is a straight line on a log scale (OD Y axis, growth time X axis, growth rate slope)
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Stationary Phase
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period when growth slows down. Occurs when cells either run out of essential nutrients, waste products build up and inhibit growth, or both. Takes more energy to make components in a cell that's larger.
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Death Phase
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Stevel Finkel tended same culture of E.Coli for over 12 years and found OD decreased, but cells still viable. Eating each other and growing mutations to survive conditions.
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Continuous Culture
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all cells in a population achieve a steady state, which allows detailed study of bacterial physiology. Requires chemostat. Useful for studies in certain growth phase
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Chemostat
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Ensures logarithmic growth by constantly adding and removing equal amounts of culture media (like human GI tract)
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Extremophiles
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Any ecological niche outside normal environmental limits: sea level, 20-40 degrees Celsius, neutral pH, 0.9% salt, ample nutrients
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Temperature requirements for growth
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Most grow at 20-25 degrees Celsius. Can affect rate of reaction by affecting enzymatic activity and changing membrane permeability. At minimum growth temperature there is a decrease in membrane fluidity and enzymatic activity. At maximum growth temp enzymes denature.
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Psychrophiles
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prefer cold temps -15 to 10 degrees Celsius. Enzymes lower freezing point, protein and membrane adaptations. Ex. Arthrobacter and Psychrobacter
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Mesophiles
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Moderate temperature 20-45 degrees Celsius, optimum 37. Most bacterial species
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Thermophiles
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heat loving 45-112 degrees Celsius. Proteins stable at high temps because - 1. do not have as many glysines so flexible and form shapes not easily disrupted, 2. amino acid terminal ends bonded with other parts so inflexible shapes, 3. lipids and fatty acids packed so not as fluid, and Taq polymerase thermostable DNA polymerase. Ex. thermus aquaticus
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Water activity/ Osmolarity
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Water Activity (aw) is measure of how much water is available for use. Osmolarity is the inverse and is a measure of the number of solute molecules in a solution.
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Plasmolysis
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Shrinkage of a cell's cytoplasm caused by hypertonic (excess of salt or sugar) environment. Most bacteria vulnerable in hypertonic environments, and cell walls prevent explosion in hypotonic
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Aquaporins
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Membrane-channel proteins that allow water to traverse membrane faster than diffusion and protect from osmotic stress. In hypertonic media bacteria import compatible solutes (K+, glutamic acid) and in hypotonic leak solutes out of cell . Osmotic pressure in cell does not have to match environment.
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Osmotic Pressure niches
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Nonhalophiles, halotolerant, halophile, and extreme halophile
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Pressure niches
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Barosensitive are low, barophiles/piezophiles live at high pressures (up to 1,000 atm/ 101mPa, often at ocean floor and also psychrophiles), and barotolernt 1-50 mPA.
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pH niches
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most prefer 6.5-7.5. Acidic food protected from most microbes. Molds and yeast wider pH range. Weak acids can pass through membranes, disrupt pH and kill cells, which is used to preserve foods. Neutrophiles 5-8 (most pathogens), acidophiles 0-5 (often chemoautotrohps who utilize sulfate as energy), alkaliphiles 9-11 (soda lakes).
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pH homeostasis
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When cells placed in pH below optimum microbes can prevent influx of protons by exchanging extracellular K+ for intracellular H+. When under alkaline conditions cells use Na+/H+ antiporter to expel Na+ and bring in H+.
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Oxygen niches
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Obligate aerobes- only grow in O2, microaerophiles- grow at lower O2 concentrations, strict anaerobe- die at O2, facultative anaerobe- live with or without O2, aerotolerant anaerobe- grow in O2 while maintaining fermentation based metabolism
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Reactive Oxygen Species (ROS)
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types of oxygen radicals that disrupt membranes, destroy DNA, proteins, etc. H atoms added to O2 to neutralize deleterious effects. Obligate anaerobes don't have enzymes to break down ROS.
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Culturing anaerobes in the lab
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1- special reducing agents (thioglycolate) or enzyme systems (oxyrase) added to ordinary liquid media, 2- anaerobe jar, 3- anaerobic chamber with glove parts, O2 removed by vacuum and replaced with N2 and CO2.
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Macronutrients
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Major elements in macromolecules. Include C, O, H, N, P, S. Ions necessary for protein function Mg2+, Ca2+ Fe2+ K+
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Micronutrients
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trace elements for enzyme function (Co, Cu, Mn, Zn) based on niche cell may have additional growth factors
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Carbon
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backbone for organic molecules and energy source (1/2 of dry weight of cell). Chemoheterotroph acquire C from organic compounds such as proteins, carbs, and lipids, Chemoautotroph capable of C fixation.
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Nitrogen
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Required to synthesize amino acids and DNA. Most bacteria decompose protein for N, some use ammonia or nitrate. A few bacteria, like photosynthetic cyanobacteria can convert atmospheric nitrogen to ammonia.
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Sulfur
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used in production of amino acids, thiamine, and biotin. Most bacteria decompose proteins for it, some us H2S or sulfate.
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Phosphorous
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DNA, RNA, ATP, phospholipids. Phosphate is a source
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Trace elements
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Inorganic elements required in small amounts by certain bacteria, usually as enzyme cofactors. Iron, copper, zinc
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Organic Growth Factors
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organic compounds obtained from the environment that cannot be synthesized in the organism. Vitamins, amino acids, purines, pyrimidines function as coenzymes and building blocks for other macromolecules
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Two main ways of isolating pure colonies
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1- dilution streaking- dragging loop across agar plate. 2- spread plate- tenfold serial dilutions on liquid culture. Small amount of each dilution plated. Bacteria grow in liquid or broth and solid (usually agar)
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Types of media
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Complex- nutrient-rich but poorly defined, synthetic- precisely defined, enriched- complex media with specific components added, selective- favor growth of one organism over the other, differential- exploit difference between two species that grow equally well, can be differential as well
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Enrichment Culture
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encourages growth of desired microbe. Example, soil sample with a few phenol degrading bacteria and many others. 1- inoculate phenol-containing medium with soil, incubate, 2- transfer 1 ml to flask of phenol medium, incubate, 3- do same to another 1 ml flask, incubate, 4- only phenol metabolizing bacteria will be growing when plated on petri dish
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Counting bacteria
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Counted directly by placing dilutions on special microscope slide - Petroff Hausser counting chamber. Microbes trapped in filter placed on solid medium or stained. Caveat is counting both viable and unviable.
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Fluorescence-activated cell sorter (FACS)
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fluorescent cells passed through orifice then a laser. Detectors measure lighter scatter in forward (size) and side (shape) directions
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Turbidity
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measure of optical density, or light absorption by microbes in a media.
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DNA microassays
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assess which RNA's made in given time or under given condition
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Two-dimensional protein gels
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separate proteins based on differences in proteins isoeletric point (1st dimension) and molecular weight (2nd)
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Deep Freezing
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pure culture placed in a liquid and quick frozen to temps between -50 and -95 C. Stored for years until thawed
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Lyophilization (freeze-drying)
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suspension of microbes quickly frozen then water removed via vacuum (sublimation). Stored for years until reintroduced with water.
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Antimicrobial control
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Sterilization- killing all living organisms, disinfection- killing all pathogens from inanimate objects, antisepsis- killing/removing all pathogens from living tissues, sanitation- reducing microbial population to safe levels
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Physical agents in antimicrobial control
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Temperature- most heat more effective, steam autoclave 121 C. Pasteurization , Filtration- micropore filters can remove microbial cells, but not viruses. Ex. HEPA filters. Irradiation- UV light, gamma light, electron beams, x-rays
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Chemical agents in microbial control
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ethanol, iodine (Wescodyne and Betadine), chlorine. Damage proteins, lipids, DNA, and used to reduce or eliminate microbial content
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Antibiotics
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chemical compounds synthesized by one microbe that kill or inhibit growth of another. Penicilin mimics part of bacterial cell wall, therefore prevents ,cell wall formation and is bactericidal
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Biocontrol
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Use of one microbe to control another. Probiotics- contain microbes that aim to restore balance to intestinal flora when ingested. Phage Therapy- aims to treat infectious diseases with a virus targeted to the pathogen, possible alternative to antibiotic resistance problem
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Cofactor
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non-protein chemical compound bound to protein, commonly enzymes, and required for biological activity. Prosthetic groups are tightly bound cofactors, co-enzymes are loosely bound cofactors
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Chemical energy/ Free energy
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Energy released by oxidation of organic to inorganic/ Energy available to do work
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How do organisms with an ETS generate PMF for flagella?
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With F1Fo ATPase transmembrane, organism can create ATP via substrate level phosphorylation, which the ATPase pumps out of the cell using energy from hydrolyzing ATP and create a PMF
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Oxidative phosphorylation
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production of ATP by coupling proton motive force across membrane. Opposed to substrate level phosphorylation
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Thermatoga maritima
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live in geothermal vents and hot springs (thermophilic). Surrounded by membranous "toga" equivalent to gram - outer membrane. Scavenges compounds for biosynthesis from environment. Can grow by anaerobic fermentation to produce lactate, acetate, CO2, and H2, or generate energy via anaerobic respiration using sulfur as an electron acceptor and generating H2.
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Geobacter
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Able to decontaminate radioactive metals and convert animal waste into electricity. Specialized pili that can conduct electrons from plasma membrane to outside of cell and transfer these electrons to metals or electrodes. Able to oxidize organic compounds, such as acetate and fumarate as C sources, and iron III oxide and III citrate as insoluble and soluble terminal electron acceptors.
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Thiomargarita namibiensis
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Largest bacterium. Preferred electron donor is sulfide which it oxidizes to elemental sulfur. Electron acceptor is nitrate which it carries in vacuole and is reduce to nitrite. Circulate between S rich and NO3 rich sediment. Chemolitotroph.
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Methanogens
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Convert various substrates to methane to produce energy. Strict anaerobes, obtain energy by converting H2 or organic compounds such as acetate and methanol and CO2 to methane. No cytochromes or quinones to carry electrons
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Chemoorganoheterotroph
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Contain cytochromes, get energy from the breakdown of methanol or acetate
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