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A comprehensive overview of various staining techniques used in microbiology, including heat fixation, chemical fixation, basic dyes, acidic dyes, simple stains, and differential staining methods such as gram staining, acid-fast staining, and endospore staining. It also delves into the structure and function of key microbial components, including the cell membrane, cell wall, peptidoglycan, flagella, and capsules. Topics related to microbial growth phases, primary and secondary metabolites, and adaptations of microbes to different environmental conditions, such as temperature and pressure. Additionally, it discusses the classification and replication of viruses, including bacteriophages, and the entry, replication, and release of animal viruses. The document also explores the human immune system's innate and adaptive responses, including the role of mucus membrane enzymes, bacteriocins, complement, and cytokines in the immune response and inflammation.
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Microbial size definition - ANSWER-organisms and acellular agents too small to be seen by the unaided eye contradictions to this definition - ANSWER--supersize microbial cells -microbial communities -viruses You are caring for a patient actively infected with Mycobacterium tuberculosis. Size of contaminated respiratory droplets are 1000- 5000 nm in size. Standard surgical masks are designed to block particles larger than 5 μm. Will wearing a standard surgical mask be an effective form of protection? - ANSWER-No, the mask protects against microbes that are 1- nanometers, and the tuberculosis particles are larger than 5 nanometers Robert Hooke - ANSWER--built first compound microscope to observe mole and cork -published Micrographia -coined the term "cell" Antoine van Leeuwenhoek - ANSWER--built single lens magnifiers -first to observe single-celled microbes, called them "small animals" Francesco Redi - ANSWER-performed an experiment disproving spontaneous generation in which he had meat in a container with no cover, one with a paper cover, and one with a gauze cover Lazzaro Spallanzani - ANSWER-disproved spontaneous generation by boiling broth and either covering it or not covering it. Observed microbial presence in broth that had no cover only Louis Pasteur - ANSWER-disproved spontaneous generation using broth and bottle- neck experiment spontaneous generation - ANSWER-living organisms can arise from non-living matter Germ theory - ANSWER-the theory that many diseases are caused by microbes (chain of infection, pure culture, colonies)
Chain of infection - ANSWER-transmission of infectious microbes Pure culture - ANSWER-culture from a single parental cell Colonies - ANSWER-distinct populations each grown from a single cell Robert Koch - ANSWER-Developed first guidelines (postulates) to establish a link between a specific microbe and disease Koch's postulates (4) - ANSWER-1) Microorganism must be present in every case of the disease and absent from healthy organisms
Gram + bacteria have (thick/thin or no) peptidoglycan layers - ANSWER-thick Gram stain procedure (long) - ANSWER-1) Add crystal violet, turning all bacteria purple.
cell wall - ANSWER-(sacculus) confers shape and rigidity to the cell and protects cell membrane, some cells have membranes but no walls two sugar precursors in peptidoglycan - ANSWER-N-acetylglucosamine (NAG) and N- acetylmuramic acid (NAM) gram-positive bacteria's peptidoglycan layers are threaded by what? - ANSWER- teichoic acids Lipoproteins are found in gram (+/-) bacteria - ANSWER-negative lipoproteins function - ANSWER-connects outer membrane to peptidoglycan layer LPS as endotoxins - ANSWER-Lipopolysaccharides overstimulate immune cells when its cell dies, causing a cytokine storm Porins - ANSWER-outer membrane holes that allow passage of nutrients; also site of antibiotic entry S-layer - ANSWER-founf in both gram + and - bacteria, is a crystalline layer of proteins and glycoproteins used to contribute to cell shape and help protect the cell from osmotic stress Nucleoid - ANSWER-region in prokaryotes where DNA is organized into loops or domains Plasmids - ANSWER-circular DNA strands that can replicate independently, often carry unique genes such as antibiotic resistance Genus mycobacterium - ANSWER-membranes contain mycolic acids instead of teichoic acids linked to arabinogalactan that links peptidoglycan Genus mycoplasma - ANSWER-Lack cell walls (pleomorphic) cannot synthesize peptidoglycan uses sterols to stabilize plasma membrane grows as fried egg appearance on agar surface contain three-layered plasma membrane essential nutrients - ANSWER-nutrients a microbe cannot make for itself, but must gather from its environment Macronutrients - ANSWER-nutrients needed in large quantity: C, N, P, H, O, S, Mg, Fe, K, and Ca micronutrients - ANSWER-nutrients needed in small quantities: Co, Cu, Mn, Md, Ni, Zn Enriched media - ANSWER-complex media to which specific blood components are added Selective media - ANSWER-favor the growth of one organism over another Differential media - ANSWER-exploit differences between two species that grow equally well Rickettsie prowawzekii - ANSWER-agent of typhus fever
N0 = original number of cells n = number of rounds of binary fission Bacterial growth curve - ANSWER- Lag phase - ANSWER-Population is metabolically active and number of cells does not increase. Length varies with species and conditions Exponential (log) phase - ANSWER-population doubles each generation and primary metabolites are synthesized. Balanced growth at a constant rate When in bacterial growth curves are the bacteria most susceptible to antibiotics? - ANSWER-exponential phase Primary metabolites - ANSWER-amino acids nucleic acids simple lipids secondary metabolites - ANSWER-antibiotics Stationary phase - ANSWER-growth curve horizontal as population growth ceases. New cells are made at the same rate as old cells die and secondary metabolites are made at beginning Death phase - ANSWER-exponential 99% of population dies Prolonged decline - ANSWER-1% of population mutates according to environment Continuous culture - ANSWER-a culture in which all cells in a population achieve a steady state, allowing detailed study of bacterial physiology Chemostat - ANSWER-ensures logarithmic growth by constantly adding and removing equal amounts of culture media Biofilms - ANSWER-most bacteria attach to surfaces rather than exist in free-floating states. Attached bacteria form complex, slime enclosed communities called biofilms. Clinically important contributor to microbial disease Biofilm formation (long) - ANSWER-1) Planktonic cells attach to nearby surfaces and coat surfaces with organic debris that more cells can attach to
-0.9% salt -ample nutrients Extremophiles - ANSWER-organisms that live outside of normal conditions, (high/low heat, pressure, etc.) Why is temperature regulation important for microbes? - ANSWER--enzymes have optimal temperature for function -high temps destroy proteins -low temperatures solidify membranes Psychrphiles - ANSWER-0-20C have enzymes adapted to function in cold temps Membrane remains semi-fluid when cold Microbes accumulate solutes to decrease freezing point How do psychrophiles keep their membrane semi-fluid in cold temperatures? - ANSWER-incorporating high levels of unsaturated fatty acids into their membranes Mesophiles - ANSWER-15-45C Thermophiles - ANSWER-40-80C enzymes adapted to function in hot temp Increased hydrogen bonding Less flexible polypeptides Numerous DNA binding proteins stabilize DNA Thermus aquaticus - ANSWER-microbe that can survive in hot temperatures by utilizing TAQ DNA polymerase Taq DNA polymerase - ANSWER-specialized DNA pol that functions in very high temperatures, one of the most widely used enzymes in biotechnology Barophiles - ANSWER-grow at pressures up to 1000 atm or 14600 psi, utilizes hydrostatic pressure to reduce membrane fluidity but other mechanisms for survival in high pressures are a mystery hypertonic medium - ANSWER-medium with high solute concentration Hypotonic medium - ANSWER-medium with low solute concentration Cells in hypertonic media - ANSWER-water will leave the cell in an attempt to equalize solute concentration, bacteria shrinks and dies Cells in a hypotonic medium - ANSWER-Water will enter cell and bacteria will swell, burst, and die. Aquaporins - ANSWER-membrane-channel proteins that allow water to traverse the membrane much faster than by diffusion to protect cell from osmotic stress How do cells adapt to hypotonic environments? - ANSWER-The cell expresses pressure-sensitive channels in plasma membrnae to allow solutes to leave the cell
3 main routes that bacteria and archaea catabolism of glucose - ANSWER-1) Glycolysis (EMP)
Geobacter and remediation - ANSWER-geobacter is used for removal of uranium from water in Colorado Geobacter oxidizes acetate to CO2, reducing uranium in the process reduced uranium precipitates out of water Sulfolobus biotechnology - ANSWER--is studied because of its enzymes that are stable at high temp and low pH -oxidizes hydrogen sulfide to sulfuric acid -microbial sulfur oxidation can cause severe environmental acidification Bacteriorhodopsin - ANSWER-seven alpha helices that span the membrane in alternating directions that surround a molecule of retinal, linked to a lysine residue A photon is absorbed by retinal, which shifts its configuration from trans to cis causing the cell ro pick up a proton This generates proton gradient that drives ATP synthesis Halobacterium and bacteriorhodopsin - ANSWER-pack their membranes with bacteriorhodopsin to maximize light absorption Which of the following statements regarding peptidoglycanis correct? A. Gram negative cells have higher concentration of it compared to Gram positive. B. It contains two alternating sugars NAG and NAM. C. It can be linked to arabinogalactan in Mycoplasma D. All of the above are correct - ANSWER-B Describe one similarity and one difference between Mycoplasma and Mycobacteria. (can be cellular structure, staining, disease, etc.) - ANSWER-Example Similarities: Both associated with respiratory infections. Both cannot be stained consistently with Gram stain procedure, etc. Example Differences: Mycoplasma has no cell wall, Mycobacteria has cell wall with arabinogalactan. Mycobacteria has mycolic acids Mycoplasma does not, etc. Describe one of Robert Hooke's contributions to the field of Microbiology. - ANSWER- Built the first compound microscope §First observations of mold, fleas, cork under a microscope §First publications (Micrographia) of observations under a microscope §Coined the term cell You perform a Gram Stain but ...ooops..forgot to add Safranin. Which of the following bacteria would appear purple after the staining procedure? (Assume all other steps performed correctly). A. Gram Negative B. Gram Positive C. Gram Negative and Gram Positive
Conjugation - ANSWER-horizontal gene transfer requiring cell contact. Genes transferred sequentially Conjugation process - ANSWER-1) Two cells are brought together by the sex pilus on the donor cell.
High-copy-numbers - ANSWER-segregate randomly to daughter cells Cases in which plasmids are advantageous to bacteria - ANSWER--resistance to antibiotics -pathogenesis -symbiosis two ways plasmids can replicate - ANSWER-Bidirectional replication Rolling-circle formation Bidirectional replication - ANSWER-starts at a single origin and occurs in two directions simultaneously Rolling circle process - ANSWER-begins at Ori One strand is nicked When synthesis of the new strand is completed the new strand is released Complementary strands are replaced (kinda confusing, look at ppt images) ParM - ANSWER-actin-like, forms long filaments on plasmids Stable filaments will drive plasmids towards opposite poles restriction endonucleases - ANSWER-enzymes that act as molecular scissors, cutting foreign DNA at specific restriction sites Restriction sites are palindromes. What does this mean? - ANSWER-both strands base pair and read the same 5'-3' direction Metagenomics - ANSWER-uses modern genomic techniques to study microbial communities directly in natural environments, bypassing the need for isolateing and cultivating individual species in the lab Transformation - ANSWER-the process of importing free DNA into bacterial cells. Cells need to be competent How to artificially mutate cells to make them competent - ANSWER-perturbing the membrane by chemical (CaCl2) or electrical (electroporation) methods Transformasome complex - ANSWER-facilitates uptake of free DNA into cells Gram positive transformation - ANSWER-competence is generated by quorem sensing. As bacteria grows, competence factor grows too. At specific levels, CF will induce a genetic program that induces the transformasome Gram-negative transformation - ANSWER-Gram-negative bacteria transform DNA without competence factors. They are either always competent or become competent when starving. Do not use transformasomes and transformation is sequence specific, limiting gene exchange between genera
Uses premise that parental (methylated) strand has proper DNA sequence, so corrects mismatch on daughter strand Mut - ANSWER-term to describe methyl-mismatch repair proteins and genes MutS - ANSWER-binds DNA mismatch and recruits other proteins to the mismatch site MutHLS - ANSWER-is recruited to mismatch by MutS and is a complex that causes looping MutH - ANSWER-cleaves the unmethylated strand Nucleotide excision repair - ANSWER-endonuclease removes a patch of single- stranded DNA containing damaged bases (does NOT distinguish between parental and daughter strands) Uvr - ANSWER-term to describe proteins and genes involved in nucleotide excision repair UvrA - ANSWER-forms a complex with UvrB that binds damaged DNA, causing a bend to occur at the site of damage UvrB - ANSWER-forms a complex with UvrB that binds damaged DNA, then recruits UvrC UvrC - ANSWER-cleaves at sites that flank the damage UvrD - ANSWER-has helicase activity that strips away the damage transcription coupled repair - ANSWER-when a cell is unable to transcribe a gene, polymerases stall during transcription and recruite Uvr proteins to assist Error-prone repair pathways - ANSWER-risk introducing mutations that operate ONLY when damage is so severe that the cell has no choice but to mutate or die SOS repair pathway - ANSWER-induced by extensive DNA damage Polymerase actions are sloppy because they lack capability for proofreading RecA - ANSWER-a protein that will regularly monitor the level of ssDNA in a cell LexA - ANSWER-protein that prevents repair gene transcription RecA and LexA experiencing extensive DNA damage - ANSWER-RecA degrades LexA SOS repair polymerases - ANSWER-Pol IV and Pol V are sloppy polymerases, cell will live if it can tolerate any mutations and other side effects SOS repair and bacterial survival - ANSWER-S. aureus is found in our nasopharynx. S. pneumoniae destroys S. aureus' DNA, triggering SOS response, which activates resident phages of S. aureus, killing it but keeping S. pneumoniae survive Vaccines - ANSWER-substances that stimulate antibody production without causing disease Transgenic - ANSWER-an organism that contains artificially introduced genetic material from another unrelated organism
Veggie vaccines - ANSWER-Incorporating vaccine (via transferable plasmids) into vegetables to generate an edible veggie vaccine Aliivibrio fischeri - ANSWER-bacteria that lives within Hawaiian bobtailed squid and produces light. Quorem sensing and A. fischeri - ANSWER-Requires an autoinducer accumulates outside of bacteria until extracellular levels become high enough that they enter the bacteria and binds toregulatory molecule, activating transcription of luciferase (bioluminescence). Extracellular autoinducer builds up during the day, and then when it is night, it enters cell and allows for bioluminescence LuxR - ANSWER-regulatory molecule that autoinducer binds to Repressors - ANSWER-bind to regulatory sequences in DNA and prevent transcription of target genes 2 mechanisms for repressor activity - ANSWER-1) Repressor binds to DNA sequence and prevents transcription. Ligand (inducer) binds to repressor, releasing it and allowing transcription
Thermotoga maritima - ANSWER-has one of the highest recorded growth temperatures of 90C, belongs to toga phylum. DUring growth, the sheath extends from the poles, followed by the outer envelope growing and then the cytoplasm growing Chloroflexus auranticus - ANSWER-belongs to phylum chloroflexus. Resides in lower levels of microbial mats under cyanobacteria. Gram NEG (atypical) and have no outer membrane Phylum cyanobacteria - ANSWER-largest, most diverse group of photosynthetic bacteria. are oxygenic and have thick peptidoglycan layer (almost as thick as gram +). Appears green because of chlorophyll Cyanobacterial mutualism - ANSWER-share many mutualistic relationships, especially in multilayered microbial mats Shapes of phylum cyanobacteria - ANSWER-filamentous or colonial Heterocysts - ANSWER-specialized cells used for nitrogen fixation produced when organism is nitrogen deprived Function of thick heterocyst walls - ANSWER-prevent oxygen diffusion into heterocyst which would inactivate nitrogenase activity, forms in communal cyanobacteria Thylakoids - ANSWER-some cyanobacteria have it, used for photosynthesis Carboxysomes - ANSWER-some cyanobacteria have them, used to fix CO two phyla in group gram positive - ANSWER-phylum firmicutes phylum actinobacteria phylum firmicutes has (high/low)-GC content - ANSWER-low Actinobacteria have (high/low)-GC content - ANSWER-high Phylum firmicutes - ANSWER-low-GC many form endospores many are pathogens Genus clostridium - ANSWER-firmicutes, rod-shaped obligate anaerobes that form spores Clostridium botulium - ANSWER-agent of foodbourne botulism, commonly found in soil and spores allow dormant survival in host until ideal (anaerobic) conditions are met Botulism - ANSWER-common source of infection is improperly preserved foods. Bacteria produce a toxin that blocks nerve function, and causes double vision, drooping eyelids, and paralysis Clostridium in the wild - ANSWER-grows in dedcaying material, and toxin is consumed by unaffected organisms (maggots) that can transmit toxin to sensitive organisms. Death of this organism perpetuates this cycle Clostridium exposure to infants - ANSWER--infant can be exposed to endospores or toxin
-consumption of honey before age 1 (due to immature gut microflora) (65% of cases) Clostridium exposure in adults - ANSWER--exposure to toxin -can be foodborne -many routes of exposure treatmend of Clostridium disease - ANSWER-intensive care, antitoxin Genus bacillus - ANSWER-one of the first bacterial genera to be classified, consists of large rod-shaped cells. Contains vegetative spores that develop inert endospores in times of starvation and stress, these spores germinate in favorable conditions, and restart vegetative growth Bacillus thuringiensis - ANSWER-most successful biological control agent yet produced spores are applied as insecticide against gypsy moth caterpillar; sporulating cell produces crystal that contains insecticidal protein What is the insecticidal protein released known as? - ANSWER-delta endotoxin Phylum actinobacteria - ANSWER-high-GC form complex multicellular filaments, some are acid-fast Genus streptomyces - ANSWER-actinobacteria aerobic non-motile inhabit soil Geosmin - ANSWER-produced by streptomyces, resulting in moist earth odor after rain nonpathogenic grow onto and into their substratum Streptomyces genome - ANSWER-have LINEAR chromosomes with telomeres Life cycle of streptomyces - ANSWER--vegetative cells form dense substrate mycelium underground -nutrient limitation/stress induces growth up into the air (aerial mycelium) -aerial mycelium cannibalize substrate mycelium for nutrients Streptomyces in biotechnology - ANSWER-used in antibiotics and anticancer How do antibiotics kill harmful bacteria? - ANSWER-selective toxicity what are some targets that antibiotics target - ANSWER-peptidoglycan differences in ribosome strucure biochemical pathway that humans do not have Broad spectrum antibiotics - ANSWER-effective against many species Narrow spectrum - ANSWER-Effective against a few or a single species Bactericidal antibiotics - ANSWER-kill target organisms Bacteriostatic antibiotics - ANSWER-prevent growth of organisms (immune system would eventually kill intruding microbe)