Microbiology Exam 1 PDF

Lecture 1: History of Microbiology ​ Spontaneous generation– The role of pneuma ○​ Life can arise from nonliving matter. Aristotle said if material contained pneuma (spirit/breath) it can arise from nonliving matter (later disproven) ​ Miasma theory- What is it?...

Lecture 1: History of Microbiology ​ Spontaneous generation– The role of pneuma ○​ Life can arise from nonliving matter. Aristotle said if material contained pneuma (spirit/breath) it can arise from nonliving matter (later disproven) ​ Miasma theory- What is it? ○​ Disease comes from particles emanating from decomposing matter- bad air ​ Germ theory: diseases results from microbial infection ○​ How it replaced spontaneous generation ​ Impact of and on Handwashing and other Aseptic techniques ​ After birth mortality rate down to 1% from washing hands with chlorine ​ Carbolic acid as disinfectant/antiseptic ​ Louis Pasteur ​ Microbes responsible for infection ​ Germ theory → germ as cause of disease ​ Endosymbiotic theory –What is it? ○​ Mitochondria and chloroplasts arose as a result of prokaryotic cells establishing a symbiotic relationship w/in a eukaryotic host ​ Scientific method– What are the steps? Observe, research, hypothesize, test via experiment, analyze, report ​ What did they do, and how did they contribute to science: contributed to germ theory ○​ Louis Pasteur ​ Swan-neck flasks w/ sterilizing broth disproving spontaneous generation ○​ John Snow ​ Revealed that cholera came from sewage and water ​ Disease not only transmitted thru air but also contaminated items (refuting miasma theory) ○​ Ignaz Semmelweis ​ Hand washing to prevent sepsis/ mortality after birth because he proposed that disease was being transferred by students performing autopsies to delivering babies ​ Disease not only transmitted thru air but also contaminated items (refuting miasma theory) ○​ Joseph Lister ​ Tried to find postsurgical infection cause and insisted on handwashing/cleanliness during surgery. Came out with antiseptic ​ Credited w/ modern microscope ○​ Florence Nightingale ​ Stats for hygiene for hospitals ○​ Robert Koch ​ Specific disease from specific microbe (miasma to germ theory) Lecture 2: Observing Microbes Prokaryote (archaea Eukaryote (fungi, Virus (HIV, & bacteria) protozoa, algae) bacteriophages) Structure Unicellular (simple) Uni/multicellular Acellular (complex) Genetic material Single circular DNA in Multiple linear DNA or RNA nucleoid region chromosomes in Both linear and nucleus circular Organization no membrane bound Membrane bound No nucleus organelles/nucleus organelles Own naming Plasma membrane Nucleus convention complex Reproduction Binary fission Mitosis and meiosis Replicate inside host (asexual) (sexual and asexual) cell Increase in size/# Cell division and differentiation Size Comparisons 5-100 um 0.05-0.1 um (biggest) (smallest) 15-100 nm Light microscope E- microscope ​ Prokaryotes ○​ Morphology ​ Coccus, bacillus, spirillum ​ Prokaryotes and Eukaryotes ○​ Describe taxonomy and binomial nomenclature ​ Capitalized, lowercase ​ Microscopy ○​ Simple vs Compound ​ Simple- light passes thru one lens ​ Compound- light passes thru 2 lenses ○​ Parts of the microscope ○​ Calculating Magnification ​ Ocular magnification x objective magnification ○​ Fluorescence microscopy- absorbs light and emits ultraviolet light for us to view ​ Importance of fluorophores ​ Used to identify pathogens, finding species, locations of molecules in a cell, distinguish live and dead cells ​ Used to identify certain diseases by observing if antibodies bind ​ Benefits and drawbacks ​ Limited by wavelengths of visible light , specimen will stay alive ○​ Electron microscope- short- wavelength e- beams ​ Benefits and drawbacks ​ Greater resolution, good for viruses and small structures, but will kill ​ Staining ​ Applying color to determine positive or negative ion ○​ Simple Stain ​ What is the purpose? To increase visibility, preserve morphology, highlighting morphological features ​ Why is it essential/beneficial for the brightfield microscope? ​ Standard microscope ​ What are the drawbacks? ​ Will kill bacteria Lecture 3: Prokaryotes Parts Structure Function Capsule polysaccharide/protein layer Protection against phagocytic outside of cell wall cells (immune cells- slippery), adheres to surfaces to grow biofilms Plasma Membrane Fluid mosaic model that Selective permeability encloses cytoplasm Cell Wall Made of peptidoglycan (sugar Protects cell from outside and aa) layers, protects environment against osmotic pressure Gram Negative Thin cell wall, porins LPS gives fever, LPS endotoxins hemorrhaging, sepsis Gram Positive teichoic acids TAc stabilize and bind Thiccer than a snicker Mycolic acids in outer cell wall endospores (for protection) Nucleoid Circular haploid (unpaired) Holds genetic material chromosome packed w/ DNA Plasmids Extrachromosomal DNA Carry genes to offer antibiotic resistance/toxins Ribosomes 70S found in cytoplasm Protein synthesis Pili Long appendages Attachment to surfaces, DNA transfer (sex pili) Fimbriae Short bristle like Attach to cells and surfaces, motility Flagellar Stiff spiral filaments Propellers in (aq) ○​ Membrane proteins: provide structural support, detect/release signals, secretion of virulence factors, ion transport ○​ Peptidoglycan: cell wall that is thick in gram (+) (anchored by teichoic acid), and thin in gram (-) ○​ Simple staining is to visualize differential is to see if gram +/-, endospores, etc ○​ Acid fast is to mycolic acids ○​ Movement ​ Flagellar- filament (tail), basal body (motor rotation), hook (connects to base) ​ Chemotaxis- bacterial movement that is dependent on chem gradients Lecture 4: Eukaryotes ​ Eukaryotes (Parts of a Eukaryote)– differences, definitions ,and any clinical applications  ○​ Cholesterol vs Hopanoids ​ Cholesterol is steroid that aids in fluidity and holding membrane together in eukaryotes ​ Hopanoid is steroid that does the same in prokaryotes ○​ Nucleus ​ Nucleolus function: rRNA biosynthesis occurs, ribosomal assembly ○​ Ribosomes ​ Eukaryotic- 80S (mitochondria/chloroplasts 70S) ​ Prokaryote- 70S ​ Free- synthesize water-soluble proteins ​ Membrane- bound- make proteins for insertion into cell membrane/export ○​ Endomembrane system- tubules, sacs, disks synthesizing and moving cell components w/in cell ​ Smooth ER- biosynthesis of lipids, carbohydrate metabolism, detoxification ​ rough ER- transport new proteins to golgi or plasma membrane ​ Golgi: modify lipids and proteins (adding carbohydrates) for exocytosis ​ Cis transports material ​ Trans accepts material ​ Lysosome digestive system engulfing and breaking down debris ○​ Peroxisome NOT part of endomembrane system, FA breakdown/ lipid synthesis ​ Produces/degrades H2O2, lipid biosynthesis ○​ Cytoskeleton- provides structural support and network for materials and anchoring ​ Microfilaments: strands of actin, exocytosis/endocytosis ​ Intermediate filaments: anchoring ​ Microtubules : roadways for cellular transport, cellular division ○​ Mitochondria ​ Ribosome type/size: eukaryotic mitochondria 70S (eukaryotic is 80S) ○​ Plasma membrane & Cell wall ​ Transport– endocytosis: engulfing into cell ​ Phagocytosis, pinocytosis, receptor- mediated endocytosis: large, small, receptors ​ Eukaryotic cells lack cell walls (most); which ones have cell walls? How does it impact drug discovery?: chitin, cellulose, silica ○​ Flagella & Cilia ​ Prokaryote: lack cilia but have flagella (H+) ​ Eukaryote: both (ATP) ​ Movement: rotates for prokaryotes, bends for eukaryotes Lecture 5: Fungi, Protozoa, Algae, Viruses ​ The four eukaryotic Kingdoms- Characteristic differences ○​ Animal- multicellular, motile, heterotrophic, complex ○​ Plant- multicellular, makes own nutrients (autotrophic) ○​ Fungi- multicellular, absorbs nutrients, chitin cell walls, exospore ○​ Protists- unicellular, heterotrophic protozoa/algae/molds, asexual (budding), very diverse, plays role in nutrient cycle but can be parasites ​ Fungi; yeast, mold, mushroom ○​ The Basic Life Cycle ○​ Unicellular (yeast) vs Multicellular (mold/mushrooms) ○​ Importance of Asexual and Sexual reproduction: has both w/ life cycles (spore formation, germinations, mycelium growth- making cell wall) ​ Protists  ○​ Characteristic difference/description of Algae vs Protozoa vs Slime/Water molds ​ Protozoa are animal like ​ Algae are plant like, photosynthetic ○​ Flagellates vs Ciliates: categorized based on what they use (they are motile) ​ Viruses: some have spikes for attachment ○​ Classification criteria: shape of capsid (how it interacts w/ host) , if has lipid membrane (how resistant it is), and nucleic acid (DNA/RNA) ○​ Genome variety: variety of genome types ○​ Taxonomy: relatively new so very messy ​ Taxa has one name ​ Capitalized and italicized Lecture 6: Microbial growth ​ Prokaryote division ○​ Binary fission: cell replication in bacteria. Cell grows and replicates DNA at origin of replication where chromosomes attach to inner membrane and goes in opposite directions until terminus is reached. The center constricts with 2 exact genetic symmetrical daughter cells. ○​ Asymmetric vs symmetric: spore formation is asymmetric ​ Doubling time: (aka generation in eukaryotes) time it takes for population to double after binary fission ​ Growth rate: determined genetically, generation time under growth conditions ○​ how it works: each division adds 2 new cells ○​ Formula: Nt = No x 2^n ​ Growth curve: reproducible growth pattern ○​ Lag: no growth, adaptive and metabolically active ○​ Log: max growth, x2 growth, most susceptible to antibiotics ○​ Stationary: plateau, secondary metabolites synthesized (antibiotics) ○​ Death: decline ​ Role of primary & secondary metabolites ○​ Primary: amino acids, nucleic acids, simple lipids (promotes growth) ○​ Secondary: protection and response to stress (low quantities) ​ Continuous vs batch culture ○​ Batch: microorganisms grown in closed culture w/ no nutrients in or out ○​ Continuous (biofilms): all cells achieve steady state w/ nutrients ​ Biofilms: ecosystems forming on surfaces. Extracellular matrix has EPS which allows permeability, hydration, and protection ○​ Formation step-by-step ○​ Clinical importance: biofilms can form in unwanted places leading to antibiotic resistance ​ Bacterial growth media: ○​ Nutrient-rich media: contains growth factors, vitamins, and essential nutrients to support variety of bacterial  ○​ Pure v mixed culture: pure- 1 microbial species grown in a specific media. Mixed has a variety ○​ Selective & differential media: non-selective support growth w/o specific inhibition. Selective inhibits growth of unwanted microorganisms. Differential makes it easy to distinguish colonies by color based on phenotype Lecture 7: Metabolism ​ Definitions ○​ Exergonic reactions: release energy, reducing power ○​ Endergonic reactions: require energy ○​ Metabolic pathways: step wise chem rxns ○​ Catabolism: exergonic, chem rearrangement of energy source ○​ Anabolism: endergonic ​ Catabolism ○​ Benefits of catabolism: reducing power (carried by NAD+/FAD+2), energy (ATP) ○​ Polymer, synthesis, breakdown: complex carbs are polymers. Synthesis is adding monomers (dehydration synthesis → ligase), breakdown is withdrawal of h2o (hydrolysis) ​ Carbohydrates ○​ Monosaccharides v Disaccharides v Polysaccharides: ​ Cellular respiration steps; ○​ know the order and location ○​ Glycolysis (EMP):2 net ATP ○​ Transition reaction:coenzyme A ○​ Krebs cycle ​ Starting molecule: pyruvate ​ End result: NADH, FADH2 ○​ Electron Transport Chain ​ Final electron acceptor O2 ​ Proton motive force, Membrane potential: H2 pumped out of cell and goes thru atp synthase ​ ATP synthase role: generates ATP thru H2 gradient ​ Cellular respiration ○​ Aerobic cellular respiration: O2 is final acceptor ○​ Anaerobic cellular respiration: uses pyruvate or other acceptors ​ Fermentation (location): type of anaerobic respiration occurring in cytoplasm ○​ What type of organisms use it?: plan B for making atp ○​ Benefits: free e- carriers, end products (ATP) are quickly produced (but not high quantity) ○​ Starting substrate: pyruvates Lecture 8: Microbial Metabolism 2  ​ Amino Acids- polymerized into proteins ○​ Structure ○​ Location ○​ Building blocks from ​ Nucleic Acids polymerized from nucleotides ○​ Structure DNA/RNA ○​ Location ○​ Building blocks from:sugar (deoxyribose) ​ Lipids composed of several subunits ○​ Structure TAG (fatty acid + glycerol), long term energy source ​ Triglyceride ​ Saturated (H bonds only) v Unsaturated (double bonds) ​ Phospholipids ​ Steroid ○​ Location ○​ Building blocks from ​ Microbial Metabolic Naming ○​ Energy, Carbon- reducing ​ Phototrophs: light to energy (plants) ​ Chemotrophs: energy from breaking chemical bonds ​ Autotrophs: inorganic carbon to organic for future catabolism ​ Heterotrophs: complex organic carbs (animals, protists) Lecture 9: Environmental conditions ​ Normal growth ○​ Extremophiles: 1 atm, temp 20-40, pH 7,.9% salt, ample nutrients ​ Optimum, minimum, maximum: best rate, lowest can grow, highest can grow ​ Temperature: ○​ Terms and their definitions: psychrophiles- adapted to cold, mesophiles- neutral temp, thermophiles- adapted to hot, hyperthermophiles- extreme ​ Oxygen: ○​ Terms and their definitions- Think metabolism too ​ Aerobes ​ Obligate aerobe- needs O2 ​ Microaerophile- low O2 ​ Anaerobe ​ Strict anaerobe- O2 is toxic ​ Facultative anaerobe- better w/ O2 but can use fermentation ​ Aerotolerant- indifferent, grows either way ○​ Reactive oxygen species: ○​ Thioglycolate medium: reducing properties, autoclaving removes O2  ​ Bacterial cell distribution in the tube: ​ pH: ○​ Terms and their definitions: ○​ Neutrophiles: ~7, most ○​ Acidophiles: low pH ○​ Alkaliphiles: high pH ​ Salt: ○​ Halophiles v Halotolerance (staphylococcus aures) ○​ Salt loving to neutral