Microbiology Midterm PDF

Chapter 1 Examples of microorganisms playing important roles in our everyday lives Decompose organic waste, generate oxygen by photosynthesis, produce chemical products (ethanol, acetone, vitamins), produce fermented foods, produce products for manufacturing (cellulose) and disease treatment (insuli...

Chapter 1 Examples of microorganisms playing important roles in our everyday lives Decompose organic waste, generate oxygen by photosynthesis, produce chemical products (ethanol, acetone, vitamins), produce fermented foods, produce products for manufacturing (cellulose) and disease treatment (insulin), constitute human microbiome, sewage treatment Are all microbes pathogenic? What are some of the ways we benefit from the activity of microorganisms? -Not all are pathogenic -Microbiome: about 40 trillion bacterial cells, composed of microbes that live in/ on the body, help maintain health, can prevent growth of pathogenic microbes, can help train immune system to discriminate threats, dysbiosis has been linked to many disease states -prevent food spoilage, understand and prevent disease, understand causes and transmission of disease to prevent epidemics What types of microorganisms exist? How do we classify/categorize them? What is the correct way to write the scientific name of a microbe? -Bacteria, Archaea and Eukarya. The first two consist completely of single-celled microbes. None of them have a nucleus. The third domain, Eukarya, consists of organisms whose cells have a nucleus. -Bacteria& Archaea (Prokaryotes) -Fungi, Protozoa, Algae, Multicellular animal parasites (e.g. helminths) (Eukaryotes) -Viruses -genus and species: italicized, genus capitalized, E.coli What are the general characteristics of bacteria, archaea, fungi, protozoa, algae, viruses? -Bacteria: prokaryotic, single celled organism, cell wall has peptidoglycan, multiply via binary fission, derive nutrition from chemicals or photosynthesis, variety of cellular morphologies and can have different appendages like flagella -Archaea: prokaryotic, no peptidoglycan, live in extreme environments (Methanogens, Extreme halophiles, extreme thermophiles), not known to cause diseases -Fungi: eukarya, nucleus surrounding DNA genetic material, chitin in cell walls, absorb organic chemicals for energy, 2 forms yeasts (unicellular) and molds& mushrooms (multicellular) -Protozoa: Eukarya, absorb or ingest organic chemicals, may be motile, free living or parasitic, preproduce sexually or asexually -Algae: eukarya, cellulose in cell walls, in freshwater saltwater and soil, photosynthesis for energy produce oxygen and carbohydrates -Virus: acellular, consist of DNA or RNA surrounded by protein coat, replicate only when living in host cell Which types of microorganisms have cell walls/which don't? bacteria (except mycoplasmas), fungi, archaea, and algae generally have cell walls protozoa, mycoplasmas, and most animal cells do not. What fields have emerged as a result of our study of microbes? -bacteriology, mycology, parasitology, immunology, virology and emerging infectious diseases Who were some of the major players that helped shaped the field of microbiology that we know today? What were their contributions/discoveries? -Hooke: cell theory, all living things are composed of cells -Leuwenhoek: first to observe microbes with lenses -Koch: criteria to help decide if organism is cause of disease (Kochs Postulates) -Fleming: first antibiotic -Pasteur: disproves spontaneous generation and discovers microbial fermentation -Lister: Aseptic Technique -Semmelweis: Significance of handwashing -Snow: cholera contaminated water Chapter 3 Convert between units of measurement -Microorganisms measured in micrometers μm (Bacteria) and nanometers nm (Virus) -nm -> μm -> mm -1m = 1x10^6 micrometers -1μm = 1000nm or 1nm = 0.001μm What are some of the different types of light microscopy that we can use? How are different light microscopes similar? Different? -brightfield, phase-contrast, fluorescence, and confocal microscopy -all use visible light to observe specimen -compound light microscope: 2 lenses, image from objective lens (4, 10, 40, 100x) is magnified again by ocular lens (10x) How does one calculate the total magnification of a specimen? Where does most of the magnification come from? -magnification= objective lens x ocular lens, objective lense What is resolution and resolving power? What does 0.4nm resolving power mean ? -resolution= ability of lenses to distinguish 2 points as separate -microscope with resolving power of 0.4nm can distinguish between points at least 0.4 nm apart -shorter wavelengths of light provide greater resolution What is the refractive index of a medium? How can we minimize refraction? -measure of light-bending ability of a medium (eg air, glass, oil) -refraction occurs when light rays bend as they pass medium with a changing index of refraction eg pencil in cup of water, occurs with microscopes too-> immersion oil to keep light from refracting when using higher magnification lenses What is brightfield and phase-contrast microscopy? Can both be performed using a compound microscope? -Brightfield: dark objects against a bright background, most common type of light microscopy -phase contrast microscopy: examination of living organisms and internal cell structures, brings together 2 sets of light rays: direct and diffracted, to form image -yes can both be used How does fluorescence and confocal microscopy differ? How are they similar? -Fluorescenct substances absorb UV light (short) and emit longer wavelengeht (visible) light -cells may be stained with dyes if the don’t naturally fluoresce -allows to visualize specific cellular structures -confocal cells stained with fluorescent dyes -short wavelength (blue) light used to excite single plane of a specimen -each plane in specimen is illuminated and 3D image constructed -can examine layers of a cell to a depth of 100 μm What are the two types of electron microscopes? How are they similar? Different? What types of images do you acquire from each? -EM uses electrons instead of light, their shorter wavelength gives greater resolution, used for 0.1nm to 50 μm eg viruses that, too small for light microscope 100 nm to 1 mm -Transmission TEM: electrons pass through ultrathin sections of specimen, specimen stained with heavy metal salts for contrasts, magnifies 10.000 to 10.000.000x, resolution 10pm -Scanning SEM: beam of electrons scans surface of specimen, 3D image, magnifies 1.000 to 500.000x, resolution 10nm What is a negative stain? What color are the organisms in a negative stain? -stain background instead of cell, maintains true size, cheap, fast -organisms are white/ colorless What are two types of differential stains? What does the Gram stain show us? How? -Gram stain and Acid-fast stain, both used to distinguish between bacteria -Gram: classifies into gram positive or negative bacteria, purple= gram positive, pink= gram negative What clinically important organism are we able to visualize with an acid-fast stain? - Mycobacterium, has waxy material in cell walls What other bacterial structures can we visualize using different stains? -capsules, endospores, flagella Chapter 4 What are the main differences between prokaryotes and eukaryotes? -pro: single circular chromosome, no nucleus, no organelles, 70S ribosomes, cell wall peptidoglycan (bacteria), binary fission, smaller, unicellular organism, -eu: paired, linear chromosomes, nucleus, organelles, 80S ribosomes, polysaccharide cell walls, mitosis and meiosis, larger How do we describe the size, shape and arrangement of bacteria? Are you able to accurately describe a bacteria if provided with only a picture? -Average size: 0.2 to 2.0 μm diameter × 2 to 8 μm length -most bacteria are monomorphic, a few pleomorphic -bacillus= rod shaped (chain) -coccus= spherical shaped (punkte) -spiral -diplo= pairs -staphylo= clusters -strepto= chains What is a glycocalyx? -external to cell wall, made of polysaccharide and/ or polypeptide -prevents phagocytosis of bacterium, adherence to surfaces, protects from attack -capsule or slime layer How to bacteria move and/or attach to surfaces? Are there more than one type of structure that allows bacteria to move? -with filamentous appendages, made up of filament, hook and basal body -flagella, axial filaments (corkscrew), fimbriae (short hairs), pili (long hairs) What is the main difference between Gram+ and Gram- cell walls? How are they structured? What are some of the important components? (Be sure to know the importance of peptidoglycan and LPS) -in bacteria it contains peptidoglycan= polymer of a repeating disaccharides in rows -LPS lipopolysaccharide: immune stimulating molecule in outer membrane of gram- -gram negative has two membranes (cell and outer), defense mechanism also contains porins to regulate exchange of nutrients -persiplasm indicates space between membranes -gram negative means its thin, when you stain it it doesn’t take up stain -positive= thick peptidoglycan, stain gets trapped -positive just one membrane, techoic acids What do atypical cell walls contain, how are they stained and what organisms/diseases do we associate with these properties? -acid-fast cell walls like gram+ cell walls, contain waxy lipid, carbolfuchsin used to stain acid.fast bacteria like mycobacterium -gram stain (CV-I) -gram positive: alcohol dehydrates peptidoglycan, crystals don’t leave, cells stain purple -negative: alcohol dissolves outer membrane, leaves hole in peptidoglycan, CV-I washes out, cells are colorless, safranin added to stain gram- cells pink What is the composition, function and importance of the plasma membrane for bacteria? -phospholipid bilayer that encloses the cytoplasm -peripheral proteins on surface -integral and transmembrane proteins penetrate membrane -selectively permeable, allows passage of some molecules others not -contains enzymes for ATP production, bacteria produce ATP on membrane -some membranes have photosynthetic pigments -damage to membrane causes leakage of cell contents What types of processes support the movement of solutes in and out of the cell? Which requires energy? Does water move freely in and out the cell? -passive processes: no energy needed >simple diffusion: move from high concentration to low >facilitated diffusion: solute combines with transporter protein, with concentration gradient >osmosis water moves from high to low concentration through aquaporins -active: move from low to how, energy in form of ATP and transport protein required, against concentration gradient What's the difference between an isotonic, hypotonic and hypertonic solution and how do these states influence the movement of water in and out of a cell? >isotonic= concentration equal inside and outside of cell, balance, water doesn’t move, cell maintains shape >hypotonic= concentration is lower outside than inside, water moves into cell, can burst >hypertonic= concentration is higher outside than inside, watter moves out, shrink What's the difference between a bacterial chromosome and plasmid? -chromosome= circular thread of DNA that contains cells genetic information -plasmid= extrachromosomal genetic elements, non crucial genes like antibiotic resistance How big are bacterial ribosomes (how big are the subunits) and what function do they serve for the cell? -site of protein synthesis, made of rRNA -complete ribosome in bacteria 70S; 50S+ 30S subunits, never adds up (sedimentation rate) What are endospores and how do they serve as a survival mechanism for bacteria? -thick-walled structures formed in some bacterial cells -produced when nutrients depleted, overcrowding occurs -resistant to desiccation, heat, chemicals and radiation What overlapping structures do prokaryotes AND eukaryotes share and are they identical? -flagella/ cilia for locomotion or moving -cell wall -plasma membranes: eu can do endocytosis (phago and pinocytosis) -cytoplasm: everything inside cell but outside nucleus -ribosomes: 80S eu, 70S pro What organelles are present in eukaryotes and what are their main functions? -nucleus: contains cells DNA -ER transport network, smooth, rough are sites of protein synthesis -Golgi: transports proteins via vesicles to plasma membrane -mitochondria, powerhouse of cell ATP production Chapter 10 What are some of the characteristics the distinguish Eukarya from Bacteria and Archaea? ->TABELLE 10.1 -archaea= prokaryotes without peptidoglycan in their cell walls What is a phylogenetic tree? How does one read it? How is a tree constructed (using what information? Hint: has to do with RNA)? -groups organisms according to common properties (fossils, genomes) -groups evolved from a common ancestor- evolutionary history -each species retains some characteristics of its ancestor What is binomial nomenclature? Why do we use this system? Can you spot the error in an improperly named organism? -used worldwide to consistently and accurately name organisms, genus+ species, italicized, E. Coli What is taxonomic hierarchy? -series of subdivisions to classify organisms (=placing them in groups of related species), shows degree of similarity among organisms Domain>Kingdom>Phylum>Class>Order>Family>Genus>Species Drunk Kings play chess on fuzzy green stools Can you interpret information from a dichotomous key/cladogram? ->Yes/ No Questions Chapter 11 How do we determine the phylogenetic relationships between bacteria? Why is this method dependable for classifying all organisms? -with a phylogenetic tree or genome sequencing, based on rRNA sequences, analzye their genetic material, rRNA slow to change over time -universal basis for comparison, rRNA same function in all organisms What are the major phyla of Gram+ and Gram- bacteria? -negative: proteobacteria -positive: What are the five major classes of proteobacteria? What are some distinguishing characteristics of this phyla? -alpha, beta, gamma, delta, epsilon -largest taxonomix group of bacteria How can we distinguish between some of the intracellular alphaproteobacteria? -some are human and plant pathogen, live in ocean, intracellular parasite What's so interesting about Wolbachia? -most common infectious bacterial genus in the world -some host species cant reproduce or survive without Wolbachia colonization Important betaproteobacteria? Distinguishing characteristics? -Burkholderia: resistance to antibiotics, causes meliodosis, in soil or contaminated water -Bordetella: whooping cough -Neisseria: gonnorrhea, meningococcal meningitis Important gammaproteobacteria? Distinguishing characteristics? -pseudomonadales: resistant to most antibiotics, capable to grow in antiseptics -Legionellales: in water -vibrionales: in aquatic habitats, cholera Important Enterobacteriales bacteria (still part of gammaproetoacteria!) -E. Coli, Salmonella, Shigella, Klebsiella, Serratia, Proteus, Yersinia (Pest), Haemophilus Important epsilonproteobacteria? Similar and distinguishing characteristics? -Camplyobacter, Heliobacter Why are cyanobacteria important? -smallest known photosynthesizing organisms, blue-green algae -important for development of life on earth, first known organism to produce oxygen How are bacteria of the phylum Chlamydiae unique? -infective stage, unique developmental cycle Why are spirochetes unique? Important medically relevant bacteria? -spiral morphology, movement via axial filaments -Treponema, Borrelia, Leptospira How are Gram+ bacteria classified? >high G+C ratio >low G+C ratio Which bacteria have we talked about that form endospores? -clostridiales, bacillus Compare Clostridiales and Bacillales? -both can cause food poisoning Important Lactobacillales? -Lactobacillus, Streptococcus, Enterococcus, Listeria Why are Mycobacterium unique? -Cell wall has outer lipid layer of mycolic acids that is waxy and water resistant >acid fast, drug resistant, slow-growing, pathogenic What is the importance of Streptomyces? -produce most of our commercially available antibiotics Chapter 12 Why are eukaryotic infections difficult to treat? -because human hosts are eukaryotes too, target own body cells with drugs, toxic for humans What are some beneficial roles that fungi play? -decompose organic matter, help plants absorb nutrients, food for human, penicillin What are the defining characteristics of fungi? (i.e. what makes up their cell wall, how do they acquire nutrients, do they undergo aerobic or anaerobic respiration, how do they divide? What kind of environments do they prefer?) -chempheterotrophs, cell wall contains chitin, yeasts& molds, fungal spores germinate and form hyphae, vegetative and aerial hyphae for nutrients and reproduction, aerobic respiration, perfrom fermentation when no oxygen, budding yeasts divide unevenly, fission yeasts divide evenly, pH 5, high sugar and salt concentration, can grow in low moisture content What does it mean for a fungi to be dimorphic? What determines which form they take? -2 forms, yeast like and mold like phase, morphological changes induced by temperature, yeast at 37 degrees and mold at 25 degrees What are some medically important fungi we discussed? -mucoromycota= bread mold -ascomycota: aspergillus, penicillium, candida albicans -Basidiomycota: mushrooms -ringworm What’s an algal bloom? Why are they dangerous? -increases in planktonic algae that can result in toxin release What is a protozoa? What are their general characteristics? -unicellular eukaryotes, inhabit water and soil, animal like nutrition, complex life cycles Important protozoa to know: Toxoplasma gondii, Plasmodium spp. -toxoplasmosis, malaria What’s a helminth? What is the general lifecycle of helminths? Which stages can be infectious (varies depending on the type of worm)? -multicellular eukaryotic animals -parasitic helminths live in hosts -egg>larva>adult, humans infected by eggs What is the difference between a definitive host and intermediate host? Accidental host? Dead-end host? -definitive= organisms that supports adult or sexually reproductive form of parasite -intermediate= supports immature or non-reproductive form, vector to reach definitive host -dead-end= infectious agents are not transmitted to other susceptible hosts What are the two main phyla of platyhelminths? What are their common their names? -Tremetodes (flukes) and cestodes (tapeworms) What is a scolex? Proglottid? What is their purpose? =head that has suckers for attachment on a tapeworm, absorb food Proglottid= body segments contain male and female reproductive organs What is cysticercosis? Hydatid cysts? Why are these difficult to treat? -cysticercosis= eggs -Hydatid cysts= tapeworm -deep seated, complexity, immune response What are roundworms? What stage of these parasites are usually infectious? -free living and parasitic, cylindrical, complete digestive system, eggs are infective What’s an arthropod vector? What are some examples of arthropod vectors and the diseases they transmit? -animals with segmented bodies, hard skeletons and jointed legs -carry pathogenic microorganism; mosquito malaria, tick Lyme disease, spotted fever Chapter 13 What are the general and distinctive characteristics of viruses? How are they distinct from bacteria? ->Table -DNA or RNA never both, no ribosomes, very small, no antibiotic Viruses are diverse and have a wide host range; however most cells infect a specific cell type in a preferred host – why are viruses limited to specific hosts/cells? Hint: what’s the first step in viral infection of a cell? -determined by specific proteins on the virus and receptors on host cells, lock and key Virus structure: What is a virion? Capsid? Envelope? Spike projections? -virion= complete viral particle, capsid= protein coat, envelope= contains spikes What is the difference between an enveloped and a non-enveloped virus? - viruses that have lipid-bilayer membranes and those that lack them How can viruses be classified/organized/categorized? -virus nucleic acid and how its mRNA is produced What are the general steps of viral infection of a host cell? Does the process of releasing new virions differ depending if the virus is enveloped or non-enveloped? -attachment, entry, uncoating, biosynthesis, maturation, release -releasing: budding (enveloped) or rupture (nonenveloped) What are retroviruses? What is an example of a retrovirus? What is unique about how retroviruses replicate within a host cell (e.g. what enzyme do they use, what do they do with their nucleic acid material)? -need to first integrate their genomes into the host genome to begin replication -transcriptase, integrase, protease There are a very limited amount of viruses that cause cancers. Which viruses are oncogenic? -Epstein-Barr virus, Hepatitis B, HPV, HTLV-1 What is a latent virus? What are some examples of viruses that lay latent that we discussed? -remains in asymptomatic host cell for long periods, can be reactivated -HHV-1, HHV-2, HHV-3 Chapter 5 What is metabolism and what are some ways that humans benefit from microbial metabolism? -buildup and breakdown of nutrients within a cell -all the chemical reactions within a living organism -provide energy and create substances that sustain life What is the difference between catabolism and anabolism? How are catabolic and anabolic reactions linked? -catabolism breaks down complex molecules, releases energy -anabolism build molecules, requires energy What is a catalyst? Enzyme? How do we name them? -speed up reactions without being consumed or altered -enzymes are biological catalysts, always end in -ase What effect does an enzyme have on a chemical reaction? (e.g. activation energy, reaction rate, substrate) -reduced activation energy -increased reaction rate -specific binding of substrates What kinds of factors effect enzyme activity? -temperature, ph, substrate concentration, inhibitors What are the different types of enzyme inhibitors? How do they work? -competitive: fill active site of enzyme and compete with substrate -non competitive: interact with another site which interfered with enzymes function (allosteric) Why is glucose such a metabolically important molecule for organisms? - What is oxidative phosphorylation? What does it involve? -phoshoprylation of ADP with input of energy= generation of ATP Is ATP generated in the same way for all organisms? Or are there different mechanisms? -aerobic (uses oxygen) and anaerovic respiration (nitrogen, sulfur) What are the three major parts of carbohydrate catabolism? What is produced from each major step? -Glycolysis= 2 ATP and 2 NADH -Krebs cycle= -Electron transport chain= Where does aerobic respiration occur in prokaryotes? What is anaerobic respiration/fermentation? How is it different from aerobic respiration and what bi-products are produced? -by product: lactic acid, ethanol, CO2 -process that generates energy from carbs and does not require oxygen -small amounts of ATP Chapter 6 Be able to classify microbes based on their preferred temperature/pH range/osmotic pressure; what are some of the unique characteristics of microbes is these categories -psychrophiles, cold, 0-25 grad, cause food spoilage -mesophiles, moderate temperature -thermophiles, heat loving 50 bis 60 grad, hot springs, compost -hyperthermophiles, over 80 grad, archaea What does facultative/obligate mean? -obligate require high osmotic pressure -facultative tolerate high osmotic pressure What is the relationship between salt concentration and osmotic pressure? -high salt causes water to move out of the cell, osmotic pressure is proportional to solute concentration What are some important chemical requirements of microbes? -carbon, nitrogen,sulfur, phosphours, trace elements, oxygen Be able to classify microbes based on their oxygen utilization/tolerance; would you be able to identify the type of organism based on their growth in a tube of growth medium -obligate aerobes require oxygen -facultative anaeroves grow via fermentation or anaerobic respiration when no oxygen available -anaerobes unable to use oxygen Aerotolerant anaerobes tolerate but cant use oxygen -microaerophiles require oxygen concentration lower than atmospheric air Biofilms - what are they, why do bacteria form them, how does it benefit the bacteria/effect the host? -microbial communitites, form slime or gels that adhere to surfaces, bacteria in biofilms secrete an inducer to attract other bacterial cells, share nutrients, shelter Basic culturing concepts: agar, media (different types and how they are unique/useful - see table 6.5) -culture medium support microbial growth -agar= jelly like substance, polysaccharide How do bacteria divide? What is generation time? Can you calculate the number of cells that would result after a certain amount of time given the generation time? -binary fission: asexual reproduction, DNA doubles and divides, two identical daughter cells -budding= division following unequal cell growth -generation time= time a cell needs to divide Phases of bacterial growth: what is happening during each phase? On what scale do we measure bacterial growth? -Lag Phase: preparing for population growth, no increase in population -Log Phase: increase in population -stationary phase: period of equilibrium, balance of death and new cells -death phase: population decreasing Chapter 7 Terminology: what's the difference between asepsis, sterile, disinfected, antisepsis, sanitized, etc. (see table) -sepsis= bacterial contamination -asepsis=absence of significant contamination -sterile= all microbial life removed and distroyed -disinfected=detroy harmful microorganism -antisepsis= destroy harmful microorganism from living tissue Alteration or damage to what structures of the cell are important factors that impact microbial survival? -number of microbes, environment, time of exposure, microbial characteristics -alteration of membrane permeability, damage to proteins, damage to nucleic acids Sterilization methods: which methods kill endospores? What is the basic parameters of each method (e.g. autoclaving, dry heat, pasteurization, filtration, radiation, etc)? -autoclave kills endospores -pasteurization reduces spoilage, doesn’t sterilize -dry heat -filtration -radiation can kill endospores What two criteria are important when considering a chemical's effectiveness at disinfecting? -concentration of disinfectant, time What is a use-dilution test? What does it tell us? What is a disk diffusion test? What does it tell us? Can you interpret the results of a disk diffusion test? -evaluates efficacy of various disinfectant -see if bacteria survived treatment -disk= efficacy of antibiotics, filter paper, look for zone of inhibition Know the the broader categories of chemical disinfectants and how they affect microbes (i.e. membrane disruption, protein inactivation, etc.) -Bisphenols: disrupt plasma membrane: gram+ -Phenol: injure lipids of plasma membrane -Bisguanides: disrupts plasma membrane -essential oils -Halogens like Iodine Why do alcohols need to be dissolved in water to be effective? -pure ethanol is ineffective Chapter 20 What is an antibiotic? Specifically, how are they produced? -metabolic products of bacteria and fungi, target different structures Identify five modes of action of antimicrobial drugs (i.e. what are they're targets?) -cell wall, plasma membrane, DNA synthesis, ribosomes, metabolic pathways Explain why isoniazid and ethambutol are antimycobacterial agents -mycobacterium contains mycolic acid, isoniazid inhibits bacterial synthesis of mycolic acid, ethambutol inhibits incorporation of mycolic acid into the cell wall