Microbiology Study Guide 1 PDF

BIOLOGY 260 MICROBIOLOGY STUDY GUIDE FOR THE FIRST LECTURE EXAM Spontaneous Generation Vs. Germ Theory of Disease ​ Spontaneous generation (Abiogenesis) living things came from non-living things ○​ rats from old clothes ○​ worms from rotten meat ○​ microbes f...

BIOLOGY 260 MICROBIOLOGY STUDY GUIDE FOR THE FIRST LECTURE EXAM Spontaneous Generation Vs. Germ Theory of Disease ​ Spontaneous generation (Abiogenesis) living things came from non-living things ○​ rats from old clothes ○​ worms from rotten meat ○​ microbes from broth ​ Germ theory of disease ○​ Living things come from other living things ○​ germs (animalcules) can invade other organisms and produce diseases ​ Redi’s Experiment ○​ 17th century ○​ Italian physicist ○​ 3 jars open, covered w/gauze, and sealed ○​ proved maggots came from flies, not the meat ​ Spallanzani’s Experiment ○​ 17th century Italian priest/scientist ○​ studied microbial growth on broth ○​ Cloudy broth = microbial growth ○​ proved microbes did not come from broth ○​ disproved abiogenesis ​ Pasteur’s Experiment ○​ 1859, French chemist ○​ swan neck flask experiment ​ Tyndall’s experiment ○​ late 1800s ○​ sealed flask experiment with boiled broth in a box ○​ air can be sterilized by settling the dust particles that carry microorganisms “Dust is the magic carpet ride for microorganisms” Works of some scientists that have direct impact to Microbiology (e.g., Leeuwenhoek, Pasteur, Koch, Lister & Semmelweis, Ehrlich, etc.) ​ Antoine Van Leeuwenhoek ○​ 1676 ○​ invented microscope (300x magnification) ○​ discovered microbial world (animalcules) ​ Louis Pasteur ○​ Father of microbiology ○​ 1857-1876 ○​ discovered anaerobic life and role of microbes in fermentation  ○​ developed “Pasteurization” process for beer and wine (for wine 56C without O2 for 30 minutes) ○​ Identified microbes that cause disease in silkworms ○​ developed first effective rabies vaccine ​ Robert Koch ○​ 1876-early 1900 ○​ demonstrated that anthrax in humans and cattle is caused by bacteria ○​ first to isolate bacteria in cultures using plates ○​ first to develop agar ○​ identified TB bacteria and developed staining method ○​ isolation of cholera causing bacteria ○​ Offered the first microbio course (Berlin) ○​ First to study malaria, typhoid fever, sleeping sickness ○​ Koch’s Postulates - series of steps to prove that an organism is the true cause of a disease) ​ Semmel Weis ○​ Austria mid 1800s ○​ First to implement sanitary practices in maternity wards to avoid puerperal fever ○​ asked interns to wash hands between morgue and maternity ward ○​ requested surgical tools to be cleaned in chlorine based disinfectants ○​ Criticized as being paranoid -> weak personality -> mental breakdown -> sent to asylum -> death at 47 ​ Lister ○​ England 1865 ○​ Developed procedures for surgical antisepsis using carbolic acid ○​ Criticized, but Continued work regardless ○​ Had more patients successfully recover than other surgeons ​ Paul Ehrlick ○​ 1878 ○​ Initiated search for “magic bullets” chemicals that target pathogens and not the host ○​ Father of chemotherapy ​ Fleming ○​ Discovered first antibiotic - penicillin ○​ Soldiers put moldy bread in bullet holes - led to accidental discovery Major Groups of microbes (characteristics, how they are similar/different) ​ Microbes: Organisms with a diameter of 1mm or less ​ Bacteria ○​ Single cell ○​ Prokaryotes: cell with no nucleus ○​ divide by binary fission (no division of nucleus) ○​ Motile/non motile, photosynthetic/nonphotosynthetic, aerobic/anerobic/facultative anaerobes (shift so anaerobic when O2 is not present, ex:coliforoms like E coli)  ○​ Average size 0.5-2.0 micrometer (1000 micrometer = 1 mm) ○​ Shapes ​ Spherical - round - coccus ​ Rod-shaped - rods - bacillus ​ Spiral - spiral - spirillum ​ Star ​ Square ​ Filamentous (source of antibiotics) ​ Pleomorphic - assumes several shapes, no cell wall (x,y,v forms) ​ Protists ○​ Mostly unicellular ○​ Eukaryotes: cells with a nucleus ​ Algae: plant like protists, usually aquatic and photosynthetic ​ Volvox ​ Diatom ​ Protozoa: animal like protists, most capable of movement ​ Amoeba ​ Fungi: mostly multicellular eukaryotes with filamentous bodies. Usually spore bearing, generally non motile, non photosynthetic ​ Yeasts (unicellular, reproduce via budding) ​ Molds ​ Mushrooms ​ Viruses ○​ Difficult to target with drugs ○​ Submicroscopic - can’t be seen with compound microscope (light based) ○​ Acellular - not a cell ○​ composed of nucleic acid, either DNA or DNA, not both ○​ Protein coat ○​ Always obligate parasite - requires live host to replicate ​ HIV ​ CoronaVirus ​ Helminthes ○​ nematodes ○​ Pathogenic worms ​ Arthropods - biological vectors of diseases ○​ Insects ○​ Mites ○​ Ticks ○​ Mosquitos ​ Ades, Anopheles, Culex (genera that carry human diseases) ​ Attracted to CO2 Importance of Microbes to Man and Ecosystem (know some) ​ Serve as agents of human plant and animal diseases  ○​ only 1% of known microbes cause disease ​ Decomposers and clears of environment ○​ recycle vital elements ○​ fungi and bacteria used to clean up oil ○​ Algae used as nuclear waste cleaners, can remove Strontium 90 from radioactive waste water ○​ Methanogens - bacteria that cleans sewer water and produces methane ​ Form symbiotic relationships with other organisms ○​ Cellulose degrading bacteria in the stomach of ruminants (cows) ○​ Nitrogen fixing bacteria in soil and root nodules convert N2 to ammonia ​ Mycorrhizal fungi absorb phosphorus and other nutrients for plants ​ Microbes are consumed directly as food by other organisms ○​ mushrooms and algae consumed by humans ​ Used in production of food and beverages ○​ Yeasts - beer, wine, bread ○​ Bacteria - yogurt, cheese, pickles, tofu ○​ xanthan gum - bacterial slime used as thickener for ice cream and chocolate ○​ Fungi - blue cheese ​ Source for antibiotics and other pharmaceutical products ○​ Penicillin from fungus ○​ Streptomycin from bacteria ○​ Botox from botulism bacteria ​ Major tools of genetic engineering ○​ used to produce insulin, hormones, and vaccines ○​ recombinant DNA technology ​ Excellent tools for research ○​ Simple structures, easy to study ○​ fast growth rates, get results in a short period of time ○​ can be mass-produced as a reasonable cost (vs lab animals) Classic Diseases and causal agents ​ Covid 19 (SARS COV 2) ○​ Highly contagious ○​ Droplet transmission ​ Bubonic plague/black death (bacteria Yersinia pestis) ○​ killed 25 million in European 14th century ○​ lasted 300 years due to lack of knowledge ○​ considered a punishment from god ​ Smallpox (virus) ○​ caused worldwide death and migration of people ○​ can live for 10 years in pustules ○​ Airborne ​ Influenza (virus) ○​ Claimed about 20 million lives  ​ Cholera (bacterium Vibrio cholera) ○​ One of the main causes of death in 3rd world countries ○​ transmitted via polluted water ​ AIDS (virus) ○​ considered one of the cruelest diseases ​ SARS (SARS COV 1) ○​ less transmittable than covid 19 ​ Mad cow disease (prions - infectious proteins) ○​ impacts beef import/export ○​ changed eating habits ​ Potato blight (fungus Phytophthora infestans) ○​ Irish potato famine ○​ starved over 1 million Irish people who fled to US ​ Coffee rust (fungus Hemilea vastatrix) ○​ wiped out coffee plantations in Sri Lanka ○​ British people switched from coffee to tea drinkers Different branches of Microbiology ​ According by type of microbe ○​ Bacteriology - bacteria ○​ Mycology - fungi ○​ Virology - virus ○​ Phycology - algae ○​ Parasitology - parasitic worms and arthropods ​ According to application ○​ Medical - ID and control of infectious disease ○​ Food - production of safe food and beverages, FDA recalls ○​ Environmental - boil orders, control of industrial wastes ○​ Agricultural - GMO, microbial fertilizers, biocontrol agents ○​ Pharmaceutical - Botox, vaccines, antibiotics ○​ Biotechnology - gene manipulation to produce products of human importance Differences/Similarities between Prokaryotes and Eukaryotes ​ Prokaryotic ○​ “pro”=before; before-nucleus ○​ Bacteria and archaea(monera) ○​ Single celled ○​ Small (0.3-2.0 μm) ○​ Cell wall made of peptidoglycans (protein-sugar complex) ○​ Cell division via binary fission ○​ No membrane bound cytoplasmic organelles ○​ Small 70s ribosomes (50s and 30s subunits) ​ Eukaryotic ○​ “Eu”=true; true-nucleus  ○​ Protists, fungi, plants, animals ○​ Mostly multicellular (protist and yeasts exceptions) ○​ Large (5-50 μm) ○​ Cell wall made of cellulose(plants)/chitin(fungi)/none(animals) ○​ Cell division via mitosis and/or meiosis ○​ Membrane bound cytoplasmic organelles (nucleus, mitochondria) ○​ Large 80s ribosomes (60s and 40s subunits) ​ All cells ○​ Cytoplasm - proteins, water, salts, the egg white ○​ Plasma membrane (cell membrane) - thin semi permeable membrane that surrounds cytoplasm ○​ DNA - genetic materia (bacteria have no nucleus) ○​ Ribosome - site of protein synthesis Functions of the different parts of Prokaryotic Cells. Know functions of all parts but most especially, cell membrane structure & unique functions in bacteria Endospore (characteristics, components, what genera of bacteria produce it, why is it a survival structure) ​ Bacteria chromosome - DNA bundled with proteins, NO membrane ​ Plasmid - extra DNA outside of chromosome, not found in all bacteria. R-plasmids: antibiotic resistance ​ Inclusion bodies (food granules) - bacterial fat, storage granules contain glycogen, gas vesicles contain air for aquatic photosynthetic bacteria ​ Endospore - Present in only 2 genera (Bacillus and Clostridium)- rare. Contains Ca and DPA (dipicolinic acid) - used for testing autoclaves ​ Ribosomes - site of protein synthesis ​ Pilus - Thinner and shorter than flagella; Fimbriae (short, used for attachment to surfaces), “F” pilus or conjunction pilus (longer, used for transfer of DNA between bacterial cells) ​ Prokaryotic flagellum - structure for locomotion; made up of protein “flagellin” and has a wavy structure ​ Capsule/slime layer - “glycocalyx” shields cell from drugs, antibiotics, and host defenses ​ Cell wall - structural support and protection from bursting due to osmotic pressure ○​ Gram positive - 60-90% peptidoglycan ○​ Gram negative - 10-20% peptidoglycan, Lipid A endotoxin layer (lipopolysaccharides) = plastic layer more resistant to chemicals/drugs/antibiotics ○​ Acid fast - NH4 ammonia) ○​ Spirochetes ​ Long spiral bacteria ​ Syphilis and Lyme disease (white tail deer host -> tick -> early arthritis in kids from overactive immune response) ○​ Mycoplasmas ​ Only bacteria without cell walls (naked bacteria) ​ Fastidious (picky eaters)  ​ Hard to grow in artificial medium ​ Walking pneumonia ○​ Chlamydia and Rickettsiae ​ Obligate parasites - can’t live outside host - can’t be cultivated ​ Thought to bee viruses ​ Chlamydia - only true bacteria without peptidoglycan - not an extremophile, so not archaea ​ Domain Eukarya ○​ Kingdom Protista ○​ Kingdom Fungi ○​ Kingdom Plantae ○​ Kingdom Animalia Domain Archaea Vs. Bacteria Methanogens, Thermophiles, Halophiles Mycoplasma, Chlamydia & Rickettsiae, Spirochetes Parts & Functions of Eukaryotic Cell - Universal components of cells = cytoplasm, cell membrane, DNA, ribosomes (virus/viral particles - no cytoplasm, nucleic acid enclose in protein coat = not a cell = not an organism = not alive) ​ Nucleus ○​ Nucleolus - RNA and proteins ○​ Nuclear chromatin - DNA and proteins ○​ Nuclear pore - holes in nuclear membrane that allows certain substances to pass ​ Mitochondria ○​ Site of ATP production ○​ Has its own circular DNA - inherited from mother only - probably evolved from bacteria cell, similar shape, membrane ○​ Inner membrane - highly folded ○​ Outer membrane - not folded ○​ Matrix - gelatinous material ○​ Cristae - compartment in the inner membrane ​ Cell membrane ○​ Similar to prokaryotic cell membrane ○​ Semi-permeable membrane ​ Cilia ○​ For movement, shorter but more numerous than flagella ○​ Made up on microfilaments and microtubules ​ Microfilaments ○​ Thin ○​ Assist with cytoplasmic movement ○​ Made of protein called “acid filaments”  ○​ Part of cytoskeleton, keep organelles in place ​ Microtubules ○​ Thick ○​ Form spindle to help with separation in mitosis and meiosis ○​ Part of cytoskeleton, provide support ○​ Make up structure of flagella and cillia ​ Centrioles (animals only) ○​ Help organize microtubule assembly called “spindle apparatus” ○​ Involved in orderly cell division ○​ Cells without centriole divide abnormally ​ Golgi bodies/apparatus - “Post office of the cell” ○​ Final modification of lipids and proteins ○​ Packaging, sorting-out, and distribution of materials throughout cell ​ Smooth endoplasmic reticulum ○​ No ribosomes attached ○​ Lipid synthesis and degradation ○​ Calcium ion storage ​ Rough endoplasmic reticulum ○​ Ribosomes attached ○​ Site of protein synthesis ​ Lysosome ○​ Contain digestive enzymes for degradation of old cell parts and microorganisms ​ Peroxisome ○​ Breakdown of lipids and detox of chemicals; ex, hydrogen peroxide, superoxide Kingdom “Protista” (not a plant, animal, or fungus - biologist dump site)- how are they classified ​ Unicellular eukaryotes (some multicellular) ​ Groupings based on mode of locomotion Plant-like Protists how they differ, examples - “Algae” ​ Euglenids (Euglenoids) ○​ Motile by single flagellum ○​ Pigmented eyespot to detect light ○​ Major producers in aquatic environments ​ Diatoms ○​ Non-motile ○​ Glass like appearance due to silica in cell wall ○​ Used in industry; abrasives for toothpaste, gloss for paint, diatomaceous earth ​ Dinoflagellates (dinos = whirling motion) ○​ Motile w/2 flagella; transverse groove/belt; other extended like tail ○​ Red tide algae - produce potent neurotoxin (saxitoxin) Animal-like protists- how they differ, examples - “Protozoa” ​ Amoeba - Loboseans/Sarcodina  ○​ Move by pseudopodia (false feet, cytoplasmic extensions) ○​ No definite shape - no cell walls ○​ Bottom of ponds, contaminated water ○​ Entamoeba histolytica - parasitic, can cause dysentery ​ Trypanosomes - Mastigophora ○​ Motile by one or more flagella ○​ Free-living or pathogenic ○​ Giardia (diplomonads) - flagellated protists w/o mitochondria (ATP production in mitochondria-like organelle); 2 nuclei; contaminated water; cause of “camper’s diarrhea” ○​ Trichomonas (parabasaplastids) - flagellated w/o mitochondria; have hydrogenosome - produces ATP while generating hydrogen; can cause vaginal infection ○​ Trypanosoma (kinetoplastids) - motile by at least one flagellum; large single mitochondria w/complex DNA; African sleeping sickness ​ Sporozoans/Apicomplexans (Plasmodium) ○​ Non-motile w/complex life cycle usually w/biological vector/carrier ○​ Parasitic - apical complex to penetrate cell membrane of host ○​ Shape indicates species ○​ Plasmodium - causes malaria; spread by mosquitoes ​ Ciliates (Paramecium) ○​ Move by cilia all over cell ○​ Largest group of protozoa that are involved in cleaning the environment ○​ Paramecium - slipper shaped ○​ Balantidium - only pathogenic ciliate; diarrhea Kingdom Fungi- How they are classified, differences between groups, examples ​ Mostly multicellular, filamentous, spore bearing, non-photosynthetic ​ Chitin cell wall ​ Mycelia - thread like structures, individual=hyphae ​ Classification based on sexual structures ​ Mycoses - diseases caused by fungi ​ Zygomycetes (molds) - sexual spores survive adverse environments; can cause food spoilage; may produce carcinogenic substances ​ Basidiomycetes (club-fungi) - sexual spores borne in club-like structure (basidiophore); many edible; some toxic/hallucinogenic; ex:Amanita muscaria, Amanita virosa, Ustilago maydis (corn smut) ​ Ascomycetes (sac-like fungi) - sexual spores borne in sac-like structure, usually 8 spores in a sac; ex: rye smut fungus, morels, cup fungi, apple scab pathogen, penicillium, yeasts, Aspergillus flavus (pathogenic fungi to nuts/grains/peanut butter, produces aflatoxin, can cause liver cancer) ​ Deuteromycetes (Fungi Imperfecti) - “imperfect fungi” because sexual stage has not been found; “transition group” once sexual stage is found, it becomes ascomycetes or  basidiomycetes; ex:Arthrobotrys (strangulates nematodes, now ascomycetes), microsporum canis (ringworm), Aspergillus niger (black mold) Binary fission- How is it different/similar to mitosis (eukaryotes) ​ Prokaryotic organisms like bacteria; no nucleus; no mitosis/meiosis ​ Prokaryotes (mitosis = eukaryotes only) ​ Few eukaryote exceptions (yeast, protozoa) ​ Cells divide into 2 genetically identical cells (same as mitosis) ​ DNA attaches to cell membrane prior to binary fission ​ No spindle apparatus to organize chromosomes ​ No stages (PMAT = mitosis only) 1.​ Attachment DNA to membrane 2.​ DNA replicates 3.​ Cell membrane and cell walls grow 4.​ Cell membrane/wall material starts growing through midsection (septum) 5.​ Cytoplasm divided in two, 2 new cells formed 6.​ Favorable condition = back to step 1 7.​ Unfavorable conditions for growth = endospore formation after step 3 (sporulation) (Bacillus and Clostridium only) (not reproductive; only in adverse conditions, metabolically inactive, not multiplying 1:1 ratio) Spore formation- What triggers sporulation and vegetative growth (binary fission) ​ Bacillus and Clostridium only ​ Triggered; exhaustion of nutrients, accumulation of toxic metabolites, drought, high temp, extreme ph ​ Asymmetrical division ​ Double membrane around endospore ​ Peptidoglycan layer forms between membranes ​ Disintegration of mother cell = layers of Ca and dipicolinic acid, spore coat made of keratin ​ Endospore will germinate in favorable conditions Bacterial Growth Curve- What happens in each phase ​ Lag phase ○​ Period of adapting to environment ○​ No increase in population ○​ Cells increase in size to prepare for cell division ○​ Cells synthesize enzymes, need large amounts of ATP for growth ○​ Agar medium = sample transferred to fresh medium ​ Log phase ○​ Exponential growth ○​ Most active metabolically; antibiotics will have greatest effect ○​ Generation time (time to double population) determined ○​ Lab culture e. Coli generation time = 15-20 minutes  ○​ Intestinal tract = 12-24 hours ​ Stationary phase​ ○​ Period where # live cells = # dead cells ○​ Depletion of nutrients starts ○​ Toxic metabolites accumulate ○​ Space becomes limited ○​ Endospores form ( can see endospore location) ​ Death & decline phase ○​ Cells lose ability to divide ○​ # dead cells increases ○​ Some cells assume unusual shapes (involution) ○​ Endospores more abundant than cells ○​ Gram stain = erroneous pink/purple mixed results; only free endospores observed, majority of cells have died 3 Mechanisms of Gene Transfer in Bacteria ​ Not sexual reproduction ○​ No fertilization/union of gametes ○​ No zygote (offspring) created, instead cells are genetically altered ○​ Gene transfer can occur between unrelated species ​ Transformation ○​ Small pieces of “naked DNA” in the environment are taken-up by bacterial cells ○​ Occurs at only certain growth stages (ex: before completion of cell wall) ○​ Plasmids and parts of chromosome from dead cells -> host cell ○​ Plasmids and cells both have negative charge = repelled away from each other ○​ In labs, transformation is enhanced by treating cells with Mg or Ca to bridge between cell and new DNA and make cells “competent” (susceptible to transformation) ○​ Can be successful (integration of nonreciprocal recombination) or fail (degradation) ○​ Transformation with DNA fragment = resistance to only one antibiotic ○​ Transformation with plasmid = resistance to 1-6 antibiotics ​ Transduction ○​ DNA is transferred by bacteriophage (virus that infects bacteria) ○​ Bacteriophage = host specific ○​ Phage injects DNA into first host ○​ Phage enzymes degrade host DNA ○​ Cell makes new phages, some phages have DNA from host (transducing phage) ○​ Transducing phage attaches to second host, injects DNA ○​ Doner DNA incorporated into recipients chromosome via recombination ○​ Frameshift mutation ​ Conjugation (bacterial mating) ○​ Direct transfer of DNA between bacteria via conjugation pilus (F-pilus) ○​ Typically between 2 related bacteria, but unrelated bacteria can also mate  ○​ Contact between donor and recipient required ○​ Larger DNA segments can be transferred - chromosome(frameshift mutation) or plasmid ○​ R plasmids (antibiotic resistance) easily transferred via mating; host can take up as much as 10 R plasmids ○​ Chemical signals called “bacterial pheromones” are believed to be involved Anabolic vs. Catabolic reactions ​ Metabolism: sum of all chemical changes that take place in living organisms ​ Catabolic - Something is broken to release energy (catastrophe) ○​ Degradative pathway ○​ Big molecules broken down into smaller ones ○​ Chemical bonds broken ○​ Exergonic: (exo=exit, onic=energy) energy-releasing pathway ○​ Ex; breakdown of glucose into CO2 and H2O with release of energy (ATP) ​ Anabolic - put things together using energy, sometimes for storage ○​ Synthetic pathway (synthesis=put together) ○​ Simple molecules combine to form complex bigger ones ○​ Chemical bonds created ○​ Endergonic: (endo=in, onic=energy) input of energy is required ○​ Ex; amino acids being linked together by peptide bonds to for proteins through dehydration synthesis Enzymes- how they work, denaturation, how inhibitors work ​ Enzymes = catalysts: speed up chemical processes without being used up in the process ​ Very specific; only act on a certain substrate ○​ Ex: Sucrase breaks down sucrose only, not any other substances ​ Namt typically ends in “ase” along with specific substrate name ​ Specificity is due to the shape of the active site where the substrate binds ​ Shape of the substrate compliments the shape of the active site; “lock and key” relationship ​ Almost all enzymes = proteins: must maintain shape to function (biologically active) ○​ Primary structure = sequence of amino acids in the chain ○​ Secondary structure = coiling of structure into helix/sheet ○​ Tertiary structure = final 3D shape of polypeptide chain after bending and folding ○​ Quaternary structure = combination of multiple polypeptide chains ​ Denaturation: the destruction of the tertiary (3D) structure of proteins; loses biological activity; can not be undone; physical factors ○​ Extreme temperature; ex: human body normal temp 98.6 F, enzymes and death occurs at 109.4 F; heat foods to eat safely ○​ Extreme pH; too many H+ or OH- may distort shape of enzyme; most bodies work at near neutral pH; body needs buffer systems; vinegar to preserve foods  ○​ Extreme ionic concentration; too many + or - ions bind to amino acids and distort the shape; ex: too much salt = denatured enzymes; salt to cure meat ​ Enzyme inhibitors = substances that prevent the formation of enzyme/substrate complex; can be temporary; chemical factors ○​ Competitive inhibitors: Binding to active site; similar shape to substrate; binds to active site, blocking substrate; some antibiotics work as competitive inhibitors ○​ Non-competitive inhibitors: Binding to site other than active site to change the shape of the enzyme; substrate can’t bind due to lack of fit