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MMiPeople Francesco Redi: scientist who tested spontaneous generation with rotting meat and maggot formation with an open container, sealed container, and gauze-covered container, and refuted spontaneous generation Needham: scientist who tested spontaneous generation with boiling chicken broth, sealing the container, and waiting a few days to assess for microbial growth, and supported spontaneous generation Spallanzani: scientist who tested spontaneous generation with further testing, Needham’s experiment, and tested with an open and closed container that was later opened, and refuted spontaneous generation Louis Pasteur: scientist who used swan-neck flasks in his experiment and definitively refuted spontaneous generation Anthony van Leeuwenhoek: scientist who was the first to observe eukaryotic microbes, calling them “wee animalcule” Robert Hooke: coined the term “cell” when looking at cork Matthias Schleiden: observed cells in plant tissue Theodor Schwann: observed cells in animal tissue Rudolf Virchow and Robert Remark: observed cells dividing to make new cells (not mitosis) Hippocrates: suggested disease has natural causes Thucydides: advocated for evidence-based analysis of cause and effect and suggested immunity after observing plague survivors didn't get sick again Marcus Terentius Varro: the first to propose that things we cannot see cause disease Ignaz Semmelweis: physician who observed the spread of disease among patients in different sides of the hospital and instituted hand washing between patients to reduce the spread of disease from patient to patient via healthcare workers Joseph Lister: surgeon who observed post-surgical infection and instituted hand washing and sterilization of medical equipment with 5% phenol solution for less disease Robert Koch: scientist who developed Koch’s postulates to determine the cause of disease and had a rivalry with Louis Pasteur John Snow: questioned the London cholera outbreak and asked questions to the people who had been infected about where they had been and what they had eaten or drank, and noticed that everyone who had cholera used one of two water pumps Classification of microbes What are the 2 domains that are composed of all microbes? Bacteria and Archaea What domain of life is composed only of some microbes? Eukarya What types of microbes do not fit into the domains of life? Viruses and Prions Prions: unicellular organisms in the domains Bacteria and Archaea with no nucleus and have cell walls Viruses: acellular and domainless (not alive) Eukaryotes: unicellular OR multicellular organisms, in domain Eukarya, have a nucleus, have membrane-bound organelles, and include fungi, algae, protazoa, and helminths How many times bigger are bacteria than viruses? 100x A cell is around how many times bigger than an individual bacteria? 10x Cell structures Know the function, general location, and whether they are shared with eukaryotes (if yes similarities/differences) of the following structures: 1. Nucleoid: contains chromosome(s) and nuclear-associated proteins that are usually haploid and circular near the center of the cell, which hold the DNA genetic information without a membrane Eukaryotes = have a nucleus, are diploid and linear Prokaryotes = have nucleoid, are haploid and circular 2. Ribosomes: work with mRNA protein synthesis, made up of proteins and RNA, found in cytoplasm Eukaryotes: 80S, 60 large, 40 small (18S sequencing) Prokaryotes: 70S, 50 large, 30 small (16S sequencing) 3. Cytoplasm: fluid inner layer 4. Fimbriae: short, bristle-like projections for attachment to surfaces 5. Endospores: not all bacteria have, protect bacteria in a dormant state/ harsh environment, found inside bacteria, sporulation = the process of becoming dormant, germination = process of becoming active 6. Plasma membrane: semipermeable, composed of lipids and proteins, controls transport into and out of cell, most inner layer before cytoplasm (ex: facilitated diffusion, active transport, diffusion, endocytosis (Eukaryotes), sterols (Eukaryotes), and cholesterol (Eukaryotes) Same for Eukaryotes 7. Cell wall: protects against harsh changing environments and osmotic stress, contains peptidoglycan in bacteria, contains Gram + and Gram - Steps of Gram stain: dye with crystal violet, iodine (mordant), alcohol (decolorizer), and safranin red If mycobacteria complete an acid-fast stain Gram + has LTA an TA and one membrane Gram - has LPS and 2 membranes 8. Capsule: protective protein shell, outermost layer 9. Pilus: medium projection, adheres to surfaces, does DNA gene transfer 10. Flagellum: long protein projections made of flagellin for movement (ex: 1= monotrichous, one at each end = amphitrichous, many at one end = lophotrichous, many flagella all over the cell = peritrichous 11. Plasmid: circular, double-stranded DNA not part of the chromosome, and can have 1-100 of the same or different plasmids to help with gene transfer, antibiotic resistance, and virulence factors, found anywhere in the cytoplasm Not part of Eukaryotes 12. Inclusion: not all bacteria have, helps with the storage of nutrients and other materials, has protein shell, and is found in cytoplasm (ex: lipid droplets store fats, volutin stores inorganic phosphates, sulfur inclusions store sulfur, gas bubbles store gas for buoyancy in water, magnetosomes store metals for movement) Not part of Eukaryotes; instead, they have vesicles for storage All cellular microbes have what four (4) components? Cell Membrane, Cytoplasm, Ribosomes, and DNA What is the only component of all cells that viruses have? Cytoplasm Know/ be able to identify the shapes of bacteria Round shape: coccus Rod shape: bacillus Vibrio: curved rod shape Short rods with combo of coccus and bacillus: coccobacillus Wavy spiral shape: Spirillum Coiled spiral shape: Spirochete Microbial growth Phases of growth Lag Phase: bacteria gear up for replication by increasing cell size, metabolism, and protein synthesis Log Phase: exponential growth phase, where bacteria actively replicate and are most susceptible to antibiotics Stationary Phase: growth curve flatlines bc bacteria are dying at same rate of growth, begin survival mode and sporulation, produce secondary metabolites, and produce virulence factors, and are low on space, nutrients, and oxygen Death Phase: bacteria die at exponential rate, increase amount of toxic waste, release spores, some spontaneously lyse to feed others, and persister cells refuse to die How do microbes replicate? Through binary fission, fragmentation, budding, and sexually What is a biofilm? Communities of bacteria (steps: colonization, attachment, replication, make EPS with antibiotic resistance, EPS kick bacteria out to replicate somewhere else) How does quorum sensing work? Bacteria want to work together, so they secrete autoinducers, and when you activate enough receptors, they activate a response Growth requirements – classifications and adaptations 1. Oxygen requirements Obligate Aerobes: need O2 to survive Obligate Anaerobes: die in presence of O2 Faculative: mostly need O2 but can survive without it Microaerophiles: need O2 for survival but not atmospheric O2 (low levels) Aerotolerant: can survive with or without oxygen Capnophiles: like high CO2 and low O2 2. pH requirements Acidophiles: low pH (2-4), high H+ environments, efflux pumps to remove H+ ions, changes membrane composition to withstand low pH Neutrophiles: neutral pH (7), found within body Alkaliphiles: basic pH (9-10), modified lipid protein structures, modified electron transport system that use Na+ instead of H+, high OH- environment 3. temperature requirements Psychrophiles: like freezing temperatures a below 0-15 degrees, die at or above 20 degrees, found in cold lakes or the ocean floor, have hydrophobic proteins to increase flexibility, have decreased secondary stabilizing bonds Psychrotolerant: cold not ideal but wont kill them, live between 4-25 degrees (fridge temperature) Mesophiles: moderate temperatures, 20-40 degrees, grow in body Thermophiles: hot environments 50-80 degrees, hot springs, geothermal soil Hyperthermophiles: very hot environments 80-110 degrees, found in hydrothermal vents, increased saturation in membranes, increased stabilizing bonds, alter amino acids to prevent denaturation 4. osmolarity requirements Hypertonic: more water out Hypotonic: more water in Isotonic: equal water in and out Halotolerant: dont require salt but can grow in high salt environments Halophiles: love salt, found in ocean and salt lakes, have increased cytoplasmic glycerol, have efflux pumps for salt 5. barometric requirements Barophile: survive high atmospheric environments like the bottom of the ocean (something at top of mountain has low atmospheric pressure) Microbial Metabolism Means of generating energy (do the processes require oxygen?, which gives the most energy?) Glycolysis: does not require O2 bc it can be used during fermentation, used 2 ATP, makes 4 ATP, NET 2 ATP Kreb’s cycle: requires O2; NET after 1 round= 1ATP, 1 NADH, 1FADH2 (x2 for second round) Electron transport: requires O2, biggest payout of ATP with NET 34 ATP Photosynthesis: does not require O2 as it is a waste product, can do oxygenic and anoxygenic Microbial genetics DNA Replication – enzymes and functions DNA gyrase: unwinds DNA (enzyme) Helicase: unzips DNA (enzyme) Single-stranded binding proteins: bind to DNA so doesnt close back up (protein) Single-stranded binding proteins: bind to DNA so doesnt close back up (protein) DNA polymerase III: lay down new DNA nucleotides, synthesizes leading and lagging strands 5’ →3’(enzyme) DNA polymerase I: removes RNA primers (enzyme) DNA Ligase: seals RNA primers (enzyme) Topoisomerase 4: separates 2 circular chromosomes Transcription and translation – enzymes and function 1. RNA polymerase: turns DNA→ mRNA (transcription) 2. Ribosomes: 30S small, 50S large, 70S total 3. tRNA: A,P, and E sites, bacteria links transcription and translation bc no nucleus, has anticodon at opposite long 3’ end, high energy bond, same active translation process as Eukaryotes Be able to do DNA base pairing, transcription, and translation (given codon table) Also know differences between prokaryotic and eukaryotic Replication, transcription, and translation Genetic Diversity – how does this work? 1. Transformation: uptake of plasmid into different bacteria and is incorporated into its genetic material 2. Transduction: bacteriophage inserts its plasmid into a bacteria (virus that infects a bacteria) 3. Conjugation: like plasmid transfer (ex: rolling circle replication), “bacterial sex” 4

Objectives come from your Unit 3 sheet and the content/examples come from the PowerPoints . ⸻ UNIT 3 COMPLETE STUDY GUIDE (Based strictly on your slides + objectives) ⸻ CHAPTER 11 — CONTROLLING MICROBIAL GROWTH Difference Between Antisepsis, Disinfection, Sanitization, Sterilization, Degerming, Decontamination Sterilization Complete destruction of all microbial life including viruses and endospores. Examples from slides: • Surgical instruments • Syringes • Packaged foods Endospores must be destroyed for something to be considered sterile. ⸻ Disinfection Destroys most vegetative pathogens on nonliving surfaces. Examples: • Disinfecting medical equipment • Hospital surfaces ⸻ Antisepsis Use of antimicrobial chemicals on living tissue. Examples: • Skin prep before surgery • Cleaning wounds ⸻ Degerming Mechanical removal of microbes by scrubbing. Example: • Handwashing ⸻ Sanitization Reduces microbial numbers to public health safe levels. Examples: • Cleaning food preparation surfaces • Restaurant sanitation ⸻ Decontamination General removal of microbes from objects or surfaces. Example: • Cleaning contaminated hospital equipment ⸻ Difference Between Static and Cidal Cidal Kills microbes. Example Bactericidal antibiotics. ⸻ Static Stops growth but does not kill. Example Bacteriostatic antibiotics. ⸻ Variables That Influence Effectiveness of Antimicrobial Methods 1. Population size Large populations require more time to kill. 2. Nature of microbes Some microbes are more resistant. Example: Bacterial endospores. 3. Temperature Higher temperature increases killing. 4. Concentration of agent 5. Contact time 6. Organic matter present Example: Blood or mucus interfering with disinfectants. 7. Mode of action of agent 8. Biofilms Biofilms protect microbes from antimicrobials. ⸻ Most Resistant vs Least Resistant Microbes Most resistant: Bacterial endospores Reason: Thick protective layers. ⸻ Less resistant: • Mycobacteria • Gram-negative bacteria • Gram-positive bacteria • Fungi • Viruses Endospores are the target of sterilization methods. ⸻ Mechanisms of Antimicrobial Agents Agents work by damaging: Cell wall Example Detergents and alcohol disrupt cell wall. ⸻ Cell membrane Effects • Loss of permeability • Leakage of molecules ⸻ Proteins Agents denature proteins. Examples • Heat • Alcohol • Strong acids ⸻ DNA and RNA Example Radiation damaging DNA. ⸻ Practical Concerns When Choosing Control Method Consider: • Does item require sterilization or disinfection? • Can item tolerate heat, pressure, radiation, chemicals? • Cost effectiveness • Safety • Ability of agent to penetrate surfaces. ⸻ PHYSICAL AND MECHANICAL METHODS ⸻ Pasteurization vs Sterilization Pasteurization: Reduces microbial numbers but does not sterilize. Used for: Milk and beverages. Sterilization: Destroys all microbes including endospores. ⸻ Boiling Kills many pathogens but may not destroy endospores. ⸻ Autoclaving Uses steam under pressure. Conditions from slides: 121°C 15 minutes 15 psi Mechanism: Denatures proteins and disrupts metabolism. ⸻ Most Rigorous Heat Method Incineration (dry heat) Burns microbes completely. ⸻ Ionizing Radiation vs UV Radiation Ionizing radiation Examples: Gamma rays X-rays Effect: Destroys DNA and proteins. Highly penetrating. ⸻ UV radiation Example: Germicidal lamps. Mechanism: Forms pyrimidine dimers (thymine dimers). Effect: DNA replication blocked. ⸻ Filtration Removes microbes from liquids or air. Examples: • Water purification • Milk filtration • Air filtration systems • HEPA filters • N95 masks HEPA filters remove 99.97% of particles. ⸻ Osmotic Pressure High salt or sugar removes water from microbes. Examples: Salt: Cured meats Sugar: Jams and jellies Causes plasmolysis and prevents growth. ⸻ Cold and Drying Cold: Slows microbial metabolism but rarely kills microbes. Drying (desiccation): Removes water necessary for microbial metabolism. Example: Freeze drying (lyophilization). ⸻ CHEMICAL METHODS ⸻ Characteristics of Good Chemical Antimicrobials • Rapid action • Effective at low concentrations • Broad spectrum • Stable • Non-toxic to tissues • Affordable • Effective in presence of organic matter ⸻ Major Chemical Agents ⸻ Halogens Examples: • Chlorine • Iodine Common example: Household bleach (sodium hypochlorite) Mechanism: Oxidizes cellular molecules and damages enzymes. ⸻ Phenols Mechanism: Disrupt cell membranes and denature proteins. Examples: Phenolic disinfectants. ⸻ Alcohols Examples: • Ethanol • Isopropanol Mechanism: Denature proteins and disrupt membranes. Common use: Hand sanitizers. ⸻ Quats Quaternary ammonium compounds. Mechanism: Disrupt membranes. Example: Lysol wipes ⸻ Peroxides Example: Hydrogen peroxide. Mechanism: Forms reactive oxygen molecules that damage cells. ⸻ Detergents / Surfactants Mechanism: Break down lipid membranes. Examples: Soap and cleaning detergents. ⸻ CHAPTER 12 — ANTIBIOTICS ⸻ Alexander Fleming Discovered penicillin in 1928 from the fungus Penicillium. ⸻ Characteristics of a Good Antimicrobial Drug • Selective toxicity • High therapeutic index • Targets unique microbial structures • Effective against pathogen • Minimal harm to microbiota ⸻ Selective Toxicity Ability of a drug to kill microbes without harming host cells. Example: Penicillin targets bacterial cell walls, which human cells lack. ⸻ Susceptibility Tests ⸻ Kirby-Bauer Disc diffusion test. Antibiotic discs placed on bacterial culture. Zone of inhibition measured. Results: Sensitive Resistant ⸻ MIC Minimum inhibitory concentration. Smallest drug concentration preventing visible growth. ⸻ MBC Minimum bactericidal concentration. Smallest concentration that kills bacteria. ⸻ Therapeutic Index TI = toxic dose / therapeutic dose Example from slides: TI of 10 safer than TI of 1.1. ⸻ Antibiotic Mechanisms ⸻ Cell Wall Inhibitors Example: Penicillin Mechanism: Prevents cross-linking of NAM-NAG peptidoglycan. Cell bursts due to osmotic pressure. Other examples: • Methicillin • Cephalosporins ⸻ Cell Membrane Disruption Examples: • Polymyxin • Daptomycin • Colistin Mechanism: Creates pores causing leakage. ⸻ Protein Synthesis Inhibitors Example: Tetracycline Mechanism: Blocks 30S ribosomal subunit. Other examples: • Erythromycin • Azithromycin • Chloramphenicol ⸻ DNA / RNA Inhibitors Example: Fluoroquinolones Examples: • Ciprofloxacin • Levofloxacin Mechanism: Inhibit DNA gyrase. ⸻ Metabolic Pathway Inhibitors Example: Sulfa drugs Block folic acid synthesis. Example drug: Bactrim. ⸻ Drugs for Eukaryotic Pathogens ⸻ Antifungals Examples: • Fluconazole • Amphotericin B • Azoles Target ergosterol in fungal membranes. ⸻ Antiprotozoal Drugs Examples: • Metronidazole • Chloroquine ⸻ Antihelminthic Drugs Examples: • Pyrantel • Mebendazole • Ivermectin ⸻ Antiviral Drugs Targets: • Viral attachment • Viral transcription/translation • Viral assembly or release Examples: Acyclovir Blocks viral DNA replication. Tamiflu Prevents influenza virus release. ⸻ HIV Drugs Target steps in HIV replication: 1 Reverse transcriptase 2 Integrase 3 Protease 4 Viral attachment Combination therapy prevents resistance. ⸻ Antibiotic Resistance ⸻ How Resistance Develops • Mutation • Natural selection • Overuse of antibiotics ⸻ Mechanisms of Resistance • Drug-destroying enzymes • Efflux pumps • Target modification • Reduced permeability ⸻ CHAPTER 13 — MICROBIOTA ⸻ Normal Microbiota Microorganisms living on body surfaces without causing disease. Examples from slides: Skin: Staphylococcus epidermidis Gut: Escherichia coli Breast milk microbes: • Bifidobacterium • Lactobacillus • Streptococcus • Clostridium ⸻ Benefits of Microbiota • Produce vitamins • Digest food • Stimulate immune system • Produce neurotransmitters • Prevent pathogen colonization ⸻ Dysbiosis Imbalance in microbiota. Associated diseases: • Diabetes • Obesity • Cancer • Asthma • Allergies • Heart disease ⸻ Microbiota Development Microbiota develop: 1 During birth 2 Through breast milk 3 Environmental exposure Stable microbiome forms by age 3. ⸻ Probiotics vs Prebiotics Probiotics: Live microbes that improve microbiota. Example: Yogurt. ⸻ Prebiotics: Food that feeds beneficial microbes. Examples: • Garlic • Onions • Asparagus • Agave • Artichokes ⸻ Fecal Microbiota Transplant Transfer of microbiota from healthy donor. Used for: Clostridioides difficile infections Success rate: 70–90%. ⸻ Virulence Factors Examples: Adhesion structures: Capsules, fimbriae Exoenzymes: Hyaluronidase Coagulase Biofilms increase resistance. ⸻ Toxins ⸻ Exotoxins Secreted protein toxins. Examples: • Cytotoxins • Neurotoxins • Enterotoxins ⸻ Endotoxins Found in gram-negative bacteria. Example: LPS containing lipid A. Effects: • Fever • Inflammation • Shock ⸻ CHAPTER 14 — EPIDEMIOLOGY ⸻ Epidemiology Study of disease frequency, distribution, and control in populations. ⸻ Epidemiological Terms Index case: First identified patient. Incidence: Number of new cases. Prevalence: Total existing cases. Mortality rate: Deaths in a population. Case fatality rate: Deaths among infected individuals. ⸻ Disease Occurrence Sporadic: Random cases. Endemic: Constant presence. Outbreak: Localized increase. Epidemic: Large regional increase. Pandemic: Worldwide epidemic. ⸻ Healthcare-Associated Infections (HAIs) Common examples: • CAUTI Catheter-associated urinary tract infection • CLABSI Central line bloodstream infection • Surgical site infections • Ventilator associated infections ⸻ Causes of HAIs • Low patient immunity • Antibiotic resistant organisms • Invasive procedures • Healthcare worker transmission Example: Healthcare workers moving between patients. ⸻ Prevention of HAIs • Medical asepsis • Surgical asepsis • Universal precautions • Infection control officers Examples: • Needlestick precautions • Surface decontamination • Barrier protection ⸻ If you want, I can also give you the 20–30 questions your professor is MOST likely to put on the exam from these slides. Micro professors tend to repeat the same exact conceptual questions every semester, and your slides have some really obvious ones.