Microbio Exam 1 Study Guide PDF

**[Χηαπτερ 1]** explain how microbes are defined. Organisms that are too small to be seen with the unaided eye; require a microscope to be seen identify what the field of Microbiology studies. The study of microscopic organisms, such as bacteria, archaea, viruses, fungi, and protozoa. This d...

**[Χηαπτερ 1]** explain how microbes are defined. Organisms that are too small to be seen with the unaided eye; require a microscope to be seen identify what the field of Microbiology studies. The study of microscopic organisms, such as bacteria, archaea, viruses, fungi, and protozoa. This discipline includes fundamental research on the biochemistry, physiology, cell biology, ecology, evolution, and the clinical aspects of microorganisms, including host response to these agents describe why defining the field of microbiology is challenging. Involves many sciences, and not all single-celled organisms are microscopic, and not all microscopic organisms are single-celled understand who is responsible for life being organized into 3 domains. Carl Woese 1977 describe the 3 domain-system of life. Bacteria, archaea, eukarya (protozoa, algae, fungi) interpret taxonomic nomenclature (binomial nomenclature) and describe briefly how it relates to how organisms are related to other organisms. Species- type of organism (or group of strains) classified according to a shared set of genes Strains- genetic variants of a species Organisms with the same genus are more closely related differentiate the major defining characteristic of prokaryotes vs eukaryotes. +-----------------------------------+-----------------------------------+ | Prokaryotes | Eukaryotes | +===================================+===================================+ | - No true nucleus/nuclear | - Membrane bound nucleus | | membrane | | | | - Larger | | - Nucleoid region | | | | | | - Smaller | | +-----------------------------------+-----------------------------------+ compare and contrast the major characteristics of each group of microorganisms Archaea, Bacteria, and Eukarya (including protozoans, algae, fungi, and helminths) and identify each as a prokaryote or eukaryote. +--------+--------+--------+--------+--------+--------+--------+--------+ | | Bacter | Archae | Protoz | Algae | Fungi- | Helmin | Viruse | | | ia | a | oa | | mycolo | ths | s, | | | | | | | gy | | viroid | | | | | | | | | s, | | | | | | | | | prions | +========+========+========+========+========+========+========+========+ | P or E | P | P | E | E | E | E | n/a | +--------+--------+--------+--------+--------+--------+--------+--------+ | Single | Single | Single | Single | Both | Single | Multi | n/a | | , | | | | | -yeast | | | | multic | | | | | | | | | ellula | | | | | Multi- | | | | r, | | | | | mold | | | | or | | | | | | | | | both | | | | | | | | +--------+--------+--------+--------+--------+--------+--------+--------+ | Nutrit | Organi | Organi | Organi | Photos | Organi | Organi | n/a | | ion | c, | c, | c, | ynthet | c | c | | | | inorga | inorga | a few | ic | | | | | | nic, | nic | photos | | | | | | | photos | | ynthet | | | | | | | ynthet | | ic | | | | | | | ic | | | | | | | +--------+--------+--------+--------+--------+--------+--------+--------+ | Cell | Yes, | Yes | No | Yes, | Yes, | No | n/a | | Walls | peptid | | | cellul | chitin | | | | | oglyca | | | ose | | | | | | n | | | | | | | +--------+--------+--------+--------+--------+--------+--------+--------+ | Motile | Common | Common | Very | Some, | More | \- | n/a | | Cells | (flage | (flage | common | often | rare | | | | | lla | lla) | (flage | flagel | | | | | | or | | lla, | la | | | | | | pili) | | cilia, | | | | | | | | | or | | | | | | | | | pseudo | | | | | | | | | pods | | | | | +--------+--------+--------+--------+--------+--------+--------+--------+ | Pathog | Yes | None | Yes | No, | Some | Yes | Yes | | ens | | yet | | but | | | | | | | | | toxins | | | | | | | | | can | | | | | | | | | cause | | | | | | | | | diseas | | | | | | | | | e | | | | +--------+--------+--------+--------+--------+--------+--------+--------+ | Extrem | Some | Yes, | More | More | More | More | n/a | | ophile | | most | rare | rare | rare | rare | | | s | | extrem | | | | | | | | | ophile | | | | | | | | | are | | | | | | | | | archae | | | | | | | | | a | | | | | | +--------+--------+--------+--------+--------+--------+--------+--------+ differentiate non-cellular microbes: viruses, viroids and prions. - Viruses (virology)- DNA or RNA genome, protein capsid (shell), may be enclosed in a lipid envelope, inert outside living host - Viroids- infectious RNAs only (no proteins) - Prions- infectious proteins (no RNA or DNA). Can cause mad cow disease, kuru, Creutzfeldt-Jakob Disease explain how non-cellular microbes relate to living cells. They require a living host to survive provide examples of historical figures and their contributions to microbiology. - Robert Hooke - First compound microscope - Micrographia book - Observed "cells" (holes in cork) - Antonie van Leeuwenhoek - Father of microbiology - Single lens magnifier - Observed single celled microbes (including bacteria) - Lazzaro Spallanzani - Sterilized sealed flask of meat broth = no bacterial growth - Bacterial cell fission - Biogenesis- development of life from preexisting life - Louis fur - New flask design that allows air in flask - Conclusion: no spontaneous generation, microbes in the air contaminate - Named vaccination - Found that exposure to attenuated/weakened strains of bacteria conferred immunity to a disease w/o causing severe symptoms - John Tyndall - Sometimes found growth in Pasteur flask - Endospores, can be killed - Florence Nightingale - Medical statistics - Ignaz Semmelweis - Infections during birth with antisepsis - Jon Snow - Collecting info can describe the spread of disease - Jenner - Used cowpox instead of human smallpox - Joseph Lister - Used chemical treatment of surgical instruments - Paul Ehrlich - Identified a chemical antimicrobial drug to treat syphilis - Theory of Immunity explain the defining features of the 4 periods of time (defined in lecture) in the field of microbiology (e.g. if I gave you an experiment would you be able to classify it into one of these 4 periods). - 10,000 BCE-1660s - Food and drink (microbial fermentation), no fridges - Evidence of microbial diseases in human mummies and art - Polio, smallpox, leprosy, tuberculosis - Diseases/plagues shape human populations - Rudimentary smallpox immunizations in China and India- exposure to lesions of disease - Diseases understood to be contagious - Microorganisms' role unidentified - Bubonic Plague (black death) - 1660s-1880s - Microscopes invented - Spontaneous generation debate- the idea that living microbes arise spontaneously - Lazzaro Spallanzani- broth flasks - Biogenesis - Louis Pasteur- S shape flask, no spontaneous generation - Endospores discovered- John Tyndall - Jenner used cowpox instead of human smallpox - 1850s-1910s (golden age) - Early techniques for classifying and identifying microbes - Gram staining invented- Hans Christian Gram - Pure cultures - Relationship between microbes and disease discovered - Germ Theory of Disease: specific diseases are caused by specific microbes - Miasma "bad air" was competing idea - Disease common in overcrowded areas - Medical statistics- Florence Nightingale - Semmelweis - Infections during birth with antisepsis - Prevention of uterine infection post birth - Joseph Lister used chemical treatments on surgical instruments - Collecting info can describe spread of disease- Jon Snow - Koch's Postulates: scientific method/criteria used to determine if a specific organism (pathogen) causes a specific disease - Needed techniques for isolating bacteria - Louis Pasteur named vaccination, found that exposure to attenuated/weakened strains of bacteria conferred immunity to a disease w/o causing severe symptoms - Epidemiology field was started - Microbes found to be metabolically diverse - Pasteur- microbial fermentation produces acetic acid or alcohol - Sergei Winogradsky- studied microbes in their natural habitats - Discovered bacteria can oxidize iron and sulfur (lithotrophy) and can Fix Nitrogen - 1900s on - Antimicrobial drug to treat syphilis- Ehrlich - Also, Theory of Immunity- our bodies make compound to fight pathogens "antibodies" - Fist natural antimicrobial drug (Penicillin)- Alexander Fleming - Understanding DNA structure -\> development of DNA sequencing - Carl Woese - 3 domains- based on rRNA sequence list ways in which microbes affect our lives (and the planet) -both destructive *and* beneficial. - Microbes are model systems for all types of molecular biology questions list ways our Microbiota important. - Community or collection of microorganisms in/on the human body - Benefits: - Digestion - Immune system development - Growth factors (vitamin B& K) - Resistance- prevent growth of pathogens through competition give examples of more recent developments in the field of microbiology. - Metagenomics: high-throughput sequencing of a microbial community - Other molecular techniques such as virla vectors (gene therapy) and CRISPR define infectious disease, pathogen, and parasite. - Pathogen: disease causing agent (including parasites) - Parasite: type of organism that may or may not be pathogenic - Infectious disease: illness caused by pathogen Textbook Q notes: - Antibiotics: - May be chemicals produced by specific microbes - A specific antibiotic can kill certain classes of microbes - Fewer antimicrobial agents are known for viruses than for bacterial pathogens - They do NOT reproduce themselves to form more antibiotics - Cyanobacteria is the class of microbes that most closely resemble the ancestor of chloroplasts - Nitrogen fixation requires bacteria or archaea - Polymerase chain reaction (PCR) amplification of DNA is now used to identify a very specific strain of a disease-causing microbe - Contradiction of microbiology definition: not all single-celled organisms are microscopic, and not all microscopic organisms are single-celled - Genome- genetic makeup of an organism - Cellular organisms: DNA-based genomes organized into chromosomes, and can replicate on their own - Viruses: smaller, simpler genomes that can be DNA or RNA-based and rely on host cells for replication **[Chapter 5]** - Describe and contrast the basic structure and function of bacterial and eukaryotic cells. - Bacterial: - Non-compartmentalized - Smaller - Circular chromosome - CW contains peptidoglycan - Eukaryotic: - Compartmentalized - Larger - Linear chromosome - List core essential components of a bacteria cell. - Envelope - Plasma/cell membrane - Cell wall - Outer membrane (G- only) - Outer layers (if present) - Cytoplasm - Gel network of proteins and other macromolecules - Ribosomes - Nucleoid region - Chromosome - Plasmids - DNA binding proteins - Categorize non-essential (but useful) components of a bacterial cell. - Capsule - Polysaccharide or protein layer outside the cell wall that protects against phagocytosis and aids in biofilm formation and adhesion to surfaces - Glycocalyx - Slime layer used for adhesion, protection, and biofilm formation - Fimbriae - Hair like protein appendages on the cell surface that is used for attachment to surfaces, host tissues, or other bacteria - Pili - Hair like protein appendages on the cell surface used for DNA transfer - Flagella - Whip like movements - Endospores - Resistant structures used for protection from extreme environments - S-layer - Protein layer outside the cell wall used for protection against environmental stressors such as pH changes - Plasmids - Small, circular DNA molecules separate from the chromosome used for carrying genes for antibiotic resistance, toxin production, or metabolic pathways - Quorum sensing molecules - Small signaling molecules used for cell to cell communication and coordinating group behaviors like biofilm formation, virulence, and bioluminescence - Explain the evolutionary process of endosymbiosis. - Larger cell engulfed smaller bacterial cells - Bacteria were incorporated by pre-eucaryotic organelles - Understand the evidence for endosymbiosis. - Mitochondria and chloroplasts - Both have double membranes - Resemble bacteria in shape and size - Bacterial-like genomes (circular, sequences) - Ribosomes like prokaryotic cells - Can divide independent of the cell - Describe size, common cell morphology (cell shape), and cellular arrangement (grouping) of prokaryotic cells. - Shapes - Bacilli- rods - Spirochetes- long corkscrew - Longer, flexible axial filament, external flagella - Cocci- spheres - Vibrio- commas - Spirilla- short spirals or helical - Shorter, rigid, external flagella - Rectangular - Club shaped - Filamentous- stringy - Pleomorphic- many shapes - Arrangements - Strepto- chains - Diplo- pairs - Tetrads- 4 - Sarcinae- 8 - Staphylo- clusters - Describe the structure and function of bacterial cell membranes. - Phospholipid bilayer and proteins - Structural support for external structures (flagella, pili) - Detecting enviro signals - Export (secretion) - Selective transport of substances - E storage and transfer - Explain how nutrients are transported across membranes and know how energy is spent to drive transport in bacteria. - Molecule permeability: - Hydrophobic (O2, CO2, N2)- freely permeable - Small, uncharged polar (H2O, glycerol)- somewhat permeable - Large, uncharged polar (glucose, sucrose)- impermeable - Ions- impermeable - Transport - Passive- nutrients move WITH concentration gradient - Simple diffusion - Facilitated diffusion - Protein channel or carrier is used - Active- AGAINST concentration gradient- requires E - Carrier molecule - Potential across a membrane - Compare and contrast bacteria and eukaryotic cells in terms of cell membranes and transport and secretion. - Bacteria - Transport across membrane - Eukaryotes - Endo- and exo- cytosis - Describe the basic structure of bacterial peptidoglycan. - Glycan chains - Short peptides (crosslink) - Describe how cell walls protect bacteria from osmotic shock. - Compare and contrast the structure and components of Gram-negative and Gram-positive cell walls in bacteria. - G negative - Stain purple - Thick CW- many peptidoglycan layers - Teichoic acids - Negative charge - Rols: cell division, cell morphology, adhesion, survival in a host - Lipoteichoic acids - Covalently attach to cell membrane - G positive - Stain pink - Thin cell wall- few peptidoglycan layers - Lipoproteins attached to outer membrane - Outer membrane - Porin protiens - Murein lipoproteins - Lipopolysaccharides (LPS) - Lipid A - Endotoxin - Antibiotic induced lysis of the cells causes release of LPS - Core polysaccharide - O polysaccharide/antigen - Variable - Identification - Understand how the structure of the bacterial cell envelope is medically relevant. - G+ - More susceptible to antibiotics like penicillin - Less resistant to immune defenses than G- - Some develop resistance - G- - More resistant to antibiotics bc of outer membrane - Endotoxin can trigger septic shock - Some antibiotics can still penetrate and kill - Describe the contribution of Rebecca Lancefield to Microbiology. - Lancefield grouping system (stereotyping streptococcus) - Serological (antibody) testing - Identified group A strep (GAS)- strep throat and rheumatic fever - Helped in the development of diagnostic test and treatments - Describe bacteria classes that do not Gram-stain well and why. - Mycobacteria - CW with peptidoglycan and mycolic acid, and waxy phenolic glycolipids - Resistant to gram staining - Help resists digestion by host (phagocytes) - Include human pathogens - Compare and contrast bacteria, archaea, and eukaryotic cells (algae, fungi) in terms of cell walls (what about protozoa and helminths). - Bacteria - Peptidoglycan CW - G+ thick peptidoglycan - G- thin PG and outer membrane - Archaea - Protein S layers - Algae - Cellulose - Fungi - Chitin - Protozoa - No CW - Flexible membrane - Helminths - Flexible outer cuticle or exoskeleton - Compare and contrast bacteria, archaea, and eukaryotic cell DNA (both nuclear and non-nuclear) in terms of genome size, topology (eg shape... think linear vs circular), DNA storage, and organization. - Bacterial DNA - Double-stranded helix - Supercoiled - Organized by DNA-binding proteins - Smaller - In loops called domains - Circular chromosome - Plasmids - Eukaryotic DNA - Linear chromosomes - Organized into chromatin: complexes of DNA and protein - Organized into domains: 1 linear chromosome = domain - Larger - Nucleus has: - 2 membranes - Nuclear pore complexes: transport - Compare and contrast bacterial chromosomes and plasmids. - Chromosomes: - Essential genes - Most often circular - 1 per cell - Plasmids - Non-essential genes - Most often much smaller - Copy \# varies (some 1-2, some continuously divide) - Replicate independently from chromosome - Often transferred to other cells (Horizontal Gene Transfer) - Compare and contrast bacteria, archaea, and eukaryotic ribosomes, in both size/sedimentation units and rRNA (how does this rRNA play a role in Carl Woese's findings). - Protein synthesis/translation - In cytoplasm - Proteins + rRNA - Sedimentation units (Svedberg units) - Prokaryotic: - 70S = 50S + 30S (odd) - [E]ukaryotic: - 80S = 60S + 40S ([e]ven) - Compare and contrast pili and stalks in bacteria in terms of both structure and function. - Pili - Adherence - Monomers- pilin - Some have slight motility (twitching and gliding) - May trigger immune response in host - Fimbriae: short attachment pili - Conjugation (sex) pilus: DNA transfer between cells - Stalks - Adherence - Membranous extensions of the cytoplasm - Secrete adhesion factors (holdfasts) - Define chemotaxis. - Rotation of the flagella that propels the cell in response to stimuli - Explain how flagellar motility and chemotaxis enable prokaryotes to respond to environmental change. - Identify polar or peritrichous flagella. - Polar: flagella on one or both ends (bipolar) - Peritrichous: around whole surface - Describe the differences between Eukaryotic and Prokaryotic flagella. - Prokaryotic flagella - Made of flagellin - E source: use electrochemical gradients (proton motive force) - Anchored in membrane and extends out of cell - Spins to move cell - Eukaryotic flagella - Made of microtubules (extensions of cytoskeleton) - Slide by each other with help of motor proteins - UNDERNEATH cell membrane - Whip-like motion - E source: ATP - Describe the structure and function of protective layers in prokaryotes: glycocalyx (slime and capsules) and S layers. - Glycocalyx - "Sugar shell" made mostly of polysaccharides (some polypeptides) - Layers: - Capsule: neatly organizes, firmly attached - Slime layer: unorganized, soft, loose - Functions: - Attachment, protection, nutrients/prevent nutrient loss - Contribute to virulence by evading phagocytosis - S Layer - Protein or glycoprotein lattice outside the peptidoglycan in SOME bacteria - Helps strengthen CW - Can be virulence factor for pathogens- makes it a better pathogen - S layers - List and describe structures that some bacteria have and their role in a bacterial lifestyle (eg think about how many different environments bacteria live in and what specialize structures could be advantageous for that life style). - Capsule - Increases virulence factor - Flagella - Helps e. coli move through intestines - Pili - Attachment to surfaces - Biofilms - Forms films in cystic fibrosis patients lungs - Cell wall - Shape, protection from osmotic stress Textbook Q notes - Inner cell membrane of G negative holds ATP synthase - Efflux excretes toxins like antibiotics - Not the same as secretion, secrete things like proteins (not toxics) - Outer membrane of G negative contains porins, murein lipoproteins, and LPS **[Chapter 7]** - Describe how catabolism converts many complex food molecules to a few kinds of catabolites. - Explain how catabolism yields energy and how the energy is stored for use. - Describe how the energy carriers, ATP and NADH, transfer energy between energy-yielding (catabolic) and energy-spending (anabolic) reactions. - Apply the terms anabolic, catabolic, and delta G (+ or -- values) to coupled reactions. - Describe how sugar is catabolized to pyruvate via glycolysis and explain how these catabolic reactions generate ATP and NADH. - Glycolysis - Input: 1 glucose, 2 ATP - Output: 2 ATP, 2 NADH, 2 pyruvate, other substrates for biosynthesis - Glucose is oxidized - Compare and contrast the alternative pathways to breakdown/oxidize glucose and sugars. What is different (in general)? - Entner-Doudoroff - Yields: 1 NADPH, NADH, ATP, 2 pyruvic acid (overlaps with glycolysis) - Uses sugar acids with carboxyl groups - E. coli uses this in intestines bc mucus contains sugar acids - Pentose Phosphate - Yields vary: \~2 NADPH, 1 ATP - Intermediates used for biosynthesis of nucleic acids and some amino acids - Not used as much for ATP but for NADPH and ribose-5-phosphate - Explain how pyruvate is further catabolized by fermentation or by the TCA cycle (when oxygen is available). - TCA - First converted to A-CoA - Releases 2 CO2, 2 NADH, 2 A-CoA - Produces 6 NADH, 2 FADH2, 2 ATP, 4 CO2 (waste) - Glucose fully oxidized - Fermentation - Want to recycle NADH to NAD+ - No O2 needed - Pyruvic acid is final e- acceptor - Describe how NADH transfers electrons to electron transport proteins of the ETS and ultimately to the terminal electron acceptor, such as O2. - - Explain how electron energy gets converted to proton motive force and ultimately ATP. - Electron energy → Proton pumping → Proton motive force → ATP production **via** ATP synthase. - List the inputs and outputs of glycolysis, preparatory step (pyruvate oxidation) and TCA cycle and the oxygenic ETC in terms of carbon (glucose, pyruvic acid, etc.) and energy (ATP, NADH, FADH~2~).  You need to know the numbers of each molecule and be able to tell me energy yields per glucose molecule.  Process C inputs E inputs C outputs E outputs ------------ ---------------- ------------------ ---------------- ------------------------ Glycolysis 1 glucose (6C) 2 ATP 2 pyruvates 2 ATP (net), 2 NADH Prep step 2 pyruvates \- 2 A-CoA, 2 CO2 2 NADH TCA cycle 2 A-CoA \- 4 CO2 6 NADH, 2 FADH2, 2 ATP ETC O2 10 NADH, 2 FADH2 H2O 34 ATP - Compare and contrast prokaryotic and eukaryotic aerobic respiration. - Explain when and why cells would use fermentation. - To regenerate NAD+ without O2 - Completes catabolism - Identify the final electron acceptor for fermentation reactions and compare/contrast lactic acid vs. ethanol fermentation. - Pyruvic acid is final e- acceptor - Lactic acid fermentation: - Lactic acid is reduced product - E.g. G+s in cheese, yogurt, pickles, sauerkraut, summer sausage - Our microbiota - Alcohol fermentation: - 2 steps: - Pyruvic acid is converted to acetaldehyde; CO2 is released - Acetaldehyde is reduced to ethanol - E.g. brewing, winemaking, and baking - Saccharomyces- yeast - Identify when and where oxygen (O~2~) is required in microbial metabolism pathways. - Describe why microbial ETCs are so diverse. When doing so, relate to anaerobic respiration, alternative energy sources, chemoautotrophs, phototrophs. *Hint:*Do all cells use have cytochrome oxidase? Why or why not? - Not all prokaryotes have cytochrome c oxidase, some have ubiquinol oxidase - Describe where (do not memorize each detailed molecule, be more general) the substrates or starting metabolites come from for biosynthesis (anabolism). - Briefly describe how cells use alternative sources of carbon. - Carbon fixation - Powered by ATP and e- carriers - Describe how lithotrophs harvest energy from their environment (don\'t need to go into too much detail only what we covered in class). - Carbon fixation - Iron, sulfur, hydrogen oxidizers - Define: chemotroph, chemoheterotroph, chemolithotroph, chemolithoheterotroph, chemoautotroph, phototroph, chemolithoheterotroph, chemoautotroph. Understand the source of electrons and carbon in these organism types. - Compare and contrast phototrophic microbial groups. - Describe how phototrophs use light to generate ATP, NADPH, and release oxygen. - 1\. Chlorophyll photoexcitation: light absorbed by pigments - Maximized using folded membranes containing antennae complexes (protein and chlorophyll) - 2\. Photosystem II - Photolysis: 2 H2O (light absorbed) -\> O2 + 4 H+ + 4e- - H+ released outside the cell increasing PMF - E- enter ETC - \~3 ATP - 3\. Photosystem I - E- get excited with light - Enter a second ETC - 4e- + 2NADP+ -\> 2NADPH + 2H+ - Compare and contrast oxygenic vs anoxygenic phototrophs. - Oxygenic - Algae and cyanobacteria - Use 2 photosystems - Chlorophylls - Thylakoid membranes (algae have chloroplasts) - Anoxygenic - Purple and green bacteria - Us H2S instead of H2O - 1 photosystem - Bacteriochlorophylls - Chromatophores & chlorosomes - Compare and differentiate chemosynthesis and photosynthesis. - Photosynthesis produces O2, chemosynthesis doesn't - Define autotroph and carbon fixation. - - Describe how an autotrophic microbes fixe CO~2~ into biomass. - Calvin cycle - Reverse TCA - Understand the general input and output of the Calvin Cycle (don\'t need to memorize all the numbers or all of the steps).  - Input: - CO2 - ATP - NADPH - Output - Glucose - ADP - NADP+ - Identify what reactions in photosynthesis produce oxygen, what reactions need light and what reactions can be done in the absence of light. - Calvin cycle does not need light - PS II produces O2 - Both photosystems need light **[Chapter 6]** - Compare heterotrophy, autotrophy, phototrophy, and chemotrophy. - Define essential nutrients and list essential nutrients in bacteria. - Describe nutritional requirements and how microbes are categorized based on carbon and energy sources (we went over this in chapter 7 as well). - Describe the nitrogen cycle and the role of microbes in the nitrogen cycle. - Describe nitrogen fixation and understand why microbes are especially important in this process. - Differentiate anaerobes from aerobes and describe how each group is cultured. - Describe the 5 different classifications of microbes in relation to oxygen utilization (obligate anaerobes, obligate aerobes, microaerophiles, facultative anaerobes, aerotolerant anaerobes), understand patterns of growth in a culture tube, and what mechanism(s) these organism use to counter reactive oxygen species. - Define fastidious organisms and auxotrophs. - Distinguish between complex and chemically defined media; list reasons you might use each type of media. - Define growth factors and understand when growth factors would be needed. - List "normal" physiological conditions. - Define extremophiles. - List and relate the different classes of microbes on the basis of their preferred environmental niches (temperature, pressure, pH, osmolarity). - Understand the biological adaptations that allow different classes of microbes to grow in extreme the different environments. - Define generation/doubling time, binary fission, and exponential growth. - Compare and contrast eukaryotic and prokaryotic cellular division. - Define primary and secondary metabolites. - List and explain the 4 phases of culture growth; describe and what is happening in each and when primary vs secondary metabolites are being produced. - Describe the purpose of continuous culture and how it correlates to other natural environment. - Describe the ways bacterial growth is measured and explain the advantages and disadvantages of each method. - Describe how biofilms develop. - Define quorum sensing and understand how quorum sensing could be beneficial during biofilm development. - Explain the importance of biofilms to microbial growth in nature and during infection. - Define endospores and understand the benefits to the bacteria that form endospores. - List the types of prokaryotic organisms that form endospores (do not need species names). - Describe the process of sporulation, and germination.