Bio 150 Exam 1.pdf

Module 1 SLO’s Module 1-A 1. What are Microorganisms (Microbes- MoO), Microbiota, Microbiome? a. Microorganism: Organisms that are too small to see with your eyes b. Microbiota: The organisms in the an ecosystem c. Microbiome: The microbial genes (DNA) in an ecosystem...

Module 1 SLO’s Module 1-A 1. What are Microorganisms (Microbes- MoO), Microbiota, Microbiome? a. Microorganism: Organisms that are too small to see with your eyes b. Microbiota: The organisms in the an ecosystem c. Microbiome: The microbial genes (DNA) in an ecosystem 2. Microbes are ubiquitous because they are found everywhere whether it be in/on living things and all ecosystems 3. What is a pathogen? a. A Pathogen is a disease causing microbe 4. Subdisciplines of microorganisms; Are they considered living beings? a. Bacteria (bacterium) : Unicellular, Prokaryotes of Bacteria Domain + bacteria kingdom (EU), cell walls (PPG), Binary fissions consumer organic + inorganic chemicals (consumers) or photosynthesis (producer) b. Archaea (Archaeon): Unicellular, prokaryotic of Archaea Domain + Archaebacteria kingdom, oldest life form, Cell walls (no PPG), extreme environments (extreme halophiles-high salt ; extreme thermophiles - high temp) c. Fungi (some Fungus): Eukaryotes of Fungi kingdom (Myceteae), Decomposition of organic matter + nutrient recycling, consume organic chemicals, d. Protozoa (Protozoan): Unicellular, Eukaryotes, non-photosynthetic (Protist kingdom), 1+ nuclei, absorb/phagocytize organic chemicals, May be mobile, Asexual reproduction to cell fusion/division, life cycles  e. Algae (Alga): Unicellular + multicellular genera (genus plural), Eukaryotes, Chromista kingdom, cell walls (cellulose), photosynthetic (oxygen +organic compounds) f. Multicellular animal parasites: Eukaryotes ( animal kingdom), parasitic helminths, life cycles (microscopic), intestinal worms, egg/larva (infective), definite host (mating), intermediate host (no mating, can grow) g. Viruses + Prions (Not living): Acellular, DNA or RNA core + protein coat, lipid layer (maybe), Reproduce only in living host cell 5. How are MoO essential to life and how? What are some things that humans can do because of mOO knowledge? a. Microbes let humans: i. Prevent disease occurrence ii. Treat diseases : Genetic therapy which removes disease causing genes iii. Prevent food spoilage iv. Produce chemicals used in medicine + industry: Fungus makes penicillin v. Mitigate industrial accidents: Using microbes to help restore the environment or clean up toxic pollinates 6. What are 2 main types of cells? How do they compare +contrast? a. The 2 main types of cells are: Prokaryotic + Eukaryotic: i. Prokaryotic cell: Has no nucleus and are unicellular, are smaller, lack organelles that are surrounded by membranes, have a rigid cell wall (shape +support), include ALL in the Bacteria + Archaea domains ii. Eukaryotic cells: Has true-membrane-bound nucleus (DNA), are unicellular or multicellular, have organelles that perform certain  functions, cell wall in plants + fungal cells, include ALL in the Eukarya domain 7. What levels of taxonomic hierarchy are most +least specifics? a. The Domain (least), Kingdom, Genus (most) 8. What is the system of scientific binomial nomenclature a. It’s a 2 name naming system that has the species genus and specific epithet i. The genus is capitalized; the epithet is lowercase ii. Typed = italicized iii. handwritten = underline iv. Doesn’t include Viruses (not living) 9. What are the 3 domains of life, describe them? a. The three domains of life are Bacteria + Archaea (Prokaryotic) and Eukarya i. Bacteria: contain prokaryotic cells ii. Archaea contain prokaryotic cells iii. Eukarya contains eukaryotic organisms 10. Differentiate the major characteristics of each group of microorganisms (criteria used to classify organisms) a. Cell type: Prokaryotic or Eukaryotic b. Unicellular or Multicellular c. Food obtaining method: Producer or Consumer ( internal digestion or external digestion + absorption) d. Biochemical (Metabolic) similarities: What it does vs what it doesn’t do e. Evolutionary history: Use gene sequence to learn how different organisms are related (Phylogenetics) 11. Explain the importance of observations made by/evidence collected by/contributions of the following: Hooke, van Leeuwenhoek, Pasteur, Semmelweis, Lister, Cohn (notes only), Koch. What is pasteurization?  a. Hooke: Reported the existence of Cells b. Van Leeuwenhoek: Father of microscopy, first to observe + draw single celled MoO (cavorting wee beasties and animalcules) c. Pasteur: microorganisms are present in the air, life doesn’t arise spontaneously, S-shaped flask kept MoO out d. Pasteurization: viable bacteria could be killed by exposure to high heat for a short time (don’t cause disease) e. Semmelweis: Handwashing advocate (prevent puerperal fever transmission) f. Lister: Disinfect surgical instruments and surgical dressings- aseptic technique in surgery (reduce/prevent surgical wound infections) g. Cohn: Classified bacteria by shape (spherical-coccus, rod-bacillus, spiral- spirochete) h. Koch: Pure cultures, 4 Koch’s postulates, logical experimental steps 12. What is spontaneous generation? What is biogenesis? What is cell theory? What is germ theory? a. Spontaneous generation: nonliving matter creates lower life organism b. Biogenesis: theory that living organisms come from preexisting life (ONLY) c. Cell Theory: All living things are made of 1+ more cells, cell is most basic unit of life, cells arise from preexisting living cells d. Germ Theory: Some diseases are caused by moo: i. moO invade humans, animals, living hosts ii. growth +reproduction within host = disease (tissue damage) iii. Germ = virus, bacterium, protist or prion that causes disease 13. Define etiology. a. The cause of disease 14. (E&D too) Be able to reiterate Koch’s postulates. What is the significance of Koch’s postulates/What is their importance? Describe limitations of the postulates. [See NOTES, OER Sections 3.2 and 15.2]  a. Suspected pathogen has to be found in EVERY case of disease (not healthy) i. Some hosts may be asymptomatic carriers (may seem healthy but they’re not) b. suspected pathogen has to isolated from host + grown in pure culture (characterized+identified) i. Some moO can’t be grown into pure culture c. Inoculate the pathogen to a healthy lab animal and it must cause the same disease (signs +symptoms) i. Some pathogens only cause disease in humans d. The pathogen from the lab animal must be isolated and compared to the original host. They must be IDENTICAL. i. Some pathogens cause several conditions +symptoms e. Importance: i. The importance of these postulates is that the cause of infectious diseases could be discovered which helps in making treatment 15. What is an asymptomatic carrier? a. A host with an infectious disease agent but have no symptoms while they’re actively shedding the pathogen (spreading) 16. Compare and contrast the overall cell structure of prokaryotes and eukaryotes. Be able to recognize structural differences and understand that it’s the differences that are significant in antibiotic drug targeting (stay tuned for more on selective toxicity later in the semester). View OER-Table 3.2 too. a. Prokaryotic cell structure: (Pro &No) i. No nucleus ii. single celled iii. Most are monomorphic iv. Few are pleomorphic  v. Smaller vi. Lack organelles vii. Rigid cell wall = rigid layer surrounding b. Eukaryotes cell structure ( Eu & TRUE) i. True membrane- bound nucleus ii. Unicellular + Multicellular eukaryotes iii. Organelles - subcellular membrane bound structures iv. Cell wall in plant + fungal cells 17. Explain the importance of observations made by/evidence collected by/contributions of Fleming. a. Discovered 1st natural antibiotic - penicillin 18. Identify the basic shapes of bacterial cells (coccus, bacillus, spirillum/spirochete, vibrio). Define pleomorphic bacteria. Identify the typical types of prokaryotic cell arrangements (staphylo-, strepto-, diplo-). a. Basic Shapes: i. Cocus (s) / Cocci (p) - spherical ii. Bacillus (s) / Bacilli (p) - rod-shaped iii. Vibrio - bent rod iv. Coccobacillus - short rod  v. Spirillum -spiral vi. Spirochete -helical b. Pleomorphic bacteria: A single species that alters their cell shape in response to their environment (shape = function) c. Prokaryotic cell arrangements: i. diplo - pair of 2 ii. Strepton - Chains (line) iii. Staphylo - Clusters 19. Describe the structure and function of the glycocalyx (capsule, slime layer). Differentiate flagella, fimbriae, and pili. (Realize that prokaryotic flagella are structurally different from eukaryotic flagella and cilia) a. Glycocalyx i. Sugar coat of polysaccharides (cell wall) lets cell to attach, adherence to surfaces + cells ii. Capsule: denser, tightly bound to cell iii. Slime layer: Less dense part of the capsule that diffuses into the surroundings b. Flagella/flagellum whip-like filament on outside of the cell wall that spin + function in mobility i. Made of flagellum proteins ( H antigens that have surface variation = specific antibody response) + rotating hook + basal body (anchor to cell wall) ii. Fimbriae/ Fimbria: allows attachment to host cell (shortest from all 3) iii. Pilus/pili: A connecting wire that lets there be a transfer of DNA from 1 cell to another by bacterial conjugation (snuggling) iv. Prokaryotic flagellum: Unmoving cork that relies on base motor for torque  v. Eukaryotic Flagellum: Beats like a whip vi. Eukaryotic cilia: Shorter and more than flagellum, wide range of movement 20. What is a biofilm? (more later) a. 1+ more moO species making a complex community 21. What comprises a bacterial envelope (this is very different from a viral envelope)? Compare and contrast the cell walls of Gram-positive bacteria, and Gram-negative bacteria, acid-fast bacteria, archaea, and mycoplasmas. Realize that a cell wall is not the same as a cell membrane and that these cannot be used interchangeably. a. Bacterial envelope: i. Outside cytoplasm + inside glycocalyx ii. Made of cell wall + cytoplasmic membrane (plasma membrane) 1. Cell wall: Outside the cell membrane + shape cell determination + structural support +over-expansion prevention ( when water enters the cell) + made of PPG b. Gram (+) bacteria cell wall: i. No outer membrane ii. Thick peptidoglycan iii. Teichoic acids (link cell wall to cell membrane), have a negative charge, makes more rigid, different surfaces = different immune response c. Gram (-) bacteria cell wall: i. Has an outer membrane ii. Thin peptidoglycan iii. Lipoprotein ( links outer membrane and PPG) Outer membrane has lipopolysaccharides (LPS, outer-leaflet), and porins (channels) iv. LPS protects inner cell membrane: 1. Has lipid A an endotoxin (inflammatory responses in animals) 2. A lot is released when the cell is dying 3. perisplasmisc space between cell membrane + cell wall d. acid-fast bacteria cell wall: i. Has a stack of PPG like (gram + cell wall) ii. Has mycolic acid (waxy lipids) embedded into PPG e. archaea cell wall: i. Wall-less or walls or walls of pseudopeptidoglycan f. mycoplasma cell wall (bacteria): i. Lacks cell wall ii. Plasma membrane with sterols 22. (important for Lab Test too) What is a Gram stain and how do we assign Gram status to bacteria? (Be able to describe each step of the procedure AND what each step is accomplishing for G(+) and G(-) bacterial cells and how). What is ultimately stained? a. The gram stain a differential staining procedure that differentiates between 2 types of bacteria based on their cell wall; what is ultimately stained is the PPG b. The gram status is assigned based on the color of the PPG (only in bacteria) is stained c. Procedure: i. Heat fix: helps bacterial cells stick onto the slide + preserves sample by killing the bacteria ii. Primary stain (crystal violet): stains the PPG of Gram + bacteria and the outer membrane of Gram (ALL appear purple) iii. Mordant (Iodine): Sets the dye because the Iodine binds to the crystal violet ( I-CV complex) and gets trapped in the PPG iv. Decolorizer (Acetone Alcohol): Removes the lipids in the outside membrane of of the Gram - taking away the purple dye ; dehydrates PPG of Gram +, but it will remain stained because of the I-CV complex v. Counter-stain: Safranin: Stains the exposed PPG of the Gram - pink and doesn’t stain the Gram + leaving it purple 23. What are AFB? Discuss the acid-fast staining procedure.PLEASE NOTE that our textbook erroneously calls the AFB, mycolic-acid rich Gram(+) cells, but since they do not Gram stain that is technically incorrect. a. AFB are acid fast bacteria that have PPG stacks like Gram + mycolic acid (waxy lipids) b. Staining Procedure: i. Heat fix: helps bacterial cells stick onto the slide + preserves sample by killing the bacteria ii. Primary stain: Carbol fuchsin + phenol which dissolves into the waxy lipids cell wall staining the cells red iii. Decolorize : acid alcohol because the waxy wall is resistant to it and will stay red meanwhile non-acid fast bacteria will be decolorized iv. Counterstain: methylene blue/Brilliant green: Non-acid fast bacteria will take up the color since they were decolorized ( G+ or G-) 24. What is lysozyme? What is LPS? What is the significance of LPS? a. Lysozyme: enzyme that’s abundant in secretion: tears, saliva, mucus, etc i. Digests disaccharides in PPG = reduces growth  b. LPS (Lipopolysaccharides): Found in the outer i. protects inner cell membrane: ii. A lot is released when the cell is dying iii. perisplasmisc space between cell membrane + cell wall 1. Made of O polysaccharide 2. Core Polysaccharides 3. Has lipid A an endotoxin (inflammatory responses in animals) 23. Understand that membranes are selectively permeable (selective permeability). a. Selective permeability is when only some molecules can pass through i. Passive transport (No energy input): simple diffusion, facilitated diffusion + osmosis ii. Active transport: Energy input (ATP) + transporter protein 24. Understand the general structure and function of the following prokaryotic cell substructures: cytoplasm, nucleoid (bacterial chromosome region), ribosome (70S) and ribosomal subunits, inclusions, endospores. a. Cytoplasm: gel-like in cell membrane i. Nucleoid: bacterial chromosome. dsDNA (circular), wrapped in proteins, plasmids ( extra dsDNA), tethered to plasma membrane of bacteria ii. Ribosome: Protein synthesis (no membrane) iii. Inclusions: Reserves of nutrientes 1. Metachromatic granules - phosphate  2. Polysaccharide granules - energy 3. sulfur granules - energy 4. Carboxysomes - energy 5. Gas vacuoles - protein cylinders for buoyancy in aquatic MoO 6. Magnetosomes - iron oxide (destroys H202) iv. Endospores: Dormant resting bodies when nutrients are depleted 1. Resistant to desiccation (drying), heat, boiling, freezing, radiation, etc 25. What is sporulation? Recognize the environmental pressures to which endospores provide resistance. What is germination? a. Sporulation: Formation of endospores ( make themselves metabolically inactive) b. Germination: Endospores return to vegetative state (metabolically active cell) when the environment is conductive 26. Understand the general structure and function of the following eukaryotic cell substructures: flagella/cilia, cytoplasm, nucleus, ribosome (80S) and ribosomal subunits, endoplasmic reticulum, Golgi, lysosome, proteasome, mitochondrion, and chloroplasts. What type of ribosomes are present in the endosymbiont-organelles? (optionally for Proteasome, see https://en.wikipedia.org/wiki/Proteasome) a. Flagella/cilia: Undulate side to side b. Cytoplasm: Inside plasma (cell cytoplasmic) membrane + outside nucleus i. Cytosol : fluid portion  ii. Cytoskeleton: Microfilaments (actin) + intermediate filaments (building block) + microtubules (tubulin) c. Plasma membrane: i. Passive transport (No energy input): simple diffusion, facilitated diffusion + osmosis ii. Active transport: Energy input (ATP) + transporter protein iii. Endocytosis: 1. Phagocytosis : pseudopods exten + engulf particles 2. Pinocytosis: Brings fluid + dissolved substances by folding inwards 3. Receptor- mediated endocytosis iv. Exocytosis : secretion d. Nucleus: Has chromatin (chromosomes) = DNA wrapped in histone proteins i. Nuclear envelope + double phospholipid bilayer (nuclear pores) ii. Nucleolus = rRNA synthesis e. Ribosomes: Protein synthesis f. ribosomal subunits: i. 80S (60S + 40S subunits) made in nucleolus (float in cytoplasm + anchored to rough ER) ii. bacterial version: 70S in mitochondria + chloroplasts g. Endoplasmic Reticulum: transport network newly synthesized + correctly folded: i. proteins - ROUGH ii. lipids - SMOOTH h. Golgi : membrane involved in post-translation + packaging + secretion of proteins i. Lysosome: Sacs (membrane- bound) that have digestive enzymes for intracellular digestion; low pH j. Proteasome: Protein complex that proteases that chop up tagged proteins k. Mitochondrion: Cellular respiration: makes ATP; has own DNA/ 70s ribosomes l. Chloroplasts: Photosynthesis; DNA/ 70s ribosomes 27. Explain the importance of observations made by/evidence collected by/contributions of Lynn Margulis with the Endosymbiotic Theory. a. Endosymbiosis: 1 organism live within another b. Endosymbiotic Theory: Origin of eukaryotes from prokaryotes i. Mitochondria + Chloroplast have origins in bacteria ii. Prokaryotic cell lost its cell wall iii. Plasma membrane enveloped nucleoid = nucleus iv. engulfed smaller bacteria = 1 organism live within another 1. Host cell provides nutrients + safety 2. symbionts make energy c. Evidence: i. Have circular chromosome ii. Have 70S iii. formed through binary fission = asexual reproduction (DNA replicates then organelle splits into 2)  iv. Porins (transport proteins) found in outer membrane like in G(-) bacterial outer membrane of cell wall v. Has inner + outer membrane (double lipid bilayer) 28. Distinguish among the 3 types of symbioses; commensalism, mutualism, parasitism. What is synergism? a. Commensalism: 1 benefits (+), other is unaffected (0) b. Mutualism: both benefit (+) c. Parasitism: 1 benefit (+), other is harmed (-) d. Synergism: relationship of 2 organisms that make results together they can only make when they’re together 29. What is a biofilm? a. Moo group where cells stick to each other on a surface + form community that resides in a matrix made by MoO (teeth, medical implements, rock, pipes) 30. What is the human microbiome (normal microbiota)? What is the Human Microbiome Project? Be able to describe your human microbiome article. a. What: Identifying + characterizing MoO that are associated in healthy + diseased humans (human microbiome) b. Article: i. Microbial cells (10) > human cells (1) ii. First phase: DNA sequence dataset + computational tools for characterizing microbiome in healthy + diseased people iii. Second phase: Created integrated datasets of biological properties from both the microbiome + host over time. 31. Understand the basics of MoO ecology. a. MoO Ecology: Relationship of organisms to each other + to the environment/ habitat 32. How do bacteria “talk” or communicate (there are 3 aspects)? What is quorum sensing? a. MoO secrete chemical messengers (message delivered) b. MoO have receptors specific for chemical messages (message received) c. Certain threshold (chemical messenger concentration), MoO respond by coordinating gene expression to produce an effect d. Quorum sensing (QS): system of stimulus + response correlated to population density. i. Moo uses QS to coordinate gene expression according to the density of their local population. 33. What is a virion? Describe the general characteristics of a typical virus? What is the nucleocapsid? Differentiate between non enveloped (naked) and enveloped viruses. Explain host specificity. a. Virion: complete infectious viral particle b. Typical virus: i. a cellular ii. obligatory intracellular parasites (can only reproduce within a living cell - intracellularly) iii. Has DNA or RNA genome (not both) + Protein coat: Capsid (capsomeres: repeating proteins) = nucleocapsid iv. Some enclosed by envelope; some are naked v. No ribosomes vi. No atp-generating mechanism vii. Majority have no metabolic enzymes viii. all are metabolically inert until infection establishes in cell ix. Host-specific: only infect a certain type of host, x. Capable of infecting more than 1+ host type xi. Host range: species spectrum the virus can infect xii. Spikers (viron surfaces) interact with host cell receptor (attachment sites) 34. Be aware that viruses infect every type of cell, including bacteria, algae, fungi, protozoa, plants, and animals. What is tissue tropism? A. Tissue tropism: only infect certain types of cells within tissues 35. What is a bacteriophage? Understand the lytic cycle and lysogeny (lysogenic cycle). a. Bacteriophage: bacterial viruses that infect bacteria, specific bacteriophages = specific bacteria, replicated in: i. Lytic cycle: Process of viral replication ending in the host cell death 1. Absorption (attachment via bacteria receptor) 2. Penetration 3. Replication of viral genome (biosynthesis) 4. Assembly of viral proteins 5. Maturation of virions 6. Lysis + release  ii. Lysogenic cycles: Process of viral replication where viral DNA integrates into host genome 1. Absorption (attachment) 2. Penetration 3. Integration of viral genome into host cell genome 36. List the steps for multiplication of an animal virus. a. Absorption / Attachment: Virus attaches to specific receptor (in/on host cell membrane) b. Penetration by endocytosis or fusion c. Uncoating of genome by viral of host enzymes d. Biosynthesis: making of DNA or RNA +proteins e. Assembly/maturation: nucleic acid + capsid proteins assemble f. Release by budding: enveloped viruses seal cellular membranes or rupture (lysis) 37. Realize that some viral ‘species’ or ‘subspecies’ are oncoviruses that can cause cancer? a. Oncogenic virus genetic material can be integrated into the host cell DNA at a certain location i. OR b. Viral products make an unstable environment in host cells leading to mutation 38. Differentiate acute viral infections from persistent (both chronic and latent) viral infections. a. Acute viral infection: a short course (rapid) + gets cleared from host b. Persistent behavior i. Chronic: Primary infection isn’t cleated + not dormant = enduring infection (host defense reduction to virus killing ability reduction) ii. Latent: Asymptomatic host cell for long; lies dormant then gets reactivated 39. What is a prion? What type of diseases do abnormal prions cause? a. Prion = Proteinaceous Infectious Particle i. No nucleic acids ii. Inherited forms + transmissible forms leading to spongiform encephalopathies (brain tissue deteriorates =sponge) : 1. Ingestion 2. transplants 3. surgical instruments b. Abnormal prions disease: i. Creutzfeldt-Jakob disease ii. Gerstmann- Straussler-Sheinker syndrome