Micro Midterm 1 PDF

Topic 1- Microbial World What is microbio? > Study of microbes how microbes interact w/food humans and how can be used , ,...

Topic 1- Microbial World What is microbio? > Study of microbes how microbes interact w/food humans and how can be used , , they Microbe : Small disease (virus) - living thing that can cause ~ Microorganism : Life, living cells /archaea, eukaryotes , bacterial Prokaryotic : "B4 nut" , no nucleus , bacteria arched ~ Eukaryotic "True nut" : , nucleus ~ ~ Prokary microorganism : arche, bacteria ~ Prokary Macro : None known - Evkary macro : Animals , plants ~ Eukary micro : algae , fungi, protozoa Robert Hooke : early microscopes first description of microbes : Fruiting structures of mold (fungi) , Antoine van Leeuwenhoek Improve microscopes, first desc. Of bacteria : 200X may, father of micro , micro : micros = 1st life ~ Why study on earth established biosphere cond , allow - multicell to evolve O ! organism , genetics , biochem, metabolism) - multi org come from micro org understand life levolution , , more than 50 %. biomass made of. - m o. - will be on earth Never ~ Benefits of m O : Fast cheap , e2 to ~ grow. , Make for indlmed prod - enzymes + molecules use , mass - Small ~ #genes, easier 2 study - Ez - genetic manip. Core features of life : not DNA or movement metabolism , by gen variation/evolution, response/adaptation , homeostasis · growth , reprod achieved.  How do what's inside ? microbes get energy? Heterotroph : Ingest preformed organic molecules (other eater Heterotroph : > - majority Protein (So % ) , enzymes be of biochem rxns structural , * > - RNA and ribosomes (IS-20% RNA/ribo) , protectantcatationa Autotroph : Produce organic molecule (self eater, CO2 e food) So % pro > - Lipids be lots of membranes , organelles (10 ) % 15-20 % RNA- Ex : Organic mol broken down by microbes to harness ATP- > Sugars + polysaccharide (6-7 %) structural + energy storage 10 % lipid , -7 % 6 - DNA 12-5 % ) informational Sugars , > - fermentation + aerobic respiration V 2-SY DNA. Microbes help biogeochem cycling (in organic -> organic) micros gone ? Weigh less · in Live diverse form microbial many dif · in grps in nature + members comm. Phylogenetic tree evkarya 3 Domains based on ribosomal RNA seq ; bacteria , archae , # What features make SSU rRNA gene sequences ideal for phylogenetic studies? V The benefits of using small subunit rRNA (SSU rRNA) genes for phylogenetic analyses is that their sequences are highly conserved and universally present in all living things and varies with constant rate. Hence, SSU rRNA genes are best suited for phylogenetic and molecular clock analysis, as they could be used to reveal evolutionary relationships between all cells, providing the first effective tool for the evolutionary classification of microorganisms. * 3 Domains : Bacteria : No nuclear membrane , membrane bound organelles are rare , plasma mem = similar to eukarya , cell wall found in almost all species (made of peptidoglycan) RNA poly , histone: histone like poly single = protein Archaea : No nuclear membrane , membrane bound organelles are rare , Plasma mem = dif than bacterk , cell wall found in almost all species (made of various mats) RNA poly single = poly , erkaryal-like RNA pol 11 has histones , Evkarya : has nuclear membrane bacteria , cell found in some species (made of various mats) many membrane bound organelles similar to wall , , plasma mem = RNA 11 111 has histones poly-RNA pol1 , , , Viruses : "alive" don't replicate outside host cell , little to biochem activity outside of technically not , no a host cell inert , + nonreactive outside host Origin of life: early earth cond = harsh , little of , 4 temp , CO2 reducing atmosphere (lots agents) of reduced compound reducing , , First life experiment : millert harold Stanley urey simulate "Spark" Reg of life: Genetic info storage able separate cell interior from external early , to catalyze biochem rxh , env. Ribozymes : RNA acting like enzymes , rxn catalyst, gen info storage, self replicating. How to achieve req for early life Micelles : hydrophilic head Early form of plasma mem , + hydrophobic tail RNA World : Prior to last universal common ancestor (LUCA) , conceived byCarl Woese Double Strand DNA : "Backup" of genetic info, more stable than RNA (not sensitive to nucleoleic attack like RNA) copy for LUCA from LUCA features: mem-bound ATP DNA-RNA-pro , , , eats CO2 (autotroph), fixes N2 into ammonia , anaerobe , thermophile Oxidizes H2 , prob. where e--energy- Cyanobacteria : 3 bilyos; e-donor leavetty ,. e- from Ho , light energy = rip e-out of tho (LUCA) ↳ ancestors produce of as toxic by product = Microbes dom = 3 Sbilyrs , fossil records largerly fossilized stromatolites (carbonate w/photosynthetic top) , coated contribute of ·. micro exist ; in pedestals micro mat on in cyanobac , Modern RNA : DNA -mRNA- > protein , RNA = Versatile Examine effects of single mutation in DNA indiv (microbial gen) : transcription > - translation Study + Compare piece of genomes to each other across domains (phylogeny origin of evk : endosymbiotic theory - prokary eats other prokary explained disproved Microbe + Disease : Louis Pasteur discovered that living organisms discriminate , btwn optical isomers all ferm, vaccine 4 anthrax , Foul cholera , rabies , pasteurization,spon gen , , developed method 4 controlling gravth , sanitation Robert Koch : Bacillus anthracs-causes anthrax (aging), mycobacterium = cause of tuberculosis Koch postulates /determine which micro cause disease) : , Disolate pathogen 2) get 4 it purified 3) infect healthy ppl 4) isolate 4 pathogen - drank it ↳ Barry Marshall Robert warren , , hellobacter pylori + stomach vicers Disease : Bubonic Prevent : antiseptic plague, native, Spanish for , hygiene, vax , antibiotics foods water , safe , Sanitary Topic 2-Bacteria ecology , Phylo. Morphology : Spherical (def ). = cocci , rod = bacillus , comma-shaped-vibrio , Spiral-Spirilla, Pleiomorphic (many shapes) - varied. Not a good indicator of phys. > morphology determined uptake efficiency /surface vol) , spirals efficient swimming (viscous turb) gliding motility (filaments) - on : nutrient : = or , bacteria 1 Some bac. assume muticell organizations hyphae (branch fila : of cells) , mycelia (tufts of hyphae) , frhomes(smooth unbranched chain of cells cell sizes : Prokary : 0 2 Nm >. 700Nm , rod shape /0. 5-0 4. um wide and 1-15Nm long) very few "large" prokary , Eukary · : 10Nm + o > 200 Nm and Steady food small : Frate of nutrient/ alot < min size due to min space, reg for genome proteins rib , , Big cells : Need waste Xchange Exceptions Thiomargarita - bigger than predators that makes them so S common in marine namibiensis up to 7000m diameter, Heide : U. : Schulz-Vogt - in. fluid Fishelsoni 700 Nm X 80 Im Some have ratio = small · Higher metabolic rate Epulopiscium 200 :V big, Sa - - faster burst like virus Faster growth · uRNA) , don't but surgeon fish , uncultured (Clostridum + 165 , ↳ gut of evolution 700 m long compared : to evk paramecium : 75 Nm · size reduc Constrained by min complement Radius : Highest S:rratio = small cell/radius Ocean = Smaller Sivratio , largest Yauger , radius low S : V = radius ↑ Siv ratio , O ⑧ ↓ radius unutrient. O I g 9 * Cytoplasm of bacteria : DNA nucleoid-made of DNA , RNA, protein , genetic info storage + gene expression chromosome packaging proteins protein , protection and compaction of genomic DNA - - Enzymes involved in Synthesis of DNA , RNA-protein , replication of genome (transcription) Regulatory Factors - protein , RNA , control of rep., transcript, translate Ribosomes protein , RNA , translation (pro Synth) - · Plasmids-DNA, variable, encode non-chromo genes for variety of fin Enzymes involved in breaking down substrates - protein , energy prod, provide anabolic precursor Inclusion bodies - many polymers, storage of carbon , Phosphate, nitrogen , sulfur Inclusion body : CPNS Gas vesicles - protein, broyancy Magnetosomes - protein , lipid ,iron , orient cell movement Cytoskeletal structures - protein, guide cell wallSynth , cell- and possibly partioning of chromo during rep area = nucleoid Largest region , house chromo + DNA rep machinery. Plasmid, DNA has antibodies How does DNA compress win nucleoid of bacteria? Several mechanisms of cations (Mg2t, K Nat) · to reduce space , use , to shield negative charges on Sugar Phosphate backbone small charged proteins - + bindz chromo to maintain cond Structure.. Topoisomerase modify , allow 4 supercoiling No mem surrounds nucleoid · No histones · cytoplasm of (tRNA etc) · = Stew Macros ribo pro , , , Inclusion bodies : Sulfur globules (sulfur storage 4 energy Polyhydroxybutyrate granule Carbon · : storage Gas Ctrl vesicle broyancy · : Microcompartment Carboxysome-loc : - of CO2 fixation rxn (RUBISCO) , protein encased , in cyanobac. Magnetosomes : organelle , direction finding (mem bound comp). > Only some bacteria orient to north pole , go 2 sediment. Depends where but more across poles ↳ chain = compass Bac series of internal pro. Cytoskeleton : , archea have too , keep everything in right place > some pro involved in cell wall Synth MreB-homolog : of actin , microfilaments , make helix · F+ S2 (homo of tubulin)-microtubule , where I divide > Other pro-move internal items - (plasmid) Cell Envelope : All layers around cyto 1) cell. mem 2) cell wall 3)mb 2nd mem , perm barrier (fividmo) , hit and push back a bit but easy 2 destroy Cytoplasmic mem : All cells have plasma mem., separate into from. ext Plasma mem : Capture energy ; ETC makes PMF (proton motive force) , used for photosynth/resp , used 2 derive energy 4 motion (flagella > Holding sensory sys : embed prodetect env changes, alter -. gene ex - > - Perm barrier ; phospho. bilayer fatty , acid + glyceral backbone connected be ester ↳ Hopanoids : sterol-like mol. to help w/ stability across temp, ranges in some bacteria Cross plasma mem : E2 lin) CO2 (out) diffuse readily, , H20 wlaquaporin pro chan Cosmosis Faci diff. + Cotransport : Pro channel more particles by lev - Conc gradient , no ATP needed , cotrans = active trans (symport ;bring in tog. and antiport (4) Ac trans-ABC transporters ; ATP need ATP bind Cassette, pro transporter moves part against conc grad , Protein Secretion : ship pro out ATP (ex ; toxins , siderophores, enzymes that break sub down ,. At found in D forms /mirror image/stereo is one Y Cell Wall : Gives cell shape , protect from osmotic lysis (mech force , matrix of cross-linked strands of peptidoglycan subunits (NAM + NAG -r There= DAP (new AA) cell wall be degraded/lysozyme attack B1-4 glycolink , break wall · can + in Ecoline walls cytoplasmic membrane - who wall , cell can't resis Osm pressure change : ruptures in hypo cond and loses in l'cytoplasmic. , dell wall membrane cell Blactam anti : Prevent peptidoglycan cross linking. Infection = cell: , anti work best wall (thick) Outer membrane Thick layer · peptidoglycan Inhibit FtsI (burst Thin cell wall again · periplas vary width - Narrow periplasmic · , outer mem made of LPS (lipopolysac) charged teichoic acid - - ↳ can harm Anti res : needInd enzyme destroys B-lactam ring , drug otherwise anti affected Not all cell wall struc Gram stain (gram are same : + and gram-) developed by Christian Gram ↳ all decolour shrinks Alc G lose large pores in gt , lock crystal · violet removes out Mem. lipids in , crystal ↳ ↳ porins large pore directlySinglestep = nutrients get in tonB pro to get nutri never enta + in Leave. periplasmic either 1 hair ↓ petri Flagella : Spiral, hollow rigid fila extending from , cell surface (loc. + #vary) , mono , amp, lop, Made of : Fila of mult. Flag pro , hook profilament + basal bod) , basal body (disk , propellers Energy 2 Spin Flagella derived from : PMF , complex stru, spins = rumble , expensive : 1000H+ repellents Chemotaxis : Chemoreceptor protein temporally sense change in [J of attractants or ⑦ Chemo : CJ attractant left Chemo : ↓[], repellent , , , right cells have internal flagella , some spirochetes have flagella in peri ↳ as they spin , rotate cell bod like corkscrew Nonflagellar motility : gliding smooth slide over surface (myxobac, cyano) - Twitching-slow , jerky using pili that extend, attatch to and pull along surface (pseudomonas aeruginosa) > Polymerization of actin in host cell for of bac into adj cells (ex ; Shigella, listerial - propulsion. shig taken up by epi cells, released from Vesicle (actin tall) , infect other, cont - ·. Adherence Molecule : Cells stick Surface , pili , fibers of pilin protein, possess pro tips for 2 on sticking ↳ Sex pillus : Dif struc used for Conjugation (send plasmid to difcell) Stalk : Ext of cell enr. tipped by "holdfast" of polysac Provide. extra surface area for nutri absorp (caulobacter, hyphomonas against host immun. Capsules : Thick polysac layer surround gramt/gram-cells. Provide adhesion, defense protect agains dessication ↳ Help bac form biofilm , protettenhance harsh survivability in env. Surface arrays (S-layers) Crystalline array of interlocking pro protect infection w/bacteriophage Gramt , Gram ; archaea : , agains predation or. Bac taxonomy : features While diff from other. Most microbes # cultured , binomial sys : Species-grp of strains Sharing common. strains Genus : grp of closely related species Bac. Taxonomy ; ↑ species -> genus > - fam- order > class - > - phylum Sgtoc Class depends on : DNA seq , size/shape , gram type , Colony morphology presence. of stru. Such as capsules or enduspores, phylmet traits , > Once class. Microbes = deposited in at least 2 culture collections ; World fed for Cult coll has database of soot coll. Pure, maint Cultures made. avail to scientists, ref Specimen deposited in cult repository. Only ~1 % Cult type strain =. Topic 3-Archaea Distinctive like bacteria genetic analyses show them to be dif prop : arche look ,. Live in inhospitable places. No known archeal human pathogens, bizzare shapes Phylogeny : Comparison of rRNA establish phylo trees Woese+ Fox studied of archaebac , first "archea" = methanogens = · , Halobac Salinarium : 3 0-S OM NaCl needed 2 dead sea , salted foods grow ,.. Pyrococcus Furious : 100 %, hydrotherm vents Picrophius Oshimae : 0. 7pH , sulfur rich volcanic areas Methanogenium Frigidum : IS , ace lake , antarctica Morph + Struc : 0 5-5Nm diameter , thermoproteus = 100 Nm , N equitans = 0 4 Shapes rod , cocci spirals Shapes (sulfolobus) , rect (thermoproteus) , Squarelhaloquadrat.... = ,. Irrey btwn arc +euk Cytoplasm Sim : to bac inclusion , bodie/microcomp (CO2 stor, gas vacuole), single circ chromo , lack mem bound nucleus, DNA rep enzymes sim 2 eukarya , histone dev = branch point Histone = Pro that DNA wraps around Cytoskel : Homologues found in both other domains. The basekarypoint · DNA wraps around Cell Envelope : All archaea possess a plasma cell wall but no outer layer dif from equir in other domains mem , , Plasma Mem : unique bilayer constr · (glycerol-1-phoslisomer of G3P)), phytanyl side chain (repeat isoprene units) / Eve linkages * Stability monolayers in * temps (stability !) · both ends very stable In arche that live in som arc ; phosphoglyceral on ,. Ignicoccus: Outer mem-periplasm like in Gram , ATP synthase enzymes in outer layer , unusual Cell Wall : pseudomrein ; like peptidoglycan, N-acetylglucosamine + N-acetylfalosaminuronic acid B1 , 3 linkages ; lysozome insensitive polysac , Cell Surface : S-layer : protect against pred/viruses, meditate adhesionCannulae : hollow glycopro tubes link cells , together to form comp network Flagellum us archaellum : Grow from base not tip Use ATP ,. Diversity : Evryarchaeota, Crenarchaeota, thaumarchaeotal low temp , oxidize ammonial , nano archaeota at Many proposed phylum : Koracheotal from URNA sea of non-culturable microges) aigararchaeota · other , Crenarchaeota ↓temp) : Thermophiles/hyperthermophiles acidophiles /low PH , acid mine drain) , barophiles (pressure , btm ocean a , Tetraether · lipids/lipid monolayer , modi pro (morex-helix , more salt bridges/side chain interactions, more arginine/tyrosine, less Cysteinelserine) Strong chaperone pro. comp , thermostable DNA-bind pro , reverse DNA gyrase enzyme to↓ supercoiling · B-Sheet (3 Strand) vs X-helix (1 better) , Eury archaeota Chalophile Salt luvr) , : Nacl [S > 1 SM , ↑ Salt. , S-34 % Salinity , ocean = 3 5 %.. Red evap pond : 02 gone , capture light energy w/bacteriorhodopsin (protein), power Atpprod intracell - Osmotic shock + loss of water : Hypollow salt , Water gain) hyper(saltwater) , iso( ) = · (1st) offset extracell [Nat] k += compat solute , , > ↑ (k+] - denature Split DNA (DNA denature > higher GC (strong bonds) , proden = acidic pro remain more stable in salt = - , Trans-resting > Phototropic : PMF (reddish (e) - No clorophyll or ETC. Bacterichopsodin ; Drive cotransport , catch light energy + makes · Cis = normal Evryarchaeota (methanogens) : Make methane take CO2 , burn Hz- methane + water energy released fix C strict anaerobes (human + Swamp Sedi) Made methane gut = , , ,. in humans combustible = gas , air in swamps Volta exp Invented battery, inverted funnel traps CH4 from swamp ignite flame : , Meth. Habitat ; Anoxic sedi-marsh/swamp , lake, moist landfill. Animal digestive tracts : animal rumen, cecum large intestine (humans ( , Geothermal Hz/CO2 fac Source (hydrotherm vents) , art. biodegrad (Sewage) , endosymbiont of anaerobic protozoa , termite gut symbionts studying : Cow hole take out termite , dig. tract, glow green TACK Superphylum : Thaum , Aig , Cren, Kor archaeota - norm temp Thaumarchaeota : (Now Nitrosopherota) separate phylum for mesophilic crenarchaeotes , ammonium Oxidizing (N cycle) Mesophile : 15-40°c, Psychrophiles - Cenarchaeum Symbiosis resides in marine Sponge , belongs to > North pacific ocean thaumarchaeot a Emerging Phyla : Korarchaeota-16sRNA seq. from hydrothermal env., no species cultivated , 1 genome available Aigarchaeota-No species critivated, 1 genome avail ; thermophile (candidatus Caldiarchaeum subterraneum( DPANN Superphylum : ultrasmall archae : ARMAN (acidic env) and Nanoarchaeum equitans obligate symbiont (hydrotherm env Nanoarchaeotalkey Member of DPANN) : Nanoarchaeum equitans (sole isolated member) , 2 other genomes avail 1 , of smallest living org on Earth , 16s URNA gene seq. ↳ Nanoarchaeum : Nano. equitans in hydrotherm Vent north of Iceland and Ignicoccus (crenarchaeota) : Obligate parasite (he said question mark) > 0 4 um. /ly. Vol of E Coli). , 0. 49Mbp genome (no met genes , only carry genes for replic.,transc., transl DPANN Superphylum : < 1 um , small genomes (1mb) , restrict Meta (unable 2 gen.. building blocks) , mutalistic or parasitic ? Asgard Superphylum Og : thought Loki was closest relative , actually Heimdall Loki/Thor Thermophilic, : group wlevkary prot 4 cell compartment· Early stages of comp cell evolution on some phylogenies , erk-like. Topic 4-Eukaryotes Morphology : mem-bound nucleus , larger than bacteria or archae, has organelles, have cell wall complex internal cytoskeleton V Organelles : Nucleus - Most of DNA here site of transc double mem , , w/pores, Outer mem. continous W/ER DNA gen , ribo + transcr. 7 ATP Mitochondrion-energy prod , double mem., has DNA , independent rep , not in amitochondriates , TCA cycle + uses ETC to make Replicate independ. Chloroplast-Photosynthesis , X2 mem has DNA , , independ rep , unique. to photosynthetic organisms , use Etc to make ATP + fixco2 -> glucose Rough ER-translation here + pro· folding , has protein-synthesizing ribosomes attatched to i t Golgi Apparatus - Modifies, sorts + transports protein , connected to ER thru vesicles. Secretory path Vacuole-Storage + Stru food vac serve as sites. of digestion , contractive vac maintain water balance , of Lysosome Digestion Macro, has dig enzymes -. Peroxisome-Breakdown fatty acid , contain many oxi enzymes (Catalase. + oxidase) ATP , double foundinamitochondriates, remnant of mitochondrion Prod of Hz mem , Hydrogenosome - + diffusion (no energy needed) + active trans (need energy) , plays role in homeostasis Plasma Mem-Phospholipid bilayer,  Function Bacteria Archaeons Eukarya Bilayer or monolayer, Isulfo- , glyco Phospho bilayer Membrane Structure Mem assembly. , hydrphillic surface , hydrophobic core phospholipid bilayer , isoprenoid Ester linkage Ether Linkage Ester linkage Lipid Structure Membrane firidity straight fatty acids Branch isoprenoid chain fatties ~ straight cyano-hopanoids * None Yes ~ Sterols Mem Mycobac-sterols * Stability Proteins Structural ↑ Abundance ↑ Abundance ↓ Abundance Bacteria Eukarya Gramt Gram Archaea Fungi Algae Protozoa Struc. Thick peptidoglycan Thin peptidoglycan varied. Methanogens : pep. ~