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Mysteries of Zhang's Research at TTU.
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Nori used as a sushi wrap is produced by growing Porphyra, a ________, in tanks. - ansred algae The electrophoretic mobility shift assay (EMSA) is utilized to monitor molecular interactions between... - ansDNA and proteins In many bacteria, the electron carrier ______ is used for biosynthesis, wereas ______ feeds the electron transport system. - ansNADPH; NADH How many turns of the Calvin cycle does it take to provide one molecule of glyceraldehyde- 3 - phosphate into the biosynthesis of glucose? - ans Which of the following is NOT a terminal electron acceptor in anaerobic respirations? - anshydrogen sulfide The recipient of Hfr conjugation _________ becomes an F+ or Hfr cell. - ansrarely The difference between generalized and specialized transduction is... - ansthat in generalized transduction, any DNA can be moved, but with specialized transduction, only certain DNA near the phage site can be moved. Mold ripening refers to the secondary _______ stage of cheese production. - ansfermentation A bacterium capable of producing methane and water from carbon dioxide and hydrogen performs a type of metabolism called _______ and, given its sources of electrons, it is a _________. - ansmethanogenesis; chemolithotroph Chemoorganotrophy is a term describing microorganisms that... - ansuse organic compounds as a source of electrons and obtain energy through fermentations or respiration What kind of mutation is produced by transposable elements? - ansinsertion _______ prevent transcription, whereas ________ stimulates transcription. - ansRepressors; activators Hydrolysis of ATP with the release of pyrophosphate is the driving force of which of the following reaction(s)? - ansDNA and RNA synthesis A derivative F plasmid that contains host DNA is called an... - ansF' plasmid How does bacteriorhodopsin couple photoexcitation with proton pumping? - ansLight- induced conformational changes of retinal cause the protein to extrude one proton. Electron transport systems are embedded in what membrane system, among others? - ansmitochondrial inner membrane thylakoids inner membrane of Gram-negative bacteria Which of the following is the most common cause of food-borne deaths in the United States?
- ansSalmonella Which form of control is the most rapid? - anstranslational control Most virus particles produced from an influenza virus infection are... - ansdefective A loss-of-function mutation could NOT be caused by... - anssilent mutation HIV-infected cells can fuse with a neighboring cell, resulting in the formation of a giant multinucleate cell called a(n)... - anssynctyium Which of the following best describes the genome of the influenza virus? - ansnegative- strand segmented DNA Once T4 DNA has been injected into host cells, all of the following virus life cycle stages take place EXCEPT... - ansT4 undergo lytic or lysogenic cycles depending on environmental factors
Mysteries of Zhang's Research at TTU.
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A modest level of ethanol enters the human circulation naturally from _______, equivalent to a fraction of a drink per day. - ansintestinal flora Herpes simplex viruses causes primary _______ infections - ansepithelial The process of importing free DNA into cells is known as... - anstransformation Production of traditionally fermented foods typically relies on ________ flora, whereas commercially fermentation generally relies on ________ - ansindigenous; starter cultures What type of reporter fusions can expose both transcriptional and translational controls? - ansgene fusions Extreme halophilic archaea exclusively utilize which kind of ion gradient? - anssodium ion The role of leader sequence in Tryp operon is to... - ansdetermine whether transcription can proceed through the genes in the operon Which pathway is utilized for carbon fixation in chloroplasts and cyanobacteria? - ansthe Calvin cycle or reductive pentose phosphate cycle Microbial biosynthetic processes require... - ansessential elements reduction energy Infection of potato crops by the fungus Phytophthora infestans is a constant menace to farmers. A biotechnological approach to prevent the recurrence of such an infestation is... - ansintroducing a wild potato gene that conveys resistance to P. infestans into commercial potato breeds Cyanobacteria have _______-based photosynthesis and are the only _______-producing bacteria - ansH2O; O Which of the following is the favored carbon source of E. coli? - ansglucose The enzyme pyruvate kinase catalyzes the conversion of phosphoenolypyruvate to pyruvate; the phosphate group is transferred to ADP to form ATP. This reaction is an example of... - ansATP synthesis by substrate-level phosphorylation Which form of control is the least reversible and most drastic? - ansalterations of DNA sequence Which of the following molecules links glycolysis with the TCA cycle, and also serves as a precursor for many biosynthetic products? - ansacetyl-CoA The purpose of a DNA protection assay is to determine the nucleotide sequence directly interacting with which macromolecules? - ansDNA-binding proteins Drug resistance arises quickly for Hepatitis C virus due to... - anshigh error rates at the hypervariable regions within the RNA genome western blot - ansdetects protein molecules southern blot - ansdetects DNA fragments northern blot - ansdetects RNA molecules eastern blot - ansdoes not exist what does western blot use - ansantibody to detect specific protein real-time PCR - ansdetermines DNA or RNA levels affinity chromatography - anspurifies protein products EMSA - ansdetermines if a protein binds DNA DNA-protection analysis - ansdetermines where in DNA protein binds two hybrid analysis (yest system) - ansdetermines whether protein x binds to protein y (protein-protein interactions)
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lactic acid is a carbon ___ molecule - ans pyruvate is a carbon ___ molecule - ans ethanol is a carbon ___ molecule - ans acetyl-coa is a carbon ___ molecule - ans gylcolysis (EMP) pathway - ansmost common yields 2 pyruvate, 2 ATP, 2NADH entner-doudoroff (ED) pathway - ansused by gut microbes feeding on gluconate (sugar acid) yields 2 pyruvate, 1 ATP, 1 NADH, 1 NADPH Pentose Phosphate Pathway (PPP) - ansgenerates c3-c7 intermediates for biosynthesis yields 1 ATP, 2NADPH Tricarboxylic Acid (TCA) Cycle - ans1 pyruvate generates 3 CO2, 4 NADH and 1 FADH2, 1 ATP generates intermediates for biosynthesis How can glucose theoretically generate 38 ATP? - ans2 ATP from glycolysis 2 ATP from TCA cycle 10 NADH (3 ATP per each) + 2 FADH2 (2 ATP per each) Glyoxylate bypass - ansglycosxylate makes a shortcut with acetyl-coa to form malate cells can generate sugar from non carbohydrate metabolites (glucogenesis) important for tuberculosis (glucose deprived) In bacteria: Two ETS generate either __ H+ for each NADH or __ H+ for each FADH2 in NADH oxidation - ans8; In eukaryotes: mitochondrial respiration is more____ and more ____ generating ___ protons per NADH. only One ETS. - anscomplex; efficient; 10- 12 F1F0 complex - ans-F0 is embedded in the membrane and movies protons
- F1 protrudes into cytoplasm and generates ATP
- can run in reverse direction to pump things out (ATP->ADP) lithotrophy - ansacquisition by oxidation of inorganic electron donors (Nitrogen or sulfur) can cause severe environmental acidification methanogenesis - ansreduction of CO2 and other single carbon compounds to methane performed only by archaea by methanogens phototrophy - ansharnessing of photoexcited electrons to power cell growth (thylakoids) bacteriorhodopsin - anssingle protein, light driven proton pump retinal-based proton pumps - ansfound in halophilic archaea Photosystem 1 (PS1) - ansDonor: H2S or Organic compound Acceptor: NAD+ or NADP+ anaerobic green sulfur bacteria (clorobia) Photosystem 2 (PS2) - ansDonor and Acceptor: bacterioclorophyll cyclic photophosphorylation anaerobic found in purple nonsulfur bacteria oxygenic Z pathway - ansincludes elements of PS1 and PS Donor: H2O (ultimately making O2) Acceptor: NADP+
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carried out by cyanobacteria and chloroplasts (thylakoids) microbes include members of which of the following groups? - ansbacteria, archaea, fungi, viruses which of the following scientist-contribution pairs is not matched correctly? - anslouis pasteur proved spontaneous generation what is robert kochs contribution - ansdeveloped the criteria for establishing a causative link betwen an infectious agent and disease what is leewunhoek's contribution - ansdiscovered individual microbes what is nightingales contributions - ansfounded medical statistics kochs postulates include all of the following except what - ansthe pathogen must be shown to contain toxins kocks postulates - ansa pure culture must be obtained, pathogne must be found in every individual suffering from the disease, the isolated pathogen must be used to infect healthy hosts, healthy individuals infected with osilated suspected pathogen must get sick with disease who performed the first vaccination - ansedward jenner who discovered the first antibiotic - ansalexander fleming who are the ancestors of mitochondria - ansproteobacteria what size are normal microbes - ans10-100um what type of microbes are less than 10um - ansprokaryotes what is the correct order of reagents in gram stain - anscrystal violet, idodine, ehtanol, safranin in fluorescence micorscopy, the specimen absorbs incident light and then re-emits a _____ energy and a _____ wavelength - anslower, longer which of the following microscopes allows the best view of bacterial flagella during motility
- ansdark-field microscope what type pf microscopy exploits differnces in refactive indices between cell parts and surroundign media as well as all live cells - ansphase-contrst microscopy scanning electron microscopy - ansspecimen is fixed and embedded, it cannot be used to view live specimen, provdes 3D image of the specimen atomic force microscope - ansmeasures van der Waals forces, example of scanning probe microscop e what is the best method to examining the presensce of a chemical structure with a diameter of 3nm? - ansx-ray crystallography what is the structure of prokaryotes that performs the same function as mitochodria in eukaryotes - anscell membrane lipids - anshave ester linkages, while those of archaea have ether linkages component of peptidoglycan - ansn-acetylmuramic acid, n-acetylglucosamine, amino acids, peptide cross-links prokaryotic outer membrane - ansfound in gram negative bacteria, contains porins, contains toxic component, contains lipopolysaccharide layer prokaryotic chromosome - anshas a single origin of replication and then DNA is replicated bidirectionally what does a stalked cell in caulobacter crescentus divide to reproduce - ansa stalked cell and a flagellated cell
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disadvantages of phage therapy - ansdifficult to administer w/o triggering immune response (OK for topical), bacteria can develop resistance just like antibiotics, can mediate horizontal gene transfer among bacteria uses sunlight for energy and CO2 as a carbon source - ansphotoautotroph ABC transporters statements - ansrequire energy, used for imports and export, largest family of transporters define selective media - ans define synthetic media - ans define differential media - ans how long does it take a bacterium with a generation time of 20 minutes to produce about a thousand cells - ans what shortest lag period would most likely be observed if a culture is transferred - ansfrom a complex medium to a fresh complex medium microbes that grow at very high pressures - anspiezophiles what type of organism will grow evenly throughout a tube of thioglycate broth medium? - ansaerotolerant anaerobe one thing organims cannot due during starvation - ansform metabolically inactive endospores what physical agents are used to prevent bacterial growth - ansautoclaving, irradiation, and freezing scanning electron microscopy is most likely used to reveal what - anssurface structures a type of microscope that exposes specimen to UV, violet, or blue light and froms and image with the light emitted at a different wavelength - ansfluorescence function of the cytoplasmic membrane of bacteria - ansretains cytoplasm and its contents, acts as a selectively permeable barrier, major site of ATP synthesis in aerobes most human pathogens are - ansmesophiles what microscope allows best view of live bacteria surface - ansatomic force microscope unit of measurement for the size of microbial cells - ansmicrometer an aquatic microbe that can only grow near the surface of the water is what - ansa phototroph what is resolution - ansthe smallest distance by which two objects can be seperated and distinguished what is the resolution of the human retina - ans~.15mm shapes of prokaryotes - ansbacilli, cocci, spiral nanometer range of human eye - ans400- 700 shorter wavelengths offer more___ - ansprecision and higher resolution what microscopy is most common in lab - ansbright field type of microscopy generate a dark image of an object over a light background - ansbright field function of fixation - ansfix the movement of internal organelles of cell. if not, the cell wall will deteriorate over time fixation - anscells are made to adhere to a slide in a fixed postition components of stain - ansconjugated double bonds or aromatic rings, and one or more postive charge differential stain - ansstains one kind of cell but not the other most important type of stain - ansgram stain 1st step of gram stain - ansCV
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2nd step of gram stain - ansiodine 3rd step of gram stain - ansdecolorizer 4th step of gram stain - anssafrinin why does the purple CV not retained in the gram negative bacteria - ansthe cell wall is thinner than that of gram positive bacteria, so it is unable to trap the dye wihthin the peptodoglycan layer what type of gram bacteria are stained blue/purple - ansgram postive what type of bacteria are stained red - ansgram negativ what is acid fast stain used for - ansdetect mycobacterium species what is spore stain used fro - ansto stain unique endospores, clostridium and bacillus. green in colore how does negative staining work - anscolors the background, with makes capsule more visible because of the negative charge of the polysaccharide what is differential interference contrast - ansmore advanced version of phased contrast explain dark field microscopy - ansdetectiion limit is not equal to the resolution limit, only the light scattered by micorbes reaches the object, sensitive to dust particles and causes artifacts explain bright field microscopy - ansstain and fixation, but sometimes it kills the cells explain phase contrast microscopy - ansincrease or enhance contrast bw cells and background. BUT you can only see large cells. hard to see individualized bacteria explain differential interference contrast - anspolarized light generates two images. more advanced version of phased contrast fluorescence microscopy - ans3D visualization (high res, bright color, vibrant) but it is very expensive fluorophore - anschemical that can absorb certain wavelengths and then emit another wave at a longer wavelength, but the handling of the equipment requires high level of skill bright field microscopy - anssimple process and portable, but it kills live cells dark field microscopy - ansallows us to detect specimens no visible in bright field, but it is prone to artifact and has low resolution phase contrast microscopy - anscan see living cells and organelles without needing to stain/fix, but cannot see single bacteria Electron Microscopy (EN) - ansalways B&W, super high res, sample must be able to absorb/block electrons. behave like waves transmission electron microscopy - anselectrons pass through the sample and reveal internal structures. like bright field microscopy Scanning electron micro (SEM) - ansshoot e- beam at surface, generates external structures. labor intensive, has to be stained Cryo EM - ansflash freeze, internal structure preserved and much harder Cryo ET - anssame procedure as cryo EM, but takes multiple images, like z stack. has to withstand bombardment of e- multiple times Scannin probe microscopy - anscan be used to observe live bacteria in water, enables nonoscale observ. of cell surfaces xray diffraction - ansmake molecule into crystal cell membrane - ansthe structure that define the existence of a cell membrane proteins & lipids - ansstructural support and signaling and communication
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thykaloid - ansonly found in cells capable of photosynthesis. the organelles here are capable of processing solar energy carboxysome - ansstorage in chloroplast for eukaryotes. trap solar energy and convert to reducing power, then used in carboxysome for sugar capsule - ansmade of polysacc and glycoprotein, outside of the regular cell wall of bacteria, use this as a protective coat from immune response s-layer - ansbacteria and archae. protection against osmotic pressure and immune response, crystallline structure, atomic microscope to see fimbrae - ansprotein based polymer, used in attachment sex pilli - ansgenetic exchange of gnes nanotubes - ansbacteria use to connect to each other, pass material from one cell to the next flagella - ansused for motilit CCW flagella - anstoward attracant CW flagella - anstumble, stops forward motion peritrichous - ansall over flagella lophotrichous - ansat both ends flagella monotrichous - ansflagella at one end chemotaxis - ansmovement of bacterium in response to chemical gradients. tells cells where attactant and infereior envirioment are (only in motile cells) many lab bacteria strains lack structures such as capsules, s-layer, pilli and nanotubes. why is that and how can you maintain these structures? - anspopulation will resemble those in lab, not nature. replicat a natural encvironment macronutrients - ansCOHNPS autotrophs - ansfix CO2, and assemble into organic molecules. generate their own biomass biomass - anstotal mass of an organism heterotrophs - anscreatures that must use preformed biomass (animals and humans) photroph - ansobtain energy from light chemotrophs - ansobtain energy from oxidation reduction rxns, transfer of e-, energy is released lithotrophs - ansuse inorganic molecules as source of e-. use electron donor, methane organotrophs - anstype of chemotroph that can only acquire e- from organic molecules PMF - ansharvest eneryg (electrochemical potential) used with membrane and gradient bacterial membrane ATP synthase - anschemical that can diffuse to any part of the cell, less restrictive to PMF, hydrolysis of ATP generates energy use of atp sythase in ATP synthess - ansAT: synthase is embedded in the membrane, flow of e from the Fo portion will cause rotation of globular flagella, rotation will begin the synthesis of ATp often the FO can reverse directions :eplain - anssometimes the cells that hydrolize ATP on the cytoplasmic site is in the opposite direction adjusting the membrane Ph diffusion - anscells can directly pick up nutrients if there is a favorable [] gradient (flow from high to low until eq) facilitated diffusion - ansrequire aid of transport proteins. does not go against [] gradient. glycerol active transport - ansrequires energy (either STP hydrolysis or PMF), brings in nutrients aginst the [] grad.
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ABC transporter - anshydrolyzes ATP into ADP plus proteins. changes shape so that it can bind to nutrient, pops outside of cell. how cells develop resistance coupled transport system - ansmovement of molecule if coupled to movement of another molecle symport - ans2 substrates in the same direction. On is moving along []G through transport, release energy, energy is used to couple movement of another molecule against [] grad antiport - ans2 substrates in opposite direction. along []g (why energy expenditure is cancelled out) group translocation - anspro only. chemical substrate will be modified once it enters cytoplasm components of group translocation - anscan save genetic capacity, no specific systems for every substrate, when the chemical is phosphorylated it can byoass [] gradient sideophores - ansbring in iron. active. cells will secrete molecules, have a high affinity for iton, diffuse back to CM, find receptor, hydrolyze ATP.. host cells will try to starve microbes synthetic media - ansevery component within media is chemically defined, must be consistent from time to time complex media - ansricher but less define, natural product, varies batch to batch enriched media - ansneeded for microbacterium, has to be spiked with something (serum, blood, plasma) selective media - ansfavors one type of bacteria, something that you allow the type of one microbes but not tohers differential media - ansdistinguish different species. expolit differences optical density - ansquickest. measure absorbance, not as direct, unable to distinguish live/dead, dormant/active direct counts - ansserial dilution, directly count cell bodies. much more direct than optical density, cannot tell live death viable counts - ansplating, streak etc. interested in the ones that are viable and capable of growing only biochemical assay - ansmeasure total amount of proteiin, ATp, and biomass. not directly correlated to cell # batch culture - ansself contained system lag phase - ansthe cells are still adjusting, no increase log phase - ansbinary fission, exponential phase. Nt=No x2^n stationary phase - ansamount of new cells are cancelled by the ones that dies, no growth. depletion of nutrients and accumulation of waste death phase - ansthe cells toxic waste builds up and the cells begin to die biofilms - ansheterogenous collaborative communites that must attach themselves to a solid surface development of biofilms - ansattach to monolayer by flagella, micro colonies (when biofilm can be detected), exopolysaccharide production, mature biofilm, dissolution and disperal cell differentiation - ansbacteria faced with environmental stress undergo complex molecular reprogramming that includes change in cell structure endospore - ansspore remains in cell body of mother cell temperature limit on bacteria - ans0-100 degrees C. 70% of every cell is water so you will not find microbes outside this range
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gram postive are more sensitve to penicillin because - ansthe thick cell wall. this type is dependent on the integrity of cell wall why is penicllin not as effective in gram - - ansthinner pep layer. they have other means to maintain cellular structure virus - ansnoncellular particle that must infect the host cell to repro Most abundant creatures on this planet - ansvirus what constitutes the virion - ansSomething that has a virion and most of its genome is DNA or RNA (not both) and a capsid protein capsid - ansforms a strucutre that protects a genome and is required in a virus cell envelope - anssimilar to CM of bac, made up of phosplipids but not all have these virion - ansnucleic acid (DNA or Rna) + protein capsis icosahedral virus - ansmost common, almost globular, 3,5,2 fold symmetry filamentous virus - anshelical. plant virus, capsid forms a spiral poylmer t4 bacteriophage - anselaborate structure, no room for organlles, evading microbe e coli. once it invades e coli, it will invade progeny and the new virus will invade bacteria poxvirus - ansanimal, envelope w/ glycoproteins, matrix, not symmetrical viroid - anspiece of RNA, major plant pathogen, does not encode but can used plant machinery to replicate, no animals because we dont have RNA dependent RNA polymerase prion - ansinfectious particle that can infect humans and animals with no nucleic acid genomes. mad cow. zombie like, converts shape what will happen if viruses are removed from earth - ansthere will not be equilibrium or genetic diversity. no recylcing of essential nutrients baltiore virus classification - ansbased on genomes, makeupe and how they generate mRNA group 1 BVC - ansdouble strnded DNA, uses it own or host polymerase for replication Group II BVC - anssingle stranded DNA, converted to double strand and requires DNA polymerase to genertae comp strain group III BVC - ansdoubel stranded RNA. require RNA depend. RNA polymerase to make mRNA and genomic RNA Group IV BVC - anssingle stranded RNA. requires RNA depend. RNA plymerase to make template for mRNA rep. does not have to be packed Group V BVC - ansdoes not translate. RNA depend RNA polym already packed in capsid (flu, ebola, rabies) Group VI BVC - ansretrovirus. RNA genome but to repro it has to be reverse transcribed to make DNA then RNA then mRNA Host recogntion and attachment - ansmediated by ligand and capsid in virus itroduction of genome into cyto plasm - ansRNA cytoplams, DNA to cytoplasm then nucleoid in ciruses Repro or replication of genome in viruses - anssynthesize and assemble vrion bacteriophage - ansa virus that parasitizes a bacterium by infecting it and reproducing inside of it lytic cylcel - anseven #, "burst" out of host. invade host, replicate itself, release dozens of progeny phases that can invade other hosts, kills hsot lysogenic phase - anstemp. phage attaches to host, sends DNA, circularized, recombines into host by site specific recombination prophage prophage - ansbacterial material of bacteriophage
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slow release bacteriophge cycle - ansbw lytic and lysogenic. phage does not integrate host chromo, phage pops up out of infected host cell slowly to prevent killing it. makes them sick bacterial host defenses - ansgenetic resistnace, restriction endonuclease, CRISPR CRISPR - ansadaptive immunity, bacterium recovers from phage infection, keep phage DNA parts, that peice will be activated if needed, then the RNA will chop it stages of animal virus life cycle - ansattachment, replication of genome, assemble of virion, exit dna virus replication - anssingle or double, uses a host cell polymerase RNA viruses replication - ansthe neg strand RNA must pack enzyme in virion. + strand can be directly translated. (((encode and RNA dependent RNA polymerase))) Retrovirus replication - ansRNA genome, has to be convereted to DNA by reverse transcript, DNA intermeditae will integrate into host genome (provirus) assemble of new virion in DNA - anssynthesis in nuclues (virion) assembly of the new vrion in RNA - anscytoplasm. depend on the organelles in euk plaque assay - ansdump virus at different dilutions until pfu=cfu batch culture - anslarge amount, invade w/phage eclipse period of batch culture - anstime virus takes to invade, assemble and exit. no death phase burst size - anshow many viral particles can be produced from a given # of host cells viral ecology - anscan select host density and diversity, will inhbit growth of other microbes when eq is disrupted, population density will decrease and host cell diversity will burst. genomes - ansall of the genetic materail that makes up an organism chromosome - anscontains gentic info in the form of genes in nucleus plasmids - anscode nonessential genes. much smaller than chromosomes single gene in prokaryotes - ansa promotor region, followed by untranslated region, then coding sequence. codes for one thing bacterial genes are (shape) - anscircular regulon - ansa single protein factor that can bind to promoter of multple organisms. any complex process require coordinated expression of many genes (can turn on and off dozens of genes at the same tiem) operon - ansa unit of linked genes that regulates other genes responsible for protein synthesis nucloid - ansnot membrane bound eukaryotes must hav - ansmembrane bound material histone like anchroing proteins - ansbind to negatively charged DNA to make sure it is clustered and condensed enough to fit into tiny cells what happens w/o DNA super coiling - ansbacterial cells do not have sufficient space to hold genome postive superocul - ansopposite directions, common among archaea that are extremophiles, rare in nature, cause bond tension and can cause breakage of DNA negative supercoil - ansDNA is underwound, generate condensed DNA, does not live in hot springs topoisomerase - ansenergy dependent (DNA packaging, replication) Topoisomerase 1 can - ansreduce superocoils, relaxed DNA Topoisomerase 2 can - ansincrease supercoils. increase tension (have ATP hydrolysis as energy source) microbes cannot package if this is absent
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differences between RNA replication adn DN replication - ansDNA replication fork can be bidrectioanlly, RNA replication is unidirectionally. RNA polymerase does not require any primer, DNA polymerase does drugs that block initation and elongation of transctiption - ansRifamycin (RNA) and acnitomycin (DNA) mRNA - ansintermediat that can be used in translation to synthesize proteins, does not have any direct function without being translated first rRNA - ansmost abundat. component for ribosmes, much longer half life than mRNA tRNA - ansbringing amino acids into translation machinery (codon and anticodon pair) sRNA - ansless than 100 nucleotides, regulate gene expression, stablize or destablize other RNA tmRNA - ansunjam tRNa that got stuck on ribosome. due to lack of proofreading (hybrid of tRNA and mRNA) catalytic RNA - ansprotein based enzymes translation from RNA to protein - ansthe production for mRNA with help of ribosomes and tRNA (initiaiton, elongation, termination) each phase in translation from RNA to protein needs what - ansa number of protein factors and energy in the from of GTP start codon - ansAUG 99% of the time (where transltion starts) stop codon - ansalways more important than start, UAG, UAA, UGA hy do some amino acids have six codons while others only have one or two? Besdes providing tolerance to mutations, what other implications does codon redundancy have? - anso Some are naturally more abundant in proteins o Synthesizes alanine is easier than trypton (many more steps, energy, resource) so this explains why these are rare o The redundancy provide buffering on mutations (especially on abundant ones) unless there is a drastic change in 1st or 2nd codon o Doesn't mean all cell use same preferences Sometimes in biotech, you cannot use gene directly because it will not be expressed directly, mus change codon preference general secretion complex - ansmajority of proteins that need to be secreted are mediated by this translocon Shine dalgardo sequence - ansonly found in RNA, not euk. helps determine right readng frame promoter region - ansfound in DNA not RNA polysoe - answhen you have mRNA that is bonded to multiple robosomes couple translation and translation - anspro only, mRNA may be trancribed from RNA polymerase and roboses bind to start translation right away (no cell E) chpaerones - ansuse ATP hydrolysis to refold a protein orthologous gene - anssame gene from difff organism paralogous - anssame gene from same cell homologs - ansorthologous and paralogous resolution - anssmallest distance by which two objects can be seperated and distinguished (HUMAN RETINA: 150UM) prokaryotes are usually - anssmller and simpler than euk
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acid fast stain - anscarbolfuschion to stain mycobacterium species spore stain - ansmalchite green used to detect spores of bacillus and clostridium differential interference contrast microscopy - ansenhances contrast superimposing one image and the specimen onto a beam of light that gnerates interferene fringes antione van leeuwonhoek - ansfirst to observe single celled microbes why should be study microbes - ansenvrio and ecology, primary producers and decomposers, food ag and industry, health and med nightingale - ansfirst nurse to use medical statistics to demonstrate the significance of mortality due to disease fleming 1929 - anspenicllium mold genertaed a substanc ethat kill bacteria microbes= - ansbacteria+archaea+protist+fungi+virus pasteur - ansswan neck dispoved spontaneous generation koch - ansfather of scientific method of mbio (posulates to determine the causality agent of disease) pastuer - ansdeveloped the first vaccines rabies piezophiles - ansmicrobes that grow at very high temps why cant bacteria grow in solutions with viery high [] of sugar - anssugar raises the solutions osmolarity a bacterium tolerates a pH range of 3-10. this represetns ______ difference in h+ ion [] - ans10,000,00 fold what can organisms do during starvation - ansundergo programmed cell death, protect against reactive oxygen species, protect against temp and pH extremes marine viruses play a role in which of the following cycles - anscarbon cycle what do all viruses contain - ansa capsid and a genome viroids are ___ agents that infect ____ - ansRNA, plants what does the bacteriophage t4 posses? - ansa icosohedral head and helical neck the baltimore system classifies viruses based on predominately what feature - ansmeans of RNA synthesis when a bacterial cell is infected by a bacteriophage the capsid - ansremains on the outside of the hsot cell some bac. virusses can insert their genome into chromo of hsot. what is that called - ansprophage genome - ansthe primary factor determining the life cycle of animal virsu the period of time whe virons are virtually undetectable - anseclipse period the sequence of one strand of DNA 5" TCGATC 3' what is the comp strand - ans5' GATCGA 3' supoercoiling is typically introduced by an enzyme calle dDNA - ansgyrase correct order of proteins involved in DNA replicatioin - ansDNAa, primase, DNA pol III, ligase primer in DNA replication ____ starter sequence with a free ___ group - ansan RNA, 3'OH noncoding sequences of euk chromo - ansintrons and pseudogenes sigma factor is required for - anstranscription initiation what can cause term of transctop - ansstem loop structure and stop codon gentic code quad as opposed to triple would be - ans what are proteasomes - ansprotein degarding organelles found in euk and archaea
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- can be seen with naked eye
- grows in GI tract of surgeonfish
- gives "live birth" to two internal offspring
- cells don't undergo binary fission Bacillales - ans-genus Bacillus
- Firmicutes
- large rod-shaped cells
- includes: B. anthrax, B. thuringiensis, and B. subtilis
- vegetative cells develop inert endospores in times of starvation and stress
- released spores germinate in favorable conditions and then restart vegetative growth Gram-Positive Bacteria - ans2 phylogenic branches:
- Phylum Firmicutes (low-GC species)
- Phylum Actinobacteria (high-GC species)
- both groups have thick cell walls that retain the Gram stain
- walls are reinforced by teichoic acids Cyanobacteria - ans-only oxygenic phototrophic prokaryotes (contain chlorophyll)
- conduct photosynthesis in thylakoids
- fix CO2 in carboxysomes
- maintain buoyancy using gas vesicles
- many fix N2 in heterocysts
- includes the single celled Synechococcuss and Prochlorococcuss
- most abundant phototrophs in oceans
- some genera are filamentous: Oscillatoria, Nostoc, and Anabaena
- these form spores called akinetes
- Pleurocapsa form colonies and reproduce through baeocytes
- Trichodesium form giant blooms Phylum Deinococcuss-Thermus - ans-in Deep-Branching Thermophiles
- have ornithine in peptidoglycan cross-bridges
- Thermus species
- moderate thermophiles
- heterotrophs
- Deinococcuss radiodurans
- not thermophilic
- resists extremely high dosage of radiation, and desiccation
- thick cell wall and S-layer Chloroflexi - ans-in Deep-Branching Thermophiles
- photoheterotrophic and moderately thermophilic
- green nonsulfur bacteria
- contain photosynthetic apparatus within chlorosomes
- forms filamentous mats in associated with thermohilic cyanobacteria Aquificae and Thermotogae - ans-in Deep-Branching Thermophiles
- most extreme bacteria hyperthermophiles
- genomes show extensive transfer of archaeal genes
- Aquifex pyrophilus- a flagellated rod
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- Thermocrinis ruber- froms filamentous mats in hydrothermal vents
- Thermotoga maritima- uses anaerobic respiration Deep-Branching Thermophiles - ans-appeared to have diverged the earliest
- includes extremophiles with similar physiology and habitat of archaea
- fastest doubling rates and high mutation rate
- includes: Aquificae, Thermotogae, Chloroflexi, and Phylum Deinococcuss-Thermus
- Chloroflexus species are thermophilic photoheterotrophs Bacterial Phyla - ans-Deep-Branching Thermophiles
- Cyanobacteria
- Gram-Positive
- Proteobacteria
- Deep-Branching Gram-Negative
- Spirochetes
- Chlamydiae, Planctomycetes, and Verrumicrobia Deltaproteobacteria - ans-Myxococcus xanthus: soil bacteria that can grow as isolated cells or aggregate into fruiting bodies (if starved)
- can disperse spherical myxospores
- Bdellovibrio species: parasitizes proteobacterial cells
- penetrates into periplasm where it uses host resources to grow Gammaproteobacteria - ans-sulfur and iron phototrophs; Chromatium
- single flagellated rods, use sulfide, produce sulfur which is deposited into cytoplasmic granules
- sulfur lithotrophs; Beggiatoa
- oxidize H2S to sulfur, deposited in periplasmic granules Enetrobacteriaceae
- versatile rods
- includes E. coli and Proteus species
- Proteus are heavily flagellated and display remarkable swarming behavior
- aerobic rods; Pseudomonas have polar flagella and are vigorous swimmers (may give up motility to develop biofilms)
- Legionella pneumophila grows intracellularly within macrophages and freshwater amoebas Betaproteobacteria - ans-photoheterotrophs; Rhadocyclus
- lithotrophs;
- nitrifiers oxidize ammonia to nitrite
- Nitrosimonas used in wastewater treatment
- sulfur and iron oxidizers; Thiobacillus
- Pathogens;
- Neisseria gonorrhoeae (humans)
- Burkholderia cepacia (animals and plants) Alphaproteobacteria - ans-photoheterophs; unicellular, Rhodobacter sphaeroids
- oligotrophs; adapted to very low nutrient concentrations
- methylotrophs; oxidize single carbon compunds; Methylobacterium
- endosymbionts; N fixers in plant roots; Rhizobium and Sinorhizobium
