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BSC 310 Exam 3 Flashcards

by: Mallory Ivy

BSC 310 Exam 3 Flashcards BSC 310

Mallory Ivy
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This contains 162 flashcards of concise but detailed terms that you need to know for Dr. Olson's third exam. If you would prefer to print out the sheets versus index cards, I have another study gui...
Dr. Olson
Class Notes
BSC 310 Olson Microbiology Regulation inducer repressor repression rna sequencing analysis gene chip endospore sporulation heterocyst isoenzymes sRNA biofilm formation global control network chemotaxis sensor kinase
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This 324 page Class Notes was uploaded by Mallory Ivy on Sunday April 3, 2016. The Class Notes belongs to BSC 310 at University of Alabama - Tuscaloosa taught by Dr. Olson in Spring 2016. Since its upload, it has received 99 views. For similar materials see Microbiology in Biology at University of Alabama - Tuscaloosa.


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Date Created: 04/03/16
454 System 1a DNA is broken into small fragments and attached to small beads. Each is placed into a well on a fiber-optic plate. DNA is amplified by PCR. Each time a base is added to the DNA strand, light is released and is measured in accordance to the nucleotide that was incorporated. 1b acidophiles 2a grow best below pH 5.5; often found in acidic thermal soils associated with volcanic activity 2b acidophilicity 3a dependent on cytoplasmic membrane stability; pH 2 above optima will cause cell to spontaneously lyse 3b activator 4a regulatory protein used in positive control; activator binding site can be several hundred base pairs upstream of the operon 4b activator protein helps RNA polymerase recognize promotor by either 5a changing DNA structure allowing the RNA pol to contact promotor more readily or can interact with RNA polymerase directly 5b aerobes 6a grow at full oxygen tensions 6b aerotolerant anaerobes 7a can tolerate and grow in the presence of O2 even though they cannot respire 7b alkaliphiles 8a -showing growth pH optima of 8 or higher; typically found in soda lakes and high- carbonate soils -some extremely alkaliphiles are also halophiles -some produce hydrolytic exoenzymes that are excreted from the cells; often added as supplements to laundry detergents to remove protein and fat stains 8b anaerobes 9a cannot respire O2 at all 9b antimicrobial agent 10a natural or synthetic chemical that kills or inhibits the growth of microorganisms 10b antimicrobial agent susceptibility assay in tubes 11a A series of tubes is inoculated with the test organism and a given amount of agent is added. After incubation, the tubes are scored for turbidity, and the MIC is the lowest concentration of agent that completely inhibits growth of test organism. 11b antiseptics 12a -aka germicides -chemicals that kill or inhibit the growth of microorganisms but are sufficiently nontoxic to animals to be applied to living tissues -some are also effective disinfectants 12b Attenuation 13a form of transcriptional control by early termination of mRNA synthesis; found in bacteria and archaea -not possible in Eukarya due to physical distance between transcription and translation 13b Attenuation in Tryptophan Operon 14a Leader sequence encodes leader peptide which contains tryptophan codons side-by-side. -If tryptophan is plentiful, the leader peptide will be synthesized and form a stem-loop, resulting in termination of transcription of remainder of operon. -If tryptophan is scarce, causes a stalled ribosome, which results in stem-loop formation that prevents termination allowing the remainder of the operon to be transcribed. 14b autoclave 15a sealed heating device that uses steam under pressure to kill microorganisms 15b autoinducer 16a specific signal molecule synthesized by the participating organism that freely diffuses across the cell envelope in both directions 16b catabolite repression 17a mechanism of global control that decides between utilizing different available carbon sources 17b Catabolite Repression Process on Lac Operon 18a When glucose is present, glucose siphons cAMP out of the cell. However, when glucose levels are low, cAMP is no longer sent out of the cell leaving it to bind to CRP. CRP forms a dimer when bound to cAMP and acts as a regulator. For the operon to be translated though, the repressor must be removed by the inducer (in this case, lactose). Lactose binds to the active repressor and thence removes it from the promotor site unblocking it for transcription. Both of these processes must occur for the lac operon to be transcribed. 18b catalase 19a converts hydrogen peroxide to water and oxygen 19b Caulobacter Differentiation 20a Swarmer= free swimming cells; cannot divide or replicate their DNA. Stalked (attached) cells- lack flagella and are attached to a surface via a stalk with a holdfast reproductive stage. Regulated by GcrA, CtrA, and DnaA i.GcrA is critical for cell division into differentiated cells and thus is active in the daughter cells only ii. CtrA is very active in flagellation 20b chromosomal islands 21a extrachromosomal elements that are not plasmids or integrated viruses; contains clusters of genes for specialized functions that are not needed for simple survival -ex: megnetosome island of Magnetospirillum -some carry a gene encoding an integrase enzyme to move it into a chromosome -target site is duplicated upon insertion; an intact tRNA gene is regenerated while the chromosomal island is inserted in place of what was to be another tRNA gene 21b -cidal agents 22a kill the microorganisms; bacteriocidal, fungicidal, etc. 22b Closed vs. Draft Genome 23a gaps in the sequence annotation is found in a draft genome whereas a closed genome has no gaps 23b compatible solutes 24a -solute that does not inhibit cellular processes in any significant way but allows halophiles to maintain a positive water balance -typically highly water-soluble organic molecules such as sugars, alcohols, or amino acid derivatives -maximum level of compatible solute is a genetically encoded characteristic 24b Connecting Unknown protein with a particular gene from genomic DNA 25a oligonucleotide probes or primers can locate the gene encoding the protein and then identify the gene after sequencing the DNA 25b Connecting unknown protein with particular gene from 2D gel system 26a 1. elute protein from gel and sequence a portion, or 2. identify protein by use of mass spectrometry 26b core genome 27a core genome is a genome found in all strains of a given species 27b corepressor 28a substance that stops enzyme synthesis (ex: arginine) 28b Culture Techniques for Aerobes 29a forced aeration is necessary so the flask or tube must be vigorously shaken or have sterilized air bubbled into the medium through a fine glass tube or porous glass disk 29b Culture Techniques for Anaerobes 30a -Bottles or tubes filled completely to the top with culture medium and fitted with leakproof closures and a reducing agent can remove any remaining O2 -obligate anaerobes can incubate in tubes or plates in a glass jar that is flushed with an O2- free gas or fitted with an O2 consumption system 30b cyclic AMP receptor protein (CRP) 31a activator protein responsible for catabolite repression; only acts when bound to cyclic adenosine monophosphate (cAMP) 31b cyclic di-guanosine monophosphate 32a another regulatory nucleotide; provides physiological changes and expression of virulence genes necessary for biofilm formation 32b decontamination 33a physical method of control that consists of treatment of an object or surface to make it safe to handle; simply removes present organisms 33b depth filter 34a -fibrous sheet or mat made from random array of overlapping paper or borosilicate fibers -important in biosafety applications such as in safety hood 34b Detecting Horizontal Gene Flow 35a 1. presence of genes that encode proteins typically found in distantly related species 2. presence of a stretch of DNA whose GC content or codon bias differs significantly from the rest of the genome 3. however, as more genomes are sequenced, using horizontal gene flow as an explanation can be nulled 35b diauxic growth 36a result of catabolite repression; cells grow first on preferred C source. Once first source is depleted, the organism undergoes a lag phase before resuming on another C source. 36b Difference between first-, second-, third-, and fourth-generations of DNA Sequencing 37a First generation- Sanger Dideoxy Method; read length 700-900 bases Second generation- 454 pyrosequencing; very large number of samples are sequenced side-by-side in the same machine requiring miniaturization and increased computing power Third generation- sequencing of single molecules of DNA based on microscopy (HeliScope Single Molecule Sequencer) or nanotechnology (Pacific Biosciences SMRT) Fourth generation- "post light sequencing" meaning optical detection is no longer used; ion torrent method or nanopore technology 37b Different Classes of Autoinducers 38a acyl homoserine lactones (AHLs), autoinducer 2, short peptides 38b differentiation in bacteria 39a formation of endospores in Gm+ Bacilli and formation of two cell types in Gm- Caulobacter (flagellated cells and those stuck to a surface) 39b disc assay for antimicrobial agent susceptibility 40a Known amounts of an antimicrobial agent are added to filter-paper discs and discs arranged on surface of uniformly inoculated agar plate. The zone of inhibition is proportional to the amount added to the disc, solubility of the agent, diffusion coefficient, and the overall effectiveness of the agent. Used to test clinically isolated pathogens for their antibiotic susceptibility. 40b disinfectants 41a -chemicals that kill microorganisms but not necessarily endospores -used on inanimate objects -important to infection control in medical settings 41b disinfection 42a physical method of control that specifically targets pathogens although it may not eliminate all microorganisms; actually kills or inhibits growth 42b DNA-binding protein 43a -interact with DNA in a sequence-specific manner, usually at inverted repeat, either act as enzymes for a specific reaction on DNA or can either block or activate transcription -does not require formation of stem-loop structure -homodimeric each divided into domains; each subunit of the dimer binds to one of the inverted repeats, thus, as a whole, the dimer binds to both DNA strands 43b effect of methylation on methyl-accepting chemotaxis proteins 44a methylated MCP is more sensitive to repellants and no longer responds to attractants and vice versa; allows cell to continue sense environment 44b effectors 45a Inducers and corepressors collectively are called effectors. Effectors assert allosteric control on their repressors. 45b emergent properties 46a behavior or properties of a particular organism that were not obvious from the original observations 46b Estimated lower limit of number of genes possible for a viable cell 47a 250-300 genes 47b Evidence that chromosomal islands have foreign origin 48a 1. extra regions are often flanked by inverted repeats suggesting they were inserted by transposition 2. the base composition and codon bias often differ significantly from that of the genome proper 3. found in some strains but not others 48b example of regulatory nucleotide 49a cyclic adenosine monophosphate and cyclic di-guanosine monophosphate (see the trend here?) 49b extreme halophiles 50a grow optimally at NaCl concentrations between 15 and 30% and are often unable to grow at all at NaCl concentrations below this 50b facultative aerobes 51a under appropriate nutrient and culture conditions they can grow in the absence of O2 but prefer to grow with O2 51b Feedback Inhibition 52a Works by allosteric enzymes; temporarily shuts off reactions in an entire biosynthetic pathway due to excess end product inhibiting an early enzyme in the pathway 52b filter sterilization 53a -used for heat sensitive liquids or gases -depth filter, membrane filter, and nucleopore filters 53b Finding a Functional ORF 54a 1. locate start and stop codons 2. most functional ORFs must be longer than 300 nucleotides but some are shorter. --> locate potential ribosome-binding sequences 3. codon bias 4. compare to similar genes in other organisms (protein homology) 54b Fourth-Generation DNA Sequencing 55a no longer uses optical detection; release of protons versus light 55b gene family 56a genes that are related in sequence to one another as a result of a common evolutionary origin 56b Genes and Proteins involved with Nitrogen Fixation (6) 57a -NifA- positive regulator for expression of nif genes -NifL- negative regulator for expression of nif genes -NtrC- active when little ammonia is present; promotes transcription of NifA (the positive regulator) -PatS- peptide produced by heterocysts that diffuses in both directions from the cell preventing the formation of more heterocysts -NtcA- transcriptional regulator that functions when α-ketoglutarate levels are high and activates transcription of hetR gene -HetR gene- controls heterocyst formation and genes to eliminate O2 and express nitrogenase 57b genomics 58a mapping, sequencing, analyzing, and comparing genomes 58b global control systems 59a regulatory mechanisms that respond to environmental signals by regulating expression of many different genes; includes flagellar genes 59b Good buffer 60a -a suite of organic molecules called Good buffers have been designed, each of which function best within a specific pH range, thus one buffer will be added to culture medium for an alkaliphile while another buffer will be used for an acidophile's culture medium -Good buffers are separate from potassium phosphate and sodium bicarbonate, which are used for neutrophiles 60b Growth Regions of Thioglycolate Broth 61a -obligate aerobes grow at the top -facultative aerobes grow throughout the tube but best near the top -microaerophiles grow near the top but not right at the top -anaerobes only grow near the bottom 61b halotolerant 62a organisms that can tolerate some level of dissolved solutes but grow best in the absence of the added solute 62b heat shock 63a another global control network that counteracts heat shock by heat shock proteins which help calls recover from temperature stress and damage; can be caused by heat, chemical exposure, and UV radiation 63b Heat Shock Regulation in E.coli 64a In low temperature, the chaperone DnaK binds to an alternative sigma factor (ribosomal polymerase H) RpoH which will be degraded. However, in high temperatures, RpoH is released while DnaK aids in refolding denatured proteins. RpoH is free to transcribe heat shock genes. 64b helix-turn-helix structure 65a A DNA-binding protein domain that consists of two helices connected by a "turn". The first helix is the recognition helix that interacts specifically with DNA. The second helix stabilizes the first. The turn is a short sequence of three AA, the first of which is typically a glycine. -ex: found in lac and trp repressors 65b Heterocyst Formation 66a -Initiated by low levels of nitrogen exhibited by elevated levels of α-ketoglutarate -These elevated levels activate NtcA which activates transcription of hetR gene (controls heterocyst formation and genes to eliminate O2 and express nitrogenase) -PatS peptide produced in heterocysts diffuses into adjacent cells 66b Heterocysts 67a cells where N2 fixation occurs, arise via monitoring of external conditions and cell-to-cell signaling 67b Hfq 68a RNA chaperones that help small RNA molecules to maintain their correct structure 68b homolog 69a genes related in sequence to an extent that implies common genetic ancestry; includes orthologs and paralogs 69b How do alkaliphiles manage bioenergetics when surrounded by such an H+ poor environment? 70a - use of sodium rather than H+, thus a sodium motive force versus a proton motive force - somehow keeps hydrogen ions close to the outer surface of the CM such that they cannot spontaneously combine with OH- to form H2O 70b hybridization 71a the process in which single-stranded, denatured DNA can form hybrid ds molecules with other ss DNA or RNA by complementary or almost complementary base pairing 71b Importance of Metabolome Analysis 72a important in study of biochemistry such as monitoring the levels of secondary metabolites (in plants or microbes) or the production of metabolites by humans in response to different conditions 72b inducer 73a substance that promotes enzyme synthesis (ex: lactose) 73b induction 74a the opposite of repression; transcription is UNBLOCKED in response to a signal; usually affects catabolic enzymes 74b insertion sequences 75a -simple transposable elements whose genes encode only transposition -found in organisms undergoing rapid evolutionary change 75b interactome 76a complete set of interactions among macromolecules within a cell; often so complex when it comes to mapping the interactions that it is more efficient to use a focused network such as the mobility protein network of Campylobacter jejuni 76b Interesting fact: the compatible solute of extremely halophilic Archaea is... 77a KCl! another salt! This salt cannot fulfill the archaea's salt-requirement but it is highly soluble in water and can aid in maintaining a positive water activity in the microbe 77b Ionizing radiation as a disinfectant 78a -EM radiation (typically X-rays) of sufficient energy to produce ions and other reactive molecular species from molecules that can cause damage to macromolecules and kill irradiated cells -unit= roetgen -efficiently kill microorganisms in bulk items such as food products and medical supplies -microbes are more resistant to IR than multicellular organisms 78b Isoenzymes 79a -Different enzymes that catalyze the same reaction but are controlled differently -typically affect branched pathways -Often diminish enzyme activity incrementally 79b labile 80a easily broken down or destroyed by... -DNA is acid-labile while RNA is alkaline- labile meaning DNA is easily destroyed by acids while RNA is destroyed by bases 80b Leader region 81a -first portion of mRNA made when under attenuation control -can fold into two different secondary structures -one structure allows further transcription while the other causes premature termination 81b leucine zipper 82a another DNA-binding protein domain that contains regularly spaced leucine residues that hold two recognition helices in the proper orientation to bind DNA 82b MALDI-TOF 83a -matrix-assisted laser desorption ionization and time of flight used in tandem to determine the mass and molecular formula of a molecule 1. sample is ionized and vaporized. 2. ions are accelerated along column toward a detector. 3. time of flight is dependent on an ion's mass/charge ratio; the smaller the ratio, the faster the ion moves 83b mechanisms for horizontal gene transfer 84a transformation, transduction, or conjugation 84b membrane filters 85a -most common in liquid sterilization -composed of high tensile strength polymers and contain a large number of tiny pores -sterilization of relatively small volumes of liquids -uses a syringe or a pump to force the liquid through the filtration apparatus into a sterile collection vessel 85b metabolome 86a complete set of metabolic intermediates and other small molecules produced in an organism 86b metagenome 87a total gene content of the organisms inhabiting and environment 87b metagenomics 88a -aka environmental genomics -analyzes polled DNA or RNA from an environmental sample containing organisms that have not been isolated and identified -community DNA can be isolated and then assembled into individual genomes -Ex: analyze presence and distribution of different taxonomic groups of bacteria 88b microaerobes 89a aerobes that can use O2 only when present at levels reduced from that in air 89b Microarrays aka gene chips 90a small solid supports to which genes or segments of genes are fixed and arrayed spatially in a known pattern 90b minimum inhibitory concentration 91a the smallest amount of the agent needed to completely inhibit the growth of a test organism; growth occurs in tubes with antimicrobial agent concentrations below the MIC 91b mobile DNA 92a segments of DNA tha tmove from one location to another within host DNA; includes transposable elements as well as insertion sequences and integrated virus genomes 92b moist heat vs dry heat 93a moist heat has a higher, and faster, penetration power of killing organisms than does dry heat 93b Most Common Methods to Survey Proteomics 94a -2D polyacrylamide gel electrophoresis -liquid chromatography 94b negative control of transcription 95a repression and induction 95b neutrophiles 96a optimal growing pH around 5.5-7.9 96b Nitrogenase Activity 97a NifA serves as a positive regulator for expression of nif genes while NifL is a negative regulator -If O2 is present, NifL is oxideized and the protein represses transcription of other nif genes -When there is little ammonia present, NtrC is active and promotes transcription of NifA 97b Noncoding RNA (ncRNA) 98a RNA molecules that are not translated into proteins; Includes tRNA and rRNA, signal recognition particles, RNA used for splicing, and sRNA 98b NrpR 99a represses genes involved in nitrogen metabolism in archaea; it is removed when α-ketoglutarate accumulates and associates with NrpR as a result of low ammonia levels 99b nucleic acid probes 100a -segments of ss nucleic acids whose identity is already known and that are used in hybridization -either radioactive or fluorescent 100b nucleopore filters 101a -made from thick polycarbonate film that is treated with radiation and then etched with uniform holes -used to isolate specimens for SEM 101b obligate anaerobe 102a inhibited or killed by O2 -Ex: Clostridium and methanogens 102b open reading frame 103a a sequence of DNA or RNA that can be translated to yield a polypeptide 103b ortholog 104a a gene found in one organism that is similar to that in ANOTHER organism but differs because of speciation -Ex: LDH in Lactobacillus is similar to all human LDH isoenzymes but differs because of speciation 104b osmophiles 105a live in environments with high sugar concentration 105b pan genome 106a the pan genome also includes the optional "additives" that is only found in some strains; pan genome increases with the number of unique strains that are sequenced 106b paralog 107a a gene within an organism whose similarity to one or more other genes in the SAME organism is the result of gene duplication -Ex: several LDH enzymes in humans 107b Pasteurization 108a uses precisely controlled heat to significantly reduce the total number of microorganisms found in milk and other liquids that would be destroyed if autoclaved *not a method of sterilization because it does not kill all organisms 108b pathogenicity islands 109a type of chromosomal island found in pathogenic strains of a bacterial species; accounts for the genome size difference between pathogenic and non-pathogenic strains while maintaining the same identity and location of genes 109b peroxidase 110a converts hydrogen peroxide with NADH to water and NAD+ 110b pH growth opitma 111a -range is typical 2-3 units of pH -refers only to the exterior environment only! 111b Picrophilus oshimae 112a Archaea that grows optimally at pH 0.7 112b positive control 113a the opposite of negative control; it enhances transcription by use of an activator that binds to an activator-binding site which signals to the RNA polymerase to bind. Promoters of positively controlled operons are poor matches for RNA polymerase.. ex: maltose-degrading enzymes 113b positive water balance 114a when solute concentration is higher within the cell than outside and thus water flows into the cell 114b Post-translational Regulation 115a Addition or removal of a small molecule to an enzyme to affect its activity -Common additions include AMP, ADP, phosphate groups, and methyl groups -Glutamine synthase is a key example- AMP added and removed by other enzymes controlled by NH3 levels. Each addition of AMP diminishes the activity of the enzyme. 115b proteomics 116a study of structure, function, and activity of an organism's proteins 116b Purpose of Microarray 117a -clinical diagnostics -view expression pattern of genes of unknown function is also revealed, yielding clues to their possible roles -also used to identify microorganisms; to differentiate between different species or organisms 117b quorem sensing 118a mechanism to evaluate the density of cells of the same kind, assess population density before starting activities that require a certain cell density to be effect (ex: toxin production, bioluminescence) 118b regulation of chemotaxis 119a 1.methyl-accepting chemotaxis proteins (MCPs) bind toan attractant (or repellant) 2.MCPs contact cytoplasmic proteins CheW which phosphorylates CheA which in turn phosphorylates CheY.Attractants decrease phosphorylation while repellants increase it. 3.CheY-Pinduces clockwise rotation of flagella resulting in a tumble while unphosphorylated CheY induces counterclockwise rotation of flagella resulting in a run 4.CheY is dephosphorylated by CheZ 5.Adaptation:CheR adds methyl groups toMCPat a constant rate while CheB removes methyl groups at a varying rate.If CheB is phosphorylated, it moves faster.This is the reset mechanism of chemotaxis. 119b regulon 120a multiple operons controlled by the same regulatory protein 120b reporter gene 121a a gene that is attached to a regulatory sequence of another gene of interest in bacteria, cell culture, animals or plants. -GFP (green fluorescent protein) 121b repression 122a PREVENTS the synthesis of an enzyme in response to a signal (corepressor); typically affects anabolic enzymes 122b resazurin 123a redox indicator dye that signals oxic regions in thioglycolate broth 123b Riboswitch 124a RNA molecule that resembles a repressor or activator but binds to metabolites to regulate gene expression -Located at 5' end of mRNA -The presence of the small molecule determines whether or not the mRNA is translated -Control is analogous to negative control -Currently only found in some bacteria, plants, and fungi 124b RNA-Seq Analysis 125a used both to measure expression of mRNA and to identify and characterize small noncoding RNAs; requires second- or third-generation sequencing 125b Sanger Dideoxy Method 126a DNA is synthesized in the presence of dideoxyribonucleotides which insert randomly and thus stop chain elongation. The DNA chains of varying length are obtained and are separated on the basis of size by gel electrophoresis. The lanes corresponded with the four dideoxyribonucleotides. The vertical position indicated the size of the fragment relative to its neighbor. The DNA sequence is read directly from the gel. Back in the day, the dideoxyribonucleotides were radioactively labeled but more recently, they've become fluorescently labeled with a different nucleotide indicated by a different color. In this case, all four reactions are run in a single lane; the results are analyzed by a computer. 126b sanitizers 127a -less harsh chemicals than disinfectants and function to reduce microbial numbers but not necessarily sterilize the object -widely used in food industry and dry handwashing 127b Shotgun Sequencing 128a preparation of DNA for sequencing where DNA fragments to be sequenced are randomly generated from larger DNA fragments 128b Small RNAs can... 129a Bind to block the RBS, open up RBS to be transcribed, increase degradation of transcript, decrease degradation of transcript 129b Sporulation in Bacillus 130a -In response to adverse growth conditions. Multiple adverse conditions result in the phosphorylation of sporulation factor proteins. -5 sensor kinases to monitor their environment (more complex than 2-component systems) 1. external adverse signals result in the phosphorylation of Spo0A 2. Spo0A phosphorylates SpoIIE 3. Spo0E removes phosphate on SpoIIAA 4.SpoIIAA binds to SpoIIAB thus booting sigma factor F off of SpoIIAB 5. sigma factor F activates sigma factor E--> early endospore genes are transcribed 6. signal from mother cell triggers synthesis of sigma factor G in endospore and pro- sigmaK in mother cell 7. signal from endospore (sigma factor G) activates sigma factor K -Cells with active Spo0A secrete a protein that lyses nearby cells of the same species whose Spo0A is not yet activated. 130b -static agents 131a only inhibit the growth of organisms; as soon as the static agent is removed, growth will resume 131b sterilants 132a -destroy all microorganisms, including endospores -in situations where it is impractical to use heat or radiation -cold sterilization= gases are used to treat objects within an enclosed device -liquid sterilants like bleach are used for instruments that cannot withstand gas or high temperatures 132b superoxide dismutase 133a converts superoxide anion to hydrogen peroxide and oxygen; works with catalase or peroxidase to remove the hydrogen peroxide by-product -found in aerobes and facultative aerobes; some aerotolerant anaerobes lack this enzyme and use a protein-free manganese complex instead -ESSENTIAL FOR AEROBES 133b superoxide reductase 134a converts superoxide anion to hydrogen peroxide without exposing the organism to oxygen -found in strict anaerobes 134b systems biology 135a the integration of different fields of research to give an overview of an organism, cell, or entire species or ecosystem 135b thioglycolate broth 136a contains a little bit of agar to make the broth viscous but still fluid; thioglycolate reacts with O2 removing oxygen from the medium except at the very surface of the medium 136b Third-Generation DNA Sequencing 137a single molecules of DNA are sequenced 137b Three Possible Functions of DNA Binding Protein 138a 1. Catalyze reactions (such as transcription by RNA polymerase) 2. Block transcription (negative regulation) 3. Activate transcription (positive regulation) 138b toxic oxygen by-products 139a -superoxide anion, hydrogen peroxide, and hydroxyl radical -whether an organism can respire O2 or not, an organism exposed to O2 will be exposed to toxic forms of oxygen 139b transcription factor B 140a Protein found in archaea that interacts with DNA and promotes transcription 140b transcriptone 141a Analogous to genome, a transcriptome is the entire complement of RNA produced under a given set of conditions 141b transduction 142a cell infected with a virus which injects and incorporates it's genome into that of the host cell 142b transformation 143a taking free genetic information from the environment 143b transposons 144a -common form of mobile DNA that moves between different host DNA molecules (such as chromosomes to plasmid); move by use of transposase -can mediate large-scale chromosomal changes 144b Trans-sRNAs complementarity 145a Trans-sRNAs are typically in intergenic regions (UTR regions that are too small to technically be introns), which limits their complementarity to their target. Hfq enhances their interaction with their mRNA target. 145b Trend of Gene Distribution in Prokaryotes 146a - metabolic genes are typically the most abundant class in prokaryotic genomes - as genome size increases, the percentage of protein synthesis genes increases - large genomes contain more genes for regulation than smaller genomes - larger genomes can also afford to encode specialized metabolic genes making them more competitive in habitats such as soil 146b Trichomonas 147a Holds record for largest gene number of any organism, yet it is a human parasite, which typically have smaller genomes. 147b two component regulatory system 148a sensor kinase (usually in cytoplasmic membrane) response regulator protein (usually in cytoplasm) 148b two main bacterial groups of microbiome 149a Bacteroidetes and Firmicutes 149b Typical genes transferred horizontally 150a virulence factors and metabolic functions 150b Using Microarray 151a -synthesizes gene segments by PCR or oligonucleotides that are designed and synthesized for each gene based on the genomic sequence -gene segments are attached to gene chip in known locations and then exposed to mRNA harvested from a microbe that was under specific growth conditions -the fluorescently labeled mRNA will attach to specific gene segments due to its "need" in the specific growth conditions -the chip can then be read and analyzed 151b UV radiation as a disinfectant 152a -between 220 and 300 nm -absorbed by DNA and can cause mutations or other serious effect on the DNA that lead to cell death -poor penetrating power, thus best used for surfaces and air 152b Variability in the Genetic Code 153a -some mitochondria use slight variations -typically use stop codons as "Sense" codons -may have arisen from selection pressure for smaller genomes -base pairing between codon and anticodon in mitochondria is much more flexible than that in cells 153b water activity (a-sub-w) 154a -the ratio of vapor pressure of air in equilibrium with a substance or solution to the vapor pressure of pure water -values vary between 0 and 1 -water flowing into cell = high water activity 154b What's so special about Encephalitozoon cuniculi? 155a Although it is a pathogenic eukaryote, it has a genome smaller than that of many prokaryotes. 155b What steps in the synthesis of a protein might be subject to regulation? 156a at transcription, translation, or before the protein is used 156b When an organism resides in a medium of low water activity, it maintains positive water balance by... 157a ...either pumping solutes into the cell from the environment or by synthesizing a cytoplasmic solute. 157b which is faster: regulation of activity of an enzyme or regulation of its synthesis? 158a regulation of activity takes a mere couple of seconds while the synthesis can take minutes 158b Which toxic-oxygen-destroying enzymes are found in aerobes? Anaerobes? 159a -Aerobes have superoxide dismutase, especially, and sometimes peroxidase and catalase. -Anaerobes use superoxide reductase 159b Why is the term "proteome" ambiguous whereas the term "genome" is not? 160a An organism's proteome can change depending on what conditions the cell is in. Therefore, it must be used in a more broad sense as all the proteins that can be present in a cell at any given time, not a specific time. 160b xerophiles 161a live in very dry environments 161b zinc finger structure 162a a DNA-binding protein domain that binds a zinc ion -typically found in regulatory proteins of eukaryotes 162b


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