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BSC 310 EXAM 3

by: Mallory Ivy

BSC 310 EXAM 3 BSC 310

Mallory Ivy
GPA 3.82

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162 terms of condensed and specific information you should know for Dr. Olson's third exam! You can convert these into flashcards or use them for last minute studying before the exam. Regardless of...
Dr. Olson
Study Guide
Microbiology Exam 3 heterocysts regulation isoenzymes sporulation attenuation global control repression induction pathogenicity islands gene transfer RNA sequence analysis
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This 21 page Study Guide was uploaded by Mallory Ivy on Sunday April 3, 2016. The Study Guide belongs to BSC 310 at University of Alabama - Tuscaloosa taught by Dr. Olson in Spring 2016. Since its upload, it has received 45 views. For similar materials see Microbiology in Biology at University of Alabama - Tuscaloosa.


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Date Created: 04/03/16
Important Terms for Exam 3 BSC 310 S16 1. Genomics – - mapping, sequencing, analyzing, and comparing genomes 2. Difference between first-, second-, third-, and fourth-generations of DNA Sequencing – - 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 3. Sanger Dideoxy Method – - 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; a computer analyzes the results. 4. Shotgun Sequencing – - preparation of DNA for sequencing where DNA fragments to be sequenced are randomly generated from larger DNA fragments 5. 454 System – - 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. Important Terms for Exam 3 BSC 310 S16 6. Third-Generation DNA Sequencing – - single molecules of DNA are sequenced 7. Fourth-Generation DNA Sequencing – - no longer uses optical detection; release of protons versus light 8. Closed vs. Draft Genome - - gaps in the sequence annotation is found in a draft genome whereas a closed genome has no gaps 9. Open reading frame – - a sequence of DNA or RNA that can be translated to yield a polypeptide 10. Finding a Functional ORF – - Locate start and stop codons - Most functional ORFs must be longer than 300 nucleotides but some are shorter. --> Locate potential ribosome- binding sequences - Codon bias - Compare to similar genes in other organisms (protein homology) 11. Estimated lower limit of number of genes possible for a viable cell – - 250-300 genes 12. Trend of Gene Distribution in Prokaryotes – - 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 13. Variability in the Genetic Code – - 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 Important Terms for Exam 3 BSC 310 S16 14. Trichomonas – - Holds record for largest gene number of any organism, yet it is a human parasite, which typically has smaller genomes. 15. What's so special about Encephalitozoon cuniculi? - Although it is a pathogenic eukaryote, it has a genome smaller than that of many prokaryotes. 16. Transcriptone – - Analogous to genome, a transcriptome is the entire complement of RNA produced under a given set of conditions 17. Microarrays aka gene chips – - small solid supports to which genes or segments of genes are fixed and arrayed spatially in a known pattern 18. Hybridization – - 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 19. Nucleic acid probes – - Segments of ss nucleic acids whose identity is already known and that are used in hybridization - Either radioactive or fluorescent 20. Using Microarray – - 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 21. Purpose of Microarray – - clinical diagnostics - View expression pattern of genes of unknown function is also revealed, yielding clues to their possible roles Important Terms for Exam 3 BSC 310 S16 - Also used to identify microorganisms; to differentiate between different species or organisms 22. RNA-Seq Analysis – - used both to measure expression of mRNA and to identify and characterize small noncoding RNAs; requires second- or third-generation sequencing 23. Most Common Methods to Survey Proteomics – - 2D polyacrylamide gel electrophoresis - Liquid chromatography 24. Connecting unknown protein with particular gene from 2D gel system – - Elute protein from gel and sequence a portion, or - Identify protein by use of mass spectrometry 25. Connecting Unknown protein with a particular gene from genomic DNA – - oligonucleotide probes or primers can locate the gene encoding the protein and then identify the gene after sequencing the DNA 26. Proteomics – - study of structure, function, and activity of an organism's proteins 27. Interactome – - 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 28. Why is the term "proteome" ambiguous whereas the term "genome" is not? - 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. 29. Metabolome – - complete set of metabolic intermediates and other small molecules produced in an organism 30. MALDI-TOF – Important Terms for Exam 3 BSC 310 S16 - 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 31. Importance of Metabolome Analysis – - 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 32. Systems biology – - the integration of different fields of research to give an overview of an organism, cell, or entire species or ecosystem 33. Emergent properties – - behavior or properties of a particular organism that were not obvious from the original observations 34. Metagenomics – - 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 35. Two main bacterial groups of microbiome – - Bacteroidetes and Firmicutes 36. Metagenome – - total gene content of the organisms inhabiting and environment 37. Homolog – - genes related in sequence to an extent that implies common genetic ancestry - includes orthologs and paralogs 38. Gene family – Important Terms for Exam 3 BSC 310 S16 - genes that are related in sequence to one another as a result of a common evolutionary origin 39. Paralog – - 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 40. Ortholog – - 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 41. Mechanisms for horizontal gene transfer - - transformation, transduction, or conjugation 42. Detecting Horizontal Gene Flow - 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 - However, as more genomes are sequenced, using horizontal gene flow as an explanation can be nulled 43. Typical genes transferred horizontally – - virulence factors and metabolic functions 44. Mobile DNA – - 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 45. Transposons – - 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 46. Insertion sequences – - simple transposable elements whose genes encode only transposition - found in organisms undergoing rapid evolutionary change 47. Pan genome - Important Terms for Exam 3 BSC 310 S16 - 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 48. Core genome – - core genome is a genome found in all strains of a given species 49. Chromosomal islands – - 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 50. Evidence that chromosomal islands have foreign origin – 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 51. Pathogenicity islands – - 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 52. Neutrophiles – - optimal growing pH around 5.5-7.9 53. Acidophiles – - grow best below pH 5.5; often found in acidic thermal soils associated with volcanic activity 54. Acidophilicity – - dependent on cytoplasmic membrane stability; pH 2 above optima will cause cell to spontaneously lyse 55. Picrophilus oshimae – - Archaea that grows optimally at pH 0.7 Important Terms for Exam 3 BSC 310 S16 56. Alkaliphiles – - 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 57. PH growth opitma – - range is typical 2-3 units of pH; refers only to the exterior environment only! 58. How do alkaliphiles manage bioenergetics when surrounded by such an H+ poor environment? - 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 59. Labile – - easily broken down or destroyed by... - Ex: DNA is acid-labile while RNA is alkaline-labile meaning DNA is easily destroyed by acids while RNA is destroyed by bases 60. Good buffer – - 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 61. Water activity (a-sub-w) – - 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 62. Positive water balance – - when solute concentration is higher within the cell than outside and thus water flows into the cell Important Terms for Exam 3 BSC 310 S16 63. Halotolerant – - organisms that can tolerate some level of dissolved solutes but grow best in the absence of the added solute 64. Extreme halophiles – - grow optimally at NaCl concentrations between 15 and 30% and are often unable to grow at all at NaCl concentrations below this 65. Osmophiles – - live in environments with high sugar concentration 66. Xerophiles – - live in very dry environments 67. When an organism resides in a medium of low water activity, it maintains positive water balance by... - ...either pumping solutes into the cell from the environment or by synthesizing a cytoplasmic solute. 68. Compatible solutes – - 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 69. Interesting fact: the compatible solute of extremely halophilic Archaea is... - 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 70. Aerobes – - grow at full oxygen tensions 71. Microaerobes – - aerobes that can use O2 only when present at levels reduced from that in air 72. Facultative aerobes – - under appropriate nutrient and culture conditions they can grow in the absence of O2 but prefer to grow with O2 Important Terms for Exam 3 BSC 310 S16 73. Anaerobes – - cannot respire O2 at all 74. Aerotolerant anaerobes – - can tolerate and grow in the presence of O2 even though they cannot respire 75. Obligate anaerobe – - inhibited or killed by O2 - Ex: Clostridium and methanogens 76. Thioglycolate broth – - 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 77. Culture Techniques for Aerobes – - 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 78. Culture Techniques for Anaerobes - - 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 79. Growth Regions of Thioglycolate Broth – - 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 80. Resazurin – - redox indicator dye that signals oxic regions in thioglycolate broth 81. Toxic oxygen by-products – - 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 82. Catalase – Important Terms for Exam 3 BSC 310 S16 - converts hydrogen peroxide to water and oxygen 83. Peroxidase – - converts hydrogen peroxide with NADH to water and NAD+ 84. Superoxide dismutase – - 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 85. Superoxide reductase – - converts superoxide anion to hydrogen peroxide without exposing the organism to oxygen - Found in strict anaerobes 86. Which toxic-oxygen-destroying enzymes are found in aerobes? Anaerobes? - Aerobes have superoxide dismutase, especially, and sometimes peroxidase and catalase. - Anaerobes use superoxide reductase 87. Decontamination – - physical method of control that consists of treatment of an object or surface to make it safe to handle; simply removes present organisms 88. Disinfection – - physical method of control that specifically targets pathogens although it may not eliminate all microorganisms; actually kills or inhibits growth 89. Moist heat vs dry heat – - moist heat has a higher, and faster, penetration power of killing organisms than does dry heat 90. Autoclave – - sealed heating device that uses steam under pressure to kill microorganisms 91. Pasteurization – Important Terms for Exam 3 BSC 310 S16 - 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 92. UV radiation as a disinfectant – - 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 93. Ionizing radiation as a disinfectant – - 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 94. Filter sterilization – - used for heat sensitive liquids or gases - Ex: depth filter, membrane filter, and nucleopore filters 95. Depth filter – - fibrous sheet or mat made from random array of overlapping paper or borosilicate fibers - Important in biosafety applications such as in safety hood 96. Membrane filters – - 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 97. Nucleopore filters – - Made from thick polycarbonate film that is treated with radiation and then etched with uniform holes - Used to isolate specimens for SEM 98. Antimicrobial agent – Important Terms for Exam 3 BSC 310 S16 - natural or synthetic chemical that kills or inhibits the growth of microorganisms 99. -Cidal agents – - kill the microorganisms; bacteriocidal, fungicidal, etc. 100. -Static agents – - only inhibit the growth of organisms; as soon as the static agent is removed, growth will resume 101. Minimum inhibitory concentration – - 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 102. Antimicrobial agent susceptibility assay in tubes – - 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. 103. Disc assay for antimicrobial agent susceptibility – - 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. 104. Sterilants – - 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 105. Disinfectants – - Chemicals that kill microorganisms but not necessarily endospores - Used on inanimate objects - Important to infection control in medical settings Important Terms for Exam 3 BSC 310 S16 106. Sanitizers – - 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 107. Antiseptics (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 108. Reporter gene – - 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) 109. What steps in the synthesis of a protein might be subject to regulation? - At transcription, translation, or before the protein is used 110. Which is faster: regulation of activity of an enzyme or regulation of its synthesis? - Regulation of activity takes a mere couple of seconds while the synthesis can take minutes 111. DNA-binding protein – - 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 112. Helix-turn-helix structure – - 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 Important Terms for Exam 3 BSC 310 S16 113. Zinc finger structure - a DNA-binding protein domain that binds a zinc ion - Typically found in regulatory proteins of eukaryotes 114. Leucine zipper – - another DNA-binding protein domain that contains regularly spaced leucine residues that hold two recognition helices in the proper orientation to bind DNA 115. Negative control of transcription - repression and induction 116. Transduction – - cell infected with a virus which injects and incorporates it's genome into that of the host cell 117. Transformation – - taking free genetic information from the environment 118. Three Possible Functions of DNA Binding Protein – 1. Catalyze reactions (such as transcription by RNA polymerase) 2. Block transcription (negative regulation) 3. Activate transcription (positive regulation) 119. Repression – - PREVENTS the synthesis of an enzyme in response to a signal (corepressor) - typically affects anabolic enzymes 120. Induction – - the opposite of repression; transcription is UNBLOCKED in response to a signal - usually affects catabolic enzymes 121. Inducer – - substance that promotes enzyme synthesis (ex: lactose) 122. Corepressor – - substance that stops enzyme synthesis (ex: arginine) 123. Effectors – - Inducers and corepressors collectively are called effectors. Effectors assert allosteric control on their repressors. 124. Activator – Important Terms for Exam 3 BSC 310 S16 - regulatory protein used in positive control; activator binding site can be several hundred base pairs upstream of the operon 125. Positive control – - 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 126. Activator protein helps RNA polymerase recognize promotor by either- - changing DNA structure allowing the RNA pol to contact promotor more readily or can interact with RNA polymerase directly 127. Regulon – - multiple operons controlled by the same regulatory protein 128. Catabolite repression – - mechanism of global control that decides between utilizing different available carbon sources 129. Global control systems – - regulatory mechanisms that respond to environmental signals by regulating expression of many different genes; includes flagellar genes 130. Diauxic growth – - 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. 131. Cyclic AMP receptor protein (CRP) – - activator protein responsible for catabolite repression; only acts when bound to cyclic adenosine monophosphate (cAMP) 132. Example of regulatory nucleotide – - cyclic adenosine monophosphate and cyclic di-guanosine monophosphate (see the trend here?) 133. Catabolite Repression Process on Lac Operon – Important Terms for Exam 3 BSC 310 S16 - 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. 134. Transcription factor B – - Protein found in archaea that interacts with DNA and promotes transcription 135. NrpR – - 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 136. Two component regulatory system – - Sensor kinase (usually in cytoplasmic membrane) - Response regulator protein (usually in cytoplasm) 137. Regulation of chemotaxis – 1. Methyl-accepting chemotaxis proteins (MCPs) bind to an attractant (or repellant) 2. MCPs contact cytoplasmic proteins CheW that phosphorylates CheA, which in turn phosphorylates CheY. Attractants decrease phosphorylation while repellants increase it. 3. 3.CheY-P induces 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 to MCP at 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. 138. Effect of methylation on methyl-accepting chemotaxis proteins – - methylated MCP is more sensitive to repellants and no longer responds to attractants and vice versa - allows cell to continue sense environment 139. Quorem sensing – Important Terms for Exam 3 BSC 310 S16 - 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) 140. Autoinducer – - specific signal molecule synthesized by the participating organism that freely diffuses across the cell envelope in both directions 141. Different Classes of Autoinducers - - acyl homoserine lactones (AHLs), autoinducer 2, short peptides 142. Cyclic di-guanosine monophosphate – - another regulatory nucleotide; provides physiological changes and expression of virulence genes necessary for biofilm formation 143. Heat shock – - 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 144. Heat Shock Regulation in E.coli – - In low temperature, the chaperone DnaK binds to an alternative σ factor (ribosomal polymerase H) RpoH that 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. 145. Differentiation in bacteria – - formation of endospores in Gm+ Bacilli and formation of two cell types in Gm- Caulobacter (flagellated cells and those stuck to a surface) 146. Sporulation in Bacillus – - 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 Important Terms for Exam 3 BSC 310 S16 2. Spo0A phosphorylates SpoIIE 3. Spo0E removes phosphate on SpoIIAA 4. 4.SpoIIAA binds to SpoIIAB thus booting σ factor F off of SpoIIAB 5. Σ factor F activates σ factor E--> early endospore genes are transcribed 6. Signal from mother cell triggers synthesis of σ factor G in endospore and pro-σ K in mother cell 7. Signal from endospore (σ factor G) activates σ factor K - Cells with active Spo0A secrete a protein that lyses nearby cells of the same species whose Spo0A is not yet activated. 147. Caulobacter Differentiation - 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 148. Heterocysts- - cells where N fixation occurs, arise via monitoring of 2 external conditions and cell-to-cell signaling 149. Nitrogenase Activity - NifA serves as a positive regulator for expression of nif genes while NifL is a negative regulator - If O2is 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 150. Heterocyst Formation - 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 151. Genes and Proteins involved with Nitrogen Fixation (6) - 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 Important Terms for Exam 3 BSC 310 S16 - 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 152. Noncoding RNA (ncRNA)- - RNA molecules that are not translated into proteins - Includes tRNA and rRNA, signal recognition particles, RNA used for splicing, and sRNA 153. Small RNAs can… - Bind to block the RBS - Open up RBS to be transcribed - Increase degradation of transcript - Decrease degradation of transcript 154. Trans-sRNAs complementarity - 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. 155. Hfq- - RNA chaperones that help small RNA molecules to maintain their correct structure 156. Riboswitch- - 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 157. Attenuation- - 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 158. Leader region- 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 159. Attenuation in Tryptophan Operon - 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. Important Terms for Exam 3 BSC 310 S16 - 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. 160. Feedback Inhibition - 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 161. Isoenzymes - Different enzymes that catalyze the same reaction but are controlled differently - Typically affect branched pathways - Often diminish enzyme activity incrementally 162. Post-translational Regulation - 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.


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StudySoup has more than 1 million course-specific study resources to help students study smarter. If you’re having trouble finding what you’re looking for, our customer support team can help you find what you need! Feel free to contact them here:

Recurring Subscriptions: If you have canceled your recurring subscription on the day of renewal and have not downloaded any documents, you may request a refund by submitting an email to

Satisfaction Guarantee: If you’re not satisfied with your subscription, you can contact us for further help. Contact must be made within 3 business days of your subscription purchase and your refund request will be subject for review.

Please Note: Refunds can never be provided more than 30 days after the initial purchase date regardless of your activity on the site.