BIOLOGY 207 1st Edition Lecture 11 Outline of Previous Lecture I. Negative ControlII. Positive ControlOutline of Current Lecture I. Sensing and signal transductionII. Regulation of developmentIII. RNA-based regulationsCurrent LectureMetabolic Regulation 2I. Sensing and signal transductiona. Cells regulate metabolism in response to many factorsi. Temperatureii. pHiii. Oxygen and nutrient available in the environmentiv. Presence and number of other cellsv. These environmental signals must be sent to the correct targetsb. Signal transduction transmits the environmental messagesi. Sensor kinase protein (enzyme that phosphorylates) on the cytoplasmic membraneii. Response regulator protein in cytoplasmiii. DNA binding protein is usually the response regulator iv. Terminating response requires phosphataseThese notes represent a detailed interpretation of the professor’s lecture. GradeBuddy is best used as a supplement to your own notes, not as a substitute.c. E. coli regulates porin proteins through signal transduction i. OmpF: large porinii. OmpC: small proteiniii. Low osmolarity (hypotonic surrounding solution) means that the cell must increase diffusion ratesiv. High osmolarity (hypertonic surrounding solution) nutrients are readily available and the diffusion rate can stay lowv. EnvZ serves as the sensor histidine kinasevi. OmpR: response regulator proteinvii. P-lated OmpR: either activator or repressor for OmpFviii. P-lated OmpR: only activator for OmpC d. Chemotaxisi. Also controlled by signal transductionii. Clockwise flagellar rotation: tumblesiii. Counterclockwise flagellar rotation: runsiv. Sensory proteins are not sensor kinases; rather they relay the messages to sensor kinases1. This is how cell is able to monitor levels of attractants and repellants to movev. CheA is the sensor kinase for chemotaxisvi. CheY determines direction of flagellar rotation1. Cannot bind to flagellar motor if CheY is unphosphorylated; counterclockwise rotation ensues (run)2. If phosphorylated, CheY binds to flagellar motor and rotates clockwise (tumble)e. Quorum sensingi. A way for cells to assess the population density of their surroundingsii. Critical density of cells must be present before particular activities are initiated iii. Autoinducers: secreted by cells utilizing quorum sensingiv. If enough cells are making these autoinducers, the level gets high enough that they trigger gene transcriptionf. Heat shocki. Response seen in all domains of lifeii. Example of global conrol (like catabolite repression and quorum sensing)iii. Mechanism used to help cells recover from heat stressiv. Largely controlled by alternative sigma factors1. RpoE and RpoH are used during heat shock responsev. DnaK: inactivates RpoH and chaperones refolding of proteins1. In normal conditions, DnaK is high and RpoH is low and promoters controlled by RpoH are not activated2. During heat shock, RpoH is high and genes are transcribed under its control; DnaK preferentially binds unfolded proteinsII. Regulation of developmenta. Prokaryotic examples:i. Formation of endospores in gram+ Ba cillusii. Formation of motile vs. stationary cells in gram- Caulobacteriii. Formation of heterocysts in nitrogen fixing Anabaenab. Endospore formationi. Triggered by unfavorable conditions1. Starvation, desiccation or harsh temperaturesii. Environment monitored by sensor kinasesiii. Phosphotransfer relay system (more complex than two-component regulatory system)iv. Controlled by four different sigma factorsv. Culminates to production of heat, radiation and chemical resistant, dormant sporesc. Caulobacteri. Gram- species of Proteobacteriaii. Found in aquatic environments with low nutrient levelsiii. Two types:1. Swarmers (free swimmers)2. Stalked (lack flagella; attach to surfaces)iv. Three proteins circulate through the cell cycle1. CtrA, DnaA and GcrA2. Phosphorylated CtrAa. Activates genes for motilityb. Inhibits DNA replicationc. Degraded by protease3. DnaAa. Rises when CtrA is degradedb. Triggers DNA replicationc. Degraded by protease4. GcrA a. Rises when DnaA is degradedb. Promotes elongation phase for replication and cell divisionc. Promotes stalk growthd. Nitrogen-fixing bacteriai. Some photosynthetic bacteria are able to fix nitrogenii. Tightly regulated due to the high energy expenditure needed for itiii. Nitrogenase (made up of two proteins) catalyzes the process1. Dinitrogenase2. Dinitrogenase reductase3. Inactivated by oxygena. Heterocysts serve as solutions to thisb. Formation triggered by nitrogen starvationc. Anoxic cells that lack photosystem 2 that arise from differentiation of vegetative cellsd. The specialized cells appear at specific intervals along the filament and monitor external conditions and cell to cell signaling e. Vegetative cells provide fixed carbon to heterocysts which in turn provide fixed nitrogen to vegetative cellsIII. RNA-based regulationsa. Small RNAs (sRNA) regulate gene expressioni. They are found in all domains of lifeii. Bind to other RNA at complementary regionsiii. Regulate expression at levels of transcription or translationiv. Can influence ribosome access to mRNAv. They can also influence mRNA stabilityb. Riboswitch RNAsi. Bind metabolites to alter gene expressionii. Does not requireiii. complementary base pairing from sRNAiv. Have coding sequence regions upstream that can bind metabolitesv. By metabolite binding, the 3D structure of RNA is alteredvi. If there is enough metabolite, translation is blockedc. Attenuationi. Transcription is prematurely terminatedii. The mRNA leader sequence is the key to attenuation; it can adopt two different conformations1. One mRNA secondary structure allows transcription to continue2. The other structure causes transcription to cease3. Works in bacteria and archaea since transcription and translation occur in the same place, but not for eukaryotesiii. Tryptophan operon1. Example of attenuation2. The operon has genes for proteins in the tryptophan biosynthetic pathway and uses multiple types of regulationa. Negative control and attenuation3. When tryptophan is abundant, transcription is terminated4. When tryptophan is limiting, transcription continues5. When tryptophan is abundant, the whole leader sequence is translated by the ribosomesa. Stem-loop (3:4) inhibits RNA polymeraseb. The cell stops making tryptophan because it now has enough6. When tryptophan is limiting, when ribosome stalls because of the lack of tryptophan-charged tRNAa. Stem-loop (2:3) allows