Lecture 191. Compare and contrast operon and regulona. Operoni. Several contiguous genes transcribed as a single mRNA under control of a single regulatory regionb. Reguloni. Multiple genes or operons in the genome under the same control mechanism2. Know the three levels of gene regulationa. Transcriptional regulationb. Translational regulationc. Post-translational regulation3. Explain how regulatory protein dimers bind to their DNA binding sitesa. They often specifically bind to short DNA sequences that are inverted repeatsb. Each protein subunit binds to one of the inverted repeats, on both strands of the DNAc. These inverted repeats are found upstream of genes or operons and play a role in controlling transcription4. Describe the typical structure of a regulating protein binding sitea. Negative controli. You have a repressor that is in an open configuration that cannot block transcriptionii. Or you have a repressor with a co-repressor in the binding site which blocked transcription. b. Enzyme inductioni. Just the repressor binds to the operator lactose not presenttranscription is blockedii. Inducer now comes to outer side of repressor and binds and transcription occurs.5. Understand which type of regulation acts the fastesta. Negative control acts fastest then it hits a plateau 6. Understand why transcription regulation saves the cell the most resources a. By not making RNA for a protein it doesn’t need7. Study the examples of operons for each type of regulatory mechanism 8. Know the function of activator and repressor proteins a. Activator- Binds to promoter region of DNA to help recruit RNA polymeraseb. Repressor- Binds to operating regions in the DNA, blocks RNA polymerase from transcribing9. Compare and contrast transcription inhibition by enzymeinhibition and enzyme induction a. Enzyme induction- most common for control of catabolic/ degradative paths b. Enzyme repression- most common for the control of biosynthetic pathways (amino acids and nucleotides)10. Know where repressor and activator binding sites are in relationship to the promoter a. Repressor- Downstreamb. Activator- Upstream11. Describe how transcription activation works a. Requires the binding of an activator protein to the DNA b. Activator protein binds the inducer c. Then it binds to the DNA at the activator binding site, allowing RNA polymerase to begin transcription 12. Explain what global control is a. One same mechanism controls the expression of many different genes13. Explain what diauxic growth is a. Two exponential growth phasesb. If two usable energy sources are available, the cells grow first on the better energy source. Growing stops when the better source is depleted but then following a lag period it resumes on the other energy source 14. Explain how diauxic growth is caused by catabolite repressiona. Catabolite repression affects over 300 enzymes b. As long as glucose is present the lac operon is not expressed andlactose is not usedc. Once glucose is depleted, catabolite repression is abolished, and then the lac operon is expressed allowing the cell tot grow in lactosed. This ensures that the better carbon source is used first15. Understand catabolite repression and know the function of the cyclic-AMP receptor protein a. Mechanism of global control that controls the use of carbon sources if more than one is presentb. Form of positive controlc. The presence of a favored carbon source represses the induction of pathways that catabolize other carbon sourcesd. Cyclic AMP is derived from a nucleic acid precursor i.e. it is a regulatory nucleotidee. Synthesized from ATP by an enzymef. Glucose inhibits the synthesis of cAMP and also stimulates cAMP transport out of the cell. When glucose enters the cell and the cAMP level is lowered, CRP cannot bind NDA and RNA polymerase fails to bind to the promoters of operons subject tocatabolite repression.g. Catabolite repression is an indirect result of the presence of a better energy source (glucose)h. The direct cause of catabolite repression is a low level of cAMP16. Predict the expression of the lac operon in given growth conditions a. LOOK AT POWERPOINT17. Explain what autoinducers area. Signal moleculeb. Usually diffuses freely across the cell envelope in wither direction18. Explain how cell concentration affects the autoinducer concentrationa. Reaches high concentrations inside the cell only if there are many cells nearby, each making the same autoinducer.b. Inside the cell, the autoinducer binds to a specific transcriptional activator protein or a sensor kinase of a two- component system,ultimately triggering transcription of specific genes19. Compare and contrast quorum sensing and two-component regulatory systems a. Quorum sensing- mechanism used by bacteria to assess population density, is an example of population dependent control of regulons by chemicals secreted by cellsb. Two component regulatory systems- About 50 different 2 component systems in bacteria, typical sequence of events in both repression and activation. Single transduction means signal comes from the outside20. Understand what methods bacteria use to sense their environment a. Can sense the nutrients, temperature, oxygen, etc. and adjust gene expression to the environmentb. Use signal transduction = transmission of an external chemical signal to relevant regulatory targets 21. Explain the 3 steps of a two-component system response a. Typical sequence of events: sensor kinase binds signal molecule and phosphorylates itself (autophosphorylation)b. Phosphate is transferred to the response regulator moleculec. Phosphorylated response regulator binds to operator on DNA (phosphatase activity = feedback loop)22. Name each component involved in the two-component system a. Sensor kinase proteinb. Response regulator protein23. Review the overall scheme of how chemicals outside the cell can cause changes in transcription inside the cell 24. Define antisense RNAs and explain how they function a. sRNAs that are made by transcribing the nontemplate strand ofthe same gene that yielded the target mRNAb. Complementary in base sequence c. Transcription often enhanced under consitions in which its target genes need to be turned off25. What are riboswitches? What are the three important regions within the riboswitch? a. Definitioni. Regions of mRNAs upstream of the ribosome binding site that regulate protein synthesis by controlling access to the RBSb. Three Important Regionsi. Upstream of the
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