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CORNELL BIOPL 3420 - 18answers16

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Plant Physiology LecturesBioPL 3420Spring 2016Lecture Topic 18 Answers to Supplementary Study QuestionsSignal Transduction1) You are working in a laboratory that is interested in understanding the signaltransduction pathway that leads to specific active defense responses in plants. Oneway to approach this problem is to generate lots of mutants and look at the mutantswhose phenotype is an altered response to a specific pathogen (compared to the wildtype). To your surprise, you find that many mutants that display altered responses tothis specific pathogen also show altered responses in other signal transductionpathways. Provide a reasonable explanation for why this might be the case. Wherewould you expect these mutations to be (what are the proteins that are encoded by themutated genes) in the case of mutants that are specific for the pathogen, and for themutants that are common to many pathways?Answer:Signal transduction pathways absolutely require that there be specificity between thesignal and the response. That is, there must always be some aspect of the signaltransduction pathway that distinguishes the response to one stimulus from another. Onthe other hand, many signal transduction pathways have common aspects as well. Forexample, changes in intracellular calcium (and those components that control Caconcentration and detect changes in Ca concentration), enzymes that are regulated bycyclic AMP, and many others are common to many types of signal transductionpathways. In the context of the question above, if you observe that a single mutationcauses alterations in several signal transduction pathways, it is likely the mutatedprotein is one of these common components of many pathways. Mutations that arespecific to a single pathway are likely to be localized at the receptor end of the pathwayor at the opposite end of the pathway directly involved in the response.2) In signal transduction pathways that regulate gene expression (as opposed to thosethat regulate the activity of enzymes), there are generally two classes of genes whosetranscription is regulated by the pathway – the early and late genes. Transcription ofthe early genes starts within minutes of the perception of the appropriate signal, whiletranscription of the late genes often is delayed by one to several hours after the signal isperceived. Very often, the proteins that are encoded by the early genes aretranscription factors, and these transcription factors regulate the expression of the lategenes. Based on this and information from lecture and your readings, explain why thereis no lag in the appearance of the early gene products and why there is a lag of an houror more in the appearance of the late gene products. I am not looking for a detaileddescription with any specific information – you answer should be completely generaland based only on information provided in lecture or the web text.Answer:For the early genes, the transcription factors that are required for their transcriptionmust be constitutively present in the cell, but in an inactive form until the proper signaltransduction pathway is activated. Very quickly (minutes or less) these transcriptionfactors for the early genes are activated and transcription of the early genes begins.The products of these early genes are themselves transcription factors, but these arespecific to the late genes. Until a sufficient amount of the transcription factors for thelate genes are present in the cell (about an hour), transcription of the late genes cannotbegin. So the difference is that for the early genes, the needed transcription factors arealready present in the cell but just not active. For the late genes, the transcriptionfactors must be produced (transcribed and translated) from the early genes.3) In both prokaryotes and eukaryotes, one of the primary stages at which gene expression is regulated is in transcription. This regulation occurs through the function ofsignal transduction pathways. I would like you to compare positive and negative regulation of gene expression between prokaryotes and eukaryotes. What aspects of regulation are the same (and may have a common evolutionary origin)? What aspects are different? I am not looking for details here, but rather a broad appreciation of this topic. However, it will likely be useful for you to use the examples of the bacterial lac and trp operons discussed in chapter 2.Answer:In both prokaryotes and eukaryotes, gene expression requires that the RNA polymerasebind to the promoter region upstream of the gene. In prokaryotes, the RNA polymerase does not require additional components to bind, but in eukaryotes, the polymerase is part of a larger transcription initiation complex involving several other proteins, includingone or more transcription factors, that regulate transcription by controlling the binding fo the polymerase to the promoter. In eukaryotes, absence of required transcription factors is a type of negative regulation. Other types of transcription factors my bind to the DNA away from the promoter region, altering the structure of the DNA to either promote or prohibit binding of the polymerase. Negative control in prokaryotes is largelythrough the use of regulatory proteins (repressors) that bind to the DNA between the promoter and the gene, preventing the polymerase from transcribing the gene. In prokaryotes, positive control is possible by proteins binding to the DNA near the promoter site, increasing promoter binding. 4) Many plant signal transduction pathways that control gene expression do so byinactivation of repressor proteins using the ubiquitin system. In signaling systemswhere the signaling molecule is membrane permeable, explain where the receptorprotein is located and the role(s) the receptor protein plays in the ubiquitin system.Imagine a signal transduction pathway in which the receptor was an integral membraneprotein but the response of the pathway was still regulation of gene expression by theubiquitin-dependent degradation of repressor proteins. Suggest a mechanism by whichthe ubiquitin system might be controlled in this scenario. I am not looking for the entiresignal transduction pathway, only the step that controls (turns on and off) the


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