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Problem 1a
In this chapter, we focused on the regulation of gene expression in eukaryotes. At the same time, we found many opportunities to consider the methods and reasoning by which much of this information was acquired. From the explanations given in the chapter:
How do we know that transcription and translation are spatially and temporally separated in eukaryotic cells?
Problem 1b
In this chapter, we focused on the regulation of gene expression in eukaryotes. At the same time, we found many opportunities to consider the methods and reasoning by which much of this information was acquired. From the explanations given in the chapter:
How do we know that DNA methylation is associated with transcriptionally silent genes?
Problem 1c
In this chapter, we focused on the regulation of gene expression in eukaryotes. At the same time, we found many opportunities to consider the methods and reasoning by which much of this information was acquired. From the explanations given in the chapter:
How do we know that core-promoter elements are important for transcription?
Problem 1d
In this chapter, we focused on the regulation of gene expression in eukaryotes. At the same time, we found many opportunities to consider the methods and reasoning by which much of this information was acquired. From the explanations given in the chapter:
How do we know that the orientation of promoters relative to the transcription start site is important while enhancers are orientation independent?
Problem 1e
In this chapter, we focused on the regulation of gene expression in eukaryotes. At the same time, we found many opportunities to consider the methods and reasoning by which much of this information was acquired. From the explanations given in the chapter:
How do we know that alternative splicing enables one gene to encode different isoforms with different functions?
Problem 1f
In this chapter, we focused on the regulation of gene expression in eukaryotes. At the same time, we found many opportunities to consider the methods and reasoning by which much of this information was acquired. From the explanations given in the chapter:
How do we know that small noncoding RNA molecules can regulate gene expression?
Problem 2
Write a short essay describing which types of trans-acting proteins bind to which type of cis-regulatory element, and how these interactions influence transcription initiation.
Problem 3
What features of eukaryotes provide additional opportunities for the regulation of gene expression compared to bacteria?
Problem 4
Describe the organization of the interphase nucleus. Include in your presentation a description of chromosome territories and interchromatin compartments.
Problem 5
Provide a brief description of two different types of histone modification and how they impact transcription.
Problem 6
Present an overview of the manner in which chromatin can be remodeled. Describe the manner in which these remodeling processes influence transcription.
Problem 7
Distinguish between the cis-acting regulatory elements referred to as promoters and enhancers.
Problem 8
Describe the manner in which activators and repressors influence the rate of transcription initiation. How might chromatin structure be involved in such regulation?
Problem 9
Many promoter regions contain CAAT boxes containing consensus sequences CAAT or CCAAT approximately 70 to 80 bases upstream from the transcription start site. How might one determine the influence of CAAT boxes on the transcription rate of a given gene?
Problem 10
Research indicates that promoters may fall into one of two classes: focused or dispersed. How do these classes differ, and which genes tend to be associated with each?
Problem 11
Explain the features of the Initiator (Inr) elements, BREs, DPEs, and MTEs of focused promoters.
Problem 12
List three types of alternative splicing patterns and how they lead to the production of different protein isoforms.
Problem 13
Consider the CT/CGRP example of alternative splicing shown in Figure 16.9. Which different types of alternative splicing patterns are represented?
Problem 14
Explain how the use of alternative promoters and alternative polyadenylation signals produces mRNAs with different - and -ends.
Problem 15
The regulation of mRNA decay relies heavily upon deadenylases and decapping enzymes. Explain how these classes of enzymes are critical to initiating mRNA decay.
Problem 16
Nonsense-mediated decay is an mRNA surveillance pathway that eliminates mRNAs with premature stop codons. How does the cell distinguish between normal mRNAs and those with a premature stop?
Problem 17
In 1998, future Nobel laureates Andrew Fire and Craig Mello, and colleagues, published an article in Nature entitled, “Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans.” Explain how RNAi is both “potent and specific.”
Problem 18
Present an overview of RNA interference (RNAi). How does the silencing process begin, and what major components participate?
Problem 19
RNAi may be directed by small interfering RNAs (siRNAs) or microRNAs (miRNAs); how are these similar, and how are they different?
Problem 20
miRNAs target endogenous mRNAs in a sequence-specific manner. Explain, conceptually, how one might identify potential mRNA targets for a given miRNA if you only know the sequence of the miRNA and the sequence of all mRNAs in a cell or tissue of interest.
Problem 21
In principle, RNAi may be used to fight viral infection. How might this work?
Problem 22
Competing endogenous RNAs act as molecular “sponges.” What does this mean, and what do they compete with?
Problem 23
How and why are eukaryotic mRNAs transported and localized to discrete regions of the cell?
Problem 24
How is it possible that a given mRNA in a cell is found throughout the cytoplasm but the protein that it encodes is only found in a few specific regions?
Problem 25
How may the covalent modification of a protein with a phosphate group alter its function?