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- In this chapter, we focused on how DNA is organized at the chromosomal level. Along the way, 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, what answers would you propose to the following fundamental questions: What is the experimental basis for concluding that puffs in polytene chromosomes and loops in lampbrush chromosomes are areas of intense transcription of RNA?
Problem 1
- In this chapter, we focused on how eukaryotic genes are regulated at the transcriptional level. Along the way, 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 promoter and enhancer sequences control the initiation of transcription in eukaryotes?
Problem 1
- In this chapter, we focused on how eukaryotic genes are regulated at the transcriptional level. Along the way, 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 1
- In this chapter, we focused on how eukaryotic genes are regulated at the transcriptional level. Along the way, 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 eukaryotic transcription factors bind to DNA sequences at or near promoter regions?
Problem 1
- In this chapter, we focused on how eukaryotic genes are regulated at the transcriptional level. Along the way, 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 there is an association between disease susceptibility in humans and regulatory DNA sequences?
Problem 1
- Write a short essay describing how cis-acting regulatory elements, activators, and chromatin modifiers are all coordinately involved in regulating transcription initiation.
Problem 2
- A number of experiments have demonstrated that areas of the genome that are transcriptionally inactive are also resistant to DNase I digestion. However, transcriptionally active areas are DNase I sensitive. Describe how DNase I resistance or sensitivity might indicate transcriptional activity.
Problem 6
Problem 10
Why doesn't polynucleotide phosphorylase (Ochoa's enzyme) synthesize RNA in vivo?
Problem 11
Refer to Table 13.1. Can you hypothesize why a synthetic RNA composed of a mixture of poly U poly A would not stimulate incorporation of ¹⁴C-phenylalanine into protein?
Problem 11
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 12
Present an overview of RNA interference (RNAi). How does the silencing process begin, and what major components participate?
Problem 13
A short RNA molecule was isolated that demonstrated a hyperchromic shift (see Chapter 10), indicating secondary structure. Its sequence was determined to be
5'-AGGCGCCGACUCUACU-3'
Propose a two-dimensional model for this molecule.Problem 13
A short RNA molecule was isolated that demonstrated a hyperchromic shift (see Chapter 10), indicating secondary structure. Its sequence was determined to be
5'-AGGCGCCGACUCUACU-3'
What DNA sequence would give rise to this RNA molecule through transcription?Problem 13
RNAi may be directed by small interfering RNAs (siRNAs) or microRNAs (miRNAs); how are these similar, and how are they different?
Problem 14
Compare the control of gene regulation in eukaryotes and bacteria at the level of initiation of transcription. How do the regulatory mechanisms work? What are the similarities and differences in these two types of organisms in terms of the specific components of the regulatory mechanisms?
Problem 14
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 15
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 15
In principle, RNAi may be used to fight viral infection. How might this work?
Problem 16
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 17
Define the process of transcription. Where does this process fit into the central dogma of molecular biology (DNA makes RNA makes protein)?
Problem 17
Explain the features of the Initiator (Inr) elements, BREs, DPEs, and MTEs of focused promoters.
Problem 18
What observations suggested the existence of mRNA?
Problem 18
Many transcriptional activators are proteins with a DNA-binding domain (DBD) and an activation domain (AD). Explain how each domain contributes to transcriptional initiation. Would you expect repressors to also have each of these domains?
Problem 19
Describe the structure of RNA polymerase in bacteria. What is the core enzyme? What is the role of the σ subunit?
Problem 19
How do the ENCODE data vastly help determine which enhancers regulate which genes?
Problem 20
Write a paragraph describing the abbreviated chemical reactions that summarize RNA polymerase-directed transcription.
Problem 21
Messenger RNA molecules are very difficult to isolate in bacteria because they are rather quickly degraded in the cell. Can you suggest a reason why this occurs? Eukaryotic mRNAs are more stable and exist longer in the cell than do bacterial mRNAs. Is this an advantage or a disadvantage for a pancreatic cell making large quantities of insulin?
Problem 22
Present an overview of various forms of posttranscriptional RNA processing in eukaryotes. For each, provide an example.
Problem 23
One form of posttranscriptional modification of most eukaryotic pre-mRNAs is the addition of a poly-A sequence at the 3' end. The absence of a poly-A sequence leads to rapid degradation of the transcript. Poly-A sequences of various lengths are also added to many bacterial RNA transcripts where, instead of promoting stability, they enhance degradation. In both cases, RNA secondary structures, stabilizing proteins, or degrading enzymes interact with poly-A sequences. Considering the activities of RNAs, what might be general functions of 3'-polyadenylation?
Problem 23
The interphase nucleus is a highly structured organelle with chromosome territories, interchromatin compartments, and transcription factories. In cultured human cells, researchers have identified approximately 8000 transcription factories per cell, each containing an average of eight tightly associated RNAP II molecules actively transcribing RNA. If each RNAP II molecule is transcribing a different gene, how might such a transcription factory appear? Provide a simple diagram that shows eight different genes being transcribed in a transcription factory and include the promoters, structural genes, and nascent transcripts in your presentation.
