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Problem 1a
Devoting a few sentences to each, describe the following structures or complexes and their effects on eukaryotic gene expression:
Promoter
Problem 1b
Devoting a few sentences to each, describe the following structures or complexes and their effects on eukaryotic gene expression:
Enhancer
Problem 1c
Devoting a few sentences to each, describe the following structures or complexes and their effects on eukaryotic gene expression:
Silencer
Problem 1d
Devoting a few sentences to each, describe the following structures or complexes and their effects on eukaryotic gene expression:
RISC
Problem 1e
Devoting a few sentences to each, describe the following structures or complexes and their effects on eukaryotic gene expression:
Dicer
Problem 2a
Describe and give an example (real or hypothetical) of each of the following:
Upstream activator sequence (UAS)
Problem 2b
Describe and give an example (real or hypothetical) of each of the following:
Insulator sequence action
Problem 2c
Describe and give an example (real or hypothetical) of each of the following:
Silencer sequence action
Problem 2d
Describe and give an example (real or hypothetical) of each of the following:
Enhanceosome action
Problem 2e
Describe and give an example (real or hypothetical) of each of the following:
RNA interference
Problem 3
What is meant by the term chromatin remodeling? Describe the importance of this process to transcription.
Problem 4
What general role does acetylation of histone protein amino acids play in the transcription of eukaryotic genes?
Problem 5
Describe the roles of writers, readers, and erasers in eukaryotic gene regulation.
Problem 6
Outline the roles of RNA in eukaryotic gene regulation.
Problem 7
What are the roles of the Polycomb and Trithorax complexes in eukaryotic gene regulation?
Problem 9
Compare and contrast the transcriptional regulation of GAL genes in yeast with that of the lac genes in bacteria.
Problem 10
The term heterochromatin refers to heavily condensed regions of chromosomes that are largely devoid of genes. Since few genes exist there, these regions almost never decondense for transcription. At what point during the cell cycle would you expect to observe the decondensation of heterochromatic regions? Why?
Problem 11
Compare and contrast promoters and enhancers with respect to their location (upstream versus downstream), orientation, and distance (in base pairs) relative to a gene they regulate.
Problem 12
What are the different chromatin classifications, and what is their relationship to gene expression?
Problem 13
Define epigenetics, and provide examples illustrating your definition.
Problem 14
What is one proposed role for lncRNAs?
Problem 15
What are the sources of dsRNA? Diagram the mechanisms by which dsRNAs are produced and processed into small RNAs.
Problem 16
How does dsRNA lead to posttranscriptonal gene silencing?
Problem 17a
A hereditary disease is inherited as an autosomal recessive trait1. The wild-type allele of the disease gene produces a mature mRNA that is 1250 nucleotides (nt) long. Molecular analysis shows that the mature mRNA consists of four exons that measure 400 nt (exon 1), 320 nt (exon 2), 230 nt (exon 3), and 300 nt (exon 4). A mother and father with two healthy children and two children with the disease have northern blot analysis performed in a medical genetics laboratory. The results of the northern blot for each family member are shown here. Identify the genotype of each family member, using the sizes of mRNAs to indicate each allele. (For example, a person who is homozygous wild type is indicated as '1250/1250.')
Problem 17b
A hereditary disease is inherited as an autosomal recessive trait1. The wild-type allele of the disease gene produces a mature mRNA that is 1250 nucleotides (nt) long. Molecular analysis shows that the mature mRNA consists of four exons that measure 400 nt (exon 1), 320 nt (exon 2), 230 nt (exon 3), and 300 nt (exon 4). A mother and father with two healthy children and two children with the disease have northern blot analysis performed in a medical genetics laboratory. The results of the northern blot for each family member are shown here. Based on your analysis, what is the most likely molecular abnormality causing the disease allele?
Problem 18a
The UG4 gene is expressed in stem tissue and leaf tissue of the plant Arabidopsis thaliana. To study mechanisms regulating UG4 expression, six small deletions of the DNA sequence upstream of the gene-coding sequence are made. The locations of deletions and their effect on UG4 expression are shown here. Explain the differential effects of deletions B and F on expression in the two tissues.
Problem 18b
The UG4 gene is expressed in stem tissue and leaf tissue of the plant Arabidopsis thaliana. To study mechanisms regulating UG4 expression, six small deletions of DNA sequence upstream of the gene-coding sequence are made. The locations of deletions and their effect on UG4 expression are shown here. Why does deletion D raise UG4 expression in leaf tissue but not in stem tissue?
Problem 18c
The UG4 gene is expressed in stem tissue and leaf tissue of the plant Arabidopsis thaliana. To study mechanisms regulating UG4 expression, six small deletions of DNA sequence upstream of the gene-coding sequence are made. The locations of deletions and their effect on UG4 expression are shown here. Why does deletion E lower expression of UG4 in leaf tissue but not in stem tissue?
Problem 19
Diagram and explain how the inducibility of a gene—for instance in response to an environmental cue—could be mediated by an activator. Then show how it could be mediated by a repressor.
Problem 20a
A muscle enzyme called ME1 is produced by transcription and translation of the ME1 gene in several muscles during mouse development, including heart muscle, in a highly regulated manner. Production of ME1 appears to be turned on and turned off at different times during development. To test the possible role of enhancers and silencers in ME1 transcription, a biologist creates a recombinant genetic system that fuses the ME1 promoter, along with DNA that is upstream of the promoter, to the bacterial lacZ (β-galactosidase) gene. The lacZ gene is chosen for the ease and simplicity of assaying production of the encoded enzyme. The diagram shows bars that indicate the extent of six deletions the biologist makes to the ME1 promoter and upstream sequences. The blue deletion labeled D is within the promoter whereas the gray bars span potential enhancer/silencer modules. The table displays the percentage of β-galactosidase activity in each deletion mutant in comparison with the recombinant gene system without any deletions.
Does this information indicate the presence of enhancer and/or silencer sequences in the ME1 upstream sequence? If so, where is/are the sequences located?