Regulation of RNA Transcription

All cells in an individual have the same genetic material but varying requirements for gene expression.

At which of the following levels can mRNA be regulated?

What is the best-understood mechanism of gene expression regulation?

The primary regulation of gene expression for most genes occurs at the level of RNA ______.

What is the role of gene regulatory proteins or transcription factors?

Transcription factors interact with the major groove of the DNA helix.

What chemical feature is uniquely presented by the major groove of DNA that allows proteins to recognize specific base pairs?

How do gene regulatory proteins interact with DNA without unzipping it?

The C-terminal ______ helix in the helix-turn-helix motif makes sequence-specific contacts in the major groove of DNA.

Which of the following structural features is characteristic of the helix-turn-helix DNA-binding motif?

Homeodomain is a special case of the zinc finger motif.

What is the function of the loop region in the helix-loop-helix (HLH) motif?

How does heterodimerization increase the range of sequences that can be recognized?

Transcription factors act on two types of gene regulatory regions: ______ and enhancers.

Which property correctly describes enhancer regions?

Eukaryotic gene regulatory regions are less complex than prokaryotic regulatory regions.

What term describes cooperative interactions that result in a greater-than-additive effect on transcription?

Name at least two mechanisms by which transcription factors regulate gene expression.

Transcription factors must be ______ activated to avoid inappropriate gene expression.

How are many transcription factors activated from an inactive state?

Post-translational modification directly regulates transcription factor's activity, but it does not change cellular localization.

What role do barrier sequences play in transcriptional control?

Match the following mRNA regulation levels with their descriptions:

Which DNA-binding motif is characterized by coordinating one or more zinc ions using amino acid side groups?

The leucine zipper motif involves an alpha helix with a hydrophobic surface on one side serving as both the dimerization region and the DNA-binding region.

What distinguishes enhancers from promoters in gene regulation?

Briefly describe the basic structure of a zinc finger motif.

The process where the growing RNA chain adopts a conformation that interferes with RNA polymerase activity, leading to premature termination of the RNA transcript, is known as transcription ______.

Which of the following describes how combinatorial control by transcription factors works?

A promoter is an independent region outside the gene, which can dramatically increase the transcription initiation.

What role is played by the Mitogen-activated protein kinase (MAPK) family in the regulation of gene expression?

Match the following DNA-binding motifs with their functions:

What is the effect of dimerization of a DNA-binding protein?

Enhancers must be located immediately upstream of the genes they regulate in order to function properly.

Transcription factors that work together to control the rate of transcription achieve ______ control of expression.

What chemical modification generally activates transcription factors?

Match the following gene regulatory proteins to the area they dominate in the fly embryo

Transcription attenuation leads to enhanced transcription of the RNA transcript.

The best understood mechanism of regulation occurs at transcriptional [blank], and involves combinatorial control by transcription factors

What can transcription activators direct to alter chromatin structure?

Dimerization of DNA-binding proteins can enhance binding and specificity by increasing the ______ area with DNA.

Eukaryotic gene regulatory regions are typically (more/less) complex than prokaryotic regulatory regions

Which of the following mechanisms primarily contribute to the regulation of gene expression at the level of mRNA?

Enhancers must be located immediately upstream of the gene they regulate.

What is the primary function of insulator elements in transcriptional control?

The helix-turn-helix motif makes sequence-specific contacts in the _______ of DNA.

A transcription factor with three different pairing partners (A, B, C) could recognize how many different DNA sequences through dimerization?

Describe how transcription factors interact with the DNA double helix to influence gene expression without disrupting its structure.

Explain how the helix-turn-helix motif facilitates sequence-specific DNA binding.

How does heterodimerization contribute to the diversity of DNA sequences that can be recognized by transcription factors?

Distinguish between the roles of promoters and enhancers in regulating gene transcription.

Explain how combinatorial control by transcription factors allows for synergistic effects on gene expression.

Describe how transcription factors regulate gene expression by influencing chromatin structure.

How do post-translational modifications of transcription factors affect their activity and localization?

How does the leucine zipper motif facilitate both dimerization and DNA binding?

Describe the role of the zinc finger motif in DNA binding by transcription factors.

Explain how the expression of the Even-skipped (Eve) gene in Drosophila embryos is regulated by combinatorial control.

How do barrier sequences and insulator elements prevent the spurious spread of transcriptional control?

Describe how the localization of a transcription factor can be regulated to control gene expression.

Explain how gene regulatory proteins can interact with the minor groove of DNA.

Provide two reasons why the regulation of RNA transcription is crucial for most genes.

Explain how the architecture of the homeodomain motif contributes to its function in DNA binding.

How can the combinatorial logic that regulates the expression of globin genes in mammals be compared to that which regulates the Eve gene in Drosophila?

Describe how transcription attenuation regulates the level of RNA transcripts.

How do transcription factors contribute to cell differentiation and the establishment of different cell types during development?

One subclass of zinc fingers coordinates zinc using cysteines and histidines; how many of each are involved and how does this arrangement occur?

Regarding transcription factors (TFs), discuss why it is important that they are selectively activated rather than constitutively active in all cells at all times.

Describe how a mutation in the promoter region of a gene could affect its transcription.

Contrast the regulatory roles of transcriptional activators and repressors.

Explain how alterations in the sequence of an enhancer region could impact gene expression.

Describe the molecular interactions that allows hydrogen bonding to occur between a DNA-binding protein and DNA's base pairs.

There is a short alpha helix contained within the Helix-loop-helix (HLH) DNA-binding Motif. What functions does the flexible loop perform?

Combinatorial control in animal development, as seen with the Even-skipped (Eve) gene expression in fly embryos, is dependent on two different types of gene regulatory proteins. What are they?

Provide an example of how transcription factors may work antagonistically.

Beyond TF's helping to unpack chromatin, list some other ways transcription factors (TF's) regulate gene expression.

Describe how combinatorial control can generate patterns during animal development.

What role does methylation play in recognition by proteins, and where does methylation typically occur?

What determines where transcription factors bind to activate/express?

If a TF is not regulated at the level of transcription, how else might it be regulated? Give an example.

What occurs when the appropriate signals activate the T cell receptor? What cascade of events does this instigate?

List some differences you might observe between eukaryotic and prokaryotic regulatory regions.

Explain why transcriptional initiation is viewed as the best understood mechanism of gene regulation, and what factor is key to this process.

How are transcription factors regulated at the level of gene transcription?

Why post-translational modifications are key to appropriate regulation in many transcription factors?

Regarding transcriptional control, compare and contrast a barrier sequence and an insulator element.

Are transcriptional enhancers generally position- and orientation-dependent or independent?

What may be an advantage of transcription factors binding to DNA outside of the DNA helix?

Transcription factors (TFs) can be regulated post-transcriptionally. Briefly outline a common mechanism for post-translational regulation of TFs and how it can modulate their activity or localization.

Explain how combinatorial control, involving multiple transcription factors, can lead to synergistic effects on gene expression.

Describe how the structure of DNA, specifically major and minor grooves, influences the binding specificity of transcription factors.

Compare and contrast the roles of promoters and enhancers in regulating gene transcription, noting their positions relative to the transcription start site and their functional characteristics.

Explain with an example, how the precise spatial expression of gene regulatory proteins in development leads to specific patterns of gene expression.