Regulation of RNA Transcription

All cells in an individual, without exception, contain exactly the same genetic material and have identical requirements for gene expression.

Which of the following is NOT a level at which mRNA can be regulated?

What is the best understood mechanism of gene expression regulation?

For most genes, where does the primary regulation of gene expression occur?

What role do gene regulatory proteins or transcription factors play?

Transcription factors can bind to and read the inside of the DNA helix to influence the binding or activity of RNA polymerase II.

Which statement best describes the information presented to transcription factors by the major groove of DNA?

How do DNA-binding proteins interact with specific base pairs without unzipping the DNA double helix?

A helix-turn-helix motif makes sequence-specific contacts in which groove of the DNA?

In the context of transcription factors, ______ refers to the association between two different members of the same class, expanding the range of DNA sequences that can be recognized.

What advantage does dimerization of DNA-binding proteins confer in transcriptional regulation?

The promoter region can drive transcription on its own, but it cannot dramatically increase transcription initiation from its corresponding promoter

Which of the following statements accurately describes enhancers?

How do transcription factors work cooperatively to regulate transcription?

Which of the following mechanisms is NOT a way that transcription factors regulate gene expression?

Transcription factors are regulated solely at the level of their own gene transcription.

What role does phosphorylation play in the regulation of transcription factors?

How might post-translational modification affect transcription factor activity?

What term describes the phenomenon where multiple gene regulatory proteins work together to control the rate of transcription?

Transcription ______ leads to premature termination of the RNA transcript, representing another level at which transcription can be regulated.

What role do barrier sequences play?

What are insulator elements?

Match the following DNA-binding motifs with their characteristics:

What is a sequence-specific DNA-binding protein primarily responsible for?

The minor groove of DNA presents a unique signature for each base pair, allowing transcription factors to easily distinguish all base pairs.

Which of the following is an important consideration regarding the energetic cost of RNA synthesis?

What type of bonding primarily mediates the interaction between a DNA-binding protein and a base-pair within the DNA double helix?

In the helix-turn-helix motif, the ______ recognition helix makes sequence-specific contacts in the major groove of DNA.

What structural feature is characteristic of the leucine zipper DNA-binding motif?

Helix-loop-helix (HLH) motifs are structurally and functionally equivalent to helix-turn-helix motifs in DNA binding.

What is the primary function of enhancers in transcriptional regulation?

What determines whether transcription factors act cooperatively or antagonistically?

Match the following scenarios with the expected level of transcription:

Transcription termination is solely determined by the presence of a termination sequence in the DNA.

How does phosphorylation control transcription factors

A single factor's expression might be different in different parts of the body, what is this called?

Give two factors that are important in determining the regulation of TF's.

______ can be reversed by binding of specific proteins to the RNA structure, allowing RNA pol to complete transcription.

Considering that a gene requires both an activator and the absence of a repressor for its expression, and given the following conditions: the activator is present, the repressor is present, and the gene is not expressed. Which of the following could explain this lack of expression?

A researcher is studying a novel transcription factor (TF) that contains a helix-loop-helix (HLH) motif but lacks a dimerization domain. Which of the following is the most likely functional consequence of this structural deficiency?

Combinatorial control of gene expression is less efficient and provides less specificity, because only one factor works at a time.

Considering that transcription factors can be regulated post-transcriptionally, describe an experiment to elucidate whether a specific transcription factor is regulated by phosphorylation?

If the concentration of Bicoid protein is uniform throughout the anterior-posterior axis of a developing Drosophila embryo, the expression pattern of the even-skipped gene would likely be ______ due to the lack of differential regulation by Bicoid.

Why is transcriptional initiation considered the best-understood mechanism of gene regulation?

Give an example of a type of gene regulation that occurs post-transcriptionally.

How do transcription factors interact with the DNA helix to influence RNA polymerase II activity?

What is the role of the major groove in DNA concerning gene regulation?

How many contacts are generally made by a gene regulator protein with DNA?

Describe the role of the recognition helix in the helix-turn-helix motif.

How does the location of amino acid side chains in zinc finger proteins contribute to their function?

Explain the function of the alpha helix in a leucine zipper motif.

In the context of DNA-binding proteins, what is the significance of heterodimerization?

Differentiate between the role of a promoter and an enhancer in RNA transcription.

What is combinatorial control of expression?

What is required for transcription to occur?

Describe how transcription factors can alter chromatin structure to regulate gene expression.

Why do transcription factors need to be selectively activated rather than always active in every cell?

Besides transcriptional regulation, how else are transcription factors regulated?

Explain how phosphorylation can regulate the activity of transcription factors.

Give an example of how cellular localization regulates transcription factors.

What is the overall effect of combinatorial control?

Define transcription attenuation.

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

Describe the significance of the fact that all cells in an individual contain the same genetic material.

How do cells respond effectively to environmental fluctuations?

Why is mRNA an important control point in gene expression?

Besides transcriptional initiation, what are other levels where mRNA can be regulated?

Why is it important to match RNA synthesis to expression requirements?

How would you describe transcription factors?

In the helix-turn-helix motif, how are DNA helices angled?

What is the larger structure of homeodomain?

In zinc finger proteins, how are zinc ions coordinated?

What is the second subclass of zinc finger proteins?

How would you concisely describe leucine zipper?

Explain the structure of helix-loop-helix (HLH).

How does dimerization of DNA-binding proteins increase contact area with DNA?

When would the promoter region be considered 'upstream'?

How is the enhancer region positioned in terms of the promoter?

In relation to activator and repressor, what interactions do transcription factors have?

What helps direct activators to direct local alterations in chromatin structure?

How are transcription factors regulated when it comes to specific cells?

How does post-translational regulation work?

Besides post-translational, what other regulation needs to be considered?

Describe how the combinatorial control of transcription factors allows for a greater diversity of gene expression patterns, using the globin gene or even-skipped gene as an example.

Explain how post-translational modifications, such as phosphorylation, can regulate the activity and localization of transcription factors, and provide an example.

Describe how the structure of DNA, specifically the major and minor grooves, contributes to the sequence-specific binding of transcription factors.

Compare and contrast the roles of promoters and enhancers in regulating gene transcription by discussing their locations, functions, and orientation dependency.

Explain how dimerization and heterodimerization contribute to the diversity and specificity of DNA binding by transcription factors.