Gene Regulation and Transcription Factors Quiz
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Questions and Answers

What is the primary function of transcription factors in gene regulation?

  • To directly alter DNA sequences to promote gene expression.
  • To modify histone proteins to regulate chromatin structure.
  • To bind to specific DNA sequences and modulate the rate of transcription. (correct)
  • To degrade mRNA transcripts and thus decrease gene expression.

Which of the following best describes the role of regulatory DNA sequences?

  • They serve as binding sites for transcription factors and other regulatory proteins. (correct)
  • They facilitate the process of mRNA translation by ribosomes.
  • They are involved in the physical packaging of DNA into chromosomes.
  • They encode the structure of proteins and other essential molecules.

What is the immediate effect of histone acetylation on gene transcription?

  • It results in a more condensed chromatin structure inhibiting transcription.
  • It causes DNA methylation leading to decreased transcription.
  • It leads to a more relaxed chromatin structure, promoting transcription. (correct)
  • It directly affects the rate of translation without affecting transcription.

Tissue-specific gene regulation is primarily due to:

<p>The selective expression and activity of specific transcription factors in different tissues. (A)</p> Signup and view all the answers

During embryonic development, what accounts for the changes in gene expression patterns?

<p>Changes in the levels of transcription factors and chromatin remodeling. (D)</p> Signup and view all the answers

Which of the following represents a short-term regulatory mechanism of gene expression?

<p>Response to growth factors and hormones. (D)</p> Signup and view all the answers

At which level does chromatin remodelling primarily regulate gene expression?

<p>Transcriptional level. (B)</p> Signup and view all the answers

Which of these is NOT a level at which gene expression is regulated?

<p>DNA Replication. (D)</p> Signup and view all the answers

What is the primary function of the core promoter during transcription initiation?

<p>To serve as the landing site for RNA Polymerase II, facilitated by transcription factors (C)</p> Signup and view all the answers

How does RNA Polymerase II recognize the specific DNA sequence where transcription should begin?

<p>It is guided to the core promoter by transcription factors (A)</p> Signup and view all the answers

What is the primary role of co-activators in gene transcription?

<p>They interact with transcription factors to enhance gene transcription (D)</p> Signup and view all the answers

What is the significance of the DNA-binding domain in transcription factors?

<p>It determines the specific DNA sequences the factor can attach to (A)</p> Signup and view all the answers

What role does the 'trans-activation/trans-repression' domain play in transcription factors?

<p>It contains binding sites for co-activators and/or co-repressors. (D)</p> Signup and view all the answers

In the context of transcription, what is a ‘ligand’?

<p>A small molecule that needs to bind certain transcription factors for activation (D)</p> Signup and view all the answers

What is the significance of the AAUAAA hexamer in mRNA during transcription termination?

<p>It signifies the end of the gene to be transcribed and is a termination signal. (A)</p> Signup and view all the answers

If a transcription factor has a mutation in its DNA-binding domain that prevents it from binding correctly to its target DNA sequence, what would be the most likely outcome?

<p>The transcription factor will not be able to regulate the transcription of its target gene. (A)</p> Signup and view all the answers

What is the process of RNA Polymerase II 'moving along the DNA', and what is its result?

<p>The RNA Polymerase II is synthesizing a complementary RNA sequence, using one strand of the DNA as template. (D)</p> Signup and view all the answers

Which of the following describes the function of the transcription factor dimerization domain?

<p>It allows some transcription factors to bind to DNA (D)</p> Signup and view all the answers

Which of the following best describes the primary role of basal transcription factors?

<p>To recruit RNA polymerase II to the gene promoter and initiate transcription. (C)</p> Signup and view all the answers

How do specific transcription factors differ from basal transcription factors?

<p>Specific transcription factors exhibit tissue-specificity and can act as activators or repressors, while basal transcription factors are ubiquitous and primarily initiators. (D)</p> Signup and view all the answers

What is the main function of enhancer and silencer elements in gene regulation?

<p>To regulate the activity of the core promoter by recruiting specific transcription factors and co-regulators. (D)</p> Signup and view all the answers

Where is the core promoter typically located in relation to the gene it regulates?

<p>Immediately upstream of the gene, within a fixed range of base pairs. (D)</p> Signup and view all the answers

How do cohesins and condensins contribute to gene regulation?

<p>They form chromatin loops, bringing enhancers/silencers into close proximity to the core promoter. (B)</p> Signup and view all the answers

What is the primary mechanism by which transcriptional activators enhance gene transcription?

<p>By recruiting co-activators to the gene promoter. (A)</p> Signup and view all the answers

What is the range of distance between enhancer/silencers and the core promoter of a gene?

<p>They can be located near or far from the core promoter, ranging from hundreds of base pairs to megabase pairs. (C)</p> Signup and view all the answers

How do specific transcription factors influence gene expression through the enhancer/silencer regions?

<p>They recruit co-activators or co-repressors to modulate the activity of the core promoter. (B)</p> Signup and view all the answers

What is the role of non-histone proteins like cohesins and condensins in gene regulation?

<p>They facilitate the formation of chromatin loops, bringing enhancer/silencer regions closer to the core promoter. (D)</p> Signup and view all the answers

Which of the following best explains the concept of transcriptional activators and repressors?

<p>They are specific factors that can increase or decrease the transcription of a gene. (A)</p> Signup and view all the answers

What is the primary effect of histone acetylation on chromatin structure?

<p>It neutralizes the positive charge on histones, reducing electrostatic interaction with DNA, and loosening chromatin. (C)</p> Signup and view all the answers

Which specialized protein domain is responsible for recognizing and binding to acetylated lysine residues on histones?

<p>Bromodomain (D)</p> Signup and view all the answers

What structural change to chromatin is associated with an increase in histone acetylation?

<p>Formation of euchromatin, which is a more open and accessible state. (D)</p> Signup and view all the answers

How do histone acetyltransferases (HATs) and histone deacetylases (HDACs) affect gene transcription?

<p>HATs open chromatin and increase gene expression, whereas HDACs condense chromatin and repress gene expression. (D)</p> Signup and view all the answers

What is the role of transcription repressors in terms of chromatin modification, in the regulation of gene expression?

<p>They recruit histone deacetylases to promote chromatin condensation and gene repression. (C)</p> Signup and view all the answers

What is the primary way that transcription activators affect chromatin structure?

<p>By recruiting histone acetyltransferases (HATs) and chromatin remodeling complexes. (D)</p> Signup and view all the answers

Which statement best describes why different cell types within an organism can exhibit different gene expression patterns?

<p>Different cell types use different transcription factors leading to different chromatin modifications. (B)</p> Signup and view all the answers

Concerning the activity of the gene, in the context of chromatin structure, what would you expect to see in a cell where a specific gene is highly expressed?

<p>High levels of both histone acetylation and chromatin accessibility (D)</p> Signup and view all the answers

What direct effect do acetyl groups have on histones that alters their interaction with DNA?

<p>They neutralize the positive charge (C)</p> Signup and view all the answers

Where would you expect to see bromodomain containing proteins?

<p>On both transcription factors and chromatin remodeling complexes (D)</p> Signup and view all the answers

What is the primary role of tissue-specific transcription factors?

<p>To regulate gene expression in a manner that is unique to specific tissues and cells. (C)</p> Signup and view all the answers

How do histone modifications contribute to tissue-specific gene expression?

<p>Histone modifications, such as acetylation, can alter chromatin structure, making it either accessible or inaccessible for transcription, resulting in tissue-specific gene expression. (A)</p> Signup and view all the answers

Which of the following statements best describes the relationship between enhancers and silencers in tissue-specific gene regulation?

<p>A silencer that is active in one tissue type, can be inactive, or even act as an enhancer, in a different tissue type. (B)</p> Signup and view all the answers

In the context of lung epithelial cell differentiation, what is the primary role of specific transcription factors?

<p>They direct distinct patterns of gene expression necessary for the unique characteristics and functions of each type of lung epithelial cell. (D)</p> Signup and view all the answers

What is the expected state of chromatin at an active enhancer in a hepatocyte?

<p>Open due to high levels of histone acetylation. (B)</p> Signup and view all the answers

How do different patterns of histone modifications lead to tissue-specific gene expression?

<p>Histone modifications alter the availability of DNA for transcription by affecting chromatin structure. (D)</p> Signup and view all the answers

What determines whether a specific enhancer will be active or inactive in a given tissue?

<p>The specific transcription factors present in the cell, coupled with the histone modification status of the enhancer itself. (A)</p> Signup and view all the answers

In a hypothetical scenario, if a gene has an active enhancer in lung fibroblasts, and an active silencer in hepatocytes, what would happen to the transcription of this gene in the two cell types?

<p>Transcription would be active in lung fibroblasts but inactive in hepatocytes. (D)</p> Signup and view all the answers

Which of the following BEST describes how transcription repressors inhibit gene transcription?

<p>By recruiting co-repressors that promote chromatin condensation, thereby blocking access to the gene promoter. (A)</p> Signup and view all the answers

What is the primary role of histone acetyltransferases (HATs) in gene regulation?

<p>To add acetyl groups to histone tails, reducing their positive charge. (A)</p> Signup and view all the answers

How do ATP-dependent chromatin remodeling enzymes primarily contribute to gene activation?

<p>By displacing nucleosomes, making DNA more accessible for transcription. (A)</p> Signup and view all the answers

What is the significance of lysine and arginine in histones?

<p>They contribute to the positive charge of histones, facilitating electrostatic interactions with negatively charged DNA. (B)</p> Signup and view all the answers

How does the formation of heterochromatin impact gene expression?

<p>It inhibits gene transcription by preventing the transcription complex from accessing the gene promoter. (A)</p> Signup and view all the answers

What is the function of histone deacetylases (HDACs)?

<p>To remove acetyl groups from lysine residues on histone tails. (C)</p> Signup and view all the answers

What two main processes are involved in opening chromatin to allow gene transcription?

<p>Nucleosome displacement and histone modifications. (B)</p> Signup and view all the answers

Describe the relationship between euchromatin and gene transcription.

<p>Euchromatin presents a more accessible structure that allows the transcription complex to bind. (D)</p> Signup and view all the answers

Flashcards

Gene Expression

The process of converting genetic information from DNA into functional proteins.

Regulation of Gene Expression

The regulation of gene expression ensures that the right genes are turned on or off at the right time and in the right place.

Transcription

The process by which a DNA sequence is copied into an RNA molecule. This is the first step in gene expression.

Translation

The process by which an RNA molecule is used to create a protein. This is the second step in gene expression.

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Chromatin Remodelling

Changes in the structure of chromatin, the complex of DNA and proteins that make up chromosomes. This can affect the accessibility of DNA to transcription factors.

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Transcription Factors

Specialized proteins that bind to specific DNA sequences and regulate gene transcription.

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Regulatory DNA Sequences

Specific DNA sequences that serve as binding sites for transcription factors. These regions can either activate or repress gene transcription.

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Histone Acetylation

A process that modifies histone proteins, making DNA more accessible to transcription factors and promoting gene transcription.

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What is the core promoter?

A non-coding DNA sequence immediately before a target gene where RNA Polymerase II binds. It's like an address that tells RNA polymerase where to start transcribing the gene.

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What are transcription factors?

Proteins that bind to specific DNA sequences and regulate the rate of gene transcription by either activating or inhibiting it. They act as on/off switches for genes.

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What is pre-initiation complex formation?

The process of RNA polymerase II attaching to the core promoter with the help of transcription factors, forming a complex that initiates transcription. It's like getting ready to build the RNA molecule.

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What is transcription elongation?

The process of RNA polymerase II moving along the DNA strand, unwinding it and using one strand as a template to synthesize a complementary RNA sequence. It's like reading a recipe and translating it into a dish.

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What is a termination signal?

A signal within the newly synthesized RNA molecule that tells RNA polymerase to stop transcription. It acts like a stop sign for the assembly line.

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What are co-activators and co-repressors?

Proteins that aid in regulating transcription by interacting with transcription factors. They can either activate or inhibit gene transcription, acting like assistants for transcription factors.

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What are protein domains?

A functional unit within a protein that allows it to interact with specific molecules, such as DNA or other proteins. These domains give proteins their unique functions.

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What is the DNA-binding domain of a transcription factor?

A domain within transcription factors that binds to specific short sequences of DNA near the target gene, allowing the transcription factor to recognize and attach to the right DNA sequence.

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What is the trans-activation/trans-repression domain?

A domain within transcription factors that interacts with co-activators or co-repressors, allowing the transcription factor to influence the activity of other proteins involved in gene transcription.

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What is the ligand-binding domain?

A domain within some transcription factors that binds to specific molecules, such as hormones, to activate the transcription factor. These transcription factors rely on signals from other molecules to become active.

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Chromatin

The complex of DNA and proteins that make up chromosomes. It can be loosely packed (euchromatin) or tightly packed (heterochromatin).

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Euchromatin

A loosely packed form of chromatin that allows genes to be transcribed.

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Heterochromatin

A tightly packed form of chromatin that prevents gene transcription.

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Chromatin Remodeling Enzymes

Enzymes that move nucleosomes along DNA, making DNA more or less accessible to transcription factors.

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Histone Acetyltransferases (HATs)

Enzymes that add acetyl groups to histones, leading to chromatin relaxation and gene activation.

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Histone Deacetylases (HDACs)

Enzymes that remove acetyl groups from histones, leading to chromatin condensation and gene repression.

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Basic Transcription Factors

Transcription factors that work in all cells and tissues. They are fundamental for recruiting RNA polymerase II to the gene promoter, which is the starting point for transcription.

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Specific Transcription Factors

Transcription factors that are specific to certain tissues. They help control gene expression in a tissue-specific manner, ensuring that the right genes are switched on or off in each tissue.

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Core Promoter

A short stretch of DNA sequence located immediately upstream (before) the gene's coding region. It marks the transcription start site and contains binding sites for basal transcription factors.

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Enhancers/Silencers

DNA sequences that can be located either before or after the gene promoter. They contain binding sites for specific transcription factors and can either enhance or repress gene transcription.

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Co-activators/Co-repressors

Specialized transcription factors that work alongside basic transcription factors to regulate gene expression. They can increase or decrease transcription by interacting with specific regions of DNA.

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Cohesins and Condensins

Proteins that help organize DNA within the nucleus, creating loops that bring enhancers/silencers physically closer to the promoter.

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Bromodomains

Proteins that contain special modules called bromodomains, which can bind to acetylated histones.

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Transcription Activators

Transcription factors that can activate gene transcription by opening chromatin. They often recruit HATs and chromatin remodeling complexes.

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Transcription Repressors

Transcription factors that can repress gene transcription by inducing chromatin condensation. They often recruit HDACs.

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Tissue-specific Transcription Factors

Specific transcription factors are found in certain tissues or cell types but not others, making them crucial for tissue-specific gene expression. They are like specialized tools for turning on and off genes within specific cells.

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Tissue-specific Enhancer Activity

Enhancers are DNA sequences that can either activate or inactivate gene expression depending on their location and the presence of specific transcription factors. They act like volume knobs for gene expression, controlling its intensity.

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Histone Modifications and Enhancer Activity

Histone acetylation and deacetylation are dynamic processes that influence chromatin structure and gene expression. Acetylation opens up chromatin, making genes more accessible to transcription factors, while deacetylation closes it, making them less accessible.

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Cell Type-specific Transcription Factors and Cell Differentiation

Cell type-specific transcription factors are essential for the development and function of different cell types. They help cells take on their specific roles and identities by regulating the expression of appropriate genes.

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Enhancer Activity

Enhancers are DNA sequences that bind to specific transcription factors, influencing gene expression by either activating or inhibiting transcription. They can act like switches for genes, determining whether they are turned on or off.

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Tissue-specific Enhancer/Silencer Activity

Lung fibroblasts and hepatocytes have different chromatin states and transcription factor profiles, leading to tissue-specific gene expression patterns.

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Tissue-specific Gene Expression

Tissue-specific gene expression is essential for normal growth and development, ensuring that different parts of the body have the appropriate functions. It helps cells specialize and work together as a cohesive system.

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Study Notes

Gene Expression & Regulation

  • Gene expression is controlled in both time and space.
  • Every cell has the same DNA, but different genes need to be "on" and "off" in different cell types.
  • Gene expression regulation is crucial for normal growth and development.
  • Gene expression is controlled at different levels

Gene Regulation During Development

  • Different genes need to be turned "on" and "off" during different stages of life to ensure proper development.
  • Different gene expression profiles are seen at different stages of life, like embryo, different months of age, etc.

Gene Regulation Overview

  • Gene regulation is divided into short-term and long-term regulation.
  • Short-term: Cells react to external environments, including growth factors and hormones.
  • Long-term: Cells have specific identities, which are passed on to daughter cells during cell division.

Gene Regulation Levels

  • Chromatin remodeling
  • Transcriptional regulation
  • Post-transcriptional regulation
  • Translational regulation

Transcription Initiation

  • RNA Pol II binds to a non-coding DNA sequence (the core promoter) before the gene.
  • Transcription factors (TFs) guide RNA Pol II to the core promoter.
  • RNA Pol II and TFs form a pre-initiation complex.
  • RNA Pol II phosphorylation at RBP1 initiates transcription.

Transcription Elongation

  • RNA Pol II detaches from the promoter, creating a transcription bubble unravelling the DNA.
  • RNA Pol II moves along one DNA strand, using it as a template to create a complementary RNA sequence.
  • Either strand can be a template depending on the promoter.
  • RNA Pol II adds nucleotides to the 3' end of the growing RNA.

Transcription Termination

  • RNA Pol II encounters a termination signal (AAUAAA).
  • Transcription stops at the termination signal.
  • RNA Pol and mRNA are released.
  • A new transcription cycle can then begin.

Transcription Factors

  • Proteins that bind to specific DNA sequences to regulate gene transcription.
  • Most transcription factors work by recruiting other proteins (co-activators or co-repressors).
  • They can activate or repress gene transcription.
  • Co-activators = proteins that increase gene transcription by interacting with transcription factors.
  • Co-repressors = proteins that decrease gene transcription by interacting with transcription factors.

Transcription Factor Domains

  • DNA-binding domain (all TFs): Recognizes specific short sequences near the target gene.
  • Trans-activation/trans-repression domain (all TFs): Contains binding sites for co-activators or co-repressors.
  • Ligand-binding domain (some TFs): Some TFs require ligand binding (e.g., hormone receptors) for activation.
  • Dimerization domain (some TFs): Some TFs need to form dimers to bind to DNA.

DNA Binding Domains

  • Specific DNA binding domains allow proteins to attach to the major groove of DNA and interact with nucleotide bases..
  • The order of amino acids in the domain determines which specific DNA sequences a TF can bind.
  • Recognizes short DNA sequences, transcription factor binding motifs (6-12 base pairs).

Basic and Specific Transcription Factors

  • Basic TFs: Found in all cells and tissues; recruit RNA polymerase II to the gene promoter.
  • Specific TFs: Show tissue specificity (e.g., heart-specific or lung-specific) and regulate gene transcription.

Regulatory DNA Sequences

  • Core promoter: Immediately upstream of the gene; contains the transcription start site (+1); required for gene transcription.
  • Enhancer/Silencer elements: Can be upstream or downstream of the gene; regulate transcription of nearby genes.
  • Contain transcription binding motifs: Recruit transcription factors (activators or inhibitors) to the target gene.

Enhancers/Silencers

  • Can be far from the gene promoter.
  • Contain binding motifs for specific transcription factors.
  • Influence core promoter activity by bringing in proteins for enhancement or repression.

Chromatin Remodeling

  • Nucleosome displacement: ATP-dependent enzymes displace nucleosomes.
  • Chromatin unravelling: Histone modifications (e.g., acetylation).

Histones

  • Highly conserved proteins with positive charges rich in lysine and arginine.
  • Globular proteins with N-terminal tails for covalent modifications (e.g., acetylation).

Histone Acetylation

  • Histone acetyltransferases (HATs): Add acetyl groups, which reduce the positive charge of histones.
  • Histone deacetylases (HDACS): Remove acetyl groups.
  • Acetylation can open chromatin structure, making DNA accessible to transcription complexes.

Bromodomains

  • Proteins that contain special modules called bromodomains.
  • These domains can bind to acetylated histones.
  • Different types of proteins contain bromodomains, in some instances, including chromatin-remodeling complexes and transcription factors.

Tissue-Specific Regulation

  • Every cell has the same DNA but distinct expression profiles due to different tissue-specific transcription factors.
  • Basal transcription factors are found in all cells, whereas specific factors dictate tissue-specificities.
  • Enhancer activity shows tissue-specificity, some enhancers being active in certain tissues and not in others.

Cell Type-Specific Transcription Factors

  • Specific transcription factors are necessary for differentiating various cell types within specific tissues (e.g., lung tissue)

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Gene Expression & Regulation (MD105) Lecture Notes PDF

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Test your knowledge on the complex mechanisms of gene regulation and the role of transcription factors. This quiz covers topics such as regulatory DNA sequences, histone modifications, and the functions of core promoters. Perfect for students studying molecular biology and genetics.

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