Gene Regulation and Chromatin Structure Quiz

Choose a study mode

Play Quiz
Study Flashcards
Spaced Repetition
Chat to Lesson

Podcast

Play an AI-generated podcast conversation about this lesson
Download our mobile app to listen on the go
Get App

Questions and Answers

What is the primary function of histone acetyltransferases (HATs)?

  • To condense chromatin, inhibiting transcription.
  • To add acetyl groups to histones, decreasing positive charge. (correct)
  • To remove acetyl groups from histones, increasing positive charge.
  • To bind to methylated histones, promoting gene silencing.

Which of the following describes euchromatin?

  • An open and accessible form of chromatin, promoting gene transcription. (correct)
  • A region rich in methylated histones, leading to gene silencing.
  • A condensed form of chromatin that inhibits gene transcription.
  • A tightly packed nucleosome structure, blocking transcription factors.

What is the role of bromodomains in gene regulation?

  • They facilitate the removal of acetyl groups from histones, repressing transcription.
  • They directly recruit RNA polymerase II to the promoter of a gene.
  • They bind to methylated DNA, leading to gene silencing.
  • They bind to acetylated histones, attracting chromatin remodeling complexes. (correct)

How can transcription repressors on silencer elements inhibit gene transcription?

<p>By inducing chromatin condensation and preventing RNA Pol II recruitment. (D)</p> Signup and view all the answers

What is a direct consequence of nucleosomes preventing transcription?

<p>Inhibition of transcription complex access to the gene promoter. (A)</p> Signup and view all the answers

What is the main type of electrostatic interaction between DNA and histones?

<p>The interaction between positively charged histones and negatively charged DNA. (A)</p> Signup and view all the answers

In the context of chromatin remodeling, what do ATP-dependent enzymes primarily facilitate?

<p>Nucleosome displacement. (D)</p> Signup and view all the answers

What is the primary reason for regulating gene expression?

<p>To make sure different cells express only the correct needed genes. (B)</p> Signup and view all the answers

Which histone modification is typically associated with gene silencing?

<p>Histone deacetylation. (C)</p> Signup and view all the answers

During which phase can the regulation of gene expression occur?

<p>At epigenetic/chromatin remodelling, transcriptional, post-transcriptional, and translational levels. (A)</p> Signup and view all the answers

What is the role of the N-terminal tail in histone proteins?

<p>To provide sites for covalent modifications. (D)</p> Signup and view all the answers

Which of the following is NOT a typical function of corepressors?

<p>Recruiting RNA Pol II. (A)</p> Signup and view all the answers

Which example is considered a short-term regulation of gene expression?

<p>Changes in gene expression in response to a growth factor. (C)</p> Signup and view all the answers

What is the role of transcription factors in gene expression?

<p>To bind to regulatory DNA sequences and control gene transcription. (A)</p> Signup and view all the answers

What is the effect of histone acetylation in the context of gene expression?

<p>It loosens chromatin, which promotes gene transcription. (D)</p> Signup and view all the answers

What is the purpose of tissue-specific gene regulation?

<p>To allow each cell type to produce only the proteins needed for its specific function. (D)</p> Signup and view all the answers

How does the information in DNA become a protein?

<p>DNA is first transcribed into mRNA, which is then translated into protein. (B)</p> Signup and view all the answers

What happens after a protein is made?

<p>Protein activity and function give rise to the observable traits of a cell or organism (B)</p> Signup and view all the answers

What is the primary function of basic transcription factors?

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

Specific transcription factors are best described by which of the following traits?

<p>They exhibit tissue-specificity and regulate gene transcription. (D)</p> Signup and view all the answers

Where is the core promoter located relative to the gene it regulates?

<p>Upstream of the gene, at a fixed position close to the start site. (B)</p> Signup and view all the answers

Which of the following best describes enhancer and silencer elements?

<p>They contain motifs for specific transcription factor binding and regulate core promoter activity from a distance. (C)</p> Signup and view all the answers

What is the main function of cohesins and condensins in gene regulation?

<p>Forming chromatin loops to bring enhancer/silencer sequences near the promoter. (D)</p> Signup and view all the answers

Which of these is NOT a characteristic of a core promoter?

<p>Binding site for specific transcription factors. (C)</p> Signup and view all the answers

How do enhancers and silencers influence gene transcription?

<p>By recruiting specific transcription factors, and through chromatin looping, they come within proximity of the core promoter to modulate its activity. (C)</p> Signup and view all the answers

What is the role of co-activators?

<p>They increase gene transcription by associating with the promoter after being recruited by transcription activators. (D)</p> Signup and view all the answers

Given the provided information, which statement about the location of enhancer/silencer elements is most accurate?

<p>They can be located upstream or downstream and at a variable distance from the gene promoter (100bp to Mbp). (A)</p> Signup and view all the answers

What is the transcription start site?

<p>The region of the core promoter where RNA synthesis begins, and it's denoted as +1. (B)</p> Signup and view all the answers

What is the primary role of transcription factors in the process of transcription?

<p>To guide RNA polymerase to the core promoter and regulate its activity. (A)</p> Signup and view all the answers

Which event signals the release of RNA Polymerase II from the promoter and the start of transcription elongation?

<p>The phosphorylation of RNA Polymerase II at RBP1. (A)</p> Signup and view all the answers

Which of the following best describes the function of co-activators in gene transcription?

<p>They increase gene transcription by interacting with transcription factors. (A)</p> Signup and view all the answers

What is the function of the DNA-binding domain found in all transcription factors?

<p>To recognize specific short DNA sequences near the target gene. (D)</p> Signup and view all the answers

What determines the specificity of a transcription factor for a particular DNA sequence?

<p>The amino acid sequence of its DNA-binding domain. (D)</p> Signup and view all the answers

How do transcription factors that act as repressors inhibit gene transcription?

<p>By recruiting co-repressors to the target gene. (B)</p> Signup and view all the answers

A transcription factor binds to a DNA sequence with the motif 'TATAAAA'. Which similar sequence is it also likely to bind to?

<p>TATATAT (C)</p> Signup and view all the answers

What is the termination signal for transcription in the newly formed mRNA?

<p>An AAUAAA hexamer. (A)</p> Signup and view all the answers

What is the role of the trans-activation/trans-repression domain found in transcription factors?

<p>To bind with co-activators or co-repressors. (B)</p> Signup and view all the answers

What is the effect of ligand binding to a transcription factor, when a ligand-binding domain is present?

<p>It is required for transcription factor activation in some cases. (B)</p> Signup and view all the answers

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

<p>Unraveling of chromatin and increased accessibility. (A)</p> Signup and view all the answers

Which protein domain is typically found in transcription factors and chromatin remodeling proteins that recognizes acetylated histones?

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

How do histone deacetylases (HDACs) contribute to gene regulation?

<p>By removing acetyl groups from histones, leading to chromatin condensation and gene repression. (A)</p> Signup and view all the answers

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

<p>Adding acetyl groups to histones, promoting gene activation. (B)</p> Signup and view all the answers

What is a consequence of recruiting histone deacetylases to a gene promoter region?

<p>Repression of gene activity due to chromatin condensation. (D)</p> Signup and view all the answers

Which of the following is a mechanism used by transcription factors to activate gene expression?

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

How does the position of acetyl groups on histones influence gene expression?

<p>The exact position of acetyl groups determines whether the gene is transcribed or repressed. (A)</p> Signup and view all the answers

How is tissue-specific gene regulation achieved given that all cells contain the same DNA?

<p>Different genes are turned 'on' and 'off' in different tissues and cell types. (B)</p> Signup and view all the answers

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

<p>To regulate gene expression specific to certain tissues and cell types (A)</p> Signup and view all the answers

Which of the following best describes the activity of enhancers?

<p>Their activity can be different in different tissues and cell types. (A)</p> Signup and view all the answers

What is the role of histone modifications, such as acetylation, in the context of enhancer activity?

<p>Histone modifications can either activate or inactivate enhancers in different tissues and cells. (A)</p> Signup and view all the answers

In the context of lung fibroblasts and hepatocytes, what is the key difference in histone modification and enhancer activity?

<p>Lung fibroblasts exhibit low histone acetylation and inactive enhancers, while hepatocytes show high histone acetylation and active enhancers. (C)</p> Signup and view all the answers

What role does the silencer play in the expression of gene X in the example?

<p>Silencers repress the expression of gene X in certain tissues. (D)</p> Signup and view all the answers

Considering the presented information on tissue-specific gene regulation, how would the activity of an enhancer differ between the two tissues?

<p>The enhancer would be active in one tissue and inactive in another. (A)</p> Signup and view all the answers

What is a possible consequence of having different sets of transcription factors in different types of lung epithelial cells?

<p>It is critical in differentiating specific types of cells and functions of lung epithelium. (D)</p> Signup and view all the answers

In the cases of the fibroblasts and the hepatocytes, how does condensed/open chromatin influence the enhancer activity?

<p>Condensed chromatin correlates with inactive enhancers, and open chromatin correlates with active enhancers. (D)</p> Signup and view all the answers

Flashcards

Gene Transcription

The process by which genetic information encoded in DNA is transcribed into RNA, which is then translated into proteins.

Gene Regulation

The process by which cells control which genes are expressed and at what levels.

Epigenetic Regulation

Changes in gene expression that are not due to alterations in the DNA sequence but are instead influenced by environmental factors or cellular signals. These changes can be inherited or reversible.

Transcription Factors

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

Signup and view all the flashcards

Regulatory DNA Sequences

Short sequences of DNA that act as binding sites for transcription factors, influencing the rate of gene transcription.

Signup and view all the flashcards

Chromatin Remodeling

The modification of DNA packaging, affecting how accessible genes are to transcription machinery and thus their expression.

Signup and view all the flashcards

Histone Acetylation

The addition of acetyl groups to histone proteins, loosening the DNA packaging and making genes more accessible to transcription factors.

Signup and view all the flashcards

Tissue-Specific Gene Expression

The process by which cells acquire and maintain their specialized functions by selectively expressing genes appropriate for their specific tissue or organ.

Signup and view all the flashcards

Core promoter

A non-coding DNA sequence located immediately upstream of a gene, where RNA polymerase II binds to initiate transcription.

Signup and view all the flashcards

Transcription factors (TFs)

Proteins that bind to specific DNA sequences and regulate the transcription of genes, either activating or inhibiting it.

Signup and view all the flashcards

Pre-initiation complex

A complex formed by RNA polymerase II and transcription factors, which is necessary for the initiation of transcription.

Signup and view all the flashcards

Transcription bubble

The process of unwinding DNA into two separate strands, creating a bubble-like structure, allowing RNA polymerase to access the template strand for transcription.

Signup and view all the flashcards

Co-activators/co-repressors

Proteins that interact with transcription factors to either activate (co-activators) or inhibit (co-repressors) gene transcription.

Signup and view all the flashcards

DNA-binding domain

A region within a transcription factor protein that is responsible for binding to DNA sequences and regulating gene transcription.

Signup and view all the flashcards

Trans-activation/trans-repression domain

A region within a transcription factor protein that allows interaction with co-activators or co-repressors to either activate or repress gene transcription.

Signup and view all the flashcards

Transcription factor binding motifs

Short DNA sequences (6-12 base pairs) that are recognized and bound by specific transcription factors.

Signup and view all the flashcards

Basic and specific transcription factors

Transcription factors are classified into two groups: basic transcription factors and specific transcription factors. Basic transcription factors are essential for the general process of transcription initiation, while specific transcription factors regulate the expression of specific genes in response to cellular cues.

Signup and view all the flashcards

Ligand-binding domain

A transcription factor that is only active when it binds to a specific ligand, such as a hormone.

Signup and view all the flashcards

Basic Transcription Factors

Transcription factors found in all cells and tissues, responsible for recruiting RNA polymerase II to the gene promoter. They act as transcriptional activators, promoting gene expression.

Signup and view all the flashcards

Specific Transcription Factors

Over 2000 transcription factors that exhibit tissue-specific expression, regulating gene transcription either as activators or repressors.

Signup and view all the flashcards

Enhancers and Silencers

Regions of non-coding DNA located near genes that control the rate of transcription. They contain binding motifs for specific transcription factors.

Signup and view all the flashcards

Basal Transcription Factors

Proteins that bind to the core promoter and recruit RNA polymerase II to the gene. They are essential for basal level transcription.

Signup and view all the flashcards

Transcriptional Activators

Transcription factors that bind to enhancers and increase gene transcription.

Signup and view all the flashcards

Transcriptional Repressors

Transcription factors that bind to silencers and decrease gene transcription.

Signup and view all the flashcards

Enhancer/Silencer Regulation

The process by which enhancer and silencer elements interact with the core promoter to regulate gene transcription from a distance. This involves chromatin looping and the recruitment of co-activators or co-repressors.

Signup and view all the flashcards

Co-activators and Co-repressors

Proteins that bridge the gap between transcription factors bound to enhancers/silencers and the core promoter, modulating transcription.

Signup and view all the flashcards

Cohesins and Condensins

Non-histone proteins that mediate the looping of chromatin, bringing enhancers and silencers into close proximity to the core promoter.

Signup and view all the flashcards

Tissue-Specific Transcription Factors

Factors that activate gene transcription in specific tissues or cell types.

Signup and view all the flashcards

Tissue-Specific Enhancer/Silencer Activity

Regions of DNA that can boost or silence gene expression depending on the cell type. They act like switches, turning genes on or off in specific tissues.

Signup and view all the flashcards

Condensed Chromatin

The state of chromatin where DNA is tightly wound around histone proteins, making genes less accessible for transcription.

Signup and view all the flashcards

Open Chromatin

The state of chromatin where DNA is loosely wound around histone proteins, making genes more accessible for transcription.

Signup and view all the flashcards

Cell Differentiation

The process by which cells acquire and maintain their specialized functions by selectively expressing genes appropriate for their specific tissue or organ.

Signup and view all the flashcards

What is histone acetylation?

Acetyl groups are added to histone proteins, loosening the DNA packaging, which allows transcription factors to access genes more easily and activate gene expression.

Signup and view all the flashcards

What is the role of bromodomains in gene regulation?

Proteins that contain bromodomains bind to acetylated histones, leading to the recruitment of chromatin remodelling proteins and transcription factors, ultimately activating gene expression.

Signup and view all the flashcards

What is the role of histone deacetylases in gene regulation?

Histone deacetylases (HDACs) remove acetyl groups from histones, tightening the DNA packaging and making genes less accessible to transcription factors, leading to gene repression.

Signup and view all the flashcards

How do transcription activators affect histone acetylation?

Transcription factors can promote gene expression by recruiting histone acetyltransferases (HATs), leading to the loosening of DNA packaging and making genes accessible for transcription.

Signup and view all the flashcards

How do transcription repressors affect histone acetylation?

Transcription factors can repress gene expression by recruiting histone deacetylases (HDACs), leading to tightening of DNA packaging, making genes inaccessible for transcription.

Signup and view all the flashcards

Why do different cells have different gene expression patterns?

Each cell in our body has the same DNA, but different cells express different sets of genes to carry out their specific functions.

Signup and view all the flashcards

What are chromatin remodelling complexes and what do they do?

Chromatin remodelling complexes are protein groups that alter the structure of chromatin, making genes more or less accessible for transcription.

Signup and view all the flashcards

How is tissue-specific gene expression controlled?

Different tissues and cell types have unique combinations of transcription factors that activate or repress specific genes, leading to specialized functions.

Signup and view all the flashcards

Chromatin opening

The process of opening chromatin, which allows RNA polymerase II (RNA Pol II) to bind and initiate transcription.

Signup and view all the flashcards

Euchromatin

A type of chromatin that is loosely packed, allowing for active transcription.

Signup and view all the flashcards

Heterochromatin

A type of chromatin that is tightly packed, preventing transcription.

Signup and view all the flashcards

RNA polymerase II (RNA Pol II)

The enzyme responsible for synthesizing RNA from a DNA template.

Signup and view all the flashcards

Silencer elements

Specific DNA sequences that bind to co-repressors, leading to gene silencing.

Signup and view all the flashcards

Co-repressors

Proteins that interact with repressors, causing chromatin condensation and inhibiting transcription.

Signup and view all the flashcards

Nucleosome

The basic unit of chromatin, consisting of DNA wrapped around histone proteins.

Signup and view all the flashcards

ATP-dependent chromatin remodeling enzymes

Enzymes that use ATP to reposition or remove nucleosomes, enabling access to DNA for transcription.

Signup and view all the flashcards

Histone modifications

Chemical modifications to histone tails that can alter their binding properties and regulate gene expression.

Signup and view all the flashcards

Study Notes

Gene Expression & Regulation

  • Gene expression is controlled in time and space. Every cell has the same DNA, but different genes need to be "on" and "off" in different cell types. This regulation is essential for cell diversity.

Lecture Objectives

  • Understanding the fundamental structures and types of transcription factors and their roles in transcriptional regulation.
  • Understanding the pivotal role of regulatory DNA sequences in regulating gene transcription.
  • Grasping the significance of histone acetylation and chromatin remodeling in the regulation of gene transcription.
  • Familiarizing with the core concepts of tissue-specific regulation of gene transcription.

Gene Regulation

  • Gene expression is regulated at various levels, including short-term (e.g., responding to external signals like growth factors or hormones) and long-term (e.g., tissue-specific identity maintained through cell division).
  • Epigenetic modifications (e.g., chromatin remodeling), transcriptional, post-transcriptional, and translational mechanisms all play a role in regulating gene expression.

Gene Expression During Development

  • Gene expression is dynamic across the life cycle. Different genes need to be "on" or "off" at various stages.

Gene Regulation During Transcription

  • DNA is transcribed into mRNA.
  • mRNA is translated into proteins.
  • Protein activity leads to a phenotype.

Transcription Initiation

  • RNA Pol II binds to a non-coding DNA region (core promoter).
  • 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 initiates transcription.

Transcription Elongation

  • RNA Pol II unwinds the DNA ("transcription bubble").
  • RNA Pol II uses one strand as a template to synthesize a complementary RNA sequence.
  • RNA Pol II adds nucleotides to the 3' end of the growing RNA molecule.

Transcription Termination

  • RNA Pol II encounters a termination signal (e.g., AAUAAA hexamer).
  • Transcription stops.
  • RNA Pol II and mRNA are released.
  • A new transcription cycle begins.

Transcription Factors

  • Transcription factors are proteins that bind specific DNA sequences and control gene transcription (activating or inhibiting).
  • Most transcription factors work with other proteins (co-activators/co-repressors) to regulate transcription.
  • Transcription factors can either activate or repress transcription. Activators recruit co-activators, and repressors recruit co-repressors.

Transcription Factor Domains

  • Transcription factors have specific structural domains for interaction with DNA or other proteins.
  • DNA-binding domains recognize specific short DNA sequences (transcription factor binding motifs).
  • Trans-activation/trans-repression domains interact with co-activators or co-repressors.
  • Some factors have ligand-binding domains (e.g., hormone receptors)
  • Some have dimerization domains (to bind to DNA in pairs).

Regulatory DNA Sequences

  • Core promoter: Immediately upstream of the gene
  • Contains the transcription start site (+1)
  • Binding sites for basal transcription factors
  • Needed for gene transcription
  • Enhancers/Silencers: Can be upstream or downstream of a gene, and affect the activity of the core promoter (increasing or decreasing).
  • Enhancers/silencers can be far from the target gene, but transcription factors bring them close through chromatin looping.

Co-activators and Co-repressors

  • Co-activators increase gene transcription by opening chromatin.
  • Co-activators recruit RNA Pol II and basal transcription factors to the promoter.
  • Co-repressors decrease gene transcription by inducing chromatin condensation.
  • Co-repressors prevent RNA Pol II recruitment to the promoter.

Histone Modifications and Chromatin Remodeling

  • Nucleosomes (DNA wrapped around histone proteins) can block access for transcription factors.
  • Chromatin remodeling enzymes (e.g. ATP-dependent chromatin remodeling enzymes) reposition or remove nucleosomes.
  • Histone modifications (e.g., acetylation) affect chromatin structure.

Histone Acetylation

  • Histone acetyltransferases (HATs) add acetyl groups to lysines on histones.
  • Histone deacetylases (HDACs) remove acetyl groups.
  • Bromodomains are special protein modules found in transcription factors, as well as chromatin remodeling complexes, which recognise acetylated lysine residues on histones.

Tissue-Specific Regulation

  • Every cell has the same genes, but different genes are expressed in different tissues and cells.
  • Tissue-specific transcription factors regulate gene transcription.
  • Enhancers/silencers have tissue-specific activity, determined by histone modifications.

Studying That Suits You

Use AI to generate personalized quizzes and flashcards to suit your learning preferences.

Quiz Team

Related Documents

More Like This

Use Quizgecko on...
Browser
Browser