Sect 7 Quiz Easy

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Questions and Answers

What is one of the learning objectives of the module?

Explain the structure of prokaryotic cells.

Describe the process of DNA replication in eukaryotes.

Define the role of promoters in gene expression. (correct)

Classify various types of cellular organelles.

Which of the following is NOT a type of transcription factor discussed in the module?

Mediator complex

Enhancers

Cis-acting factors

Transcriptional activators in bacterial cells (correct)

What is epigenetic regulation primarily associated with?

Alterations in RNA splicing.

Changes in chromosome condensation. (correct)

Increased mutation rates in DNA.

Physical changes in gene sequences.

Which term refers to the silencing of genes by mechanisms like DNA methylation?

Gene silencing Signup and view all the answers

What characterizes adaptive radiation as discussed in the context?

Multiple species rapidly evolve from a common ancestor. Signup and view all the answers

What structure inhibits the binding of RNA polymerases required for transcription initiation?

Condensed chromatin Signup and view all the answers

What is the primary role of enhancers in gene expression?

To increase the efficiency of transcriptional activation. Signup and view all the answers

What is the primary role of activator proteins in gene expression?

Promote chromatin decondensation Signup and view all the answers

Which RNA polymerase is very sensitive to a-amanitin?

RNA Pol II Signup and view all the answers

Which RNA polymerase is primarily responsible for transcribing mRNA in eukaryotic cells?

RNA polymerase II Signup and view all the answers

Which RNA polymerase is responsible for synthesizing mRNA?

RNA Pol II Signup and view all the answers

What does the term 'cis-acting elements' refer to?

DNA sequences that influence the transcription of neighboring genes. Signup and view all the answers

What remains phosphorylated during active transcription in RNA Pol II?

C-terminal domain (CTD) Signup and view all the answers

Which type of RNA does RNA Pol III primarily synthesize?

tRNAs Signup and view all the answers

What is a key structural difference between yeast RNA polymerases and E.coli RNA polymerase?

Presence of a C-terminal domain Signup and view all the answers

What effect do repressor proteins have on chromatin state?

Condense chromatin Signup and view all the answers

What role do transcription factors play in gene expression?

They stimulate or repress transcription. Signup and view all the answers

Where are enhancer elements typically located in relation to a promoter?

Up to 50,000 bp upstream or downstream from a promoter. Signup and view all the answers

What characterizes trans-acting elements?

They can regulate genes regardless of their location on DNA. Signup and view all the answers

What method can be used to detect protein-DNA interactions?

Footprinting and gel-shift assays. Signup and view all the answers

In yeast, what are upstream activating sequences (UASs) analogous to in higher eukaryotes?

Promoter-proximal elements. Signup and view all the answers

How do transcription factors typically bind to DNA?

By binding to promoter-proximal elements and enhancers. Signup and view all the answers

What is the approximate number of transcription factors that the human genome codes for?

<ol start="2000"> <li></li> </ol> Signup and view all the answers

What is the primary function of enhancers in eukaryotic cells?

To stimulate transcription of associated genes. Signup and view all the answers

What role does the mediator play in transcription?

It facilitates the connection between transcription factors and RNA polymerase II. Signup and view all the answers

How does flexibly structured DNA influence transcription?

It allows enhancers to interact with distant promoters. Signup and view all the answers

What is necessary for the expression of a specific gene in a cell?

Specific activators required for that gene's transcription. Signup and view all the answers

What generally occurs during the elongation phase of transcription by RNA Pol II?

Transcription continues beyond 200 bases in a highly processive manner. Signup and view all the answers

Why are heterochromatin regions significant in transcription?

They are condensed regions making DNA less accessible to transcription factors. Signup and view all the answers

What can modulate the activity of transcription factors?

Levels and activities of activators and repressors. Signup and view all the answers

What occurs after RNA Pol II transcribes the polyadenylation site?

Elongation continues for a variable distance beyond the polyadenylation site. Signup and view all the answers

What are the three levels at which transcription activation and repression occur?

Changes in chromatin structure, modulation of activators and repressors, and direct influence on transcription-initiation complexes. Signup and view all the answers

What occurs in a gel-shift assay when a DNA fragment is complexed to protein?

Its band location shifts. Signup and view all the answers

What are the two distinct functional domains of transcriptional activators?

DNA-binding domain and activation domain. Signup and view all the answers

What is the main function of repressors in gene transcription?

They inhibit gene transcription. Signup and view all the answers

How do modular domains in transcription factors interact?

They can interact when DNA-binding domains are separated. Signup and view all the answers

Which situation can determine the outcome of gene transcription?

The competition between activators and repressors. Signup and view all the answers

How can the roles of modular domains in transcription factors be demonstrated?

Using deletion constructs. Signup and view all the answers

What might some repressors do to the binding of activators?

They allow activators to bind while inhibiting them. Signup and view all the answers

What common feature do both activators and repressors share?

They have modular structures with functional domains. Signup and view all the answers

What is the role of the hydrophobic leucine stripe in leucine-zipper proteins?

It allows for dimerization. Signup and view all the answers

Basic helix-loop-helix (bHLH) proteins are characterized by which structural feature?

A nonhelical loop separating two a helices. Signup and view all the answers

Which type of interaction can activate the transcription factor CREB?

Conformational change induced by a ligand. Signup and view all the answers

What is a potential function of the acidic activation domains in transcription factors?

Interacting with other proteins for transcriptional activation. Signup and view all the answers

How do the transcription-control regions of most genes behave regarding transcription factors?

Contain binding sites for multiple transcription factors. Signup and view all the answers

What effect does the binding of an antagonistic ligand, such as tamoxifen, have on transcription factors?

It stabilizes a non-activating structure. Signup and view all the answers

Which of the following best describes the coiled-coil structure of dimerized proteins?

It is stabilized by hydrophobic interactions. Signup and view all the answers

Which of the following best describes the general purpose of transcription factors?

To regulate gene expression. Signup and view all the answers

Study Notes

Learning Objectives

Students will be able to compare and contrast gene expression in prokaryotic and eukaryotic organisms.
Students will be able to compare eukaryotic RNA polymerases and the genes those polymerases transcribe.
Students will be able to describe RNA pol II promoters and general transcription factors.
Students will be able to define the role of cis-acting elements, promoter-proximal elements, and enhancers in tissue-specific transcription.
Students will be able to describe different categories of transcription factors that act at cis-acting elements.
Students will be able to describe epigenetic regulation of genes by DNA methylation and IncRNA inactivation of the X chromosome.
Students will be able to define activation, repression, cis-element, trans factors, enhancesome, hyper- and hypo-acetylation, condensation and decondensation of chromosomes, mediator complex, and gene silencing. Students will also define epigenetics, IncRNA, DNase 1 footprinting, EMSA, CpG islands, and the CTD domain of RNA pol II.
Students will be able to compare transcription initiation in RNA Pol I, III, and II.

Text

Verse: God gives each organism a body suited to its own kind. (Corinthians 15:38-39).
Biological Basis of Speciation: Speciation is driven by genome changes that allow natural selection for species members better adapted to the environment.
Problems in Current Understanding: Current models struggle with the rate at which species adapt (adaptation happening within a few decades is difficult to explain). There are also significant similarities in genomes of divergent species that are not accounted for.
Adaptive Radiation Example: Darwin's Finches: Evolution suggests that natural disasters can be a trigger for adaptive radiation (the diversification of a single species into multiple species). Darwin's Finches, known for their beak forms and functions, are a good example of this, with beaks and bodies changing to allow them to eat different foods (nuts, fruits, insects).
Epigenetic Changes: Recent research suggests epigenetic changes are a more accurate explanation for rapid environmental changes like the ones observed in Darwin's Finches, rather than subtle base-pair mutations in their genome.
Epigenetic Changes in Darwin's Finches: Studies have confirmed that populations of Darwin's finches in rural and urban areas have substantial epigenetic differences linked to environmental changes from urbanization, even though there's little genetic variation.

Introduction (Topic 7)

Gene Expression: The entire process where the information encoded in a gene is translated into a protein.
Components of Gene Expression: Transcription initiation, RNA polymerization/elongation, and transcription termination.
Constitutive (Housekeeping) Genes: Genes that are constantly expressed in growing cells during all stages.
Inducible Genes: Genes whose expression is regulated by the cell's needs.
Differential Gene Expression: Gene expression that varies between different cells or at different stages of development

General Overview of Eukaryotic Gene Control and RNA Polymerases

Optimization: Gene control in bacteria and single-celled eukaryotes is mostly about optimizing growth and division in response to the environment.
Multicellular Organisms: In multicellular organisms, gene control is critical for precise development and differentiation; it often isn't reversible.
Transcriptional Control: In eukaryotes, the primary way to regulate gene expression is by regulating transcription. This involves specific regulatory DNA sequences (cis-control elements) interacting with regulatory proteins (trans factors).
Chromatin State: Inactive genes are in condensed chromatin, which prevents the binding of RNA polymerases and transcription factors that are needed for initiation.
Activators: Proteins which bind to control elements near transcription start sites or enhancer elements.
Repressors: Proteins that bind to control elements, causing chromatin condensation and inhibition of polymerase binding.

RNA Polymerases

Three RNA polymerases catalyze different RNA production (Pol I for rRNA, Pol II for mRNA, tRNA, and other small stable RNAs).
RNA polymerase differs in their sensitivity to a-amanitin.
Each Pol has different subunit structures.

RNA Pol II Promoters and General Transcription Factors

Protein-coding genes: Transcribed by RNA polymerase II.
Regulatory Sequences:
- Promoters : Sites of transcription initiation, where RNA Pol II binds.
- Promoter-proximal elements: Located close to the start site, help regulate gene expression.
- Enhancers: Located further away from the start site, usually stimulating transcription by RNA Pol II binding.
General Transcription Factors: Proteins required for transcription initiation by RNA Pol II.
- Assembly of a complex that positions RNA Pol II at initiation sites and allows it begin transcription.
- The complex assembly is stepwise.

Promoter Structure

TATA box: Common in rapidly transcribed genes, typically located 25-30 base pairs upstream from the start site.
Innitiator (Inr): Less common than TATA boxes, most have cytosine(-1) and adenine(+1) at the start site.

General Transcription Factors (GTFs) on Pol II Promoters

TFIID: Binds to TATA box; composed of TBP and TAFs which assists RNA Pol II initiation.
TFIIA, TFIIB, and TFIIF: Assist in transcription via interaction with DNA and Pol II.
TFIIE, and TFIIH: Complete the preinitiation complex, facilitating DNA unwinding, and help with RNA polymerase II phosphorylation.

Regulatory Sequences in Protein-Coding Genes

Promoter-proximal elements: Control regions near the start site of transcription.
Enhancers (or UASs) located upstream and/or downstream : Control regions far from the start site; typically stimulate transcription.
Methods to identify regulatory sequence (e.g., 5' deletion)
Yeast:
- The transcriptional activation sequences in yeast function similarly to promotor -proximal and enhancer elements.

Transcriptional Activators/Repressors

Modular Structure: Transcription factors often have DNA-binding domains and activation or repression domains, which are separated by linker regions.
DNA-binding domains: They bind specific DNA sequences.
Activation/Repression domains: Interact with other proteins, such as co-activator or co-repressors, to modulate transcription rates.
Protein-DNA Interactions: Techniques like DNase I footprinting show protein interaction with DNA sequences.
Gel-shift assay: Used to detect protein bound to DNA.

Epigenetic Control of Transcription

Epigenetics: Changes in gene expression that are not due to changes in the DNA sequence, but due to DNA methylation and post-translational modification of histones.
Histone Modification (e.g. acetylation/deacetylation), and DNA methylation are maintained after cell replication.
DNA methylation: Modifying the CpG DNA motifs and associated proteins in mammalian genomes.
Methyl markers (e.g., H3K9 methylation) on nucleosomes are frequently associated with heterochromatin-associated proteins and lead to repression of gene expression.

In vivo Polymerase II Initiation

Enhancers: Regions with multiple clustered binding sites for transcription factors; binding of such factors results in a nucleoprotein complex (called "enhancerome")
Mediator complex: Large multi-protein complex which acts as a bridge between transcriptional activators and RNA polymerase II and stimulates transcription.
Cell type specificity: In vivo initiation requires specific sets of transcriptional activators for a given cell type.

Other Transcription Systems

Other RNA polymerases have analogous methods of initiation.
Their transcription factors differ in their structure and function when compared to other RNA polymerases.

Regulation of Transcription Factor Activity

Ligand Binding: Many transcription factors respond to ligands, like hormones; this conformational change can alter how these proteins interact with other factors.
Covalent Modification: Factors can be regulated by covalent modification such as phosphorylation to alter their activity.
Nuclear Receptors: Hormone-activated transcription factors which share a common domain architecture that regulate transcription in response to hormone action.
Peptide Hormons: Cannot diffuse across cellular membranes and must activate cellular receptor proteins and associated pathways to affect transcription.

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Description

This quiz covers key concepts in molecular biology regarding gene expression in prokaryotic and eukaryotic organisms. Students will compare RNA polymerases, transcription factors, and the role of epigenetics in gene regulation. It's essential for understanding the mechanisms of transcription and the influence of cis-acting elements and enhancers.