Gene Expression and Transcription Regulation
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Questions and Answers

What is a method by which transcription factors can undergo conformational changes?

  • Inhibition by metal ions
  • Decreased pH levels
  • Covalent modification, such as phosphorylation (correct)
  • Temperature fluctuations

Which of the following correctly describes the role of lipid-soluble hormones?

  • They function solely as repressive agents
  • They can only alter cell functions in the same cell
  • They diffuse through plasma and nuclear membranes to affect distant cells (correct)
  • They regenerate nuclear receptors

What type of receptor structure is shared by all nuclear receptors?

  • A unique N-terminal domain that functions as activation domains (correct)
  • An identical transmembrane domain
  • A conserved binding region for RNA polymerase
  • A common C-terminal region for DNA replication

How do receptors generally bind to their response elements on DNA?

<p>As homodimers or heterodimers (B)</p> Signup and view all the answers

Which specific element do estrogen receptors bind to?

<p>Estrogen receptor response element (ERE) (D)</p> Signup and view all the answers

In the context of RXR-TR heterodimeric nuclear receptors, what determines their activity?

<p>The binding of hormones to the ligand-binding site (D)</p> Signup and view all the answers

What kind of response elements do thyroid hormone receptors bind to?

<p>Direct repeats of ERE separated by 4 bp (A)</p> Signup and view all the answers

What determines whether the RXR-TR complex acts as a repressor or an activator of transcription?

<p>Whether or not the hormone occupies the ligand-binding site (B)</p> Signup and view all the answers

What are the primary functions of cis-acting elements in gene expression?

<p>They act as regulatory sites for transcription factors. (A)</p> Signup and view all the answers

Which RNA polymerase is primarily responsible for transcribing protein-coding genes in eukaryotes?

<p>RNA polymerase II (B)</p> Signup and view all the answers

What role does DNA methylation play in gene regulation?

<p>It silences gene expression by condensing chromatin structure. (C)</p> Signup and view all the answers

How do transcription factors interact with cis-acting elements?

<p>They bind to these elements to regulate transcription. (B)</p> Signup and view all the answers

What is a major characteristic of adaptive radiation as explained by Darwin's finches?

<p>It involves rapid diversification due to environmental challenges. (A)</p> Signup and view all the answers

Which of the following best describes 'epigenetics'?

<p>It encompasses non-sequence changes that affect gene activity. (C)</p> Signup and view all the answers

What defines the role of enhancers in tissue-specific transcription?

<p>They act independently of the promoter regions. (C)</p> Signup and view all the answers

What is the significance of the CTD domain of RNA polymerase II?

<p>It plays a role in RNA processing events. (C)</p> Signup and view all the answers

What were some of the foods that Darwin's finches adapted to eat due to changes in their beaks and bodies?

<p>Nuts, fruits, and insects (C)</p> Signup and view all the answers

What is considered a better explanation for how Darwin's finches respond to environmental changes?

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

In studies of Darwin's finches, what was found to have substantial differences between urban and rural populations?

<p>Epigenetic differences (A)</p> Signup and view all the answers

What does the term 'epimutations' refer to in the context of DNA methylation patterns?

<p>Heritable changes in gene expression (D)</p> Signup and view all the answers

Which of the following is NOT a factor that contributes to epigenetic changes in Darwin's finches?

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

What is suggested about the relationship between phylogenetic distance and epimutations?

<p>Epimutations are more abundant with increasing phylogenetic distance (A)</p> Signup and view all the answers

What does the concept of an epigenome encompass?

<p>The chemical modifications regulating gene expression (C)</p> Signup and view all the answers

What could potentially explain the high degree of genomic sequence similarities between species, according to recent studies?

<p>The role of the epigenome in defining species characteristics (C)</p> Signup and view all the answers

What is the primary function of the TATA box in gene transcription?

<p>To initiate transcription by binding RNA polymerase II (C)</p> Signup and view all the answers

Which of the following best describes cis-acting elements in eukaryotic transcription?

<p>Elements that act only on genes located on the same DNA molecule (A)</p> Signup and view all the answers

What role does the DSIF factor play in transcription?

<p>It promotes RNA polymerase II to act as a processive enzyme (A)</p> Signup and view all the answers

How far can eukaryotic cis-acting elements be located from their promoter?

<p>Often several kilobases away (A)</p> Signup and view all the answers

What is true about the RNA polymerase II transcribing complex?

<p>It possesses a clamp domain that aids in transcription (C)</p> Signup and view all the answers

What is the major role of promoter-proximal elements?

<p>To regulate transcription of nearby genes (A)</p> Signup and view all the answers

What is a significant characteristic of enhancers in eukaryotic transcription?

<p>They can stimulate transcription from distant sites (D)</p> Signup and view all the answers

Which RNA polymerase is responsible for transcribing protein-coding genes?

<p>RNA polymerase II (D)</p> Signup and view all the answers

What is the primary structure that allows DNA-binding domains to interact with specific sequences?

<p>Noncovalent interactions between amino acid side chains (A)</p> Signup and view all the answers

Which structural motif is found in the DNA-binding domain of the bacteriophage 434 repressor?

<p>Helix-turn-helix (C)</p> Signup and view all the answers

What is the characteristic structure of zinc-finger proteins?

<p>A polypeptide chain folded around a central Zn2+ ion (B)</p> Signup and view all the answers

What type of residues bind the Zn2+ ion in the most common C2H2 zinc-finger motif?

<p>Two Cysteine and two Histidine residues (B)</p> Signup and view all the answers

How do C2H2 zinc-finger proteins typically interact with DNA?

<p>As a monomer that wraps around the DNA double helix (A)</p> Signup and view all the answers

Which of the following is NOT a type of DNA-binding domain classified in eukaryotic transcription factors?

<p>Beta-sheet proteins (D)</p> Signup and view all the answers

In the context of homeodomain proteins, what is the significance of the homeobox motif?

<p>It contains conserved sequences that are key for function (C)</p> Signup and view all the answers

How is the C4 type zinc-finger different from the C2H2 type zinc-finger?

<p>It includes four Cys that bind the Zn2+ ion (A)</p> Signup and view all the answers

What role does TSIX lncRNA play in the regulation of X-chromosome inactivation?

<p>It represses the effect of XIST lncRNA on the active X chromosome. (C)</p> Signup and view all the answers

What is the primary function of XIST lncRNA in female mammals?

<p>To initiate X-chromosome inactivation on one X chromosome. (D)</p> Signup and view all the answers

How does XIST lncRNA maintain X inactivation throughout embryogenesis and adult life?

<p>By maintaining association with repression complexes and DNA methylation. (D)</p> Signup and view all the answers

What occurs during very early embryogenesis concerning TSIX lncRNA?

<p>Both X chromosomes express TSIX lncRNA, preventing XIST expression. (A)</p> Signup and view all the answers

Which statement accurately describes the action of XIST lncRNA?

<p>It acts in cis by remaining with the inactive X chromosome. (B)</p> Signup and view all the answers

What is the mechanism through which lncRNAs like HOTAIR operate?

<p>By interacting with repression complexes to repress genes in trans. (D)</p> Signup and view all the answers

What is the main role of DNA methylation in relation to X inactivation?

<p>It serves to maintain the inactivated state of the X chromosome. (C)</p> Signup and view all the answers

Which transcription system involves processes analogous to that of Pol II?

<p>Both Pol I and Pol III. (D)</p> Signup and view all the answers

Flashcards

Transcription Factors

Proteins that bind to DNA to regulate gene expression.

Active/Inactive Conformation

Transcription factors exist in different shapes that determine their ability to work for or against gene expression.

Ligand Binding

Turning transcription factors on to work in gene expression by interacting with a molecule (ligand).

Covalent Modification

The effect transcription factors in gene expression, via chemical additions to the protein molecule, e.g., phosphorylation.

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Nuclear Receptors

Transcription factors that respond to lipid-soluble hormones.

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Hormone-Binding Domain

The part of a nuclear receptor that binds to the hormone.

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Response elements

Specific DNA sequences that nuclear receptors bind to to influence gene expression.

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Hormonal Control of Nuclear Receptors

Hormones control whether nuclear receptors activate or repress gene expression based on different configurations.

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Gene Expression (Prokaryotes vs. Eukaryotes)

Gene expression differs in prokaryotes and eukaryotes. Prokaryotes have simpler regulation, while eukaryotes have more complex processes, including compartmentalization (nucleus).

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Eukaryotic RNA Polymerases

Eukaryotic cells have different RNA polymerases (Pol I, Pol II, Pol III) that transcribe different types of genes.

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RNA Pol II Promoters

RNA polymerase II promoters have specific sequences that recruit general transcription factors to start transcription.

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Cis-acting elements

DNA sequences that regulate gene expression from within the same gene's vicinity

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Transcription Factors

Proteins that bind to DNA and either activate or repress gene transcription.

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Epigenetic Regulation

Changes in gene expression that are not due to changes in the DNA sequence.

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Adaptive Radiation

Diversification of a species into many new forms, often following a major environmental change.

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Speciation (Molecular Basis)

Genome changes (mutations) drive the natural selection of adapted species, but the accumulation of mutations takes a long time and the similarity of genomes of divergent species is a problem.

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Darwin's Finches

A group of finch species found on the Galapagos Islands known for their diverse beak shapes and sizes, enabling them to eat different foods.

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Epigenetics

Changes in gene expression that do not involve alterations to the underlying DNA sequence.

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Epimutations

Epigenetic alterations in DNA methylation patterns.

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DNA Methylation

A common epigenetic modification where a methyl group is added to DNA, affecting gene expression.

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Genetic Variation

Differences in the DNA sequences between individuals or populations.

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Phylogenetics

The study of evolutionary relationships among species.

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Epigenome

The complete set of epigenetic modifications to DNA and histone proteins, regulating gene expression.

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Environmental Factors

External factors like urbanization and changes in food availability that may lead to epigenetic changes.

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RNA polymerase II

A type of RNA polymerase responsible for transcribing protein-coding genes in eukaryotes.

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Promoters in Eukaryotes

DNA sequences that initiate transcription, specifying where RNA polymerase binds and starts transcribing.

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TATA box

A common promoter sequence in eukaryotic genes that helps position RNA polymerase II.

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Cis-acting elements

DNA sequences that regulate gene expression on the same DNA molecule.

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Trans-acting proteins

Proteins that bind to regulatory DNA sequences (cis-acting elements) to control gene expression.

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Transcription elongation factor (e.g., DSIF)

A protein that aids in the RNA polymerase's function.

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Transcriptional control regions

Multiple DNA sequences in eukaryotes that control the expression of protein-coding genes.

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Transcriptional start site (+1)

The specific DNA base pair where mRNA synthesis begins.

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DNA-binding domains

Specific protein regions that bind to DNA sequences, regulating gene expression.

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Helix-Turn-Helix motif

A common DNA-binding structural pattern, often found in proteins, utilizing a-helices.

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Homeodomain

A 60-residue DNA-binding motif similar to helix-turn-helix, frequently found in homeotic genes.

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Zinc-finger proteins

Common protein group binding to DNA, characterized by zinc ion binding to polypeptide chains.

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C2H2 zinc finger

A type of zinc-finger motif where each finger has two Cys and two His residues around a Zn2+ ion.

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Bacteriophage 434 repressor

A protein that binds as a dimer to specific DNA regions, regulating gene expression.

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Recognition helix

The alpha-helix in a DNA-binding domain that directly interacts with the DNA base pairs.

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Half-sites

Adjacent sections of DNA where each monomer of DNA-binding proteins binds to.

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lncRNA X-chromosome inactivation

Xist lncRNA inactivates an X chromosome in female mammals by spreading along the chromosome, associating with repression complexes.

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XIST lncRNA action

XIST lncRNA only works on the same chromosome (cis) and interacts with a co-repressor to recruit repression complexes.

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TSIX lncRNA role

TSIX lncRNA represses XIST's effect, preventing X inactivation in early embryos; its production is repressed later during differentiation.

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X-inactivation mechanism

XIST and TSIX act to silence one X chromosome during embryonic development; the decision for inactivation is random, choosing either Xp from the egg or Xm from the sperm.

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lncRNA repression in trans

Some lncRNAs, like HOTAIR, repress genes on different chromosomes (trans), a different mode than XIST.

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XIST function in inactivation

XIST lncRNA attracts repression complexes (including histone deacetylases) to condense DNA of the inactive X chromosome.

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X inactivation maintenance

X inactivation in adult cells is maintained by repression complexes & DNA methylation at CpG islands, ensuring that the same X chromosome remains inactive.

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Transcription by Pol I & Pol III

Transcription initiation using RNA polymerase I (Pol I) and RNA polymerase III (Pol III) is similar to that of RNA polymerase II (Pol II).

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Study Notes

Learning Objectives

  • Students will be able to compare and contrast gene expression in prokaryotes and eukaryotes.
  • Students will be able to compare eukaryotic RNA polymerases and the genes they transcribe.
  • Students will be able to describe RNA polymerase II promoters and general transcription factors.
  • Students will be able to define the roles of cis-acting elements, promoter-proximal elements, and enhancers in tissue-specific transcription.
  • Students will be able to describe different categories of transcription factors.
  • Students will be able to describe epigenetic regulation of genes by DNA methylation and lncRNA inactivation.
  • Students will be able to define activation, repression, cis-elements, trans factors, enhancers, hyper- and hypoacetylation, chromosome condensation and decondensation, mediator complex, gene silencing, epigenetics, lncRNA, DNase I footprinting, EMSA, and CpG islands and the CTD domain of RNA polymerase II.
  • Students will be able to compare transcription initiation in RNA polymerase I, III, and II.

Gene Expression in Prokaryotes and Eukaryotes

  • Prokaryotic and eukaryotic gene expression differ in process optimization
  • Gene regulation in multicellular organisms is often not reversible, unlike prokaryotes used for development and cellular differentiation.

Speciation

  • Speciation is facilitated by genome changes and natural selection
  • It is argued that accumulation of significant mutations over time to develop adaptive differences is needed. Fast adaptations are not easily explained by subtle base pair changes.
  • Adaptive radiation is an example where organisms diversify into new forms due to a sudden environmental change. Darwin's finches demonstrate this (adaptations in beaks and bodies for different food types).

Epigenetics

  • Epigenetics studies heritable changes that are independent of DNA sequence
  • Epigenetic variations in Darwin's finches were found to correspond well with environmental variations, not genetic differences, as opposed to standard Darwinian models.

Gene Expression: An Entire Process

  • The entire process involves decoding the information into a protein.
  • Includes transcription and translation.
  • Constitutive or housekeeping genes are active during all cell cycle stages.
  • Inducible or regulated genes are controlled based on cellular needs.

Overview of Eukaryotic Gene Control and RNA Polymerases

  • Bacterial cells and single-celled eukaryotes optimize gene control for growth and division responses to the environment
  • Gene control in multicellular organisms is needed for differentiation and is generally not reversible as opposed to prokaryotes
  • The transcriptional control is a primary means of regulation in eukaryotes. Cis-control elements (DNA sequences) are associated with genes. Trans factors (proteins) bind to these cis-elements to regulate gene activation or repression.
  • Inactive genes are usually condensed chromatin, restricting RNA polymerase access.
  • Transcriptional factors (bind to control elements) are responsible for positioning RNA polymerase and controlling transcription initiation and rate or repression,

RNA Polymerases

  • There are 3 eukaryotic RNA polymerases (Pol I, II, and III).
  • Different polymerases have different sensitivities to a-amanitin. Pol I is insensitive, Pol II is very sensitive, and Pol III has intermediate sensitivity.
  • Each polymerase transcribes different types of RNA products. (Pol I transcribes ribosomal RNA, Pol II transcribes messenger RNA and other non-coding RNAs, and Pol III transcribes transfer RNA and other small RNAs.)
  • Polymerases have core subunits, similar across types, along with other unique subunits.

RNA Polymerase II Promoters and General Transcription Factors

  • Eukaryotic genes transcribed by RNA Pol II are regulated by multiple cis-acting control regions (e.g., promoters, proximal elements, enhancers).
  • Activators bind to enhancer regions to stimulate transcription, while repressors bind to prevent transcription.
  • General transcription factors (TFs) regulate RNA polymerase II positioning and initiation by sequence-specific binding.

Promoters

  • The TATA box is a highly conserved promoter sequence.
  • Initiators are less frequent but also regulate initiation.
  • CpG islands are CG-rich regions that are often associated with genes transcribed at lower rates. They are typically unmethylated.

General Transcription Factors (TFIIs)

  • TFIID is an initial factor that binds the TATA box, thus positioning for RNA polymerase II initiation.
  • Other factors (TFIIA, TFIIB, TFIIF, TFIIE, TFIIH) combine to create a complete preinitiation complex.
  • TFIIH has kinase activity that phosphorylates Pol II's CTD, thus initiating the elongation/synthesis phase.

Regulatory Sequences in Protein-Coding Genes

  • Promoter-proximal elements are close to a start site and work with enhancers.
  • Enhancers are distant from a start site and control transcription by binding transcription factors for activation or repression.
  • These regions and associated factors are often cell-type specific.

Modular Transcription Factors

  • Transcriptional activators and repressors are modular, with DNA-binding domains for sequence recognition and activation or repression domains to interact with other components of the transcriptional machinery (e.g., mediator).
  • Interactions often are influenced by protein-protein interactions and specific amino acids in the involved sequences.

Multiple Transcription Factor Binding Sites

  • Genes often have multiple binding sites for different transcriptional factors, allowing for combinatorial control.
  • This combination allows for the specific activation or repression of certain genes in diverse cell types, or across cell cycles,
  • Binding combinations and the factors involved are regulated, which creates flexibility in gene control.

Epigenetic Regulation of Transcription

  • Epigenetic regulation involves alterations that alter gene expression without affecting the DNA sequence.
  • Such alterations can be sustained even after cell division.
  • Examples include DNA methylation (at CpG islands) and histone modifications (like methylation, acetylation, ubiquinations)(which affect accessibility of DNA for protein-binding),

Other Transcription Systems

  • Three main RNA polymerases (Pol I, II, III).
  • Pol I and Pol III use similar mechanisms (but different specific factors and promoter locations) to RNA Pol II.
  • Mitochondrial and chloroplast DNA have specific transcription factors or polymerases.

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Description

This quiz focuses on comparing gene expression in prokaryotes and eukaryotes, with an emphasis on RNA polymerases, transcription factors, and gene regulation mechanisms. Students will explore the nuances of transcriptional control, including the roles of various elements and epigenetic factors. Dive into the complexities of gene activation and repression through this comprehensive assessment.

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