Sect 7 Quiz Easy

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.

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.