Transcription Factors Overview
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Questions and Answers

The core promoter is the binding site for ______ factors.

general transcription

The ______ is a DNA sequence found in the core promoter region that indicates the point at which a genetic sequence can be found, read, and decoded.

TATA Box

The ______ is the simplest functional promoter that can direct transcription without a TATA Box.

Inhibitor Element

DPE, or ______ ______, functions cooperatively with the INR for the binding of TFIID in transcription of core promoters in the absence of the TATA Box.

<p>Downstream Promoter Elements</p> Signup and view all the answers

Which of the following are considered regulatory promoter elements? (Select all that apply)

<p>Enhancer</p> Signup and view all the answers

Transcription factors are RNA molecules that bind to specific DNA sequences.

<p>False</p> Signup and view all the answers

The transcription factor has a ______ signal which allows the protein to get into the nucleus and get to the DNA.

<p>nuclear localization</p> Signup and view all the answers

Transcription factors have ______ domains, which is where they bind to specific DNA sequences.

<p>DNA binding</p> Signup and view all the answers

Transcription factors can have activating or repressing domains that regulate whether the gene is needed or not.

<p>True</p> Signup and view all the answers

What is the function of the WRKY22 protein?

<p>The WRKY22 protein binds to the TTGACC/T DNA sequence and is activated to confer submergence tolerance in Arabidopsis, indicating its role in plant stress response.</p> Signup and view all the answers

Explain the role of the bHLH domain in transcription factors.

<p>The bHLH domain is crucial for the binding of transcription factors to DNA and facilitates their role in epithelial-mesenchymal transition (EMT) and tumorigenesis.</p> Signup and view all the answers

Describe the function of the zinc finger domain in the regulation of HIV.

<p>Zinc finger proteins play a key role in the transcriptional regulation of HIV by binding to DNA and regulating the expression of the HIV promoter. They also cooperate with KRAB-ZFPs to control HIV expression.</p> Signup and view all the answers

Explain how the leucine zipper domain facilitates DNA binding.

<p>Leucine zipper domains consist of alpha-helices that contain a leucine residue every seventh amino acid. These domains dimerize, forming a Y-shaped structure that allows them to bind to two different major grooves within the DNA molecule, enhancing gene regulation.</p> Signup and view all the answers

Describe the function of the Rel homology domain (RHO) in the Rel family of transcription factors.

<p>The Rel homology domain, which contains a DNA-binding region and a protein-protein interaction domain, enables Rel family transcription factors to participate in various cellular processes, including dorsoventral patterning and the immune response. It interacts with other Rel family members and enhances their functionality.</p> Signup and view all the answers

Describe the mechanism of DNA binding by the helix-turn-helix motif.

<p>The helix-turn-helix motif consists of two alpha-helices connected by a short turn. The last helix, commonly referred to as the recognition helix, inserts into the major groove of DNA, mediating base-specific DNA recognition and allowing for specific gene regulation.</p> Signup and view all the answers

Explain the mechanism of DNA binding by the homeodomain.

<p>Homeodomains are DNA-binding motifs similar to helix-turn-helix motifs but have a three-helix structure. They recognize and bind to DNA in a specific manner, primarily via interactions in the major groove, and play crucial roles in regulating gene expression and developmental processes.</p> Signup and view all the answers

What is the function of the NAC domain in plants?

<p>The NAC domain is a DNA-binding motif found in transcription factors that regulate various developmental processes in plants, including leaf spine formation, plant growth, and stress response. By binding to specific DNA sequences, they control gene expression and contribute to overall plant development and adaptation to environmental challenges.</p> Signup and view all the answers

What are the roles of the different eukaryotic RNA polymerases?

<p>RNA polymerase I is responsible for synthesizing ribosomal RNA (rRNA), which is essential for ribosome assembly and protein synthesis. RNA polymerase II transcribes messenger RNA (mRNA), which carries genetic information from DNA to the ribosomes. RNA polymerase III produces transfer RNA (tRNA), which helps transport amino acids to the ribosome for protein synthesis. RNA polymerases IV and V are specific to plants and are involved in RNA-directed DNA methylation, a crucial epigenetic process.</p> Signup and view all the answers

What are the roles of general transcription factors for RNA polymerase II?

<p>General transcription factors play critical roles in the initiation of transcription by RNA polymerase II. They bind to promoter regions in the DNA sequence, specifically the TATA box, and recruit RNA polymerase II to the initiation site, facilitating the start of transcription.</p> Signup and view all the answers

Which step of transcription involves unwinding of DNA to expose the template strand?

<p>Initiation</p> Signup and view all the answers

What is the function of the C-terminal domain (CTD) of RNA polymerase II?

<p>The C-terminal domain (CTD) of RNA polymerase II is a highly phosphorylated tail that plays crucial roles in regulating transcription. During initiation, TFIIH phosphorylates the CTD, allowing RNA polymerase II to escape from the initiation complex and begin elongation. The CTD is also involved in RNA processing, including capping, splicing, and polyadenylation.</p> Signup and view all the answers

Mutations that result in the loss of kinase function for TFIIH are lethal because TFIIH loses its ability to phosphorylate, and no RNA can be made or proteins.

<p>True</p> Signup and view all the answers

What is the function of FACT in transcription?

<p>FACT, or Facilitated Chromatin Transcription, is a complex of proteins responsible for disassembling and reassembling nucleosomes as RNA polymerase II moves through the DNA. This process allows RNA polymerase II to bypass histone-bound DNA and transcribe genes that are packaged within chromatin.</p> Signup and view all the answers

Explain how the transcription bubble is formed during transcription.

<p>The transcription bubble is formed as RNA polymerase II separates the two strands of DNA. RNA polymerase II binds to the promoter region and unwinds the DNA, creating a bubble that allows for the template strand to be exposed and transcribed into RNA. The unwinding of the DNA molecule proceeds in a small segment, typically about 25 base pairs, allowing for efficient transcription.</p> Signup and view all the answers

During termination of transcription, RNA polymerase II continues to transcribe DNA while the pre-mRNA is cut off and released.

<p>True</p> Signup and view all the answers

Explain the function of the 5' exonuclease XRN2 in mRNA processing.

<p>XRN2, a 5' exonuclease found in eukaryotes, is responsible for degrading mRNA transcripts that are either incomplete or aberrant. It works by removing nucleotides from the 5' end of the RNA molecule, effectively degrading the transcript and ensuring the quality of mRNA present within the cell.</p> Signup and view all the answers

RNA polymerase I is responsible for the synthesis of ribosomal RNA (rRNA), which is essential for ribosome assembly and protein synthesis.

<p>True</p> Signup and view all the answers

RNA polymerase III transcribes mRNA, which contains the genetic code for proteins.

<p>False</p> Signup and view all the answers

Which of the following factors is involved in the initiation of transcription by RNA polymerase I?

<p>UBFI</p> Signup and view all the answers

Explain the mechanism of termination of transcription by RNA polymerase I.

<p>The termination of transcription by RNA polymerase I is facilitated by a specific transcription termination factor called TTF-1. TTF-1 binds to the newly synthesized rRNA transcript downstream of the termination site, signaling RNA polymerase I to detach from the DNA template and end transcription.</p> Signup and view all the answers

RNA polymerase III utilizes the same general transcription factors as RNA polymerase II for initiation.

<p>False</p> Signup and view all the answers

What is the purpose of processing rRNA?

<p>Processing rRNA is essential for ensuring that the ribosome, the protein synthesis machinery within cells, is assembled correctly. rRNA undergoes a series of modifications, including cleavage, methylation, and pseudouridylation, which are crucial for the proper folding and formation of the functional ribosomal subunits.</p> Signup and view all the answers

The processing of rRNA, tRNA, and mRNA involves the action of ribozymes.

<p>True</p> Signup and view all the answers

What is the purpose of 5' capping of mRNA?

<p>5' capping of mRNA is essential for protecting the mRNA from degradation by exonucleases. The 7-methylguanosine cap, added to the 5' end of the mRNA, serves as a protective barrier and a recognition signal for nuclear export, facilitating the efficient translation of the mRNA into protein.</p> Signup and view all the answers

The addition of a poly A tail to mRNA occurs at the 5' end of the mRNA.

<p>False</p> Signup and view all the answers

What are the functions of NELF and DSIF in mRNA processing?

<p>NELF and DSIF are negative elongation factors that associate with RNA polymerase II and pause elongation during transcription. They play a role in controlling the rate of transcription and ensuring that mRNA transcripts are produced efficiently and correctly.</p> Signup and view all the answers

Explain the role of P-TEFb in mRNA processing.

<p>P-TEFb, or Positive Transcription Elongation Factor b, is a kinase that phosphorylates NELF and DSIF, releasing them from RNA polymerase II and allowing transcription to resume. This process is crucial for regulating the rate of transcription and ensuring the efficient production of mRNA transcripts.</p> Signup and view all the answers

Describe the role of the polyadenylation signal in mRNA processing?

<p>The polyadenylation signal, typically AAUAAA, is a sequence within the mRNA transcript that marks the end of transcription. It signals the cleavage of the pre-mRNA transcript and triggers the addition of a poly A tail to the 3' end. These events are crucial for mRNA stability, nuclear export, and translation efficiency.</p> Signup and view all the answers

What is the function of the spliceosome?

<p>The spliceosome is a large molecular complex responsible for removing introns from pre-mRNA transcripts and splicing together exons, creating a mature mRNA molecule that can be translated into proteins.</p> Signup and view all the answers

Explain the function of the snRNAs in splicing.

<p>Small nuclear RNAs (snRNAs), components of the spliceosome, play critical roles in guiding the splicing process. They recognize and bind to specific sequences within the pre-mRNA, including splice sites and the branch point, and facilitate the precise removal of introns and the joining of exons.</p> Signup and view all the answers

Histone acetylation is often associated with increased transcription, while histone deacetylation is often associated with repressed transcription.

<p>True</p> Signup and view all the answers

Histone methylation can either activate or repress transcription depending on the specific amino acid residue that is methylated.

<p>True</p> Signup and view all the answers

Explain how chromatin remodeling factors regulate gene expression.

<p>Chromatin remodeling factors are proteins that alter the structure of chromatin, the complex of DNA and histone proteins. They can slide histone proteins along the DNA, expose specific DNA sequences, or even remove histones from the DNA. These actions can modulate access for transcription factors to DNA, influencing gene expression levels.</p> Signup and view all the answers

LncRNAs can act as scaffolds to recruit chromatin remodeling factors, ensuring that the transcription region is accessible.

<p>True</p> Signup and view all the answers

Explain how tRNAs are activated for use in translation.

<p>tRNAs are activated by attaching the correct amino acid to their acceptor arm. This process is catalyzed by aminoacyl tRNA synthetases, enzymes that use ATP to attach the appropriate amino acid to the tRNA, ensuring that the tRNA is ready to deliver the amino acid to the ribosome during translation.</p> Signup and view all the answers

Ribosomes are composed of two subunits, a large subunit that catalyzes peptide bond formation and a small subunit that binds to mRNA.

<p>True</p> Signup and view all the answers

Explain the roles of the three sites within the ribosome (A, P, and E sites).

<p>The A site (aminoacyl site) is where the incoming charged tRNA, carrying the next amino acid, binds. The P site (peptidyl site) is where the tRNA with the growing polypeptide chain is bound. The E site (exit site) is where the deacylated tRNA, without an amino acid, exits the ribosome after its amino acid has been added to the polypeptide chain.</p> Signup and view all the answers

The process of translation initiation involves the assembly of the ribosome, the binding of the initiator tRNA, and the binding of mRNA to the ribosome.

<p>True</p> Signup and view all the answers

What is the function of eIF3 in translation initiation?

<p>eIF3, a eukaryotic initiation factor, is a protein complex that binds to the small ribosomal subunit and prevents it from prematurely associating with the large ribosomal subunit.</p> Signup and view all the answers

Explain the role of eIF2 in translation initiation.

<p>eIF2, another key eukaryotic initiation factor, is responsible for delivering the initiator tRNA, carrying the methionine amino acid, to the small ribosomal subunit.</p> Signup and view all the answers

What is the role of the eIF4 complex in translation initiation?

<p>The eIF4 complex plays a critical role in the binding of mRNA to the small ribosomal subunit. eIF4E, a component of the eIF4 complex, binds to the 5' cap of the mRNA transcript.</p> Signup and view all the answers

Explain the function of eIF5B in translation initiation.

<p>eIF5B is a GTPase that acts as a catalyst for the joining of the large ribosomal subunit to the small ribosomal subunit complex.</p> Signup and view all the answers

During translation elongation, what is the role of eEF1a?

<p>eEF1a, a eukaryotic elongation factor, binds to the newly synthesized aminoacyl tRNA, delivering it to the A site on the ribosome.</p> Signup and view all the answers

During translation elongation, GTP is hydrolyzed to GDP, providing the energy for the ribosome to move one codon along the mRNA transcript.

<p>True</p> Signup and view all the answers

What are the three stop codons that signal the termination of translation?

<p>The three stop codons that signal the termination of translation are UAA, UAG, and UGA.</p> Signup and view all the answers

Explain the role of release factors in translation termination.

<p>Release factors are proteins that bind to the A site on the ribosome when a stop codon is encountered in the mRNA transcript.</p> Signup and view all the answers

Organelles, such as mitochondria and chloroplasts, have their own translation machinery, which is similar to that of bacteria.

<p>True</p> Signup and view all the answers

Study Notes

Transcription Factors

  • Transcription factors are proteins that bind to specific DNA sequences.
  • Core promoter is the binding site for general transcription factors.
  • TATA box is a DNA sequence in the core promoter region, indicating the start of a gene.
  • INR (Inhibitor Element) is a simple functional promoter that controls transcription without a TATA box.
  • DPE (Downstream Promoter Elements) cooperatively work with INR to bind TFIID in transcription without a TATA box.
  • Core promoters are about 60 nucleotides.
  • Regulatory Promoters are where specific transcription factors bind that are necessary to activate specific genes.
  • Enhancers are upstream distant enhancers and repressors that are 1000 to 10,000 base pairs from transcription start sites and bend the DNA to contact the start site.
  • Transcription factors have a nuclear localization signal for entry into the nucleus.
  • DNA binding domains allow transcription factors to bind to specific DNA sequences.
  • Activating and repressing domains regulate whether a gene is needed or not.

DNA Binding Domains

  • Basic Helix-Loop-Helix (bHLH): Contains two alpha-helices for DNA binding.
  • Zinc finger: Contains 3 base pairs for DNA interactions, involves Zn ions. An example includes HIV regulation.
  • Leucine Zipper (ZIP): Contains alpha-helices with leucine residues every 7th amino acid; binds to 2 different major grooves of DNA.
  • Rel homology domain (RHO): Contains an internal DNA binding region and recognition loop.
  • Homeodomain: Contains an alpha helix and amino acid residues to contact DNA.

Helix-Turn-Helix (HTH)

  • The last helix in HTH motif is the recognition helix which inserts into the DNA major groove for recognizing specific DNA locations.
  • Examples include Lac repressor.
  • Used in DNA repair and RNA metabolism.

RNA polymerase functions

  • RNA polymerase I makes ribosomal RNA (rRNA).
  • RNA polymerase II makes messenger RNA (mRNA), microRNA (miRNA), and long noncoding RNA (IncRNA).
  • RNA polymerase III makes transfer RNA (tRNA).
  • RNA polymerases IV and V make plant-specific RNA for DNA methylation.

General transcription factors for RNA polymerase II

  • TFIID, TFIIB, TFIIF, TFIIE, TFIIH
  • Mediators join in the beginning of initiation
  • Phosphorylation of RNA Polymerase II CTD is done by TFIIH, leading to release of RNA polymerase for elongation

RNA Polymerase I

  • Initiation: Upstream binding factor (UBF) and factor 1 (SLF1) bind to promoter. Then, polymerase I binds to and moves away after the polymerase is released.
  • Elongation is the same as RNA polymerase II.
  • Termination: TFII-1

RNA Polymerase III

  • Initiation: TFIIB and polymerase III
  • Elongation: Same as RNA polymerase II
  • Termination: Section of 4–7 Us signals end of gene

RNA Processing

  • 5.8s, 18s, and 28s rRNA are made from a single transcript.
  • 5s rRNA comes from a different transcript.
  • Pseudouradine is formed from the isomerization of ribose.
  • rRNA are processed through methylation and snoRNPs.
  • tRNA are processed through cleavage and CCA addition.
  • mRNA is processed through 5' capping, splicing, and 3' polyadenylation.
  • 5' capping prevents degradation.
  • Splicing removes introns and joins exons.
  • 3' polyadenylation adds a poly-A tail to stabilize mRNA.

RNA Processing (small nuclear ribonucleoproteins; snRNPs)

  • Small nuclear RNAs (U1, U2, U4, U5, and U6) are part of the spliceosome.
  • These form a complex that recognizes the splice sites, removes introns, and joins exons together.
  • Additional snRNAs bind and catalyze splicing.

Epigenetics

  • Affects transcription by controlling areas of tightly packed or loosely packed chromatin.
  • Acetylation/deacetylation - Histone acetylation (associated with transcription) and deacetylation (associated with repression).
  • Methylation- affects transcription depending on the active and non active sites.
  • Phosphorylation- may change the function of the tail with adding methyl, acetyl or phosphate groups.
  • Chromatin remodeling factors loosen and tighten histones to make areas accessible to allow or prevent transcription.
  • Non-coding RNA (ncRNA) affects expression positively or negatively.

Translation

  • tRNA activation for translation involves specific enzymes (aminoacyl-tRNA synthetases). Each amino acid requires its own synthetase.
  • Eukaryotic ribosomes (80S) are composed of a large subunit (60S) and a small subunit (40S).
  • mRNA, ribosome subunits, and initiator tRNA assemble during initiation.
  • Elongation factors bring charged tRNAs and position new amino acids for peptide bond formation.
  • Termination occurs with release factors at stop codons.

Translation Elongation

  • eEF1a brings in next charged tRNA, checks for match, peptide bond formed by ribosome.
  • Translocation occurs, tRNA moves to next sites.

Translation Termination

  • Release factors bind to stop codons.
  • Peptide chain released from tRNA and ribosome subunits disconnect.

Translation in organelles

  • Mitochondria and chloroplasts have their own translation machinery.

Protein Degradation

  • Proteins tagged with ubiquitin are targeted for degradation by the proteasome.
  • Steps involve E1 ubiquitin-activating enzyme, E2 ubiquitin-conjugating enzyme, and E3 ubiquitin ligase.
  • Tagged proteins are recognized by the proteasome and unfolded, leading to degradation.

Proteasome

  • Made of two subunits (26s and 20s)
  • 26s- the regulatory subunit (19s) lid recognizes Poly Ub.
  • 20s- the catalytic subunit.
  • Protein unfolding and breakdown occurs in the proteasome.

ER-stress response (UPR)

  • ER stress involves accumulation of misfolded proteins.
  • UPR response lowers global protein production, upregulates membrane lipid biosynthesis, increases ERAD (ER Associated Degradation) pathway, expands secretory pathway.
  • Chronic UPR leads to apoptosis.

Post-Translational Processing

  • Protein folding/unfolding is crucial for function.
  • Enzymes like protein disulfide isomerase and peptidyl prolyl isomerase help in folding proteins.
  • Chaperones and chaperonins assist in proper protein folding and prevent aggregation.
  • Glycosylation: Addition of sugars to proteins.
  • Lipidation: Addition of lipids to proteins.

Proteolysis

  • Cleavage of a polypeptide to activate protein from inactive precursor.
  • Steps include signal peptide removal and polypeptide chain cleavage, activating proteins.

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Description

This quiz covers essential concepts related to transcription factors, including their role in gene expression and the different elements of core promoters. Learn about the significance of the TATA box, INR, DPE, and regulation through enhancers. Test your understanding of how these components work together in transcription regulation.

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