transcription

• What is the TATA box in the eukaryotic promoter?

  A DNA sequence rich in thymine and adenine that is located approximately $30 \text{ bp}$ upstream of the start site

  
• What is the role of the TATA box in the eukaryotic promoter?

  It acts as a binding site for general transcription factors and assists in the assembly of the preinitiation complex

  
• Name two general transcription factors that bind to the eukaryotic promoter

  TBP (TATA binding protein) and TFIID

  
• What is the function of TBP in the preinitiation complex?

  It binds to the TATA box and helps bend the DNA to facilitate preinitiation complex assembly

  
• What is the name of the multisubunit protein complex that contains TBP?

  TFIID

  
• What is the role of TFIID in the preinitiation complex?

  It is essential for promoter recognition, binding, and preinitiation complex assembly

  
• What steps are involved in the formation of the preinitiation complex?

  • Binding of TBP and TFIID to the TATA box in the eukaryotic promoter
  • Recruitment of additional general transcription factors such as TFIIF, TFIIIH, and TFIIH to form the complex

  
• Which RNA polymerase initiates transcription in eukaryotes?

  RNA polymerase II

  
• What is the role of TFIIH in the preinitiation complex?

  It is responsible for DNA unwinding and phosphorylation of RNA polymerase II's CTD

  
• How does the C-terminal domain (CTD) of RNA polymerase II function in transcription elongation?

  • Phosphorylation of the CTD by TFIIH triggers the transition from initiation to elongation
  • Facilitates the binding of factors necessary for transcription elongation, such as splicing machinery

  
• What is the abbreviation for RNA polymerase II?

  Pol II

  
• What occurs once RNA polymerase II binds to the preinitiation complex?

  It initiates transcription and begins moving along the DNA template during elongation

  
• What are the primary roles of TFIIF in the preinitiation complex?

  Assists TFIID binding to the promoter and helps in RNA polymerase II recruitment and stability

  
• What is the function of TFIIIH in the preinitiation complex?

  It is involved in DNA unwinding and phosphorylating the CTD of RNA polymerase II

  
• What component of RNA polymerase II is phosphorylated by TFIIH?

  The C-terminal domain (CTD)

  
• If TFIIH were mutated and unable to phosphorylate the CTD of RNA polymerase II, what would be the expected outcome?

  • Initiation would occur normally, but the transition to elongation would be impaired
  • Transcription elongation would be reduced or completely inhibited

  
• What is the name of the enzyme responsible for catalyzing the addition of ribonucleotides during transcription elongation?

  RNA polymerase

  
• What are the two main components of the transcription initiation complex?

  • Core enzymes of RNA polymerase
  • Transcription factors

  
• What does the term "zipper" refer to in the context of transcription elongation?

  It refers to the separated DNA strands allowing access to the template strand

  
• What is the role of the "rudder" structure in RNA polymerase during transcription elongation?

  To unwind and separate the DNA double helix

  
• How does the movement of core enzymes in RNA polymerase ensure fidelity during transcription elongation?

  • RNA polymerase moves along the DNA template ensuring that only complementary ribonucleotides are added
  • It continuously catalyzes the formation of phosphodiester bonds between ribonucleotides

  
• What happens to the growing mRNA transcript as RNA polymerase moves along the DNA template?

  • RNA polymerase adds complementary ribonucleotides to the transcript
  • The transcript continues to grow in the $5' \rightarrow 3'$ direction

  
• What is the main function of RNA polymerase holoenzyme?

  • To catalyze the synthesis of RNA from a DNA template

  
• What components make up the RNA polymerase holoenzyme?

  • Core enzyme
  • Sigma factor

  
• What does the term "holoenzyme" refer to in RNA polymerase?

  The complete RNA polymerase enzyme complex consisting of the core enzyme and sigma factor.

  
• How does the RNA polymerase holoenzyme initiate transcription?

  • It recognizes and binds to the promoter region of DNA
  • It unwinds the DNA double helix to expose the template strand
  • It initiates RNA synthesis at the transcription start site

  
• How would the removal of the sigma factor affect the activity of RNA polymerase holoenzyme?

  Removal of the sigma factor would prevent RNA polymerase from recognizing and binding to the promoter region, thus reducing or eliminating transcription initiation.

  
• What role does the sigma factor play in RNA polymerase holoenzyme?

  The sigma factor is responsible for recognizing and binding to the promoter region of DNA, enabling accurate initiation of transcription.

  
• What are the major steps in transcription initiation by RNA polymerase holoenzyme?

  1. Binding to the promoter region
  2. Unwinding the DNA double helix
  3. Initiation of RNA synthesis at the transcription start site

  
• What are the primary components of the gene control region?

  Regulatory sequence, spacer DNA, promoter.

  
• What is the function of spacer DNA in the gene control region?

  • Separates the regulatory sequence from the promoter

  
• What is the role of the TATA box in the promoter?

  It serves as a binding site for general transcription factors.

  
• What enzyme facilitates the transcription of gene X?

  RNA polymerase II.

  
• What are the general transcription factors?

  • Proteins that bind to the TATA box

  
• What is the purpose of the promoter in the gene control region?

  It is the region where RNA polymerase II binds to initiate transcription.

  
• What is the role of gene regulatory proteins in gene expression?

  • They bind to the regulatory sequence to influence the initiation of transcription

  
• What binds to the regulatory sequence in gene X’s control region?

  Gene regulatory proteins.

  
• What are the main components involved in gene activation?

  • Activators
  • Enhancers
  • Co-activators
  • Mediator
  • General transcription factors
  • RNA polymerase II
  • TATA box
  • Promoter

  
• How does an activator protein facilitate gene activation?

  By binding to the enhancer region, it recruits co-activators and mediator complexes, leading to the assembly of general transcription factors and RNA polymerase II at the promoter to initiate transcription.

  
• What is the role of an enhancer in gene activation?

  The enhancer is a DNA sequence that binds activator proteins, increasing the rate of transcription initiation of the associated gene by bringing together activator proteins, co-activators, and mediator complexes.