Transcription Factors — Notes OmpathStudy

--- TRANSCRIPTION FACTORS AND RNA POLYMERASE IN EUKARYOTES AND PROKARYOTES 1. RNA POLYMERASE IN PROKARYOTES VS. EUKARYOTES A. Prokaryotic RNA Polymerase In prokaryotic organisms (such as bacteria), transcription is carried out by a single RNA polymerase enzyme . This RNA polymerase does not require additional transcription factors to initiate transcription. Instead, the enzyme recognizes specific promoter sequences with the help of a sigma (σ) factor that enables the enzyme to locate the transcription start site. Once transcription begins, the σ factor is released , allowing the core enzyme to elongate the RNA transcript. B. Eukaryotic RNA Polymerase Eukaryotic transcription is more complex and requires three distinct RNA polymerases : RNA Polymerase I – Synthesizes rRNA (except 5S rRNA). RNA Polymerase II – Synthesizes mRNA, some small nuclear RNAs (snRNAs), and microRNAs. RNA Polymerase III – Synthesizes tRNA, 5S rRNA, and other small RNAs. RNA Polymerase II, which transcribes mRNA , requires multiple transcription factors to recognize and bind to promoter regions, initiate transcription, and regulate gene expression. 2. TRANSCRIPTION FACTORS IN EUKARYOTES A. Definition and Role Transcription factors (TFs) are regulatory proteins that assist RNA polymerase in initiating transcription by recognizing and binding to promoter regions. They help in unwinding DNA, stabilizing RNA polymerase binding , and regulating gene expression . B. Transcription Factors for RNA Polymerase II RNA Polymerase II requires six essential transcription factors , which are collectively called General Transcription Factors (GTFs) . These factors are necessary for the initial stages of transcription and help in: Recruiting RNA Polymerase II to the promoter region . Unwinding DNA at the transcription start site . Stabilizing the transcription complex . Regulating the initiation process . C. The Six General Transcription Factors for RNA Polymerase II Each transcription factor has specific roles in the formation of the transcription initiation complex : TFIID (TATA-Binding Protein, TBP) Structure & Function : Contains TBP (TATA-Binding Protein) , a monomeric protein that recognizes the TATA box , a conserved promoter sequence. TBP binding to the TATA box is the first step in transcription initiation . TFIID also contains TAFs (TBP-associated factors) , which help regulate transcription and provide specificity to different promoters. Key Role : Initiates transcription by binding to the TATA box in the regulatory region of the gene. TFIIA Structure & Function :A multimeric protein composed of three subunits. It stabilizes the binding of TFIID (TBP) to the TATA box. Enhances RNA polymerase II recruitment to the promoter. Key Role : Ensures stability of the transcription initiation complex. TFIIB Structure & Function :A monomeric protein that binds to TFIID (TBP) . Helps position RNA Polymerase II correctly at the transcription start site. Recruits TFIIF and RNA Polymerase II to form the pre-initiation complex. Key Role : Bridges the interaction between TBP and RNA Polymerase II , ensuring accurate transcription start site selection. TFIIF Structure & Function :A multimeric protein with two subunits. Binds tightly to RNA Polymerase II , preventing it from binding non-specifically to DNA . Helps RNA Polymerase II bind specifically to the correct promoter . Key Role : Prevents random DNA binding and stabilizes RNA Polymerase II during initiation. TFIIE Structure & Function :A multimeric protein with two subunits. Recruits TFIIH , an essential transcription factor with enzymatic activity. Plays a role in DNA unwinding , allowing the transcription machinery to access the DNA template. Key Role : Facilitates DNA opening by recruiting TFIIH . TFIIH Structure & Function :A multimeric protein with 12 subunits. Contains helicase activity , which unwinds DNA at the transcription start site . Phosphorylates RNA Polymerase II , activating it for elongation. Involved in nucleotide excision repair (NER) , a DNA repair mechanism that corrects transcription errors. Key Role : Unwinds DNA to allow transcription initiation. Phosphorylates RNA Polymerase II to trigger the elongation phase . Plays a role in DNA repair . 3. FORMATION OF THE TRANSCRIPTION INITIATION COMPLEX The process of transcription initiation follows these steps: TFIID (TBP) binds to the TATA box , marking the transcription start site. TFIIA stabilizes TFIID binding . TFIIB bridges TBP and RNA Polymerase II , recruiting the enzyme to the promoter. TFIIF binds to RNA Polymerase II , preventing it from interacting with non-specific DNA sequences. TFIIE recruits TFIIH , which begins DNA unwinding . TFIIH unwinds DNA and phosphorylates RNA Polymerase II , allowing it to transition from initiation to elongation. Once this complex is assembled and RNA Polymerase II is activated, transcription begins. 4. DNA REPAIR DURING TRANSCRIPTION TFIIH is involved in transcription-coupled DNA repair . It recr