eukaryote transcripton 1

Which RNA polymerase transcribes protein-coding genes in eukaryotes?

RNA polymerase II 🧬 → transcribes mRNA (protein-coding genes).

Why is eukaryotic transcription more complex than prokaryotic transcription?

DNA is packaged into nucleosomes 🧶, RNA Pol II cannot bind promoters alone ❌, and general transcription factors (GTFs) are required 🧩.

What does RNA polymerase I transcribe?

RNA Pol I transcribes large rRNAs: 28S, 18S, and 5.8S 🧠.

What does RNA polymerase II transcribe?

RNA Pol II transcribes mRNA and most snRNA and snoRNA ✍️.

What does RNA polymerase III transcribe?

RNA Pol III transcribes tRNA, 5S rRNA, and some small RNAs 🔬.

What is the core promoter?

The DNA region around the +1 transcription start site that is required for transcription initiation 🚦.

What is the TATA box and where is it located?

A core promoter element with consensus TATAAAA, located ~25 bp upstream of the start site 📍.

What percentage of eukaryotic promoters contain a TATA box?

About 30% of promoters contain a TATA box ⚖️.

What is the initiator (INR) element?

A core promoter sequence at the start site that helps recruit TFIID and can work with or without a TATA box 🎯.

What is the downstream promoter element (DPE)?

A core promoter element located +28 to +32 bp downstream that helps TFIID bind 📐.

What are upstream sequence elements (USEs)?

Short DNA sequences ~100 bp upstream that bind transcription factors to enhance regulated expression or tissue-specific expression 🎚.

Give examples of upstream sequence elements and what binds them.

GC box binds Sp1 🧲 and

CAAT box binds C/EBP (CTF).

What two conditions must upstream sequence elements meet to function?

They must be in the correct orientation 🔄 and the correct distance from the promoter 📏.

What is an enhancer?

A DNA element that increases transcription by binding activator proteins, even when far away from the gene 🚀.

How do enhancers differ from upstream sequence elements?

Enhancers work at long distances and any orientation 🛰️, while USEs must be close and correctly positioned 📍.

Where can enhancers be located?

Upstream, downstream, or within introns of a gene 🧬.

How do enhancers increase transcription?

They bind activators that interact with the Mediator complex to recruit RNA Pol II more efficiently 🤝.

What is the pre-initiation complex (PIC)?

A large protein complex that assembles at the promoter to start transcription 🏗️.

Which factor binds first during PIC assembly?

TFIID binds first 🥇.

What are the components of TFIID?

TBP (TATA-binding protein) and TAFs (TBP-associated factors) 🧩.

What is the role of TBP?

TBP binds the TATA box and bends DNA to help assemble the PIC 🪢.

What is the correct order of pre-initiation complex assembly?

TFIID → TFIIA & TFIIB → RNA Pol II → TFIIF → TFIIE → TFIIH 🧱➡️.

What is the role of TFIIA and TFIIB?

They stabilise TFIID and help recruit RNA Pol II ⚓.

What is the role of TFIIF?

It escorts RNA Pol II to the promoter and stabilises its binding 🤲.

Why is TFIIH an important ?

It has helicase, ATPase, and kinase activity and controls the start of elongation ⭐.

What are the functions of TFIIH?

It unwinds DNA 🧵 and phosphorylates the CTD (C-terminal domain) of RNA Pol II 🔋.

What does phosphorylation of the RNA Pol II CTD cause?

Release of most TFs 🚪, conformational change of Pol II 🔄, and recruitment of elongation factors 🏃.

What is the transition from initiation to elongation?

TFIIH phosphorylates the CTD, allowing RNA Pol II to leave the promoter and begin productive elongation ▶️.

Why does the PIC alone produce only low levels of transcription?

It lacks enhancer-bound activators and Mediator interaction, so recruitment is inefficient ⚠️.

How is cell fate determined at the transcriptional level?

By specific gene expression patterns controlled by transcription factors and external signals 🧬.

Why can the same DNA sequence be expressed differently in different cells?

Each cell type has a unique combination of transcription factors 🧠.

What classic experiment demonstrated enhancer function?

Deletion of a 72 bp enhancer from SV40 (Simian Virus 40) caused a 100-fold drop in transcription 📉.

Why can mutations in introns affect gene expression?

Because introns can contain enhancers (sequences) that regulate transcription 🧩.