Transcription Regulation in RNA Polymerase II

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Questions and Answers

What role does the phosphorylation of Serine-5 by TFIIH play during transcription elongation?

It promotes the uncoupling of RNA Polymerase II from the pre-initiation complex. (correct)

It alters the sequence of the RNA being transcribed.

It irreversibly binds RNA Polymerase to the promoter region.

It enhances the acidity of the carboxyl-terminal domain.

Which transcription factors remain associated with the transcription machinery after the initiation complex is formed?

TFIIB and TFIIE

TFIID (correct)

TFIIB and TFIID

TFIIE and TFIIH

What characteristic of RNA Polymerase II's carboxyl-terminal domain (CTD) facilitates its interaction with transcription factors?

It contains polar, uncharged amino acids structured in a repeating domain. (correct)

It has a rigid structure that limits flexibility.

It is rich in hydrophobic residues, allowing it to repel other proteins.

It is composed of only charged amino acids.

How does the phosphorylation of the CTD affect the RNA Polymerase II during transcription?

It triggers the promotion of mRNA 5' capping. Signup and view all the answers

Which feature of TFIID allows it to play a role in initiating the formation of the pre-initiation complex (PIC)?

Its binding to the TATA box on the DNA. Signup and view all the answers

What is the primary function of the CAAT Box in the proximal promoter?

To recruit transcription factors and enhance binding efficiency of RNA polymerase II Signup and view all the answers

Which element is specifically responsible for binding hormone receptors?

HRE (Hormone Response Element) Signup and view all the answers

How far upstream from the start site can enhancers operate?

Up to 50,000 base pairs Signup and view all the answers

Which transcription factor is associated with the GC Box?

SP1 Signup and view all the answers

What role do specific response elements play in gene regulation?

They allow for gene expression regulation in response to environmental or cellular signals Signup and view all the answers

What is the primary function of RNA Pol II during the elongation phase of transcription?

To incorporate nucleotides into the growing mRNA molecule Signup and view all the answers

What is the typical length of the DNA-RNA hybrid region during transcription elongation?

8-9 base pairs Signup and view all the answers

What occurs to the pyrophosphate (PPi) released during RNA synthesis?

It undergoes hydrolysis into two inorganic phosphates Signup and view all the answers

During elongation, how does RNA Pol II determine the correct nucleotide to incorporate into the mRNA?

By pairing the incoming nucleotides with the DNA template through hydrogen bonds Signup and view all the answers

What type of supercoiling occurs in the DNA ahead of RNA Pol II during transcription?

Positive supercoiling Signup and view all the answers

Why is the 3' OH group of the previous nucleotide important in transcription?

It binds to the 5' α-phosphate of the incoming nucleotide Signup and view all the answers

Which enzyme relieves the supercoiling tension created during transcription?

Topoisomerase Signup and view all the answers

In which direction does RNA polymerase synthesize the RNA molecule?

5' to 3' Signup and view all the answers

What is the primary role of the Pre-Initiation Complex (PIC) in eukaryotic transcription?

To position RNA polymerase II and denature the DNA Signup and view all the answers

What is the primary function of RNA polymerase II during transcription?

To bind to DNA and initiate transcription Signup and view all the answers

Which proteins bind to the TATA box during the formation of the Pre-Initiation Complex?

TFIID consisting of TBP and TAFs Signup and view all the answers

What is the function of TFIIH in the Pre-Initiation Complex?

Phosphorylates sites on RNA Pol II to start elongation Signup and view all the answers

Which component is NOT required for translation in the cytoplasm?

RNA polymerase II Signup and view all the answers

What type of complex is formed between RNA Pol II and TFIIF?

A specific binding complex within the PIC Signup and view all the answers

What is the end product of transcription after processing?

Messenger RNA (mRNA) Signup and view all the answers

Which of the following roles does TFIIA play in the Pre-Initiation Complex assembly?

It stabilizes the PIC structure Signup and view all the answers

In the context of transcription, what does the 'sense strand' refer to?

The strand that codes for the RNA and is identical in sequence to the mRNA Signup and view all the answers

What is the significance of the ATP-driven transcription bubble formed at the promoter site?

It allows DNA to unwind for transcription to occur Signup and view all the answers

Which of the following best describes the role of transcription factors?

They assist RNA polymerase II in initiating transcription Signup and view all the answers

Which sequence marks the beginning of transcription?

Transcription Start Site (+1) Signup and view all the answers

What occurs during transcription initiation in relation to nucleotides?

A phosphodiester bond is formed between the first two nucleotides Signup and view all the answers

Which protein provides a specific binding site for RNA Polymerase II within the PIC?

TFIIB Signup and view all the answers

During the process of translation, which structure is primarily responsible for synthesizing proteins?

Ribosome Signup and view all the answers

How many proteins typically make up the Pre-Initiation Complex (PIC)?

Approximately 100 proteins Signup and view all the answers

What differentiates the coding strand from the antisense strand in DNA?

The coding strand's sequence is identical to the newly formed mRNA strand Signup and view all the answers

Which of the following statements about transcriptional activators is accurate?

They bind to coactivators that then connect to the PIC Signup and view all the answers

What is the primary role of the promoter region in eukaryotic transcription?

Binding of RNA polymerase Signup and view all the answers

Which of the following elements is specifically recognized by the TATA-binding protein (TBP)?

TATA box Signup and view all the answers

How far upstream from the transcription start site (TSS) does the proximal promoter typically extend?

About 250 to 40 base pairs Signup and view all the answers

Which transcription factor recognizes the B recognition element (BRE) in human promoters?

TFIIB Signup and view all the answers

What is the consensus sequence for the TATA box in eukaryotic promoters?

TATAWAWR Signup and view all the answers

What is located about 28-32 nucleotides downstream of the transcription start site and plays a role in transcription initiation?

Downstream promoter element (DPE) Signup and view all the answers

Which of the following is NOT a core promoter element found in eukaryotic transcription?

Enhancer region Signup and view all the answers

What is the primary function of proximal promoter elements?

To regulate the timing and level of gene expression Signup and view all the answers

Study Notes

Molecular Mechanisms of Disease

This course, HSS2305, covers molecular mechanisms of disease.
The diagrams and lecture content refer to cell structure and processes.
The course material moves through eukaryotic gene transcription and translation.
A central dogma is described: DNA, transcription, RNA, translation, and protein.

Eukaryotic Gene Transcription and Translation

Eukaryotic gene transcription and translation are key topics.
Transcription is the process of creating mRNA from DNA.
Translation converts mRNA into proteins.
A detailed process of transcription and translation was presented.
Post-transcriptional modifications to mRNA were noted.

From Genes to Proteins overview

The Central Dogma of molecular biology (DNA --> RNA--> Protein) is described through a diagram.
The process of mRNA synthesis from DNA template is emphasized.
RNA polymerase is a key enzyme in transcription.
The process of translation, converting mRNA to protein, is discussed with a diagram.

From Genes to Proteins (Complex) Overview

A more complex depiction of the process is shown.
mRNA, post-transcriptional modification, translation, ribosomal proteins, cytosol and others are visible.
A diagram shows the nucleus and cytosol with the movement of mRNA during translation, as well as other elements like tRNA and ribosomes.

Protein Synthesis (Video)

A video presentation discussing protein synthesis (DNA, transcription, translation) and folding was referenced.
The video is identified with a URL.

Transcription (Summary)

Transcription is the synthesis of RNA from a DNA template within the nucleus.
Starting material includes DNA, RNA polymerase II, and transcription factors.
The end product is messenger RNA.

Translation (Summary)

Translation is the synthesis of proteins from mRNA in the cytoplasm.
Starting material includes mRNA, ribosomal RNA, transfer RNA, and ribosomal proteins.
The end product is a polypeptide.

Sense vs Antisense DNA Strands

The coding strand's sequence is identical to the mRNA sequence, except for uracils replacing thymines.
The template strand is the opposite strand.

Transcription (General)

Both DNA strands encode genes.
The DNA strand of a gene has ~3.6 x 10^4 base pairs.
Several other important elements or factors for transcription are referred to.

Transcription - RNA Polymerase

RNA polymerase binds to DNA and initiates transcription at promoter regions.
It incorporates nucleotides into an RNA strand complementary to the DNA template strand.

Eukaryotic RNA Polymerases

Prokaryotes use single RNA polymerase for transcription of all types of RNA.
Eukaryotes use three different RNA polymerases (I, II, and III) in transcription.
Specific RNA polymerases have unique roles.
Enzymes and molecules required for initiation and more are discussed.

Eukaryotic Transcription - RNA Polymerase

RNA polymerase is DNA-dependent, RNA polymerase, and synthesizes RNA from DNA in the 5' to 3' direction.
A diagram shows elements like Enhancer sites (-50,000 to + 50,000), proximal elements, and core promoters.
other important elements like BRE, TATA box, Inr, and DPE are named.

Eukaryotic Transcription

Transcription factors, general and specific factors,
TFII (A,B,D,E,F,H)
TBP (TATA binding protein) and TAFs (TBP-associated factors) are presented as important elements.
The need for the initiation complex (PIC) is noted.

Gene Promoter Overview

The promoter region is a site on DNA where RNA polymerase binds for transcription initiation.
It dictates which strand acts as the template (anti-sense) for mRNA creation.
Specific sequences (sometimes referred to as elements) within the promoter region are highlighted. (ex. core and proximal)

Eukaryotic Transcription Core Promoter

Core promoters contain elements like the TATA box or initiator sequence (INR) and others.
Consensus sequences within the promoter motifs, (e.g., BRE, TATA, Inr, and DPE) are shown.
Their locations, relative to the start site, and function in eukaryotic transcription.

Eukaryotic Transcription - Core Promoter Elements

The initiator elements (INR) overlap with transcription start sites.
Consensus sequences for the elements like (e.g., YYANWYY,
Downstream promoters, for instance, RGWYV(T)
Elements and factors for promoter regions are detailed.

Eukaryotic Transcription - Proximal Promoter Elements

Proximal promoter elements contain specific binding sites (e.g., CAAT box, GC box) for transcription factors.

Eukaryotic Transcription - Enhancer Regions

Enhancer regions can be located far from the promoter and can increase transcriptional activity.

Eukaryotic Transcription - Pre-Initiation Complex (PIC)

A large, multi-protein complex that forms at the promoter prior to transcription initiation.
Various components like TBP, TAFs, TFIIA, TFIIB, TFIIE, TFIIF, and TFIIH are identified.

Eukaryotic Transcription - Formation of PIC

Stages in PIC formation are presented with diagrams, showing the roles of TFII(Bs, etc.) factors to initiate the formation of the PIC and position RNA polymerase at gene start sites.

Eukaryotic Transcription - Initiation

Transcription initiation involves the formation of a phosphodiester bond between the first two nucleotides of the RNA transcript.
RNA polymerase continues moving along the DNA template.

Eukaryotic Transcription- Elongation

Extension of the RNA molecule using a DNA template is shown.
RNA polymerase incorporating new nucleotides.
The DNA-RNA hybrid and supercoils are described.
Topoisomerases play a role here.

Eukaryotic Transcription - Elongation Factors

Various elongation factors (like P-TEFb and others) influence the elongation process.
They regulate the rate and accuracy of transcription.

Eukaryotic Transcription - Termination

Termination is described including sequences in prokaryotic and eukaryotic cells.
Processing steps and the addition of adenines (polyadenylation) to form the 3' tail of mRNA are described.

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Description

This quiz explores the critical aspects of transcription regulation involving RNA Polymerase II, including the role of phosphorylation on the carboxyl-terminal domain and the factors associated with the transcription machinery during initiation and elongation. Test your understanding of the pre-initiation complex and the functionality of transcription factors.