Biology Chapter: Transcription Mechanisms

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Questions and Answers

What is a key characteristic of a strong promoter?

RNA polymerase binds weakly

Fewer transcripts are made

Significantly deviates from consensus sequence

Same as the consensus sequence (correct)

Where is the TATA box located in eukaryotic promoters?

Upstream from the Pribnow box

At the initiation site

19-27 bases before the startpoint (correct)

Within the gene it promotes

What distinguishes eukaryotic promoters used for RNA polymerase III?

Contains a bipartite structure

Located in the promoter region

Located within the gene it promotes (correct)

Found upstream of the Pribnow box

Which of the following mutations causes a deviation from the consensus sequence?

A mutation that alters the TATAAT sequence Signup and view all the answers

What is the primary role of auxiliary proteins in eukaryotic promoters?

Facilitate RNA polymerase binding Signup and view all the answers

What effect does a weak promoter have on RNA polymerase binding?

RNA polymerase binds weakly Signup and view all the answers

What do general transcription factors do?

Direct the level of transcription from core promoters Signup and view all the answers

What feature is common to all eukaryotic promoters?

They are specific to each type of RNA polymerase Signup and view all the answers

What is the first step during transcription initiation by RNA polymerase?

Binding to the promoter Signup and view all the answers

Which boxes are part of the general structure found in eukaryotic promoters?

CAAT box, GC box, and TATA box Signup and view all the answers

How does RNA polymerase add nucleotides during transcription elongation?

One at a time to the growing RNA chain Signup and view all the answers

What characterizes Rho-independent termination of transcription?

It ends in a stretch rich in GC Signup and view all the answers

Which of the following is TRUE about gene-specific transcription factors?

They interact and activate specific genes Signup and view all the answers

What triggers the termination of transcription in the Rho-dependent process?

Rho helicase releases the transcript after Rho binds Signup and view all the answers

What is the role of RNA polymerase during transcription?

It catalyzes the formation of RNA from a DNA template Signup and view all the answers

Which type of transcription termination requires ATP?

Rho-dependent termination Signup and view all the answers

What is the main product of transcription?

RNA Signup and view all the answers

Which enzyme is primarily responsible for transcription?

RNA polymerase Signup and view all the answers

What are the three general steps involved in transcription?

Initiation, elongation, termination Signup and view all the answers

What is the role of the promoter in transcription?

It serves as a binding site for RNA polymerase Signup and view all the answers

How does RNA polymerase build the RNA strand?

By adding ribonucleotides to the 3' end Signup and view all the answers

What is a primary transcript in transcription?

The immediate product of RNA polymerase Signup and view all the answers

Which type of RNA is specifically not produced by transcription?

DNA Signup and view all the answers

In which part of the cell does transcription occur in prokaryotes?

Cytoplasm Signup and view all the answers

What indicates the nucleotide position number (+1) in the DNA template?

The first RNA nucleotide added Signup and view all the answers

What is a characteristic of eukaryotic RNA polymerase II?

It synthesizes mRNA Signup and view all the answers

Study Notes

Chapter Objectives

Describe the features of transcription
Discuss the requirements and steps in transcription
Explain the different mechanisms in RNA processing

Transcription

Transcription is a DNA-dependent synthesis of RNA
Template: DNA
Product:
- Messenger RNA (mRNA)
- Ribosomal RNA (rRNA)
- Transfer RNA (tRNA)
- miRNA, siRNA, and other regulatory RNAs

Features of Transcription

It involves certain regions of DNA that code for RNA, but other regions do not.
It consists of three general steps: initiation, elongation, termination.
It is the major point of control of gene expression.
The main enzyme for transcription is RNA polymerase.

RNA Polymerase

DNA-directed
Adds ribonucleotides to the 3' end of the RNA chain.
Builds RNA in the 5' to 3' direction.
Can initiate synthesis of strands on DNA templates.
Makes an error for every 10⁴-10⁶ ribonucleotides incorporated.
Has no proofreading ability.
Prokaryotic vs. Eukaryotic

Bacterial RNA Polymerase Subunits

2α - aids in promoter recognition
β - binds ribonucleotide substrate
β' - binds DNA template
σ - recognizes and binds tightly to promoter
ω - facilitates assembly
2αββ' = core enzyme; (2αββ')σ = holoenzyme

Eukaryotic RNA Polymerases

Three types of eukaryotic RNA polymerases (I, II, and III)
I - located in the nucleolus, transcribes rRNA.
II - located in the nucleoplasm, transcribes hnRNA (precursor of mRNA).
III - located in the nucleoplasm, transcribes tRNA, 5s rRNA, and small stable RNAs.

Definition of Some Terms

Gene - basic unit of a gene which extends from the promoter to the terminator.
Promoter - a sequence that "promotes" or helps gene expression; the binding site for RNA polymerase.
Terminator - the end of a gene sequence.
Upstream - regions close to the promoter.
Downstream - regions farther away from the promoter.
(+1) - base pair in DNA which corresponds to the first RNA nucleotide added by RNA polymerase.
(+) - nucleotide position number toward the direction of transcription.
(−) - nucleotide position number toward the opposite/away from the direction of transcription.
Consensus sequence - nucleotide sequence that, when aligned, have certain nucleotides that appear frequently at particular positions.

Prokaryotic Promoter

Consensus sequence of -35 sequence and -10 sequence.
Upstream from Pribnow box.

Eukaryotic Promoters

One promoter for each type of RNA polymerase because there is a specific RNA polymerase for each type.
Types:
- For RNA polymerase II: promoter for RNA pol II.
- For RNA polymerase I: promoter for RNA pol I
  - Includes upstream control element (UCE) and core promoter.
- For RNA polymerase III: promoter for RNA pol III, located within the gene.
General structure: includes TATA box, CAAT box, and GC box.
Roles:
- A-T rich region simplifies initial RNA polymerase binding.
- The location relative to the startpoint affects RNA polymerase binding.
- Auxillary protein binding facilitates RNA polymerase binding.

Promoter Mutation

Two types of promoter mutation:
- 1. mutation - causes deviation from the consensus sequence.
- 1. mutation - causes a given sequence to become more/exactly similar to an established consensus sequence.

General Transcription Factors

Necessary protein factors for the transcription of any eukaryotic gene.
Sufficient to direct transcription from many core promoters.
Position RNA polymerase at the appropriate position.

Assembly of Transcription Initiation Complex in Eukaryotes

Steps of TFs binding to DNA and other TFs.

Gene-specific Transcription Factors

Proteins involved in the interaction and activation of particular genes or groups of genes.
Different sets in different cell types result in different patterns.
Examples include steroid hormone receptors and myogenic proteins.

Transcription Initiation

RNA polymerase binds to a promoter.
RNA polymerase melts the DNA.
RNA polymerase remains stationary.
RNA polymerase incorporates the first ribonucleotide.
RNA polymerase retains all three phosphate groups.

Transcription Elongation

Nucleotides are added one by one to the growing RNA chain..
5' to 3' in the direction of RNA growth
Rapid, about 50 nucleotides/sec in E. coli.

Transcription Termination

RNA polymerase stops transcription at designated sequence signals.
- Two types:
  - Rho-independent
  - Rho-dependent

Two Types of Termination

Rho-independent: Simple termination; no need for rho factor. Ends in a stretch of GC-rich sequences from the mRNA that forms a hairpin structure that facilitates termination
Rho-dependent: Termination that requires a protein called rho; a characteristic sequence is required; usually less GC rich and there isn't a sequence of UUUU's at the end of the RNA. Rho binds to the RNA at a recognition site, pursuing RNA pol until it catches up and unwinds the DNA-RNA helix, causing the transcript to release.

Additional Information Summarized

Rifampicin binds to bacterial RNA polymerase and inhibits transcription initiation.

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Description

Explore the essential features and processes of transcription in this quiz. Learn about the requirements, steps involved, and the role of RNA polymerase in synthesizing RNA from DNA. Test your understanding of different types of RNA and the importance of transcription in gene expression.