Eukaryotic Transcription: L14-15

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Questions and Answers

What is the primary function of activation domains in transcription factors?

To bind DNA and activate transcription (correct)

To inhibit transcription in gene expression

To provide structural integrity to DNA

To prevent protein interactions

What is required for transcription factors with basic binding domains to bind to DNA?

They require a DNA-binding motif.

They must be localized to the nucleus.

They need to be phosphorylated.

They must dimerise. (correct)

In the domain swap experiment, which region from Transcription Factor 2 was determined to have the activation domain?

Region C

Region B (correct)

Region A

None of the regions

Which type of amino acid composition is characteristic of acidic activation domains?

High in acidic amino acids Signup and view all the answers

Which type of transcription factor is C/EBP identified as?

Basic zipper TF Signup and view all the answers

What is one example of a transcription factor that possesses a glutamine-rich activation domain?

Oct-2 Signup and view all the answers

Which of the following describes a characteristic of transcription factors with basic binding domains?

They need a dimerisation motif. Signup and view all the answers

What is the expected outcome when a domain with no specific structure is tested for activation capability?

It may lead to either activation or inhibition Signup and view all the answers

Which three types of DNA binding domains are most common in transcription factors?

Zinc fingers, Basic binding domains, Helix-turn-helix Signup and view all the answers

How are steroid hormone receptors classified in terms of transcription factor activity?

By their responsiveness and regulation of activity. Signup and view all the answers

What is the primary purpose of DNA binding domains in transcription factors?

To bind specifically to DNA sequences Signup and view all the answers

Which transcription factor is specific for B-cells and shows a modular structure?

Oct-2 Signup and view all the answers

How do zinc finger domains interact with DNA?

By using a-helices that contact the major groove Signup and view all the answers

What role does the zinc ion (Zn2+) play in zinc finger domains?

It stabilizes the structure of the finger Signup and view all the answers

What characteristic is common to helix-turn-helix structures in transcription factors?

They have a fixed angle between two helices Signup and view all the answers

Which of the following statements about homeodomains is true?

They have a prominent role in binding to the major groove of DNA Signup and view all the answers

What does the term 'modular structure' refer to in the context of transcription factors?

The presence of distinct regions for binding and function Signup and view all the answers

Which domain is involved in the activation or inhibition of transcription in transcription factors?

Activation or inhibitory domain Signup and view all the answers

What mechanism is primarily used by co-repressors to inhibit transcription?

Interacting with the transcription initiation complex (PIC) Signup and view all the answers

How do histone de-acetylases (HDAC) contribute to the regulation of transcription?

By removing acetyl groups from histones Signup and view all the answers

What is one effect of Tamoxifen in the treatment of breast cancer?

It alters the conformation of the estrogen receptor to favor co-repressor binding Signup and view all the answers

In eukaryotic transcription, what is the role of the C-terminal domain (CTD) of RNA Pol II?

To provide binding sites for RNA processing machinery Signup and view all the answers

Which of these is NOT a function of the transcription factors (TFs)?

Recruiting ribosomes to mRNA Signup and view all the answers

What distinguishes eukaryotic transcription from prokaryotic transcription?

Eukaryotic transcription takes place in the nucleus Signup and view all the answers

What is the role of the branch point in RNA splicing?

It acts as a nucleophile during the cleavage at the splice sites. Signup and view all the answers

Which strand of RNA is cleaved first in the splicing process?

The 5’ splice site. Signup and view all the answers

What is a characteristic of the elongation phase of eukaryotic transcription?

The C-terminal domain (CTD) of RNA Pol II is phosphorylated Signup and view all the answers

What role do co-activators play in transcription regulation?

Facilitate interaction with RNA polymerase II Signup and view all the answers

What type of reaction is primarily involved in intron removal during RNA splicing?

Transesterification. Signup and view all the answers

Which of the following best describes the termination of eukaryotic transcription?

It extends beyond the gene and requires additional processing Signup and view all the answers

What happens to the intron after it is spliced out of the RNA molecule?

It is degraded in the cell. Signup and view all the answers

What is formed when the exons are ligated together?

The mature mRNA. Signup and view all the answers

Why is the addition of a 5’ cap important for mRNA?

It stabilizes the mRNA and marks it for transport. Signup and view all the answers

What specifically occurs during the second step of RNA splicing?

The 3’OH group attacks the 3’ splice site. Signup and view all the answers

Which of the following is NOT a characteristic of RNA splicing?

It requires the presence of ribosomal RNA. Signup and view all the answers

What is the function of RNA triphosphatase in the capping process?

To remove the gamma-phosphate from the RNA Signup and view all the answers

Which enzyme is responsible for adding the GMP to the 5' end of the RNA?

Guanylyltransferase Signup and view all the answers

What linkage is formed between the added GMP and the 5' terminal base of the transcript?

5'-5' linkage Signup and view all the answers

What is added to the guanine during the capping process?

A methyl group Signup and view all the answers

Which of the following is NOT a role of the 5' cap in mRNA?

It assists in DNA replication Signup and view all the answers

What is the most abundant cap added to mRNA?

m7G cap Signup and view all the answers

What is the main component recognized by cap-binding complexes (CBCs)?

The 5' cap structure Signup and view all the answers

Why is the highly phosphorylated CTD of RNAP II significant?

It provides binding sites for capping enzymes Signup and view all the answers

Study Notes

Transcriptional Regulation in Eukaryotes

Eukaryotic transcription factors (TFs) are proteins that regulate gene expression.
TFs have specific structures that allow them to bind to DNA and initiate or inhibit transcription.
TFs are identified and purified using bioinformatics analysis of whole-genome sequencing data.
Mutation analysis (observational or interventional) of upstream regions of genes can reveal sequences that control transcription.

Transcription Factor Structure

Transcription factors are amino acid-based proteins.
Their 3-dimensional structure is critical for their function.
Structure is modular; one region binds to DNA, another binds to other components.
Examples include Oct-2 (an octamer TF specific for B-cells) recognizing a conserved octanucleotide sequence (5'-ATGCAAAT-3').
Transcription factors have domains for different functions: DNA-binding, activation (or inhibitory) domains.

DNA Binding Domains

Three main types: zinc fingers, helix-turn-helix, and basic binding domains.
Zinc fingers: loops of 23 amino acids, often multiple per TF, linkers between fingers (7-8 amino acids), and an alpha helix contacting the major groove of DNA.
Helix-turn-helix: two helices at a fixed angle, recognition helix binds the major groove of DNA, typically present as dimers where recognition helices are separated by one turn of DNA helix.
Basic binding domains: transcription factors with basic binding motifs cannot bind to DNA solely, but must dimerise. Leucine zipper and helix-loop-helix are examples.

Transcription Factor Activity

Steroid hormone receptors (e.g., vitamin D receptor, glucocorticoid receptor, estrogen receptor, androgen receptor) exhibit activity regulated by location due to responsivness.
DNA-binding domains of steroid hormone receptors have high sequence homology (43-97%).

Transcription Factors Activate Transcription:

TF activation domains may work through direct interaction with the pre-initiation complex (PIC) or by recruiting co-activators.
Co-activators may interact with the PIC or alter chromatin structure (e.g., acetylation of histone amino-acid tails).
Histone acetyltransferase (HAT) activity is an example of co-activator-mediated modification of chromatin.

Transcription Factors Inhibit Transcription

TF inhibitory domains repress transcription either by binding to DNA/blocking other transcription factors, binding to the pre-initiation complex (PIC), or recruiting co-repressors.
Co-repressors may interact with the PIC or alter chromatin structure (e.g., de-acetylation of histone amino-acid tails).

RNA Processing

The processes of capping, splicing, and polyadenylation occur in the nucleus, and are critical to the conversion of pre-messenger RNA to messenger RNA.

5' Capping

The 5' cap is a 7-methylguanosine cap added to the 5' end of the mRNA.
Capping enzymes are bound to the RNA polymerase II C-terminal domain (CTD).
This process includes three steps: RNA triphosphatase, Guanylyltransferase, and Methyltransferase.
Essential for efficient translation, stabilisation and transport of mRNA.
The 5' cap protects mRNA from degradation.
The 5' cap helps distinguish mRNA from other types of RNA.

RNA Splicing

Introns are removed and exons are joined together by splicing mechanisms.
Three classes (nuclear pre-mRNA splicing involving spliceosomes, group II self-splicing, group I self-splicing).
Mechanisms of removal include conserved sequence motifs such as GU and AG sites, and branch points, and involve transesterification reactions.

Quality Control of 5' Capping

Improperly capped RNA is recognised and degraded by quality control mechanisms.
Example of mechanisms in yeast include Rai1-Rat1 heterocomplexes and exoribonuclease activity.
Mammalian DXO in the nucleus has mRNA-decapping activities.

Viruses and mRNA Production

Some viruses (e.g., influenza) hijack the host cell's machinery to produce their mRNA.
They do this by cap snatching, where viral RNA-dependent RNA polymerase (RdRp) uses the 5’ cap from pre-existing host mRNA.

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Description

Test your knowledge about the functions and characteristics of transcription factors, specifically focusing on activation and DNA binding domains. This quiz covers key questions regarding the composition and classification of transcription factors, their roles in gene expression, and specific examples of activation domains. Ideal for students studying molecular biology or biochemistry.