Eukaryotic Transcription Flashcards

Flashcards covering eukaryotic transcription processes, factors, and regulation.

RNA Polymerase I Promoter

Located upstream of rRNA genes, recognized by core binding factor (CBF).

RNA Polymerase I Transcription Factors

TFIIIA, TFIIIB, TFIIIC are required for initiation.

RNA Polymerase II Promoter

Typically contains a TATA box (-30 region) and initiator (Inr) sequences.

Function of General Transcription Factors (GTFs)

Pre-initiation complex (PIC) assembly and transcription initiation.

Examples of General Transcription Factors (GTFs)

TFIID (contains TATA-binding protein or TBP), TFIIA, TFIIB, TFIIF, TFIIE, TFIIH

Function of C-terminal domain (CTD) of RNA Pol II

Involved in recruiting RNA processing factors.

RNA Polymerase III Promoter

Contains A and B box sequences.

RNA Polymerase III Transcription Factors

Necessary for tRNA and 5S rRNA transcription initiation.

RNA Polymerase I Termination

Occurs via a torpedo mechanism or protein-dependent termination.

Factors Involved in RNA Polymerase I Termination

Specific termination factors like TSL (termination factor) are involved.

RNA Polymerase II Termination (Torpedo Model)

After RNA cleavage, Rat1 exonuclease degrades remaining RNA.

Polyadenylation in RNA Polymerase II Termination

Signals termination at the 3' end of the transcript.

RNA Polymerase III Termination

Occurs through the formation of a hairpin loop and U-rich sequence.

Post-Transcription Event in RNA Polymerase III Termination

RNA is cleaved, and the polymerase dissociates.

Mechanism of Actinomycin D

Intercalates between the DNA bases, preventing RNA polymerase movement.

Effect of Actinomycin D on Transcription

Blocks transcription by preventing elongation.

Mechanism of Cordycepin

Nucleoside analog that leads to chain termination during RNA synthesis.

Key Structural Feature of Cordycepin

Lacks a 3' hydroxyl group.

Function of Transcription Factors

Specific DNA-binding motifs used to recognize target sequences.

Helix-Turn-Helix (HTH) Motif

Two α-helices connected by a turn; one helix fits into the DNA major groove.

Occurrence of Helix-Turn-Helix (HTH) Motif

Common in prokaryotic repressors and some eukaryotic TFs.

Zinc Finger Motif

Contains a zinc ion coordinated by cysteine and histidine residues.

DNA Binding Mechanism of Zinc Finger Motif

The “finger” fits into the DNA major groove.

Occurrence of Zinc Finger Motif

Found in many eukaryotic TFs (e.g., steroid hormone receptors).

Leucine Zipper Motif

Two α-helices with leucines every 7 amino acids, forming a dimer.

DNA Binding Mechanism of Leucine Zipper Motif

DNA binding occurs via adjacent basic regions.

Example of Leucine Zipper Motif

Jun-Fos (AP-1) transcription factor.

Helix-Loop-Helix (HLH) Motif

Two α-helices connected by a loop; allows dimerization.

DNA Binding Mechanism of Helix-Loop-Helix (HLH) Motif

Binds DNA through basic regions.

Occurrence of Helix-Loop-Helix (HLH) Motif

Found in TFs involved in development and differentiation.

Eukaryotic Gene Promoter

Core region includes the TATA box (around –30), where RNA Pol II binds via TFIID (TBP).

Upstream Regulatory Elements

Include enhancers, silencers, CAAT boxes, and GC-rich regions.

Function of Upstream Regulatory Elements

Bind specific transcription factors to modulate expression.

5′ Untranslated Region (5′ UTR)

Between the transcription start site and start codon; helps regulate translation.

Exons

Coding sequences.

Introns

Non-coding sequences removed by splicing.

3′ Untranslated Region (3′ UTR)

Follows the stop codon; includes signals for polyadenylation and mRNA stability.

Pre-Initiation Complex (PIC) Formation

Assembly of GTFs and RNA Pol II at the core promoter.

Function of TFIID (with TBP)

Binds the TATA box.

Role of Promoter

TATA box positions RNA Pol II correctly.

Function of Upstream Regulatory Sequences (Enhancers)

Enhancers bind activator proteins that loop DNA to interact with the PIC.

Function of Upstream Regulatory Sequences (Silencers)

Silencers bind repressors to inhibit transcription.

Function of TFIIH (Helicase)

Has helicase activity to unwind DNA.

Function of TFIIH (Kinase)

Kinase activity phosphorylates the CTD of RNA Pol II, triggering transcription start.

Result of Phosphorylation of RNA Pol II

Once phosphorylated, RNA Pol II escapes the promoter and begins elongation.

Recognition of TATA Box

Recognized by TBP (TATA-binding protein), a subunit of TFIID.

Function of TBP

TBP binds and bends DNA to recruit GTFs and RNA Pol II.

Recognition of CAAT Box

Recognized by CBF (CAAT-binding factor) or NF-Y.

Function of CAAT Box

Enhances promoter activity and increases transcription efficiency.

Recognition of GC Box

Recognized by SP1 (specificity protein 1).

Function of GC Box

SP1 binds GC-rich regions and helps recruit RNA Pol II and co-activators.

Euchromatin

Accessible to transcription machinery; associated with active gene expression.

Heterochromatin

Inaccessible to transcription machinery; associated with gene silencing.

Effect of Acetylation on Histones

Loosens chromatin, promoting transcription.

Effect of Methylation on Histones

Can activate or repress transcription, depending on the context.

Effect of Deacetylation on Histones

Condenses chromatin, repressing transcription.

Function of Chromatin Remodeling Complexes

Use ATP to reposition or evict nucleosomes, making DNA more accessible.

Examples of Chromatin Remodeling Complexes

SWI/SNF, ISWI, CHD, and INO80 families.

RNA Interference (RNAi)

Uses siRNAs or miRNAs to degrade or inhibit the translation of target mRNAs.

Gene Knockdown

Achieved by introducing synthetic siRNAs or shRNAs.

Role of RISC complex in RNAi-mediated knockdown

Targets and silences specific mRNA sequences, reducing gene expression.

Synthesis (Transcription) of Eukaryotic mRNA

RNA polymerase II synthesizes pre-mRNA (hnRNA) in the nucleus.

Function of 5' Cap

Protects mRNA, facilitates export, and aids in translation initiation.

Function of Poly-A Tail

Increases mRNA stability, helps with mRNA export, and regulates translation.