Eukaryotic Transcription and RNA Modification

Flashcards covering key concepts and terminology related to eukaryotic transcription and RNA modification processes.

RNA pol I

Transcribes all rRNA genes (except for the 5S rRNA)

RNA pol II

Transcribes all protein-encoding (structural) gene (all mRNAs) and some snRNA genes needed for splicing

RNA pol III

Transcribes all tRNA genes and the 5S rRNA gene and microRNA genes

Core promoter

A relatively short sequence that typically consists of the TATA box, a transcriptional start site, and one or more downstream promoter elements (DPEs)

Activators

Stimulate transcription

Repressors

Inhibit transcription

Regulatory elements

Short DNA sequences that affect the binding of RNA polymerase to the promoter

Cis-acting elements

DNA sequences that exert their effect only over a particular gene; example: TATA box, enhancers, and silencers

Trans-acting elements

Regulatory proteins that bind to such DNA sequences

Three categories of proteins required for transcription to occur at the promoter

RNA polymerase II, six different proteins called general transcription factors (GTFs), and a protein complex called mediator

RNA polymerase II

The enzyme that catalyzes the linkage of nucleotides in the 5′ to 3′ direction, using DNA as a template

TFIID

Composed of TATA-binding protein (TBP) and other TBP-associated factors (TAFs); recognizes the TATA box of eukaryotic protein-coding gene promoters

TFIIA

Binds to TFIID and promotes its binding to the TATA box

TFIIB

Binds to TFIID and then enables RNA polymerase II to bind to the core promoter; also promotes TFIIF binding

TFIIF

Binds to RNA polymerase II and plays a role in its ability to bind to TFIIB and the core promoter; also plays a role in the ability of TFIIE and TFIIH to bind to RNA polymerase II

TFIIE

Plays a role in the formation or the maintenance (or both) of the open complex; it may exert its effects by facilitating the binding of TFIIH to RNA polymerase II and regulating the activity of TFIIH

TFIIH

A multisubunit protein that has multiple roles; certain subunits act as helicases and promote the formation of the open complex; other subunits phosphorylate the carboxyl terminal domain (CTD) of RNA polymerase II, which releases its interaction with TFIIB, thereby allowing RNA polymerase II to proceed to the elongation phase

Mediator

A multisubunit complex that mediates the effects of regulatory transcription factors on the function of RNA polymerase II

Allosteric model

After transcribing the polyadenylation signal sequence, RNA polymerase II is destabilized and dissociates from the DNA

Torpedo model

An exonuclease binds to the 5' end of the RNA that is still being transcribed and degrades it in a 5' to 3' direction

Exons

Coding sequences

Introns

Intervening sequences

Capping

The attachment of a 7-methylguanosine cap (m7G) to the 5′ end of mRNA

polyA tailing

The attachment of a string of adenine-containing nucleotides to the 3′ end of mRNA at a site where the mRNA is cleaved

exonucleases

cleave a covalent bond between two nucleotides at one end of a strand

endonucleases

can cleave bonds within a strand

A ribozyme

RNase P

Splicing among group I and II introns

Self-splicing

Pre-mRNA splicing

Requires the aid of structure known as the spliceosome

Functions of spliceosome subunits

Bind to an intron sequence and precisely recognize the intron- exon boundaries, Hold the pre-mRNA in the correct configuration, and Catalyze the chemical reactions that remove introns and covalently link exons

Alternative splicing

A pre-mRNA with multiple introns can be spliced in different ways to generate mature mRNAs with different combinations of exons

Splicing factors

proteins that regulate alternative splicing, including splicing repressors and splicing enhancers

Splicing repressors

Prevent splicing

Splicing enhancers

Facilitate splicing

RNA editing

Change in the base sequence of an RNA after it is already made