Regulation of Gene Expression in Eukaryotic Cells – Vocabulary Review

This set of vocabulary flashcards covers the key enzymes, factors, sequences and processes involved in eukaryotic transcription, RNA processing and overall gene expression control, as presented in Dr. Pritchett’s lecture.

RNA Polymerase

Enzyme that synthesizes RNA from a DNA template during transcription.

RNA Polymerase I

Eukaryotic polymerase that transcribes most ribosomal RNA (rRNA).

RNA Polymerase II

Polymerase responsible for making mRNA, microRNA and many other RNA transcripts.

RNA Polymerase III

Polymerase that produces tRNA, 5S rRNA and other small RNAs.

mRNA (messenger RNA)

Protein-coding RNA molecule generated by RNA Pol II and translated into polypeptide.

rRNA (ribosomal RNA)

Structural and catalytic RNA component of ribosomes, mainly transcribed by RNA Pol I.

tRNA (transfer RNA)

Adaptor RNA that brings amino acids to the ribosome; made by RNA Pol III.

miRNA (microRNA)

Short non-coding RNA that post-transcriptionally regulates gene expression.

lncRNA (long non-coding RNA)

RNA >200 nt that is not translated but can regulate chromatin and transcription.

Transcription

Process of copying DNA information into RNA by RNA polymerase.

Transcription Initiation

First stage of transcription when RNA polymerase is recruited to DNA and the DNA helix is unwound.

Transcription Elongation

Stage in which RNA polymerase moves 3′→5′ along template, synthesizing RNA 5′→3′.

Transcription Termination

Final stage when RNA polymerase disengages and the RNA transcript is released.

Promoter

DNA region upstream of a gene that directs RNA polymerase where to begin transcription.

Transcription Start Site (TSS)

Exact nucleotide position in the promoter where RNA synthesis begins.

General Transcription Factors (GTFs)

Set of proteins required by eukaryotic RNA Pol II to initiate transcription at most promoters.

TFIID

GTF that recognizes the TATA box and initiates assembly of the transcription machinery.

TFIIB

GTF that binds BRE sequences and positions RNA Pol II at the TSS.

TFIIA

GTF that stabilizes TFIID binding at certain promoters.

TFIIF

GTF that stabilizes RNA Pol II–TFIIB interaction and recruits TFIIE and TFIIH.

TFIIE

GTF that attracts and regulates TFIIH.

TFIIH

GTF with helicase activity that unwinds DNA at the TSS and helps release RNA Pol II from the promoter.

Pre-initiation Complex (PIC)

Assembly of RNA Pol II with GTFs at a promoter before RNA synthesis begins.

Transcription Bubble

Locally unwound DNA region within which RNA polymerase synthesizes RNA.

Sense Strand

DNA strand whose sequence matches the RNA transcript (except T/U) and is not used as template.

Antisense Strand

DNA strand that serves as the template for RNA synthesis.

Enhancer

Distant DNA element bound by activator proteins that increases transcription of specific promoters.

Chromatin Modifier

Protein that alters histones or DNA to influence chromatin structure and transcription.

Transcription Elongation Factors

Proteins that assist RNA Pol II during elongation by overcoming nucleosome barriers and coordinating RNA processing.

5′ Cap

Modified guanine nucleotide added to the 5′ end of nascent mRNA for stability and ribosome recruitment.

Poly(A) Tail

String of adenines added to the 3′ end of mRNA that enhances stability and translation.

Torpedo Model

Termination model where a 5′→3′ exonuclease degrades the downstream RNA and dislodges RNA Pol II.

Allosteric Model

Termination model proposing that a conformational change in RNA Pol II causes it to release the DNA.

T-tract

Run of thymidines in the DNA template implicated in pausing/termination of RNA Pol II.

Exon

Expressed sequence that remains in mature mRNA after splicing.

Intron

Non-coding sequence removed from pre-mRNA during splicing.

5′ UTR

Untranslated region at the 5′ end of mRNA upstream of the start codon.

3′ UTR

Untranslated region at the 3′ end of mRNA downstream of the stop codon.

Alternative Splicing

Process by which different combinations of exons are joined to generate multiple mRNA transcripts from one gene.

Gene Expression Regulation (levels)

Control can occur during transcription, RNA processing, RNA transport/localization, mRNA stability/translation, and protein function/degradation.