RNA Transcription and Processing

Vocabulary practice flashcards based on Dr. Lehman's lecture on RNA transcription, RNA classes, eukaryotic pre-mRNA processing, splicing mechanisms, and small RNA-mediated gene silencing.

Ribose

The five-carbon pentose sugar found in RNA nucleotides, distinguished from deoxyribose by the presence of a hydroxyl ($-\text{OH}$) group on the \text{#2} carbon.

Uracil

A pyrimidine base found in RNA that pairs with adenine via two hydrogen bonds during transcription and can also pair with guanine during RNA folding.

Ribozyme

An RNA molecule capable of catalyzing specific biochemical reactions, functioning analogously to protein enzymes.

Messenger RNA (mRNA)

A class of RNA that serves as an intermediate between DNA and protein, carrying the protein-coding genetic information from the genome to the translational machinery.

Functional RNA

A broad class of RNA molecules that do not encode proteins but instead carry out biological roles as final, active RNA products (e.g., tRNA, rRNA, snRNA, miRNA, and siRNA).

Transfer RNA (tRNA)

A functional RNA molecule responsible for bringing the correct amino acid to mRNA during translation in the cytoplasm.

Ribosomal RNA (rRNA)

A class of functional RNA that constitutes the primary structural and catalytic components of the ribosome.

Small Nuclear RNA (snRNA)

A class of eukaryotic nuclear RNAs that associate with protein factors to form snRNPs within the spliceosome, assisting in the excision of introns from pre-mRNAs.

Asymmetric Transcription

The principle that for any given gene, only one of the two complementary DNA strands serves as the template strand for RNA synthesis.

Template Strand

The specific DNA strand read by RNA polymerase in the $3' \rightarrow 5'$ direction to direct the synthesis of RNA in the complementary $5' \rightarrow 3'$ direction.

Coding Strand

The non-template DNA strand whose nucleotide sequence is identical to the synthesized RNA transcript (with uracil replacing thymine).

Promoter

A conserved, regulatory DNA region upstream of the transcription initiation site where RNA polymerase binds to initiate RNA synthesis.

Pribnow Box

An essential bacterial promoter consensus sequence ($\text{TATAAT}$) centered roughly $10\,\text{bp}$ upstream ($-10$ region) from the transcription initiation site.

5' Untranslated Region (5' UTR)

The region of an mRNA transcript located between the transcription initiation site ($+1$) and the protein translation start codon ($\text{ATG}/\text{AUG}$).

RNA Polymerase Holoenzyme

The complete bacterial transcription initiation complex consisting of the core enzyme ($2\alpha$, $\beta$, $\beta'$, and $\omega$) joined by a sigma ($\sigma$) factor.

Sigma Factor ($\sigma$)

A bacterial polymerase subunit (such as $\sigma^{70}$) that specifically binds the $-35$ and $-10$ promoter regions, melts the DNA helix around $-10$, and dissociates after transcription initiation.

Transcription Bubble

The unwound region of single-stranded DNA maintained by RNA polymerase during elongation, exposing the template strand for ribonucleotide addition.

Rho-Independent Termination

A bacterial transcription termination mechanism mediated by an inverted repeat that forms an RNA hairpin loop followed by a poly-U stretch, causing release of the RNA transcript without protein assistance.

Rho-Dependent Termination

A bacterial termination mechanism where the Rho protein factor recognizes and binds a Rho utilization site ($\text{rut}$), tracks along the transcript, and unwinds the DNA-RNA hybrid when RNA polymerase pauses.

RNA Polymerase I

The eukaryotic enzyme localized to the nucleolus that transcribes all ribosomal RNA (rRNA) species except for $5\text{S}$ rRNA.

RNA Polymerase II

The eukaryotic enzyme localized in the nucleoplasm responsible for transcribing all nuclear genes that encode proteins into mRNA.

RNA Polymerase III

The eukaryotic enzyme located in the nucleoplasm that transcribes transfer RNA (tRNA), $5\text{S}$ rRNA, and small nuclear RNAs.

General Transcription Factors (GTFs)

A set of eukaryotic protein factors that assemble on promoter elements (such as the TATA box) to correctly position core RNA polymerase II at the transcription start site.

TATA Box (Hogness Box)

A conserved eukaryotic core promoter element centered roughly $25$ to $30\,\text{bp}$ upstream of the start site with the consensus sequence $\text{TATAAA}$, recognized by TATA-binding protein (TBP).

Carboxyl-Terminal Domain (CTD)

The tail region of the $\beta$ subunit of eukaryotic RNA polymerase II whose reversible phosphorylation coordinates co-transcriptional capping, splicing, and polyadenylation.

5' Methylguanine Cap

A chemical cap structure added co-transcriptionally to the $5'$ end of eukaryotic pre-mRNA to protect the transcript from enzymatic degradation and facilitate translation.

Poly(A) Tail

A tract of $150$ to $200$ adenine nucleotides appended to the $3'$ end of eukaryotic mRNA following cleavage during co-transcriptional processing.

Exon

An expressed region of a eukaryotic gene that is retained in the mature mRNA after splicing and contains coding sequence for proteins.

Intron

An intervening non-coding intragenic sequence in pre-mRNA transcripts that is excised by RNA splicing before nuclear export and translation.

Spliceosome

A multi-component ribonucleoprotein machine composed of five small nuclear RNAs (snRNAs) and associated proteins that catalyzes the excision of introns and ligation of exons.

snRNP

A small nuclear ribonucleoprotein particle composed of an snRNA complexed with specific proteins; subunits of the spliceosome.

Canonical Splice Sites

The conserved dinucleotide boundaries of eukaryotic introns, characterized by a $\text{GU}$ sequence at the $5'$ splice site and an $\text{AG}$ sequence at the $3'$ splice site in RNA.

Lariat

The looped, branched RNA structure formed during the first trans-esterification step of splicing when the $5'$ end of an intron covalently links to a conserved branch point adenine.

Alternative Splicing

A regulatory mechanism where exons of a pre-mRNA can be joined in differential arrangements, allowing a single gene to encode multiple distinct protein isoforms.

MicroRNA (miRNA)

Small regulatory non-coding RNAs ($21\text{--}24\,\text{nt}$) transcribed by RNA polymerase II that form hairpins and repress translation or promote degradation of target mRNAs encoded by different genes.

Small Interfering RNA (siRNA)

Short ($21\text{--}24\,\text{nt}$) double-stranded RNA molecules derived from foreign elements or antisense transcripts that silence the specific genetic sequences from which they originate.

Dicer

A double-strand-specific endonuclease that cleaves precursor double-stranded RNA into short duplex fragments of approximately $21\text{--}24\,\text{bp}$.

RNA-Induced Silencing Complex (RISC)

A protein complex containing an Argonaute core that incorporates a single-stranded small RNA guide strand to target and degrade complementary mRNAs or inhibit their translation.

Argonaute (AGO)

The central catalytic protein subunit within the RISC complex possessing endonuclease activity that mediates target mRNA destruction or translational suppression.