Module 12: RNA — Transcription and Processing

Comprehensive vocabulary flashcards covering RNA types, prokaryotic and eukaryotic transcription mechanisms, RNA processing, splicing, RNA interference, and CRISPR systems.

Informational RNA

RNA that carries information used in translation.

Messenger RNA (mRNA)

RNA that carries information from which a protein is translated; prokaryotic mRNA typically lacks processing and can encode multiple proteins, whereas eukaryotic mRNA is processed and typically encodes one.

Functional RNA

RNA that performs a cellular or molecular function without being translated into protein.

Transfer RNA (tRNA)

Functional RNA that transports specific amino acids during translation.

Ribosomal RNA (rRNA)

Functional RNA molecules that form the structural and catalytic components of ribosomes.

Small Nuclear RNA (snRNA)

Functional RNA that helps splice primary RNA transcripts into mature mRNA.

Small Nucleolar RNA (snoRNA)

Functional RNA that assists in rRNA processing.

Small Cytoplasmic RNA (scRNA)

Functional RNA that directs protein trafficking in eukaryotic cells.

miRNA and siRNA

Small functional RNAs that promote mRNA degradation or inhibit translation.

CRISPR RNA (crRNA)

RNA that participates in a prokaryotic CRISPR defense system.

Long Noncoding RNA (lncRNA)

Noncoding RNA transcripts whose functions include dosage compensation.

Transcription

The enzymatic synthesis of RNA from a DNA template.

Template DNA Strand

The antisense/anti-coding DNA strand read in the 3′ to 5′ direction by RNA polymerase to synthesize complementary RNA.

Non-Template DNA Strand

The coding/sense DNA strand whose nucleotide sequence matches the synthesized RNA, except thymine replaces uracil.

RNA Polymerase Holoenzyme

The bacterial transcription enzyme complex consisting of the core enzyme combined with a sigma factor.

Promoter

A DNA regulatory sequence located upstream of the transcription start site that signals RNA polymerase to initiate transcription.

Bacterial Promoter Consensus Regions

Conserved DNA sequence regions located approximately −35 and −10 upstream of the +1 transcription start site.

Sigma Factor

A bacterial protein subunit that recognizes specific promoter sequences and correctly positions RNA polymerase.

5′ UTR

The untranslated leader region of an mRNA located between the +1 transcription start site and the first ATG translation start codon.

Transcription Bubble

A locally unwound region of DNA where RNA polymerase synthesizes RNA.

Direct Termination

Bacterial transcription termination triggered directly by an intrinsic terminator sequence without requiring auxiliary proteins.

Rho-Dependent Termination

Bacterial transcription termination in which Rho protein binds to the rut site and facilitates RNA release from RNA polymerase.

rut Site

A specific sequence on an RNA transcript to which the Rho termination protein binds.

RNA Polymerase I

The eukaryotic enzyme dedicated specifically to the synthesis of rRNA.

RNA Polymerase II

The eukaryotic enzyme responsible for synthesizing mRNA and certain noncoding RNAs.

RNA Polymerase III

The eukaryotic enzyme responsible for synthesizing tRNA, snRNA, and scRNA.

TATA Box

A conserved promoter DNA sequence located approximately 30 base pairs upstream of the eukaryotic transcription start site.

TATA-Binding Protein (TBP)

A subunit of the TFIID complex that binds directly to the TATA box sequence.

TFIID

A general transcription factor complex containing TBP that aids in recognizing eukaryotic promoters.

Preinitiation Complex (PIC)

An assembly formed at eukaryotic promoters comprising six general transcription factors (TFIIs) and RNA polymerase II.

Carboxyl-Terminal Domain (CTD)

The repeated tail structure of eukaryotic RNA polymerase II that undergoes reversible phosphorylation and dephosphorylation to coordinate transcription and mRNA processing.

5′ Cap

A modified structure added to the 5′ end of eukaryotic pre-mRNA that protects the molecule from degradation and is required for translation.

Poly(A) Tail

A stretch of about 150–200 adenine residues added to the 3′ end of eukaryotic mRNA following cleavage downstream of a polyadenylation signal.

Polyadenylation Signal Sequences

Specific sequence motifs on eukaryotic transcripts (AAUAAA or AUUAAA) recognized by cleavage machinery about 20 bases before the poly(A) addition site.

Intron

A noncoding intervening sequence within a primary RNA transcript that is excised during RNA splicing.

Exon

A segment of a primary RNA transcript that is retained and joined together to form mature RNA.

Spliceosome

A large ribonucleoprotein complex that removes introns and ligates exons during pre-mRNA splicing.

snRNPs

Small nuclear ribonucleoproteins (including U1, U2, U4, U5, and U6) that align splice sites and assemble the functional spliceosome.

GU–AG Rule

The rule describing the conserved boundary nucleotides of introns, where introns typically start with a 5′ GU and end with a 3′ AG.

Lariat

A looped, lasso-like RNA structure formed by an excised intron during the two-step splicing reaction.

Alternative Splicing

The differential joining of distinct exon combinations from a single pre-mRNA transcript, producing multiple distinct protein isoforms.

Joan Steitz

The scientist recognized for foundational work linking snRNAs to pre-mRNA splicing.

Sidney Altman

The scientist who demonstrated the catalytic nature of RNA through studies of ribonuclease P in 1979.

Tom Cech

The scientist who discovered self-splicing RNA in Tetrahymena in 1981.

RNA World Hypothesis

The evolutionary hypothesis proposing that early life forms relied on RNA both to store genetic information and to catalyze biochemical reactions.

Gene Silencing

The selective shutting off of gene expression so that no functional protein is produced.

Andrew Fire and Craig Mello

The researchers who demonstrated double-stranded RNA (dsRNA)-induced gene silencing in 1998.

Double-Stranded RNA (dsRNA)

An RNA duplex consisting of a sense RNA strand paired with a complementary antisense RNA strand that triggers RNA interference.

David Baulcombe

The researcher who established the connection between short RNAs and dsRNA-mediated post-transcriptional gene silencing.

Transgene Silencing

The phenomenon in which an introduced foreign gene is successfully incorporated into an organism but fails to produce protein.

Cosuppression

The simultaneous post-transcriptional silencing of both an introduced transgene and its homologous endogenous gene, first documented in petunias by Richard Jorgensen.

CRISPR

Clustered regularly interspaced short palindromic repeats; a bacterial adaptive immune system providing defense against invading viral DNA.

CRISPR Arrays

Genomic DNA segments in bacteria that store captured fragments of DNA from past viral infections to maintain molecular memory.

Cas9

An RNA-guided endonuclease that cleaves viral DNA during infections and is adapted for targeted genome editing.