RNA Transcription and Processing - Vocabulary

Vocabulary flashcards covering key terms and definitions related to RNA synthesis, transcription, processing, and regulation in both prokaryotic and eukaryotic cells.

RNA

Ribonucleic acid; polymer of ribonucleotides with ribose sugar and phosphate backbone; bases A, U, C, G (uracil replaces thymine); often single-stranded.

Transcription

Process of copying RNA from a DNA template to produce mRNA, tRNA, rRNA, or microRNA.

mRNA (messenger RNA)

RNA that carries the genetic code from DNA to the ribosome for protein synthesis.

tRNA (transfer RNA)

RNA that delivers specific amino acids to the ribosome during translation.

rRNA (ribosomal RNA)

RNA component of ribosomes; essential for protein synthesis.

microRNA (miRNA)

Small non-coding RNA that inhibits translation or promotes degradation of target mRNA.

Initiation (transcription)

First step where RNA polymerase binds the promoter and forms the transcription bubble.

Elongation (transcription)

RNA polymerase extends the new RNA strand by adding nucleotides as it moves along the template.

Termination (transcription)

Process that ends transcription; can be intrinsic (rho-independent) or rho-dependent.

Promoter

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

TATA box

Promoter element rich in A/T recognized by TBP, aiding RNA polymerase binding and start site determination.

Pribnow box

Bacterial promoter element around -10 recognized by sigma factor; part of promoter specificity.

RNA polymerase

Enzyme that synthesizes RNA using a DNA template; reads 3'→5' and makes RNA 5'→3'.

Sigma factor (s factor)

Bacterial protein that directs RNA polymerase to specific promoters by recognizing -10 and -35 regions.

Core enzyme

RNA polymerase subunits capable of elongation without promoter-specific initiation.

Holoenzyme

Core enzyme plus sigma factor; capable of promoter-specific initiation.

Template strand

DNA strand used to synthesize the complementary RNA sequence.

Coding strand

DNA strand whose sequence is identical to the RNA transcript (T replaces U); not used as template.

Transcription bubble

Region where DNA is unwound to allow RNA synthesis to occur.

5' to 3' synthesis

RNA is synthesized in the 5' to 3' direction while the template is read 3' to 5'.

Rho-dependent termination

Termination of transcription requiring the Rho factor to disengage RNA polymerase.

Intrinsic (Rho-independent) termination

Terminating mechanism relying on a hairpin structure in RNA followed by a U-rich tail.

Operon

Prokaryotic gene cluster under a single promoter and operon enables co-transcription of multiple genes.

RNA polymerase I

Eukaryotic RNA polymerase that transcribes most rRNA genes, including 18S-28S-5.8S precursor.

RNA polymerase II

Eukaryotic RNA polymerase that transcribes mRNA and some snRNA.

RNA polymerase III

Eukaryotic RNA polymerase that transcribes tRNA and 5S rRNA.

TBP (TATA-binding protein)

Basal transcription factor that binds the TATA box to help recruit RNA polymerase II.

TFII

Basal transcription factors required for transcription by RNA polymerase II (e.g., TFIIA, TFIIB, etc.).

5' capping

Addition of a 7-mutually methylated guanine cap to the 5' end of pre-mRNA to regulate export and translation.

3' polyadenylation

Addition of a poly(A) tail to the 3' end of pre-mRNA after transcription termination.

AAUAAA

Polyadenylation signal sequence in pre-mRNA directing poly(A) tail addition.

CPSF

Cleavage and polyadenylation specificity factor; part of 3' end processing machinery.

CstF

Cleavage stimulation factor; participates in 3' end processing of pre-mRNA.

PAP

Poly(A) polymerase; enzyme that adds the poly(A) tail.

PABP

Poly(A) binding protein; stabilizes the poly(A) tail and aids export/translation.

Splicing

Removal of introns and joining of exons in pre-mRNA; performed by the spliceosome.

Spliceosome

Ribonucleoprotein complex (with snRNPs U1, U2, U4/U5/U6) that catalyzes RNA splicing.

5' splice site

Intron boundary at the 5' end, typically with GU consensus.

3' splice site

Intron boundary at the 3' end, typically with AG consensus.

Branch site

Internal intron sequence important for lariat formation during splicing.

Ribosome structure (40S/60S/80S)

Ribosome subunits: 40S (small) and 60S (large) form 80S ribosome in cytoplasm for translation.

18S/28S/5.8S rRNA

Ribosomal RNA components derived from the 45S precursor and assembled into ribosomal subunits.

5S rRNA

Ribosomal RNA component transcribed by RNA polymerase III and included in the 60S subunit.

tRNA cloverleaf

Secondary structure of tRNA with acceptor stem, D loop, anticodon loop, and TΨC loop.

CCA addition

Post-transcriptional addition of CCA at 3' end of tRNA for amino acid attachment.

Nuclear pore transport

Export of mature mRNA from the nucleus to the cytoplasm through nuclear pores.

Thalassemia TATA box mutation

Thalassemia caused by promoter mutation in the TATA box affecting transcription of β-globin.

Actinomycin D

Antibiotic that binds DNA and inhibits transcription by intercalation; affects both prokaryotes and eukaryotes.

Rifampin

Antibiotic that inhibits bacterial RNA polymerase, blocking elongation.

Amanitin

Toxin from death cap mushroom; inhibits eukaryotic RNA polymerases, most potent on Pol II.