RNA Transcription & Processing - CHAPTER 8

Vocabulary flashcards covering key concepts from RNA transcription, processing, and regulation as presented in the notes.

Central dogma of biology

Describes the flow of genetic information: DNA → RNA → Protein; includes transcription and translation (with updates like reverse transcription).

Transcription

Synthesis of an RNA molecule from a DNA template by RNA polymerase.

Translation

Process by which mRNA directs the synthesis of a polypeptide (protein) at the ribosome.

DNA

Repository of genetic information; double-stranded molecule that serves as the template for RNA.

RNA

Single-stranded nucleic acid made of ribonucleotides; contains uracil instead of thymine and ribose sugar.

Antisense strand (template strand)

DNA strand used by RNA polymerase to synthesize RNA; complementary to the RNA transcript.

Sense strand (coding strand)

DNA strand whose sequence corresponds to the RNA transcript (T is replaced by U in RNA).

RNA polymerase

Enzyme that synthesizes RNA by adding ribonucleotides to a growing chain using a DNA template.

Uracil

RNA base that pairs with adenine; replaces thymine in RNA.

Ribonucleotides vs deoxyribonucleotides

RNA uses ribose with a 2'-OH group; DNA uses deoxyribose (lacks 2'-OH).

mRNA (messenger RNA)

RNA that encodes the amino acid sequence of a protein; translated into a polypeptide.

tRNA (transfer RNA)

RNA that carries amino acids to the ribosome and matches them to mRNA codons.

rRNA (ribosomal RNA)

RNA component of ribosomes; works with proteins to synthesize proteins.

snRNA (small nuclear RNA)

RNA component of spliceosomes involved in pre-mRNA splicing.

miRNA and siRNA

Small regulatory RNAs; miRNA regulates gene expression; siRNA mediates RNA interference.

Telomerase RNA

RNA component providing a template for synthesis of telomere repeats.

Pre-mRNA vs mature mRNA

Pre-mRNA is the initial transcript; mature mRNA is processed (capped, tailed, spliced) and exported.

5' cap

Modified guanine added to the 5' end of pre-mRNA; protects from degradation and aids export/translation.

3' polyadenylation tail (poly-A tail)

Addition of a long string of adenines at the 3' end of mRNA; protects, exports, and enhances translation.

Intron

Noncoding sequence removed during splicing.

Exon

Coding sequence retained in mature mRNA after splicing.

Spliceosome

RNA-protein complex that removes introns and ligates exons during splicing.

Lariat intron

Looped intron structure formed during splicing via a 2'-5' phosphodiester bond.

Branch site

Intronic site rich in pyrimidines containing an invariant adenine needed for lariat formation.

Alternative splicing

Process by which a single gene can yield multiple mRNA transcripts by varying exon inclusion.

Dscam

Drosophila gene with extensive alternative splicing producing thousands of isoforms.

Promoter

DNA sequence upstream of a gene that binds RNA polymerase and transcription factors to initiate transcription.

Promoter consensus sequences (-10, -35)

Conserved bacterial promoter elements: -10 (Pribnow box) 5'-TATAAT-3' and -35 5'-TTGACA-3'.

Pribnow box

The -10 promoter consensus sequence in bacteria: 5'-TATAAT-3'.

-35 consensus sequence

The -35 promoter consensus sequence: 5'-TTGACA-3'.

Sigma factor

Bacterial transcription factor subunit that directs RNA polymerase to promoter sites.

Holoenzyme

RNA polymerase core enzyme plus a sigma factor; capable of initiating transcription.

Core RNA polymerase

Catalytic enzyme that synthesizes RNA but cannot initiate without sigma factor.

Promoter recognition

Process by which RNA polymerase holoenzyme binds promoter via promoter sequences and sigma factor.

Transcription initiation

Binding to promoter, unwinding DNA near the -10 region, and starting RNA synthesis at +1.

Transcription elongation

RNA polymerase extends the growing RNA chain; sigma subunit may dissociate after initial nucleotides.

Transcription termination

End of transcription; can be intrinsic (RNA hairpin + U-rich tail) or Rho-dependent.

Intrinsic termination

Termination driven by inverted repeats in DNA forming a hairpin in RNA followed by U-rich sequence.

Rho-dependent termination

Termination requiring the Rho helicase binding to a rut site on nascent RNA.

Eukaryotic transcription

Multiple RNA polymerases (I, II, III) and numerous transcription factors; introns/exons and chromatin structure.

RNA pol II promoter elements

Promoter elements for RNA polymerase II include TATA box, CAAT box, GC-rich box.

TATA box

Promoter element around -25 with consensus 5'-TATAAA-3'.

CAAT box

Promoter element near -80; often works with GC box to promote transcription.

GC box

GC-rich promoter element typically around -90 or further upstream.

Enhancers

DNA elements that increase transcription; can be far from promoter and act via DNA looping.

Silencers

DNA elements that repress transcription by inhibiting enhancer/promoter activity.

RNA pol II CTD

Carboxyl-terminal domain of RNA polymerase II; coordinates capping, splicing, and polyadenylation.

5' cap (capping enzymes)

Enzymes add a 5' cap to nascent mRNA, protecting it and aiding processing and translation.

Polyadenylation signal (AAUAAA)

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

Polyadenylation factors

Proteins such as CPSF, CStF, CF I/CF II, PAP, and PABP that mediate 3' end processing and tail addition.

Torpedo model of termination

Model in which a torpedo RNase degrades the residual uncapped RNA after cleavage, triggering Pol II release.

Spliceosome assembly steps

U1 binds 5' splice site; U2 binds branch site; U4/U5/U6 assemble; U4 dissociates to activate splicing.

Intron splicing signals

5' splice site GU; 3' splice site AG; branch point adenine essential for splicing.

Coupling of transcription and processing

CTD coordinates capping, splicing, and polyadenylation with transcription in eukaryotes.

Chromatin

DNA-protein complex; its structure regulates accessibility of DNA to transcription.

Promoter elements (eukaryotes)

Diverse promoter elements; TATA box is common, with CAAT box and GC box variably located.

Promoter recognition factors

Transcription factors that bind promoter DNA and assist RNA Pol II binding and initiation.

Direction of transcription (template vs coding)

RNA polymerase reads the template strand 3'→5'; the RNA transcript grows 5'→3' and mirrors the coding strand (with U instead of T).

mRNA export and translation

After processing, mature mRNA is exported to the cytoplasm for translation by ribosomes.