Ch. 38: RNA Processing in Eukaryotes

heterogenous nuclear RNA (hnRNA)

all RNA in the nucleus

messenger RNA (mRNA)

intermediate that carries genetic information from DNA to ribosomes for protein production, heterogenous in size and base composition, comprises 5% of RNA in cell, made by RNA pol. II

transfer RNA (tRNA)

decodes mRNA to protein by specifying which codon corresponds to which amino acid, transfers amino acids onto growing protein chain during translation, forms secondary structure, made by RNA pol. III

ribosomal RNA (rRNA)

structural and catalytic component of the ribosome (60%) that binds mRNA and recruits tRNA, most abundant type of RNA in cell, site of translation, made by RNA pol. I

small nucleolar RNA (snoRNA)

part of a complex involved in rRNA processing

small nuclear RNA (snRNA)

structural component of spliceosomes, needed for mRNA processing

microRNA (miRNA)

short, single-stranded RNA (=20 nucleotides) that block expression of complementary mRNA to regulate gene expression

RNA processing

the molecular events that allow primary RNA transcripts (pre-RNA) to become mature RNA that the cell can use

rRNA processing

small nucleolar ribonucleoproteins (snoRNPs) modify some of the nucleotides to make them more stable by methylating them, then the 45S precursor is cleaved so only the modified regions remain

tRNA processing

endonuclease removes nucleotides from 5’ end, 3’ trailer sequence removed by exonuclease, tRNA nucleotidyl transferase adds CCA to 3’ end, intron removed by endonuclease and products are joined by ligase to create the anti codon

carboxy-terminal domain (CTD)

what coordinates splicing and transcription

7-methyl guanosine cap (m⁷G)

protects mRNA from degradation by exonucleases, required for splicing of 1st intron, and site of binding for translation

phosphohydrolase

removes a phosphate at the 5’ end of mRNA

guanalyltransferase

attaches a guanine monophosphate group (from GTP) at the 5’ end, “upside-down”

the N-7 base, and the 2’ OH groups on 1st few riboses

which portions of the 5’ cap are methylated

polyA tail

250 adenosine residues added to 3’ end of mRNA to increase time required for nucleases to reach coding regions

splicing

utilizes spliceosomes (snRNPs and >150 proteins) to remove introns and join exons, happens as mRNA is made not sequentially

functions of introns

regulate gene expression (enhancers), involved in alternative splicing, generates miRNA to regulate transcription, sites for RNA-binding proteins, pace cellular functions

5’ end of intron-exon junction

contains sequence ^5’AGGUAAGU^3’ with the first GU from the 5’ end marking beginning of first intro

3’ end of intron-exon junction

marked by stretch of pyrimidines/pyrimidine tract (Py)_n followed by any base, a C, and then the intron ends with AG

branch site of intron

located 20-50 nucleotides away from the 3’ end of the intron, site of the first transesterification reaction

spliceosomes

small nuclear ribonuclear protein complexes (snRNPs) that associate with the pre-mRNA

catalytic snRNAs

U2 and U6 facilitate transesterification reactions that remove introns and join exons

first transesterification reaction

catalytic core (U2 and U6 snRNPs) catalyzes this between 5’ end of intron and branch point adenosine, creating lariat structure

lariat structure

loop of intron formed from branch point A + G transesterification

second transesterification reaction

U2, U6 and U5 leads to this reaction between 3’ end of first exon and the 5’ end of second exon, releasing lariat intron, spliced exon, and snRNPs

de-branching enzyme

linearizes lariat intron

splice variants

when splicing is regulated to create alternative forms of protein, pre-mRNA is spliced in different patterns, important for protein diversity

RNA editing

changes the proteins encoded by mRNA by deaminating cytosine to uracil which generates a stop codon

tRNA acceptor stem

the site where the amino acid is covalently attached to the tRNA on the adenosine (of CCA) at the 3’ end of this stem

anticodon arm

contains 3 base sequence that binds to the complementary codon in the mRNA

inosine

a deamination of guanine that can baypically found in the anticodon arm, used to stabilize tRNA