Transcription and RNA Processing (1B) - MCAT Biological and Biochemical Foundations of Living Systems

A sequence retained in mature mRNA after splicing (may be coding or UTR). Exons contain the sequences that form the final mRNA, including coding regions and untranslated regions.

RNA is synthesized in the $5' \to 3'$ direction. RNA polymerase adds nucleotides to the 3' end of the growing chain, ensuring antiparallel synthesis complementary to the template.

RNA polymerase moves along the template $3' \to 5'$. This direction allows the enzyme to read the template and synthesize RNA in the 5' to 3' direction antiparallel to it.

Template (antisense) strand. It serves as the direct template for RNA synthesis, with complementary base pairing to the nascent RNA strand.

Coding (sense, non-template) strand. It has the same sequence as the RNA (with T for U), not used as the template during transcription.

Pre-mRNA (primary transcript, hnRNA). This unprocessed RNA includes introns and requires capping, splicing, and polyadenylation to become mature mRNA.

RNA polymerase II. It is specialized for transcribing genes that code for proteins, distinguishing it from polymerases for rRNA and tRNA.

RNA polymerase I. It primarily synthesizes ribosomal RNA components essential for ribosome assembly in the nucleolus.

RNA polymerase III. It is responsible for small RNA molecules involved in translation and ribosome function.

TATA box. This AT-rich sequence helps position RNA polymerase II at the transcription start site in eukaryotic promoters.

Pribnow box ($-10$ element). This TATAAT consensus sequence is crucial for promoter recognition and initiation of transcription in bacteria.

Spliceosome (snRNP-containing complex). The spliceosome uses snRNPs to recognize splice sites and catalyze intron removal via transesterification.

$-35$ element (recognition site for sigma factor). This TTGACA sequence is recognized by the sigma factor to facilitate RNA polymerase binding in prokaryotes.

GU (in RNA; GT in DNA). This conserved sequence marks the intron-exon boundary, facilitating recognition by the spliceosome.

Sigma ($\sigma$) factor. It associates with core RNA polymerase to recognize specific promoter sequences and initiate transcription.

TATA-binding protein (TBP) within TFIID. TBP binds the TATA box, recruiting other factors to assemble the preinitiation complex for transcription.

Coupled transcription and translation. In prokaryotes, the absence of a nucleus allows ribosomes to attach to nascent mRNA during ongoing transcription.

Multiple genes transcribed as one polycistronic mRNA. Operons enable coordinated regulation of related genes by transcribing them into a single mRNA in prokaryotes.

$7$-methylguanosine linked by a $5'\text{–}5'$ triphosphate. This modified guanosine cap is added co-transcriptionally to protect the 5' end of eukaryotic pre-mRNA.

Protects mRNA and promotes translation initiation and export. The cap shields mRNA from degradation, facilitates nuclear export, and aids ribosome binding for translation.

AAUAAA polyadenylation signal. This consensus sequence recruits cleavage factors to cut the pre-mRNA downstream, enabling polyadenylation.

Poly(A) tail added by poly(A) polymerase. After cleavage at the polyadenylation site, poly(A) polymerase adds adenine residues enzymatically without a template.

AG (in RNA; AG in DNA). This dinucleotide signals the end of the intron, enabling precise ligation of exons during splicing.

Increases mRNA stability and enhances translation efficiency. The tail protects against exonucleases and interacts with initiation factors to improve translation rates.