In eukaryotes, when does RNA processing occur relative to transcription?
It can happen both during transcription (co-transcriptional) and after termination (post-transcriptional).
Why do transcription and translation not occur simultaneously in eukaryotes?
There is spatial separation between the nucleus (transcription) and cytoplasm (translation), allowing for additional RNA processing to occur.
What are the three major ways eukaryotic pre-mRNA is processed before nuclear export?
Transcripts are capped at the 5’ end, introns are removed by splicing, and 3’ ends are cleaved and polyadenylated.
What part of RNA Polymerase II is required for recruiting factors for capping, splicing, and 3’-RNA processing?
The C-terminal domain (CTD) tail.
The _____ of the CTD in each heptapeptide repeat is required for transcript elongation and recruitment of processing factors.
phosphorylation
What general term describes the collection of all transcripts made by RNA Polymerase II in the nucleus?
Heterogeneous Nuclear RNA (hnRNA).
What is the name of the complex formed when hnRNA is covered with proteins during transcription?
Heterogeneous nuclear ribonucleoprotein (hnRNP).
What unique structural feature characterizes the 5’ 7-methylguanosine cap on eukaryotic RNAPII transcripts?
A 5’ to 5’ triphosphate linkage of 7-methylguanosine to the initial nucleotide of the RNA.
List two critical functions of the 5’ cap on eukaryotic mRNA.
It protects the mRNA from 5’-exoribonuclease degradation and stimulates translation.
At what point during transcription is the 5’ cap added to the nascent RNA chain?
It is added soon after RNAPII starts transcription, when the chain is about 20-30 nucleotides long.
Which enzyme removes the terminal γ-phosphate from the 5’ end of the growing RNA chain during the first step of capping?
RNA triphosphatase.
Which enzyme attaches GMP from GTP to the diphosphate at the 5’ end of the RNA, forming the 5’→5’ linkage?
RNA guanylyltransferase.
Which enzyme adds a methyl group to position 7 of the capping guanine nucleotide?
RNA (guanine-7) methyltransferase.
mRNA 3’ ends are produced by cleavage of the pre-mRNA between a conserved AAUAAA element and a _____ element.
G/U-rich sequence
What protein complex recognizes and binds to the AAUAAA polyadenylation signal on pre-mRNA?
Cleavage and polyadenylation specificity factor (CPSF).
What protein complex binds to the G/U-rich sequence downstream of the poly(A) site to aid in cleavage?
Cleavage stimulation factor (CstF).
What is the canonical polyadenylation signal (PAS) sequence found in most eukaryotic pre-mRNAs?
5’-AAUAAA-3’
How does the poly(A) tail protect mRNA from degradation?
It serves as a binding site for cytoplasmic poly(A)-binding protein I (PAB I), which resists 3’-exonuclease action.
Which enzyme is responsible for adding the adenine nucleotides to form the poly(A) tail?
Poly(A) polymerase (PAP).
The initial, slow phase of polyadenylation adds about 12 nucleotides. What protein is required for the subsequent rapid phase of polyadenylation?
Nuclear poly(A) binding protein II (PABII).
What is the ‘allosteric model’ of transcription termination?
It proposes that transcription through the PAS causes a conformational change in RNAPII, reducing its processivity and promoting termination.
What is the ‘torpedo model’ of transcription termination?
It proposes that after RNA cleavage, a 5’-3’ exoribonuclease degrades the remaining nascent RNA and collides with RNAPII, dislodging it.
What are the non-coding sequences within a gene that are removed from pre-mRNA during processing?
Introns.
What are the coding sequences within a gene that are joined together after splicing to form mature mRNA?
Exons.
