Transcription and RNA Processing (1B) - Bio & Biochem

1. What is the definition of an intron in a eukaryotic gene?

   A transcribed sequence removed from pre-mRNA during splicing. Introns are non-coding regions excised to join exons, allowing for mature mRNA formation in eukaryotes.

2. What is added to the $3'$ end of most eukaryotic mRNAs after cleavage, and what enzyme adds it?

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

3. What is an operon in bacteria?

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

4. What is the main functional consequence of adding a $5'$ cap to eukaryotic mRNA?

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

5. Which eukaryotic RNA polymerase transcribes most rRNA (the $28S$, $18S$, and $5.8S$ rRNAs)?

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

6. What is the typical $3'$ splice acceptor dinucleotide at the end of an intron in pre-mRNA?

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

7. What is the bacterial promoter consensus sequence located near $-35$ called?

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

8. What is the direction of RNA synthesis by RNA polymerase relative to the growing RNA strand?

   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.

9. What is the definition of an exon in a eukaryotic gene?

   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.

10. What is the DNA strand called that is directly read by RNA polymerase to make RNA?

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

11. What is the major purpose of the poly(A) tail on eukaryotic mRNA?

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

12. What is the typical $5'$ splice donor dinucleotide at the start of an intron in pre-mRNA?

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

13. What is the chemical identity of the $5'$ cap added to eukaryotic pre-mRNA?

    $7$-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.

14. Which RNA-protein complex catalyzes removal of introns from eukaryotic pre-mRNA?

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

15. Which general transcription factor binds the TATA box to initiate eukaryotic transcription?

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

16. Which bacterial transcription factor confers promoter specificity to RNA polymerase holoenzyme?

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

17. What is the name of the process in bacteria where translation begins on an mRNA while it is still being transcribed?

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

18. What is the sequence signal in eukaryotic pre-mRNA that typically triggers cleavage and polyadenylation?

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

19. Which eukaryotic RNA polymerase transcribes mRNA (protein-coding genes)?

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

20. Which eukaryotic RNA polymerase transcribes tRNA and the $5S$ rRNA?

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

21. What is the direction of RNA polymerase movement along the DNA template strand during transcription?

    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.

22. What is the bacterial promoter consensus sequence located near $-10$ called?

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

23. What is the immediate RNA product made by RNA polymerase II before processing in eukaryotes?

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

24. What is the core promoter element in many eukaryotes located about $-25$ from the start site?

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

25. What is the DNA strand called that matches the RNA sequence except that DNA has T instead of U?

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

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