MCAT Biological and Biochemical Foundations of Living Systems Flashcards: 1b Transcription Rna Processing

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This deck focuses on 1b Transcription Rna Processing, giving you a quick way to review the definitions, rules, and examples that matter most for MCAT Biological and Biochemical Foundations of Living Systems.

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Work through these flashcards in short sessions. Try to answer each prompt before flipping the card, then revisit any cards you miss until the explanation feels automatic.

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

Answer: 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.

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

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

Flashcard 3: What is an operon in bacteria?

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

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

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

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

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

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

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

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

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

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

Answer: 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.

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

Answer: 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.

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

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

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

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

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

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

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

Answer: $7$-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.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Answer: 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.

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

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

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

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

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

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

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

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