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Questions and Answers
What is the primary function of RNA?
Which type of RNA is primarily responsible for bringing amino acids to the ribosome?
Where is rRNA primarily produced?
What is the typical lifespan of mRNA in prokaryotes?
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Which component differentiates uracil from thymine?
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What type of bonding holds the primary structure of RNA together?
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Which statement about mRNA in eukaryotes is correct?
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Which structural feature is a unique characteristic of RNA?
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Which RNA polymerase is responsible for synthesizing mRNA precursors?
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What is the approximate range of base pairs upstream of the transcriptional start site that the core promoter includes?
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Which transcription factor is specifically characterized by its binding to the TATA box?
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What component of TFIIH is involved in separating DNA strands during transcription?
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What is one role of the kinase subunit of TFIIH during transcription?
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How are RNA strands synthesized during transcription?
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Which of the following is NOT one of the precursors used in RNA synthesis?
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What percentage of human genes possess a TATA box?
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What is the primary distinction between transcription in prokaryotes and eukaryotes?
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Which of the following processes is involved in the modification of mRNA in eukaryotic cells?
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What initiates transcription in both prokaryotes and eukaryotes?
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What role does the sigma (σ) subunit play in prokaryotic transcription?
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What is the composition of RNA polymerase in Escherichia coli?
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Which statement is true about mRNA produced in prokaryotic cells?
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What forms the initiation bubble during transcription?
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Which of the following best describes the process of transcription initiation in eukaryotes?
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What is the relationship between the template strand of DNA and RNA during transcription?
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What primarily distinguishes Rho-dependent termination from Rho-independent termination?
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What is a characteristic error rate of RNA polymerase compared to DNA polymerase III?
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In the context of transcription termination, what is a function of the Rho protein?
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What structural feature is commonly found in the terminator region that aids in transcription termination?
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What happens during Rho-independent transcription termination?
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Which strand serves as a template for RNA synthesis?
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What is the main structural consequence of the stem-loop formation during RNA transcription termination?
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What is the primary function of the Rho factor during transcription?
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Which proteins are responsible for binding to the termination sequences in eukaryotic mRNA processing?
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What is the purpose of adding a polyA-tail to mRNA?
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What role do spliceosomes play in mRNA processing?
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How does post-transcriptional processing differ in prokaryotes compared to eukaryotes?
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What does the addition of a modified guanine nucleotide to the 5’ end of mRNA accomplish?
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Which of the following statements about the role of exonucleases in mRNA synthesis is true?
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Study Notes
RNA Function
- RNA primarily functions in protein synthesis through translation.
- Carries genetic information read by ribosomes to produce proteins.
- Three main types:
- mRNA: Transfers information for protein synthesis, rapidly degraded by nucleases.
- rRNA: Forms the structural components of ribosomal subunits, possesses peptidyl transferase activity. Highly stable, comprises the majority of cellular RNA.
- tRNA: Transports amino acids to the ribosome, highly stable.
- Other RNA functions include RNA editing, gene regulation, and RNA interference.
rRNA Production
- Synthesized in the nucleolus.
- rRNA transcription influences DNA structure.
- Genes responsible for rRNA are continuously transcribed, residing in a region of the chromosome that is less tightly compacted.
RNA Structure
- RNA contains ribose as its sugar molecule.
- Contains uracil instead of thymine, differing by a methyl group.
- Uracil pairs with adenine alongside thymine.
- Typical size ranges from 60 to 20,000 bases.
- Can form double helix structures.
- RNA strands can fold back on themselves, forming short, antiparallel double-helical segments, creating "stems" (base-paired portions) and "loops" (unpaired portions).
- Hybridization: RNA can pair with DNA to form DNA-RNA hybrids.
- Prokaryotes vs. Eukaryotes:
- In prokaryotes, mRNA has a shorter lifespan (about 3 minutes), leading to rRNA comprising over 80% of bacterial RNA, and mRNA constituting about 3%.
- Most human mRNAs persist for 1 to 10 hours.
- Prokaryotic mRNA can code for multiple proteins.
Primary RNA Structure
- Nucleotides linked by 5'-3' phosphodiester bonds between ribose sugars.
- Ribose has a molecular formula of C5H10O5, with a predominant D-ribose form and a less common L-ribose form.
Secondary and Tertiary RNA Structures
- Base pairing through hydrogen bonds forms the foundation of RNA's secondary structure.
- RNA tertiary structure results from folding, yielding a three-dimensional shape consisting of helices and grooves.
DNA Transcription: Overview
- Significant differences exist in transcription between prokaryotes and eukaryotes:
- Location: Prokaryotic transcription occurs in the cytoplasm, while eukaryotic transcription takes place in the nucleus.
- DNA Accessibility: Prokaryotic DNA is more accessible to RNA polymerase compared to eukaryotic DNA. Eukaryotic DNA is wrapped around histones to form nucleosomes and further packed into chromatin.
- mRNA Modification: Prokaryotic mRNA is not modified after transcription; eukaryotic mRNA undergoes RNA splicing, 5' capping, and poly A tail addition.
Pre-initiation of Transcription
- RNA polymerase and cofactors (general transcription factors) bind to DNA, unwinding it to create an initiation bubble.
- This bubble exposes a single DNA strand, permitting RNA polymerase access. Approximately 14 to 17 base pairs are exposed at a time.
Initiation of Transcription in Prokaryotes
- Begins with RNA polymerase binding to the promoter region of DNA.
Initiation of Transcription in Eukaryotes
- More complex; mediated by transcription factors that facilitate RNA polymerase binding and initiation.
Sigma Subunit in Prokaryotic Transcription
- RNA polymerase synthesizes RNA from DNA.
- Genes start with a promoter sequence, which RNA polymerase initially identifies.
- Bacterial RNA polymerase consists of a core enzyme (α2ββ′ω) and a loosely attached sigma (σ) subunit.
- σ subunit recognizes the promoter, while the core enzyme synthesizes RNA.
- Sigma factors determine the specificity of promoter DNA binding and RNA synthesis initiation.
- The first discovered sigma factor was sigma70 (σ70) in Escherichia coli.
- RNA polymerase exists in two forms:
- Core polymerase (α2ββ'ω) can inefficiently and nonspecifically transcribe DNA.
- Holoenzyme (α2ββ’σω70), formed when the sigma subunit (σ70) adds to the core polymerase, enables specific promoter binding and efficient transcription initiation.
RNA Polymerase in Eukaryotes
- RNA polymerase I: Synthesizes the precursor of 5.8S, 18S, and 28S rRNA in the nucleolus.
- RNA polymerase II: Synthesizes mRNA precursors.
- RNA polymerase III: Synthesizes small RNAs, including tRNAs and 5S rRNA.
Eukaryotic Promoters
- Highly variable.
- The core promoter consists of 30 to 40 base pairs upstream of the transcriptional start site, serving as an assembly point for general transcription factors, functionally analogous to the bacterial σ subunit.
- These factors are named TF (transcription factor), followed by the RNA polymerase number and an identifying letter.
- RNA polymerase must bind to the promoter-associated transcription factors before transcription can begin.
- A key promoter element is the TATA box (consensus TATAAAA), located 25 to 30 base pairs upstream of the start site.
- Transcription factors assemble on TATA box-containing promoters in a specific order:
- TATA-binding protein (TBP) binds to the TATA box. TBP comprises one subunit of transcription factor IID (TFIID).
- TBP-associated factors (TAFs) assemble on TBP while it's bound to the TATA box.
- Additional transcription factors join the complex.
- TFIIH, composed of ten subunits, including ATP-dependent helicases and a protein kinase, is essential for the complex.
- Transcription commences when RNA polymerase II binds to the assembled transcription factors.
- TFIIH's helicase components separate DNA strands during transcription, while its kinase subunit phosphorylates RNA polymerase II on multiple serine and threonine residues.
- Phosphorylated RNA polymerase attracts proteins required for elongation and mRNA modification.
Alternative Promoter Assembly
- Less than 10% of human genes possess a TATA box; alternative preinitiation complex assembly mechanisms exist:
- Certain TAFs bind to both TBP and promoter elements other than the TATA box.
DNA to RNA Transcription: Elongation
- RNA synthesis proceeds in a 5' to 3' direction.
- ATP, GTP, CTP, and uridine triphosphate (UTP) serve as precursors.
- RNA polymerase does not require a primer.
- Initiates a new chain by positioning the first nucleotide.
- The template DNA strand is antiparallel and complementary to the RNA transcript.
- The coding strand is identical to the RNA transcript (with uracil replaced by thymine).
- RNA polymerase lacks proofreading nuclease activity.
- Error rate is approximately 1:10,000, significantly higher than DNA polymerase III.
- Template strand = antisense = plus = noncoding strand.
- Non-template strand = sense = minus = coding strand.
Termination of Transcription in Prokaryotes
- Two primary mechanisms: Rho-dependent and Rho-independent.
Rho-Independent Termination
- Transcription continues until encountering a terminator sequence.
- Most terminators contain a palindrome, a sequence reading the same forward and backward, like "Madam, I'm Adam."
- Upon transcription, the palindrome forms a stem-loop structure in the RNA transcript due to internal base pairing, causing RNA polymerase to dissociate from the template and release the RNA transcript.
- The terminator region typically contains an inverted repetitive pattern followed by an adenine-rich region (AAAA).
- The inverted repeat sequence allows hydrogen bonding to create a hairpin loop structure, halting RNA polymerase activity.
- A U-rich region follows the hairpin loop, where weak interactions occur between the U bases of the transcript and A bases of the template.
- These interactions destabilize the RNA-DNA hybrid, causing separation and termination.
- No energy requirement.
Rho-Dependent Termination
- One of the two mechanisms for prokaryotic transcription termination.
- Involves the Rho factor protein, which possesses helicase activity.
- The Rho protein binds to the RNA transcript and moves alongside RNA polymerase in a 5'-3' direction.
- This movement facilitates the breaking of hydrogen bonds between the DNA template and the RNA transcript.
- As Rho factor approaches the transcription bubble, it separates the DNA-RNA hybrid, releasing the transcript and terminating transcription.
Eukaryotic Transcription Termination
- Termination sequences at the end of mRNA attract proteins (CPSF and CstF), forming a loop.
- Two enzymes (CF1 and CF2) bind, cleaving the RNA strand.
- PolyA polymerase (PAP) adds a polyA tail, a series of adenine nucleotides, to the cleaved 3' end, stabilizing it with polyA binding proteins (PABP).
- A polyA tail of 50 to 250 adenines is added.
- Exonucleases degrade the remaining mRNA being synthesized, outpacing synthesis and ensuring complete termination.
- The 5' cap and polyA tail interact via associated proteins, forming a loop.
Modifying RNA after Transcription
- Chemical modifications after transcription are known as post-transcriptional processing.
- Prokaryotic mRNA rarely undergoes processing due to the immediate initiation of translation.
- Eukaryotic mRNA undergoes extensive processing:
- Intron removal: Introns are non-coding sequences removed from the mRNA. Exons, the coding sequences, remain.
- 5' capping and 3' polyA tail addition: These modifications protect the mRNA from nucleases, guide mRNA into the cytoplasm and to ribosomes, and regulate translation initiation.
- Post-transcriptional processing occurs during transcription, initiated by proteins recruited by phosphorylated RNA polymerase.
- 5' capping: A modified guanine nucleotide is attached in a reverse orientation to the 5' end of the mRNA. This cap protects the mRNA from 5'-exonucleases, assists in nuclear export, ribosomal binding, and translation initiation.
- Intron removal (splicing): Introns are removed by spliceosomes, complexes containing five small RNAs (U1, U2, U4, U5, and U6) and associated proteins, forming small nuclear ribonucleoprotein particles (snRNPs). Approximately 50 proteins participate in splicing.
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Description
This quiz explores the essential functions of RNA in protein synthesis, including the roles of mRNA, rRNA, and tRNA. It also covers the biochemical structure of RNA, comparing it to DNA and highlighting its unique components. Test your understanding of RNA synthesis and its various functions in the cell.
