Harper's Biochemistry Chapter 36 - RNA Synthesis, Processing, & Modification

Considering the intricacies of eukaryotic mRNA synthesis, which modification would MOST severely impede the transition from pre-mRNA to mature mRNA, thereby disrupting downstream cellular processes?

In a hypothetical scenario involving a novel eukaryotic cell line, researchers discover a mutation that results in a complete absence of snRNA synthesis. Based on your understanding of RNA processing, which of the following cellular outcomes would MOST immediately and directly arise from this deficiency?

If a researcher introduces a synthetic, non-hydrolyzable analog of GTP into a eukaryotic cell undergoing active mRNA transcription, which phase of transcription would be MOST directly affected, considering the known roles of GTP-dependent processes in gene expression?

Consider a eukaryotic cell line engineered to express an exogenous gene with an abnormally short poly(A) tail. Predict the MOST likely downstream consequence of this modification on the fate of the corresponding mRNA transcript.

In studying a novel regulatory mechanism in eukaryotic transcription, you identify a protein that selectively binds to a specific sequence within the primary transcript, leading to increased recruitment of decapping enzymes. Which of the following outcomes would MOST likely result from the activity of this protein?

A researcher discovers that a particular eukaryotic cell line expresses a mutant form of RNA polymerase II that is incapable of being phosphorylated on its C-terminal domain (CTD). Which of the following processes would be MOST directly impaired in these cells?

Imagine a scenario where a novel chemical compound selectively inhibits the function of the exosome complex within a eukaryotic cell. What immediate effect would this compound MOST likely have on the cellular pool of RNA transcripts?

You are investigating a rare genetic disorder characterized by the accumulation of abnormally long and improperly processed rRNA precursors within the nucleolus. Which of the following enzymatic deficiencies would MOST likely underlie this phenotype?

Upon analyzing a mutant cell line, you discover that a specific mRNA transcript exhibits significantly enhanced stability compared to its wild-type counterpart, despite no changes in its coding sequence. Further investigation reveals a disruption in the 3' UTR. Which of the following mechanisms is MOST likely responsible for the observed increase in mRNA stability?

In a study examining the dynamics of mRNA localization within a highly polarized eukaryotic cell, you observe that a particular mRNA transcript is actively transported to a specific cellular compartment via a motor protein-dependent mechanism. Disruption of which mRNA structural element would MOST directly impair this localization process?

Considering the differential transcription of genomic DNA in eukaryotes, which statement best describes the synergistic interplay between RNA polymerases and accessory factors in generating specific mRNA precursor molecules?

In mammalian mRNA-encoding genes, the presence of introns necessitates precise RNA splicing. If a mutation impairs the spliceosome's ability to differentiate between authentic and pseudo-splice sites within an mRNA precursor, what is the MOST probable outcome?

During mRNA splicing, a critical step involves the formation of a lariat structure. Which biochemical activity is MOST directly responsible for catalyzing the phosphodiester bond rearrangement that forms this structure?

A novel therapeutic approach aims to inhibit mRNA processing to suppress the expression of an oncogene. If a drug selectively inhibits the guanylyl transferase responsible for capping mRNA precursors, what downstream effect would MOST directly compromise mRNA function?

Imagine you are studying a newly discovered eukaryotic organism with a unique mRNA splicing mechanism. After performing deep sequencing of nuclear and cytoplasmic RNA, you observe that a subset of mRNAs in the cytoplasm still contains intronic sequences and lacks typical splice junctions. Furthermore, these mRNAs are efficiently translated. What is the MOST plausible explanation for this observation?

During the normal functioning of a cell, precursor mRNA molecules undergo processing to become functional mRNAs that are available for translation. What is the MOST significant impact on mRNA processing that would result from a complete loss of function of the exosome?

Consider a scenario where a novel mutation in a eukaryotic cell impairs the function of the CTD (C-terminal domain) of RNA Polymerase II (involved in coordinating mRNA processing events). Which of the following outcomes is MOST likely to be observed?

A research team discovers a novel RNA-binding protein (RBP) in mammalian cells. Experiments reveal that this RBP specifically binds to a conserved sequence element located within the 3' UTR of a subset of mRNA transcripts. Further analysis shows that overexpression of this RBP leads to increased stability and enhanced translation of its target mRNAs. Which of the listed mechanisms is MOST LIKELY to mediate the observed effects of this RBP?

A researcher is investigating the impact of alternative splicing on protein diversity in a specific tissue. Using high-throughput RNA sequencing (RNA-seq), they identify numerous instances of exon skipping, intron retention, and alternative 5' or 3' splice site selection within mRNA transcripts. However, upon closer examination, they find that a significant proportion of these alternatively spliced transcripts are rapidly degraded by cellular surveillance mechanisms and do not contribute to the proteome. What conclusion is MOST justified by these findings?

Consider a scenario in which a cell is subjected to oxidative stress. This stress triggers a signaling cascade that ultimately leads to the phosphorylation of specific splicing factors. How might this post-translational modification of splicing factors MOST directly influence gene expression in response to the stress?

In the intricate machinery of eukaryotic mRNA synthesis, consider a scenario where a novel analog of ATP is introduced, one that competitively inhibits the activity of RNA polymerase II's CTD kinase. Which of the subsequent processes would be MOST severely compromised?

Imagine a groundbreaking experiment where researchers successfully engineer a eukaryotic cell line devoid of detectable levels of U1 snRNP. Considering the established roles of snRNPs in mRNA processing, which of the following outcomes would MOST immediately and directly arise from this deficiency?

Suppose a researcher introduces a chemically modified, non-functional analog of the TATA-binding protein (TBP) into a eukaryotic cell undergoing active mRNA synthesis. Assuming this analog competitively binds to TATA boxes, which phase of transcription would be MOST directly affected?

Consider a meticulously designed experiment involving a eukaryotic cell line genetically engineered to express an exogenous gene with a mutation that prevents the addition of the 5' cap structure. Based on your understanding of mRNA processing and stability, predict the MOST likely downstream consequence of this modification on the fate of the corresponding mRNA transcript.

In the quest to decipher novel regulatory mechanisms in eukaryotic transcription, you identify a protein that selectively binds to a specific sequence within a subset of primary transcripts, leading to the enhanced recruitment of the CCR4-NOT deadenylase complex. Which of the ensuing outcomes would be MOST likely to ensue as a result of the activity of this protein?

A researcher isolates a mutant eukaryotic cell line expressing an altered form of mRNA export receptor Tap/NXF1 exhibiting impaired binding affinity for FG-nucleoporins. Which downstream effect would MOST predictably arise in these cells?

Imagine a scenario where a newly synthesized chemical compound selectively inhibits the activity of snoRNPs (small nucleolar RNAs) within a eukaryotic cell. Considering their diverse roles in guiding post-transcriptional modifications, what immediate effect would this compound MOST likely exert on the cellular pool of RNA transcripts?

You are investigating a novel genetic mutation that disrupts the function of the nuclear exosome complex within a eukaryotic cell. What immediate effect would this mutation MOST likely have on the cellular pool of RNA transcripts?

Upon analyzing a unique mutant cell line, you discover that a specific mRNA transcript coding for a crucial cell cycle regulator exhibits significantly reduced stability compared to its wild-type counterpart, despite no apparent alterations in its coding sequence. Further investigation reveals a disruption in the AU-rich elements (AREs) located in the 3' UTR of this mRNA. Which of the following mechanisms is MOST likely responsible for the observed decrease in mRNA stability?

In a meticulous study examining the dynamics of mRNA localization within a highly polarized eukaryotic cell, you observe that a particular mRNA transcript encoding a synaptic protein is actively transported to the distal dendrites via a kinesin-dependent mechanism. Perturbation of which mRNA structural element would MOST directly abrogate this localization process?

In a groundbreaking experiment, researchers synthesize a novel analog of UTP modified with a highly reactive chemical group that, upon incorporation into an elongating RNA transcript, covalently crosslinks the transcript to any proximal protein within a 5 Å radius. If this modified UTP is introduced into a eukaryotic nucleus actively undergoing transcription, which of the subsequent experimental steps would provide the MOST definitive identification of proteins directly and transiently interacting with the nascent RNA transcript during elongation?

Consider a scenario in which a previously uncharacterized nuclear exoribonuclease is discovered. This enzyme exhibits a unique substrate preference, selectively degrading RNA transcripts that have undergone extensive adenosine-to-inosine (A-to-I) editing within their 3' UTRs. Which of the following cellular consequences would MOST likely arise from the targeted inhibition of this exoribonuclease?

Imagine a scenario where a bacterial pathogen secretes a highly specific enzyme that selectively cleaves the CTD (C-terminal domain) of eukaryotic RNA polymerase II within host cells. Which of the following cellular events would be MOST immediately and severely compromised as a direct consequence of this enzymatic activity, thus disrupting the host's gene expression program?

Suppose a research team discovers a novel class of small molecule inhibitors that specifically target and disrupt the association of the U4/U6 snRNP complex within the spliceosome. What immediate effect would this class of inhibitors MOST likely have on pre-mRNA splicing?

In a synthetic biology experiment, a researcher constructs a modified mRNA molecule containing a series of tandemly repeated guanine quadruplex (G-quadruplex) structures within its 5' UTR. Assuming that these G-quadruplexes are stable and efficiently formed in vivo, which of the following outcomes would MOST likely be observed regarding the translation of this mRNA?

Consider a scenario within a eukaryotic cell where a mutation arises that completely abolishes the function of the enzyme responsible for adding the 5' cap structure to mRNA transcripts. What is the MOST likely consequence of this mutation on the stability and translatability of mRNA within this cell?

Imagine a scenario in which a researcher is investigating a novel RNA modification that alters the secondary structure of a specific subset of pre-mRNA molecules. This modification causes the affected pre-mRNAs to fold into exceptionally stable and compact tertiary structures. Which of the following splicing outcomes is MOST probable for these modified pre-mRNAs?

In a hypothetical experiment, researchers develop a method to selectively and irreversibly alkylate all adenosine residues within the poly(A) tail of mRNA molecules in vivo. What is the MOST likely downstream consequence of this alkylation on mRNA function and fate?

Consider a situation in which a cell is exposed to a sudden and drastic shift in environmental temperature, leading to widespread protein misfolding and cellular stress. This stress triggers a signaling pathway that activates a specific kinase capable of phosphorylating serine/arginine-rich (SR) proteins involved in splicing regulation. Which of the following splicing patterns would be MOST likely induced by this stress-activated kinase?

Assume a scenario in which a researcher discovers a novel eukaryotic cell line that lacks the ability to perform adenosine-to-inosine (A-to-I) RNA editing. Detailed analysis reveals that this deficiency is due to a complete absence of functional ADAR (adenosine deaminase acting on RNA) enzymes. Which of the following consequences would MOST likely arise from this ADAR deficiency in the cell line?

In a groundbreaking experiment, researchers have developed a technique to selectively inhibit the activity of all three eukaryotic RNA polymerases (I, II, and III) within a living cell. Considering the immediate and direct consequences of this inhibition, which of the following cellular processes would be the MOST rapidly and comprehensively disrupted?

A research team isolates a eukaryotic cell line exhibiting a novel mutation wherein the gene encoding the CCR4-NOT deadenylase complex is constitutively overexpressed and hyperactive. Given the complex's role in mRNA degradation, which of the following downstream effects would be MOST likely observed in this mutant cell line?

A scientist is studying a rare genetic disorder characterized by severe defects in mRNA splicing. Upon closer examination, they discover that affected individuals possess a mutation that disrupts the proper folding and assembly of the U2 snRNP. Given the role of U2 snRNP in spliceosome function, what specific consequence would MOST directly contribute to the observed splicing defects?

In the quest to engineer synthetic mRNA molecules with enhanced stability and translational efficiency for therapeutic applications, a research team synthesizes a series of modified mRNA transcripts containing various combinations of chemical modifications, structural elements, and regulatory sequences. Which of the following modifications would MOST synergistically enhance both the stability and translational efficiency of the synthetic mRNA in a mammalian cell?

A research scientist is investigating a novel class of RNA-binding proteins (RBPs) that appear to regulate mRNA stability in response to cellular stress. Using CLIP-seq (Crosslinking and Immunoprecipitation sequencing), the scientist identifies that one of these RBPs, named 'StressRBP', binds preferentially to AU-rich elements (AREs) within the 3' UTR of a specific subset of mRNAs encoding stress-response proteins. However, surprisingly, overexpression of StressRBP leads to increased, rather than decreased, stability of its target mRNAs. Which of the following mechanisms would BEST explain this paradoxical observation?

A researcher discovers a novel mutation in a eukaryotic cell line that results in the complete loss of function of the enzyme responsible for catalyzing the formation of the 7-methylguanosine (m7G) cap structure at the 5' end of mRNA transcripts. Considering the multifaceted roles of the m7G cap, which of the following cellular outcomes would MOST directly and comprehensively compromise mRNA function?

In a hypothetical scenario, researchers develop a novel class of synthetic molecules that selectively inhibit the activity of RNA helicases involved in ribosome biogenesis within the nucleolus of eukaryotic cells. Considering the critical functions of these RNA helicases, which of the following specific steps in ribosome assembly would be MOST severely impaired by these molecules?

A research team is investigating the effects of a novel chemical compound on mRNA splicing in a human cell line. They observe that treatment with the compound leads to a significant increase in the inclusion of a specific exon within a subset of mRNA transcripts. Further analysis reveals that the compound directly enhances the binding affinity of the SR protein SF2/ASF to an exonic splicing enhancer (ESE) element located within the regulated exon. Which of the following mechanisms is MOST likely responsible for the observed increase in exon inclusion?

Consider a groundbreaking study in which researchers successfully develop a CRISPR-based genome editing strategy to precisely delete all AU-rich elements (AREs) from the 3' untranslated region (UTR) of a specific mRNA transcript encoding a potent inflammatory cytokine. Assuming that the AREs normally function to promote mRNA decay, which of the following outcomes would be MOST likely observed in cells expressing the ARE-deleted mRNA?

Researchers are investigating the effects of a novel chemotherapeutic agent on mRNA processing in cancer cells. They discover that this agent selectively inhibits the activity of the DDX3 RNA helicase, which is known to play a crucial role in mRNA export from the nucleus to the cytoplasm. Given the function of DDX3, which of the following cellular outcomes would be MOST directly affected by this agent?

Within the context of eukaryotic mRNA maturation, predict the downstream consequences of a CRISPR-mediated knockout of the gene encoding the spliceosome-associated DEAD-box RNA helicase, Prp22, on global gene expression.

Considering the complexities of RNA polymerase II (Pol II) transcription termination in mammalian cells, what outcome would be MOST likely if a cell line were engineered to express a catalytically inactive version of CPSF (Cleavage and Polyadenylation Specificity Factor) that retains its RNA-binding affinity?

A research team discovers a novel cis-regulatory element within the introns of a specific set of mammalian genes. This element recruits a complex that induces local chromatin remodeling, leading to increased histone methylation and transcriptional repression. How would the disruption of this element via CRISPR-Cas9 MOST likely affect the expression of these genes?

In a scenario modeling the evolution of RNA processing mechanisms, imagine a primitive eukaryotic cell where the major pathway for mRNA degradation is dependent on a single exoribonuclease that degrades RNA from the 5' end. What adaptation would provide the GREATEST selective advantage for mRNA stability in this cellular environment?

Consider a hypothetical scenario in which a viral pathogen has evolved a mechanism to directly interfere with the host cell's mRNA splicing machinery. This virus expresses a protein that specifically binds to and inactivates the SF1 protein, a critical component of the spliceosome's commitment complex. What is the MOST likely consequence of this viral interference on host gene expression?

A researcher identifies a novel RNA-binding protein (RBP) that specifically interacts with a conserved stem-loop structure located within the 3' UTR of a subset of mRNAs encoding proteins involved in cell cycle progression. Further experiments reveal that binding of this RBP leads to translational repression of its target mRNAs under conditions of nutrient deprivation. Which mechanism is MOST likely responsible for this RBP-mediated translational control?

Imagine that you are designing a synthetic mRNA molecule for gene therapy purposes. To maximize its stability and translational efficiency within a target cell, which combination of modifications would be MOST effective, assuming the cell possesses functional RNA surveillance and degradation pathways?

A research team discovers a novel form of RNA modification in the 3' UTR of specific mRNA transcripts. This modification involves the enzymatic conversion of cytosine to 5-methylcytosine (5mC), a modification typically associated with DNA. What is the MOST plausible consequence of this RNA methylation on the fate and function of the affected mRNAs?

Consider a scenario in which a eukaryotic cell is exposed to a chemical agent that specifically inhibits the activity of the CCR4-NOT deadenylase complex. What immediate and direct effect would this agent have on the global population of mRNA molecules within the cell?

In a groundbreaking experiment, researchers develop a method to selectively and completely deplete a specific cell type of all known RNA N6-methyladenosine (m6A) demethylases (enzymes that remove m6A marks). What is the MOST likely consequence of this global m6A demethylase knockout on gene expression and cellular function within these cells?

Eukaryotic DNA-dependent RNA polymerases can independently transcribe genomic DNA without the need for accessory factors.

The majority of mammalian mRNA-encoding genes feature a continuous sequence of protein-coding regions, uninterrupted by non-coding sequences.

RNA splicing is a process that modifies precursor molecules into functional mRNAs ready for translation, and is not crucial for removing non-coding regions.

RRNAs, tRNAs and mRNAs are processed in both prokaryotes and eukaryotes.

In mammals, gene transcription is generally unaffected by hormonal as well as developmental stimuli.

RNA splicing converts end-modified precursor molecules into mRNAs that are functional for translation.

Eukaryotic mRNA encoding genes possess no similarities to their prokaryotic counterparts.

Introns are protein coding sequences.

Altered rates of protein synthesis can arise from mRNA processing events.

RRNAs are never processed and modified.

RNA synthesis in eukaryotes depends solely on a single type of DNA-dependent RNA polymerase.

Initiation, elongation, and termination are the primary stages involved in synthesizing a primary transcript.

Regions of DNA upstream from the initiation site and protein factors regulate the termination of transcription.

All RNA molecules have the same lifespan within a cell.

Errors in mRNA processing cannot lead to disease.

Eukaryotic cells possess two major classes of RNA: protein-coding RNAs (mRNAs) and non-coding RNAs.

Ribosomal RNAs (rRNAs) constitute approximately 80% of the total RNA in a cell and are highly unstable.

Transfer RNAs (tRNAs) represent a minor fraction (less than 1%) of the total RNA within the cell.

Messenger RNA molecules are synthesized directly in their mature, active form.

Variations in gene expression allow organisms to adapt to environmental changes.

Match the RNA type with its function:

Match the term with its description:

Match the RNA type with its approximate percentage of total RNA in eukaryotic cells:

Match the enzyme with its role in RNA synthesis:

Match the step with its role in mRNA processing:

Match the term with its description in the context of RNA synthesis:

Match the feature with its location:

Match the RNA class with its general stability:

Match the following RNA types with their function:

Match the terms related to gene expression with their function: