Case-Based MCQs on RNA Structure and Function: Test Your Knowledge

Case 1: RNA Virus Mutation

A researcher is studying a new RNA virus. Unlike DNA viruses, RNA viruses mutate more rapidly. The researcher finds that this rapid mutation is linked to the virus’s single-stranded RNA structure.

Question 1:
Why does the single-stranded nature of RNA contribute to the high mutation rate in RNA viruses?

A) RNA lacks a complementary strand for error correction during replication
B) RNA is inherently unstable and cannot carry genetic information accurately
C) RNA viruses mutate because they do not have a genetic code
D) RNA is double-stranded in viruses, which causes frequent mutations
E) RNA contains thymine instead of uracil, leading to replication errors

Correct Answer: A

Explanation: Unlike DNA, which has a complementary strand that allows for error-checking mechanisms (such as DNA polymerase proofreading), single-stranded RNA lacks this redundancy. RNA-dependent RNA polymerases (RdRp) used by RNA viruses lack proofreading ability, leading to frequent mutations. This is why RNA viruses, like influenza and SARS-CoV-2, evolve quickly.

Case 2: RNA Folding and Function

A molecular biologist is analyzing an RNA molecule involved in enzyme-like activity. Although RNA is single-stranded, the molecule has folded into a complex 3D shape.

Question 2:
What allows single-stranded RNA to fold into complex structures despite not being double-stranded like DNA?

A) RNA molecules always remain linear and do not fold
B) RNA can form internal base-pairing interactions, such as hairpin loops
C) RNA is unstable and breaks apart instead of folding
D) RNA folds only when it binds to DNA to form a hybrid structure
E) RNA folding is only possible in viruses, not in normal cells

Correct Answer: B

Explanation: The single-stranded nature of RNA allows it to fold into complex secondary and tertiary structures through intramolecular base pairing (e.g., hairpin loops, stem-loops). This folding is crucial for its function, as seen in ribosomal RNA (rRNA) and catalytic RNA molecules like ribozymes, which play structural and enzymatic roles in the cell.

Case 3: RNA in Gene Regulation

A team of geneticists is studying microRNA (miRNA), a type of RNA that plays a role in gene regulation. They observe that miRNA binds to messenger RNA (mRNA) and prevents the production of certain proteins.

Question 3:
How does the single-stranded structure of RNA contribute to its role in gene regulation?

A) It allows RNA to form complementary base pairs with mRNA to regulate gene expression
B) RNA’s single-stranded nature prevents it from interacting with other molecules
C) Single-stranded RNA is unable to fold into regulatory structures
D) RNA’s single-stranded nature makes it too unstable to participate in gene regulation
E) RNA cannot interact with mRNA because it lacks a double-stranded structure

Correct Answer: A

Explanation: MicroRNAs (miRNAs) and small interfering RNAs (siRNAs) bind to complementary sequences on mRNA due to their single-stranded nature, allowing them to silence genes by preventing translation or triggering degradation. This is a key process in RNA interference (RNAi) and post-transcriptional gene regulation.

Case 4: Ribosomal RNA and Protein Synthesis

A student is analyzing ribosomal RNA (rRNA) and notices that, despite being single-stranded, rRNA has a complex, stable three-dimensional structure within ribosomes.

Question 4:
Why is the single-stranded structure of rRNA important for protein synthesis?

A) It allows rRNA to form a rigid, double-helix structure similar to DNA
B) rRNA can fold into functional secondary and tertiary structures for ribosome assembly
C) The single-stranded nature of rRNA prevents it from interacting with ribosomal proteins
D) Single-stranded rRNA is only important for viral replication, not protein synthesis
E) The ribosome requires a single-stranded rRNA to avoid binding with transfer RNA (tRNA)

Correct Answer: B

Explanation: The single-stranded nature of rRNA allows it to fold into intricate shapes, forming the core structural and catalytic components of ribosomes. This enables ribosomes to bind mRNA, coordinate tRNA positioning, and catalyze peptide bond formation, making protein synthesis possible.

Case 5: RNA Stability and Function

A pharmaceutical company is developing RNA-based drugs, such as mRNA vaccines. However, they find that RNA degrades quickly in the body, requiring modifications to increase its stability.

Question 5:
Why is single-stranded RNA more prone to degradation than double-stranded DNA?

A) RNA contains thymine, which makes it unstable in the cellular environment
B) RNA is attacked by ribonucleases (RNases) due to its exposed single strand
C) RNA does not degrade easily and is more stable than DNA
D) The single-stranded structure of RNA prevents it from being recognized by enzymes
E) RNA molecules are always found in a protected environment and never degrade

Correct Answer: B

Explanation: Unlike DNA, single-stranded RNA is more exposed to enzymatic attack by ribonucleases (RNases), which rapidly degrade RNA in the cell. Additionally, RNA contains ribose sugar, which has an extra hydroxyl (-OH) group at the 2′ position, making it chemically more reactive and prone to hydrolysis. Chemical modifications (e.g., in mRNA vaccines) can be used to protect RNA from rapid degradation to improve stability.

Case 6- Eukaryotic mRNA and the 7-methylguanosine triphosphate cap

A researcher is studying the modifications of eukaryotic mRNA and notices that a 7-methylguanosine triphosphate cap is added to the 5′ end.

What is the primary function of this 5′ cap?

A) It prevents the mRNA from folding into secondary structures
B) It enhances mRNA stability and protects it from exonuclease degradation
C) It marks the mRNA for rapid degradation in the cytoplasm
D) It serves as a termination signal during transcription
E) It prevents ribosomes from binding to the mRNA for translation

Correct Answer: B

Explanation: The 5′ cap (7-methylguanosine triphosphate cap) is essential for mRNA stability and protects it from exonuclease degradation. It also facilitates ribosome recognition and translation initiation in eukaryotic cells. Without this modification, mRNA would degrade rapidly.

Case 7: Capping and Tailing in Prokaryotes vs. Eukaryotes

A scientist compares eukaryotic and prokaryotic mRNA processing. She finds that while eukaryotic mRNA undergoes capping and tailing, bacterial mRNA lacks these modifications.

Why do prokaryotic mRNAs not require capping and tailing?

A) Prokaryotic mRNAs are stable and do not degrade easily
B) Prokaryotic transcription and translation occur simultaneously, reducing the need for protection
C) Prokaryotic mRNAs are always double-stranded, preventing degradation
D) The ribosome in prokaryotes does not require a 5′ cap for translation
E) Prokaryotic mRNA uses poly-G tailing instead of poly-A tailing

Correct Answer: B

Explanation: In prokaryotes, transcription and translation occur simultaneously (coupled transcription-translation), meaning mRNA does not need additional stability mechanisms like 5′ capping and poly-A tailing. Instead, bacterial mRNA has a shorter half-life and is rapidly degraded once its function is complete.

Case 8: mRNA Vaccines and Capping Efficiency

A pharmaceutical company is developing an mRNA-based vaccine for a viral infection. During clinical trials, researchers observe that certain vaccine formulations result in low protein expression and rapid degradation of the mRNA inside cells. Further analysis reveals that these formulations contain mRNA with an improperly added 5′ cap.

Which of the following best explains why an incomplete or missing 5′ cap leads to poor protein expression?

A) The mRNA is unable to leave the nucleus and remains trapped inside
B) The ribosome cannot efficiently bind to the mRNA for translation initiation
C) The poly-A tail compensates for the missing 5′ cap, so translation is unaffected
D) mRNA without a cap gets rapidly translated but forms non-functional proteins
E) Capping is only required in bacterial mRNA, not human mRNA

Correct Answer: B

Explanation: The 5′ cap (7-methylguanosine triphosphate cap) is essential for translation initiation because it serves as a recognition site for eukaryotic initiation factors (eIFs) and ribosomes. If the cap is missing or incomplete, the mRNA is not recognized efficiently by the ribosome, leading to poor translation and reduced protein expression, which is critical for mRNA vaccine efficacy.

Case 9: Cancer Therapy and Poly-A Tail Length

A cancer researcher is investigating mRNA stability in tumor cells and finds that certain oncogenes (cancer-causing genes) have mRNAs with unusually long poly-A tails. The researcher hypothesizes that this modification contributes to increased oncogene expression and tumor progression.

Why would an abnormally long poly-A tail lead to higher oncogene expression in cancer cells?

A) Longer poly-A tails protect mRNA from degradation, allowing prolonged translation
B) Longer tails cause mRNA to be rapidly degraded, preventing tumor growth
C) The poly-A tail serves as a binding site for tumor-suppressor proteins
D) Poly-A tails block the ribosome from translating oncogenic proteins
E) Poly-A tail length does not affect oncogene expression in cancer cells

Correct Answer: A

Explanation: The poly-A tail at the 3′ end of mRNA enhances stability and prevents premature degradation by exonucleases. In cancer, longer poly-A tails extend mRNA half-life, allowing continuous oncogene translation, which contributes to uncontrolled cell growth and tumor progression. Targeting poly-A tail length has been explored as a potential cancer therapy.

Case 10: Genetic Disease and mRNA Processing Defects

A child presents with developmental delays, immune dysfunction, and recurrent infections. Genetic sequencing reveals a mutation in a gene encoding an enzyme involved in mRNA capping. Laboratory tests show that the patient’s cells produce unstable mRNA, leading to defective protein synthesis.

Which of the following best explains how a mutation in mRNA capping enzymes could contribute to the patient’s symptoms?

A) Uncapped mRNA degrades rapidly, reducing essential protein levels needed for normal function
B) The mutation prevents mRNA from being translated entirely, halting all protein production
C) Uncapped mRNA leads to excessive immune activation and autoimmune disease
D) Cells produce an excess of non-functional capped mRNA, leading to toxic protein buildup
E) The mutation affects only mitochondrial mRNA, leaving nuclear mRNA translation intact

Correct Answer: A

Explanation: The 5′ cap protects mRNA from degradation and promotes translation. A mutation in capping enzymes results in uncapped or improperly capped mRNA, leading to rapid degradation and reduced protein synthesis. This can disrupt immune function, development, and metabolic processes, contributing to genetic disorders and immune deficiencies.

Case 11: tRNA Mutations and Protein Synthesis Disorders

A patient presents with muscle weakness, lactic acidosis, and neurological abnormalities. Genetic testing reveals a mutation in a mitochondrial tRNA gene affecting its structure and function. The doctor suspects a mitochondrial disease.

How does a mutation in tRNA contribute to mitochondrial disorders?

A) tRNA mutations impair ribosomal RNA synthesis, preventing translation
B) Defective tRNA reduces the efficiency of protein synthesis in mitochondria
C) Mutated tRNA only affects nuclear-encoded proteins, not mitochondrial proteins
D) tRNA mutations cause excess protein production, leading to cell toxicity
E) Mitochondrial tRNA is not essential for cellular function

Correct Answer: B

Explanation: Mitochondria have their own tRNA molecules, which are essential for translating mitochondrial-encoded proteins. Mutations in mitochondrial tRNA genes can impair protein synthesis, reducing energy production (ATP) and leading to mitochondrial disorders like MELAS (Mitochondrial Encephalopathy, Lactic Acidosis, and Stroke-like episodes).

Case 12: Chemotherapy and tRNA Function

A cancer patient is undergoing chemotherapy with a drug that inhibits tRNA charging (aminoacylation), preventing tRNA from binding to amino acids. The patient develops severe side effects, including anemia and muscle wasting.

Why does inhibiting tRNA charging lead to these clinical symptoms?

A) Uncharged tRNA molecules block ribosome function, halting protein synthesis
B) The drug directly destroys ribosomes, preventing translation
C) tRNA is only needed for non-essential proteins, so the drug should not cause side effects
D) The inhibition affects only viral protein synthesis, not human cells
E) Cells compensate by increasing tRNA production, preventing major effects

Correct Answer: A

Explanation: Aminoacyl-tRNA synthetases charge tRNA molecules by attaching amino acids to them. If this process is blocked, tRNA cannot deliver amino acids to the ribosome, halting translation and leading to reduced protein synthesis. This explains the side effects, as actively dividing cells (e.g., in the bone marrow and muscles) require continuous protein production.

Case 13: tRNA and Antibiotic Action

A bacterial infection is being treated with an antibiotic that specifically binds to the A-site of the bacterial ribosome, preventing tRNA from delivering amino acids.

How does this antibiotic stop bacterial growth?

A) It blocks ribosomal RNA synthesis, preventing ribosome formation
B) It prevents tRNA from entering the ribosome, stopping protein elongation
C) It destroys bacterial DNA, preventing transcription
D) It causes excessive tRNA function, leading to toxic protein buildup
E) It selectively degrades bacterial tRNA molecules

Correct Answer: B

Explanation: Some antibiotics, like tetracyclines, bind to the A-site of the ribosome, preventing aminoacyl-tRNA from binding and blocking protein elongation. This stalls bacterial protein synthesis, leading to bacterial death or growth inhibition without harming human cells, as human ribosomes have a different structure.

Case 14: tRNA in Neurodegenerative Disease

A neurologist is studying a rare neurodegenerative disorder linked to mutations in genes encoding tRNA-modifying enzymes. Patients exhibit progressive cognitive decline, tremors, and muscle weakness.

How could defective tRNA modification contribute to neurodegeneration?

A) Modified tRNA prevents proper folding of neuronal proteins
B) tRNA modifications are required for efficient translation and protein homeostasis
C) tRNA mutations only affect non-neuronal cells, so they are unlikely to cause brain damage
D) Loss of tRNA function causes excessive protein synthesis, leading to toxic aggregates
E) Neurons do not rely on tRNA, so the mutation should not affect brain function

Correct Answer: B

Explanation: tRNA modifications (e.g., methylation, pseudouridylation) are essential for proper codon recognition and translation fidelity. Defective modifications can lead to misfolded proteins and impaired neuronal function, contributing to neurodegenerative diseases like pontocerebellar hypoplasia and other tRNA-linked disorders.

Case 15: tRNA in Autoimmune Diseases

A patient with an autoimmune disease is found to have autoantibodies targeting tRNA synthetases. The patient presents with muscle inflammation, joint pain, and lung disease. The doctor diagnoses anti-synthetase syndrome.

What is the likely mechanism by which autoantibodies against tRNA synthetases cause disease?

A) They block tRNA synthesis, preventing transcription
B) They prevent tRNA from being charged with amino acids, leading to defective protein synthesis
C) They destroy ribosomes, preventing mRNA from binding
D) They directly degrade all forms of tRNA, leading to cell death
E) They enhance protein synthesis, leading to immune overactivation

Correct Answer: B

Explanation: Autoantibodies against tRNA synthetases (e.g., anti-Jo-1 antibodies) interfere with tRNA charging, reducing protein synthesis efficiency. This disrupts cellular function, particularly in muscle and lung tissues, leading to the symptoms of anti-synthetase syndrome, an autoimmune disorder seen in some cases of myositis and interstitial lung disease.

Case 16: Antibiotics Targeting Peptidyl Transferase

A patient is diagnosed with bacterial pneumonia and is prescribed chloramphenicol, an antibiotic known to inhibit peptidyl transferase activity in bacterial ribosomes. After starting the medication, the patient experiences bone marrow suppression, leading to anemia.

How does inhibition of peptidyl transferase by chloramphenicol contribute to its antibacterial effect?

A) It prevents the ribosome from initiating translation
B) It blocks elongation by preventing peptide bond formation between amino acids
C) It causes ribosomes to degrade, stopping protein synthesis completely
D) It prevents mRNA from binding to the ribosome
E) It accelerates protein synthesis, leading to bacterial cell lysis

Correct Answer: B

Explanation: Peptidyl transferase is the enzymatic component of the ribosome that catalyzes peptide bond formation between amino acids during translation. Chloramphenicol inhibits this activity in bacterial ribosomes, preventing protein elongation and stopping bacterial growth. However, in rare cases, it can also affect mitochondrial ribosomes in human cells, leading to bone marrow suppression and anemia.

Case 17: Ribosomal RNA (rRNA) and Peptidyl Transferase Activity

A medical student is studying the role of ribosomal RNA (rRNA) in protein synthesis. She learns that the peptidyl transferase enzyme is not a protein but is instead a function of ribosomal RNA within the large ribosomal subunit.

Which of the following best describes the role of rRNA in peptidyl transferase activity?

A) rRNA provides structural support but does not participate in catalysis
B) rRNA serves as the enzymatic component that catalyzes peptide bond formation
C) rRNA acts as a primer for mRNA transcription
D) rRNA transports amino acids to the ribosome for peptide bond formation
E) rRNA functions only in mRNA splicing and does not participate in translation

Correct Answer: B

Explanation: The peptidyl transferase activity is catalyzed by ribosomal RNA (rRNA), specifically within the large ribosomal subunit (23S rRNA in prokaryotes and 28S rRNA in eukaryotes). This is an example of ribozyme activity, where RNA, rather than protein, carries out enzymatic functions, facilitating peptide bond formation between amino acids during translation.

Case 18: Ribosomal RNA Damage and Protein Synthesis

A patient is exposed to a toxin that specifically modifies the 28S rRNA in the eukaryotic ribosome, leading to the inactivation of peptidyl transferase activity. As a result, the patient develops symptoms of rapidly progressing cell death in tissues with high protein turnover, such as the gastrointestinal tract and bone marrow.

Why does damage to ribosomal RNA result in impaired protein synthesis?

A) Ribosomal RNA is responsible for decoding mRNA codons during translation
B) Ribosomal RNA is necessary for attaching the ribosome to mRNA
C) Peptidyl transferase activity, which forms peptide bonds, is a function of rRNA
D) Ribosomal RNA prevents degradation of transfer RNA (tRNA) molecules
E) Damage to ribosomal RNA blocks DNA replication, leading to cell death

Correct Answer: C

Explanation: Peptidyl transferase is a ribozyme (catalytic RNA) that catalyzes peptide bond formation. If 28S rRNA in eukaryotic ribosomes is damaged, the ability of the ribosome to link amino acids together is lost, halting protein synthesis. This explains why toxins targeting rRNA, such as ricin, cause widespread cellular damage, particularly in tissues that rely on high levels of protein synthesis.

Case 19: Functional Differences Between DNA and RNA

A medical student is studying nucleic acids and their roles in cellular function. She notes that DNA serves as genetic storage, while RNA plays multiple roles in gene expression.

Which of the following is NOT a function of RNA?

A) Serving as a template for protein synthesis
B) Carrying amino acids to the ribosome
C) Storing genetic information long-term
D) Catalyzing peptide bond formation in ribosomes
E) Regulating gene expression through small RNA molecules

Correct Answer: C

Explanation: DNA serves as the long-term storage of genetic information, while RNA is involved in gene expression, translation, and enzymatic functions. Messenger RNA (mRNA), transfer RNA (tRNA), ribosomal RNA (rRNA), and regulatory RNAs (miRNA, siRNA) all contribute to protein synthesis and gene regulation.

Question 20: Structural Flexibility of RNA vs. DNA

A scientist isolates an RNA molecule and observes that it forms secondary structures like hairpin loops and stem-loops. However, DNA does not typically form such structures in cells.

What allows RNA to adopt these complex structures while DNA remains mostly double-stranded?

A) RNA contains uracil, which increases its ability to form hydrogen bonds
B) RNA’s single-stranded nature allows it to fold into complex shapes
C) RNA lacks nucleotides, so it forms loops instead of a helix
D) DNA does not have a phosphate backbone, preventing it from folding
E) DNA and RNA form identical structures, but RNA is more flexible

Correct Answer: B

Explanation: RNA is single-stranded, allowing it to fold into complex secondary and tertiary structures through intramolecular base pairing. These structures are critical for functions such as ribosome assembly, enzymatic activity (ribozymes), and gene regulation.

Case 21: RNA Splicing and Disease

A patient with spinal muscular atrophy (SMA) has a mutation affecting the splicing of mRNA, leading to incomplete protein formation.

Which RNA component is directly involved in the splicing process?

A) tRNA
B) Ribosomal RNA
C) Small nuclear RNA (snRNA)
D) MicroRNA (miRNA)
E) Messenger RNA (mRNA)

Correct Answer: C (Small nuclear RNA – snRNA)

Explanation: snRNA, as part of the spliceosome, recognizes splice sites and removes introns from pre-mRNA, ensuring proper exon joining. Mutations in splicing factors can lead to diseases like SMA and certain cancers.

Case 22: Non-Coding RNA and Gene Regulation

A cancer research team finds that certain microRNAs (miRNAs) suppress oncogene expression by binding to complementary mRNA sequences.

What is the primary function of miRNA in gene regulation?

A) miRNA inhibits ribosome assembly
B) miRNA promotes mRNA degradation or translation repression
C) miRNA enhances transcription of target genes
D) miRNA facilitates tRNA function in translation
E) miRNA repairs damaged RNA molecules

Correct Answer: B (miRNA promotes mRNA degradation or translation repression)

Explanation: MicroRNAs (miRNAs) bind to mRNA targets, leading to mRNA degradation or translation suppression, playing a crucial role in post-transcriptional gene regulation.

Case 23: RNA Viruses and Mutability

RNA viruses, such as influenza and HIV, mutate rapidly, leading to frequent vaccine updates.

Why do RNA viruses have higher mutation rates than DNA viruses?

A) RNA viruses lack a proofreading mechanism
B) RNA viruses encode more stable genetic material than DNA viruses
C) RNA viruses have multiple double-stranded genomes
D) RNA viruses replicate only inside the nucleus
E) RNA viruses lack a phosphodiester backbone

Correct Answer: A (RNA viruses lack a proofreading mechanism)

Explanation: RNA-dependent RNA polymerases (RdRp) lack proofreading activity, leading to higher mutation rates in RNA viruses, making them highly adaptable.

Case 24: Ribosomal RNA and Cell Function

A cell biologist treats eukaryotic cells with a drug that selectively inhibits the 28S rRNA function in ribosomes.

What would be the most direct effect of this drug on the cell?

A) Blockage of mRNA transcription
B) Inhibition of peptide bond formation in translation
C) Prevention of ribosome assembly
D) Activation of DNA repair mechanisms
E) Increase in mRNA degradation

Correct Answer: B (Inhibition of peptide bond formation in translation)

Explanation: The 28S rRNA in eukaryotic ribosomes possesses peptidyl transferase activity, essential for peptide bond formation during protein synthesis.

Case 25: RNA Interference as a Therapeutic Approach

A new cancer therapy involves small interfering RNA (siRNA), which selectively silences oncogene expression.

How does siRNA function in gene silencing?

A) siRNA binds DNA to prevent transcription
B) siRNA inhibits ribosome function
C) siRNA degrades complementary mRNA, preventing translation
D) siRNA modifies histones to repress gene expression
E) siRNA replaces defective mRNA in the cell

Correct Answer: C (siRNA degrades complementary mRNA, preventing translation)

Explanation: siRNA is a double-stranded RNA molecule that guides the RNA-induced silencing complex (RISC) to degrade target mRNA, blocking protein production.