RNA polymerase structure and function US Medical PG Practice Questions and MCQs
Practice US Medical PG questions for RNA polymerase structure and function. These multiple choice questions (MCQs) cover important concepts and help you prepare for your exams.
RNA polymerase structure and function US Medical PG Question 1: You are seeing a patient in clinic who recently started treatment for active tuberculosis. The patient is currently being treated with rifampin, isoniazid, pyrazinamide, and ethambutol. The patient is not used to taking medicines and is very concerned about side effects. Specifically regarding the carbohydrate polymerization inhibiting medication, which of the following is a known side effect?
- A. Vision loss (Correct Answer)
- B. Paresthesias of the hands and feet
- C. Cutaneous flushing
- D. Arthralgias
- E. Elevated liver enzymes
RNA polymerase structure and function Explanation: ***Vision loss***
- The "carbohydrate polymerization inhibiting medication" refers to **ethambutol**, which inhibits **arabinosyl transferase** (involved in mycobacterial cell wall arabinogalactan synthesis)
- **Ethambutol** causes **optic neuritis**, leading to **decreased visual acuity**, **red-green color blindness**, and potentially **irreversible vision loss**
- **Regular ophthalmologic monitoring** is essential during ethambutol therapy
*Paresthesias of the hands and feet*
- This describes **peripheral neuropathy** caused by **isoniazid**
- Isoniazid interferes with **pyridoxine (vitamin B6) metabolism**, leading to neurotoxicity
- Risk factors include malnutrition, diabetes, alcoholism, and pregnancy
- Prevented by **pyridoxine supplementation**
*Cutaneous flushing*
- Not a characteristic side effect of first-line anti-tuberculosis medications
- More commonly associated with niacin or certain allergic/vasodilatory reactions
*Arthralgias*
- Classic side effect of **pyrazinamide**, often affecting small joints
- Caused by **pyrazinamide-induced hyperuricemia** (inhibits renal uric acid excretion)
- May require dose adjustment or discontinuation if severe
*Elevated liver enzymes*
- **Hepatotoxicity** can occur with **rifampin**, **isoniazid**, and **pyrazinamide**
- Requires regular monitoring of liver function tests during TB treatment
- Most common serious adverse effect of combination TB therapy
RNA polymerase structure and function US Medical PG Question 2: A 25-year-old male is brought to the emergency department by his friends after a camping trip. He and his friends were in the woods camping when the patient started experiencing severe right upper quadrant abdominal pain after foraging and ingesting some wild mushrooms about 3 hours earlier. The patient is lethargic on exam and appears jaundiced. He has scleral icterus and is severely tender to palpation in the right upper quadrant. He has scattered petechiae on his extremities. Liver function tests are:
Serum:
Na+: 134 mEq/L
Cl-: 100 mEq/L
K+: 4.2 mEq/L
HCO3-: 24 mEq/L
Urea nitrogen: 50 mg/dL
Glucose: 100 mg/dL
Creatinine: 1.4 mg/dL
Alkaline phosphatase: 400 U/L
Aspartate aminotransferase (AST, GOT): 3278 U/L
Alanine aminotransferase (ALT, GPT): 3045 U/L
gamma-Glutamyltransferase (GGT): 100 U/L
The most likely cause of this patient’s clinical presentation acts by inhibiting which of the following molecules?
- A. RNA polymerase II (Correct Answer)
- B. RNA polymerase III
- C. Topoisomerase
- D. RNA polymerase I
- E. Prokaryote RNA polymerase
RNA polymerase structure and function Explanation: ***RNA polymerase II***
- The clinical presentation with severe hepatotoxicity (jaundice, elevated AST/ALT, RUQ pain, petechiae, lethargy) following wild mushroom ingestion is highly suggestive of poisoning by **Amanita phalloides** (death cap mushroom).
- The primary toxin in *Amanita phalloides* is **alpha-amanitin**, which specifically inhibits **RNA polymerase II**, thereby halting mRNA synthesis and leading to cellular death, particularly in rapidly dividing cells and hepatocytes.
*RNA polymerase III*
- **RNA polymerase III** is responsible for synthesizing **tRNA** and **5S ribosomal RNA**.
- While essential for cell function, it is not the primary target of amanitin toxins, and its inhibition would not directly cause the severe hepatotoxicity observed.
*Topoisomerase*
- **Topoisomerases** are enzymes that regulate the supercoiling of **DNA** during replication, transcription, and repair.
- While critical for cell survival, they are not the target of the toxins found in *Amanita phalloides* mushrooms.
*RNA polymerase I*
- **RNA polymerase I** is responsible for synthesizing most **ribosomal RNA (rRNA)**.
- While also essential, it is less sensitive to **alpha-amanitin** than RNA polymerase II, requiring much higher concentrations for inhibition.
*Prokaryote RNA polymerase*
- **Prokaryote RNA polymerase** is fundamentally different in structure and function from eukaryotic RNA polymerases.
- **Alpha-amanitin** specifically targets eukaryotic RNA polymerases and has no significant inhibitory effect on prokaryotic RNA polymerase.
RNA polymerase structure and function US Medical PG Question 3: An investigator is studying the genetic profile of an isolated pathogen that proliferates within macrophages. The pathogen contains sulfatide on the surface of its cell wall to prevent fusion of the phagosome and lysosome. She finds that some of the organisms under investigation have mutations in a gene that encodes the enzyme required for synthesis of RNA from a DNA template. The mutations are most likely to reduce the therapeutic effect of which of the following drugs?
- A. Pyrazinamide
- B. Ethambutol
- C. Rifampin (Correct Answer)
- D. Streptomycin
- E. Levofloxacin
RNA polymerase structure and function Explanation: ***Rifampin***
- **Rifampin** specifically targets bacterial **DNA-dependent RNA polymerase**, inhibiting **RNA synthesis**. Mutations in the gene encoding this enzyme would directly reduce rifampin's binding and effectiveness.
- The description of the pathogen thriving within macrophages and using **sulfatide to evade lysosomal fusion** strongly suggests **Mycobacterium tuberculosis**, a bacterium for which rifampin is a cornerstone treatment.
*Pyrazinamide*
- **Pyrazinamide** is a prodrug that, once converted to **pyrazinoid acid**, disrupts **mycobacterial membrane potential** and metabolism. Its primary target is not RNA synthesis.
- Its efficacy is pH-dependent and it acts optimally in acidic environments, such as within macrophages, but mutations affecting RNA synthesis would not directly compromise its action.
*Ethambutol*
- **Ethambutol** inhibits **arabinosyl transferase**, an enzyme essential for the synthesis of the **mycobacterial cell wall component arabinogalactan**.
- Its mechanism of action is distinct from RNA synthesis, thus mutations affecting RNA polymerase would not impact its efficacy.
*Streptomycin*
- **Streptomycin** is an **aminoglycoside antibiotic** that binds to the **30S ribosomal subunit**, inhibiting bacterial **protein synthesis**.
- This mechanism is unrelated to DNA-dependent RNA polymerase, so mutations in RNA synthesis enzymes would not affect streptomycin's action.
*Levofloxacin*
- **Levofloxacin** is a **fluoroquinolone antibiotic** that inhibits **bacterial DNA gyrase (topoisomerase II)** and **topoisomerase IV**, thereby blocking DNA replication and transcription.
- While it affects processes related to DNA, its direct target is not the DNA-dependent RNA polymerase enzyme itself, distinguishing it from rifampin's specific mechanism.
RNA polymerase structure and function US Medical PG Question 4: Replication in eukaryotic cells is a highly organized and accurate process. The process involves a number of enzymes such as primase, DNA polymerase, topoisomerase II, and DNA ligase. In which of the following directions is DNA newly synthesized?
- A. 3' --> 5'
- B. N terminus --> C terminus
- C. C terminus --> N terminus
- D. 3' --> 5' & 5' --> 3'
- E. 5' --> 3' (Correct Answer)
RNA polymerase structure and function Explanation: ***5' --> 3'***
- DNA polymerase can only add **nucleotides** to the 3' end of a growing strand, meaning synthesis always proceeds in a **5' to 3' direction**.
- This is true for both the **leading strand** (synthesized continuously) and the **lagging strand** (synthesized discontinuously via Okazaki fragments).
*3' --> 5'*
- While the parental template strand is read in the 3' to 5' direction, the *newly synthesized* DNA strand is always built in the **opposite, antiparallel 5' to 3' direction**.
- DNA polymerase lacks the ability to add new nucleotides to the **5' phosphate group** of the growing strand.
*N terminus --> C terminus*
- This directional notation refers to the synthesis of **proteins**, where amino acids are added to the C (carboxyl) terminus of the growing polypeptide chain.
- It does not apply to the synthesis direction of **nucleic acids (DNA or RNA)**.
*C terminus --> N terminus*
- This directional notation is incorrectly applied; protein synthesis always proceeds from the **N (amino) terminus to the C (carboxyl) terminus**.
- This has no relevance to the synthesis direction of **DNA**.
*3' --> 5' & 5' --> 3'*
- Although DNA replication involves two strands, one is synthesized continuously in the **5' → 3' direction (leading strand)** and the other discontinuously, but still *each fragment* is synthesized in the **5' → 3' direction (lagging strand)**.
- No new DNA strand is synthesized in the **3' → 5' direction**.
RNA polymerase structure and function US Medical PG Question 5: A group of researchers is studying molecules and DNA segments that are critical for important cellular processes in eukaryotic cells. They have identified a region that is located about 28 bases upstream of the 5’ coding region. This region promotes the initiation of transcription by binding with transcription factors. Which of the following regions have these researchers most likely identified?
- A. TATA Box (Correct Answer)
- B. RNA polymerase II
- C. Small nuclear ribonucleoprotein (SnRNPs)
- D. DNA methyltransferase
- E. CAAT Box
RNA polymerase structure and function Explanation: ***TATA Box***
- The **TATA box** is a core promoter element found in eukaryotic genes, typically located **25-35 base pairs upstream** of the transcription start site.
- It plays a crucial role in initiating transcription by serving as a binding site for **transcription factors**, which in turn recruit **RNA polymerase II**.
*RNA polymerase II*
- **RNA polymerase II** is the enzyme responsible for transcribing protein-coding genes into mRNA.
- While essential for transcription, it is an enzyme that binds to the promoter region (which includes the TATA box), rather than a regulatory DNA sequence itself.
*Small nuclear ribonucleoprotein (SnRNPs)*
- **SnRNPs** are components of the spliceosome, involved in the **splicing of pre-mRNA** to remove introns.
- They are involved in post-transcriptional modification, not in the initiation of transcription.
*DNA methyltransferase*
- **DNA methyltransferase** is an enzyme involved in **DNA methylation**, a process that typically represses gene expression.
- This enzyme modifies DNA, but it is not a DNA region that promotes transcription initiation.
*CAAT Box*
- The **CAAT box** is another common promoter element in eukaryotes, usually located further **upstream (70-80 base pairs)** from the transcription start site.
- While it also binds transcription factors and influences transcription initiation, its location is generally *more distant* than the 28 bases upstream described, making the TATA box a more accurate fit for the given distance.
RNA polymerase structure and function US Medical PG Question 6: A group of microbiological investigators is studying bacterial DNA replication in E. coli colonies. While the cells are actively proliferating, the investigators stop the bacterial cell cycle during S phase and isolate an enzyme involved in DNA replication. An assay of the enzyme's exonuclease activity determines that it is active on both intact and demethylated thymine nucleotides. Which of the following enzymes have the investigators most likely isolated?
- A. DNA ligase
- B. Telomerase
- C. Primase
- D. DNA topoisomerase
- E. DNA polymerase I (Correct Answer)
RNA polymerase structure and function Explanation: ***DNA polymerase I***
- **DNA polymerase I** possesses **5' to 3' exonuclease activity**, which is crucial for removing **RNA primers** (intact nucleotides) laid down by primase during DNA replication.
- This 5' to 3' exonuclease activity also allows it to excise damaged DNA, including DNA containing **demethylated thymine nucleotides**.
- It also has 3' to 5' exonuclease activity for proofreading.
- **Key distinction:** While DNA polymerase III (the main replicative enzyme) only has 3' to 5' exonuclease activity, DNA polymerase I has **both** 3' to 5' and 5' to 3' exonuclease activities, making it essential for primer removal and DNA repair.
*DNA ligase*
- **DNA ligase** functions to form a **phosphodiester bond** between adjacent nucleotides to seal nicks in the DNA backbone, but it does not have exonuclease activity.
- Its primary role is in joining Okazaki fragments and repairing single-strand breaks.
*Telomerase*
- **Telomerase** is a specialized reverse transcriptase that extends the telomeres at the ends of eukaryotic chromosomes, but is not present in prokaryotes like *E. coli*.
- It uses an RNA template to synthesize DNA, and it lacks exonuclease activity.
*Primase*
- **Primase** is an RNA polymerase that synthesizes short **RNA primers** on the DNA template, providing a starting point for DNA synthesis.
- It is involved in synthesizing primers, not in removing or excising nucleotides, and has no exonuclease activity.
*DNA topoisomerase*
- **DNA topoisomerases** relieve supercoiling in DNA during replication and transcription by cutting and rejoining DNA strands.
- While they act on DNA, their function is to manage topological stress, and they do not exhibit exonuclease activity on nucleotides.
RNA polymerase structure and function US Medical PG Question 7: Although nucleotide addition during DNA replication in prokaryotes proceeds approximately 20-times faster than in eukaryotes, why can much larger amounts of DNA be replicated in eukaryotes in a time-effective manner?
- A. Eukaryotes have multiple origins of replication (Correct Answer)
- B. Eukaryotes have helicase which can more easily unwind DNA strands
- C. Eukaryotes have fewer polymerase types
- D. Eukaryotes have less genetic material to replicate
- E. Eukaryotes have a single, circular chromosome
RNA polymerase structure and function Explanation: ***Eukaryotes have multiple origins of replication***
- Eukaryotic chromosomes are much larger than prokaryotic chromosomes and require multiple origins of replication to complete DNA synthesis within a reasonable timeframe.
- Each origin of replication initiates simultaneously, allowing DNA synthesis to occur at many sites along the chromosome, effectively increasing the overall speed of replication.
- This compensates for the slower rate of nucleotide addition by DNA polymerase in eukaryotes compared to prokaryotes.
*Eukaryotes have helicase which can more easily unwind DNA strands*
- While helicase activity is crucial for unwinding DNA, there is no evidence to suggest that eukaryotic helicases are significantly more efficient or faster at unwinding DNA compared to prokaryotic helicases in a way that would account for the large difference in overall replication time.
- The rate of DNA unwinding by helicase is a factor in replication speed, but it does not overcome the fundamental limitation of a single origin of replication in prokaryotes.
*Eukaryotes have fewer polymerase types*
- Eukaryotic cells actually have **more** types of DNA polymerases than prokaryotic cells, each specialized for different functions like replication, repair, and mitochondrial DNA synthesis.
- The number of polymerase types does not directly relate to the speed or efficiency of overall DNA replication in terms of replicating large amounts of DNA.
*Eukaryotes have less genetic material to replicate*
- Eukaryotic organisms typically have significantly **more** genetic material (a larger genome size) than prokaryotic organisms, not less.
- If eukaryotes had less genetic material, the question itself about effective replication of "much larger amounts of DNA" would be contradictory.
*Eukaryotes have a single, circular chromosome*
- Eukaryotic cells have **multiple, linear chromosomes** within a membrane-bound nucleus, not a single circular chromosome.
- Prokaryotic cells typically have a single, circular chromosome located in the nucleoid region.
- The linear structure of eukaryotic chromosomes with multiple origins is actually what enables efficient replication of large genomes, making this statement both factually incorrect and contradictory to the mechanism in question.
RNA polymerase structure and function US Medical PG Question 8: A drug that inhibits mRNA synthesis has the well-documented side effect of red-orange body fluids. For which of the following is this drug used as monotherapy?
- A. Brucellosis
- B. Tuberculosis
- C. Methicillin-resistant staphylococcus aureus infection
- D. Mycobacterium avium intracellulare infection
- E. Neisseria meningitidis prophylaxis (Correct Answer)
RNA polymerase structure and function Explanation: ***Neisseria meningitidis prophylaxis***
- The drug described is **rifampin**, which inhibits bacterial **DNA-dependent RNA polymerase**, thereby blocking **mRNA synthesis** and causes characteristic **red-orange discoloration of body fluids** (tears, urine, sweat).
- Rifampin is used as **monotherapy** for **prophylaxis** against **Neisseria meningitidis** infection in close contacts of infected patients.
- This is the **only indication** where rifampin monotherapy is appropriate, as prophylaxis requires short-term use where resistance development is not a concern.
*Tuberculosis*
- Rifampin is a **first-line agent** for tuberculosis treatment and a cornerstone of all TB regimens.
- However, it is **never used as monotherapy** for TB due to rapid development of resistance.
- Standard TB treatment requires **multidrug therapy** with rifampin, isoniazid, pyrazinamide, and ethambutol (RIPE) for initial phase.
*Methicillin-resistant Staphylococcus aureus infection*
- Rifampin is sometimes used in **combination** with other antibiotics (e.g., vancomycin, daptomycin) to treat **MRSA infections**, especially those involving **prosthetic devices** or **biofilms**.
- It is **not used as monotherapy** for active MRSA infections due to extremely high rates of spontaneous resistance.
*Mycobacterium avium intracellulare infection*
- **Mycobacterium avium complex (MAC)** infections require a multidrug regimen, typically including **macrolides (azithromycin or clarithromycin)**, **ethambutol**, and sometimes **rifabutin** (a rifamycin derivative preferred over rifampin).
- **Monotherapy is never appropriate** for MAC infections due to resistance concerns and treatment failure.
*Brucellosis*
- **Brucellosis** treatment requires **combination therapy**, typically **doxycycline plus rifampin** for 6 weeks or longer.
- **Rifampin monotherapy** is inadequate for eradicating Brucella infection and leads to treatment failure and resistance development.
RNA polymerase structure and function US Medical PG Question 9: A scientist wants to determine if a specific fragment is contained within genome X. She uses a restriction enzyme to digest the genome into smaller fragments to run on an agarose gel, with the goal of separating the resulting fragments. A nitrocellulose blotting paper is then used to transfer the fragments from the agarose gel. A radiolabeled probe containing a complementary sequence to the fragment she is searching for is incubated with the blotting paper. Which of the following is the RNA equivalent of this technique?
- A. RT-PCR
- B. Western blot
- C. qPCR
- D. Northern blot (Correct Answer)
- E. Southern blot
RNA polymerase structure and function Explanation: **Northern blot**
- The technique described in the question, involving **restriction enzyme digestion**, **agarose gel electrophoresis**, **blotting onto a membrane**, and **hybridization with a labeled probe**, is characteristic of a **Southern blot** for DNA
- The **Northern blot** is the analogous technique used to detect and quantify **RNA** sequences, following the same principles of separation by size and detection by hybridization with a complementary probe
- Both Southern and Northern blots use the same workflow: separate nucleic acids by size on gel → transfer to membrane → detect with complementary probe
*RT-PCR*
- **Reverse transcriptase polymerase chain reaction (RT-PCR)** is used to amplify specific **RNA** sequences by first converting **RNA** into **complementary DNA (cDNA)** using reverse transcriptase, followed by standard PCR
- Unlike Northern blot, it is an **amplification technique** rather than a direct visualization method via blotting
*Western blot*
- **Western blot** is a technique used to detect and identify specific **proteins**, not nucleic acids
- It involves **gel electrophoresis** to separate proteins by size, followed by transfer to a membrane and detection using **antibodies** rather than nucleic acid probes
*qPCR*
- **Quantitative polymerase chain reaction (qPCR)**, also known as real-time PCR, is a technique used to **quantify DNA or RNA** (after reverse transcription) in real-time
- It measures the accumulation of fluorescent signal during the PCR reaction, allowing for real-time monitoring and quantification, which is fundamentally different from a blotting technique
*Southern blot*
- The description in the question *is* a **Southern blot**, which is used for **DNA** detection, not RNA
- Since the question asks for the **RNA equivalent** of the described technique, and Southern blot detects DNA, Northern blot is the correct answer
RNA polymerase structure and function US Medical PG Question 10: A 24-year-old man is brought to the emergency department by his brother because of a 3-hour history of lethargy and confusion. The brother says that 2 days ago, the patient ate several large-capped mushrooms he had foraged in the woods. After eating the mushrooms, he developed severe, bloody diarrhea that has since resolved. His pulse is 140/min, respirations are 26/min, and blood pressure is 98/62 mm Hg. Examination shows dry mucous membranes and tenderness to deep palpation in the right upper quadrant. Serum studies show a serum AST concentration of 2335 U/L and ALT concentration of 2294 U/L. Inhibition of which of the following processes is the most likely cause of this patient's condition?
- A. Parasympathetic activation
- B. Messenger RNA synthesis (Correct Answer)
- C. Microtubule polymerization
- D. Cell depolarization
- E. ATP production
RNA polymerase structure and function Explanation: ***Messenger RNA synthesis***
- This patient's symptoms, including **severe gastrointestinal upset** followed by apparent recovery and then **hepatic encephalopathy** (lethargy, confusion, elevated AST/ALT), are classic for **Amanita phalloides (death cap mushroom) poisoning**.
- The primary toxin, **α-amanitin**, specifically inhibits **RNA polymerase II**, thereby blocking **mRNA synthesis** and leading to hepatocyte death and liver failure.
*Parasympathetic activation*
- This is characteristic of poisoning by muscarinic agonists (e.g., *Inocybe* or *Clitocybe* mushrooms), causing symptoms like **salivation, lacrimation, urination, defecation, gastrointestinal cramping, and emesis (SLUDGE)**.
- While initial GI symptoms might overlap, the severe liver damage and delayed presentation of encephalopathy are inconsistent with sole parasympathetic overactivation.
*Microtubule polymerization*
- Inhibition of microtubule polymerization is associated with toxins like **colchicine** or **vincristine**, which can cause gastrointestinal toxicity and myelosuppression.
- It does not directly explain the severe hepatotoxicity and delayed onset of liver failure seen in this patient.
*Cell depolarization*
- This mechanism is associated with neurotoxins that affect ion channels, such as those found in some species of *Gyromitra* mushrooms (producing **monomethylhydrazine**) or *Psilocybe* (containing **psilocybin**).
- While neurotoxicity can occur, the prominent and severe liver failure points away from cell depolarization as the primary mechanism in this case.
*ATP production*
- Toxins that inhibit ATP production (e.g., cyanide, carbon monoxide, some mitochondrial poisons) cause widespread cellular dysfunction and can lead to multi-organ failure.
- While severe liver failure will eventually impair ATP production, α-amanitin's direct mechanism is earlier in the protein synthesis pathway (mRNA synthesis), leading to a delayed, but profound, impact on cellular function and viability.
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