Nucleic Acid Biochemistry — MCQs
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Deamination of methylated cytosine will produce which of the following?
Gout is a disorder of -
Which of the following is a disorder of purine metabolism?
Which form of DNA is predominantly seen in living cells under physiological conditions?
Triplex DNA is a clue to which of the following?
A patient presents with increased levels of Hypoxanthine and Xanthine in the blood, along with hypouricemia. Which enzyme deficiency is responsible for this condition?
Clinical manifestations of Lesch-Nyhan syndrome are due to the defective recycling of which of the following?
Which of the following is not involved in the synthesis of pyrimidines?
Thermo-stability in DNA is contributed mostly by:
What is the main catabolic product of purine nucleotides in humans?
Nucleic Acid Biochemistry Indian Medical PG Practice Questions and MCQs
Question 131: Deamination of methylated cytosine will produce which of the following?
- A. Thymine (Correct Answer)
- B. Adenine
- C. Xanthine
- D. Guanine
Explanation: ### Explanation **1. Why Thymine is Correct:** Cytosine undergoes spontaneous deamination to form **Uracil**. However, in DNA, cytosine is frequently methylated at the 5th carbon (5-methylcytosine) by DNA methyltransferase, a process essential for gene silencing and epigenetic regulation. When **5-methylcytosine** undergoes deamination, the amino group is replaced by a carbonyl group, directly converting it into **Thymine** (5-methyluracil). **2. Why Other Options are Incorrect:** * **Adenine & Guanine:** These are purines. Deamination of cytosine (a pyrimidine) cannot result in a purine structure. * **Xanthine:** This is an intermediate in purine catabolism produced by the deamination of **Guanine**. (Note: Deamination of Adenine produces Hypoxanthine). **3. Clinical Pearls & High-Yield Facts for NEET-PG:** * **The "Mutation Hotspot":** Because thymine is a natural base in DNA, the repair enzyme *Uracil DNA Glycosylase* cannot recognize this specific deamination product as "damaged." Consequently, C → T transitions at methylated CpG islands are the most common cause of single-point mutations in humans. * **Uracil in DNA:** Spontaneous deamination of *unmethylated* cytosine produces Uracil. This is why DNA uses Thymine instead of Uracil—it allows the cell to identify deaminated cytosine as "foreign" and initiate Base Excision Repair (BER). * **Summary of Deamination:** * Cytosine → Uracil * 5-Methylcytosine → **Thymine** * Adenine → Hypoxanthine * Guanine → Xanthine
Question 132: Gout is a disorder of -
- A. Purine metabolism (Correct Answer)
- B. Pyrimidine metabolism
- C. Ketone metabolism
- D. Protein metabolism
Explanation: **Explanation:** **Gout** is a clinical syndrome characterized by hyperuricemia (elevated serum uric acid levels), leading to the deposition of monosodium urate crystals in joints and soft tissues. **Why Purine Metabolism is Correct:** Uric acid is the final metabolic breakdown product of **purine nucleotides** (Adenine and Guanine) in humans. The pathway involves the conversion of purines to Xanthine, which is then oxidized by the enzyme **Xanthine Oxidase** to form Uric Acid. Gout occurs when there is either an overproduction of uric acid (due to enzyme defects like PRPP synthetase overactivity) or, more commonly, decreased renal excretion. **Why Other Options are Incorrect:** * **Pyrimidine Metabolism:** The end products of pyrimidine catabolism (Cytosine, Uracil, Thymine) are highly water-soluble compounds like **β-alanine** and **β-aminoisobutyrate**, which are easily excreted and do not cause crystal deposition. * **Ketone Metabolism:** Disorders here lead to ketoacidosis or hypoglycemia, not urate deposition. * **Protein Metabolism:** While purines are found in nucleoproteins, "protein metabolism" generally refers to amino acid breakdown, which primarily results in **urea** formation via the urea cycle. **High-Yield Clinical Pearls for NEET-PG:** * **Lesch-Nyhan Syndrome:** A deficiency of **HGPRT** (salvage pathway) leading to extreme hyperuricemia and self-mutilation. * **Drug of Choice:** **Allopurinol** (a suicide inhibitor of Xanthine Oxidase) for chronic gout; **NSAIDs** for acute attacks. * **Von Gierke’s Disease:** A glycogen storage disease that causes secondary gout due to increased PPP activity and lactic acid competing with uric acid for renal excretion. * **Microscopy:** Gout crystals are **needle-shaped** and show **strong negative birefringence** under polarized light.
Question 133: Which of the following is a disorder of purine metabolism?
- A. Hyperammonemia
- B. Gout (Correct Answer)
- C. Orotic aciduria
- D. Hepatolenticular degeneration (Wilson's disease)
Explanation: **Explanation:** **Gout** is the correct answer because it is a clinical syndrome resulting from the deposition of monosodium urate crystals in joints and tissues. This occurs due to **hyperuricemia**, which is an elevation of uric acid—the final breakdown product of **purine metabolism** in humans. Key enzymes involved in purine pathways, such as PRPP synthetase (overactivity) or HGPRT (deficiency in Lesch-Nyhan syndrome), are frequently implicated in secondary gout. **Analysis of Incorrect Options:** * **Hyperammonemia (A):** This is a disorder of the **Urea Cycle** (protein/amino acid metabolism), resulting from the body's inability to detoxify ammonia into urea. * **Orotic aciduria (B):** This is a disorder of **pyrimidine metabolism**. It typically results from a deficiency of the bifunctional enzyme UMP synthase, leading to a buildup of orotic acid and megaloblastic anemia. * **Hepatolenticular degeneration (D):** Also known as Wilson’s disease, this is a disorder of **copper metabolism** caused by mutations in the *ATP7B* gene, leading to copper accumulation in the liver and brain. **High-Yield Clinical Pearls for NEET-PG:** * **Rate-limiting step of Purine Synthesis:** Glutamine PRPP amidotransferase. * **Lesch-Nyhan Syndrome:** An X-linked recessive deficiency of **HGPRT** (salvage pathway), characterized by hyperuricemia, self-mutilation, and mental retardation. * **Von Gierke’s Disease (G6Pase deficiency):** Often presents with secondary gout due to increased shunting of G6P into the Pentose Phosphate Pathway, increasing Ribose-5-Phosphate and subsequent purine synthesis. * **Drug of Choice:** **Allopurinol** (a suicide inhibitor of Xanthine Oxidase) is used for chronic gout to lower uric acid levels.
Question 134: Which form of DNA is predominantly seen in living cells under physiological conditions?
- A. A
- B. C
- C. B (Correct Answer)
- D. Z
Explanation: ***B*** - **B-form DNA** is the most stable conformation under **physiological conditions** with normal hydration levels and **Watson-Crick base pairing**. - It features a **right-handed double helix** with **10.5 base pairs per turn** and **major and minor grooves** that are well-defined for protein binding. *A* - **A-form DNA** occurs under **dehydrated conditions** or in **RNA-DNA hybrids**, making it less common in living cells. - It has a **wider, shorter helix** with **11 base pairs per turn** and is predominantly found in laboratory conditions, not physiological environments. *C* - **C-form DNA** is an **intermediate form** that exists at **low humidity** and specific salt conditions. - This form is **rarely observed** in biological systems and represents a **transitional state** between A and B forms. *Z* - **Z-form DNA** is a **left-handed double helix** that forms under **high salt concentrations** and specific base sequences (GC-rich). - While it may exist **transiently** in some cellular processes, it represents less than **1%** of cellular DNA under normal physiological conditions.
Question 135: Triplex DNA is a clue to which of the following?
- A. Hoogsteen Pairing (Correct Answer)
- B. Palindromic sequences
- C. Large number of guanosine repeats
- D. Polypyrimidine tracts
Explanation: **Explanation:** **1. Why Hoogsteen Pairing is Correct:** Triplex DNA (Triple-helical DNA) occurs when a third strand of DNA winds around a standard B-form double helix. This is made possible by **Hoogsteen base pairing**, which differs from the standard Watson-Crick pairing. In Hoogsteen pairing, the third strand occupies the **major groove** of the duplex and forms hydrogen bonds with the purine bases (Adenine or Guanine) of the existing Watson-Crick pairs. This requires the purine to use its N7 and C6 positions for bonding, rather than the usual N1 and C6 positions. **2. Analysis of Incorrect Options:** * **B. Palindromic sequences:** These are sequences that read the same 5' to 3' on both strands. They are characteristic of **Hairpin or Cruciform structures** and are recognition sites for restriction endonucleases, not triplex DNA. * **C. Large number of guanosine repeats:** While G-rich sequences can form unique structures, they typically form **G-quadruplexes** (four-stranded DNA), often found in telomeres, rather than triplexes. * **D. Polypyrimidine tracts:** While triplex DNA often involves homopurine-homopyrimidine stretches, the *mechanism* that defines the triplex structure itself is the specific Hoogsteen hydrogen bonding. **High-Yield Clinical Pearls for NEET-PG:** * **H-DNA:** Intramolecular triplex DNA is also known as H-DNA. It can induce genomic instability and is often found in promoter regions. * **Z-DNA:** A left-handed helix with a zigzag sugar-phosphate backbone, often seen in sequences with alternating purines and pyrimidines (e.g., CGCGCG). * **Therapeutic Potential:** Triplex-forming oligonucleotides (TFOs) are being researched for gene therapy to site-specifically inhibit transcription or induce site-specific mutations.
Question 136: A patient presents with increased levels of Hypoxanthine and Xanthine in the blood, along with hypouricemia. Which enzyme deficiency is responsible for this condition?
- A. Hypoxanthine-guanine phosphoribosyltransferase (HGPrtase)
- B. Xanthine oxidase (Correct Answer)
- C. Adenosine deaminase
- D. Acyclovir resistance protein (APRTase)
Explanation: **Explanation:** The correct answer is **Xanthine oxidase**. **1. Why Xanthine Oxidase is correct:** Xanthine oxidase (XO) is the key enzyme in the final stages of purine catabolism. It catalyzes two critical steps: the conversion of **Hypoxanthine to Xanthine** and the subsequent conversion of **Xanthine to Uric Acid**. A deficiency in this enzyme (Xanthinuria) leads to a metabolic block. Consequently, Hypoxanthine and Xanthine cannot be converted into uric acid, leading to their accumulation in the blood and urine, while serum uric acid levels drop significantly (**Hypouricemia**). **2. Why the other options are incorrect:** * **HGPRTase:** Deficiency causes **Lesch-Nyhan Syndrome**. This leads to a failure of the purine salvage pathway, causing an *increase* in uric acid production (Hyperuricemia) and gout-like symptoms, not hypouricemia. * **Adenosine deaminase (ADA):** Deficiency leads to **Severe Combined Immunodeficiency (SCID)** due to the toxic accumulation of dATP in lymphocytes. It does not typically present with isolated hypouricemia. * **APRTase:** Deficiency leads to the formation of **2,8-dihydroxyadenine renal stones**. It affects adenine metabolism but does not cause the specific triad of high hypoxanthine/xanthine and low uric acid. **Clinical Pearls for NEET-PG:** * **Xanthinuria:** Often asymptomatic but can lead to **Xanthine stones** (radiolucent) in the urinary tract. * **Allopurinol:** A drug used in gout that acts as a suicide inhibitor of Xanthine Oxidase, mimicking this deficiency to lower uric acid levels. * **Hypouricemia Differential:** Consider Xanthine oxidase deficiency, Fanconi syndrome (renal loss), or severe liver disease.
Question 137: Clinical manifestations of Lesch-Nyhan syndrome are due to the defective recycling of which of the following?
- A. Purines (Correct Answer)
- B. Methylcobalamin
- C. Pyrimidines
- D. Thiamine
Explanation: **Explanation:** **Lesch-Nyhan Syndrome (LNS)** is an X-linked recessive disorder caused by a complete deficiency of the enzyme **Hypoxanthine-Guanine Phosphoribosyltransferase (HGPRT)**. This enzyme is central to the **Purine Salvage Pathway**, which recycles free purine bases (Hypoxanthine and Guanine) back into nucleotides (IMP and GMP). 1. **Why Purines is Correct:** In LNS, the inability to recycle purines leads to two major consequences: * **Hyperuricemia:** Unsalvaged purines are instead shunted into the degradation pathway, resulting in excessive production of Uric Acid. * **Increased De Novo Synthesis:** The lack of salvage leads to low levels of IMP/GMP, which normally inhibit the rate-limiting enzyme *PRPP Glutamyl Amidotransferase*. Without this feedback inhibition, *de novo* purine synthesis increases, further exacerbating uric acid production. 2. **Why Other Options are Incorrect:** * **Methylcobalamin (B12):** Deficiency leads to Megaloblastic anemia and Subacute Combined Degeneration of the spinal cord, not purine recycling issues. * **Pyrimidines:** Pyrimidine metabolism defects (e.g., Orotic Aciduria) involve different enzymes like UMP Synthase and do not cause the neurological symptoms seen in LNS. * **Thiamine (B1):** Deficiency causes Beriberi or Wernicke-Korsakoff syndrome, affecting carbohydrate metabolism (Pyruvate Dehydrogenase). **High-Yield Clinical Pearls for NEET-PG:** * **Classic Triad:** Hyperuricemia (Gout/Renal stones), Intellectual disability, and **Self-mutilation** (characteristic lip/finger biting). * **Biochemical Marker:** Elevated **PRPP** (Phosphoribosyl pyrophosphate) levels and low HGPRT activity. * **Treatment:** Allopurinol or Febuxostat (to manage uric acid), but these do not reverse neurological symptoms. * **Orange Sand:** Look for "orange sand" in the diapers of affected infants (Urate crystals).
Question 138: Which of the following is not involved in the synthesis of pyrimidines?
- A. Glutamine
- B. CO2
- C. Aspartic acid
- D. Glycine (Correct Answer)
Explanation: In pyrimidine synthesis, the parent ring structure is constructed from three simple precursors: **Glutamine**, **CO2**, and **Aspartic acid**. Unlike purine synthesis, which is a complex multi-step assembly on a ribose sugar, the pyrimidine ring is synthesized first and then attached to PRPP. **Why Glycine is the correct answer:** Glycine is a major contributor to the **purine** ring (providing carbons 4 and 5 and nitrogen 7), but it plays **no role** in the synthesis of pyrimidines. This is a classic "distractor" in biochemistry exams, as students often confuse the precursors of purines with those of pyrimidines. **Explanation of other options:** * **Glutamine (Option A):** Provides the amide nitrogen (N3) of the pyrimidine ring. It is the substrate for the rate-limiting enzyme, Carbamoyl Phosphate Synthetase II (CPS-II). * **CO2 (Option B):** Provides Carbon-2 of the pyrimidine ring. * **Aspartic acid (Option C):** This is the most significant contributor, providing the bulk of the ring (Nitrogen-1 and Carbons 4, 5, and 6). **High-Yield Clinical Pearls for NEET-PG:** * **Rate-limiting enzyme:** CPS-II (located in the cytosol), inhibited by UTP and activated by PRPP. * **Leflunomide:** An immunosuppressant used in Rheumatoid Arthritis that inhibits **Dihydroorotate dehydrogenase**, blocking pyrimidine synthesis. * **Orotic Aciduria:** Caused by a deficiency of UMP Synthase; presents with megaloblastic anemia that does not respond to B12/Folate and the presence of orotic acid crystals in urine. * **Mnemonic for Pyrimidine atoms:** **"CAD"** — **C**O2, **A**spartate, and **D**erivative of Glutamine (Ammonia).
Question 139: Thermo-stability in DNA is contributed mostly by:
- A. A=T base pairs
- B. G≡C base pairs (Correct Answer)
- C. Molecular base stacking
- D. Antiparallel arrangement
Explanation: **Explanation:** The thermo-stability of the DNA double helix refers to its resistance to denaturation (melting) when exposed to heat. **Why G≡C base pairs are the correct answer:** The stability of DNA is primarily determined by the hydrogen bonding between nitrogenous bases. According to Chargaff’s rules, Guanine (G) pairs with Cytosine (C) via **three hydrogen bonds**, whereas Adenine (A) pairs with Thymine (T) via only **two hydrogen bonds**. The additional hydrogen bond in G≡C pairs provides significantly higher thermal stability. Consequently, DNA sequences with a high **GC content** have a higher **Melting Temperature (Tm)**—the temperature at which 50% of the DNA becomes single-stranded. **Analysis of Incorrect Options:** * **A. A=T base pairs:** These contain only two hydrogen bonds, making them easier to break with heat compared to GC pairs. * **C. Molecular base stacking:** While hydrophobic interactions and van der Waals forces between stacked bases contribute to the overall structural stability of the helix, the specific "thermo-stability" tested in competitive exams traditionally focuses on the strength of the inter-strand hydrogen bonding (GC content). * **D. Antiparallel arrangement:** This refers to the 5'→3' and 3'→5' orientation of the strands. While essential for the double helix geometry, it is not the primary determinant of thermal resistance. **High-Yield Clinical Pearls for NEET-PG:** * **Tm (Melting Temperature):** Directly proportional to the GC content and the length of the DNA molecule. * **Hyperchromicity:** When DNA denatures (melts), its UV light absorption at **260 nm increases**. This is a common laboratory method to monitor DNA denaturation. * **TATA Box:** Promoters often contain AT-rich regions (like the TATA box) because the lower number of hydrogen bonds allows for easier "melting" or opening of the DNA strands during the initiation of transcription.
Question 140: What is the main catabolic product of purine nucleotides in humans?
- A. Ammonia and CO2
- B. Ammonia
- C. Uric Acid (Correct Answer)
- D. CO2 and Water
Explanation: **Explanation:** In humans and higher primates, the final degradation product of purine metabolism (Adenine and Guanine) is **Uric Acid**. This process occurs primarily in the liver. Adenosine and Guanosine are converted into **Xanthine**, which is then oxidized by the enzyme **Xanthine Oxidase** to form Uric Acid. Because humans lack the enzyme *Urate Oxidase (Uricase)*, we cannot further break down uric acid into the more soluble allantoin, making uric acid the terminal excretory product excreted in urine. **Analysis of Options:** * **Option A & D (Ammonia, CO2, and Water):** These are the end products of **Pyrimidine** catabolism (Cytosine, Uracil, and Thymine). Pyrimidines are highly soluble and break down into β-alanine and β-aminoisobutyrate, eventually yielding CO2 and NH3. * **Option B (Ammonia):** While ammonia is produced during the deamination of amino acids and certain steps of nucleotide breakdown, it is not the "main" end product of the purine ring itself; it is typically converted to urea in the liver. **High-Yield Clinical Pearls for NEET-PG:** * **Rate-limiting enzyme:** PRPP Synthetase/Amidotransferase (Synthesis); **Xanthine Oxidase** (Catabolism). * **Gout:** Hyperuricemia (Uric acid >7 mg/dL) leads to the deposition of **Monosodium Urate crystals** in joints (Tophi). * **Lesch-Nyhan Syndrome:** Deficiency of **HGPRT** (salvage pathway) leads to excessive de novo purine synthesis and massive overproduction of uric acid, characterized by self-mutilation and mental retardation. * **Pharmacology Link:** **Allopurinol** and **Febuxostat** treat gout by inhibiting Xanthine Oxidase.
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Regulation of Gene Expression
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Mutations and DNA Repair
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Purine Metabolism and Disorders
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