Nucleic Acid Biochemistry Practice Questions

Q: A person presented with swelling of the right 3rd toe. X-ray shows deposition of multiple crystals. A defect in which of the following pathways caused the problem?

Uric acid pathway. ***Uric acid pathway*** - Swelling of the toe with **crystal deposition** on X-ray is characteristic of **gout**, caused by **monosodium urate crystals** depositing in joints due to hyperuricemia. - Defects in **uric acid metabolism** lead to increased uric acid production or decreased excretion, resulting in crystal formation and joint inflammation. *Purine salvage pathway* - While **HGPRT deficiency** (Lesch-Nyhan syndrome) can cause hyperuricemia, it's a secondary effect rather than the primary pathway defect causing gout. - The purine salvage pathway defect would present with **neurological symptoms** and **self-mutilation** in severe cases, not isolated joint swelling. *Urea cycle* - The **urea cycle** is involved in **ammonia detoxification** and nitrogen disposal, not uric acid metabolism. - Defects cause **hyperammonemia** with neurological symptoms like confusion and coma, not crystal arthropathy. *CORI cycle* - The **CORI cycle** involves **lactate-glucose interconversion** between muscle and liver during exercise and fasting. - This metabolic pathway has no relation to **uric acid production** or crystal deposition in joints.

Q: Triple bonds are found between which base pairs?

Cytosine–Guanine. ### Explanation **Core Concept: Watson-Crick Base Pairing** In the DNA double helix, nitrogenous bases pair specifically via hydrogen bonds. The stability of the DNA structure depends on these bonds. * **Cytosine (C) and Guanine (G)** form **three (triple) hydrogen bonds**. This is due to the specific arrangement of hydrogen bond donors (amino and imino groups) and acceptors (carbonyl and ring nitrogens) on their respective rings. * **Adenine (A) and Thymine (T)** form only **two (double) hydrogen bonds**. **Analysis of Options:** * **Option B (Correct):** Cytosine and Guanine share three hydrogen bonds. Because of this extra bond, G-C rich DNA sequences are more stable and require higher temperatures to denature (higher Melting Temperature, $T_m$). * **Option A (Incorrect):** Adenine and Thymine pair via two hydrogen bonds. In RNA, Adenine pairs with Uracil, also via two bonds. * **Options C & D (Incorrect):** These represent Purine-Purine (A-G) or Pyrimidine-Pyrimidine (C-T) pairings. Under normal physiological conditions, these do not occur because they would distort the uniform width of the DNA helix. **NEET-PG High-Yield Pearls:** 1. **Melting Temperature ($T_m$):** The $T_m$ of DNA is directly proportional to the G-C content. Higher G-C content = Higher $T_m$. 2. **Chargaff’s Rule:** In double-stranded DNA, the amount of $A=T$ and $G=C$; therefore, Total Purines = Total Pyrimidines. 3. **Bond Strength:** The C-G bond is stronger than the A-T bond. This is why "TATA boxes" (A-T rich regions) are found in promoter sequences—they are easier for the cell to "unzip" to initiate transcription. 4. **Clinical Correlation:** Drugs like **Dactinomycin** (Actinomycin D) exert their effect by intercalating specifically into the minor groove of DNA at G-C rich cytotoxic sites, inhibiting RNA synthesis.

Q: A 3-year-old male child presents with severe self-mutilation behavior (repetitive biting of his lips and fingers causing scarring), choreoathetosis, spasticity, and intellectual disability. Laboratory investigations reveal elevated serum uric acid levels. Which of the following enzymes is likely to be deficient in this child?

HGPRTase. ***HGPRTase*** - **HGPRTase deficiency** causes **Lesch-Nyhan syndrome**, characterized by **self-mutilation behavior**, **hyperuricemia**, and **neurological abnormalities** in male children. - The deficiency leads to accumulation of **hypoxanthine** and **guanine**, causing excessive **uric acid production** and developmental delays. *Adenosine deaminase* - **ADA deficiency** causes **severe combined immunodeficiency (SCID)**, presenting with recurrent infections and immune system failure. - Does not cause **self-mutilation** or **hyperuricemia**, but rather **lymphopenia** and **opportunistic infections**. *APRTase* - **APRTase deficiency** leads to **2,8-dihydroxyadenine nephropathy** with kidney stone formation and renal dysfunction. - Does not present with **neurological symptoms** or **behavioral abnormalities** like self-mutilation. *Acid maltase* - **Acid maltase deficiency** causes **Pompe disease**, a glycogen storage disorder affecting muscles and heart. - Presents with **muscle weakness**, **cardiomegaly**, and **hepatomegaly**, not hyperuricemia or self-mutilation.

Q: The melting temperature of DNA is directly proportional to which of the following?

The percentage of Guanine-Cytosine (GC) base pairs. **Explanation:** The **Melting Temperature (Tm)** is defined as the temperature at which 50% of double-stranded DNA denatures into single strands. This process involves breaking the hydrogen bonds between complementary base pairs. **Why Option A is correct:** The stability of the DNA helix is primarily determined by the hydrogen bonding between bases. **Guanine (G) and Cytosine (C)** are held together by **three hydrogen bonds**, whereas Adenine (A) and Thymine (T) are held by only two. Because triple bonds require more thermal energy to break than double bonds, DNA with a higher **GC content** has a higher melting temperature. Therefore, Tm is directly proportional to the percentage of GC pairs. **Why other options are incorrect:** * **Option B:** Increasing AT base pairs decreases the overall stability of the helix because they only possess two hydrogen bonds. Thus, Tm is inversely proportional to AT content. * **Option C:** While the total energy required to denature a very long molecule is higher, the *temperature* at which it melts (Tm) is fundamentally a function of the base composition (GC ratio) and ionic strength, rather than the absolute length of the polymer in a clinical/biochemical context. **High-Yield Facts for NEET-PG:** * **Hyperchromicity:** Denatured (single-stranded) DNA absorbs more UV light at **260 nm** than double-stranded DNA. This increase in absorbance is used to measure Tm. * **Ionic Strength:** Tm also increases with higher salt concentrations (e.g., $Na^+$) because cations neutralize the negative charges on the phosphate backbone, reducing repulsion between strands. * **Formamide:** This chemical lowers the Tm by disrupting hydrogen bonds, often used in labs to denature DNA at lower temperatures.

Q: Nucleic acids absorb UV light maximally at which wavelength?

260 nm. ### Explanation **1. Why 260 nm is Correct:** Nucleic acids (DNA and RNA) contain nitrogenous bases (purines and pyrimidines) which possess **conjugated double bond systems**. These aromatic rings undergo resonance, allowing them to absorb ultraviolet (UV) light. The maximum absorption (λmax) occurs at **260 nm**. This property is routinely used in laboratories for the **quantitation** of DNA and RNA; the concentration of a sample can be calculated based on its absorbance at this specific wavelength using the Beer-Lambert Law. **2. Analysis of Incorrect Options:** * **280 nm (Option B):** This is the peak absorption wavelength for **proteins**. It is due to the presence of aromatic amino acids, primarily **Tryptophan** and Tyrosine. The ratio of absorbance at 260/280 nm is a critical high-yield index used to assess the purity of nucleic acid samples (a ratio of ~1.8 for DNA and ~2.0 for RNA indicates high purity). * **410 nm (Option C):** This falls within the visible light spectrum (violet). This wavelength is associated with the **Soret peak** of heme-containing proteins like hemoglobin. * **320 nm (Option D):** This wavelength is often used as a background correction in spectrophotometry because neither nucleic acids nor proteins absorb significantly here. **3. High-Yield Clinical Pearls for NEET-PG:** * **Hyperchromicity:** When DNA is denatured (double strand to single strand), its absorbance at 260 nm **increases**. This is known as the Hyperchromic effect. * **Tm (Melting Temperature):** The temperature at which 50% of DNA is denatured. DNA with higher **G-C content** has a higher Tm because G-C pairs have three hydrogen bonds compared to two in A-T pairs. * **Purity Check:** If the 260/280 ratio is <1.8, it suggests protein contamination in the DNA sample.

Q: Which arm of tRNA binds it to the ribosomal surface?

Pseudouridine arm. ### Explanation The correct answer is **B. Pseudouridine arm**. Transfer RNA (tRNA) has a characteristic "cloverleaf" secondary structure with four major arms, each serving a distinct functional role during translation. **1. Why the Pseudouridine arm is correct:** The **TψC arm** (where ψ represents pseudouridine) is named for the presence of the sequence Ribothymidine-Pseudouridine-Cytidine. This arm is responsible for **binding the tRNA molecule to the ribosomal surface**, specifically to the 5S rRNA of the large ribosomal subunit (60S in eukaryotes, 50S in prokaryotes). This interaction ensures the tRNA is correctly positioned within the A, P, or E sites during protein synthesis. **2. Why the other options are incorrect:** * **DHU arm (A):** Contains Dihydrouridine. Its primary role is **recognition by the specific Aminoacyl-tRNA synthetase** enzyme, ensuring the correct amino acid is attached to the tRNA. * **Acceptor arm (C):** This is the 3' end of the tRNA (ending in the sequence **CCA**). It is the site where the **amino acid is covalently attached** via an ester bond. * **Anticodon arm (D):** Contains the three-nucleotide anticodon sequence that **recognizes and base-pairs with the complementary codon** on the mRNA strand. ### High-Yield NEET-PG Pearls: * **Smallest RNA:** tRNA is the smallest (75–90 nucleotides; 4S) and is also known as "Soluble RNA." * **Post-transcriptional modifications:** tRNA is rich in unusual bases (Pseudouridine, Dihydrouridine, Methylguanosine). * **The "Adapter Molecule":** Termed by Francis Crick because it bridges the gap between mRNA codons and amino acids. * **Variable Arm:** The length of this arm determines the classification of tRNA into Class 1 (short) or Class 2 (long).

Q: A female patient complains of swelling and pain in her great toe. Her uric acid level is found to be high. A drug that reduces uric acid levels is prescribed. Which of the following enzymes should the drug inhibit?

Xanthine oxidase. ***Xanthine oxidase*** - **Xanthine oxidase** catalyzes the conversion of hypoxanthine to xanthine and xanthine to uric acid in the purine degradation pathway - **Xanthine oxidase inhibitors** (allopurinol, febuxostat) are the mainstay drugs for chronic management of hyperuricemia and gout - By inhibiting this enzyme, these drugs reduce uric acid production, lowering serum uric acid levels and preventing crystal deposition in joints - The clinical presentation of **podagra** (acute pain and swelling of the great toe) with elevated uric acid is classic for **acute gouty arthritis** *Lysyl oxidase* - Involved in cross-linking collagen and elastin in connective tissue formation - Not related to purine metabolism or uric acid synthesis - Inhibition would affect collagen strength, not uric acid levels *Homogentisate oxidase* - Enzyme in the tyrosine degradation pathway - Deficiency causes alkaptonuria (accumulation of homogentisic acid) - Not involved in purine metabolism *Urease* - Bacterial enzyme that hydrolyzes urea to ammonia and carbon dioxide - Found in bacteria like *Helicobacter pylori* and *Proteus* species - Not involved in human uric acid synthesis or metabolism

Q: What is the treatment of the condition shown due to absence of enzyme marked as $X$ ?

Uridine. ***Uridine*** - **Hereditary orotic aciduria** results from a deficiency in **UMP synthase**, leading to an inability to synthesize pyrimidines and a subsequent buildup of orotic acid. - Supplementation with **Uridine** provides a source of pyrimidines that bypasses the enzymatic block, thereby alleviating **megaloblastic anemia** and reducing orotic acid excretion. *Sodium benzoate* - This agent is primarily used in the management of **urea cycle disorders** to promote nitrogen excretion by conjugating with glycine. - It has no effect on the **pyrimidine synthesis pathway** and would not resolve the symptoms associated with UMP synthase deficiency. *L-arginine* - This is a supplement used to replenish intermediates in the **urea cycle**, specifically for treating conditions like **ornithine transcarbamylase deficiency**. - While orotic aciduria can occur in urea cycle defects, UMP synthase deficiency is a primary metabolic block that **L-arginine** cannot correct. *L-carnitine* - **L-carnitine** is vital for the transport of long-chain fatty acids into the mitochondria for **beta-oxidation**. - It is used to treat **carnitine deficiency** or organic acidemias, but it plays no role in the production of **nucleotide bases** or the treatment of orotic aciduria.

Q: Which type of bonds are represented by the dotted lines in the image? (AIIMS Nov 2017)

Hydrogen bond. ***Hydrogen bond*** - The dotted lines in the image represent the weak, non-covalent interactions between the **nitrogenous bases** on opposite strands of the DNA double helix. - Specifically, these are **hydrogen bonds** formed between complementary base pairs (Adenine with Thymine via two hydrogen bonds, and Guanine with Cytosine via three hydrogen bonds). *Covalent bond* - **Covalent bonds** involve the sharing of electron pairs between atoms and are much stronger than hydrogen bonds. - In DNA, covalent bonds form the **sugar-phosphate backbone** of each strand and link the nitrogenous bases to the deoxyribose sugars. *Ionic bond* - **Ionic bonds** involve the electrostatic attraction between oppositely charged ions, formed by the complete transfer of electrons. - While ions (like magnesium or sodium) interact with DNA, the dotted lines specifically represent the inter-strand forces between bases, which are not ionic. *Phosphodiester* - A **phosphodiester bond** is a specific type of covalent bond that links the 3' carbon of one deoxyribose sugar to the 5' carbon of the next deoxyribose sugar via a phosphate group, forming the backbone of a single DNA strand. - The dotted lines are between the two DNA strands, not within a single strand's backbone.

Question 1

A person presented with swelling of the right 3rd toe. X-ray shows deposition of multiple crystals. A defect in which of the following pathways caused the problem?

Accepted Answer

Uric acid pathway

Answer

Purine salvage pathway

Answer

Urea cycle

Answer

CORI cycle

Question 2

Triple bonds are found between which base pairs?

Accepted Answer

Cytosine–Guanine

Answer

Adenine–Thymine

Answer

Adenine–Guanine

Answer

Cytosine–Thymine

Question 3

A 3-year-old male child presents with severe self-mutilation behavior (repetitive biting of his lips and fingers causing scarring), choreoathetosis, spasticity, and intellectual disability. Laboratory investigations reveal elevated serum uric acid levels. Which of the following enzymes is likely to be deficient in this child?

Accepted Answer

HGPRTase

Answer

Adenosine deaminase

Answer

APRTase

Answer

Acid maltase

Question 4

Deficiency of purine nucleoside phosphorylase causes which of the following?

Accepted Answer

Cellular immunodeficiency

Answer

Complement deficiency

Answer

Humoral immunodeficiency

Answer

Combined immunodeficiency

Question 5

The melting temperature of DNA is directly proportional to which of the following?

Accepted Answer

The percentage of Guanine-Cytosine (GC) base pairs

Answer

The percentage of Adenine-Thymine (AT) base pairs

Answer

The length of the DNA molecule

Answer

None of the above

Question 6

Nucleic acids absorb UV light maximally at which wavelength?

Accepted Answer

260 nm

Answer

280 nm

Answer

410 nm

Answer

320 nm

Question 7

Which arm of tRNA binds it to the ribosomal surface?

Accepted Answer

Pseudouridine arm

Answer

DHU arm

Answer

Acceptor arm

Answer

Anticodon arm

Question 8

A female patient complains of swelling and pain in her great toe. Her uric acid level is found to be high. A drug that reduces uric acid levels is prescribed. Which of the following enzymes should the drug inhibit?

Accepted Answer

Xanthine oxidase

Answer

Lysyl oxidase

Answer

Homogentisate oxidase

Answer

Urease

Question 9

What is the treatment of the condition shown due to absence of enzyme marked as $X$ ?

Accepted Answer

Uridine

Answer

Sodium benzoate

Answer

L-arginine

Answer

L-carnitine

Question 10

Which type of bonds are represented by the dotted lines in the image? (AIIMS Nov 2017)

Accepted Answer

Hydrogen bond

Answer

Covalent bond

Answer

Ionic bond

Answer

Phosphodiester

Nucleic Acid Biochemistry — MCQs

Nucleic Acid Biochemistry — MCQs

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