Nucleic Acid Biochemistry Practice Questions

Q: A patient presents with skin cancer and hyperpigmentation that worsens with sunlight exposure. Which of the following DNA repair mechanisms is most likely defective in this condition?

Nucleotide excision repair. ***Nucleotide excision repair*** - This mechanism is responsible for repairing large, bulky DNA lesions, most notably **pyrimidine dimers** caused by **UV radiation** (sunlight). - A defect in NER is the underlying cause of **Xeroderma Pigmentosum**, which presents with severe photosensitivity, hyperpigmentation, and a significantly increased risk of **skin cancer** (melanoma and non-melanoma). *Base excision repair* - Primarily repairs **small, non-helix-distorting lesions** caused by spontaneous factors (like deamination) or oxidative damage, such as single base modifications. - Defective BER is implicated in hereditary cancers like MUTYH-associated polyposis (MAP), which is not associated with **UV-induced skin pathology**. *Non-homologous end joining (NHEJ)* - Responsible for repairing **double-strand breaks (DSBs)** in DNA, usually in the G0/G1 phase of the cell cycle. - While critical for genome stability, defects in NHEJ lead to severe immunodeficiency (due to impaired V(D)J recombination) and are not the primary cause of susceptibility to **solar-induced skin cancer**. *Mismatch repair* - Corrects errors (mismatched bases) incorporated during **DNA replication** that escape proofreading. - Defective MMR leads to a high frequency of microsatellite instability, characteristic of conditions like **Hereditary Non-polyposis Colorectal Cancer (HNPCC)** or Lynch syndrome, but not the primary cause of photosensitivity and UV-related skin cancer.

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

Uridine. ***Correct: Uridine*** - **Hereditary orotic aciduria** is caused by deficiency of UMP synthase (which has two enzymatic activities: orotate phosphoribosyltransferase and orotidine-5'-monophosphate decarboxylase) in the **pyrimidine synthesis pathway** - The enzyme deficiency leads to accumulation of **orotic acid** and impaired production of pyrimidine nucleotides - Clinical features include **megaloblastic anemia** (not responsive to vitamin B12 or folate), **growth retardation**, and **developmental delays** - **Oral uridine supplementation** is the specific treatment as it bypasses the enzymatic block, providing an exogenous source of pyrimidine nucleotides - Uridine is converted to UMP by uridine kinase, normalizing pyrimidine levels and alleviating symptoms *Incorrect: Sodium benzoate* - Used to treat **hyperammonemia** in urea cycle disorders by conjugating with glycine to form hippurate, facilitating nitrogen excretion - Not relevant to pyrimidine synthesis defects - Would not address the underlying pyrimidine deficiency or megaloblastic anemia *Incorrect: L-arginine* - A conditionally essential amino acid and key intermediate in the **urea cycle** - Used in treating urea cycle disorders like **argininosuccinic aciduria** and **citrullinemia** - Has no role in pyrimidine metabolism or treatment of orotic aciduria *Incorrect: L-carnitine* - Essential for **fatty acid oxidation** by transporting long-chain fatty acids into mitochondria - Used in primary carnitine deficiency and disorders of fatty acid metabolism - Not involved in pyrimidine synthesis pathway or treatment of nucleotide deficiencies

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.

Q: A patient presents with a skin rash that is exaggerated on sun exposure. What is the repair mechanism involved in this condition?

Nucleotide excision repair. ***Nucleotide excision repair*** - This mechanism is responsible for repairing **bulky lesions** in DNA, such as **pyrimidine dimers** caused by **UV radiation** from sun exposure. - Patients with defects in nucleotide excision repair (e.g., **xeroderma pigmentosum**) are highly sensitive to sunlight and develop skin rashes, pigment changes, and skin cancers. *Base excision repair* - This pathway primarily corrects **small damaged bases** that do not cause significant distortion of the DNA helix, such as deaminated, oxidized, or alkylated bases. - It does not primarily address the bulky lesions induced by UV light that cause exaggerated sun sensitivity. *Mismatch repair* - This system corrects errors, like **mismatched base pairs**, that are incorporated during DNA replication. - It is not directly involved in repairing DNA damage caused by environmental factors like UV radiation. *Double stranded DNA break repair* - This mechanism repairs **double-strand breaks** in DNA, which are highly deleterious lesions caused by ionizing radiation or oxidative stress. - While critical for genome stability, it is not the primary repair pathway for UV-induced DNA lesions or the direct cause of sun sensitivity.

Q: Deamination of methylated cytosine forms which of the following?

Thymine. ***Thymine*** - Deamination of **5-methylcytosine** removes the amine group at the 4-position and replaces it with a keto group, forming **thymine**. - This reaction can lead to a common type of point mutation, as the DNA repair machinery might fail to distinguish this naturally occurring base from normal thymine. *Uracil* - **Uracil** is formed by the deamination of **unmethylated cytosine**, not methylated cytosine. - Uracil is a base found in RNA but not typically in DNA, so its presence in DNA signals a repair event. *Cytosine* - **Cytosine** is the original base before deamination occurs; deamination is a chemical modification that changes cytosine into another base. - If a base remains cytosine, it means deamination has not taken place. *Guanine* - **Guanine** is a purine base and is structurally unrelated to cytosine or its deamination products. - Deamination primarily affects pyrimidine bases like cytosine and uracil, not purines like guanine.

Q: Which bases are present in human DNA?

Adenine-guanine-cytosine-thymine. ***Adenine- guanine-cytosine-thymine*** - DNA (deoxyribonucleic acid) in humans, and most other organisms, is composed of four nitrogenous bases: **adenine (A), guanine (G), cytosine (C), and thymine (T)**. - These bases are paired specifically: **adenine with thymine (A-T)** and **guanine with cytosine (G-C)**, forming the rungs of the DNA double helix. *None of the above* - This option is incorrect because there is a definitive set of bases that make up human DNA, as described in the correct option. - The fundamental building blocks of human DNA are well-established and universally recognized in biology. *Adenine-guanine- cytosine-uracil* - This list of bases is characteristic of **RNA (ribonucleic acid)**, not DNA. - In RNA, **uracil (U)** replaces thymine (T), meaning RNA contains adenine (A), guanine (G), cytosine (C), and uracil (U). *Adenine-guanine-thiamine- uracil* - This option incorrectly includes **thiamine**, which is a **vitamin (B1)** and not a nitrogenous base found in nucleic acids. - It also incorrectly includes **uracil**, which is found in RNA, not DNA.

Q: Which organelle contains its own DNA apart from the nucleus?

Mitochondria. ***Mitochondria*** - Mitochondria contain their own **circular DNA (mtDNA)**, which is inherited maternally, and their own ribosomes. - This DNA encodes for some proteins essential for **cellular respiration** and its own replication, supporting the endosymbiotic theory. *RER* - The **Rough Endoplasmic Reticulum (RER)** is characterized by the presence of **ribosomes** on its surface. - It plays a crucial role in the **synthesis and modification of proteins** designated for secretion or insertion into membranes, but does not contain DNA. *Golgi complex* - The **Golgi complex** is involved in **modifying, sorting, and packaging proteins and lipids** for secretion or delivery to other organelles. - It consists of flattened sacs called cisternae but does not possess DNA. *SER* - The **Smooth Endoplasmic Reticulum (SER)** is involved in **lipid synthesis**, **detoxification** of drugs and poisons, and **calcium ion storage**. - Unlike mitochondria, it does not contain its own genetic material.

Q: Which is a product of purine metabolism?

Uric acid. ***Uric acid*** - **Uric acid** is the final breakdown product of **purine metabolism** in humans. - It's formed from the oxidation of **xanthine** by the enzyme **xanthine oxidase**. *Xanthine* - **Xanthine** is an intermediate compound in the purine metabolic pathway, but not the final product in humans. - It is converted to **uric acid** via the enzyme **xanthine oxidase**. *Beta alanine* - **Beta-alanine** is a **non-proteogenic amino acid** and is a breakdown product of **pyrimidine metabolism**, not purine. - It is involved in the synthesis of **carnosine**, a buffer in muscle tissue. *Urea* - **Urea** is the primary end product of **protein (amino acid) metabolism** in mammals, representing the main way the body excretes **nitrogen**. - It is produced in the **urea cycle** in the liver and is unrelated to purine breakdown.

Q: Which part of DNA is most susceptible to radiation?

Nucleotides. ***Nucleotides*** - Radiation primarily damages DNA at the **nucleotide level**, with the deoxyribose sugar component being most susceptible to ionizing radiation. - Radiation causes **hydroxyl radical formation** that attacks the sugar-phosphate backbone, leading to single-strand and double-strand breaks. - Purine and pyrimidine bases within nucleotides can also undergo radiation-induced modifications, causing **mutations** and loss of genetic information. *Nucleosides* - Nucleosides (base + sugar without phosphate) are not the functional unit within DNA strands. - While the sugar moiety is susceptible, nucleosides as isolated units are not the primary consideration when discussing **DNA strand damage**. - Radiation damage occurs to nucleotides as they exist in the DNA polymer, not to free nucleosides. *Double helix* - The double helix is the **overall structural configuration** of DNA, not a specific chemical component. - Radiation damages the double helix by affecting its constituent nucleotides, particularly through **sugar-phosphate backbone breaks**. - Double helix disruption is a consequence of nucleotide-level damage. *Phosphate groups* - Phosphate groups link nucleotides together but are relatively **less susceptible** to direct radiation damage compared to the deoxyribose sugar. - The phosphodiester bonds can be broken as a secondary effect of **sugar radical formation**, rather than being the primary target of radiation.

Q: What will happen to DNA if salt is added to it: (PGI Dec 2008)

Increase Melting point (Tm). ***Increase Melting point (Tm)*** - Adding **salt (ions)** to DNA stabilizes the **double helix structure** by shielding the negatively charged phosphate backbone. - This increased stability requires a **higher temperature** to break the hydrogen bonds and denature the DNA, thus increasing the melting point (Tm). *Not affect Tm* - This is incorrect because **ion concentration** is a significant factor influencing the stability of the DNA double helix. - Changes in salt concentration directly impact the electrostatic interactions within the DNA molecule. *Melting leads to denaturation of DNA* - While it's true that **melting refers to the denaturation** (separation of strands) of DNA, this option does not answer what happens *to the melting point* when salt is added. - DNA melting is a process, and the question asks about the effect of salt on the physical property of its melting temperature (Tm). *Decrease Tm* - This would occur if the DNA double helix were destabilized, for example, by reducing the **ionic strength** or adding denaturing agents. - Salt, by providing positive ions, actually helps stabilize the DNA structure, making it harder to denature.

Question 1

A patient presents with skin cancer and hyperpigmentation that worsens with sunlight exposure. Which of the following DNA repair mechanisms is most likely defective in this condition?

Accepted Answer

Nucleotide excision repair

Answer

Base excision repair

Answer

Mismatch repair

Answer

Non-homologous end joining (NHEJ)

Question 2

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 3

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

Question 4

A patient presents with a skin rash that is exaggerated on sun exposure. What is the repair mechanism involved in this condition?

Accepted Answer

Nucleotide excision repair

Answer

Base excision repair

Answer

Mismatch repair

Answer

Double stranded DNA break repair

Question 5

Deamination of methylated cytosine forms which of the following?

Accepted Answer

Thymine

Answer

Uracil

Answer

Cytosine

Answer

Guanine

Question 6

Which bases are present in human DNA?

Accepted Answer

Adenine-guanine-cytosine-thymine

Answer

None of the above

Answer

Adenine-guanine-cytosine-uracil

Answer

Adenine-guanine-thiamine-uracil

Question 7

Which organelle contains its own DNA apart from the nucleus?

Accepted Answer

Mitochondria

Answer

RER

Answer

Golgi complex

Answer

SER

Question 8

Which is a product of purine metabolism?

Accepted Answer

Uric acid

Answer

Xanthine

Answer

Beta alanine

Answer

Urea

Question 9

Which part of DNA is most susceptible to radiation?

Accepted Answer

Nucleotides

Answer

Nucleosides

Answer

Double helix

Answer

Phosphate groups

Question 10

What will happen to DNA if salt is added to it: (PGI Dec 2008)

Accepted Answer

Increase Melting point (Tm)

Answer

Not affect Tm

Answer

Melting leads to denaturation of DNA

Answer

Decrease Tm

Nucleic Acid Biochemistry — MCQs

Nucleic Acid Biochemistry — MCQs

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