Molecular Biology and Genomics Practice Questions

Q: Which one of the following binds to specific nucleotide sequences that are upstream of the start site of transcription?

RNA polymerase. ### Explanation **1. Why RNA Polymerase is Correct:** Transcription initiation requires **RNA polymerase** to recognize and bind to specific DNA sequences known as **promoters**. These promoter sequences (such as the TATA box in eukaryotes or the Pribnow box in prokaryotes) are located **upstream** (5' direction) of the transcription start site (+1). In eukaryotes, RNA polymerase II, along with general transcription factors, forms the pre-initiation complex at these sites to ensure that the gene is transcribed at the correct location and frequency. **2. Why the Other Options are Incorrect:** * **Helicase (A):** This enzyme is primarily involved in **DNA replication**. It breaks hydrogen bonds to "unzip" the double helix at the replication fork. It does not specifically bind upstream promoters to initiate transcription. * **Histone Protein (B):** Histones are structural proteins around which DNA wraps to form nucleosomes. While they regulate DNA accessibility, they bind to DNA non-specifically via electrostatic interactions (positive charge of histones to negative charge of DNA) rather than specific upstream nucleotide sequences. * **Primase (C):** This is an RNA polymerase used in **DNA replication** to synthesize short RNA primers. It provides a 3'-OH group for DNA polymerase to begin synthesis; it does not initiate gene transcription at promoter sites. **3. Clinical Pearls & High-Yield Facts for NEET-PG:** * **RNA Polymerase Types (Eukaryotes):** * **Pol I:** rRNA (except 5S) * **Pol II:** mRNA (and snRNA, miRNA) — *Target of alpha-amanitin poisoning.* * **Pol III:** tRNA and 5S rRNA. * **Promoter Sequences:** The **TATA box** (Hogness box) is usually located at -25 bp, while the **CAAT box** is further upstream at -75 bp. * **Rifampicin:** A key antitubercular drug that acts by inhibiting **bacterial DNA-dependent RNA polymerase**, preventing transcription initiation.

Q: The process underlying differences in the expression of a gene, according to which parent has transmitted it, is called –

Genomic imprinting. **Explanation:** **1. Why Genomic Imprinting is Correct:** Genomic imprinting is an epigenetic process where certain genes are expressed in a **parent-of-origin-specific manner**. Although an individual inherits two copies of a gene (one from each parent), imprinting "silences" one copy through **DNA methylation** or histone modification. Therefore, the phenotype of the offspring depends entirely on which parent transmitted the active allele. **2. Analysis of Incorrect Options:** * **Anticipation (A):** Refers to the phenomenon where a genetic disorder (typically Trinucleotide Repeat Disorders like Huntington’s or Fragile X) becomes more severe or appears at an earlier age in successive generations. * **Mosaicism (B):** The presence of two or more populations of cells with different genotypes in one individual, arising from a post-zygotic mutation (e.g., Mosaic Turner Syndrome). * **Non-penetrance (C):** Occurs when an individual carries a dominant disease-causing mutation but does not manifest any clinical symptoms of the disease. **3. High-Yield Clinical Pearls for NEET-PG:** * **Classic Examples:** The best-known examples of imprinting involve **Chromosome 15q11-q13**: * **Prader-Willi Syndrome:** Deletion of the *paternal* allele (Maternal imprinting). Features: Obesity, hypotonia, and hypogonadism. * **Angelman Syndrome:** Deletion of the *maternal* allele (Paternal imprinting). Features: "Happy Puppet," seizures, and ataxia. * **Mechanism:** It occurs during **gametogenesis** (oogenesis or spermatogenesis) and is primarily mediated by **DNA Methyltransferase**. * **Uniparental Disomy (UPD):** If a child inherits both copies of a chromosome from one parent (and none from the other), it can result in imprinting disorders even without a deletion.

Q: Leiden mutation is classified as which type of mutation?

Mis-sense mutation. **Factor V Leiden** is the most common inherited cause of hypercoagulability (thrombophilia). It is caused by a specific point mutation in the *F5* gene. ### 1. Why Mis-sense Mutation is Correct A **mis-sense mutation** occurs when a single nucleotide change results in a codon that codes for a different amino acid. In Factor V Leiden, a single base substitution occurs at position 1691 (**G → A**), which leads to the replacement of the amino acid **Arginine with Glutamine** at position 506 (**Arg506Gln**). * **Biochemical Pathology:** This mutation occurs at the specific cleavage site where **Activated Protein C (APC)** normally inactivates Factor Va. The structural change renders Factor Va resistant to cleavage (APC resistance), leading to a prothrombotic state and increased risk of Venous Thromboembolism (VTE). ### 2. Why Other Options are Incorrect * **Non-sense mutation:** This involves a point mutation that creates a premature stop codon (UAG, UAA, UGA), resulting in a truncated, usually non-functional protein. * **Frame shift mutation:** This occurs due to the insertion or deletion of nucleotides (not in multiples of three), which shifts the reading frame and alters all subsequent amino acids. * **Trinucleotide repeat mutation:** This involves the expansion of specific three-base sequences (e.g., CAG in Huntington’s disease or CGG in Fragile X syndrome). ### 3. Clinical Pearls for NEET-PG * **Inheritance:** Autosomal Dominant. * **Key Finding:** Activated Protein C (APC) resistance. * **Clinical Presentation:** Recurrent Deep Vein Thrombosis (DVT) and Pulmonary Embolism (PE). * **Diagnosis:** Screening is done via the APC resistance test (clotting assay); confirmation is via PCR for the G1691A mutation. * **High-Yield Fact:** Heterozygotes have a 5-10 fold increased risk of thrombosis, while homozygotes have an 80-fold increased risk.

Q: RNA dependent DNA polymerase is:

Reverse transcriptase. **Explanation:** The central dogma of molecular biology typically flows from DNA to RNA to Protein. However, certain viruses and cellular processes utilize **Reverse Transcriptase**, an enzyme that catalyzes the synthesis of DNA using an RNA template. This process is known as **Reverse Transcription**. 1. **Why Reverse Transcriptase is correct:** The name of a polymerase is derived from the template it reads and the product it synthesizes. An **RNA-dependent DNA polymerase** reads an **RNA** template to synthesize a complementary **DNA** strand (cDNA). This enzyme is crucial for the replication of retroviruses like HIV and is also found in human telomerase (which uses an internal RNA template to extend telomeres). 2. **Why other options are incorrect:** * **DNA polymerase:** This is typically a **DNA-dependent DNA polymerase**, as it uses a DNA template to replicate DNA during the S-phase of the cell cycle. * **RNA polymerase:** This is a **DNA-dependent RNA polymerase**, which reads a DNA template to synthesize RNA (Transcription). * **Phosphokinase:** This is a general term for enzymes that catalyze the transfer of phosphate groups (phosphorylation) and is not involved in template-directed nucleic acid synthesis. **High-Yield Clinical Pearls for NEET-PG:** * **HIV/AIDS:** Reverse transcriptase is the primary target for **NRTIs** (e.g., Zidovudine, Tenofovir) and **NNRTIs** (e.g., Efavirenz). * **Telomerase:** A specialized reverse transcriptase (TERT) that maintains chromosomal stability; its activity is high in cancer cells and stem cells. * **PCR Technology:** In **RT-PCR**, reverse transcriptase is used to convert viral RNA (like SARS-CoV-2) into DNA before amplification. * **Hepatitis B Virus:** Unlike other DNA viruses, HBV uses a reverse transcriptase step during its replication cycle.

Q: Which one of the following causes a frame-shift mutation?

Deletion. **Explanation:** **1. Why Deletion is Correct:** Genetic code is read in non-overlapping triplets called **codons**. A **Frame-shift mutation** occurs when the number of nucleotides inserted or deleted is **not a multiple of three**. This shifts the "reading frame" of the mRNA during translation. * **Deletion** of one or two nucleotides changes every subsequent codon downstream of the mutation. This usually results in a completely different amino acid sequence and often creates a premature **stop codon (UAA, UAG, UGA)**, leading to a truncated, non-functional protein. **2. Why the Other Options are Incorrect:** * **Options B & C (Transversion):** Substitution of a purine for a pyrimidine (or vice versa) is a **Point Mutation**. This only affects a single codon. It may result in a missense, nonsense, or silent mutation, but it does *not* shift the reading frame. * **Option D (Transition):** This is a point mutation where a purine is replaced by another purine (A↔G) or a pyrimidine by another pyrimidine (C↔T). Like transversions, transitions do not alter the reading frame. **Clinical Pearls & High-Yield Facts for NEET-PG:** * **Duchenne Muscular Dystrophy (DMD):** Caused by a **frame-shift mutation** (deletion) in the dystrophin gene, leading to a severe phenotype. * **Becker Muscular Dystrophy:** Caused by a **non-frame-shift** (in-frame) mutation, resulting in a milder phenotype. * **Tay-Sachs Disease:** Often caused by a 4-base pair insertion (frame-shift) in the HEXA gene. * **Cystic Fibrosis:** The most common mutation ($\Delta$F508) is an **in-frame deletion** of 3 nucleotides (one amino acid), meaning it is *not* a frame-shift mutation.

Q: What is the approximate number of base pairs in a human chromosome?

3 billion. **Explanation:** The human genome consists of the total genetic material stored within our cells. To answer this question correctly, it is vital to distinguish between the **haploid** and **diploid** genome sizes. 1. **Why 3 Billion is Correct:** The **haploid** human genome (the content of a single set of 23 chromosomes found in a sperm or egg cell) consists of approximately **3.2 to 3.3 billion base pairs**. In the context of standard medical examinations like NEET-PG, this is frequently rounded to **3 billion base pairs** (or 3 Gb). This represents the "blueprint" of a single human set of instructions. 2. **Analysis of Incorrect Options:** * **3.3 Billion (Option C):** While technically more precise for the haploid genome, standard textbooks and examiners often use "3 billion" as the benchmark figure. However, if the question asks for the **diploid** content (found in somatic cells), the answer would be approximately **6.6 billion base pairs**. * **3 Million / 5 Million (Options A & D):** These figures are far too small for eukaryotes. For comparison, the *Escherichia coli* (prokaryotic) genome is approximately 4.6 million base pairs. **High-Yield Clinical Pearls for NEET-PG:** * **Coding vs. Non-coding:** Only about **1–1.5%** of the human genome actually codes for proteins (exons). * **Mitochondrial DNA (mtDNA):** Unlike the nuclear genome, mtDNA is circular, double-stranded, and contains only **16,569 base pairs** encoding 37 genes. * **The "C-Value Paradox":** Genome size does not necessarily correlate with the complexity of the organism. * **Repeat Sequences:** Nearly 50% of the human genome consists of repetitive sequences (e.g., LINEs, SINEs, and satellite DNA), which are crucial for chromosomal structural integrity and regulation.

Q: The normal and mutated sequences of RNA coding for a protein are given below. Normal sequence: AGC-GCC-GAA-AGA-AAG-AUG-ACG. Mutated sequence: AGC-GCC-GAA-UGA-AAG-AUG-ACG. What type of mutation is shown above?

Nonsense mutation. ### Explanation **1. Why Nonsense Mutation is Correct:** A **nonsense mutation** occurs when a single nucleotide substitution results in a **premature stop codon** (UAA, UAG, or UGA) within the mRNA sequence. * **Normal sequence:** ...GAA-**AGA**-AAG... (AGA codes for Arginine) * **Mutated sequence:** ...GAA-**UGA**-AAG... (UGA is a Stop Codon) The conversion of an amino acid codon (AGA) into a stop codon (UGA) leads to the premature termination of translation, resulting in a truncated, usually non-functional protein. **2. Analysis of Incorrect Options:** * **A. Missense mutation:** This involves a point mutation that changes one amino acid to a *different* amino acid (e.g., GAA to GUA). Here, the protein is not truncated but altered. * **C. Silent mutation:** This is a point mutation that changes the codon but, due to the **degeneracy of the genetic code**, it still codes for the *same* amino acid. There is no change in the protein primary structure. * **D. Frame shift mutation:** This occurs due to the **insertion or deletion** of nucleotides (not divisible by 3). This shifts the entire reading frame downstream. In this question, the number of nucleotides remains the same; only one base is substituted. **3. NEET-PG High-Yield Pearls:** * **Stop Codons:** Remember them as **U** **A**re **A**way (UAA), **U** **G**o **A**way (UGA), and **U** **A**re **G**one (UAG). * **Transition vs. Transversion:** In this case, Adenine (Purine) changed to Uracil (Pyrimidine), which is a **Transversion**. * **Clinical Correlation:** Nonsense mutations are responsible for severe phenotypes in diseases like **Duchenne Muscular Dystrophy** and certain types of **β-Thalassemia**. * **Aminoglycosides:** At low doses, drugs like Gentamicin can sometimes induce "translational read-through" of premature stop codons, a concept being researched for treating nonsense mutation-related genetic disorders.

Q: BRD4 is required for stimulating kinase activity of which of the following?

P-TEFB. **Explanation:** **BRD4 (Bromodomain-containing protein 4)** is a key epigenetic "reader" protein that recognizes acetylated lysine residues on histones. Its primary function in transcription is to recruit and activate the **Positive Transcription Elongation Factor b (P-TEFb)**. 1. **Why P-TEFb is correct:** Transcription by RNA Polymerase II often "pauses" shortly after initiation. To resume elongation, P-TEFb (a cyclin-dependent kinase complex consisting of CDK9 and Cyclin T1) must phosphorylate the C-terminal domain (CTD) of RNA Polymerase II. BRD4 acts as a scaffold that recruits P-TEFb to active promoters and enhancers, directly stimulating its kinase activity to release the paused polymerase. 2. **Why other options are incorrect:** * **HEXIM1:** This is an inhibitory protein. It binds to P-TEFb and 7SK snRNA to form an inactive complex, sequestering P-TEFb and preventing transcription. BRD4 actually competes with HEXIM1 to release P-TEFb from this inhibited state. * **HOX-B:** These are homeobox genes involved in body patterning during development. While their expression may be regulated by epigenetic factors, they are not kinases stimulated by BRD4. * **7SK snRNA:** This is a small nuclear RNA that acts as a structural scaffold for the *inactivation* of P-TEFb, not a kinase stimulated by BRD4. **Clinical Pearls for NEET-PG:** * **BET Inhibitors:** Drugs targeting BRD4 (e.g., JQ1) are being heavily researched as potent anti-cancer agents (especially in NUT midline carcinoma and AML) because they prevent the recruitment of P-TEFb to oncogenes like *c-MYC*. * **HIV Link:** The HIV Tat protein competes with BRD4 to recruit P-TEFb to the viral LTR, which is essential for viral replication. * **Keywords:** Bromodomain (acetyl-lysine reader), CDK9, RNA Pol II elongation.

Q: Which of the following enzymatic activities is possessed by the ribosome?

Peptidyl transferase. **Explanation:** The ribosome is a complex molecular machine responsible for protein synthesis (translation). The core enzymatic activity of the ribosome is **Peptidyl transferase**, which catalyzes the formation of peptide bonds between adjacent amino acids. **1. Why Peptidyl Transferase is Correct:** During the elongation phase of translation, the peptidyl transferase activity transfers the growing polypeptide chain from the tRNA in the P-site to the amino acid attached to the tRNA in the A-site. In prokaryotes (70S), this activity is located in the **23S rRNA** of the large (50S) subunit. In eukaryotes (80S), it resides in the **28S rRNA** of the 60S subunit. Because the catalyst is an RNA molecule rather than a protein, the ribosome is classified as a **Ribozyme**. **2. Why Other Options are Incorrect:** * **Peptidase:** These are enzymes that break peptide bonds (proteolysis), whereas the ribosome forms them. * **Aminoacyl tRNA synthetase:** These enzymes are located in the cytosol, not the ribosome. They are responsible for "charging" tRNA by attaching the correct amino acid to its corresponding tRNA (requires ATP). * **GTPase:** While elongation factors (like EF-Tu and EF-G) possess GTPase activity to provide energy for translation, this is an extrinsic property of the factors themselves, not an intrinsic enzymatic activity of the ribosomal structure. **Clinical Pearls for NEET-PG:** * **Antibiotic Target:** Several antibiotics inhibit the peptidyl transferase center, most notably **Chloramphenicol**. * **Ribozyme Concept:** The fact that rRNA (not protein) catalyzes peptide bond formation is a high-yield "RNA World" hypothesis concept. * **Shine-Dalgarno Sequence:** In prokaryotes, the 16S rRNA (small subunit) recognizes this sequence to initiate translation.

Question 1

Which one of the following binds to specific nucleotide sequences that are upstream of the start site of transcription?

Accepted Answer

RNA polymerase

Answer

Helicase

Answer

Histone protein

Answer

Primase

Question 2

The process underlying differences in the expression of a gene, according to which parent has transmitted it, is called –

Accepted Answer

Genomic imprinting

Answer

Anticipation

Answer

Mosaicism

Answer

Non-penetrance

Question 3

Leiden mutation is classified as which type of mutation?

Accepted Answer

Mis-sense mutation

Answer

Non-sense mutation

Answer

Frame shift mutation

Answer

Trinucleotide repeat mutation

Question 4

RNA dependent DNA polymerase is:

Accepted Answer

Reverse transcriptase

Answer

DNA polymerase

Answer

RNA polymerase

Answer

Phosphokinase

Question 5

Which one of the following causes a frame-shift mutation?

Accepted Answer

Deletion

Answer

Substitution of purine for pyrimidine

Answer

Substitution of pyrimidine for purine

Answer

Transition

Question 6

What is the approximate number of base pairs in a human chromosome?

Accepted Answer

3 billion

Answer

3 million

Answer

3.3 billion

Answer

5 million

Question 7

The normal and mutated sequences of RNA coding for a protein are given below. Normal sequence: AGC-GCC-GAA-AGA-AAG-AUG-ACG. Mutated sequence: AGC-GCC-GAA-UGA-AAG-AUG-ACG. What type of mutation is shown above?

Accepted Answer

Nonsense mutation

Answer

Missense mutation

Answer

Silent mutation

Answer

Frame shift mutation

Question 8

All of the following statements about human mitochondrial DNA are true EXCEPT:

Accepted Answer

It has a low mutation rate.

Answer

It is circular.

Answer

AGA is a stop codon.

Answer

It contains very few untranslated sequences.

Question 9

BRD4 is required for stimulating kinase activity of which of the following?

Accepted Answer

P-TEFB

Answer

HEXIMI

Answer

HOX-B

Answer

TSKsnRNA

Question 10

Which of the following enzymatic activities is possessed by the ribosome?

Accepted Answer

Peptidyl transferase

Answer

Peptidase

Answer

Aminoacyl tRNA synthetase

Answer

GTPase

Molecular Biology and Genomics — MCQs

Molecular Biology and Genomics — MCQs

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