Molecular Biology and Genomics Practice Questions

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.

Q: In the lac operon, transcription is inhibited by binding into which site?

Operator site. ### Explanation The **lac operon** is a classic model of prokaryotic gene regulation, specifically an **inducible system** used by *E. coli* to metabolize lactose. **Why the Operator site is correct:** The **Operator (O site)** is a segment of DNA located between the promoter and the structural genes. In the absence of lactose, a **repressor protein** (encoded by the *lacI* gene) binds specifically to the operator. This binding creates physical steric hindrance, preventing **RNA polymerase** from moving forward from the promoter to the structural genes (*lacZ, lacY, lacA*), thereby inhibiting transcription. This is known as **negative control**. **Analysis of Incorrect Options:** * **A. Promoter site:** This is the binding site for **RNA polymerase**. While transcription *starts* here, inhibition occurs because the repressor blocks the polymerase's progress at the operator, not because the repressor binds to the promoter itself. * **C. CAP site:** The Catabolite Activator Protein (CAP) binds here to **stimulate** transcription when glucose levels are low (via cAMP). This represents **positive control**, not inhibition. * **D. None of the above:** Incorrect, as the operator is the definitive site of repressor-mediated inhibition. ### High-Yield Clinical Pearls for NEET-PG: * **Inducer:** Allolactose (an isomer of lactose) is the natural inducer that binds to the repressor, causing it to detach from the operator. * **IPTG:** A synthetic, non-metabolizable inducer often used in laboratory experiments. * **Constitutive Expression:** Mutations in the *i* gene (repressor) or the operator site lead to "constitutive" expression, where enzymes are produced regardless of lactose presence. * **Glucose Effect:** High glucose levels inhibit Adenylate Cyclase, leading to low cAMP and decreased CAP binding, ensuring the cell prefers glucose over lactose (Catabolite repression).

Q: Which DNA or RNA fragment, which is radioactive or chemically labile, is used to detect a specific fragment?

Probe. **Explanation:** **1. Why the Correct Answer is Right:** A **Probe** is a single-stranded sequence of DNA or RNA (typically 10–1000 nucleotides long) used to detect the presence of a complementary nucleic acid sequence. To be functional, a probe must be **labeled**—either radioactively (e.g., with $^{32}P$) or chemically (e.g., with fluorescent dyes or biotin). Through the process of **hybridization**, the probe binds specifically to its target sequence, allowing researchers to visualize and identify specific genes or fragments in techniques like Southern Blotting (DNA detection) or Northern Blotting (RNA detection). **2. Why Incorrect Options are Wrong:** * **Okazaki fragments:** These are short, newly synthesized DNA fragments formed on the **lagging strand** during DNA replication. They are biological intermediates, not diagnostic tools. * **Antibody:** These are proteins used to detect specific **antigens** (proteins), not DNA/RNA fragments. They are the primary tool in Western Blotting and ELISA. * **Epitope:** This is the specific part of an **antigen** molecule to which an antibody attaches. It is a structural component of a protein, not a detection fragment. **3. NEET-PG High-Yield Clinical Pearls:** * **Southern Blot:** Used for DNA (Mnemonic: **S**outhern = **D**NA). * **Northern Blot:** Used for RNA (Mnemonic: **N**orthern = **R**NA). * **Western Blot:** Used for Proteins (Mnemonic: **W**estern = **P**rotein). * **Probes in Medicine:** Fluorescent In-Situ Hybridization (**FISH**) uses fluorescent probes to detect chromosomal abnormalities like trisomies (Down Syndrome) or gene amplifications (HER2/neu in breast cancer). * **Stringency:** The conditions (temperature and salt concentration) under which a probe hybridizes. High stringency ensures the probe binds only to a perfectly matched sequence.

Q: Which of the following statements is TRUE about the iron-responsive element (IRE)?

It forms a stem-loop structure in messenger RNA.. **Explanation:** The **Iron-Responsive Element (IRE)** is a specific, non-coding sequence of nucleotides that forms a characteristic **stem-loop (hairpin) structure** in the untranslated regions (UTRs) of certain messenger RNAs (mRNAs). This mechanism allows the cell to regulate iron homeostasis at the post-transcriptional level through the action of **Iron Regulatory Proteins (IRPs)**. **Why Option A is correct:** The IRE is defined by its secondary structure—a stem-loop. When iron levels are low, IRPs bind to these loops. Depending on the location of the loop (5' or 3' UTR), this binding either inhibits translation or stabilizes the mRNA. **Analysis of Incorrect Options:** * **Option B:** In **Transferrin Receptor (TfR) mRNA**, the IREs are located in the **3' UTR**. Binding of IRP here stabilizes the mRNA, preventing its degradation and increasing receptor synthesis to bring more iron into the cell. * **Option C:** In **Ferritin mRNA**, the IRE is located in the **5' UTR**. Binding of IRP here acts as a physical block to the ribosome, inhibiting translation to prevent excess iron storage when iron is scarce. * **Option D:** The IRP does not degrade the IRE. Instead, it protects the mRNA from **ribonucleases** (in the case of TfR) or blocks the **initiation complex** (in the case of Ferritin). **High-Yield Clinical Pearls for NEET-PG:** * **High Iron Levels:** Iron binds to IRP, causing it to detach from the mRNA. This leads to **increased Ferritin** synthesis (storage) and **decreased Transferrin Receptor** synthesis (reduced uptake). * **Aconitase Connection:** IRP-1 is bifunctional; when iron is abundant, it functions as the enzyme **c-aconitase** in the cytosol. * **Mnemonic:** **F**erritin = **F**ive prime (5') UTR; **T**ransferrin Receptor = **T**hree prime (3') UTR.

Q: Methylation of cytosine is associated with which of the following?

Decreased expression of gene. **Explanation:** DNA methylation is a key **epigenetic mechanism** used by cells to control gene expression without altering the underlying DNA sequence. **Why Option C is Correct:** Methylation typically occurs at **CpG islands** (regions with a high frequency of Cytosine-Guanine dinucleotide pairs) located in or near gene promoters. The enzyme **DNA Methyltransferase (DNMT)** adds a methyl group to the 5th carbon of the cytosine ring, forming 5-methylcytosine. This modification leads to **decreased gene expression (gene silencing)** via two primary mechanisms: 1. **Physical hindrance:** The methyl groups physically prevent the binding of transcription factors to the promoter. 2. **Chromatin Remodeling:** Methylated DNA recruits **Methyl-CpG-binding domain proteins (MBDs)**, which further recruit histone deacetylases (HDACs). This leads to chromatin condensation (formation of heterochromatin), making the DNA inaccessible for transcription. **Why Other Options are Incorrect:** * **Option A:** While spontaneous deamination of 5-methylcytosine can lead to a Thymine mutation (a common cause of single nucleotide polymorphisms), methylation itself is a physiological regulatory process, not a primary mutational event. * **Option B:** Increased expression is generally associated with **DNA hypomethylation** or **Histone Acetylation**. * **Option D:** Methylation has a profound effect on cellular identity, X-inactivation, and genomic imprinting. **NEET-PG High-Yield Pearls:** * **Mnemonic:** **M**ethylation **M**utes DNA; **A**cetylation **A**ctivates DNA. * **Genomic Imprinting:** Methylation is the basis for Prader-Willi and Angelman syndromes (differential methylation of maternal/paternal alleles). * **Fragile X Syndrome:** Characterized by hypermethylation of the FMR1 gene due to CGG triplet repeat expansion. * **Cancer:** Hypermethylation of tumor suppressor genes (like *p16*) is a common finding in many malignancies.

Q: Which type of RNA is synthesized using a DNA template but does not code for proteins?

cDNA. ### Explanation The question asks for an RNA type synthesized from a DNA template that does not code for proteins. However, there is a **conceptual error in the provided key**: **cDNA (complementary DNA)** is not a type of RNA; it is DNA synthesized from an RNA template via reverse transcription. In a standard NEET-PG context, the correct answer for "non-coding RNA synthesized from DNA" would typically be **tRNA or rRNA**. **1. Analysis of the Options:** * **cDNA (Option D - Marked Correct):** This is factually incorrect as a type of RNA. cDNA is **DNA** synthesized from a messenger RNA (mRNA) template using the enzyme **Reverse Transcriptase**. It is used in RT-PCR and gene cloning because it lacks introns. * **tRNA (Option A) & rRNA (Option C):** These are the correct biological answers. Both are synthesized from a DNA template (via RNA Polymerase III and I, respectively) and are **non-coding RNAs**, meaning they do not translate into proteins but function in protein synthesis. * **mRNA (Option B):** This is synthesized from DNA but is **coding RNA**, as it carries the genetic blueprint to the ribosome for translation into proteins. **2. High-Yield NEET-PG Pearls:** * **RNA Polymerase I:** Synthesizes rRNA (except 5S). * **RNA Polymerase II:** Synthesizes mRNA and snRNA. * **RNA Polymerase III:** Synthesizes tRNA and 5S rRNA. * **Reverse Transcriptase:** An RNA-dependent DNA polymerase used by retroviruses (like HIV) and in labs to create cDNA. * **Non-coding RNAs (ncRNA):** Include tRNA, rRNA, miRNA, and snRNA; they regulate gene expression and protein synthesis but are never translated. **Note for Students:** If this specific question appears with "cDNA" as the key, it is likely a technical error in the question bank. Always remember: **cDNA = DNA from RNA.**

Q: In which of the following techniques are oligonucleotide primers used?

Polymerase Chain Reaction (PCR). **Explanation:** **Correct Option: B. Polymerase Chain Reaction (PCR)** PCR is an *in vitro* enzymatic method used to amplify specific DNA sequences. The process requires **oligonucleotide primers**, which are short, single-stranded DNA sequences (usually 15–30 nucleotides long) complementary to the target DNA's flanking regions. These primers provide a free 3'-OH group, allowing **Taq Polymerase** to initiate DNA synthesis. Without these specific primers, the polymerase cannot bind and extend the DNA chain. **Analysis of Incorrect Options:** * **A. RFLP:** This technique relies on **Restriction Endonucleases** to cut DNA at specific recognition sites. The fragments are then separated by electrophoresis and visualized using labeled probes, not primers. * **C. FISH:** This technique uses fluorescently labeled **DNA/RNA probes** to detect and locate specific gene sequences directly on intact chromosomes. It is a hybridization technique, not an amplification technique requiring primers. * **D. Chromosomal Walking:** While this method is used to sequence long stretches of DNA by using the end of one cloned fragment as a probe to find the next, the fundamental tool used to identify overlapping clones is a **probe**, not a primer-driven amplification (though modern variations may use PCR, the classical definition relies on genomic library screening). **NEET-PG High-Yield Pearls:** * **PCR Steps:** Denaturation (94°C) → Annealing (55°C; where primers bind) → Extension (72°C). * **Components of PCR:** Template DNA, Primers, dNTPs, and Heat-stable DNA polymerase (Taq). * **Clinical Use:** PCR is the gold standard for diagnosing viral loads (e.g., HIV, Hepatitis C) and detecting genetic mutations.

Question 1

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

Accepted Answer

P-TEFB

Answer

HEXIMI

Answer

HOX-B

Answer

TSKsnRNA

Question 2

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

Accepted Answer

Peptidyl transferase

Answer

Peptidase

Answer

Aminoacyl tRNA synthetase

Answer

GTPase

Question 3

In the lac operon, transcription is inhibited by binding into which site?

Accepted Answer

Operator site

Answer

Promoter site

Answer

CAP site

Answer

None of the above

Question 4

Which DNA or RNA fragment, which is radioactive or chemically labile, is used to detect a specific fragment?

Accepted Answer

Probe

Answer

Okazaki fragment

Answer

Antibody

Answer

Epitope

Question 5

Somatic mutations involve:

Accepted Answer

Frame-shift alteration in coding nucleotides

Answer

Deletion

Answer

Plasmid mediated

Answer

None

Question 6

Which of the following statements is TRUE about the iron-responsive element (IRE)?

Accepted Answer

It forms a stem-loop structure in messenger RNA.

Answer

It is located in the 5' untranslated region (UTR) of transferrin mRNA.

Answer

It is located in the 3' untranslated region (UTR) of ferritin mRNA.

Answer

The IRE-binding protein causes the degradation of the IRE.

Question 7

Which of the following tests is NOT used in epigenetics?

Accepted Answer

HPLC

Answer

ChIP-on-ChIP

Answer

Bisulfite sequencing

Answer

Methylation-sensitive restriction enzyme digestion

Question 8

Methylation of cytosine is associated with which of the following?

Accepted Answer

Decreased expression of gene

Answer

Mutation

Answer

Increased expression of gene

Answer

No effect

Question 9

Which type of RNA is synthesized using a DNA template but does not code for proteins?

Accepted Answer

cDNA

Answer

tRNA

Answer

mRNA

Answer

rRNA

Question 10

In which of the following techniques are oligonucleotide primers used?

Accepted Answer

Polymerase Chain Reaction (PCR)

Answer

Restriction Fragment Length Polymorphism (RFLP)

Answer

Fluorescence In Situ Hybridization (FISH)

Answer

Chromosomal walking

Molecular Biology and Genomics — MCQs

Molecular Biology and Genomics — MCQs

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