Molecular Biology and Genomics Practice Questions

Q: Which of the following methods cannot be used to detect subtelomeric fractions in children with idiopathic MR?

Laser diode index. **Explanation:** Subtelomeric rearrangements (deletions or duplications) are a significant cause of idiopathic mental retardation (MR), accounting for approximately 5–10% of cases. Detecting these micro-aberrations requires high-resolution molecular cytogenetic techniques. **Why "Laser Diode Index" is the correct answer:** A **Laser Diode** is a semiconductor device used in optical fiber communications and barcode readers; it is **not a diagnostic medical technique** for genetic analysis. There is no established "Laser Diode Index" used in cytogenetics or the detection of chromosomal fractions. **Analysis of Incorrect Options:** * **FISH (Fluorescence In Situ Hybridization):** Historically the "gold standard" for detecting subtelomeric deletions. It uses fluorescent probes specific to the telomeric regions to visualize missing or extra segments under a microscope. * **MALDI (Matrix-Assisted Laser Desorption/Ionization):** This is a type of Mass Spectrometry (MALDI-TOF). It is used for high-throughput analysis of DNA fragments and can detect single nucleotide polymorphisms (SNPs) and small deletions/insertions in subtelomeric regions. * **Array CGH (Comparative Genomic Hybridization):** Currently the first-line investigation for children with unexplained developmental delay or MR. It provides a much higher resolution than standard karyotyping, allowing for the detection of submicroscopic copy number variants (CNVs) across the entire genome, including subtelomeres. **Clinical Pearls for NEET-PG:** * **First-line investigation** for idiopathic MR/Developmental Delay: **Array CGH** (Microarray). * **Standard Karyotyping** resolution is ~5 Mb; subtelomeric rearrangements are often <5 Mb, necessitating molecular techniques. * Common subtelomeric syndrome: **22q13.3 deletion syndrome** (Phelan-McDermid syndrome).

Q: What is telomerase?

RNA dependent DNA polymerase. **Explanation:** **Telomerase** is a specialized enzyme responsible for maintaining the length of telomeres (the repetitive TTAGGG sequences at the ends of eukaryotic chromosomes). 1. **Why Option B is Correct:** Telomerase is a **ribonucleoprotein** complex. It contains an internal RNA template (known as TERC) that it uses to synthesize complementary DNA sequences. Because it uses an **RNA template** to synthesize **DNA**, it is functionally an **RNA-dependent DNA polymerase** (a type of reverse transcriptase). This activity prevents the "end-replication problem," where chromosomes shorten with each cell division. 2. **Why Other Options are Incorrect:** * **Option A (DNA-dependent RNA polymerase):** These enzymes (like RNA Polymerase I, II, and III) use DNA as a template to synthesize RNA (transcription). * **Option C (RNA-dependent RNA polymerase):** These are primarily found in RNA viruses (e.g., Poliovirus, SARS-CoV-2) to replicate their RNA genomes; they are not naturally occurring in human telomere maintenance. * **Option D (DNA-dependent DNA polymerase):** These are standard DNA polymerases (e.g., Pol $\alpha, \delta, \epsilon$) used in semi-conservative DNA replication. **High-Yield Clinical Pearls for NEET-PG:** * **Cellular Aging:** Telomerase is active in germ cells, stem cells, and cancer cells, but is **absent or low in most somatic cells**, leading to cellular senescence (the Hayflick limit). * **Cancer:** Approximately 85-90% of cancer cells upregulate telomerase to achieve **replicative immortality**. * **Components:** It consists of **TERT** (Telomerase Reverse Transcriptase - the catalytic protein) and **TERC** (Telomerase RNA component - the template). * **Clinical Correlation:** Mutations in telomerase components can lead to **Dyskeratosis Congenita**, characterized by bone marrow failure and premature aging.

Q: The same amino acid can be coded by multiple codons due to which phenomenon?

Degeneracy. **Explanation:** The correct answer is **Degeneracy**. In the genetic code, there are 64 possible codons but only 20 standard amino acids. This redundancy, where multiple different codons specify the same single amino acid, is termed "Degeneracy." This phenomenon primarily occurs due to the **Wobble Hypothesis**, which states that the third base of the codon (the 3' end) has less stringent base-pairing requirements with the anticodon of tRNA. For example, Leucine, Serine, and Arginine are each coded by six different codons. **Analysis of Incorrect Options:** * **B. Frame-shift mutation:** This occurs when the addition or deletion of nucleotides (not in multiples of three) shifts the reading frame of the mRNA, usually resulting in a completely different protein sequence or a premature stop codon. * **C. Transcription:** This is the biological process of copying a segment of DNA into RNA by the enzyme RNA polymerase. It is a step in gene expression, not a property of the genetic code itself. * **D. Mutation:** This is a general term for any permanent alteration in the DNA sequence. While mutations can lead to changes in codons, they do not define the inherent redundancy of the genetic code. **High-Yield Clinical Pearls for NEET-PG:** * **Universality:** The genetic code is the same in almost all organisms (Exceptions: Mitochondrial DNA, where UGA codes for Tryptophan instead of a Stop codon). * **Non-overlapping & Commaless:** The code is read sequentially, three bases at a time, without skipping any bases. * **Unambiguous:** While one amino acid can have many codons (Degeneracy), **one specific codon always codes for only one amino acid.** * **Initiation Codon:** AUG (Methionine); **Stop Codons:** UAA, UAG, UGA.

Q: What is true about Restriction Fragment Length Polymorphism (RFLP)?

Detects mutation. **Explanation:** **Restriction Fragment Length Polymorphism (RFLP)** is a molecular biology technique used to detect variations in DNA sequences. It relies on the principle that a specific **mutation** (single nucleotide polymorphism) can either create or abolish a recognition site for a **restriction endonuclease** enzyme. 1. **Why Option A is Correct:** When a mutation occurs at a restriction site, the enzyme fails to cut the DNA at that specific point, or it may cut at a new site. This results in DNA fragments of varying lengths (polymorphism) when separated by gel electrophoresis. Therefore, RFLP is primarily used to **detect mutations** that alter restriction sites. 2. **Why Other Options are Incorrect:** * **Option B:** Trinucleotide repeats (e.g., in Fragile X or Huntington’s) are typically detected using PCR or Southern Blotting to measure expansion size, rather than RFLP. * **Option C:** While large deletions can change fragment size, RFLP is specifically designed to identify variations at specific restriction enzyme recognition sequences. Deletions are more accurately detected by Comparative Genomic Hybridization (CGH) or multiplex PCR. * **Option D:** Restriction enzymes can produce either "sticky ends" (overhangs) or "blunt ends." Producing blunt ends is not a defining characteristic or a requirement for RFLP analysis. **Clinical Pearls for NEET-PG:** * **Applications:** RFLP is used in forensic science (DNA fingerprinting), paternity testing, and identifying genetic carriers for diseases like **Sickle Cell Anemia** (where a mutation destroys the *MstII* enzyme site). * **Key Requirement:** You must have a specific DNA probe that complementary binds to the region of interest. * **Evolution:** RFLP has largely been replaced by faster, PCR-based SNP genotyping, but remains a fundamental concept in genetic linkage analysis.

Q: Phenotypic expression of a gene depending on the parent of origin is referred to as _______

Genomic imprinting. **Explanation:** **Genomic Imprinting** is an epigenetic process where certain genes are expressed in a parent-of-origin-specific manner. While most autosomal genes are expressed from both alleles, imprinted genes are "silenced" (usually via DNA methylation) in either the egg or the sperm. Therefore, the phenotype of the offspring depends entirely on which parent transmitted the active allele [1]. **Analysis of Incorrect Options:** * **B. Mosaicism:** Refers to the presence of two or more populations of cells with different genotypes in one individual, derived from a single zygote (e.g., Turner syndrome mosaicism 45,X/46,XX). * **C. Anticipation:** A phenomenon where a genetic disorder becomes more severe or appears at an earlier age in succeeding generations. This is typically seen in **Trinucleotide Repeat Disorders** (e.g., Huntington’s disease, Fragile X). * **D. Nonpenetrance:** Occurs when an individual carries a dominant disease-causing mutation but does not exhibit any clinical symptoms of the disease. **High-Yield Clinical Pearls for NEET-PG:** * **Prader-Willi Syndrome:** Deletion of the **paternal** copy of chromosome 15q11-q13 (Maternal imprinting). Features: Hyperphagia, obesity, and hypogonadism. * **Angelman Syndrome:** Deletion of the **maternal** copy of the same region (Paternal imprinting) [1]. Features: Inappropriate laughter ("Happy Puppet"), ataxia, and seizures. * **Uniparental Disomy (UPD):** When an individual receives two copies of a chromosome from one parent and none from the other; this is a common mechanism for imprinting disorders [1].

Q: Which sequence is present immediately downstream of the Shine-Dalgarno sequence in prokaryotes?

AUG. **Explanation:** In prokaryotic translation initiation, the **Shine-Dalgarno (SD) sequence** plays a critical role in mRNA recognition. It is a purine-rich leader sequence (typically AGGAGG) located approximately 8 base pairs upstream of the start codon. The SD sequence is complementary to the 3' end of the **16S rRNA** (part of the 30S ribosomal subunit). This base-pairing ensures that the ribosome is correctly positioned so that the P-site is aligned directly over the **AUG start codon**, which is located immediately downstream. This alignment is essential for the initiation of protein synthesis and ensures the correct reading frame is established. **Analysis of Options:** * **Option A (AUG):** Correct. This is the universal start codon in prokaryotes (coding for N-formylmethionine) and is positioned downstream of the SD sequence to initiate translation. * **Options B, C, and D (UAG, UGA, UAA):** Incorrect. These are **Stop Codons** (Amber, Opal, and Ochre, respectively). Their presence immediately downstream of an SD sequence would result in immediate termination of translation rather than initiation. **High-Yield Facts for NEET-PG:** * **Kozak Sequence:** The eukaryotic functional equivalent of the Shine-Dalgarno sequence, which helps the 40S subunit identify the start codon. * **16S rRNA:** A component of the small ribosomal subunit (30S) in prokaryotes; its interaction with the SD sequence is a classic example of RNA-RNA interaction. * **Streptomycin:** An aminoglycoside that acts by binding to the 30S subunit, interfering with the initiation complex and the reading of the mRNA.

Q: All are processing reactions in tRNA, except?

Poly A tailing. **Explanation:** Post-transcriptional modification is essential for converting precursor tRNA (pre-tRNA) into functional mature tRNA. **Why Poly A tailing is the correct answer:** **Polyadenylation (Poly A tailing)** is a characteristic processing step for **mRNA**, not tRNA. In eukaryotes, a tail of 200–250 adenine residues is added to the 3’ end of mRNA to enhance stability and facilitate translation initiation. In contrast, adding a Poly A tail to tRNA or rRNA in some organisms actually signals for their degradation rather than maturation. **Analysis of incorrect options (Processing steps that DO occur in tRNA):** * **CCA tailing:** All mature tRNAs have a **CCA sequence** at their 3’ end, which is the attachment site for amino acids. While prokaryotic tRNA genes often encode this, eukaryotic tRNAs require the enzyme *nucleotidyltransferase* to add it post-transcriptionally. * **Methylation of bases:** tRNA undergoes extensive base modifications (e.g., methylation, pseudouridylation) to stabilize its tertiary structure and ensure precise codon-anticodon pairing. * **Trimming of 5’ end:** Pre-tRNA contains "leader" and "trailer" sequences. The 5’ leader sequence is removed by **RNase P** (a ribozyme), while the 3’ trailer is removed by RNase D. **High-Yield Clinical Pearls for NEET-PG:** * **RNase P** is a classic example of a **ribozyme** (RNA acting as a catalyst). * **Intron removal:** Some eukaryotic tRNAs contain introns in the anticodon loop; these are removed by a unique **endonuclease** rather than the standard spliceosome used for mRNA. * **Unusual Bases:** tRNA contains modified bases like **Dihydrouridine (D-loop)** and **Pseudouridine (TψC loop)**, which are diagnostic features of its "cloverleaf" secondary structure.

Question 1

Which of the following methods cannot be used to detect subtelomeric fractions in children with idiopathic MR?

Accepted Answer

Laser diode index

Answer

FISH

Answer

MALDI

Answer

Array comparative genomic hybridization

Question 2

What is telomerase?

Accepted Answer

RNA dependent DNA polymerase

Answer

DNA dependent RNA polymerase

Answer

RNA dependent RNA polymerase

Answer

DNA dependent DNA polymerase

Question 3

The same amino acid can be coded by multiple codons due to which phenomenon?

Accepted Answer

Degeneracy

Answer

Frame-shift mutation

Answer

Transcription

Answer

Mutation

Question 4

What is true about Restriction Fragment Length Polymorphism (RFLP)?

Accepted Answer

Detects mutation

Answer

Recognizes trinucleotide repeat

Answer

Detects deletion

Answer

Blunt ends are produced

Question 5

Nonsense mutation is seen in which of the following conditions?

Accepted Answer

Thalassemia

Answer

AIHA

Answer

Sickle cell anemia

Answer

Hemophilia

Question 6

Phenotypic expression of a gene depending on the parent of origin is referred to as _______

Accepted Answer

Genomic imprinting

Answer

Mosaicism

Answer

Anticipation

Answer

Nonpenetrance

Question 7

Which of the following statements regarding the microarray technique is false?

Accepted Answer

It can detect Robertsonian translocations.

Answer

Its core principle is DNA hybridization.

Answer

It is also known as a DNA chip or biochip.

Answer

It can detect deletions and insertions.

Question 8

Which sequence is present immediately downstream of the Shine-Dalgarno sequence in prokaryotes?

Accepted Answer

AUG

Answer

UAG

Answer

UGA

Answer

UAA

Question 9

All are processing reactions in tRNA, except?

Accepted Answer

Poly A tailing

Answer

CCA tailing

Answer

Methylation of bases

Answer

Trimming of 5’ end

Question 10

Which of the following is true about DNA polymerase in eukaryotes?

Accepted Answer

β is associated with repair

Answer

Components are α, β, γ, δ, ε

Answer

γ is associated with repair

Answer

δ is associated with synthesis of mitochondrial DNA

Molecular Biology and Genomics — MCQs

Molecular Biology and Genomics — MCQs

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