Molecular Biology and Genomics — MCQs

Molecular Biology and Genomics Indian Medical PG Practice Questions and MCQs

Question 831: Which of the following techniques can be used to detect single base pair substitutions?

A. FISH
B. Southern blot
C. PCR (Correct Answer)
D. Restriction Fragment Length Polymorphism (RFLP)

Explanation: ***PCR (with sequencing or allele-specific methods)*** - **PCR-based techniques** are the most versatile methods for detecting single base pair substitutions (point mutations) - **Allele-specific PCR** can directly detect known point mutations by using primers specific to mutant or wild-type alleles - **PCR followed by Sanger sequencing** is the gold standard for identifying any single base pair substitution - **High-resolution melting (HRM) analysis** after PCR can detect mutations based on melting curve differences - PCR amplification is the foundation that enables these detection methods *FISH (Fluorescence in situ hybridization)* - FISH detects **large chromosomal abnormalities** such as aneuploidy, translocations, large deletions, and duplications - It visualizes chromosomal-level changes using fluorescent probes - **Not sensitive enough** to detect single base pair changes, as these are too small to visualize cytogenetically *Southern blot* - Southern blot detects **large DNA rearrangements**, insertions, deletions, or copy number variations - Analyzes restriction enzyme fragments separated by gel electrophoresis - **Generally cannot detect** single base pair substitutions unless they create or abolish a restriction enzyme recognition site - Even when applicable, PCR-based methods are more efficient and sensitive *Restriction Fragment Length Polymorphism (RFLP)* - RFLP can detect single base pair substitutions **only if** they create or abolish a **restriction enzyme recognition site** - Classic example: **Sickle cell mutation** (GAG→GTG in β-globin gene) abolishes an MstII restriction site - **Limited applicability** - can only detect the subset of point mutations that affect restriction sites - PCR-based methods are preferred as they can detect **any** single base pair substitution, not just those affecting restriction sites

Question 832: Which of the following best defines genomic imprinting?

A. Different expression of a gene depending on the parent of origin. (Correct Answer)
B. Expression of genes silenced on one chromosome through random X-inactivation.
C. Parent-specific gene expression due to chromosomal deletions only.
D. Uniparental disomy is a condition where both alleles come from one parent.

Explanation: ***Different expression of gene depending on parent of origin*** - Genomic imprinting refers to the phenomenon where genes are expressed in a parent-of-origin-specific manner, affecting gene expression based on whether the allele is inherited from the mother or father [1]. - This can lead to different phenotypic outcomes and is critical in various genetic disorders [1]. *Angelman syndrome is due to maternal deletion of chromosome 15* - Angelman syndrome is caused by a **paternal deletion** of chromosome 15 and maternal disomy, not a deletion from the mother [1]. - The maternal genes on this chromosome are typically imprinted and thus not expressed in the absence of the paternal contribution [1]. *Prader-Willi syndrome is paternal deletion of chromosome 15* - Prader-Willi syndrome is actually a result of a **maternal deletion** or paternal imprinting of chromosome 15, leading to loss of function of paternal genes . - The absence of these paternal genes causes the manifestations of the syndrome, making this statement incorrect . *Uniparental disomy is a condition where both alleles come from one parent, not genomic imprinting* - While uniparental disomy involves both alleles coming from one parent, it does **not directly relate to** genomic imprinting, which modulates the expression based on the parental origin [1]. - Uniparental disomy can lead to imprinting disorders only if the involved genes are subject to genomic imprinting [1]. **References:** [1] Kumar V, Abbas AK, et al.. Robbins and Cotran Pathologic Basis of Disease. 9th ed. Genetic Disorders, pp. 181-183.

Question 833: What is the technique for accurate quantification of gene expression?

A. PCR
B. Real-Time Reverse Transcriptase PCR (Correct Answer)
C. Reverse Transcriptase PCR
D. Northern blot

Explanation: ***Real-Time Reverse Transcriptase PCR*** - This technique allows for the **quantification of gene expression** by concurrently reverse-transcribing RNA to cDNA and amplifying it while monitoring the accumulation of DNA in real-time using fluorescent reporters. - The ** threshold cycle (Ct) value** is inversely proportional to the initial amount of target mRNA, enabling precise quantification. *Northern blot* - This method is used to detect **RNA sequences** and can provide semi-quantitative data about gene expression levels based on band intensity. - However, it is generally **less sensitive** and provides less precise quantification compared to real-time PCR. *PCR* - **Standard PCR** amplifies DNA, but it is not directly used for gene expression quantification as it starts with DNA templates. - While it can be used to detect the presence of a gene, it does not quantify its expression without further modifications or additional steps like reverse transcription and real-time monitoring. *Reverse Transcriptase PCR* - This technique involves **reverse transcribing RNA into cDNA** and then performing standard PCR to amplify the cDNA. - While it confirms the presence of mRNA and allows for cDNA amplification, it is a **qualitative or semi-quantitative** method for expression, as the endpoint detection does not accurately reflect initial mRNA concentration due to plateau effects.

Question 834: Which phase of the cell cycle does not have a fixed duration?

A. S phase (DNA synthesis)
B. M phase (mitosis)
C. G1 phase (cell growth) (Correct Answer)
D. G2 phase (preparation for mitosis)

Explanation: ***G1*** - The **G1 phase** of the cell cycle is variable in length and can differ significantly between cell types and conditions, unlike S, M, and G2 phases [1][2]. - Cells can spend an **indeterminate amount of time** in G1, depending on factors like nutrients and signals for division [2]. *S* - The **S phase** is characterized by a fixed duration where **DNA replication** occurs, and is critical for cell division [1]. - It typically has a well-defined time frame in the cell cycle that is consistent across different cells [1]. *M* - The **M phase** (mitosis) requires a set duration to ensure that the **cell divides** accurately and equally into two daughter cells [2]. - Fluctuations in this phase can result in aberrant cell division and aneuploidy. *G2* - The **G2 phase** also has a consistent timeframe dedicated to preparing the cell for mitosis, focusing on DNA repair and organelle duplication [2]. - The cell ensures readiness for division during this phase, which is critical for genomic integrity. **References:** [1] Cross SS. Underwood's Pathology: A Clinical Approach. 6th ed. (Basic Pathology) introduces the student to key general principles of pathology, both as a medical science and as a clinical activity with a vital role in patient care. Part 2 (Disease Mechanisms) provides fundamental knowledge about the cellular and molecular processes involved in diseases, providing the rationale for their treatment. Part 3 (Systematic Pathology) deals in detail with specific diseases, with emphasis on the clinically important aspects., pp. 78-79. [2] Kumar V, Abbas AK, et al.. Robbins and Cotran Pathologic Basis of Disease. 9th ed. With Illustrations By, pp. 37-38.

Question 835: Gene silencing refers to a gene that would be expressed under normal circumstances being switched off by cell machinery. Which one of the following cellular components is not involved in gene silencing?

A. Double stranded RNA
B. siRNA
C. Micro-RNA
D. Ribosomal RNA (Correct Answer)

Explanation: ***Micro-RNA*** - **Micro-RNAs** play a crucial role in gene regulation by binding to complementary sequences in mRNA, leading to gene silencing or degradation [1]. - They are involved in post-transcriptional regulation, effectively controlling gene expression at the **mRNA level** [1]. *Si RNA* - While **small interfering RNA (siRNA)** is also involved in gene silencing, it operates through a slightly different mechanism, primarily within RNA interference pathways. - SiRNAs typically require specific machinery for their function and are not the primary agents of gene silencing described in the question. *Double stranded RNA* - **Double-stranded RNA (dsRNA)** can induce silencing but serves primarily as a trigger for the RNA interference pathway rather than being the active component in gene silencing itself. - It is often utilized in research and therapeutic contexts but does not directly engage in the gene silencing process. *Ribosomal RNA* - **Ribosomal RNA (rRNA)** is primarily involved in protein synthesis and the structural component of ribosomes, with no role in gene silencing mechanisms. - It serves as a scaffold for ribosome assembly and is not implicated in the regulation of gene expression. **References:** [1] Kumar V, Abbas AK, et al.. Robbins and Cotran Pathologic Basis of Disease. 9th ed. With Illustrations By, pp. 16-18.

Question 836: Phenotypic expression of a gene depending on the parent of origin is referred to as:

A. Genomic imprinting (parent-of-origin gene expression) (Correct Answer)
B. Mosaic genetic variation
C. Nonpenetrance of genotype
D. Genetic anticipation

Explanation: ***Genomic imprinting (parent-of-origin gene expression)*** - **Genomic imprinting** is an epigenetic phenomenon where gene expression is dependent on whether the gene was inherited from the mother or the father. - This results in monoallelic expression of specific genes, with only one copy (maternal or paternal) being active. *Mosaic genetic variation* - **Mosaicism** refers to the presence of two or more populations of genetically different cells in one individual, all derived from a single zygote. - This typically arises from a somatic mutation during development, not from differential expression based on parental origin. *Nonpenetrance of genotype* - **Nonpenetrance** occurs when individuals carrying a disease-causing genotype do not express the associated phenotype. - This concept relates to the presence or absence of a phenotype, not the differential expression based on parental origin. *Genetic anticipation* - **Genetic anticipation** is the phenomenon where the symptoms of a genetic disorder become more severe and/or appear at an earlier age in successive generations. - This is commonly observed in disorders caused by expansions of trinucleotide repeats, such as Huntington's disease, and is distinct from parent-of-origin gene expression.

Question 837: Which of the following genes of Hepatitis B virus encodes for DNA polymerase?

A. X gene
B. C gene
C. P gene (Correct Answer)
D. S gene

Explanation: ***P gene*** - The **P gene** (polymerase gene) of the **hepatitis B virus (HBV)** encodes for the viral DNA polymerase. - This **DNA polymerase** is crucial for both reverse transcription of pregenomic RNA and DNA synthesis during viral replication. *X gene* - The **X gene** of HBV encodes for the **HBx protein**, which is a transcriptional transactivator and plays a role in hepatocarcinogenesis. - It does not encode for DNA polymerase. *C gene* - The **C gene** of HBV encodes for the **HBcAg (hepatitis B core antigen)** and **HBeAg (hepatitis B e antigen)**. - These proteins are involved in viral assembly and immune modulation, respectively, not DNA synthesis. *S gene* - The **S gene** of HBV encodes for the **HBsAg (hepatitis B surface antigen)**, which is involved in viral entry into host cells and is the primary antigen used in vaccines. - It does not encode for the viral DNA polymerase.

Question 838: When a gene is expressed exclusively from the allele inherited from one parent while the allele from the other parent is silenced, what is this phenomenon known as?

A. Genomic imprinting (Correct Answer)
B. Mosaicism
C. Alleles
D. Chimerism

Explanation: ***Genomic imprinting*** - **Genomic imprinting** is an epigenetic phenomenon where certain genes are expressed in a **parent-of-origin-specific manner**. - This means that depending on whether the gene was inherited from the **mother or the father**, only one copy (maternal or paternal) is expressed, while the other is silenced. *Mosaicism* - **Mosaicism** describes the presence of **two or more cell lines** with different genotypes within a single individual, originating from a single zygote. - This typically arises from a **post-zygotic mutation** or chromosomal abnormality during early embryonic development. *Alleles* - **Alleles** are different forms of a **single gene** located at the same locus on homologous chromosomes. - An individual inherits **two alleles** for each gene, one from each parent, but both are usually expressed unless one is recessive. *Chimerism* - **Chimerism** refers to an individual composed of cells from **two or more different zygotes**, meaning the cells originate from different genetic lineages. - This can occur through processes like **fusion of two embryos** or organ transplantation.

Question 839: Preferential expression of a gene depending upon the parent of origin is called:

A. Mosaicism
B. Genomic imprinting (Correct Answer)
C. Alleles
D. Chimerism

Explanation: ***Genomic imprinting*** * Genomic imprinting refers to the **epigenetic phenomenon** where the expression of certain genes is determined by whether they are inherited from the mother or the father. * This involves **DNA methylation** and histone modifications that lead to transcriptional silencing of either the maternal or paternal allele. *Mosaicism* * **Mosaicism** occurs when an individual has two or more genetically different cell lines originating from a single zygote. * It does not relate to parent-of-origin gene expression but rather to the presence of **different genotypes** within the same individual's cells. *Alleles* * **Alleles** are different forms of a gene located at the same locus on homologous chromosomes. * While alleles are involved in inheritance, their definition does not inherently describe the **parent-of-origin expression** pattern. *Chimerism* * **Chimerism** is the presence of cells from two or more different individuals in one individual, usually originating from the fusion of two or more zygotes. * This is different from genomic imprinting, which involves differential gene expression based on the **parental origin** of a gene within a single individual's genome.

Question 840: What is the term used to describe the process where complementary single-stranded DNA molecules bind together to form a double helix in molecular biological methods?

A. DNA-DNA hybridization
B. DNA annealing (Correct Answer)
C. DNA-DNA ligation
D. DNA denaturation

Explanation: ***DNA annealing*** - **Annealing** is the specific term used in molecular biology to describe the process where two **complementary single-stranded DNA** molecules bind together through base pairing to form a double helix. - This term is commonly used in techniques like **PCR** (polymerase chain reaction), where primers anneal to template DNA during the annealing step. - The process involves **controlled cooling** that allows complementary sequences to recognize and bind to each other through hydrogen bonding. *DNA-DNA hybridization* - **Hybridization** is a broader, more general term that encompasses any pairing of complementary nucleic acid strands (DNA-DNA, DNA-RNA, or RNA-RNA). - While annealing is a type of hybridization, in molecular biology practice, "annealing" specifically refers to the binding step in enzymatic reactions like PCR. - Hybridization is more commonly used to describe probe-target binding in techniques like Southern blotting or in situ hybridization. *DNA-DNA ligation* - **Ligation** is an entirely different process involving the enzymatic joining of two **DNA fragments** using **DNA ligase**. - This creates a **phosphodiester bond** between the 3'-hydroxyl and 5'-phosphate ends of adjacent DNA strands, not base pairing between complementary strands. *DNA denaturation* - **Denaturation** (or melting) is the **opposite process** where a double-stranded DNA molecule separates into two single strands by breaking hydrogen bonds between base pairs. - This typically occurs through **heating** or chemical treatment and is the step that precedes annealing in PCR cycles.

Practice by Chapter

DNA Replication and Repair Mechanisms

Practice Questions

Transcription Factors and Gene Regulation

Practice Questions

Epigenetics and DNA Methylation

Practice Questions

RNA Processing and Splicing

Practice Questions

miRNA and RNA Interference

Practice Questions

Protein Synthesis and Post-Translational Modifications

Practice Questions

Genomics and Human Genome Project

Practice Questions

Single Nucleotide Polymorphisms

Practice Questions

Gene Therapy Approaches

Practice Questions

CRISPR-Cas9 and Genome Editing

Practice Questions

DNA Fingerprinting and Forensics

Practice Questions

Molecular Basis of Genetic Diseases

Practice Questions

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