Molecular Biology and Genomics Practice Questions

Q: What is the repair mechanism associated with CRISPR-cas9?

Non-homologous end joining. ***Non-homologous end joining*** - **CRISPR-Cas9** creates a **double-strand break (DSB)** in DNA, which is primarily repaired by **non-homologous end joining (NHEJ)**. - **NHEJ** is the **predominant repair pathway** in most cells, accounting for 60-90% of DSB repairs. - **NHEJ** is an error-prone repair mechanism that ligates the broken ends directly, often leading to small **insertions or deletions (indels)** causing gene knockout. - Note: **Homology-directed repair (HDR)** is another CRISPR-associated mechanism used for precise editing when a donor template is provided, but **NHEJ is the primary endogenous repair pathway**. *Mismatch repair* - This mechanism corrects errors that arise during **DNA replication**, such as incorrect base pairing. - It does not repair **double-strand breaks** induced by CRISPR-Cas9. *Nucleotide excision repair* - This pathway removes **bulky DNA adducts** and lesions, such as those caused by UV radiation. - It is not involved in repairing **CRISPR-Cas9 induced double-strand breaks**. *Base excision repair* - This mechanism corrects **damaged or modified bases**, typically single base changes, without affecting the sugar-phosphate backbone significantly. - It handles different types of DNA damage than the **double-strand breaks** generated by CRISPR-Cas9.

Q: Which of the following molecular analysis methods is used to detect RNA?

RT-PCR. ***RT-PCR*** - **Reverse transcriptase polymerase chain reaction (RT-PCR)** is a molecular method that first converts **RNA into complementary DNA (cDNA)** using reverse transcriptase before amplification via PCR. - This technique is commonly used to detect and quantify specific **RNA sequences**, such as viral RNA or gene expression levels. *Western blot* - **Western blot** is a laboratory technique used to detect specific **proteins** in a sample. - It involves separating proteins by size using gel electrophoresis, transferring them to a membrane, and then detecting the target protein using specific antibodies. *G banding* - **G banding** is a cytogenetic technique used to produce a visible **karyotype** by staining condensed chromosomes. - This method is primarily used to detect large-scale structural changes in chromosomes, not to detect RNA. *Sanger's method* - **Sanger's method**, also known as **dideoxy sequencing**, is a DNA sequencing technique. - It is used to determine the exact order of **nucleotides within a DNA molecule**, not to detect RNA directly.

Q: Steps of PCR in sequence are?

Denature DNA, Anneal Primers, Extend DNA. ***Denature DNA, Anneal Primers, Extend DNA*** - This sequence represents the three fundamental steps of each PCR cycle, ensuring accurate and efficient **DNA amplification**. - **Denaturation** separates the double-stranded DNA template, **annealing** allows primers to bind to specific sequences, and **extension** synthesizes new DNA strands. *Denature DNA, Extend DNA, Anneal Primers* - This order is incorrect because **primer annealing** must occur before DNA extension can begin. - Primers provide the necessary starting points for the **DNA polymerase** to synthesize the new strands. *Anneal Primers, Extend DNA, Denature DNA* - This sequence is incorrect as the **template DNA** must first be denatured to separate the strands before primers can anneal to them. - If the DNA is not denatured, the primers cannot access their target sequences. *Extend DNA, Anneal Primers, Denature DNA* - This order is incorrect because **DNA extension** is the final step, occurring only after denaturation and primer annealing. - The polymerase requires both a denatured template and bound primers to initiate synthesis.

Q: All are added to PCR, except:

Dideoxynucleotide. ***Dideoxynucleotide*** - **Dideoxynucleotides (ddNTPs)** are chain-terminating nucleotides that lack a 3'-hydroxyl group, preventing further phosphodiester bond formation and DNA strand elongation. They are primarily used in **Sanger sequencing**, not standard PCR. - In PCR, the goal is to amplify DNA segments, which requires continued strand synthesis, making ddNTPs unsuitable as they would halt the amplification process. *Thermostable DNA polymerase* - **Thermostable DNA polymerase** (e.g., Taq polymerase) is a crucial component of PCR, responsible for synthesizing new DNA strands during the extension phase. - Its thermostability allows it to withstand the high temperatures used during the denaturation step in each cycle without losing activity. *Template DNA* - **Template DNA** is the specific DNA sequence that needs to be amplified, serving as the blueprint for the PCR reaction. - The primers anneal to the template DNA, dictating the region that will be copied. *Deoxynucleotide* - **Deoxynucleotides (dNTPs)** are the basic building blocks of DNA (dATP, dCTP, dGTP, dTTP) that are incorporated by DNA polymerase to synthesize new DNA strands. - They provide the raw materials for the "extension" phase of PCR, where the DNA polymerase adds nucleotides complementary to the template strand.

Q: Restriction fragment length polymorphism is used for:

Genetic mapping and identification. ***Genetic mapping and identification*** - **Restriction fragment length polymorphism (RFLP)** exploits variations in DNA sequences that create or abolish **restriction enzyme recognition sites**, leading to fragments of different lengths. - These polymorphic fragments serve as **genetic markers** to map genes on chromosomes and identify specific genes or genetic regions. *Detection of gene mutations* - While RFLP can detect some mutations by altering restriction sites, it is not the primary or most efficient method for general **gene mutation detection**. - Techniques like **DNA sequencing** or **PCR-based assays** are typically more sensitive and comprehensive for direct mutation analysis. *Paternity testing* - RFLP was historically used for **paternity testing** by comparing inheritance patterns of polymorphic markers between child and alleged father. - However, it has largely been replaced by more advanced and faster methods like **short tandem repeat (STR) analysis** due to higher discriminatory power and lower DNA requirements. *Forensic analysis* - Similar to paternity testing, RFLP was an early technique employed in **forensic analysis** for DNA fingerprinting to identify individuals. - Modern forensic DNA analysis predominantly uses **STR profiling**, which offers greater resolution, speed, and requires smaller, less degraded samples.

Q: PCR is primarily a

DNA amplification technique. ***Correct: DNA amplification technique*** - **Polymerase Chain Reaction (PCR)** is a laboratory technique used to make millions of copies of a specific DNA segment - This amplification allows for easier detection, analysis, and manipulation of even very small amounts of DNA - PCR uses repeated cycles of heating and cooling with DNA polymerase to exponentially amplify target DNA sequences *Incorrect: DNA sequencing technique* - **DNA sequencing** determines the exact order of nucleotides within a DNA molecule, which is different from PCR's primary function - While PCR products can be sequenced afterward, PCR itself does not determine the nucleotide sequence - Sequencing is a separate technique (e.g., Sanger sequencing, Next-generation sequencing) *Incorrect: DNA degradation technique* - **DNA degradation** involves the breakdown of DNA molecules, typically by nucleases or chemical/physical processes - PCR's purpose is to **synthesize and increase** the amount of DNA, not to break it down - This is the opposite of what PCR does *Incorrect: All of these* - PCR has a specific primary function: **DNA amplification** - It is not a combination of amplification, sequencing, and degradation techniques - While PCR can be part of a workflow that includes sequencing, its primary role is amplification only

Q: Mitochondrial DNA inheritance is transmitted from:

Mother. ***Mother*** - **Mitochondrial DNA (mtDNA)** is exclusively inherited from the mother. - This is because the **egg cell** contributes the cytoplasm, including mitochondria, to the zygote, while the sperm primarily contributes nuclear DNA. *Father* - The father primarily contributes **nuclear DNA** during fertilization. - While sperm do contain mitochondria, these are typically **degraded** or excluded from the fertilized egg. *Grandmother* - This option confuses **lineage** with **direct transmission**. - The question asks about immediate parental transmission, which is from the **mother**, not the grandmother. - While mtDNA follows a maternal lineage (grandmother → mother → child), the direct source is always the mother. *Grandfather* - A grandfather does not transmit mtDNA to his offspring. - The inheritance pathway for mtDNA is strictly **maternal**.

Q: ChIP is used for :

Protein DNA interactions and histone modifications. ***Protein DNA interactions and histone modifications*** - **Chromatin immunoprecipitation (ChIP)** is a molecular biology technique used to investigate the **interaction of specific proteins with DNA**. - It allows for the identification of DNA regions bound by a particular protein, including **transcription factors** and **histone modification patterns**. *Movement of proteins* - Techniques like **fluorescence recovery after photobleaching (FRAP)** or **single-particle tracking** are used to study the movement of proteins. - ChIP is primarily focused on the physical binding of proteins to DNA, not their dynamic movement within a cell. *Study of aneuploidy* - **Aneuploidy**, which is an abnormal number of chromosomes, is typically studied using techniques such as **karyotyping**, **FISH (fluorescence in situ hybridization)**, or **comparative genomic hybridization (CGH)**. - ChIP does not directly assess chromosomal number or large-scale chromosomal aberrations. *Amplify DNA* - **Polymerase Chain Reaction (PCR)** is the primary method used to **amplify DNA** sequences. - While ChIP often concludes with PCR to analyze the immunoprecipitated DNA, its core purpose is not amplification itself but rather the isolation of protein-bound DNA.

Q: Which of the following enzymes is used in Recombinant DNA research for Homopolymer tailing?

Terminal transferase. ***Terminal transferase*** - **Terminal transferase** is an enzyme that adds **deoxyribonucleotides** to the 3'-hydroxyl terminus of a DNA strand **independently of a template**. - This capability makes it ideal for **homopolymer tailing**, where a series of identical nucleotides (e.g., poly-A or poly-T tails) are added to the ends of DNA molecules to facilitate cloning. *S1 nuclease* - **S1 nuclease** is a single-strand specific **endonuclease** that degrades single-stranded DNA or RNA. - Its primary use is in removing **single-stranded overhangs** or converting **sticky ends to blunt ends**, not in adding nucleotide tails. *Polynucleotide kinase* - **Polynucleotide kinase** catalyzes the transfer of the **gamma-phosphate from ATP to the 5'-hydroxyl terminus** of DNA or RNA. - It is used for **labeling DNA/RNA fragments** or for phosphorylation prior to ligation, not for adding long homopolymer tails. *Reverse transcriptase* - **Reverse transcriptase** is a **DNA polymerase** that synthesizes a DNA strand from an RNA template (reverse transcription). - Its main roles are in **cDNA synthesis** from mRNA and in the study of retroviruses, not in adding homopolymer tails to DNA.

Q: Two transgenic plants were genetically engineered using Recombinant DNA technology. One plant was transformed using a plasmid vector with GFP (Green Fluorescent Protein) gene and another plant was transformed with a complete Luciferase bioluminescent system (including luciferase gene and luciferin substrate availability). Which of these two plants will glow spontaneously in the dark?

Plant with Luciferase Gene. ***Plant with Luciferase Gene*** - The plant transformed with the **complete bioluminescent system**, including the **luciferase gene** and **luciferin substrate**, will glow spontaneously because luciferase acts on luciferin to produce light through a chemical reaction. - The question explicitly states "complete Luciferase bioluminescent system (including luciferase gene and luciferin substrate availability)," indicating all necessary components for bioluminescence are present. - **Bioluminescence** is light produced by living organisms through chemical reactions, requiring both enzyme (luciferase) and substrate (luciferin). *Both plants* - This is incorrect because the plant with the **GFP gene** alone will not glow spontaneously in the dark. - GFP requires **excitation by an external light source** (e.g., UV or blue light) to fluoresce, so it cannot contribute to spontaneous glowing. - Only the luciferase-transformed plant produces light spontaneously. *Plant with GFP Gene* - **GFP** (Green Fluorescent Protein) is **fluorescent**, not bioluminescent; it absorbs light at one wavelength and emits it at another wavelength. - GFP does not generate its own light in the dark and requires **illumination with an appropriate light source** (blue or ultraviolet light) to excite the protein and produce visible fluorescence. - Without external light excitation, GFP remains invisible in darkness. *None of the options* - This is incorrect because the plant equipped with a **complete luciferase bioluminescent system** is specifically designed to produce light spontaneously. - All required components (luciferase enzyme and luciferin substrate) are present and functional, enabling autonomous light production in the dark.

Question 1

What is the repair mechanism associated with CRISPR-cas9?

Accepted Answer

Non-homologous end joining

Answer

Mismatch repair

Answer

Nucleotide excision repair

Answer

Base excision repair

Question 2

Which of the following molecular analysis methods is used to detect RNA?

Accepted Answer

RT-PCR

Answer

Western blot

Answer

G banding

Answer

Sanger's method

Question 3

Steps of PCR in sequence are?

Accepted Answer

Denature DNA, Anneal Primers, Extend DNA

Answer

Denature DNA, Extend DNA, Anneal Primers

Answer

Anneal Primers, Extend DNA, Denature DNA

Answer

Extend DNA, Anneal Primers, Denature DNA

Question 4

All are added to PCR, except:

Accepted Answer

Dideoxynucleotide

Answer

Thermostable DNA polymerase

Answer

Template DNA

Answer

Deoxynucleotide

Question 5

Restriction fragment length polymorphism is used for:

Accepted Answer

Genetic mapping and identification

Answer

Detection of gene mutations

Answer

Paternity testing

Answer

Forensic analysis

Question 6

PCR is primarily a

Accepted Answer

DNA amplification technique

Answer

DNA sequencing technique

Answer

All of these

Answer

DNA degradation technique

Question 7

Mitochondrial DNA inheritance is transmitted from:

Accepted Answer

Mother

Answer

Father

Answer

Grandmother

Answer

Grandfather

Question 8

ChIP is used for :

Accepted Answer

Protein DNA interactions and histone modifications

Answer

Movement of proteins

Answer

Study of aneuploidy

Answer

Amplify DNA

Question 9

Which of the following enzymes is used in Recombinant DNA research for Homopolymer tailing?

Accepted Answer

Terminal transferase

Answer

S1 nuclease

Answer

Polynucleotide kinase

Answer

Reverse transcriptase

Question 10

Two transgenic plants were genetically engineered using Recombinant DNA technology. One plant was transformed using a plasmid vector with GFP (Green Fluorescent Protein) gene and another plant was transformed with a complete Luciferase bioluminescent system (including luciferase gene and luciferin substrate availability). Which of these two plants will glow spontaneously in the dark?

Accepted Answer

Plant with Luciferase Gene

Answer

Both plants

Answer

Plant with GFP Gene

Answer

None of the options

Molecular Biology and Genomics — MCQs

Molecular Biology and Genomics — MCQs

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