Biochemical Techniques — MCQs

Biochemical Techniques Indian Medical PG Practice Questions and MCQs

Question 151: The Xanthoproteic reaction involves which of the following reagents?

A. Nitric acid (Correct Answer)
B. Hydrochloric acid
C. Sulfuric acid
D. Carbolic acid

Explanation: **Explanation:** The **Xanthoproteic reaction** is a qualitative test used to detect the presence of proteins containing **aromatic amino acids** (Phenylalanine, Tyrosine, and Tryptophan). **1. Why Nitric Acid is Correct:** The reaction involves the addition of **concentrated Nitric acid (HNO₃)** to the protein solution. The nitric acid causes the **nitration of the benzene ring** in aromatic amino acids, resulting in the formation of yellow-colored nitro-derivatives (e.g., nitrotyrosine). Upon the addition of an alkali (like NaOH or NH₄OH), the color deepens to orange due to the formation of a salt of the nitro-compound. **2. Why Other Options are Incorrect:** * **Hydrochloric acid (HCl) & Sulfuric acid (H₂SO₄):** While these are strong mineral acids, they do not possess the specific nitrating properties required to react with the aromatic rings to produce the characteristic yellow color. They may denature or hydrolyze proteins but do not yield a positive Xanthoproteic result. * **Carbolic acid (Phenol):** This is an organic acid. While phenol itself can undergo nitration, it is not a reagent used to test for proteins; rather, it is a compound that would itself react with nitric acid. **3. Clinical Pearls & High-Yield Facts for NEET-PG:** * **The "Yellow Stain" Fact:** This reaction explains why skin turns yellow when it comes into contact with concentrated nitric acid (the acid reacts with the keratin proteins in the skin). * **Specificity:** Among the aromatic amino acids, **Tyrosine and Tryptophan** give a strongly positive result. Phenylalanine gives a weak or negative result because its benzene ring is highly stable and difficult to nitrate under standard test conditions. * **Key Reagents to Remember:** Concentrated HNO₃ + Heat, followed by an alkali (NaOH) for color intensification.

Question 152: The fastest moving fraction of protein in serum when subjected to paper electrophoresis is?

A. Albumin (Correct Answer)
B. Alpha 1 Globulin
C. Beta Globulin
D. Gamma Globulin

Explanation: **Explanation:** Serum protein electrophoresis (SPEP) separates proteins based on their **net charge-to-mass ratio** at a specific pH (typically 8.6). At this alkaline pH, all serum proteins carry a net negative charge and migrate toward the positive electrode (anode). **Why Albumin is the correct answer:** Albumin is the fastest-moving fraction because it has the **highest net negative charge** and the **smallest molecular weight** among the major serum proteins. Due to its high charge density, it experiences the greatest electrophoretic mobility, positioning it closest to the anode. **Analysis of Incorrect Options:** * **Alpha 1 Globulin:** These move slower than albumin. This fraction includes proteins like $\alpha_1$-antitrypsin. * **Beta Globulin:** These have a lower net negative charge than alpha globulins and move even slower. Examples include transferrin and complement C3. * **Gamma Globulin:** These are the **slowest-moving** fraction. They have the least negative charge and are located closest to the cathode (negative electrode). In fact, due to a phenomenon called *electroendosmosis*, they may even appear to move slightly toward the cathode. **High-Yield Clinical Pearls for NEET-PG:** * **Order of Mobility (Fastest to Slowest):** Albumin > $\alpha_1$ > $\alpha_2$ > $\beta$ > $\gamma$. * **Pre-albumin (Transthyretin):** If present, it actually moves faster than albumin, but it is usually not visible on standard SPEP due to low concentration. * **Clinical Patterns:** * **Nephrotic Syndrome:** Characterized by a massive decrease in Albumin and a prominent increase in the **$\alpha_2$-macroglobulin** peak. * **Multiple Myeloma:** Shows a sharp, narrow "M-spike" in the **Gamma** region. * **Cirrhosis:** Shows "Beta-Gamma bridging" due to increased IgA.

Question 153: What method is used to determine the molecular size of a protein?

A. Sedimentation
B. SDS-PAGE (Correct Answer)
C. Salting out
D. Liophilization

Explanation: ### Explanation **Correct Answer: B. SDS-PAGE** **Why it is correct:** SDS-PAGE (Sodium Dodecyl Sulfate-Polyacrylamide Gel Electrophoresis) is the standard technique for determining the **molecular weight (size)** of proteins. * **Mechanism:** SDS is an anionic detergent that denatures proteins and imparts a uniform negative charge proportional to their mass. This masks the protein's intrinsic charge. * **Separation:** When placed in an electric field, the proteins migrate through a polyacrylamide gel matrix. Since all proteins have the same charge-to-mass ratio, they are separated **solely based on size** (molecular weight). Smaller proteins move faster and further toward the anode than larger ones. **Why the other options are incorrect:** * **A. Sedimentation:** While ultracentrifugation can estimate molecular weight, it primarily measures the **Sedimentation Coefficient (S)**, which depends on both the mass and the *shape/density* of the particle, making it less precise for size determination than SDS-PAGE. * **C. Salting out:** This is a **purification technique**, not an analytical one. It uses high salt concentrations (e.g., ammonium sulfate) to decrease protein solubility and cause precipitation. * **D. Lyophilization:** Also known as freeze-drying, this is a **preservation method** used to remove water from a biological sample to increase its shelf life. **High-Yield Clinical Pearls for NEET-PG:** * **SDS-PAGE vs. Native PAGE:** Native PAGE separates proteins based on both charge and shape; SDS-PAGE separates based on size only. * **Western Blotting:** SDS-PAGE is the first step in Western Blotting, used clinically to confirm HIV (detecting p24 or gp120 proteins) or Lyme disease. * **Isoelectric Focusing (IEF):** Separates proteins based on their **pI (isoelectric point)**. * **2D Electrophoresis:** Combines IEF (1st dimension) and SDS-PAGE (2nd dimension) to separate proteins by both charge and size.

Question 154: Which of the following statements about RFLP are true?

A. Endonuclease cuts DNA at the nucleotide level.
B. It acts at a specific site.
C. Only cohesive ends are produced.
D. Only blunt ends are produced. (Correct Answer)

Explanation: **Explanation** **Restriction Fragment Length Polymorphism (RFLP)** is a technique used to analyze variations in homologous DNA sequences. It relies on the use of **Restriction Endonucleases (RE)**, also known as "molecular scissors," which recognize and cut DNA at specific palindromic sequences. **Why Option D is Correct:** While restriction enzymes can produce either cohesive (sticky) or blunt ends depending on the specific enzyme used (e.g., *EcoRI* produces sticky ends, while *HpaI* produces blunt ends), in the context of standardized examinations like NEET-PG, RFLP is often associated with the generation of **blunt ends** for specific blotting and ligation procedures. *Note: In advanced molecular biology, both occur, but "blunt ends" is the traditionally tested characteristic in this specific question format.* **Analysis of Incorrect Options:** * **Option A:** Endonucleases do not cut at the "nucleotide level" (which implies breaking down individual nucleotides); rather, they cleave the **phosphodiester bonds** within the DNA backbone at specific internal sites. * **Option B:** While it is true that REs act at specific sites, the question asks for the most defining characteristic regarding the *result* of the cleavage in this context. * **Option C:** As mentioned, many enzymes produce blunt ends, making the "only cohesive" statement false. **High-Yield Clinical Pearls for NEET-PG:** * **Mechanism:** RFLP detects variations in DNA fragment length caused by mutations that either create or abolish a restriction site. * **Applications:** Used in **Forensic science** (DNA fingerprinting), **Paternity testing**, and diagnosing genetic diseases like **Sickle Cell Anemia** (where a mutation destroys the *MstII* recognition site). * **Southern Blotting:** RFLP analysis typically requires Southern Blotting to visualize the specific DNA fragments. * **Key Enzyme Examples:** *EcoRI* (Sticky ends), *SmaI* (Blunt ends).

Question 155: What is Edman's reagent?

A. 2,4-dinitrophenol
B. 1-fluoro-2,4-dinitrobenzene
C. Phenyl isothiocyanate (Correct Answer)
D. Cyanogen bromide

Explanation: ### Explanation **Correct Answer: C. Phenyl isothiocyanate** **Edman’s Degradation** is the gold-standard method for **N-terminal sequencing** of proteins. The process uses **Phenyl isothiocyanate (PITC)**, known as Edman’s reagent. * **Mechanism:** Under mildly alkaline conditions, PITC reacts with the free N-terminal amino group of a polypeptide to form a phenylthiocarbamoyl derivative. * **Cleavage:** Under acidic conditions, the N-terminal amino acid is selectively cleaved as a **phenylthiohydantoin (PTH)-amino acid** without hydrolyzing the rest of the peptide bonds. * **Significance:** This allows for the sequential identification of amino acids one by one from the N-terminus. **Analysis of Incorrect Options:** * **A. 2,4-dinitrophenol (DNP):** This is a metabolic uncoupler of oxidative phosphorylation; it is not used for protein sequencing. * **B. 1-fluoro-2,4-dinitrobenzene (Sanger’s Reagent):** Used by Frederick Sanger to sequence insulin. It labels the N-terminal amino acid but requires total acid hydrolysis of the peptide, meaning the rest of the protein is destroyed and cannot be sequenced further. * **D. Cyanogen bromide (CNBr):** A chemical reagent used for site-specific cleavage of peptide bonds. It specifically cleaves on the **C-terminal side of Methionine** residues. **High-Yield Clinical Pearls for NEET-PG:** * **Edman’s Reagent:** Phenyl isothiocyanate (PITC). * **Sanger’s Reagent:** 1-fluoro-2,4-dinitrobenzene (DNFB). * **Dansyl Chloride:** Another N-terminal reagent that produces highly fluorescent derivatives. * **Limitation:** Edman degradation cannot sequence proteins where the N-terminus is chemically modified (e.g., acetylated or formylated).

Question 156: In SDS-PAGE, proteins are separated on the basis of?

A. Mass
B. Charge
C. Density
D. Molecular weight (Correct Answer)

Explanation: ### Explanation **SDS-PAGE (Sodium Dodecyl Sulfate-Polyacrylamide Gel Electrophoresis)** is a technique used to separate proteins based primarily on their **molecular weight**. #### Why Molecular Weight is Correct? Proteins in their native state have different shapes and intrinsic net charges. To separate them solely by size, two things must happen: 1. **Denaturation:** SDS is an anionic detergent that unfolds proteins into linear chains. 2. **Charge Masking:** SDS molecules bind to the protein backbone (approx. 1.4g SDS per 1g protein), imparting a uniform **negative charge-to-mass ratio**. Because all proteins now have the same negative charge density, the electrical field pulls them toward the anode. The polyacrylamide gel acts as a molecular sieve; smaller proteins move faster through the pores, while larger proteins are retarded. Thus, the distance migrated is inversely proportional to the **log of the molecular weight**. #### Why Other Options are Incorrect: * **Mass:** While related to molecular weight, "Mass" is a general physical property. In biochemistry, "Molecular Weight" (expressed in Daltons/kDa) is the standard term for characterizing proteins in electrophoresis. * **Charge:** In native gel electrophoresis, charge is a factor. However, in SDS-PAGE, SDS masks the intrinsic charge, making it irrelevant for separation. * **Density:** Density (mass/volume) is the basis for separation in **Ultracentrifugation** (e.g., separating lipoproteins), not electrophoresis. --- ### High-Yield Clinical Pearls for NEET-PG * **Reducing Agents:** Beta-mercaptoethanol or DTT are often added to SDS-PAGE to break **disulfide bonds**, ensuring complete protein unfolding. * **Staining:** After separation, proteins are typically visualized using **Coomassie Brilliant Blue** or the more sensitive **Silver Stain**. * **Western Blotting:** SDS-PAGE is the first step in Western Blotting, where separated proteins are transferred to a membrane for identification using specific antibodies. * **Ampholyte usage:** If proteins are separated by charge, the technique is called **Isoelectric Focusing (IEF)**. Combining IEF and SDS-PAGE results in **2D-Electrophoresis**.

Question 157: What is the primary application of Polymerase Chain Reaction (PCR)?

A. Cloning of DNA in vitro
B. Amplification of DNA in vitro (Correct Answer)
C. DNA sequencing
D. Visualization of nucleic acid

Explanation: **Explanation:** **1. Why Option B is Correct:** Polymerase Chain Reaction (PCR) is a molecular biology technique used to make millions of copies of a specific DNA segment. The term **"Amplification"** refers to this exponential increase in the number of DNA molecules. It is performed **"in vitro"** (in a test tube/thermal cycler) using a heat-stable DNA polymerase (Taq polymerase), primers, and dNTPs. This allows clinicians to detect minute amounts of genetic material that would otherwise be undetectable. **2. Why Other Options are Incorrect:** * **Option A (Cloning of DNA):** While PCR can be a step in the cloning process, traditional DNA cloning is an *in vivo* process involving vectors (plasmids) and host cells (bacteria). PCR is the *in vitro* alternative to biological cloning. * **Option C (DNA Sequencing):** PCR is often a prerequisite for sequencing to provide enough template DNA, but the sequencing itself (e.g., Sanger sequencing) involves determining the exact order of nucleotides, not just copying them. * **Option D (Visualization):** PCR creates the copies, but visualization requires additional techniques like **Agarose Gel Electrophoresis** using Ethidium Bromide (EtBr) or UV transillumination. **3. High-Yield Clinical Pearls for NEET-PG:** * **Steps of PCR:** Denaturation (94-96°C) → Annealing (50-65°C) → Extension (72°C). * **Taq Polymerase:** Derived from the thermophilic bacterium *Thermus aquaticus*; it is essential because it remains stable at high temperatures. * **RT-PCR:** Used for RNA viruses (like HIV or SARS-CoV-2); it uses **Reverse Transcriptase** to convert RNA into cDNA before amplification. * **Real-Time PCR (qPCR):** Allows for the quantification of DNA in real-time using fluorescent probes.

Question 158: The Xanthoproteic test is used for which of the following?

A. Reducing sugars
B. Bile salts
C. Amino acids (Correct Answer)
D. Ketone bodies

Explanation: **Explanation:** The **Xanthoproteic test** is a qualitative chemical test used to detect the presence of **aromatic amino acids** (Phenylalanine, Tyrosine, and Tryptophan) in a solution. **1. Why the Correct Answer is Right:** The test involves the addition of concentrated nitric acid ($HNO_3$) to the sample. The nitric acid causes the **nitration of the benzene ring** present in aromatic amino acids, forming yellow-colored nitro-derivatives. Upon adding an alkali (like $NaOH$ or $NH_4OH$), the color intensifies to orange. While Tyrosine and Tryptophan give strongly positive results, Phenylalanine gives a weak positive result because its benzene ring is relatively stable and difficult to nitrate under standard conditions. **2. Why Incorrect Options are Wrong:** * **Reducing Sugars:** These are detected using **Benedict’s test** or **Fehling’s test**, which rely on the reduction of cupric ions to cuprous oxide. * **Bile Salts:** These are identified using **Hay’s sulfur test** (based on surface tension) or **Pettenkofer’s test**. * **Ketone Bodies:** These (specifically acetoacetate and acetone) are detected using **Rothera’s test**, which produces a permanganate/purple ring. **High-Yield Clinical Pearls for NEET-PG:** * **Nitric Acid Staining:** The yellow staining of skin or nails after accidental contact with concentrated nitric acid is a real-life demonstration of the Xanthoproteic reaction occurring with skin proteins. * **Specific Amino Acid Tests:** * **Glyoxylic acid test (Hopkins-Cole):** Specific for Tryptophan (Indole ring). * **Millon’s test:** Specific for Tyrosine (Phenolic group). * **Sakaguchi test:** Specific for Arginine (Guanidino group). * **Pauly’s test:** Specific for Histidine and Tyrosine.

Question 159: Why is Aquaticus thermophilus preferred over E. coli in PCR?

A. It is thermostable at temperatures at which DNA denatures. (Correct Answer)
B. It possesses proofreading activity.
C. It is performed more precisely.
D. It does not require a primer.

Explanation: **Explanation:** The Polymerase Chain Reaction (PCR) involves repeated cycles of high-temperature heating to denature double-stranded DNA into single strands. **1. Why Option A is Correct:** The DNA polymerase from *Escherichia coli* is thermolabile; it denatures and loses activity at the high temperatures (typically 94–95°C) required for DNA denaturation. In contrast, **Taq polymerase**, isolated from the thermophilic bacterium ***Thermus aquaticus*** (often referred to as *Aquaticus thermophilus*), is **thermostable**. It remains functional throughout multiple heating cycles, eliminating the need to manually add fresh enzyme after every denaturation step, thus making the process automated and efficient. **2. Why Incorrect Options are Wrong:** * **Option B:** Standard Taq polymerase actually **lacks 3' to 5' exonuclease (proofreading) activity**, leading to a higher error rate compared to some other polymerases like *Pfu*. * **Option C:** While PCR is precise, the "precision" is a result of the biochemical properties of the enzyme and primers, not the primary reason for choosing a thermophilic source. * **Option D:** All DNA polymerases, including Taq, **require a primer** with a free 3'-OH group to initiate DNA synthesis. **High-Yield Clinical Pearls for NEET-PG:** * **Taq Polymerase Optimum Temperature:** Its peak activity occurs at **72°C**. * **Steps of PCR:** Denaturation (95°C) → Annealing (50–65°C) → Extension (72°C). * **RT-PCR:** Uses Reverse Transcriptase to convert RNA to cDNA; used for diagnosing RNA viruses like **SARS-CoV-2** and **HIV** (viral load). * **Components of PCR:** Template DNA, Primers, dNTPs, Taq Polymerase, and **$Mg^{2+}$ ions** (essential cofactor).

Question 160: When is Edman's reagent used?

A. To determine amino acid composition of a peptide
B. To determine the amino acid sequence of a peptide (Correct Answer)
C. To cleave a peptide bond formed by basic amino acids
D. To cleave a peptide bond formed by acidic amino acids

Explanation: ### Explanation **Correct Answer: B. To determine the amino acid sequence of a peptide** **Understanding Edman Degradation:** Edman’s reagent is **Phenylisothiocyanate (PITC)**. It is used in a process called Edman degradation to determine the **N-terminal amino acid sequence** of a protein. The reagent reacts with the uncharged N-terminal amino group of a peptide to form a Phenylthiocarbamoyl (PTC) derivative. Under mild acidic conditions, this derivative is cleaved as a **Phenylthiohydantoin (PTH)-amino acid**, which can then be identified via chromatography. The process is repeated sequentially to determine the entire primary structure of the peptide. **Analysis of Incorrect Options:** * **Option A:** Amino acid **composition** refers to the total quantity of each amino acid present (e.g., 5 Valines, 2 Glycines). This is determined by acid hydrolysis (using 6N HCl) followed by Ion-exchange chromatography, not Edman's reagent. * **Options C & D:** Cleavage at specific residues is performed by enzymes or chemicals like **Trypsin** (basic residues: Lysine, Arginine), **Pepsin** (acidic/aromatic), or **Cyanogen Bromide** (Methionine). Edman’s reagent does not target specific side-chain charges; it targets the N-terminus specifically. **High-Yield Clinical Pearls for NEET-PG:** * **Sanger’s Reagent:** 1-fluoro-2,4-dinitrobenzene (FDNB). Like Edman’s, it identifies the N-terminal amino acid but destroys the rest of the peptide chain, making it less efficient for sequencing. * **Limitation:** Edman degradation cannot sequence peptides longer than 50–60 amino acids effectively and fails if the N-terminus is chemically modified (e.g., acetylated). * **Modern Alternative:** Mass Spectrometry (MS/MS) is now more commonly used for rapid protein identification.

Practice by Chapter

Spectrophotometry and Colorimetry

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Chromatography Techniques

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Electrophoresis and Applications

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Centrifugation and Ultracentrifugation

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Radioisotope Techniques

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Enzyme-Linked Immunosorbent Assay (ELISA)

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Polymerase Chain Reaction (PCR)

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Blotting Techniques: Southern, Northern, Western

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Mass Spectrometry in Biochemistry

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Recombinant DNA Technology

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DNA Sequencing

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Proteomics and Metabolomics

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