Section 4: Bioprocess Engineering and Process Biotechnology
Mass transfer in bioprocesses (kLa)
Subtopic: Fundamentals of Mass transfer in bioprocesses (kLa)
Question Statement:
An analysis of DNA-protein interactions was carried out using all DNA-protein complexes
in the protein data bank (PDB). The frequency distribution of four amino acid residues,
represented as P, Q, R and S, occurring in non-covalent interactions between the protein and
DNA backbone is shown below.
Which one of the following is correct?
Options:
(A) P-Lys, Q-Arg, R-Gln, S-Glu
(B) P-Gln, Q-Glu, R-Lys, S-Arg
(C) P-Asn, Q-Asp, R-Arg, S-Lys
(D) P-His, Q-Glu, R-Gln, S-Lys
Official Answer Key:
A
Step-by-Step Solution & Explanation
### **Official Solution & Step-by-Step Derivation (GATE BT 2018 Q.47)**
**1. Governing Concept & Question Classification**:
- **Section**: BT
- **Question Type**: **MCQ** (2 Marks)
- **Topic**: Biochemistry / Structural Biology (DNA-Protein Interactions & Residue Frequencies)
**2. Detailed Step-by-Step Analysis**:
- The DNA backbone is polyanionic due to the negatively charged phosphodiester phosphate groups ($pO_4^-$).
- In structural surveys of all DNA-protein complexes in the Protein Data Bank (PDB):
- **Positively charged basic amino acids** (Lysine, Lys, and Arginine, Arg) interact electrostatically with the negatively charged DNA backbone with the highest frequency:
- **Lysine (Lys)** and **Arginine (Arg)** dominate non-covalent interactions (salt bridges and hydrogen bonds) with phosphate oxygens, represented by the highest bars **P** and **Q**.
- **Polar uncharged amino acids** (such as **Glutamine, Gln**, and Asparagine, Asn) interact at intermediate frequency via hydrogen bonding with the deoxyribose sugars and backbone oxygens, represented by bar **R**.
- **Negatively charged acidic amino acids** (**Glutamate, Glu**, and Aspartate, Asp) suffer strong electrostatic repulsion from the negatively charged phosphate backbone, occurring at the lowest frequency, represented by the smallest bar **S**.
- Matching: **P-Lys, Q-Arg, R-Gln, S-Glu**.
- **Option-by-Option Evaluation**:
- **Option (A) [CORRECT]**: P-Lys, Q-Arg, R-Gln, S-Glu correctly reflects the electrostatic ranking (basic residues most abundant, acidic residues least abundant due to charge repulsion).
- **Option (B) [INCORRECT]**: Places polar Gln and acidic Glu at the highest frequencies.
- **Option (C) [INCORRECT]**: Incorrectly places basic residues at the bottom.
- **Option (D) [INCORRECT]**: Assigns Glu to the second-highest frequency, which contradicts electrostatic principles.
**3. Final Answer / Verification Summary**:
- **Official GATE Answer Key**: **A**
- **Scoring Criteria**: +2.0 Marks (Negative marking: -0.67 marks).
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