Introduction to protein engineering MCQs With Answer

Introduction to protein engineering MCQs With Answer

Protein engineering integrates biochemistry, molecular biology and computational design to modify protein structure and function for therapeutic and industrial applications. This concise introduction for B. Pharm students covers core concepts—protein structure, enzyme kinetics, mutagenesis methods (site-directed, error-prone PCR), directed evolution, rational design, phage display, expression systems, post-translational modifications, stability optimization, and assays for activity and binding. Emphasis is placed on drug design, biosimilars, biopharmaceutical production, and regulatory considerations. These multiple-choice questions (MCQs) with answers reinforce practical knowledge required for formulation, bioprocessing, and novel therapeutic development. Now let’s test your knowledge with 30 MCQs on this topic.

Q1. What is the primary goal of protein engineering in pharmaceutical development?

• To sequence the genome of therapeutic organisms
• To design and modify proteins to enhance therapeutic properties
• To create synthetic DNA for vaccines
• To develop new small-molecule drugs exclusively

Correct Answer: To design and modify proteins to enhance therapeutic properties

Q2. Which technique is commonly used for introducing specific amino acid changes at a chosen site?

• Random mutagenesis by UV light
• Site-directed mutagenesis
• Mass spectrometry
• Western blotting

Correct Answer: Site-directed mutagenesis

Q3. Directed evolution primarily relies on which two iterative processes?

• Cloning and sequencing
• Mutation and selection/screening
• Protein purification and crystallization
• In silico docking and molecular dynamics

Correct Answer: Mutation and selection/screening

Q4. Which expression system is often preferred for producing therapeutic monoclonal antibodies?

• Escherichia coli
• Saccharomyces cerevisiae
• CHO (Chinese hamster ovary) cells
• Plant chloroplasts

Correct Answer: CHO (Chinese hamster ovary) cells

Q5. Phage display is a method used to:

• Measure enzyme kinetics in vivo
• Display peptide or protein variants on bacteriophage for ligand selection
• Sequence antibody genes directly from serum
• Encode proteins into plasmids for bacterial expression only

Correct Answer: Display peptide or protein variants on bacteriophage for ligand selection

Q6. Which computational approach predicts protein structures or designs new sequences?

• Polymerase chain reaction
• Rosetta or homology modeling
• ELISA
• Isoelectric focusing

Correct Answer: Rosetta or homology modeling

Q7. Error-prone PCR is most useful when the goal is to:

• Create a single targeted amino acid substitution
• Introduce a library of random mutations across a gene
• Precisely delete large genomic regions
• Measure protein stability by calorimetry

Correct Answer: Introduce a library of random mutations across a gene

Q8. Which post-translational modification is critical for many therapeutic glycoproteins’ activity and half-life?

• Phosphorylation
• Glycosylation
• Methylation
• Lipidation

Correct Answer: Glycosylation

Q9. When improving enzyme thermostability, which strategy is commonly employed?

• Removing all disulfide bonds
• Introducing stabilizing mutations such as proline substitutions and salt bridges
• Increasing the number of hydrophobic residues on the surface
• Reducing the molecular weight drastically

Correct Answer: Introducing stabilizing mutations such as proline substitutions and salt bridges

Q10. Which assay is commonly used to quantify enzyme catalytic efficiency?

• Western blot
• Kinetic measurement of Km and Vmax
• Isoelectric focusing
• SDS-PAGE

Correct Answer: Kinetic measurement of Km and Vmax

Q11. Alanine scanning mutagenesis is primarily used to:

• Determine effects of individual residues on protein stability or binding by systematic substitution with alanine
• Insert glycosylation sites into a protein
• Label proteins with fluorescent probes
• Amplify genes for cloning

Correct Answer: Determine effects of individual residues on protein stability or binding by systematic substitution with alanine

Q12. Codon optimization for expression in E. coli aims to:

• Alter the protein’s amino acid sequence
• Improve translational efficiency by matching codon usage to host tRNA abundance
• Increase glycosylation
• Introduce post-translational modifications

Correct Answer: Improve translational efficiency by matching codon usage to host tRNA abundance

Q13. Which analytical method provides high-resolution structural information about proteins?

• NMR spectroscopy and X-ray crystallography
• ELISA
• SDS-PAGE
• UV-Vis spectrophotometry

Correct Answer: NMR spectroscopy and X-ray crystallography

Q14. For screening large variant libraries, which technique enables rapid single-cell sorting based on binding or activity?

• Gel electrophoresis
• Fluorescence-activated cell sorting (FACS)
• Standard plate reader only
• Mass spectrometry

Correct Answer: Fluorescence-activated cell sorting (FACS)

Q15. Which factor is most important when designing a therapeutic protein to reduce immunogenicity?

• Maximizing hydrophobic surface exposure
• Humanizing sequences and removing T-cell epitopes
• Adding bacterial tags for purification
• Increasing protein aggregation propensity

Correct Answer: Humanizing sequences and removing T-cell epitopes

Q16. Which technique couples genotype and phenotype for selection of improved proteins?

• Southern blotting
• Phage display or yeast display
• ELISA without linkage
• Spectrophotometric enzyme assays only

Correct Answer: Phage display or yeast display

Q17. Which parameter describes protein stability as the temperature where 50% of protein is unfolded?

• KM
• Tm (melting temperature)
• pI
• Isoelectric point

Correct Answer: Tm (melting temperature)

Q18. In rational design of a binding interface, which information is most useful?

• Primary amino acid sequence only
• High-resolution 3D structure of the protein-ligand complex
• Cell growth rate data
• Generic codon usage tables

Correct Answer: High-resolution 3D structure of the protein-ligand complex

Q19. Which modification can improve a protein drug’s serum half-life?

• Increasing protease-sensitive sites
• PEGylation or Fc-fusion
• Removing glycosylation sites
• Adding degradation tags

Correct Answer: PEGylation or Fc-fusion

Q20. What is the role of molecular chaperones in recombinant protein expression?

• They degrade recombinant proteins
• They assist in proper protein folding and reduce aggregation
• They truncate proteins post-translationally
• They glycosylate proteins in bacteria

Correct Answer: They assist in proper protein folding and reduce aggregation

Q21. Which sequencing technology is most useful to analyze diversity of mutant libraries after selection?

• Sanger sequencing only
• Next-generation sequencing (NGS)
• Western blot analysis
• Edman degradation

Correct Answer: Next-generation sequencing (NGS)

Q22. In antibody engineering, “humanization” refers to:

• Converting human antibodies into mouse antibodies
• Altering non-human antibody sequences to resemble human frameworks while retaining antigen binding
• Adding sugar moieties to antibodies
• Fusing antibodies to toxins

Correct Answer: Altering non-human antibody sequences to resemble human frameworks while retaining antigen binding

Q23. Which parameter indicates catalytic efficiency combining affinity and turnover?

• kcat/Km
• IC50
• Molecular weight
• pKa

Correct Answer: kcat/Km

Q24. What is the main advantage of cell-free protein synthesis systems in engineering?

• They always produce glycosylated proteins
• Rapid expression and screening without cell viability constraints
• Unlimited folding capacity equivalent to mammalian cells
• They eliminate the need for DNA templates

Correct Answer: Rapid expression and screening without cell viability constraints

Q25. Which method can identify residues critical for ligand binding by systematic randomization and selection?

• Site-directed alanine scanning only
• Combinatorial library screening with deep sequencing
• UV-visible spectroscopy
• Isoelectric focusing

Correct Answer: Combinatorial library screening with deep sequencing

Q26. Why is aggregation a major concern for biopharmaceutical proteins?

• Aggregates improve therapeutic potency
• Aggregates can reduce efficacy and increase immunogenicity
• Aggregates lower production costs
• Aggregation makes proteins more soluble

Correct Answer: Aggregates can reduce efficacy and increase immunogenicity

Q27. In rational enzyme redesign, substituting which residue often increases rigidity and can stabilize local structure?

• Glycine to proline
• Tryptophan to alanine
• Serine to threonine
• Leucine to isoleucine

Correct Answer: Glycine to proline

Q28. Which regulatory consideration is critical for engineered protein therapeutics?

• Demonstrating consistent manufacture, purity, potency, and safety including immunogenicity assessment
• Only labeling color is regulated
• No documentation of host cell proteins is necessary
• Regulations do not apply to biosimilars

Correct Answer: Demonstrating consistent manufacture, purity, potency, and safety including immunogenicity assessment

Q29. Which approach integrates machine learning to predict beneficial mutations in protein engineering?

• Classical PCR without data
• Data-driven sequence-to-function models trained on experimental datasets
• Manual trial-and-error without computational tools
• Only classical homology modeling with no statistics

Correct Answer: Data-driven sequence-to-function models trained on experimental datasets

Q30. Which purification tag is commonly used to facilitate affinity purification of recombinant proteins?

• GFP tag only for purification
• His-tag (polyhistidine)
• Ribosomal RNA tag
• Ubiquitin degradation tag

Correct Answer: His-tag (polyhistidine)

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