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Questions and Answers
What is the main goal of protein engineering?
What is the main goal of protein engineering?
- To study natural protein folding.
- To understand DNA replication.
- To explore RNA modifications.
- To create proteins with desired functions. (correct)
Which of the following is a key advantage of directed evolution?
Which of the following is a key advantage of directed evolution?
- Always yields a perfect protein in one cycle.
- Utilizes non-natural amino acids exclusively.
- Requires no prior structural knowledge. (correct)
- Eliminates the need for screening.
Which of the following best describes rational design?
Which of the following best describes rational design?
- Uses machine learning for optimization.
- Requires detailed structural and functional knowledge of the protein. (correct)
- Mimics natural selection in vitro.
- Relies on random mutagenesis for diversity.
Which amino acid contains a thiol group useful for bioconjugation?
Which amino acid contains a thiol group useful for bioconjugation?
Which of these is not a post-translational modification?
Which of these is not a post-translational modification?
What is the primary limitation of Solid-Phase Peptide Synthesis (SPPS)?
What is the primary limitation of Solid-Phase Peptide Synthesis (SPPS)?
Which of the following describes a key feature of Cell-Free Protein Synthesis (CFPS)?
Which of the following describes a key feature of Cell-Free Protein Synthesis (CFPS)?
What is a primary advantage of recombinant DNA technology in protein synthesis?
What is a primary advantage of recombinant DNA technology in protein synthesis?
What is the most common glycosylation type in antibodies?
What is the most common glycosylation type in antibodies?
Which PTM stabilizes protein structure via covalent bonding?
Which PTM stabilizes protein structure via covalent bonding?
Which PTM adds a negatively charged group to proteins?
Which PTM adds a negatively charged group to proteins?
Which of the following PTMs typically regulates transcription?
Which of the following PTMs typically regulates transcription?
What is the target functional group of NHS esters in bioconjugation?
What is the target functional group of NHS esters in bioconjugation?
Which reagent is commonly used for thiol-specific cross-linking?
Which reagent is commonly used for thiol-specific cross-linking?
What is the purpose of bifunctional cross-linkers like NHS-PEG-Maleimide?
What is the purpose of bifunctional cross-linkers like NHS-PEG-Maleimide?
Which type of reaction is typically used for hydroxyl groups in tyrosine?
Which type of reaction is typically used for hydroxyl groups in tyrosine?
Which functional group in histidine enables metal coordination?
Which functional group in histidine enables metal coordination?
What is the principle of Top-Down Mass Spectrometry?
What is the principle of Top-Down Mass Spectrometry?
How does SILAC enable quantification of proteins?
How does SILAC enable quantification of proteins?
Which tool is most commonly used for structural prediction in protein engineering?
Which tool is most commonly used for structural prediction in protein engineering?
Which of the following describes a LOCKR protein system?
Which of the following describes a LOCKR protein system?
What is the role of fluorescent protein bioconjugation to antibodies?
What is the role of fluorescent protein bioconjugation to antibodies?
Why is click chemistry considered bioorthogonal?
Why is click chemistry considered bioorthogonal?
Which of the following is a unique feature of cell-free protein synthesis?
Which of the following is a unique feature of cell-free protein synthesis?
Which amino acid is most commonly glycosylated in antibodies?
Which amino acid is most commonly glycosylated in antibodies?
What is a common use of periodate oxidation?
What is a common use of periodate oxidation?
Which PTM is commonly used to target proteins for degradation?
Which PTM is commonly used to target proteins for degradation?
Which cross-linking reagent is a zero-length cross-linker?
Which cross-linking reagent is a zero-length cross-linker?
What is the effect of phosphorylation on protein charge?
What is the effect of phosphorylation on protein charge?
What is a key limitation of directed evolution?
What is a key limitation of directed evolution?
Flashcards
What is the goal of protein engineering?
What is the goal of protein engineering?
Protein engineering aims to create proteins with new or improved properties.
What are the methods of protein engineering?
What are the methods of protein engineering?
Protein engineering involves modifying existing proteins or creating new ones.
Why is protein structure important in protein engineering?
Why is protein structure important in protein engineering?
Understanding protein structure and function is crucial for successful protein engineering.
What are the ways to alter a protein's sequence?
What are the ways to alter a protein's sequence?
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How do computers aid protein engineering?
How do computers aid protein engineering?
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What is directed evolution in protein engineering?
What is directed evolution in protein engineering?
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What is rational design in protein engineering?
What is rational design in protein engineering?
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What are the applications of protein engineering?
What are the applications of protein engineering?
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How does protein engineering impact enzymes?
How does protein engineering impact enzymes?
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How does protein engineering solve problems?
How does protein engineering solve problems?
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Study Notes
Protein Engineering Exam MCQs - General Concepts
- Protein engineering goal: Create proteins with desired functions
- Directed evolution advantage: Does not require prior structural knowledge
- Rational design key: Detailed structural and functional knowledge of the protein is needed
- Bioconjugation amino acid: Cysteine (contains a thiol group)
- Post-translational modification (not): Recombinant DNA insertion
- Rational design: Mimics natural selection in vitro, needs detailed structural & functional knowledge of the protein
- Directed evolution: Requires no prior structural knowledge; doesn't necessarily yield a perfect protein in one cycle; utilizes non-natural amino acids, but screening is still required
Protein Synthesis
- Solid-Phase Peptide Synthesis (SPPS) limitation: Difficulty synthesizing large proteins
- Cell-Free Protein Synthesis (CFPS) key feature: Enables rapid incorporation of non-natural amino acids
- Recombinant DNA advantage: Enables large-scale protein production in host cells.
- Recombinant DNA primary advantage: Allows large-scale protein production in host cells - avoids problems of using live cells
- Primary limitations of SPPS (Solid Phase Peptide Synthesis): Inability to incorporate non-natural amino acids, difficulty in synthesizing large proteins, requirement of living cells for synthesis, and lack of precision in amino acid coupling
Post-Translational Modifications (PTMs)
- Common Antibody Glycosylation type: N-linked glycosylation
- Stabilizes Protein Structure: Disulfide bond formation (via covalent bonding)
- Negatively charged group addition: Phosphorylation
- Transcription regulation PTM: Ubiquitination
Bioconjugation and Cross-Linking
- NHS esters target functional group: Amine (-NH2)
- Thiol-specific cross-linking agent: Maleimide
- Bifunctional cross-linker purpose: To link two different types of functional groups
- Hydroxyl group reaction: Periodate oxidation
- Metal coordination: Imidazole group (in histidine)
Techniques in Protein Engineering
- Top-Down Mass Spectrometry principle: Fragmentation/analysis of intact proteins
- SILAC protein quantification: Uses isotopically labeled amino acids for synthesis.
- Structural prediction tool: AlphaFold
- LOCKR protein system: A method to create isotopically labeled proteins
- Fluorescent protein bioconjugation use with Antibodies: Enables detection and visualization
- Click chemistry: Bioorthogonal, meaning it works without interfering with native biomolecules in living systems
- Cell-free protein synthesis advantage: Eliminates the need for transcription and translation machinery
- Commonly glycosylated amino acid in antibodies: Asparagine
Advanced Concepts/Questions
- Zero-length cross-linker: EDC
- Phosphorylation effect on protein charge: Introduces a negative charge
- Directed evolution limitation: Requires extensive structural knowledge, screening is resource-intensive
- Common use for periodate oxidation: Introducing thiol groups into proteins.
- PTM commonly used for protein degradation: Ubiquitination.
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