This set of Protein Engineering Assessment Questions and Answers focuses on “Rational Approach for De-novo Protein Design”.
1. In rational design, knowledge of the structure and function of the protein is taken into consideration.
a) False
b) True
View Answer
Explanation: The above statement is true. In rational design, knowledge of the structure and function of the protein is taken into consideration. This is done by making rationally designed changes in the gene of the protein.
2. Which of the following is done for the directed evolution of the proteins with an unknown structure?
a) Site-directed mutagenesis
b) Specific mutations
c) Non-random mutations
d) Random changes (mutations)
View Answer
Explanation: Random changes (mutations) are performed for the directed evolution of the proteins with unknown structures. After, this a mutant form of protein with desired properties is chosen.
3. Subtilisin (a protease) is inactivated by bleach due to the presence of which amino acid?
a) Cysteine at 23
b) Serine at 32
c) Alanine 33
d) Methionine at 22
View Answer
Explanation: Subtilisin (a protease) is inactivated by bleach due to the presence of methionine at 22. Subtilisin is added in the detergent to improve the efficiency of laundry detergents. However, subtilisin is inactivated by bleach. This inactivation is due to oxidation of the amino acid methionine at position 22 of the subtilisin molecule.
4. Which of the following mutation in subtilisin makes it resistant to inactivation by bleach?
a) Serine 32 → glycine
b) Alanine 33 → methionine
c) Cysteine 23 → valine
d) Methionine 22 → alanine
View Answer
Explanation: Methionine 22 → alanine mutation in subtilisin makes it resistant to inactivation by bleach. This engineered subtilisin shows high activity and stability and now many laundry detergents contain cloned, engineered subtilisin.
5. Which of the following is a strategy in protein engineering attempts to create improved protein molecules based on the three-dimensional structure and the relationship between structure and function?
a) Natural evolution
b) Directed evolution
c) Irrational design
d) Rational design
View Answer
Explanation: The rational design is a strategy in protein engineering attempts to create improved protein molecules based on the three-dimensional structure and the relationship between structure and function. Hence, it is also called as knowledge-based design.
6. Which of the following process involves the determination of the three-dimensional structure of a protein and representing it graphically and mathematically on a computer?
a) Irrational design
b) Directed evolution
c) Natural evolution
d) Rational design
View Answer
Explanation: X-ray crystallography is used to provide the three-dimensional structure of a protein. Rational design involves the determination of the three-dimensional structure of the protein and representing it graphically and mathematically on a computer.
7. Which of the following step in rational design allows predictions to be made particularly in the realm of the effect of mutations on structure-based properties?
a) Site-directed mutagenesis
b) X-ray crystallography
c) Protein assay
d) Computer modeling
View Answer
Explanation: The step in rational design that allows predictions to be made particularly in the realm of the effect of mutations on structure-based properties is computer modeling. Site-directed mutagenesis, x-ray crystallography, and protein assay do not allow for predicting the effect of mutations on structure-based properties.
8. Which of the following is the final, but an essential component of rational design?
a) X-ray crystallography
b) Computer modeling
c) Protein assay
d) Site-directed mutagenesis
View Answer
Explanation: Site-directed mutagenesis is the final, but an essential component of rational design. In the final step, variants of the native protein are made by recombinant (r) DNA techniques. The rDNA method of choice is commonly site-directed mutagenesis, in which one amino acid at a particular location is replaced with another.
9. In the rational design of proteins, once variant proteins are made and purified the new protein is evaluated to see if the desired property is achieved.
a) False
b) True
View Answer
Explanation: The above statement is true. In the rational design of proteins, once variant proteins are made and purified the new protein is evaluated to see if the desired property is achieved. If the desired property is not achieved, the information obtained in the evaluation is used in the second round of crystallography modeling and mutagenesis.
10. What is the missing component in the flow diagram of the rational design of proteins given below?
a) Protein-ligand assay
b) Structure visualization
c) Structure prediction
d) Site-directed mutagenesis
View Answer
Explanation: The missing component in the flow diagram of the rational design of proteins shown above is site-directed mutagenesis. This is because the computer modeling step provides us with probable target locations of mutation, making changes at these locations can potentially result in the desired protein variant.
11. Cellulose is a hybrid enzyme.
a) False
b) True
View Answer
Explanation: The above statement is true. Cellulose is a hybrid enzyme. Hybrid enzymes are commonly found in nature. Cellulose consists of a binding domain that serves to anchor the enzyme to cellulose and a catalytic domain to facilitate chain hydrolysis.
12. Which step is performed after the variant protein is expressed and purified?
a) Protein manipulation
b) Computer-aided modeling
c) Site-directed mutagenesis
d) Evaluation of desired property
View Answer
Explanation: After the variant, protein is expressed and purified it is evaluated for desired properties. This is done to access protein for desired changes. Protein manipulation, computer-aided modeling, and site-directed mutagenesis are not performed after the variant protein is expressed and purified.
13. Rational protein design is a high throughput protein engineering.
a) True
b) False
View Answer
Explanation: The above statement is false. Rational protein design is not a high throughput protein engineering. Irrational protein design is a high throughput protein engineering. Rational protein design is knowledge-based engineering of proteins with desired characteristics.
14. X-ray crystallography is not required in each and every cycle of rational protein design.
a) True
b) False
View Answer
Explanation: The above statement is false. X-ray crystallography is required in each and every cycle of rational protein design. It develops the 3-D structure of proteins which is then visualized using computer-aided models. Then predictions are made for making changes in the protein with the help of the structure obtained.
15. Only one cycle of rational protein design is sufficient to get a protein with desired characteristics.
a) True
b) False
View Answer
Explanation: The above statement is false. Only one cycle of rational protein design is not sufficient to get a protein with desired characteristics. Several cycles of rational protein design are required to finally obtain a protein variant with the desired characteristics.
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