Protein Engineering Questions for Campus Interviews

This set of Protein Engineering Questions and Answers for Campus interviews focuses on “Chemical Synthesis of Peptides – 2”.

1. What is the total number of dipeptides and tripeptides that can be formed when two solutions of different amino acids are mixed?
a) Twenty-four
b) Sixteen
c) Ten
d) Twelve
View Answer

Answer: d
Explanation: The total number of dipeptides and tripeptides that can be formed when two solutions of different amino acids are mixed is twelve. E.g. if those two different amino acids are trp and cys then the possible combinations of dipeptides and tripeptides are trp-cys, trp-trp, cys-cys, cys-trp, cys-cys-cys, trp-trp-trp, trp-cys-cys, cys-trp-cys, cys-cys-trp, trp-trp-cys, trp-cys-trp, and cys-trp-trp. This can also be calculated by using the formula given below,
Formula: n=x^y
Where x=number of different amino acids used,
y=number amino acid positions in the peptides.
Hence, n=2³+2²
n=12.

2. The side group of serine is protected by which of the following protecting groups?
a) A tertiarybutyloxycarbonyl (tBOC)
b) 2,2,5,7,8-pentamethylchroman-6-sulphonyl group (PMC)
c) A triphenylmethyl group (Trt)
d) A tertiary butyl group (tBu)
View Answer

Answer: d
Explanation: The side group of serine is protected by the tertiary butyl group (tBu). Serine has a hydroxyl group in its side chain. Hence, it cannot be protected by tertiarybutyloxycarbonyl (tBOC), 2,2,5,7,8-pentamethylchroman-6-sulphonyl group (PMC), or triphenylmethyl group (Trt).

3. The coupling reaction in the SPPS is catalyzed by which of the following?
a) 1,4-dicyclohexylcarbodiimide
b) 2,3-dicyclohexylcarbodiimide
c) 1,2-dicyclohexylcarbodiimide
d) 1,3-dicyclohexylcarbodiimide
View Answer

Answer: d
Explanation: In the coupling reaction the FMOC protected amino acid is reacted with the last amino acid attached to the polyamide. The coupling reaction in the SPPS is catalyzed by 1,3-dicyclohexylcarbodiimide. In the reaction process, 1,3-dicyclohexylcarbodiimide (DCC) is itself reduced to 1,3-dicyclohexylurea (DCU).

4. In the deprotection step of SPPS, the FMOC group is removed with the help of which of the following reagent?
a) Fluorobenzene
b) Trifluoroacetic acid
c) 1,3-dicyclohexylcarbodiimide
d) Piperidine
View Answer

Answer: d
Explanation: In the deprotection step of SPPS, the FMOC group is removed with the help of piperidine. Piperidine is a cyclic secondary amine. This is a trans amidification reaction.

5. How many combinations of tripeptides can be formed if two solutions of different amino-acids are mixed?
a) Twelve
b) Sixteen
c) Thirty-two
d) Eight
View Answer

Answer: d
Explanation: Eight different combinations of tripeptides can be formed if two solutions of different amino-acids are mixed. E.g. if those two different amino acids are trp and cys then the possible combinations of tripeptides are cys-cys-cys, trp-trp-trp, trp-cys-cys, cys-trp-cys, cys-cys-trp, trp-trp-cys, trp-cys-trp, and cys-trp-trp. This can also be calculated by using the formula given below,
Formula: n=x^y
Where x=number of different amino acids used,
y=number amino acid positions in the peptides.
Hence, n=2³
n=8.

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6. The side group of cysteine is protected by which of the following protecting groups?
a) 2,2,5,7,8-pentamethylchroman-6-sulphonyl group (PMC)
b) A tertiary butyl group (tBu)
c) A tertiarybutyloxycarbonyl (tBOC)
d) A triphenylmethyl group (Trt)
View Answer

Answer: d
Explanation: The side group of cysteine is protected by a triphenylmethyl group (Trt). The side chain of cysteine contains a sulfhydryl group. Hence, it cannot be protected by tertiarybutyloxycarbonyl (tBOC), 2,2,5,7,8-pentamethylchroman-6-sulphonyl group (PMC), or triphenylmethyl group (Trt).

7. If the yield for each amino acid addition in SPPS is 99 % then, what will be the overall yield of a 40 amino acid peptide?
a) 64.1 %
b) 76.8 %
c) 86.9 %
d) 66.9 %
View Answer

Answer: d
Explanation: If the yield for each amino acid addition in SPPS is 99 % then, the overall yield of a 40 amino acid peptide would be around 66.9 %. This can be calculated by using the formula given below.
Formula: Y=yx(\(\frac{y}{100}\))^n-1
Where Y=the overall yield
y=yield for each amino acid addition
n=number of amino acids in the peptide
Hence, Y=99x(\(\frac{99}{100}\))^40-1
Y=66.9%.

8. How many combinations of tetrapeptides can be formed if two solutions of different amino-acids are mixed?
a) Twelve
b) Nine
c) Twenty-four
d) Sixteen
View Answer

Answer: d
Explanation: Sixteen different combinations of tetrapeptides can be formed if two solutions of different amino-acids are mixed. This can also be calculated by using the formula given below,
Formula: n=x^y
Where x=number of different amino acids used,
y=number amino acid positions in the peptides.
Hence, n=2⁴
n=16.

9. The side group of lysine is protected by which of the following protecting groups?
a) A tertiary butyl group (tBu)
b) A triphenylmethyl group (Trt)
c) 2,2,5,7,8-pentamethylchroman-6-sulphonyl group (PMC)
d) A tertiarybutyloxycarbonyl (tBOC)
View Answer

Answer: d
Explanation: The side group of lysine is protected by a tertiarybutyloxycarbonyl (tBOC). The side chain of lysine contains positively charged ammonium ion. Hence, it cannot be protected by tertiarybutyloxycarbonyl (tBOC), 2,2,5,7,8-pentamethylchroman-6-sulphonyl group (PMC), or triphenylmethyl group (Trt).

10. How many combinations of tripeptides can be formed if three solutions of different amino-acids are mixed?
a) Twenty-four
b) Nine
c) Sixteen
d) Twenty-seven
View Answer

Answer: d
Explanation: Twenty-seven different combinations of tripeptides can be formed if three solutions of different amino-acids are mixed. This can also be calculated by using the formula given below,
Formula: n=x^y
Where x=number of different amino acids used,
y=number amino acid positions in the peptides.
Hence, n=3³
n=27.

11. Once the synthesis of the peptide is complete, it is removed from the polyamide with the help of which reagent?
a) 1,3-dicyclohexylcarbodiimide
b) Piperidine
c) Fluorobenzene
d) Trifluoroacetic acid
View Answer

Answer: d
Explanation: Once the synthesis of the peptide is complete, it is removed from the polyamide with the help of a reagent known as trifluoroacetic acid (TFA). The side-chain protecting groups are also removed at this stage.

12. If the yield for each amino acid addition in SPPS is 99.99 % then, what will be the overall yield of a 50 amino acid peptide?
a) 98.2 %
b) 99.1 %
c) 99.9 %
d) 99.5 %
View Answer

Answer: d
Explanation: If the yield for each amino acid addition in SPPS is 99.99 % then, the overall yield of a 50 amino acid peptide would be 99.5 %. This can be calculated by using the formula given below.
Formula: Y=y x (\(\frac{y}{100}\))^n-1
Where Y=the overall yield
y=yield for each amino acid addition
n=number of amino acids in the peptide
Hence, Y=99.99 x (\(\frac{99.99}{100}\))^50-1
Y=99.5%.

13. How many combinations of tetrapeptides can be formed if three solutions of different amino-acids are mixed?
a) Ninety-one
b) Eighty-six
c) Seventy-two
d) Eighty-one
View Answer

Answer: d
Explanation: Eighty-one different combinations of tetrapeptides can be formed if three solutions of different amino-acids are mixed. This can also be calculated by using the formula given below,
Formula: n=x^y
Where x=number of different amino acids used,
y=number amino acid positions in the peptides.
Hence, n=3⁴
n=81.

14. The side group of arginine is protected by which of the following protecting groups?
a) A triphenylmethyl group (Trt)
b) A tertiary butyl group (tBu)
c) A tertiarybutyloxycarbonyl (tBOC)
d) 2,2,5,7,8-pentamethylchroman-6-sulphonyl group (PMC)
View Answer

Answer: d
Explanation: The side group of arginine is protected by a 2,2,5,7,8-pentamethylchroman-6-sulphonyl group (PMC). The side chain of arginine contains a positively charged ammonium group. Hence, it cannot be protected by tertiarybutyloxycarbonyl (tBOC), 2,2,5,7,8-pentamethylchroman-6-sulphonyl group (PMC), or triphenylmethyl group (Trt).

15. How many combinations of dipeptides can be formed if four solutions of different amino-acids are mixed?
a) Four
b) Six
c) Eight
d) Sixteen
View Answer

Answer: d
Explanation: Sixteen different combinations of dipeptides can be formed if four solutions of different amino-acids are mixed. This can also be calculated by using the formula given below,
Formula: n=x^y
Where x=number of different amino acids used,
y=number amino acid positions in the peptides.
Hence, n=4²
n=16.

Sanfoundry Global Education & Learning Series – Protein Engineering.

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