Protein 1st and 2nd Structures

 Protein 1st and 2nd Structures

1) Formation of a peptide bond produces _____ as a byproduct.

1. A) ammonia
2. B) carbon dioxide
3. C) water
4. D) H⁺
5. E) OH^–

2) What type of plot allows one to investigate the likely phi and psi angles of the peptide backbone?

1. A) Hill
2. B) Lineweaver-Burk
3. C) Hanes-Woolf
4. D) Ramachandran
5. E) Michaelis-Menten

3) What level of protein structure is composed of a-helices, b sheets, and turns?

1. A) primary
2. B) secondary
3. C) tertiary
4. D) quaternary
5. E) both secondary and tertiary

4) What is the charged group(s) present in the peptide GLPQ at a pH of 7?

1. A) –NH₃⁺
2. B) –COO^–
3. C) –NH₂⁺
4. D) –NH₃⁺and –COO^–
5. E) All the charged groups are present.

5) At a pH of 12, what is the charged group(s) present in the peptide GLPQ?

1. A) –NH₃⁺
2. B) –COO^–
3. C) –NH₂⁺
4. D) –NH₃⁺and –COO^–
5. E) All the charged groups are present.

7) In the following peptide, which amino acid is the N-terminus?

Phe-Ala-Gly-Arg

1. A) Phe
2. B) Ala
3. C) Gly
4. D) Arg
5. E) Phe and Arg

8) Why is the peptide bond planar?

1. A) Bulky side chains prevent free rotation around the bond.
2. B) It contains partial double-bond character, preventing rotation.
3. C) Hydrogen bonding between the NH and C=O groups limits movement.
4. D) All of the answers are correct.
5. E) None of the answers is correct.

9).  Write chemical structures of trans and cis isomers of the peptide Ser-Pro and Circle the most like conformation the peptide bond tend to have.

The bond indicated in the Cis Ser-Pro structure represents the most likely peptide bond to be formed. This is because the Cis structure is more stable than the Trans structure and is more favored (Creese & Cooper, 2016).

10) Draw the Newman projections of the amino acid residue S in peptide MST, showing the values of Φ = -90 and Ψ = +180.

The phi (Φ) presented in the Newman projection structure (A) is -90⁰ and constitutes four atoms. They include a carbonyl carbon, an alpha-carbon, the amide nitrogen, and the following carbonyl carbon. The angle Φ depends on the offset of the n^th residue’s carbonyl atom from the carbonyl atom (n+1)^th (Fang et al., 2018). The backbone nitrogen attached to the nth residue from the (n+1)^th nitrogen defines the angle psi (ψ). In the Newman projection structure (B), the (ψ) is formed between two nitrogen atoms at the carbon atom attached to a carbonyl group (Li et al., 2017). Both the ψ and Φ angles are formed on the alpha carbon atom, as indicated in the structures A and B. Finally, the structural rotation on Φ and ψ angles is independent of each other.

References

Creese, A. J., & Cooper, H. J. (2016). Separation of cis and trans Isomers of Polyproline by FAIMS Mass Spectrometry. Journal of The American Society for Mass Spectrometry, 27(12), 2071-2074.

Fang, C., Shang, Y., & Xu, D. (2018). Prediction of protein backbone torsion angles using deep residual inception neural networks. IEEE/ACM transactions on computational biology and bioinformatics, 16(3), 1020-1028.

Li, H., Hou, J., Adhikari, B., Lyu, Q., & Cheng, J. (2017). Deep learning methods for protein torsion angle prediction. BMC bioinformatics, 18(1), 417.