This set of Protein Engineering Multiple Choice Questions & Answers (MCQs) focuses on “Structure Function Relationships – Zinc Fingers”.
1. Regulatory proteins have only protein-DNA interacting domains.
a) True
b) False
View Answer
Explanation: The above statement is false. The regulatory proteins contain domains not only for DNA binding but also for protein-protein interaction. Examples include many eukaryotic transcription factors that function as gene activators.
2. Which among the following motifs contain a positively charged ion?
a) Leucine zippers
b) H-T-H motif
c) Homeobox
d) Zinc fingers
View Answer
Explanation: The zinc finger DNA-binding motif contains a positively charged zinc ion. There is a single Zn+2 ion in the core structure of the zinc motif. This Zn+2 ion is coordinated with four amino acid residues.
3. The positively charged Zn+2 ion in the zinc finger interacts directly with the negatively charged phosphate in DNA.
a) True
b) False
View Answer
Explanation: The above statement is false. In zinc fingers, the elongated loop is held together at the base by a single Zn+2 ion. The Zn+2 ions do not itself interact with DNA.
4. Zn+2 ions in zinc fingers are coordinated to which amino acid residues?
a) 2 Met and 2 Cys
b) 4 Val or 2 Met and 2 Cys
c) 2 Ala and 2 Gly
d) 4 Cys or 2 Cys and 2 His
View Answer
Explanation: The zinc ion is coordinated to four of the following residues: 4 Cys or 2 Cys and 2 His. This coordination of zinc with the amino acids stabilizes this small structural motif. Thus, the Zn+2 ions do not directly interact with the DNA.
5. What is the average length of the elongated loop in zinc fingers?
a) 20 amino acid residues
b) 10 amino acid residues
c) 40 amino acid residues
d) 30 amino acid residues
View Answer
Explanation: The average length of the elongated loop in zinc fingers is 30 amino acid residues. This loop is held together at the base by a single Zn+2 ion. These ions form a coordination bond with the amino acid residues in the loop.
6. The interaction of a single zinc finger with DNA is typically very strong.
a) True
b) False
View Answer
Explanation: The above statement is false. The interaction of a single zinc finger with DNA is typically weak and many DNA-binding proteins have multiple zinc fingers that substantially enhance binding by interacting simultaneously with the DNA.
7. Zinc fingers can also function as which of the following?
a) Lipid-binding motif
b) Carbohydrate-binding motif
c) Ribosome-binding motif
d) RNA-binding motif
View Answer
Explanation: Zinc fingers can also function as an RNA-binding motif. E.g. in certain proteins that bind eukaryotic mRNAs and act as translational repressors. Zinc fingers do not function as a lipid-binding motif, carbohydrate-binding motif, and ribosome-binding motif.
8. Zinc fingers in found in many eukaryotic DNA-binding motifs.
a) False
b) True
View Answer
Explanation: The above statement is true. Zinc fingers in found in many eukaryotic DNA-binding motifs. There are few known examples of the zinc finger motifs in bacterial proteins.
9. Which of the following is not true for zinc fingers?
a) It contains a beta-sheet domain
b) It contains an alpha-helix domain
c) It contains Zn+2 ion
d) It contains Ca+2 ion
View Answer
Explanation: Zinc fingers contain a beta-sheet domain, an alpha-helix domain, and a Zn+2 ion. It does not contain a Ca+2 ion. Zn+2 ion forms a coordination bond with the amino acid residues in the extended loop of the zinc fingers.
10. Zinc fingers are not able to interact with which of the following?
a) DNA
b) RNA
c) Poly-ADP-ribose
d) ATP
View Answer
Explanation: Zinc fingers are not able to interact with ATP molecules because they do not have specificity for them. Whereas zinc fingers can interact with DNA, RNA, and Poly-ADP-ribose. Moreover, it can also interact with other proteins.
11. Zinc fingers do not have a role in which of the following processes?
a) Transcriptional regulation
b) Ubiquitin-mediated protein degradation
c) Signal transduction
d) Cellular transport
View Answer
Explanation: Zinc fingers do not have a role in cellular transport. Whereas, zinc fingers have a role in transcriptional regulation, ubiquitin-mediated protein degradation, and signal transduction. Moreover, it also has a role in DNA repair, actin targeting, cell migration, and various other processes.
12. Most regulatory proteins have discrete DNA-binding domains, which contain one or more relatively small groups. What are these groups called?
a) Excretory motifs
b) Regulatory motifs
c) Catalytic motifs
d) Structural motifs
View Answer
Explanation: The regulatory proteins that interact closely and specifically with the DNA, have discrete DNA-binding domains. These domains contain a relatively small group of recognizable and characteristic structural motifs.
13. The side chains of which amino acid residues are not hydrogen-bonded to bases in the DNA?
a) Gln residue
b) Lys residue
c) Glu residue
d) Ala residue
View Answer
Explanation: Ala residue cannot be hydrogen-bonded to bases in the DNA. Hence, these residues are not present in the DNA-binding domains of regulatory proteins. Gln, Lys, and Glu residues can form hydrogen bonds with the bases in the DNA. Hence, Gln, Lys, and Glu residues are mostly present in the DNA-binding domains of regulatory proteins.
14. What is the approximate length of DNA-binding domains of regulatory proteins?
a) 100-500 amino acid residues
b) 50-60 amino acid residues
c) 5-10 amino acid residues
d) 60-90 amino acid residues
View Answer
Explanation: The approximate length of DNA-binding domains of regulatory proteins is about 60-90 amino acid residues. To interact with bases in the major groove of DNA a protein requires a relatively small substructure that can stably protrude from the protein surface.
15. Which of the following is a feature of DNA-binding sites for regulatory proteins?
a) Cytosine rich sequence
b) Guanine rich sequence
c) CpG repeats
d) Palindromic sequence
View Answer
Explanation: Palindromic sequence is a feature of DNA-binding sites for regulatory proteins. The DNA-binding sites for regulatory proteins are often inverted repeats of short DNA sequences. This DNA sequence is a palindrome. Multiple subunits of a regulatory protein bind cooperatively at these sites.
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