Bioinformatics Questions and Answers Part-1

1. What is the length of a motif, in terms of amino acids residue?
a) 30- 60
b) 10- 20
c) 70- 90
d) 1- 10

Answer: b
Explanation: A typical motif is 10-20 amino acids long. For e.g. Zn-finger motif. Hence it is also referred to as super secondary structure. This motif is seen in transcription factors.

2. On average, what is the length of a typical domain?
a) About 100 residues
b) About 300 residues
c) About 500 residues
d) About 900 residues

Answer: a
Explanation: The predicted optimal number of residues, which corresponds to the maximum free energy of unfolding, is 100. This is in agreement with a statistical analysis derived from their experimental structures of motifs. For too short chain, change in enthalpy of internal interactions is not favorable enough for folding because of the limited number of inter-residue contacts. And a long chain is also unfavorable for a single domain.

3.Which of the following is false about the ‘loop’ structure in proteins?
a) They connect helices and sheets
b) They are more tolerant of mutations
c) They are more flexible and can adopt multiple conformations
d) They are never the components of active sites

Answer: d
Explanation: Loops are frequently components of active sites as they are flexible in nature and as they are situated on the surface of the structure. Besides, they vary in length and 3-D configurations which give even more chances to be component of active sites.

4. Which of the common structural motifs are described wrongly?
a) β-hairpin – adjacent antiparallel strands
b) Greek key – 4 adjacent antiparallel strand
c) β-α-β – 2 parallel strands connected by helix
d) β-α-β – 2 antiparallel strands connected by helix

Answer: d
Explanation: In motif, two adjacent β parallel strands are connected by an α helix from the C-terminus of strand 1 to the N-terminus of strand. Most protein structures that contain parallel beta-sheets are built up from combinations of such β-α-βmotifs.

5. Which of the following least describes Long Loop β-hairpins?
a) They are Often referred to as a ‘random coil’ conformation
b) Generally they are referred to as the β-meander supersecondary structure
c) Loop looks similar to the Greek Letter Ω
d) Wide-range of conformations with very specific sequence preferences

Answer: d
Explanation: They are wide-range of conformations with no particular sequence preferences. As the name suggests ‘meander’ the conformation they possess is also quite unspecified. Addition to that Long loop β-hairpins are special case of Ω loops, that explains a lot about their structural preferences.

6. Motifs that can form α/β horseshoes conformation are rich with which protein residue?
a) Proline
b) Arginine
c) Valine
d) Leucine

Answer: d
Explanation: Specific pattern of Leucine residues, strands form a curved sheet with helices on the outside. Leucine-rich repeats (LRRs) are 20-29-residue sequence motifs present in a number of proteins with diverse functions. The primary function of these motifs appears to be to provide a versatile structural framework for the formation of protein-protein interactions.

7. Which of the following wrongly describes protein domains?
a) They are made up of one secondary structure
b) Defined as independently foldable units
c) They are stable structures as compared to motifs
d) They are separated by linker regions

Answer: a
Explanation: Protein domains are made up of two or more motifs i.e. the secondary structure to form stable and folded 3-D structures. They are conserved part of the protein sequence and can evolve, function, and exist independently of the rest of the protein chain.

8. The protein structural motif domain- helix loop helix are contained by all of the following except ________
a) Scleraxis
b) Neurogenins
c) Transcription Factor 4
d) Leucine zipper

Answer: d
Explanation: Leucine zipper is associated with gene regulation and contains alpha helix with leucine at every 7th amino acid. While rest of them are under one of the largest families of dimerizing transcription factors

9. Which of the following is not the function of Short Linear Motifs?
a) Irreversible cleavage of the peptide at the SLiM
b) Reversible cleavage of the peptide at the SLiM
c) Moiety addition at targeted sites on SLiM
d) Structural modifications of the peptide backbone

Answer: a
Explanation: Short Linear Motifs are short stretches of protein sequence that mediate protein-protein interaction. SLiMs can act as recognition sites of endo-peptidases resulting in the irreversible cleavage of the peptide at the SLiM.

10. In the zinc finger, which residues in this sequence motif form ligands to a zinc ion?
a) Cysteine and histidine
b) Cysteine and arginine
c) Histidine and proline
d) Histidine and arginine

Answer: a
Explanation: In the zinc finger, which is found in a widely varying family of DNA-binding proteins, cysteine and histidine residues in this sequence motif form ligands to a zinc ion whose coordination is essential to stabilize the tertiary structure.