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This quiz contains multiple-choice problems on protein motifs, motif and domain databases using regular expressions and statistical models, protein family databases, global and local sequence alignments, dot matrix sequence comparison and Bayesian statistics.
What is the length of a motif, in terms of amino acids residue?
30- 60
10- 20
70- 90
1- 10
On average, what is the length of a typical domain?
About 100 residues
About 300 residues
About 500 residues
About 900 residues
Which of the following is false about the ‘loop’ structure in proteins?
They connect helices and sheets
They are more tolerant of mutations
They are more flexible and can adopt multiple conformations
They are never the components of active sites
Which of the common structural motifs are misdescribed?
β-hairpin – adjacent antiparallel strands
Greek key – 4 adjacent antiparallel strand
β-α-β – 2 parallel strands connected by helix
β-α-β – 2 antiparallel strands connected by helix
Motifs that can form α/β horseshoes conformation are rich with which protein residue?
Proline
Arginine
Valine
Leucine
Which of the following misdescribes protein domains?
They are made up of one secondary structure
Defined as independently foldable units
They are stable structures as compared to motifs
They are separated by linker regions
Which of the following least describes long loop β-hairpins?
They are often referred to as a ‘random coil’ conformation
Generally they are referred to as the β-meander supersecondary structure
Loop looks similar to the Greek Letter Ω
Wide-range of conformations with very specific sequence preferences
Which of the following is not the function of short linear motifs?
Irreversible cleavage of the peptide at the SLiM
Reversible cleavage of the peptide at the SLiM
Moiety addition at targeted sites on SLiM
Structural modifications of the peptide backbone
In the zinc finger, which residues in this sequence motif form ligands to a zinc ion?
Cysteine and histidine
Cysteine and arginine
Histidine and proline
Histidine and arginine
Which of the following is not an advantage of the statistical models’ methods in analyzing protein motifs?
Sequence information is preserved from a multiple sequence alignment and expresses it with probabilistic models
Statistical models allow partial matches and compensate for unobserved sequence patterns using pseudo-counts
Statistical models have stronger predictive power than the regular expression based approach, even when they are derived from a limited set of sequences
The comparative flexibility is less in case of these methods when compared to regular expressions methods
Which of the following programs or databases is for regulated sites curated from scientific literature for motif scanning?
ENSEMBL
ORegAnno
MAST
Clover
Which of the following is not an advantageous feature or algorithm of the database PRINTS?
This program breaks down a motif into even smaller non-overlapping units called ‘fingerprints’, which are represented by unweighted PSSMs
To define a motif, at least a majority of fingerprints are required to match with a query sequence
A query that has simultaneous high-scoring matches to a majority of fingerprints belonging to a motif is a good indication of containing the functional motif
The difficulty to recognize short motifs when they reach the size of single fingerprints
In which of the following multipurpose packages is the Gibbs sampling algorithm used?
Consensus
BEST
AlignACE
PhyloCon
Which of the following is untrue in case of the database BLOCKS?
The alignments are automatically generated using the same data sets used for deriving the BLOSUM matrices
The derived ungapped alignments are called ‘blocks’, which are usually longer than motifs, are subsequently converted to PSSMs
A weighting scheme and pseudo counts are subsequently applied to the PSSMs to account for underrepresented and unobserved residues in alignments
The functional annotation of blocks is not consistent with that for the motifs
When did Needleman-Wunsch first describe the algorithm for global alignment?
