Sequence Alignment
Sequence
Alignment
Protein
Motifs and Domain Prediction
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
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Answer
Answer:
b
Explanation:
A typical motif
is 10-20 amino acids long. For e.g. the 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
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Answer
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
View
Answer
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 components 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 a helix
d)
β-α-β – 2 antiparallel strands connected by a helix
View
Answer
Answer:
d
Explanation:
In motif, two adjacent β parallel strands are connected by an α helix from the
C[1]terminus
of strand 1 to the N-terminus of the strand. Most protein structures that contain
parallel
beta-sheets
are built up from combinations of such β-α-β motifs.
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 super secondary structure
c)
Loop looks similar to the Greek Letter Ω
d)
Wide-range of conformations with very specific sequence preferences
View
Answer
Answer:
d
Explanation:
They are a wide range of conformations with no particular sequence preferences.
As
the name
suggests ‘meander’ the conformation they possess is also quite unspecified. In addition
to that
Long loop β-hairpins are a special cases of Ω loops, which 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
View
Answer
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
View
Answer
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 a 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 is contained by all of the
following except________
a)
Scleraxis
b)
Neurogenins
c)
Transcription Factor 4
d)
Leucine zipper
View
Answer
Answer:
d
Explanation:
Leucine zipper is associated with gene regulation and contains alpha-helix with
leucine
at every 7th amino acid. While the 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
View
Answer
Answer:
a
Explanation:
Short Linear Motifs are short stretches of the protein sequence that mediate
protein[1]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
View
Answer
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.
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