Conservation of gene order due to operon structure is _______ so interactions of proteins specific to eukaryotes cannot be detected by method of Conservation of gene order.

not applicable to archea genomes

not applicable to prokaryote genomes

applicable to eukaryote genomes

not applicable to eukaryote genomes

Interactions between proteins can be predicted computationally by looking for sets of genes that occur as a _______

multiple genes in at least one genome

single gene in at least one genome

multiple genes in at least one genome

multiple genes in various genomes

In Multiple conformation rigid-body method, a ligand is assumed to be able to adopt a number (N) of different _______ that are computed _____ the ligand being docked into the receptor.

high-energy conformations, prior to

low-energy conformations, after

low-energy conformations, prior to

high-energy conformations, prior to

high-energy conformations, after

In case of Protein-ligand docking, ______ ligands are often _____ in adapting their shape to fit the receptor binding pocket.

large molecule, highly flexible

small molecule, highly flexible

large molecule, highly flexible

Proteins are dynamic entities that undergo _______

illimitable or total conformational change of amino acid side-chains when in solution

only fluctuation of flexible loop regions about equilibrium positions when in solution

only limited conformational change of amino acid side-chains when in solution

both limited conformational change of amino acid side-chains and fluctuation of flexible loop regions about equilibrium positions when in solution

illimitable or total conformational change of amino acid side-chains when in solution

An approach for predicting ______ to look for cases across a set of genomes where _____ are part of the same gene in one genome resulted in gene fusion method.

protein interactions, two orthologs

gene interactions, only three to four orthologs

gene interactions, two orthologs

protein interactions, two or more orthologs

protein interactions, two orthologs

Which of the following is untrue about Electrostatic Complementarity?

The electrostatic properties of biomolecules play an important role in determining interactions

The burial of charged residues at protein-protein/DNA interfaces is thought to be generally net destabilizing with the hydrophobic effect being the primary driving force

Charged groups involved in the biomolecular interface are often stabilized by other polar or oppositely charged groups on the interacting molecule

Charged groups involved in the biomolecular interface are often stabilized by similar polar or same charged groups on the interacting molecule

Which of the following is untrue about Hydrophobicity?

The hydrophobic effect plays a dominant role in the folding of proteins

Hydrophobic residues aggregate away from contact with water

Hydrophobic residues aggregate to form hydrophobic cores with more polar residues

Hydrophobic residues form the solvent accessible surface but restrict the solubility of the protein

Which of the following is true regarding Protein flexibility?

Methods have been described for the introduction of side-chain flexibility to protein-ligand docking only

Methods have been described for the introduction of side-chain flexibility to both protein-ligand and protein-protein docking

Methods have been described for the introduction of side-chain flexibility to protein-ligand docking only

The Mean Field principle is rarely used in this

Methods have been described for the introduction of side-chain flexibility to protein-protein docking only

Domains that are part of a multidomain protein are ______

nethier co-regulated nor colocalized

not co-regulated but colocalized

co-regulated and but not colocalized

The ______ is an ongoing community-wide experiment on the comparative evaluation of protein-protein docking for structure prediction.

Chronological Assignment of Prediction of Interactions (CAPRI)

Chronological Assessment of Prediction of Interactions (CAPRI)

Critical Assignment of Prediction of Interactions (CAPRI)

Critical Assessment of Prediction of Interactions (CAPRI)

Which of the following is incorrect about Purification of protein complexes followed by mass spectrometry?

Affinity purification based on the epitope will then extract all the proteins attached to the bait protein from cell lysates

Isolating protein complexes from cells allows identification of interactions between ensembles of proteins instead of just pairs

Systematic purification of complexes on a large scale is done by tagging hundreds of genes with an epitope

UnLike in the yeast-two-hybrid assay, this does not involve chimeric genes

Affinity purification based on the epitope will then extract all the proteins attached to the bait protein from cell lysates

Almost ______ engage in interactions with domains from their own family when one includes oligomeric proteins.

one fifith of all known families

one fourth of all known families

Which of the following is untrue about Grid Representation?

To speed up the matching process the topology of the protein can be simplified from atomic level detail to a series of cubic elements

To speed up the matching process discretizing the 3-dimensional space using a grid is done

Discretizing allows very fast computer matching using search methods such as Fourier transform

Fourier transform is hardly used in computer matching

63 + Mcqs in Protein Protein Interactions in Bioinformatics Page 1 McqOptions

1.	When comparing pairs of genes or sets of genes in different genomes for this purpose, it is not mandatory for the genes to be orthologs.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» C. May be True or False

Discussion

2.	Conservation of gene order due to operon structure is _______ so interactions of proteins specific to eukaryotes cannot be detected by method of Conservation of gene order.
A.	not applicable to archea genomes
B.	not applicable to prokaryote genomes
C.	applicable to eukaryote genomes
D.	not applicable to eukaryote genomes
Answer» E.

Discussion

3.	In a quantitative assessment of this method (Conservation of gene order) using the genome of the parasitic organism Mycoplasma genitalium as a benchmark.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

Discussion

4.	Interactions between proteins can be predicted computationally by looking for sets of genes that occur as a _______
A.	single gene in at least one genome
B.	multiple genes in at least one genome
C.	multiple genes in various genomes
D.	single gene in various genomes
Answer» B. multiple genes in at least one genome

Discussion

5.	Experimentation is most desirable over computational methods by every means.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» C. May be True or False

Discussion

6.	Across the different types of catalytic families, the position of the two domains with respect to one another varied, but only within a range of about ______
A.	20°
B.	10°
C.	90°
D.	80°
Answer» D. 80°

Discussion

7.	In Multiple conformation rigid-body method, a ligand is assumed to be able to adopt a number (N) of different _______ that are computed _____ the ligand being docked into the receptor.
A.	low-energy conformations, after
B.	low-energy conformations, prior to
C.	high-energy conformations, prior to
D.	high-energy conformations, after
Answer» C. high-energy conformations, prior to

Discussion

8.	In case of Protein-ligand docking, ______ ligands are often _____ in adapting their shape to fit the receptor binding pocket.
A.	small molecule, highly flexible
B.	large molecule, highly flexible
C.	large molecule, more flexible
D.	small molecule, less flexible
Answer» B. large molecule, highly flexible

Discussion

9.	Proteins are dynamic entities that undergo _______
A.	only fluctuation of flexible loop regions about equilibrium positions when in solution
B.	only limited conformational change of amino acid side-chains when in solution
C.	both limited conformational change of amino acid side-chains and fluctuation of flexible loop regions about equilibrium positions when in solution
D.	illimitable or total conformational change of amino acid side-chains when in solution
Answer» D. illimitable or total conformational change of amino acid side-chains when in solution

Discussion

10.	In the assessment of methods to predict protein-protein interactions, one third of such pairs were found to physically interact, and an additional third to belong to the same metabolic pathway or functional process.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

Discussion

11.	An approach for predicting ______ to look for cases across a set of genomes where _____ are part of the same gene in one genome resulted in gene fusion method.
A.	gene interactions, only three to four orthologs
B.	gene interactions, two orthologs
C.	protein interactions, two or more orthologs
D.	protein interactions, two orthologs
Answer» D. protein interactions, two orthologs

Discussion

12.	Due to the requirement for co-regulation as well as colocalization, the method is mostly limited to certain classes of protein-protein interactions.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

Discussion

13.	The disadvantage of Multiple conformation rigid-body method is that the active conformation may be missed as the result of a minor structural difference not considered in the ______ ligand conformations. Where, the N is the number of low-energy conformations.
A.	N +1
B.	N
C.	N²
D.	N/2
Answer» C. N²

Discussion

14.	Oligomers are often obligate complexes meaning that the free-energy cost of dissociation is high and they exist as oligomers under physiological conditions.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

Discussion

15.	In Property-based measures, displaying physical properties on the molecular surface of molecules can help to guide molecular docking.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

Discussion

16.	Which of the following is untrue about Electrostatic Complementarity?
A.	The electrostatic properties of biomolecules play an important role in determining interactions
B.	The burial of charged residues at protein-protein/DNA interfaces is thought to be generally net destabilizing with the hydrophobic effect being the primary driving force
C.	Charged groups involved in the biomolecular interface are often stabilized by other polar or oppositely charged groups on the interacting molecule
D.	Charged groups involved in the biomolecular interface are often stabilized by similar polar or same charged groups on the interacting molecule
Answer» E.

Discussion

17.	Which of the following is untrue about Hydrophobicity?
A.	The hydrophobic effect plays a dominant role in the folding of proteins
B.	Hydrophobic residues aggregate away from contact with water
C.	Hydrophobic residues aggregate to form hydrophobic cores with more polar residues
D.	Hydrophobic residues form the solvent accessible surface but restrict the solubility of the protein
Answer» E.

Discussion

18.	Members of a stable complex are often co-regulated and thus will be detected by the method of Conservation of gene order.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

Discussion

19.	The most detailed experimental information about protein-protein interactions comes from three-dimensional structures.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

Discussion

20.	Genes that are consistently part of the same operon across different, distantly related genomes are likely to be part of the same protein complex or functional process across all species.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

Discussion

21.	In Grid representation, the lowest score represents the best surface complementarity for a given translational scan.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» C. May be True or False

Discussion

22.	The phylogenetic profile method relies on detection of orthologs (or homologs, in a variation of the method) in a set of genomes.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

Discussion

23.	The linkers between the catalytic domain and the Rossmann domain were conserved in each family.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

Discussion

24.	The investigation (Aloy and Russel) of domain combinations in multidomain proteins by Bashton and Chothia focuses on two-domain proteins belonging to the Rossmann domain family.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

Discussion

25.	Which of the following is true regarding Protein flexibility?
A.	Methods have been described for the introduction of side-chain flexibility to both protein-ligand and protein-protein docking
B.	Methods have been described for the introduction of side-chain flexibility to protein-ligand docking only
C.	The Mean Field principle is rarely used in this
D.	Methods have been described for the introduction of side-chain flexibility to protein-protein docking only
Answer» B. Methods have been described for the introduction of side-chain flexibility to protein-ligand docking only

Discussion

26.	Domains that are part of a multidomain protein are ______
A.	nethier co-regulated nor colocalized
B.	not co-regulated but colocalized
C.	co-regulated and but not colocalized
D.	co-regulated and colocalized
Answer» E.

Discussion

27.	Typical motions of proteins will be primarily treated by a rigid body model for docking.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» C. May be True or False

Discussion

28.	Structural analyses on small sets of proteins have shown that the domains from a pair of families bind to each other with the same geometry in multi-domain proteins and in transient interactions.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

Discussion

29.	In the phylogenetic profile method for predicting protein interaction, presence or absence of orthologous genes is scored across a variety of genomes.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

Discussion

30.	Stochastic methods can guarantee reaching a global optimal solution and the methods are computationally costly in comparison to the other methods.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» C. May be True or False

Discussion

31.	Genetic methods (genetic algorithms and evolutionary programming) store multiple solutions. These solutions form a population of members.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

Discussion

32.	In a Monte Carlo simulation the score (or energy) is calculated at each step and compared to the previous step. The probability of accepting the step is given by _________ where ΔE is the difference in energy; kB is Boltzmann’s constant and T the temperature.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

Discussion

33.	In Stochastic search methods, they include methods such as Monte Carlo simulation, simulated annealing, Tabu search, genetic algorithms and evolutionary programming.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

Discussion

34.	An understanding of the importance of different factors in a particular interaction is important if confidence in the results is required. Which of the following are not those factors?
A.	Shape
B.	Hydrophobicity
C.	Electrostatics
D.	pH
Answer» E.

Discussion

35.	The ______ is an ongoing community-wide experiment on the comparative evaluation of protein-protein docking for structure prediction.
A.	Chronological Assignment of Prediction of Interactions (CAPRI)
B.	Chronological Assessment of Prediction of Interactions (CAPRI)
C.	Critical Assignment of Prediction of Interactions (CAPRI)
D.	Critical Assessment of Prediction of Interactions (CAPRI)
Answer» E.

Discussion

36.	There was little degree of success in docking an antibody-antigen complex in the second challenge for the protein-protein docking evaluation.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

Discussion

37.	In case of protein-protein docking, the level of success is dependent on the system under study.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

Discussion

38.	In a similar way to structure prediction methods models can be evaluated using RMSD to measure the similarity between two molecular complexes.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

Discussion

39.	The GRASP and VRLM have been incorporated into the GRASS server.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

Discussion

40.	The popular program RasMol can be made to view molecular properties by assigning those properties to the temperature factor column of the sdf file in question only.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» C. May be True or False

Discussion

41.	Information about shape, hydrophobicity, electrostatics, evolutionary relationships and conformational flexibility is not always available and the search for a universally applicable scoring function as well as an adequate treatment of conformational flexibility is ongoing.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

Discussion

42.	Visualization methods are very important in viewing molecular properties on molecules. Of particular note is the rendering of molecular surfaces according to their various properties (that can be expressed numerically).
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

Discussion

43.	In practical circumstances there exists an experimental structure of the complex.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

Discussion

44.	Which of the following is incorrect about Purification of protein complexes followed by mass spectrometry?
A.	Isolating protein complexes from cells allows identification of interactions between ensembles of proteins instead of just pairs
B.	Systematic purification of complexes on a large scale is done by tagging hundreds of genes with an epitope
C.	UnLike in the yeast-two-hybrid assay, this does not involve chimeric genes
D.	Affinity purification based on the epitope will then extract all the proteins attached to the bait protein from cell lysates
Answer» D. Affinity purification based on the epitope will then extract all the proteins attached to the bait protein from cell lysates

Discussion

45.	In the Interaction map of domain families, the interactions of one family represent the sum of all the interactions of domains in that family.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

Discussion

46.	In protein domain family interaction map, the physical contacts of the domains in different families are represented by the lines between the nodes.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

Discussion

47.	In order to understand the geometry of domain combinations, different structures of homologous pairs of domains must be studied.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

Discussion

48.	Almost ______ engage in interactions with domains from their own family when one includes oligomeric proteins.
A.	one fifith of all known families
B.	one fourth of all known families
C.	all of all known families
D.	half of all known families
Answer» E.

Discussion

49.	Most domain families only interact with one or two other families, while a few families are extremely versatile in their interactions and are connected to many families.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

Discussion

50.	Which of the following is untrue about Grid Representation?
A.	To speed up the matching process the topology of the protein can be simplified from atomic level detail to a series of cubic elements
B.	To speed up the matching process discretizing the 3-dimensional space using a grid is done
C.	Discretizing allows very fast computer matching using search methods such as Fourier transform
D.	Fourier transform is hardly used in computer matching
Answer» E.

Discussion

Explore topic-wise MCQs in Bioinformatics.

When comparing pairs of genes or sets of genes in different genomes for this purpose, it is not mandatory for the genes to be orthologs.

Conservation of gene order due to operon structure is _______ so interactions of proteins specific to eukaryotes cannot be detected by method of Conservation of gene order.

In a quantitative assessment of this method (Conservation of gene order) using the genome of the parasitic organism Mycoplasma genitalium as a benchmark.

Interactions between proteins can be predicted computationally by looking for sets of genes that occur as a _______

Experimentation is most desirable over computational methods by every means.

Across the different types of catalytic families, the position of the two domains with respect to one another varied, but only within a range of about ______

In Multiple conformation rigid-body method, a ligand is assumed to be able to adopt a number (N) of different _______ that are computed _____ the ligand being docked into the receptor.

In case of Protein-ligand docking, ______ ligands are often _____ in adapting their shape to fit the receptor binding pocket.

Proteins are dynamic entities that undergo _______

In the assessment of methods to predict protein-protein interactions, one third of such pairs were found to physically interact, and an additional third to belong to the same metabolic pathway or functional process.

An approach for predicting ______ to look for cases across a set of genomes where _____ are part of the same gene in one genome resulted in gene fusion method.

Due to the requirement for co-regulation as well as colocalization, the method is mostly limited to certain classes of protein-protein interactions.

The disadvantage of Multiple conformation rigid-body method is that the active conformation may be missed as the result of a minor structural difference not considered in the ______ ligand conformations. Where, the N is the number of low-energy conformations.

Oligomers are often obligate complexes meaning that the free-energy cost of dissociation is high and they exist as oligomers under physiological conditions.

In Property-based measures, displaying physical properties on the molecular surface of molecules can help to guide molecular docking.

Which of the following is untrue about Electrostatic Complementarity?

Which of the following is untrue about Hydrophobicity?

Members of a stable complex are often co-regulated and thus will be detected by the method of Conservation of gene order.

The most detailed experimental information about protein-protein interactions comes from three-dimensional structures.

Genes that are consistently part of the same operon across different, distantly related genomes are likely to be part of the same protein complex or functional process across all species.

In Grid representation, the lowest score represents the best surface complementarity for a given translational scan.

The phylogenetic profile method relies on detection of orthologs (or homologs, in a variation of the method) in a set of genomes.

The linkers between the catalytic domain and the Rossmann domain were conserved in each family.

The investigation (Aloy and Russel) of domain combinations in multidomain proteins by Bashton and Chothia focuses on two-domain proteins belonging to the Rossmann domain family.

Which of the following is true regarding Protein flexibility?

Domains that are part of a multidomain protein are ______

Typical motions of proteins will be primarily treated by a rigid body model for docking.

Structural analyses on small sets of proteins have shown that the domains from a pair of families bind to each other with the same geometry in multi-domain proteins and in transient interactions.

In the phylogenetic profile method for predicting protein interaction, presence or absence of orthologous genes is scored across a variety of genomes.

Stochastic methods can guarantee reaching a global optimal solution and the methods are computationally costly in comparison to the other methods.

Genetic methods (genetic algorithms and evolutionary programming) store multiple solutions. These solutions form a population of members.

In a Monte Carlo simulation the score (or energy) is calculated at each step and compared to the previous step. The probability of accepting the step is given by _________ where ΔE is the difference in energy; kB is Boltzmann’s constant and T the temperature.

In Stochastic search methods, they include methods such as Monte Carlo simulation, simulated annealing, Tabu search, genetic algorithms and evolutionary programming.

An understanding of the importance of different factors in a particular interaction is important if confidence in the results is required. Which of the following are not those factors?

The ______ is an ongoing community-wide experiment on the comparative evaluation of protein-protein docking for structure prediction.

There was little degree of success in docking an antibody-antigen complex in the second challenge for the protein-protein docking evaluation.

In case of protein-protein docking, the level of success is dependent on the system under study.

In a similar way to structure prediction methods models can be evaluated using RMSD to measure the similarity between two molecular complexes.

The GRASP and VRLM have been incorporated into the GRASS server.

The popular program RasMol can be made to view molecular properties by assigning those properties to the temperature factor column of the sdf file in question only.

Information about shape, hydrophobicity, electrostatics, evolutionary relationships and conformational flexibility is not always available and the search for a universally applicable scoring function as well as an adequate treatment of conformational flexibility is ongoing.

Visualization methods are very important in viewing molecular properties on molecules. Of particular note is the rendering of molecular surfaces according to their various properties (that can be expressed numerically).

In practical circumstances there exists an experimental structure of the complex.

Which of the following is incorrect about Purification of protein complexes followed by mass spectrometry?

In the Interaction map of domain families, the interactions of one family represent the sum of all the interactions of domains in that family.

In protein domain family interaction map, the physical contacts of the domains in different families are represented by the lines between the nodes.

In order to understand the geometry of domain combinations, different structures of homologous pairs of domains must be studied.

Almost ______ engage in interactions with domains from their own family when one includes oligomeric proteins.

Most domain families only interact with one or two other families, while a few families are extremely versatile in their interactions and are connected to many families.

Which of the following is untrue about Grid Representation?

In Multiple conformation rigid-body method, a ligand is assumed to be able to adopt a number (N) of different ___ that are computed _ the ligand being docked into the receptor.

In case of Protein-ligand docking, __ ligands are often _ in adapting their shape to fit the receptor binding pocket.

An approach for predicting __ to look for cases across a set of genomes where _ are part of the same gene in one genome resulted in gene fusion method.