This set of Bioinformatics Multiple Choice Questions & Answers (MCQs) focuses on “Protein – Protein Interactions”.
1. The physical contacts between domains are crucial for the functioning of the cellular machinery.
Explanation: Interactions between domains occur in multidomain proteins, in stable complexes and in transient interactions between proteins that also exist independently. Experimental approaches for the large-scale determination of protein interactions are emerging. Theoretical analyses based on protein structures have unraveled some of the overall principles and features of the way domains evolved to interact with each other.
2. There exist three types of interactions between domains. Which of the following is not one of them?
a) Stable complex
b) Transient interaction
c) Multi-domain protein
d) Unstable interaction
Explanation: Interactions between domains determine the structure of multidomain proteins, in which there are several domains on one polypeptide chain. Given that all proteins consist of domains, interactions between domains also occur between the proteins that are permanently associated in stable complexes and proteins that interact transiently, but also exist independently of each other.
3. Stable complexes consist of proteins that are _____ associated with each other, like many ____ proteins for instance.
a) temporarily, oligomeric
b) temporarily, monomeric
c) permanently, oligomeric
d) permanently, monomeric
Explanation: Well-known stable complexes include the histone octamer, the ribosome and DNA and RNA polymerases. Transient interactions on the other hand are all those protein-protein interactions that occur between proteins that also exist independently.
4. Sets of proteins that are part of stable complexes and sets of proteins involved in transient interactions ____ in terms of the similarity in gene expression among the set of proteins.
a) are similar
c) are same
d) show similar function
Explanation: Proteins permanently associated in a stable complex need to be present or absent in the cell at the same time. Analysis of microarray data by Gerstein and co-workers by methods along the lines, has shown that the members of stable complexes in the yeast Saccharomyces cerevisiae have highly correlated gene expression patterns.
5. Correlation of gene expression for pairs of transiently interacting proteins is ______ compared to randomly chosen pairs of proteins.
a) not significant
b) only marginally significant
c) totally significant
d) significant to much extent
Explanation: In prokaryotes, genes are co-regulated if they are a member of the same operon, and many proteins that are members of the same stable complex are part of the same operon. For instance, Ouzounis and Karp determined that over 90% of the enzymes that are in stable complexes in E. coli metabolic pathways are adjacent on the E. coli chromosome.
6. Membership in a stable complex also differs from transient interaction in terms of evolutionary constraints upon sequence divergence.
Explanation: Thus the proteins in stable complexes are more similar across species, having higher sequence identity between orthologs, than the proteins in transient interactions. A calculation by Teichmann showed that there are significant differences between the average values for sequence identities between S. cerevisiae and S. pombe orthologs in stable complexes, transient interactions and monomers.
7. For proteins in stable complexes the average sequence identity is 46%, while for proteins in transient interactions it is 41%.
Explanation: (Proteins not known to be involved in any type of interaction have an average sequence identity of 38 %) One of the main reasons for this is the surface area involved in interfaces of stable complexes which is larger than in transient complexes. Sequence divergence may be slower in order to conserve these extensive interfaces.
8. Which of the following is incorrect about Yeast-two-hybrid screens?
a) The yeast-two-hybrid system uses the transcription of a reporter gene driven by the Gal4 transcription factor to monitor whether or not two proteins are interacting
b) The DNA-binding domain chimeric protein will not bind upstream of the reporter gene
c) If the activation domain chimeric protein interacts with the DNA-binding domain chimeric protein, the reporter gene will be transcribed
d) Disadvantages of the method are that only pairwise interactions are tested, and not interactions that can only take place when multiple proteins come together, as well as a high false positive rate
Explanation: If the interaction between two proteins, A and B, is being tested, one of their genes would be fused to the DNA-binding domain of the Gal4 transcription factor (Gal4-DBD) while the other would be fused to the activation domain (Gal4-AD). The DNA-binding domain chimeric protein will bind upstream of the reporter gene. This experiment can be carried out hundreds or even thousands of times on microassay plates, as in the case of the study by Uetz and colleagues on S.cerevisiae (yeast) interactions. Each array element on these plates contains yeast cells transformed with a particular combination of two plasmids, one carrying the DNA-binding domain chimeric protein and the other the activation domain chimeric protein.
9. 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
Explanation: Like in the yeast-two-hybrid assay, this is done by making chimeric genes that are introduced into cells. The principle of mass spectrometric identification of proteins is that the protein is chopped into fragments by tryptic digestion, and the mass of each fragment is measured by matrix-assisted laser desorption/ ionization-time-of-flight mass spectrometry (MALDI-TOF MS). This measurement is so accurate that the combination of amino acids in each fragment can be calculated and compared to a database of all the proteins in the proteome of the organism in order to find the correct one.
Sanfoundry Global Education & Learning Series – Bioinformatics.
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