This set of Bioinformatics Multiple Choice Questions & Answers (MCQs) focuses on “Protein Interactions”.
1. Which of the following is untrue regarding the classic yeast two-hybrid method?
a) It is used for the detection of Protein interactions
b) Method that relies on the interaction of “bait” and “prey” proteins in molecular constructs in yeast
c) DNA-binding domain and a trans-activation domain don’t necessarily interact
d) In this strategy, a two-domain transcriptional activator is employed as a helper for determining protein–protein interactions
View Answer
Explanation: The two domains which are a DNA-binding domain and a trans-activation domain normally interact to activate transcription. However, molecular constructs are made such that each of the two domains is covalently attached to each of the two candidate proteins (bait and prey).
2. If the bait and prey proteins _______ they bring the DNA-binding and trans-activation domains in such close proximity that they reconstitute the function of the transcription activator, turning ____ the expression of a reporter gene as a result. Which of the following is not the correct pair of blanks?
a) physically interact, on
b) do not interact, on
c) do not interact, off
d) stop interacting, off
View Answer
Explanation: Molecular constructs are made such that each of the two domains is covalently attached to each of the two candidate proteins. If the two candidate proteins do not interact, the reporter gene expression remains switched off.
3. Which of the following is untrue regarding the classic yeast two-hybrid method?
a) Protein–protein interaction networks of yeast and a small number of other species have been subsequently determined using this method
b) This technique is a high throughput approach
c) Each bait and prey construct has to be prepared individually to map interactions between all proteins
d) It has been systematically applied to study interactions at the whole proteome level
View Answer
Explanation: This technique is essentially a low throughput approach. A major flaw in this method is that it is an indirect approach to probe protein–protein interaction and has a tendency to generate false positives (spurious interactions) and false negatives (undetected interactions). It has been estimated from proteome-wide characterizations that the rate of false positives can be as high as 50%.
4. An alternative approach to determining protein–protein interactions is to use a large-scale affinity purification technique that involves attaching fusion tags to proteins and purifying the associated protein complexes in an affinity chromatography column.
a) True
b) False
View Answer
Explanation: The purified proteins are then analyzed by gel electrophoresis followed by MS for identification of the interacting components. The protein microarray systems mentioned above also provide a high throughput alternative for studying protein–protein interactions.
5. Which of the following is untrue regarding the Predicting Interactions Based on Domain Fusion?
a) It is based on gene fusion events
b) Predicting protein–protein interactions is called the “Rosetta stone” method
c) A fused protein often reveals relationships between its domain components
d) A fused protein doesn’t necessarily reveal about the relationships between its domain components
View Answer
Explanation: The rationale goes like this: if A and B exist as interacting domains in a fusion protein in one proteome, the gene encoding the protein is a fusion gene. Their homologous gene sequences A and B existing separately in another genome most likely encode proteins interacting to perform a common function. Conversely, if ancestral genes A and B encode interacting proteins, they may have a tendency to be fused together in other genomes during evolution to enhance their effectiveness.
6. When the two domains are located in two different proteins, to preserve the same functionality, their close proximity and interaction have to be preserved as well.
a) True
b) False
View Answer
Explanation: In this method, by studying gene/protein fusion events, protein–protein interactions can be predicted. This prediction rule has been proven to be rather reliable and since successfully applied to a large number of proteins from both prokaryote and eukaryotes.
7. The justification behind Rosetta stone method is that when two domains are fused in a single protein, they have to be in _______ proximity to perform a common function.
a) distant
b) close
c) extremely distant
d) extremely close
View Answer
Explanation: When the two domains are located in two different proteins, to preserve the same functionality, their close proximity and interaction have to be preserved as well. Therefore, by studying gene/protein fusion events, protein–protein interactions can be predicted.
8. In Predicting Interactions Based on Gene Neighbors if a certain gene linkage is found to be indeed conserved across divergent genomes, it can be used as a strong indicator of formation of an operon that encodes proteins that are functionally and even physically coupled.
a) True
b) False
View Answer
Explanation: This rule of predicting protein–protein interactions holds up for most prokaryotic genomes. For eukaryotic genomes, gene order may be a less potent predictor of protein interactions than a tight co-regulation for gene expression.
9. Which of the following is untrue regarding the predicting Interactions Based on Phylogenetic Information?
a) Proteins do not operate as a complex
b) This method detects the co-presence or co-absence of orthologs across a number of genomes
c) Protein interactions can be predicted using phylogenetic profiles
d) Phylogenetic profile are defined as patterns of gene pairs that are concurrently present or absent across genomes
View Answer
Explanation: The logic behind the co-occurrence approach is that proteins normally operate as a complex. If one of the components of the complex is lost, it results in the failure of the entire complex. Under the selective pressure, the rest of the nonfunctional interacting partners in the complex are also lost during evolution because they have become functionally unnecessary.
10. Which of the following is untrue regarding the STRING?
a) Search Tool for the Retrieval of Interacting Genes/Proteins
b) Functional associations include only the direct protein-protein interactions
c) It is based on combined evidence of gene linkage, gene fusion and phylogenetic profiles
d) It is a web server that predicts gene and protein functional associations
View Answer
Explanation: Functional associations include both direct and indirect protein-protein interactions.
Indirect interactions can mean enzymes in the same pathway sharing a common substrate or proteins regulating each other in the genetic pathway.
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