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Bioinformatics Practice Test Questions: Global Approaches for Studying Protein – Protein Interactions
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Avg score: 64% • Most missed: “Experimentation is most desirable over computational methods by every means.”

The yeast two-hybrid method allows the mapping of binary or pair-wise interactions, protein chips are suited to detect protein–protein, pro- tein–lipid and other protein–ligand interactions.

Topics include: Protein – Protein Interactions, Structural Analyses of Domain Interactions, & The Use of Gene Order & Phylogeny to Predict Protein – Protein Interactions.

Bioinformatics Practice Test Questions: Global Approaches for Studying Protein – Protein Interactions
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25 Questions

1. 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.
2. Interactions between proteins can be predicted computationally by looking for sets of genes that occur as a _______
3. In the phylogenetic profile method for predicting protein interaction, presence or absence of orthologous genes is scored across a variety of genomes.
4. The most detailed experimental information about protein-protein interactions comes from three-dimensional structures.
5. There exist three types of interactions between domains. Which of the following is not one of them?
6. In order to understand the geometry of domain combinations, different structures of homologous pairs of domains must be studied.
7. Which of the following is incorrect about Yeast-two-hybrid screens?
8. 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.
9. Almost ______ engage in interactions with domains from their own family when one includes oligomeric proteins.
10. Domains that are part of a multidomain protein are ______
11. 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.
12. In a quantitative assessment of this method (Conservation of gene order) using the genome of the parasitic organism Mycoplasma genitalium as a benchmark.
13. 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.
14. Members of a stable complex are often co-regulated and thus will be detected by the method of Conservation of gene order.
15. 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.
16. 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.
17. 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.
18. 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.
19. Experimentation is most desirable over computational methods by every means.
20. Due to the requirement for co-regulation as well as colocalization, the method is mostly limited to certain classes of protein-protein interactions.
21. For proteins in stable complexes the average sequence identity is 46%, while for proteins in transient interactions it is 41%.
22. 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 ______
23. The linkers between the catalytic domain and the Rossmann domain were conserved in each family.
24. Correlation of gene expression for pairs of transiently interacting proteins is ______ compared to randomly chosen pairs of proteins.
25. Stable complexes consist of proteins that are _____ associated with each other, like many ____ proteins for instance.

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