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This quiz contains multiple-choice problems on protein and domain interactions, gene order, use and phylogeny to predict proteins.
There exist three types of interactions between domains. Which of the following is not one of them?
Stable complex
Transient interaction
Multi-domain protein
Unstable interaction
Stable complexes consist of proteins that are __ associated with each other, like many __ proteins.
temporarily, oligomeric
temporarily, monomeric
permanently, oligomeric
permanently, monomeric
Sets of proteins that are part of stable complexes and sets of proteins involved in transient interactions __ in terms of gene expression similarity among the set of proteins.
Are similar
Differ
Are the same
Show similar function
The correlation of gene expression for pairs of transiently interacting proteins is __ compared to randomly chosen pairs of proteins.
Not significant
Only marginally significant
Totally significant
Significant to much extent
Membership in a stable complex differs from transient interaction in terms of evolutionary constraints upon sequence divergence. True or false?
True
False
The average sequence identity for proteins in stable complexes is 46%, whilst it is 41% for proteins in transient interactions. True or false?
True
False
Interactions between proteins can be computationally predicted by looking for sets of genes that occur as a
Single gene in at least one genome
Multiple genes in at least one genome
Multiple genes in various genomes
Single gene in various genomes
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. True or false?
True
False
The conservation of gene order due to operon structure is __, so interactions of proteins specific to eukaryotes cannot be detected by gene order conservation.
Not applicable to archaea genomes
Not applicable to prokaryote genomes
Applicable to eukaryote genomes
Not applicable to eukaryote genomes
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 the gene fusion method.
gene interactions, only three to four orthologs
gene interactions, two orthologs
protein interactions, two or more orthologs
protein interactions, two orthologs
Domains that are part of a multidomain protein are
Neither co-regulated nor colocalized
Not co-regulated but colocalized
Co-regulated and but not colocalized
Co-regulated and colocalized
The most detailed experimental information about protein-protein interactions comes from three-dimensional structures. True or false?
True
False
Physical contact between domains is crucial for cellular machinery functioning. True or false?
True
False
Which of the following statements is incorrect regarding yeast-two-hybrid screens?
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
The DNA-binding domain chimeric protein will not bind upstream of the reporter gene
If the activation domain chimeric protein interacts with the DNA-binding domain chimeric protein, the reporter gene will be transcribed
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
Which of the following statements is incorrect regarding the purification of protein complexes followed by mass spectrometry?
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
