Protein-Protein Interactions: A Comprehensive Guide for Bioinformatics Students

Question 1

Which technique involves capturing specific protein complexes using antibodies to identify their interacting partners?

Accepted Answer

Co-immunoprecipitation

Answer

Mass spectrometry

Answer

Yeast two-hybrid

Answer

Protein microarray

Question 2

Which type of protein-protein interaction exhibits a stable and durable association?

Accepted Answer

Obligate

Answer

Transient

Answer

Conditional

Answer

Cooperative

Question 3

Which software tool is commonly employed for analysis and visualization of protein-protein interaction networks?

Accepted Answer

Cytoscape

Answer

BLAST

Answer

ClustalW

Answer

PyMOL

Question 4

Which approach utilizes engineered proteins to investigate the spatial orientation and dynamics of protein-protein interactions?

Accepted Answer

Förster resonance energy transfer (FRET)

Answer

Protein crystallization

Answer

Circular dichroism (CD) spectroscopy

Answer

Nuclear magnetic resonance (NMR) spectroscopy

Question 5

Which concept describes the combined effect of multiple protein-protein interactions in a specific biological process?

Accepted Answer

Cooperativity

Answer

Modularity

Answer

Hierarchy

Answer

Redundancy

Question 6

Which computational method leverages a database of known protein-protein interactions to predict interactions in novel proteins?

Accepted Answer

Machine learning

Answer

Homology modeling

Answer

Molecular docking

Answer

Phylogenetics

Question 7

Which technique is commonly used to identify protein-protein interactions based on proximity, where proteins that are close together are likely to be interacting?

Accepted Answer

Co-immunoprecipitation

Answer

Western blotting

Answer

Mass spectrometry

Answer

Molecular docking

Question 8

What type of protein structure is mainly involved in protein-protein interactions, providing the physical interface for interactions between proteins?

Accepted Answer

Quaternary structure

Answer

Primary structure

Answer

Secondary structure

Answer

Tertiary structure

Question 9

What is the significance of protein interaction networks in understanding cellular processes?

Accepted Answer

They reveal pathways and functional modules involved in specific cellular functions

Answer

They indicate the absolute abundance of proteins in the cell

Answer

They predict protein localization based on interacting partners

Answer

They determine the post-translational modifications of proteins

Question 10

Which type of protein interaction is characterized by permanent covalent bonds between amino acid side chains, forming stable and long-lasting complexes?

Accepted Answer

Covalent

Answer

Obligatory

Answer

Transient

Answer

Non-specific

Question 11

What is the key challenge in analyzing the vast amount of protein interaction data generated by high-throughput technologies?

Accepted Answer

Integrating, interpreting, and managing the large and complex datasets

Answer

Storing and maintaining the data securely and efficiently

Answer

Acquiring accurate and reliable data from experimental techniques

Answer

Visualizing the data effectively to identify patterns and relationships

Question 12

Which of the following is NOT a direct experimental method for detecting protein-protein interactions?

Accepted Answer

Protein interaction databases

Answer

Co-immunoprecipitation

Answer

Proximity ligation assay

Answer

Fluorescence resonance energy transfer

Question 13

Which of the following is a well-known database for experimentally determined protein-protein interactions?

Accepted Answer

IntAct

Answer

Protein Data Bank (PDB)

Answer

UniProt

Answer

KEGG

Question 14

Which technique relies on crosslinking reagents to capture protein-protein interactions within a living organism?

Accepted Answer

Chemical crosslinking

Answer

Co-immunoprecipitation

Answer

Yeast two-hybrid system

Answer

Bioinformatics prediction

Question 15

What is the fundamental principle underlying the yeast two-hybrid system?

Accepted Answer

Reporter gene activation based on proximity

Answer

Isolation of interacting proteins through affinity purification

Answer

Crosslinking of interacting proteins

Answer

Computational analysis of protein sequences

Question 16

Which of the following is not considered a type of protein-protein interaction interface?

Accepted Answer

Covalent

Answer

Homotypic

Answer

Heterotypic

Answer

Electrostatic

Question 17

What is the primary purpose of protein interaction databases in bioinformatics?

Accepted Answer

Storing and sharing information on protein interactions

Answer

Predicting protein-protein interactions

Answer

Analyzing protein interaction networks

Answer

Designing drugs that target protein interactions

Question 18

Which experimental technique relies on precipitation of protein complexes using specific antibodies to identify protein-protein interactions in living cells in real-time?

Accepted Answer

Co-immunoprecipitation

Answer

Molecular docking

Answer

NMR spectroscopy

Answer

Mass spectrometry

Question 19

What is the primary purpose of employing crosslinking agents in protein-protein interaction studies?

Accepted Answer

To stabilize protein-protein interactions for downstream analysis

Answer

To increase binding affinity between interacting proteins

Answer

To identify the specific amino acids involved in the interaction

Question 20

Which bioinformatics resource is specifically designed to provide comprehensive information on known protein-protein interactions?

Accepted Answer

STRING

Answer

GenBank

Answer

PubMed

Question 21

What is a distinct advantage offered by the yeast two-hybrid system for identifying protein-protein interactions?

Accepted Answer

High-throughput screening capability

Answer

Direct observation of protein-protein complexes

Answer

Analysis of transient interactions

Answer

Detection of weak interactions

Question 22

What is the term used to describe the specific three-dimensional structure formed at the contact surface of two interacting proteins?

Accepted Answer

Interface

Answer

Domain

Answer

Conformation

Answer

Motif

Question 23

Which computational approach can be utilized to predict protein-protein interactions based solely on the amino acid sequences of the involved proteins?

Accepted Answer

Machine learning

Answer

NMR spectroscopy

Answer

Molecular dynamics simulation

Answer

X-ray crystallography

Question 24

What is the fundamental significance of protein-protein interactions in the context of cellular processes?

Accepted Answer

They orchestrate various cellular functions and signaling pathways

Answer

They provide structural support to cells

Answer

They protect cells against environmental stressors