Protein-Protein Interactions: A Comprehensive Guide for Medical Students

Question 1

Which of the following is NOT a characteristic of protein-protein interaction interfaces?

Accepted Answer

Covalent

Answer

Homotypic

Answer

Heterotypic

Answer

Hydrophobic

Question 2

How do mutations affect protein-protein interactions?

Accepted Answer

Disrupt binding by altering the protein's binding site

Answer

Enhance binding by increasing protein affinity

Answer

Have no effect on binding because mutations don't affect protein structure

Answer

Increase binding specificity by making the protein more selective

Question 3

The equilibrium dissociation constant (K_d) of a protein-protein interaction provides a measure of:

Accepted Answer

Binding affinity

Answer

Specificity

Answer

Cooperativity

Answer

Allostery

Question 4

Which technique is commonly employed in in vitro studies to investigate protein-protein interactions?

Accepted Answer

Co-immunoprecipitation

Answer

Chromatography

Answer

Electrophoresis

Answer

Mass spectrometry

Question 5

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

Accepted Answer

Covalent interface

Answer

Homodimer interface

Answer

Heterodimer interface

Answer

Non-covalent interface

Question 6

Which of the following is an example of a protein-protein interaction that is critical in cell signaling processes?

Accepted Answer

Receptor-ligand binding

Answer

Antigen-antibody binding

Answer

Enzyme-substrate binding

Answer

Protein-nucleic acid binding

Question 7

Which amino acid side chain forms covalent disulfide bonds that contribute to the stability of protein complexes?

Accepted Answer

Cysteine

Answer

Serine

Answer

Asparagine

Question 8

What is the primary mechanism by which proteins achieve specificity in their interactions?

Accepted Answer

Complementary surface shape and charge distribution

Answer

Covalent bond formation

Answer

Induced fit

Answer

Random collisions

Question 9

Which of the following is NOT a type of protein complex?

Accepted Answer

Monomers

Answer

Homodimers

Answer

Heterodimers

Answer

Homotetramers

Question 10

Which computational tool is commonly used for predicting protein-protein interactions?

Accepted Answer

Molecular docking

Answer

Protein BLAST

Answer

Sequence alignment

Answer

Gene ontology analysis

Question 11

How have protein-protein interactions influenced the evolutionary development of biological systems?

Accepted Answer

Enhanced complexity and adaptability

Answer

Diminished genetic diversity

Answer

Impeded cellular efficiency

Answer

No significant evolutionary impact

Question 12

Which fundamental force primarily drives stable protein-protein interactions?

Accepted Answer

Van der Waals forces

Answer

Covalent bonds

Answer

Hydrogen bonding

Answer

Ionic bonds

Question 13

Which factor primarily determines the specificity of protein-protein interactions?

Accepted Answer

A combination of all three factors

Answer

Shape complementarity of binding surfaces

Answer

Presence of compatible amino acid side chains

Answer

Overall protein charge

Question 14

Which techniques can be employed to disrupt protein-protein interactions for functional analysis?

Accepted Answer

A combination of all three techniques

Answer

Site-directed mutagenesis

Answer

Chemical cross-linking

Answer

RNA interference

Question 15

Which post-translational modification can modulate protein-protein interactions?

Accepted Answer

All of the above modifications

Answer

Phosphorylation

Answer

Ubiquitination

Answer

Glycosylation

Question 16

Which characteristic feature is common to protein-protein interaction networks?

Accepted Answer

All of the above features

Answer

High level of interconnectedness

Answer

Organization into functional modules

Answer

Scale-free topology

Question 17

Which database provides comprehensive information on protein-protein interactions?

Accepted Answer

All of the above databases

Answer

UniProt

Answer

IntAct

Answer

BioGRID

Question 18

Which experimental technique is commonly used to investigate protein-protein interactions by isolating protein complexes based on their specific binding affinities?

Accepted Answer

Co-immunoprecipitation

Answer

Western blotting

Answer

Radioactive labeling

Answer

Electron microscopy

Question 19

Which type of protein complex exhibits a fixed stoichiometry and is highly stable?

Accepted Answer

Oligomeric complex

Answer

Transient complex

Answer

Multimeric complex

Answer

Heterodimeric complex

Question 20

How do post-translational modifications (PTMs) impact protein-protein interactions? Provide specific examples of modifications that can alter binding affinity and specificity.

Accepted Answer

PTMs can modify protein structure and charge, creating new binding sites or disrupting existing ones.

Answer

PTMs solely affect protein stability, not their interactions.

Answer

PTMs are only found on proteins secreted from cells.

Answer

PTMs have no effect on protein-protein interactions.

Question 21

Which technique employs fluorescence to detect protein-protein interactions within living cells?

Accepted Answer

FRET

Answer

Co-immunoprecipitation

Answer

Cross-linking

Answer

Protein microarrays

Question 22

Which of the following experimental techniques is widely used to analyze protein-protein interactions, including the identification of protein complexes and studying protein-protein binding properties?

Accepted Answer

Co-immunoprecipitation

Answer

Polymerase Chain Reaction (PCR)

Answer

Western blotting

Answer

Mass spectrometry

Question 23

The physical forces that hold protein complexes together are collectively known as:

Accepted Answer

Non-covalent bonds

Answer

Ionic interactions

Answer

Covalent bonds

Answer

Hydrogen bonds

Question 24

A common interaction motif found in protein-protein interfaces is known as:

Accepted Answer

Leucine zipper

Answer

Helix-turn-helix

Answer

Zinc finger

Answer

Immunoglobulin-like fold

Question 25

A primary functional consequence of protein-protein interactions is the formation of:

Accepted Answer

Functional protein complexes

Answer

Denaturation of proteins

Answer

Proteolysis

Question 26

The change in protein conformation that occurs upon protein-protein binding is known as:

Accepted Answer

Induced fit

Answer

Ligand binding

Answer

Protein folding

Answer

Allosteric regulation

Question 27

In the context of drug discovery, protein-protein interaction studies are particularly relevant for:

Accepted Answer

Identifying potential drug targets

Answer

Diagnostics

Answer

Protein purification

Answer

Understanding protein evolution

Question 28

What is the key factor that determines the selectivity of protein-protein interactions?

Accepted Answer

Shape complementarity

Answer

Hydrophobicity

Answer

Charge distribution

Question 29

Which of the following techniques is commonly used to measure protein-protein binding affinity?

Accepted Answer

Surface Plasmon Resonance (SPR)

Answer

Protein crystallization

Answer

Gel electrophoresis

Answer

Western blotting

Question 30

What is the primary functional role of protein complexes in cells?

Accepted Answer

Facilitating cellular processes and functions

Answer

Transporting molecules

Answer

Storing genetic information

Answer

Providing structural support

Question 31

What is the distinction between a protein homodimer and a protein heterodimer?

Accepted Answer

Homodimers consist of identical subunits, while heterodimers are composed of different subunits.

Answer

Homodimers are larger than heterodimers.

Question 32

Protein-protein interactions are crucial for cell signaling because they:

Accepted Answer

Allow cells to respond to external stimuli and communicate with each other.

Answer

Are involved in DNA replication

Answer

Provide energy for cellular processes

Question 33

Which of the following represents an example of a protein-protein interaction mediated by a small molecule?

Accepted Answer

Ligand-receptor binding

Answer

Antibody-antigen binding

Answer

Protein-DNA binding

Answer

Enzyme-substrate binding

Question 34

Targeting protein-protein interactions holds potential therapeutic significance because:

Accepted Answer

It could lead to the development of novel drugs for treating diseases associated with protein misfolding or dysregulation.

Answer

It could improve the efficiency of protein production in biotechnology

Question 35

What is the primary mechanism by which protein-protein interactions contribute to protein function?

Accepted Answer

Protein-protein interactions primarily contribute to protein function by forming protein complexes with specific biological functions.

Answer

Regulating gene expression and transmitting signals are not primary mechanisms by which protein-protein interactions contribute to protein function.

Answer

While protein-protein interactions can have various effects, their primary contribution to protein function is through the formation of protein complexes.

Question 36

Which of the following techniques is commonly employed to investigate protein-protein interactions in research laboratories?

Accepted Answer

Immunoprecipitation is a widely used technique for studying protein-protein interactions, allowing researchers to isolate and identify specific protein complexes.

Answer

Flow cytometry is primarily used for cell analysis and sorting, not specifically for studying protein-protein interactions.

Answer

Electrophoresis is often used to separate proteins but not specifically for studying protein-protein interactions.

Answer

PCR is a technique used for amplifying DNA, not directly for studying protein-protein interactions.

Question 37

What is the primary function of chaperone proteins in relation to protein-protein interactions?

Accepted Answer

Chaperone proteins play a crucial role in assisting the folding, assembly, and stability of proteins, facilitating their proper interactions.

Answer

Chaperones promote protein-protein interactions rather than preventing them.

Answer

Breaking down proteins is typically carried out by proteases, not chaperones.

Answer

Transporting proteins is not a primary function of chaperone proteins.

Question 38

Provide an example of a protein-protein interaction that is involved in signal transduction pathways.

Accepted Answer

Receptor-ligand binding is a crucial protein-protein interaction that initiates signal transduction pathways by transmitting signals across cell membranes.

Answer

Hydrophobic interactions are not specific to signal transduction pathways.

Answer

Enzyme-substrate binding is primarily involved in enzymatic reactions, not signal transduction.

Answer

Antigen-antibody binding is involved in the immune response, not directly in signal transduction.

Question 39

Explain the fundamental difference between a protein-protein interaction and a covalent bond.

Accepted Answer

Protein-protein interactions are non-covalent and reversible, involving weaker forces such as hydrogen bonding, electrostatic interactions, and hydrophobic interactions. Covalent bonds, on the other hand, are irreversible chemical bonds that involve the sharing of electrons between atoms.

Answer

While protein-protein interactions can be weaker than covalent bonds, this is not the only distinguishing factor.

Question 40

Which of the following is NOT a recognized type of protein-protein interaction?

Accepted Answer

Covalent bonding is not considered a type of protein-protein interaction because it involves the formation of irreversible chemical bonds between atoms, unlike the non-covalent interactions that characterize protein-protein interactions.

Answer

Hydrogen bonding is a type of non-covalent interaction commonly found in protein-protein interactions.

Answer

Electrostatic interactions are another type of non-covalent interaction that contributes to protein-protein binding.

Question 41

Which of the following techniques is frequently used to investigate protein-protein interactions?

Accepted Answer

Co-immunoprecipitation

Answer

X-ray crystallography (provides structural information but does not directly study interactions)

Answer

DNA sequencing (not directly relevant to protein-protein interactions)

Question 42

The equilibrium dissociation constant (Kd) of a protein-protein interaction primarily indicates its:

Accepted Answer

Binding affinity (lower Kd indicates stronger binding)

Answer

Kinetics (not captured by Kd, which represents equilibrium)

Answer

Specificity (not directly measured by Kd)

Answer

Enthalpy (not directly measured by Kd)

Question 43

Which of the following types of protein-protein interactions results from the formation of covalent bonds?

Accepted Answer

Disulfide bond (covalent bond between cysteine residues)

Answer

Ionic bond (non-covalent interaction)

Answer

Van der Waals force (non-covalent interaction)

Answer

Hydrogen bond (non-covalent interaction)

Question 44

In which environment does the hydrophobic effect primarily contribute to protein-protein interactions?

Accepted Answer

Aqueous environments (hydrophobic interactions drive nonpolar residues to cluster together, away from water)

Answer

Nonpolar environments (hydrophobic interactions are less significant in nonpolar environments)

Answer

Vacuum (not a relevant environment for protein-protein interactions)

Answer

Organic solvents (interactions in organic solvents are primarily driven by different forces)

Question 45

Which of the following is a critical factor influencing the selectivity of protein-protein interactions?

Accepted Answer

Protein structure (complementary shapes and binding surfaces determine specificity)

Answer

Salt concentration (can affect binding affinity but not necessarily specificity)

Answer

Temperature (can affect binding affinity but not necessarily specificity)

Question 46

Protein complexes are assemblies of multiple proteins that primarily serve to:

Accepted Answer

Perform specific biological functions (complexes often have specialized roles)

Answer

Are always highly stable (not necessarily true, some complexes are dynamic)

Answer

Have no clear biological significance (not supported by evidence)

Answer

Form spontaneously and randomly (not accurate, they are usually regulated)

Question 47

Which of the following methods is commonly used to detect protein-protein interactions within living cells?

Accepted Answer

Proximity ligation assay (detects close proximity of proteins using antibody-mediated ligation)

Answer

Microarray analysis (not specifically designed for detecting protein-protein interactions in cells)

Answer

Western blotting (not suitable for detecting interactions in living cells)

Question 48

The aggregation of proteins into amyloid fibrils exemplifies a pathological:

Accepted Answer

Protein-protein interaction (abnormal interactions lead to aggregation)

Answer

Protein-carbohydrate interaction (not a direct characteristic of amyloid fibrils)

Answer

Protein-lipid interaction (not a direct characteristic of amyloid fibrils)

Answer

Protein-nucleic acid interaction (not a direct characteristic of amyloid fibrils)

Question 49

Which approach is commonly employed to selectively disrupt protein-protein interactions?

Accepted Answer

Small molecule inhibitors (designed to bind and interfere with interactions)

Answer

Antibody binding (can disrupt interactions but is not a general approach)

Answer

RNA interference (targets RNA, not directly relevant to protein-protein interactions)

Answer

Gene knockout (prevents protein expression, not specific to interactions)

Question 50

Which of the following factors primarily determines the strength of a protein-protein interaction?

Accepted Answer

The number and type of non-covalent interactions between the interacting protein surfaces

Answer

The presence of a specific amino acid sequence at the interaction interface

Answer

The pH of the surrounding environment

Answer

The size of the interacting proteins

Question 51

Which of the following experimental techniques can be employed to measure the dissociation constant (Kd) of a protein-protein interaction?

Accepted Answer

Surface Plasmon Resonance (SPR)

Answer

Immunoprecipitation

Answer

Gel electrophoresis

Answer

Western blotting

Question 52

A protein complex formed by two proteins with high affinity is likely to have a:

Accepted Answer

Low Kd value

Answer

Kd value that is independent of concentration

Answer

No Kd value

Answer

High Kd value

Question 53

The specificity of a protein-protein interaction is primarily determined by:

Accepted Answer

The shape and chemical properties of the interacting surfaces

Answer

The size of the interacting proteins

Answer

The presence of a specific amino acid sequence at the interaction interface

Question 54

Which of the following is an example of a protein complex involved in regulating gene expression?

Accepted Answer

Transcription factors binding to DNA

Answer

Actin filaments in muscle contraction

Answer

Hemoglobin carrying oxygen

Answer

Collagen fibers in connective tissue

Question 55

What is the primary purpose of a protein-protein interaction network?

Accepted Answer

To map and visualize the interactions between proteins within a cell or organism

Answer

To determine the amino acid sequence of a protein

Answer

To predict the three-dimensional structure of a protein

Question 56

Disrupting a protein-protein interaction can have significant effects on cellular function. Which of the following approaches could be used to disrupt such an interaction?

Accepted Answer

Developing small molecule inhibitors that bind to the interaction interface

Answer

Decreasing the pH of the cellular environment

Answer

Increasing the concentration of the interacting proteins

Question 57

Which of the following is NOT a widely used method for studying protein-protein interactions in a high-throughput manner?

Accepted Answer

X-ray crystallography

Answer

Protein microarrays

Answer

Affinity purification followed by mass spectrometry

Answer

Yeast two-hybrid (Y2H) screening