Protein Function Prediction: Master the Art of Computational Protein Analysis

Question 1

Which of the following sequence-based methods is commonly used for protein function prediction?

Accepted Answer

Homology searching

Answer

Gene ontology analysis

Answer

Molecular docking

Answer

Structure-based threading

Question 2

What type of information does a hidden Markov model (HMM) use to predict protein function?

Accepted Answer

Amino acid sequences

Answer

Protein structures

Answer

Gene expression data

Answer

Protein-protein interaction networks

Question 3

When selecting a database for homology searching, which of the following is NOT a crucial consideration?

Accepted Answer

Operating system compatibility

Answer

Reliability of annotations

Answer

Database size

Answer

Coverage of species

Question 4

What is the primary reason for using evolutionary information in protein function prediction?

Accepted Answer

Identification of conserved functional regions

Answer

Phylogenetic tree construction

Answer

Multiple sequence alignment generation

Answer

Protein subcellular localization prediction

Question 5

How does homology modeling differ from molecular docking?

Accepted Answer

Homology modeling predicts protein structure, while molecular docking predicts interactions.

Answer

Molecular docking predicts protein structure, while homology modeling predicts interactions.

Answer

Both homology modeling and molecular docking predict protein structure.

Answer

Both homology modeling and molecular docking predict protein interactions.

Question 6

What is the significance of GO terms in protein function prediction?

Accepted Answer

Providing a structured vocabulary for describing protein functions

Answer

Creating protein interaction networks

Answer

Identifying potential disease-causing mutations

Answer

Predicting protein localization

Question 7

Computational methods for predicting protein function have limitations. Describe these limitations and explain how experimental validation can improve the accuracy of these predictions.

Accepted Answer

Experimental validation can help identify and correct errors in computational predictions.

Answer

Computational approaches can only predict functions of highly conserved, well-studied proteins.

Answer

Experimental validation is not needed for accurate protein function prediction.

Answer

Computational approaches can accurately predict the functions of all proteins in an organism.

Question 8

Which protein function prediction method leverages sequence alignment and evolutionary information?

Accepted Answer

Homology modeling

Answer

Sequence alignment

Answer

Molecular docking

Question 9

Which of the following is **not** a commonly used computational approach for protein function prediction?

Accepted Answer

Wet-lab experiments

Answer

Gene ontology analysis

Answer

Sequence homology search

Answer

Structure prediction

Question 10

The BLAST algorithm is primarily used for:

Accepted Answer

Searching for similar sequences in a database

Answer

Annotating gene functions

Answer

Identifying protein-protein interactions

Answer

Predicting protein structure

Question 11

Which structural feature is a reliable indicator of protein function?

Accepted Answer

Active site

Answer

Tertiary structure

Answer

Quaternary structure

Answer

Secondary structure

Question 12

The GO (Gene Ontology) database primarily provides:

Accepted Answer

Annotations of gene and protein functions

Answer

Protein sequences

Answer

Protein structures

Question 13

Machine learning approaches for protein function prediction typically use:

Accepted Answer

Large datasets of known protein sequences and functions

Answer

Physical models of protein structures

Answer

Quantum computing algorithms

Question 14

The Swiss-Prot database is known for its:

Accepted Answer

High-quality manually curated protein annotations

Answer

User-friendly web interface

Answer

Comprehensive collection of protein sequences

Answer

Advanced protein structure visualization tools

Question 15

Which of the following bioinformatics tools is PRIMARILY used for predicting protein function from amino acid sequence?

Accepted Answer

BLAST

Answer

PyMOL

Answer

Clustal Omega

Answer

RasMol

Question 16

You are analyzing a novel protein sequence. Which method would be MOST suitable for predicting its function based on similarity to proteins with known functions?

Accepted Answer

Homology-based inference

Answer

Phylogenetic analysis

Answer

Molecular dynamics simulations

Answer

Ab initio structure prediction

Question 17

What information is NOT typically used by machine learning algorithms for protein function prediction?

Accepted Answer

Protein's 3D structure visualization

Answer

Domain architecture

Answer

Amino acid composition

Answer

Physicochemical properties of amino acids

Question 18

Which database is a comprehensive resource for protein families, domains, and functional sites?

Accepted Answer

Pfam

Answer

PDB

Answer

UniProt

Answer

GenBank

Question 19

A protein is predicted to contain a transmembrane helix. What function is this protein MOST likely to be involved in?

Accepted Answer

Cellular transport

Answer

DNA replication

Answer

Carbohydrate metabolism

Answer

Protein synthesis

Question 20

What is a key limitation of using Gene Ontology (GO) terms for protein function prediction?

Accepted Answer

GO annotations can be incomplete or inaccurate.

Answer

GO is not widely used in the scientific community.

Answer

GO terms are not hierarchical.

Answer

GO terms are only applicable to prokaryotic proteins.

Question 21

You identify a protein with a significant sequence similarity to a known enzyme. What can you MOST confidently infer about the novel protein?

Accepted Answer

It may have a similar enzymatic function.

Answer

It will be involved in the same metabolic pathway.

Answer

It will have the exact same enzymatic function.

Answer

It will be localized to the same cellular compartment.

Question 22

What is the MAIN advantage of using a combination of different methods for protein function prediction?

Accepted Answer

Increased prediction accuracy and confidence

Answer

Simplified data interpretation

Answer

Elimination of the need for experimental validation

Answer

Reduced computational cost

Question 23

Which experimental technique can be used to validate the predicted function of a protein?

Accepted Answer

Enzyme activity assay

Answer

Gel electrophoresis

Answer

DNA sequencing

Answer

Polymerase chain reaction (PCR)

Question 24

What is the significance of predicting protein function in drug discovery?

Accepted Answer

Identifying potential drug targets for specific diseases

Answer

Optimizing agricultural practices

Answer

Developing new biofuels