This set of Bioinformatics Multiple Choice Questions & Answers (MCQs) focuses on “Protein Sorting”.
1. Which of the following is an incorrect statement about the terminologies related to protein sorting?
a) Subcellular localization is an integral part of protein functionality
b) Many proteins exhibit functions only after being transported to certain compartments of the cell
c) All the proteins exhibit functions after being transported to certain compartments of the cell
d) Protein sorting is also known as protein targeting
Explanation: The study of the mechanism of protein trafficking and subcellular localization is the field of protein sorting, which has become one of the central themes in modern cell biology. Identifying protein subcellular localization is an important aspect of functional annotation, because knowing the cellular localization of a protein often helps to narrow down its putative functions.
2. For many eukaryotic proteins, newly synthesized protein precursors have to be transported to specific membrane-bound compartments and be proteolytically processed to become functional.
Explanation: These compartments include chloroplasts, mitochondria, the nucleus, and peroxisomes. To carry out protein translocation, unique peptide signals have to be present in the nascent proteins, which function as “zip codes” that direct the proteins to each of these compartments.
3. Once the proteins are translocated within the organelles, protease cleavage takes place to remove the signal sequences and generate mature proteins.
Explanation: It is an example of posttranslational modification. Even in prokaryotes, proteins can be targeted to the inner or outer membranes, the periplasmic space between these membranes, or the extracellular space. The sorting of these proteins is similar to that in eukaryotes and relies on the presence of signal peptides.
4. The signal sequences have a _________ consensus but contain some specific features. They all have a ______ core region preceded by one or more positively charged residues.
a) weak, hydrophilic
b) weak, hydrophobic
c) strong, hydrophilic
d) strong, hydrophilic
Explanation: However, the length and sequence of the signal sequences vary tremendously. Peptides targeting mitochondria, for example, are located in the N-terminal region.
5. The signal sequences are typically _______ residues long, rich in _____ charged residues such as arginines as well as hydroxyl residues such as serines and threonines, but devoid of ______ charged residues.
a) 28 to 80, positively, negatively
b) 300 to 800, negatively, positively
c) 28 to 80, negatively, positively
d) 300 to 500, positively, negatively
Explanation: They have the tendency to form amphiphilic α-helices. These targeting sequences are cleaved once the precursor proteins are inside the mitochondria.
6. Chloroplast localization signals are also located in the __________ terminus and are about 25 to 100 residues in length, containing very few _______ charged residues but many hydroxylated residues such as serine.
a) N, negatively
b) C, negatively
c) C, positively
d) N, positively
Explanation: Chloroplast localization signals are also called transit Peptides. An interesting feature of the proteins targeted for the chloroplasts is that the transit signals are bipartite.
7. Chloroplast localization signals consist of two adjacent signal peptides, one for targeting the proteins to the stromaportion of the chloroplast before being cleaved and the other for targeting the remaining portion of the proteins to the thylakoids.
Explanation: Localization signals targeting to the nucleus are variable in length (seven to forty-one residues) and are found in the internal region of the proteins. They typically consist of one or two stretches of basic residues with a consensus motif K(K/R)X(K/R). Nuclear signal sequences are not cleaved after protein transport.
8. Which of the following is an incorrect statement about SignalP?
a) It only uses neural networks
b) It only uses HMMs
c) It is a web-based program that predicts subcellular localization signals
d) It uses both neural networks and HMMs
Explanation: The neural network algorithm combines two different scores, one for recognizing signal peptides and the other for protease cleavage sites. The HMM-based analysis discriminates between signal peptides and the N-terminal transmembrane anchor segments required for insertion of the protein into the membrane.
9. Which of the following is not one of the training sets in SignalP?
c) Gram-positive bacteria
d) Gram-negative bacteria
Explanation: This distinction is necessary because there are significant differences in the characteristics of the signal peptides from these organisms. Therefore, appropriate datasets need to be selected before analyzing the sequence. The program predicts both the signal peptides and the protease cleavage sites of the query sequence.
10. TargetP is a neural network-based program, similar to SignalP.
Explanation: It predicts the subcellular locations of eukaryotic proteins based on their N-terminal amino acid sequence only. It uses analysis output from SignalP and feeds it into a decision neural network, which makes a final choice regarding the target compartment.
Sanfoundry Global Education & Learning Series – Bioinformatics.
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