This set of Bioinformatics Multiple Choice Questions & Answers (MCQs) focuses on “Functional Classification of Genes”.
1. GeneQuiz focuses on deriving a predicted protein function, based on a variety of available evidence, including the evaluation of the similarity to the closest homolog in a database.
Explanation: GeneQuiz is an integrated system for large-scale biological sequence analysis that uses a variety of search and analysis methods using current sequence databases. By applying expert rules to the results of the different methods, GeneQuiz creates a compact summary of findings.
2. Which of the given statement is incorrect regarding MAGPIE?
a) It analyzes the genome using a set of automated processes
b) It is designed for high-throughput genome sequence analysis
c) It is unable to locate potential promoters
d) It automatically annotates genomic sequence data and maintains a daily up-to-date record in response to user queries about one or more genomes
Explanation: The system also uses a set of rules in logic programming to make decisions that may be used to interpret information from various sources. It has been used to locate potential promoters, terminators, start codons, Shine-Dalgarno sites, DNA motif sites, co-transcription units, and putative operons in microbial genomes. These sites are shown on a map display of the genome that may be edited.
3. Which of the given statement is incorrect?
a) Paralogous sequences, frequently are found to have dissimilar functions
b) An early classification scheme for eight related groups of E. coli genes included categories for enzymes, transport elements
c) An early classification scheme for eight related groups of E. coli genes included categories for regulators, membranes, structural elements, protein factors, leader peptides, and carriers
d) Ninety percent of E. coli genes related by significant sequence similarity fell into these same broad categories
Explanation: Genes that are significantly similar in an organism, i.e., paralogous sequences, frequently are found to have a related biological function. This discovery follows the expected origin of paralogs by gene duplication events, leaving one copy to perform the original function and producing a second copy to develop a new function not too distant from the original one under evolutionary selection.
4. The designation ECa.b.c.d conveys information. Which of the following is not one of it?
a) One of twelve main classes of biochemical reactions
b) The group of substrate molecule
c) The nature of chemical bond that is involved in the reaction
d) Designation for acceptor molecules (cofactors)
Explanation: Option “One of twelve main classes of biochemical reactions” should be ‘one of six main classes of biochemical reactions’. The Enzyme Commission numbers formulated by the Enzyme Commission of the International Union of Biochemistry and Molecular Biology provide a detailed way to classify enzymes based on the biochemical reactions they catalyze.
5. An approach to classification of genes that encode enzymes is to examine relationships among multiple enzymes that perform the same biochemical function in the same organism.
Explanation: Although catalyzing the same reaction, these enzymes showed variations in metabolic regulation of their activity. More than one-half of multiple enzymes in E. coli share significant sequence similarity; i.e., they are paralogs. However, the remainder do not share any sequence similarity.
6. Other functional classification schemes for genes include a broader category for genes involved in the same biological process, e.g., a three-group scheme for energy-related, information-related, and communication-related genes has also been used.
Explanation: By this scheme, plants devote more than one-half of their genome to energy metabolism. Whereas, animals devote one-half of their genome to communication-related functions.
7. Two species that have recently diverged from a common ancestor might be expected to have a ________ set of genes and ________ chromosomes with these genes positioned along the chromosomes in the same order.
a) distinct, similar
b) similar, distinct
c) similar, dissimilar
d) similar, similar
Explanation: Over evolutionary time, the sequence of each pair of genes will slowly diverge, as the species diverge and other changes such as gene duplication and gene loss change the gene content. In addition, the order of genes also changes over evolutionary time as a result of chromosomal rearrangements.
8. Which of the given statement is incorrect about the observations made with regard to gene order?
a) Order is highly conserved in closely related species
b) Order in closely related species becomes changed by rearrangements over evolutionary time
c) As more and more rearrangements occur, there will no longer be any correspondence in the order of orthologous genes on the chromosome of one organism with that of a second organism
d) Order is less conserved in closely related species
Explanation: Order is more conserved in closely related species. Another observation is that the groups of genes that have a similar biological function tend to remain localized in a group or cluster.
9. Which of the given statement is incorrect about the Chromosomal Rearrangements?
a) Comparison of the number of rearrangements in a given period of evolutionary history may vary significantly from one organism to the next
b) If gene A has a neighboring gene B, then if an ortholog of A occurs in another genome, there is an increased probability of an ortholog of B also occurring in the other organism
c) If gene A has a neighboring gene B, then if an ortholog of A occurs in another genome, the B ortholog is more likely to be a neighbor of the A ortholog of the genome of the second species if the two species are more divergent
d) In general, the order of orthologs is not well conserved in prokaryotes when the genomes have diverged sufficiently that the orthologs have < 50% identity
Explanation: The B ortholog is less likely to be a neighbor of the A ortholog of the genome of the second species if the two species are more divergent. By classifying genes using a nine class functional classification scheme, several genes falling into the same functional category are clustered together on the chromosomes of both of these organisms, and the clusters are in a similar order.
10. Which of the given statement is incorrect?
a) In a given organism or species, genes are found in a given order that is maintained on the chromosomes from one generation to the next
b) Genes with a related function are frequently found to be distorted on a chromosome
c) A possibility is that there is genetic variation (alleles) within each gene in a cluster of a given species and that only certain allelic combinations of different genes are compatible
d) Clustering of related genes presumably provides an evolutionary advantage to a species
Explanation: Genetic analysis has revealed that genes with a related function are frequently found to be clustered at one chromosomal location. As genome-by-genome comparisons of the chromosomes of related species are made and the rearrangements are discovered, a further challenge to computational and evolutionary biologists is to estimate the number and types of rearrangements that have occurred and also to determine when they occurred. For example, a comparison of the mouse and human chromosomes reveals many rearrangements.
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