Collegedunia Team Content Curator
Content Curator
Bioinformatics is a hybrid science that connects biological data with information storage, dissemination, and analysis techniques to help scientists in a variety of fields, including biomedicine. Applying computation and analysis tools to collect and process biological data is characterized as bioinformatics.
It usually refers to genes, DNA, RNA, or proteins, and it's especially useful when comparing genes and other sequences in proteins and even other sequences within an organism or between organisms, searching for evolutionary relationships between organisms and determining the function of DNA and protein sequences using patterns found across DNA and protein sequences.
Also Read: RNA Interference
Ques 1. Which among the following statements about ENTREZ is false?
- It has a number of forms to fill out in order to get a Medline reference for a molecular biology sequence database.
- It offers a set of forms to fill out in order to obtain a DNA or protein sequence.
- The ENTREZ database provides a simple way to access sequence databases.
- It's a resource created only by the National Centre for Biotechnology Information's team.
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Ans. d
Explanation: The National Centre for Biotechnology Information and the National Library of Medicine, both in Bethesda, Maryland, put together this resource. After selecting a protein or DNA sequence to look for at the aforementioned site, a new Web page appears with a form to complete for the search. Thus, option d is the answer.
Ques 2. MEME is abbreviated as which of the following?
- Multiple Expectation Maximisation for Motif Elicitation
- Mega Expectation Maximisation for Motif Elicitation
- Micro Expectation Maximisation for Motif Extraction
- Multiple Expectation Maximisation for Motif Extraction
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Ans. a
Explanation: Multiple Expectation Maximisation for Motif Elicitation is an internet-based software that searches for themes in DNA or protein sequences using the EM method. To tackle the local minimum problem, it employs a modified EM algorithm.
Ques 3. Which among the following tools is not a dot plot analysis software?
- DOTMATCHER
- LALIGN
- DOTLET
- SIMMI
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Ans. d
Explanation: Various softwares are currently available for the interpretation of dot plots. SIM is one of these programmes that uses the dot-plot method, which is incorrectly shortened.
Ques 4. Which of the following statements about the assumptions used in the Dayhoff scoring matrix construction method is correct?
- The degree of mutability of sites does not differ.
- Each amino acid position is believed to be equally mutable.
- Each amino acid position is believed to be not equally changeable.
- Each amino acid position is believed to be immutable at all times.
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Ans. b
Explanation: Each amino acid position is considered to be equally malleable in this process, despite the fact that sites vary greatly in their degree of mutability. In molecular genetics, mutagenesis hot spots are well-known, and variations in the mutability of various amino acid positions in proteins.
Ques 5. The procedure for determining the relative positions of genes on a chromosome is referred to as?
- Gene tracking
- Genome mapping
- Genome walking
- Chromosome walking
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Ans. b
Explanation: Genome mapping is a technique for identifying and recording the locations of genes on a chromosome as well as the distances between them. The important landmarks in an organism's genome are highlighted in a genome map.
Ques 6. Which of the following statements concerning protein's 'loop' structure is false?
- They link helices and sheets together.
- Mutation tolerance is higher in them.
- They are more adaptable and can take on a variety of shapes.
- They are never the components of active sites
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Ans. d
Explanation: Because of their flexibility and location on the structure's surface, loops are widely used as part of active sites. Furthermore, they come in a variety of lengths and 3-D layouts, giving them even more opportunities to be part of busy sites.
Ques 7. Which of the following statements about protein domains is incorrect?
- They consist of a single secondary structure.
- Defined as foldable components that can be folded independently of one another.
- In comparison to motifs, they are more stable structures.
- Linker regions serve as a barrier between them.
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Ans. a
Explanation: Protein domains are composed of two or even more motifs (secondary structure) that come together to produce stable and folded three-dimensional structures. They are a conserved portion of the protein sequence that can evolve, operate, and exist separately from the remainder of the protein chain.
Ques 8. Which of the following statements about pairwise sequence alignment is incorrect?
- Sequence alignment is the most basic technique in this type of comparison.
- It's a crucial initial step toward analysing the structural and functional properties of newly discovered sequences.
- This is the method of comparing sequences by looking for common character sequences and creating residue-residue correspondence between related sequences.
- It's a method for aligning multiple sequences.
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Ans. d
Explanation: The method of aligning two sequences is known as pairwise sequence alignment, and it provides the foundation for database similarity searches and multiple sequence alignment. Sequence comparison is gradually becoming progressively relevant as new biological sequences are created at an exponential rate, allowing operational and evolutionary inference of a novel protein from proteins already in the database.
Ques 9. Which of the following statements regarding evolution is false?
- Macromolecules can be viewed as molecular fossils that record thousands of years of evolution.
- These biological macromolecules' building blocks, nucleotide bases and amino acids, form linear sequences that dictate the molecules' main structure.
- Evolution has produced DNA and proteins.
- Changes in molecular sequences are negligible.
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Ans. d
Explanation: Molecular sequences exhibit unexpected modifications over this time period, some of which are determined during the evolution process. As the selected sequences accrue mutations and deviate over time, evidence of evolution may still be visible in some regions of the sequences, allowing the common ancestry to be determined.
Ques 10. Which of the following does not have anything to do with multiple sequence alignment?
- A protein multiple alignment can reveal a number of conserved and functionally important amino acid residues.
- Multiple sequence alignment is also required for phylogenetic study of sequence families and the prediction of secondary and tertiary structures of proteins.
- Degenerate polymerase chain reaction (PCR) primers based on numerous related sequences can be designed using multiple sequence alignment.
- This method does not contribute significantly to the development of degenerate polymerase chain reaction (PCR) primers.
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Ans. d
Explanation: Heuristic techniques are most commonly employed in application. Designing degenerate (PCR) primers based on many related sequences can benefit from multiple sequence alignment.
Ques 11. Which of the following statements regarding DCA is false?
- It full form is Divide-and-Conquer Alignment
- It functions by dividing each sequence into two smaller pieces.
- Further divisions are forbidden if the segments are not short enough
- The breaking points in the procedure are defined by the sequences' regional similarity.
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Ans. c
Explanation: This is a web-based software that is actually semi-exhaustive due to the usage of heuristics for key compute phases. If the portions aren't long enough, additional divisions are made. Dynamic programming is used to align each set of subsequences when the lengths of the sequences hit a predetermined threshold. The short alignments are then merged head to tail to form a multiple alignment that spans the complete length of all sequences.
Ques 12. Which of the following statements concerning the PILEUP programme is false?
- It is the MSA programme, which is part of the Genetics Computer Group's sequence analysis software suite.
- It has been owned by Oxford Communications since 1997 and is commonly used due to its popularity and availability.
- The Needleman- Wunsch dynamic programming approach is used to align the sequences pair by pair.
- It employs a method for MSA that is fundamentally opposite to CLUSTALW.
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Ans. d
Explanation: For MSA, PILEUP employs an approach that is quite similar to CLUSTALW. The sequences are pairwise aligned using the Needleman- Wunsch dynamic programming approach, and the scores are utilised to generate a tree using the unweighted pair-group method with arithmetic averages. The generated tree is then used to direct the alignment of the sequences and groupings of sequences that are the most closely linked. The Needleman-Wunsch algorithm produces a global alignment as a result of the process.
Ques 13. Which of the following statements about the stabilising Forces is incorrect?
- Noncovalent forces keep secondary to quaternary protein structures together
- They involve electrostatic interactions but not van der Waals forces, and hydrogen bonding
- In a protein structure, electrostatic interactions provide a substantial stabilising force
- Excess negative charges in one location are neutralised by positive charges in another region, resulting in electrostatic interactions
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Ans. b
Explanation: Electrostatic interactions, van der Waals forces, and hydrogen bonding are all part of stabilising forces. Salt bridges form between oppositely charged residues as a result of this process. Electrostatic interactions have a pretty long range of operation (15 Å). Hydrogen bonds are electrostatic interactions that involve hydrogen from one residue and oxygen from another, analogous to dipole–dipole interactions. Hydrogen bonds can form between atoms in the main chain and atoms in the side chain.
Ques 14. In terms of protein structural comparison, which of the following statements is incorrect?
- Finding distant protein homologs requires a comparative method.
- The conservation of protein structures is substantially higher than that of sequences.
- The conservation of protein structures is substantially lower than that of protein sequences.
- Proteins can have similar structures even though their sequences aren't identical
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Ans. c
Explanation: One of the most basic techniques in protein structure investigation is structural comparison. Structure comparison can often uncover distant evolutionary links between proteins that would otherwise be impossible to discover using only a sequence-based alignment technique. Furthermore, protein structure comparison is required for structural classification of proteins into different food groups.
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Ques 15. Which of the following statements about transmembrane proteins is false?
- They make up up to 30% of all cellular proteins.
- They are in charge of many key functions in a cell, including signal transduction, cross-membrane transport, and energy conversion.
- Membrane proteins are also extremely important in biomedicine.
- They aren't medicinal targets or receptors
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Ans. d
Explanation: Membrane proteins are also extremely important in biomedicine since they are frequently used as therapeutic targets in pharmaceutical research. Integral membrane proteins are divided into two categories: α-helical and β-barrel. Only α-helices, which are present in the cytoplasmic membrane, are found in most transmembrane proteins. Several membrane proteins have β-strands that form β- barrel topology, which is a cylindrical structure made up of antiparallel β-sheets.
Ques 16. Which of the following statements concerning genomic mapping is false?
- It doesn’t lead to the comprehension of a genome structure
- It helps determine the relative positions of genes.
- It entails identifying characteristics.
- It helps identifying mutations
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Ans. a
Explanation: Genome mapping, which is the act of finding relative locations of genes, mutations, or features on a chromosome, is the first step in comprehending a genome's structure. The order and relative distances of genetic markers on a chromosome are described as a low-resolution technique to mapping genomes.
Ques 17. Which of the following statements concerning DNA sequencing is incorrect?
- The Sanger method is now used on a regular basis
- DNA polymerases aren't used in this method.
- This involves the construction of DNA chains of various lengths.
- Dideoxynucleotides are used to stop DNA synthesis.
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Ans. b
Explanation: DNA polymerases are utilised to create DNA chains. Fluorescent dyes are used to identify the dideoxynucleotides, which cause DNA synthesis to stop at sites containing all four bases, leading to nested fragments that differ in length by a single base. The banding patterns in the gel disclose the DNA sequence when the tagged DNA is electrophoresed.
Ques 18. Which of the following statements about genome economy is incorrect?
- It's a phenomenon in which fewer genes produce more proteins.
- This is a key method used by eukaryotic organisms to achieve phenotypic diversity.
- This is a key method used by eukaryotic organisms to achieve a wide range of genotypic diversity.
- There are a variety of underlying genetic pathways that contribute to genome economy.
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Ans. c
Explanation: Alternative splicing, which means the splicing event that unites distinct exons from a single gene to generate different transcripts, is a significant process responsible for protein variety. Exon shuffling, a comparable mechanism that links exons from various genes to generate additional transcripts, is also found in eukaryotes. Alternative splicing and exon shuffling are known to occur in around two-thirds of human genes during expression, resulting in 90 percent of total proteins.
Ques 19. Which of the following statements about Gene Order Comparison is not correct?
- Synteny is the preservation of the order of a set of related genes across genomes.
- Gene order is substantially more conserved than gene sequences in general.
- Gene order is substantially less conserved than gene sequences in general.
- It is, in fact, rare among diverse species.
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Ans. b
Explanation: In reality, gene order conservation between divergent species is rare. As a result, syntenic relationships are usually compared between lineages that are very close. If syntenic links for certain genes are found across divergent prokaryotes, they can often reveal vital information about the genes' functional relationships. Thus, Gene order is substantially less conserved than gene sequences.
Ques 20. Which of the following statements about MAGPIE is incorrect?
- It uses a series of automated processes to analyse the genome.
- It's made for high-throughput genomic sequence analysis.
- It can't seem to find any suitable promoters.
- In response to user inquiries about one or more genomes, it intelligently annotates genomic sequence data and keeps a daily up-to-date record.
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Ans. c
Explanation: The system also makes judgments based on a set of logic programming rules that may be used to evaluate data from multiple sources. In microbial genomes, it has been used to find potential promoters, terminators, start codons, Shine-Dalgarno sites, DNA motif sites, co-transcription units, and putative operons. These locations are displayed on a map of the genome that can be modified.
Ques 21. Which of the following statements is false?
- Genes are located in a specific order in a given organism or species, which is retained on the chromosomes from generation to generation.
- On chromosomes, genes with related functions are usually discovered to be distorted.
- It's possible that each gene in a cluster of a given species has genetic variation (alleles) and that only specific allelic combinations of distinct genes are compatible.
- A species' evolutionary advantage may be gained by clustering related genes.
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Ans. b
Explanation: Genes with similar functions are commonly concentrated at one chromosomal region, according to genetic research. As genome-by-genome comparisons of related species' chromosomes are done and rearrangements are identified, computational and evolutionary biologists face a new challenge: estimating the number and kinds of rearrangements that have happened, as well as determining when they occurred. A comparison of the mouse and human being chromosomes, for example, reveals several rearrangements.
Ques 22. Out of the following options, which one is an example of a Homology and similarity tool?
- RasMol
- BLAST
- PROSPECT
- EMBOSS
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Ans. b
Explanation: BLAST or Basic Local Alignment Search Tool (BLAST) is also a homology and similarity tool that finds parts of local similarity between nucleotide or protein sequences. BLAST compares nucleotide or protein sequences to sequence databases. It calculates the significance of matches statistically. BLAST helps to deduce functional and evolutionary relationships between sequences and helps identify members of gene families.
Ques 23. SWISS-PROT protein sequence database began in which year?
- 1986
- 1992
- 1987
- 1988
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Ans. c
Explanation: SWISS-PROT is an annotated protein sequence database. It was created at the Department of Medical Biochemistry of the University of Geneva. SWISS-PROTT has been a collaborative effort between the Department and the European Molecular Biology Laboratory (EMBL) since 1987.
Ques 24. Who created the first Bioinformatics database?
- Pearson
- Dayhoff
- Richard Durbin
- Michael.J.Dunn
Ans. b
Explanation: Margaret O. Dayhoff was one of the founders of the bioinformatics database. Margaret O. Dayhoff created the first public comprehensive, computerized, and publicly accessible database of protein sequences, The Atlas of Protein Sequence and Structure (1965).
Ques 25. When did the first molecular biology server ExPASy commence its operation?
- 1997
- 1983
- 1992
- 1993
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Ans. d
Explanation: ExPASy started operating in 1993, as the first WWW server in the field of life sciences. Other than its main site in Switzerland, seven mirror sites in different continents are currently serving the user community.
Ques 26. In medical applications, the ultimate goal of gene mapping is to disease genes.
- True
- False
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Ans. a
Explanation: Once the gene gets cloned, determination of the DNA sequence can take place. Also, the study of the target protein is carried out.
Ques 27. Which of the following feature of Bayesian methods is the disadvantage?
- Computationally Bayesian methods are better
- They are used to calculate the evolutionary distance
- A specific mutational model is required
- A length and distance that gives the highest overall probability may be determined
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Ans. c
Explanation: One disadvantage of the Bayesian approach is that a specific mutational model is required, whereas other methods, such as the maximum likelihood approach, can be used to estimate the best mutational model as well as the distance. Computationally, however, the Bayesian method is much more practical.
Ques 28. Which of the following is incorrect regarding sequence homology?
- When two sequences are descended from a common evolutionary origin, they are said to share homology
- When two sequences are descended from a common evolutionary origin, they are said to have a homologous relationship
- It is an important concept in sequence analysis
- Two sequences can have a homologous relationship even if have do not have a common origin
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Ans. d
Explanation: Homologous relationships are more accurate when sequences have a common evolutionary origin. A related term is sequence similarity, which is the percentage of aligned residues that are similar in physiochemical properties such as size, charge, and hydrophobicity.
Ques 29. What is used to generate parameters for the extreme distribution?
- A single score of a shuffled sequence
- Basic optimal score computed at the beginning of the test
- The pool of alignment scores from the unshuffled sequences
- The pool of alignment scores from the shuffled sequences
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Ans. a
Explanation: Maximum scores are obtained through repeated shuffling. Then the pool of alignment scores from the shuffled sequences is used to generate parameters for the extreme distribution. The original alignment score is then compared against the distribution of random alignments to determine whether the score is beyond random chance.
Ques 30. For the 10-residue DNA sequence example, there are _______ possible starting sites for a 20-residue-long site.
- 31
- 52
- 44
- 81
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Ans. d
Explanation: For the 10-residue DNA sequence example, there are 100 – 20 +1 possible starting sites for a 20-residue-long site. Where the first one is at position 1 in the sequence ending at 20 and the last beginning at position 81 and ends at 100 (there is not enough sequence for a 20-residue-long site beyond position 81).
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