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Correct answer is (a) Prokaryotes

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.

Right answer is (a) True

To explain: Similarly, an UNSUPERVISED analysis does not assume PREDEFINED categories, but identifies data categories ACCORDING to actual similarity patterns. The unsupervised analysis is also called clustering, which is to GROUP patterns into clusters of genes with correlated PROFILES.

The correct option is (a) The two-color microarray uses multiple dyes at times

To explain: The most common type of microarray protocol is the two-color microarray, which involves labeling one set of cDNA from an experimental CONDITION with one dye (Cy5, red FLUORESCENCE) and another set of cDNA from a reference condition (the controls) with another dye (Cy3, GREEN fluorescence). When the two differently labeled cDNA samples are mixed in equal quantity and ALLOWED to HYBRIDIZE with the DNA probes on the chips, gene expression patterns of both samples can be measured simultaneously.

The correct answer is (b) This technique is a high throughput APPROACH

Best EXPLANATION: This technique is essentially a low throughput approach. A major flaw in this method is that it is an indirect approach to probe protein–protein interaction and has a tendency to generate FALSE positives (spurious interactions) and false NEGATIVES (undetected interactions). It has been estimated from proteome-wide characterizations that the rate of false positives can be as high as 50%.

Correct answer is (a) 28 to 80, POSITIVELY, negatively

To explain: They have the tendency to FORM amphiphilic α-helices. These targeting SEQUENCES are cleaved once the precursor proteins are inside the MITOCHONDRIA.

The CORRECT answer is (C) There is no screening of vector contaminants

The explanation: The process INCLUDES a preprocessing step that removes vector contaminants and MASKS repeats. Vecscreen, can be used to screen out bacterial vector sequences. This is FOLLOWED by a clustering step that associates EST sequences with unique genes.

Right choice is (c) All the proteins exhibit functions after being transported to certain COMPARTMENTS of the cell

To explain: 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.

Correct OPTION is (a) True

The explanation is: Given a cDNA sequence, one can search SAGE libraries for possible SAGE tags and PERFORM “virtual” NORTHERN blots that indicate the relative abundance of a tag in a SAGE library. Each output is hyperlinked to a particular UNIGENE entry with sequence annotation.

The correct OPTION is (b) This approach is quite less efficient than the EST analysis

The explanation is: If an average clone has a size of 700 bp, it can contain up to 50 sequence tags (15 bp each), which means that the SAGE method can be at least fifty times more efficient than the brute force EST SEQUENCING and counting. THEREFORE, the SAGE analysis has a better chance of detecting weakly expressed GENES.

The CORRECT option is (a) posttranslational, covalent

Explanation: Disulfide bonds are important for maintaining the STABILITY of certain types of proteins. The disulfide prediction is the prediction of paring potential or BONDING states of cysteines in a PROTEIN.

The correct OPTION is (a) True

To elaborate: 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.

The correct ANSWER is (a) True

For explanation I would say: Further characterization involves determination of amino acid composition, peptide mass fingerprints, and sequences USING mass spectrometry (MS). Finally, database searching is needed for protein IDENTIFICATION.

The CORRECT ANSWER is (C) It stands for Squared analysis of gene expression

The explanation is: In this method, SHORT fragments of DNA (usually 15 base pairs [bp]) are excised from cDNA sequences and used as UNIQUE markers of the gene transcripts. The sequence fragments are termed tags. They are subsequently concatenated (linked together), cloned, and sequenced.

Right OPTION is (d) They are typically in the range of 800 to 900 nucleotides in LENGTH

Explanation: ESTs are typically in the range of 200 to 400 nucleotides in length obtained from EITHER the 5’end or 3’end of cDNA inserts. Libraries of cDNA clones are prepared through reverse transcription of isolated mRNA populations by using oligo (dT) primers that hybridize with the poly (A) tail of MRNAS and ligation of the cDNAs to cloning vectors.

The correct option is (c) DISULFIDE, three

To elaborate: This problem can be TACKLED by using PROFILES constructed from multiple sequence alignment. It can also be tackled by using RESIDUE contact POTENTIALS calculated based on the local sequence environment.

The correct choice is (d) Despite of all the failures, the translation the sequences is smooth

To explain: Common errors ALSO include frameshift errors and artifactual stop codons, resulting in failures of translating the sequences. In ADDITION, there is often contamination by vector sequence, introns (fromunspliced RNAs), RIBOSOMAL RNA (rRNA), mitochondrial RNA, among OTHERS. ESTs represent only partial sequences of genes.

Correct OPTION is (a) True

For 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.

The correct choice is (B) It only uses HMMs

Easy 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.

The correct choice is (a) True

To explain: For such TESTS, it is common to use a P-value cutoff of .05, which MEANS a confidence level of 95% to distinguish the data groups. This level also corresponds to a GENE expression level with two standard deviations from the MEAN of distribution.

Correct option is (c) CORRECTLY sequenced SAGE tag ALWAYS corresponds to SEVERAL genes

Easy explanation: To improve the sensitivity and SPECIFICITY of SAGE detection, the lengths of the tags need to be increased for the technique. There are some comprehensive software tools for SAGE analysis viz. SAGEmap, SAGEXPROFILER.

The correct answer is (c) Bayesian algorithm is not involved in ProFound

To EXPLAIN I would say: In ProFound, A Bayesian algorithm is used. It RANKS the DATABASE MATCHES according to the probability of database sequences producing the peptide mass fingerprints.

The correct option is (a) True

Explanation: The RAPID accumulation of EST sequences has prompted the establishment of public and private databases to archive the data. The mentioned database is regularly updated to reflect the progress of various EST SEQUENCING PROJECTS. Each newly submitted EST sequence is subject to a database search. If a strong SIMILARITY to a known gene is FOUND, it is annotated accordingly.

Right answer is (a) True

The best EXPLANATION: In this method, by STUDYING gene/protein fusion events, protein–protein interactions can be predicted. This prediction rule has been PROVEN to be rather reliable and SINCE successfully applied to a LARGE number of proteins from both prokaryote and eukaryotes.

Right option is (b) weak, hydrophobic

To explain I would say: HOWEVER, the LENGTH and sequence of the signal sequences VARY tremendously. PEPTIDES targeting mitochondria, for example, are located in the N-terminal region.

The correct OPTION is (b) False

For explanation I would SAY: It is a web-based program that allows a “virtual subtraction” of an expression profile of one library (e.g., normal tissue) from another (e.g., diseased tissue). Comparison of the TWO LIBRARIES can provide information about overexpressed or silenced genes in normal versus diseased tissues.

Right CHOICE is (a) k-means clustering produces a dendrogram

Easiest explanation: In contrast to hierarchical clustering algorithms, k-means clustering does not PRODUCE a dendrogram, but instead classifies DATA through a single STEP partition. The value of k is normally randomly set but can be adjusted if RESULTS are found to be unsatisfactory.

The correct choice is (a) True

The best I can EXPLAIN: This rule of predicting PROTEIN–protein interactions holds up for most prokaryotic genomes. For eukaryotic genomes, gene order may be a LESS potent PREDICTOR of protein interactions than a tight co-regulation for gene expression.

Correct OPTION is (a) True

The best explanation: There are TWELVE database search TOOLS in this server dedicated to protein identification based on MS data. For example, the AACompIdent PROGRAM identifies proteins based on PI, MW, and amino acid composition and compares these values with theoretical compositions of all proteins in SWISS-PROT/TrEMBL.

Correct ANSWER is (c) Even in reality, the protease digestion is always PERFECT in MS

Easiest explanation: In reality, protease digestion is RARELY perfect, OFTEN generating partially digested products as a result of missed cuts at expected cutting sites. Peptides RESULTING from MALDI-MS are also charged, which increases their mass slightly.

Correct OPTION is (c) Membrane proteins are largely hydrophilic and readily solubilized

Easy explanation: Membrane proteins are largely hydrophobic and not readily solublized. They tend to aggregate in the aqueous medium of a two-dimensional gel. To overcome this problem, membrane proteins can be fractionated USING SPECIALIZED protocols and then electrophoresed using optimized buffers containing zwitterionic detergents. Subfractionation can be carried out to separate nuclear, cytosol, cytoskeletal, and other subcellular FRACTIONS to boost the concentrations of rare proteins and to reveal subcellular localizations of the proteins.

The CORRECT option is (a) True

Easy explanation: This comprehensive package includes four interlinked PROGRAMS, TIGR spot finder (for image analysis), MIDAS (for data normalization), MEV (for CLUSTERING analysis and visualization), and MADAM (for data MANAGEMENT). The package provides different data normalization schemes and clustering options. Other Similar Clustering Programs are EPCLUST, SOTA.

Right option is (a) It is an EST database that the similar type of clustering method from UniGene

The BEST I can explain: BLAST and FASTA are used to identify sequence overlaps. In the sequence assembly STAGE, both TIGR Assembler and CAP3 are used to construct contigs, producing a so-called tentative consensus (TC). To prevent chimerism, transcripts are clustered only if they match FULLY with known genes.

Right ANSWER is (a) True

To explain I WOULD say: The purified proteins are then analyzed by gel electrophoresis followed by MS for identification of the INTERACTING components. The protein microarray systems MENTIONED above ALSO provide a high throughput alternative for studying protein–protein interactions.

Right option is (a) True

Easiest explanation: The PCR amplification STEP involved in the SAGE procedure means that it requires only a minute quantity of sample MRNA. This compares FAVORABLY to the requirement for a much larger quantity of mRNA for MICROARRAY experiments, which may be impossible to obtain under certain circumstances.

Correct option is (a) True

Easy explanation: In MALDI-MS, for example, the peptides are charged with POSITIVE ions and forced through an analyzing tube with a magnetic field. Peptides are analyzed in the gas phase. Because smaller peptides are deflected more than larger ones in a magnetic field, the peptide fragments can be separated according to molecular MASS and charges. A DETECTOR generates a spectrum that DISPLAYS ion intensity as a function of the mass-to-charge RATIO.

The correct answer is (d) EXTREMELY close

The explanation is: When the two domains are LOCATED in two different proteins, to preserve the same functionality, their close proximity and interaction have to be preserved as well. Therefore, by studying gene/protein FUSION EVENTS, protein–protein interactions can be PREDICTED.

Right choice is (a) True

The best 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.

Correct answer is (a) The proteolysis doesn’t generate a PATTERN according to molecular weight

Easy EXPLANATION: The proteolysis generates a UNIQUE pattern of peptide fragments of VARIOUS MWs, which is termed a peptide fingerprint. The fragments can be ANALYZED with MS, a high-resolution technique for determining molecular masses. Currently, electro-spray ionization MS and matrix-assisted laser desorption ionization (MALDI) MS are commonly used.

Correct option is (b) Studies have indicated that the GENE expression measurements from these methods are highly inconsistent with each other

Easiest explanation: SAGE has the POTENTIAL to allow discovery of new, yet unknown gene TRANSCRIPTS. Because is able to measure all the mRNA expressed in a sample, it becomes possible.

Right answer is (b) do not interact, on

The explanation is: Molecular CONSTRUCTS are made such that each of the two domains is COVALENTLY attached to each of the two candidate PROTEINS. If the two candidate proteins do not interact, the reporter gene EXPRESSION remains switched off.

Correct answer is (b) It doesn’t USE SVM approach

BEST explanation: Hyperplane, which has been trained to recognize known protein sequence motifs, SEPARATES the kernels into different classes. Each SEPARATION is compared with known motif classes, most of which are related to posttranslational modification. The best match with a known class defines the functional motif.

Correct option is (a) a linear or nonlinear mathematical function

Easiest explanation: It is used to best separate true signals from noise. The algorithm has more ENVIRONMENTAL variables included that may be required for the enzyme modification. After training the algorithm with sufficient STRUCTURAL FEATURES, it is able to correctly RECOGNIZE many POSTTRANSLATIONAL modification patterns.

The correct OPTION is (a) True

For explanation: This requires the software programs to be able to STRETCH or maneuver one of the gels relative to the other to find a COMMON geometry. When the reference spots are aligned properly, the rest of the spots can be subsequently COMPARED automatically.