Interview MCQ Set 1
1. Experimentation is most desirable over computational methods by every means.
Answer: b [Reason:] Computational methods for predicting protein-protein interactions are desirable as experimental determination is time-consuming and expensive. Several prediction methods are based on the observation that if two proteins are part of the same complex, it is favorable for the two interaction partners to be co-expressed and co-regulated.
2. Interactions between proteins can be predicted computationally by looking for sets of genes that occur as a _______
a) single gene in at least one genome
b) multiple genes in at least one genome
c) multiple genes in various genomes
d) single gene in various genomes
Answer: a [Reason:] Interactions between proteins can be predicted computationally by looking for sets of genes that occur as a single gene in at least one genome. Or it can be done by looking for prokaryotic genes that have conserved adjacent gene order across several genomes.
3. Genes that are consistently part of the same operon across different, distantly related genomes are likely to be part of the same protein complex or functional process across all species.
Answer: a [Reason:] This is because they have been selected to remain as a co-regulated unit throughout the extensive shuffling of gene order that takes place in prokaryote genomes. Thus conservation of gene order across different, distantly related genomes has been used as a method for predicting protein interactions.
4. When comparing pairs of genes or sets of genes in different genomes for this purpose, it is not mandatory for the genes to be orthologs.
Answer: b [Reason:] When comparing pairs of genes or sets of genes in different genomes for this purpose, it is important to ensure that the genes are truly equivalent, in other words that they are orthologs, as opposed to merely similar genes. This is frequently done by only accepting a pair of proteins as orthologs if they are ‘bi-directional best hits’. This means that both proteins are the best match to each other when searching against the other proteome. The other extreme would be to consider proteins as equivalent if they share just one of many domains, for instance.
5. Members of a stable complex are often co-regulated and thus will be detected by the method of Conservation of gene order.
Answer: a [Reason:] As much it is true proteins which are part of the same metabolic pathway or part of the same biological process can also be co-regulated. Therefore, although some of the genes detected as interacting by this method physically interact, others are just functionally associated with each other.
6. In a quantitative assessment of this method (Conservation of gene order) using the genome of the parasitic organism Mycoplasma genitalium as a benchmark.
Answer: a [Reason:] Huynen and colleagues found that two-thirds to four-fifths of the general interactions detected correspond to physical interactions and another 13% correspond to a metabolic or non-metabolic pathway. Genes those are physically associated with each other while being regulated and expressed individually will not be detected by this method.
7. Conservation of gene order due to operon structure is_______, so interactions of proteins specific to eukaryotes cannot be detected by method of Conservation of gene order.
a) not applicable to archea genomes
b) not applicable to prokaryote genomes
c) applicable to eukaryote genomes
d) not applicable to eukaryote genomes
Answer: d [Reason:] Co-regulation of genes in eukaryotes can be inferred by similarity in the expression patterns of genes. A comparison of co-expressed yeast and worm genes showed that 90% of those pairs of genes with conserved co-expression are members of stable complexes. Thus, the principle of conserved co-regulation across distantly related organisms applies to stable complexes in both prokaryotes and eukaryotes, and can be used as a prediction tool in both.
8. An approach for predicting ______ to look for cases across a set of genomes where _____ are part of the same gene in one genome resulted in gene fusion method.
a) gene interactions, only three to four orthologs
b) gene interactions, two orthologs
c) protein interactions, two or more orthologs
d) protein interactions, two orthologs
Answer: c [Reason:] The prediction is then that the orthologs that are on separate genes in the other genomes interact with each other. In the case of gene fusion, the fused proteins are not only co-regulated, as in conservation of gene order described above, but also permanently colocalized in the cell. The additional requirement of colocalization beyond just co-regulation poses a further limitation on the prediction method.
9. Domains that are part of a multidomain protein are ______
a) nethier co-regulated nor colocalized
b) not co-regulated but colocalized
c) co-regulated and but not colocalized
d) co-regulated and colocalized
Answer: d [Reason:] Therefore, members of stable complexes as well as consecutive enzymes may be involved in gene fusions. However elements of signal transduction chains are seldom part of the same gene, for instance, as it is an essential part of their function that they can be regulated and localized independently.
10. Due to the requirement for co-regulation as well as colocalization, the method is mostly limited to certain classes of protein-protein interactions.
Answer: a [Reason:] Those classes are members of the same stable complex and proteins in the same metabolic pathway. In their assessment of computational methods for prediction of all types of protein interactions, Huynen and colleagues found that two-thirds of the interactions detected in this way were between proteins that physically interact and another 15% between proteins part of the same metabolic pathway. The remaining interactions involved hypothetical proteins of unknown function.
11. The phylogenetic profile method relies on detection of orthologs (or homologs, in a variation of the method) in a set of genomes.
Answer: a [Reason:] If the pattern of ortholog presence or absence is the same in a group of proteins, then these proteins are clustered together as belonging to the same functional class. A method that appears to reliably predict a loose functional correlation between proteins is the phylogenetic profile method developed by Pellegrini and colleagues.
12. In the assessment of methods to predict protein-protein interactions, one third of such pairs were found to physically interact, and an additional third to belong to the same metabolic pathway or functional process.
Answer: a [Reason:] As mentioned, one third of such pairs were found to physically interact. The phylogenetic patterns of clusters of orthologous groups of proteins deposited in the COG database of Koonin and co-workers could in principle be used for prediction in the same way.
13. In the phylogenetic profile method for predicting protein interaction, presence or absence of orthologous genes is scored across a variety of genomes.
Answer: a [Reason:] This is represented by presence or absence of a dot in the row. Genes that have the same pattern of presence or absence across genomes are predicted to interact.
14. Structural analyses on small sets of proteins have shown that the domains from a pair of families bind to each other with the same geometry in multi-domain proteins and in transient interactions.
Answer: a [Reason:] Most domain families engage in interactions with one or two other types of families, but a few families are very versatile and interact with many families. These versatile families are ubiquitously useful families such as P-loop nucleotide triphosphate hydrolases and Rossmann domains.
15. The most detailed experimental information about protein-protein interactions comes from three-dimensional structures.
Answer: a [Reason:] The 3-D structure gives the most conformation of the structure. It is likely that complexed protein structures will be solved more frequently in the wake of the structural genomics projects.
Interview MCQ Set 2
1. Which of the following DC motor has the poorest speed control?
a) Differentially compounded motor
b) Cumulatively compounded motor
c) Shunt motor
d) Series motor
Answer: d [Reason:] DC series motor at no load condition gives infinite speed ideally. Practically it will damage all the armature circuit. Thus, as the load is reduced speed of the motor will go on increasing rapidly. So, speed control is very poor in series motor.
2. In variable speed motor ____________
a) Stronger commutating field is needed at low speed than at high speed
b) Weaker commutating field is needed at low speed than at high speed
c) Same commutating field is needed at low speed and at high speed
d) Cannot be determined
Answer: b [Reason:] According to commutating fields of machine, speed and overall performance of a machine is determined. For low speeds of motor in a variable speed motor we need weaker commutating field.
3. The speed of a motor falls from 1200 rpm at no-load to 1050 rpm at rated load. The speed regulation of the motor is ____________
Answer: b [Reason:] Speed of regulation of DC series motor is given by ratio of difference of no-load speed and full load speed with full load speed. Thus, in this case, speed regulation = (1200-1050)/1050= 14.28%.
4. Which of the following is not the method of speed control in DC series motor?
b) Tapped-field control
c) Variable resistance in series with armature
d) Series- parallel control
Answer: c [Reason:] Diverter means adding a variable resistance in parallel with field winding. Tapped field control is the method where field ampere turns are adjusted in steps by varying the number of turns included in the circuit. In series parallel method field winding is connected so that it will form two parts.
5. For speed reversal, field control method is suitable.
Answer: b [Reason:] Field control method is not suited to applications needing speed reversal; since the only way to reverse speed is to disconnect the motor from the source and reverse the field/armature polarity. The field circuit being highly inductive, it is normally the armature which is reversed.
6. For large motors what is the ratio of compensating winding is required for increasing the speed of the motor?
Answer: a [Reason:] For motors requiring a wide range of speed control, the field ampere-turns are much smaller than the armature ampere-turns at high speeds causing extreme distortion of the flux density in the air-gap. This leads to poor commutation. Compensating winding can be used to increase the speed range which can be 2 to 1 for large motors.
7. In diverter resistor field control method of DC series motor, variable resistor is added ________
a) In parallel with field
b) In series with field
c) In parallel with armature
d) In parallel with load
Answer: a [Reason:] Diverter is a small variable resistor, which is connected in parallel with field winding. By varying this resistance value, the field current and consequently the field ampere-turns can be varied and speed can be controlled.
8. Why it is advisable to use inductively wound diverter resistor?
a) To make speed control on more range
b) For long-life of machine
c) Cost efficient
d) To avoid oscillations in speed
Answer: d [Reason:] One precaution to be taken in this method in order to avoid oscillations in speed initiated by load changes is to use an inductively wound diverter resistor. Thus, speed controlled output will vary smoothly when load is changed.
9. For higher diverter resistance, speed-torque characteristic will lie ____________
a) Above speed-torque characteristic of lower resistance
b) Below speed-torque characteristic of lower resistance
c) On the speed-torque characteristic of lower resistance
d) Cannot say
Answer: b [Reason:] Speed-torque characteristic for decreasing values of diverter resistance or decreasing value of kd will lie above of the previous or lower value of diverter resistance. Thus, for higher diverter value curve will lie below the previous one.
10. In tapped field control method ____________
a) A variable resistor is connected in parallel
b) A variable resistor is connected in series
c) Field winding is made with more out pins
d) Another field winding is added with the previous one
Answer: c [Reason:] In tapped field control of the DC series motor a field winding is simply tapped at various points and many out pins taken, so that any out pin can be connected and particular part of field winding will be selected in the circuit, while other part is made open.
11. Which of the following method will not give many speed values for a DC series motor?
c) Field tapped
d) All field control methods will give many speed values
Answer: b [Reason:] In series-parallel method, field winding is equally divided in two parts which are connected in series and parallel with respect to each other. Thus, in series connection we’ll get one speed and in parallel mode we’ll get one speed. These 2 speeds are only possible.
12. In series-parallel speed control method ______________
a) Speed given by parallel connection is more
b) Speed given by series connection is more
c) Both speeds can be equal
d) Will depend on other parameters
Answer: a [Reason:] In parallel case, total ampere turns will be exactly half of the ampere turns of the series case. Since speed of any DC motor is inversely proportional to the MMF or flux or ampere turns developed, speed of the parallel control method will always large than the series one.
13. Where diverters are used?
a) In shunt motors
b) In series motors
c) In both motors
d) All other motors except shunt and series motors
Answer: b [Reason:] Diverters are used in series motors for speed control, they are not used in shunt motors. Since, shunt field winding resistance is very high, if we connect a diverter across shunt field winding, total current will flow through diverter and it will almost short circuit the shunt field winding. This will increase the motor speed to a very high value.
14. What will happen to the speed of a series motor if the temperature of armature resistance is increased?
a) Not change
d) Cannot be determined
Answer: b [Reason:] In a DC series motor, when the resistance increases due to rise in temperature, the IR drop in the circuit will increase, which reduces the effective voltage applied to the armature, hence speed decreases due to the direct proportionality.
Interview MCQ Set 3
1. What are the pipelining stages include?
a) Fetch, Decode, Write
b) Fetch, Decode, Execute
c) Fetch, Execute, Write
d) Fetch, Decode, Execute, Write
Answer: a [Reason:] ARM7 core has 3-stage pipeline that increase instruction flow through processor up to three times. So each instruction is executed in 3 stages:
Fetch – instruction is fetched from memory and placed in pipeline
Decode – instruction is fetched and data-path signals prepared for next cycle
Execute – instruction from prepared data-path reads from registry bank, shifts operand to ALU and writes generated result to dominant register.
2. What is pipe lining?
a) Non linear
c) Linear and Non linear
d) Sometimes both
Answer: b [Reason:] Pipeline is linear, which means that in simple data processing processor executes one instruction in single clock cycle which while individual instruction takes three clock cycles.
3. What are the no of pins that are in the ARM7 processors?
a) 65 pin with QFP
b) 45 Pin with QFP
c) 45 pin with LLC
d) 65 pin with DIP
Answer: d [Reason:] The ARM7 family members have different packages, such as DIP(Dual In Line), QFP(Quad Flap Package), LLC(Leadless Chip Carrier) they all have 40 pin that are dedicated to different functions. Especially 8051 has a Quad Flap Package.
4. Using what the processor wake-up from power-down?
a) External Interrupts
b) Internal interrupts
c) Serial Programming
d) Program Counter
Answer: a [Reason:] The AVR7 processor wakes up from power down mode via external interrupt or BOD.
5. What is the flash memory for LPC2141?
Answer: b [Reason:] It is the first series of ARM7. This memory is used for both code and data storage. Programming of the flash memory may be accomplished in several ways. It can also be programmed in system via serial port.
6. What are the categories in the vectored interrupt controller?
a) Fast interrupt request
b) Non vectored interrupt request
c) Non-vectored IQR
d) Fast interrupt request, Non vectored interrupt request, and Non-vectored IQR
Answer: d [Reason:] The vectored Interrupt controller accepts all the interrupts request inputs and categorizes them as Fast Interrupt Request, Vectored Interrupt Request, and Non Vectored IQR as defined by programmable settings. The programmable assignment scheme means that priorities of interrupts from the various peripherals can be dynamically assigned and adjusted.
7. Each peripheral has an interrupt line?
Answer: a [Reason:] Each peripheral device has one interrupt line connected to the Vectored Interrupt Controller, but may have several internal interrupt flags. Individual interrupt flags may also represent more than one interrupt source.
8. What is pin connect block?
a) All pins are having a function without reserved
b) Some pins are Reserved
c) Pins have more than one function
d) Multiplexing of some pins
Answer: c [Reason:] The pin connect block allows selected pins of the microcontroller to have more than one function. Configuration registers control the multiplexers to allow connection between the pin and the on chip peripherals.
9. What is the size of ADC and DAC?
a) 16 bit
b) 10 bit
c) 8 bit
d) 32 bit
Answer: b [Reason:] The converters are single 10-bit successive approximation analog to digital converters. While, ADC0 has 6 channels, ADC1 has 8 channels. And DAC output voltage is the vref voltage.
10. How many processors are used in the Instruction pipelining?
Answer: a [Reason:] Pipelining is a technique for implementing instruction level parallelism within a single processor. Pipelining attempts to keep every part of the processor busy with some instructions, by dividing incoming instructions into the series of a sequential steps.
11.Which signal is used for pipelining on bis cycle in ARM710T?
Answer: b [Reason:] The signal BTAN[1:0] is placed by one bus cycle. This pipelining should be taken into account when these signals are being decoded. The value of BTRAN[1:0] indicates whether the next bus cycle is a data cycle or an address cycle.
12. _______ pin can be used to extend memory access in whole cycle increments.
Answer: c [Reason:] BWAIT pin can be used to extend memory access in whole cycle increments. BWAIT is driven by the selected slave during the low phase of BCLK.
13. How many DC-DC converters interfaces in ARM7100?
Answer: d [Reason:] ARM7100 has two programmable duty ratio 96KHz clock output which are intended to be used as drivers for DC to DC converter in the PSU subsystems.
14. The ARM7TDMI-S uses which pipelining?
Answer: b [Reason:] A 3-stage pipelining is used, so instructions are executed in three stages: Fetch, Decode, Execute.
15. The ARM7TDMI-S processor has __________ types of memory cycle.
Answer: c [Reason:] The ARM7TDMI-S processor has 4 types of memory cycle: Non sequential cycle, Sequential cycle, cp processor register transfer cycle, internal cycle.
Interview MCQ Set 4
1. Which of the given statement is incorrect about proteome analyses?
a) For BLAST, setting an effective database size appropriate for each search and program is important
b) Due to the large number of comparisons that must be made in these types of analyses and due to the volume of program output, the procedure must be automated on a local machine using Perl scripts or a similar method and a database system
c) BLAST is used for obtaining a correct statistical evaluation of alignment scores
d) BLAST does not give statistical evaluation of alignment scores
Answer: d [Reason:] Each protein encoded by the genome is used as a query in database similarity searches to identify similar database proteins, some having a known structure or function. Additional searches of EST databases can be used to identify additional relatives of the query sequence.
2. An all-against-all analysis requires first making a database of the proteome. This database is then sequentially searched by each individual protein sequence of the proteome using a rapid database similarity search tool such as _______
Answer: a [Reason:] P values of WU-BLAST are similar to E values of NCBI BLAST (Rubin et al. 2000) for values of P and E < 0.05. This analysis generates a matrix of alignment scores, each with an E value and corresponding alignment for each pair of proteins. Also, the E value of an alignment score is the probability that an alignment score as good as the one found would be observed between two random or unrelated sequences in a search of a database of the same size.
3. Evolutionary modeling can include a various types of analyses. Which is mostly not one of them?
a) The prediction of chromosomal rearrangements
b) Eu/Hetero-chromatin structures
c) Duplications at gene, chromosomal and full genome level
d) Duplications at the protein domain level
Answer: b [Reason:] Option b indicates the structural studies. Also as mentioned, analysis of the prediction of chromosomal rearrangements that preceded the present arrangement is done (e.g., a comparison of mouse and human chromosomes).
4. Which of the given statement is incorrect about Clusters of functionally related genes?
a) In microbial genomes, genes specifying a metabolic pathway may be contiguous on the genome where they are coregulated transcriptionally in an operon by a common promoter
b) In related organisms, gene order on the chromosome is least likely to be conserved
c) As the relationship between the organisms decreases, local groups of genes remain clustered together, but chromosomal rearrangements move the clusters to other locations
d) The function of a particular gene can sometimes be predicted, given the known function of a neighboring, closely linked gene
Answer: b [Reason:] In related organisms, both gene content of the genome and gene order on the chromosome are likely to be conserved.
5. Which of the given statement is incorrect about Orthologs?
a) In comparing two proteomes, a common standard is to require that for each pair of orthologs, the first of the pair is the best hit when the second is used to query the proteome of the first
b) To identify orthologs, each protein in the proteome of an organism is used as a query in a similarity search of a database comprising the proteomes of only one different organism
c) The best hit in each proteome is likely to be with an ortholog of the query gene
d) Orthologs are genes that are so highly conserved by sequence in different genomes that the proteins they encode are strongly predicted to have the same structure and function and to have arisen from a common ancestor through speciation
Answer: b [Reason:] To identify orthologs, each protein in the proteome of an organism is used as a query in a similarity search of a database comprising the proteomes of one or more different organisms.
6. In protein/domain analysis, each protein in the predicted proteome is again used as a query of a curated protein sequence database such as ____ in order to locate similar domains and sequences. To find orthologs, very low E value scores (E<10<20) for the alignment score and an alignment that includes 60–80% of the query sequence are generally required in order to avoid matches to paralogs.
Answer: d [Reason:] The domain composition of each protein is also determined by searching for matches in domain databases such as Interpro. The analysis reveals how many domains and domain combinations are present in the proteome, and reveals any unusual representation that might have biological significance. The number of expressed genes in each family can also be compared to the number in other organisms to determine whether or not there has been an expansion of the family in the genome.
7. In all-against-all self comparison, A comparison is made in which every protein is used as a query in a similarity search against a database composed of the rest of the proteome, and the significant matches are identified by a low expect value.
Answer: a [Reason:] Many proteins comprise different combinations of a common set of domains, proteins that align along most of their lengths (80% identity is a conservative choice). Hence they are chosen to select those that have a conserved domain structure.
8. Processed pseudogenes are also derived from a functional gene and they contain introns and a promoter.
Answer: b [Reason:] Processed pseudogenes are also derived from a functional gene, but they do not contain introns and lack a promoter; hence, they are not expressed. The origin of these pseudogenes is probably due to reverse transcription of the mRNA of the functional gene and insertion of the cDNA copy into a new chromosomal location by a LINE1 reverse transcriptase.
9. Pseudogenes are DNA sequences that were derived from distinct genes but which have acquired mutations that are deleterious to function in the same period of time.
Answer: b [Reason:] Pseudogenes are DNA sequences that were derived from a functional copy of a gene but which have acquired mutations that are deleterious to function. For e.g. the pseudogene TRY5 is similar to the nearby functional gene TRY4.
10. New gene functions are thought to be gained by duplication of an existing gene creating two tandem copies.
Answer: a [Reason:] Functional differentiation then occurs between the copies by mutation and selection. However, because most mutations are deleterious, and because only one gene copy may be needed for function, there is a strong tendency of one copy to accumulate mutations that render the gene nonfunctional.
Interview MCQ Set 5
1. In the program COGNITOR each protein in the proteome is used as a query of a database of protein clusters.
Answer: a [Reason:] The database was made by performing an all-by-all genome comparison across a spectrum of prokaryotic organisms and a portion of the yeast proteome. Orthologous pairs of sequence were then merged with clusters or orthologous pairs (COGs) for multiple proteomes.
2. WU-BLAST produces P scores and BLAST (NCBI) produces E scores where _____
a) E = ln (1 + P2)
b) E = ln (1 – P2)
c) E = ln (1 + P)
d) E = ln (1 – P)
Answer: d [Reason:] For values less than 0.05, E = P. The choice of a < 10-20 score is a conservative one for identification of orthologs that should have a similar domain structure.
3. In Proteolysis and fragment sequencing, Protein spots may be excised from a two-dimensional protein gel and subjected to a combination of amino acid sequencing and cleavage analyses using the techniques of mass spectrometry and high-pressure liquid chromatography.
Answer: a [Reason:] Genome regions that encode these sequences can then be identified and the corresponding gene located. A similar method may be used to identify the gene that encodes a particular protein that has been purified and characterized in the laboratory.
4. In Protein 2D gel Electrophoresis, Individual proteins produced by the genome can be separated to _____ by this method and specific ones identified by various _______
a) smaller extent, biochemical and immunological tests
b) a large extent, biochemical and immunological tests
c) a large extent, biochemical tests only
d) smaller extent, purely mechanical tests
Answer: b [Reason:] Moreover, changes in levels of proteins in response to an environment signal can be monitored in much the same way as a microarray analysis is performed. Microarrays only detect untranslated mRNAs, whereas a two-dimensional gel protein analysis detects translation products, thus revealing an additional level of regulation.
5. In Metabolic pathways and regulation, as genes are identified in a new genome sequence, some will be found that are known to act sequentially in a metabolic pathway or to have a known role in gene regulation in other organisms.
Answer: a [Reason:] From this information, the metabolic pathways and metabolic activities of the organism will become apparent. In some cases, the apparent absence of a gene in a well-represented pathway may lead to a more detailed search for the gene. Clustering of genes in the pathway on the genome of a related organism can provide a further hint as to where the gene may be located.
6. _______ of the Drosophila sequence is composed of TEs and _____ is heterochromatic regions that do not include genes.
a) one-fourth, one-third
b) one-fifth, one-fourth
c) one-sixth, one-eighth
d) one-sixth, one-third
Answer: d [Reason:] Hence, in the euchromatic regions, the gene density in the Drosophila genome is one gene per 9 kb. Despite the fact that the lower number of predicted genes in Drosophila is smaller than that of the other genomes, the amount of functional diversity, as evidenced by protein family representation, is similar.
7. Yeast is about ______ compact than E. coli.
a) fivefold, less
b) threefold, more
c) twofold, less
d) twofold, more
Answer: c [Reason:] Of the remaining genomes, C. elegans and A. thaliana have approximately the same density of genes (one gene per 6 kb). Drosophila is the least dense in this comparison (one gene per 14 kb).
8. The ________ are _______by genetic structure to retroviruses.
a) STR retrotransposons, related
b) LTR retrotransposons, related
c) STR transposons, related
d) LTR retrotransposons, not related
Answer: b [Reason:] There are three main subclasses of these TEs—the long terminal repeat (LTR) retrotransposons, retroposons, and retrovirus-like elements with LTRs. Class I elements encode a reverse transcriptase and use RNA mediated mechanisms of transcription.
9. Which of the given statement is incorrect?
a) As in an all-by-all protein comparison within a proteome, a matrix of alignment scores with E values is made, and the most closely related sequences in the two organisms are identified
b) To perform a between-proteome analysis, proteome databases are made for the known and predicted genes of two or more genomes
c) Each protein of one proteome is selected in turn as a query of the proteome of another organism or the combined proteome of a group of organisms
d) Each protein of one proteome is selected in turn as a query of the proteome of another single organism only
Answer: d [Reason:] This analysis can predict orthologs. In other words proteins have an identical function attributable to descent of the respective genes from a common ancestor.
10. The higher the E value, the more significant the alignment between a pair of matching sequences.
Answer: b [Reason:] The lower the E value, the more significant the alignment between a pair of matching sequences. The E value of an alignment score is the probability that an alignment score as good as the one found would be observed between two random or unrelated sequences in a search of a database of the same size.