Category: Objective Questions

Bioinformatics Multiple Choice Questions on “Protein Family Databases”.

1. Which of the following statements about COG is incorrect regarding its features?
A. Currently, there are 4,873 clusters in the COG databases derived from unicellular organisms
B. It is constructed by comparing protein sequences encoded in forty-three completely sequenced genomes, which are mainly from prokaryotes, representing thirty major phylogenetic lineages
C. The interface for sequence searching in the COG database is the COGnitor program, which is based on gapped BLAST
D. It is a protein family database based on structural classification
Answer: D
Explanation: COG which stands for Cluster of Orthologous Groups, is a protein family database based on phylogenetic classification. Because orthologous proteins shared by three or more lineages are considered to have descended through a vertical evolutionary scenario, if the function of one of the members is known, functionality of other members can be assigned.

2. Which of the following statements about InterPro is incorrect regarding its features?
A. Protein relatedness is defined by the P-values from the BLAST alignments
B. The most closely related sequences are grouped into the lowest level clusters
C. More distant protein groups are merged into higher levels of clusters
D. The outcome of this cluster merging is a tree-like structure of functional categories
Answer: A
Explanation: InterPro is a database of clusters of homologous proteins similar to COG. Protein relatedness is defined by the E-values from the BLAST alignments. The database further provides gene ontology information for protein cluster at each level as well as keywords from InterPro domains for functional prediction.

3. Pfam is available at four locations around the world. Which of the following is not one of them?
A. UK
B. Sweden
C. US
D. Japan
Answer: D
Explanation: Pfam is available at four locations around the world each providing a core set of functionality for accessing each family. They are US, UK, Sweden and France. Documentation on the content and use of Pfam is available via the web.

4. Which of the following is not a member database of InterPro?
A. SCOP
B. HAMAP
C. PANTHER
D. Pfam
Answer: A
Explanation: The signatures from InterPro come from 11 member databases viz. CATH-Gene3D, HAMAP, PANTHER, Pfam, PIRSF, PRINTS, ProDom, PROSITE, SMART, SUPERFAMILY, TIGRFAMs.

5. Which of the following statements about SCOP is incorrect regarding its features?
A. Proteins with the same shapes but having little sequence or functional similarity are placed in different super families, and are assumed to have only a very distant common ancestor
B. Proteins having the same shape and some similarity of sequence and/or function are placed in ‘families’, and are assumed to have a closer common ancestor
C. SCOP was created in 1994 in the Centre of Protein Engineering and the University College London
D. It aims to determine the evolutionary relationship between proteins
Answer: C
Explanation: SCOP, Structural Classification of Proteins, was created in 1994 in the Centre of Protein Engineering and the Laboratory of Molecular Biology. It was maintained by Alexey G. Murzin and his colleagues in the Centre for Protein Engineering until its closure in 2010 and subsequently at the Laboratory of Molecular Biology in Cambridge, England.

6. What is the source of protein structures in SCOP and CATH?
A. Uniprot
B. Protein Data Bank
C. Ensemble
D. InterPro
Answer: B
Explanation: The source of protein structures in SCOP is PDB (Protein Data Bank). PDB is a secondary database which means it has protein structures derived from primary databases that have the protein sequences. UNIPROT is a primary database.

7. Which of the following statements about SUPERFAMILY database is incorrect regarding its features?
A. Sequences can be submitted raw or FASTA format
B. Sequences must be submitted in FASTA format only
C. It searches the database using a superfamily, family, or species name plus a sequence, SCOP, PDB or HMM ID’s
D. It has generated GO annotations for evolutionarily closed domains and distant domains
Answer: B
Explanation: SUPERFAMILY is a database of structural and functional annotation for all proteins and genomes. It classifies amino acid sequences into known structural domains, especially into SCOP super families. Sequences can be amino acids, a fixed frame nucleotide sequence, or all frames of a submitted nucleotide sequence. Up to 1000 sequences can be run at a time.

8. Which of the following statements about PRINTS and ProDom databases is incorrect regarding its features?
A. PRINTS is a compendium of protein fingerprints
B. Usually the motifs do not overlap, but are separated along a sequence, though they may be contiguous in 3D-space
C. Current versions of ProDom are built using a novel procedure based on recursive BLAST searches
D. ProDom domain database consists of an automatic compilation of homologous domains
Answer: C
Explanation: Current versions of ProDom are built using a novel procedure based on recursive PSI-BLAST searches and not just BLAST searches. And PRINTS is indeed a compendium of protein fingerprints. A fingerprint is a group of conserved motifs used to characterise a protein family; its diagnostic power is refined by iterative scanning of UniProt.

9. Which of the following statements about CATH-Gene3D and HAMAP databases is incorrect regarding its features?
A. CATH-Gene3D describes protein families and domain architectures in complete genomes
B. In CATH-Gene3D the functional annotation is provided to proteins from single resource
C. HAMAP profiles are manually created by expert curators they identify proteins that are part of well-conserved bacterial, archaeal and plastid-encoded proteins families or subfamilies.
D. HAMAP stands for High-quality Automated and Manual Annotation of microbial Proteomes
Answer: B
Explanation: In CATH-Gene3D Protein families are formed using a Markov clustering algorithm, followed by multi-linkage clustering according to sequence identity. Mapping of predicted structure and sequence domains is undertaken using hidden Markov models libraries representing CATH and Pfam domains. Functional annotation is provided to proteins from multiple resources. Functional prediction and analysis of domain architectures is available at the website.

10. Which of the following statements about PANTHER and TIGRFAMs databases is incorrect regarding its features?
A. TIGRFAMs provides a tool for identifying functionally related proteins based on sequence homology
B. TIGRFAMs is a collection of protein families, featuring curated multiple sequence alignments, hidden Markov models (HMMs) and annotation
C. Hidden Markov models (HMMs) are not used in PANTHER
D. PANTHER is a large collection of protein families that have been subdivided into functionally related subfamilies, using human expertise
Answer: C
Explanation: In PANTHER the subfamilies model the divergence of specific functions within protein families, allowing more accurate association with function (human-curated molecular function and biological process classifications and pathway diagrams), as well as inference of amino acids important for functional specificity. Hidden Markov models (HMMs) are built for each family and subfamily for classifying additional protein sequences.

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Bioprocess Engineering Multiple Choice Questions on “Role of Diffusion in Bioprocessing”.

1. The size of eddy is proportional to the streamline flow.
A. True
B. False
Answer: B
Explanation: Turbulence in fluids produces bulk mixing on a scale equal to the smallest eddy size. Within the smallest eddies, flow is largely streamline so that further mixing must occur by diffusion of fluid components. Mixing on a molecular scale therefore relies on diffusion as the final step in the mixing process.

2. Diffusion maintains the concentration difference between high and low concentrations.
A. True
B. False
Answer: B
Explanation: Molecular diffusion is the movement of component molecules in a mixture under the influence of a concentration difference in the system. It occurs in the direction required to destroy the concentration difference. If the gradient is maintained by constantly supplying material to the region of high concentration and removing it from region of low concentration, diffusion will continue.

3. The total rate of oxygen uptake is proportional to the concentration of __________
A. Medium
B. Liquid
C. Number of cells
D. Gas
Answer: C
Explanation: The concentration of cell increases during course of batch culture and the total rate of oxygen uptake is proportional to the no. of cell present. The rate of oxygen consumption per cell also known as oxygen uptake rate (OUR):
Q_o = q_ox
Where: Q_o = oxygen uptake rate per volume broth (gL^-1 s^-1)
q_o = specific oxygen transfer rate (gg^-1 s^-1).

4. Which one of the following is not the type of transfer in molecular diffusion?
A. Density
B. Mass
C. Momentum
D. Energy
Answer: A
Explanation: The molecular transfer equations of Newton’s law for fluid momentum, Fourier’s law for heat, and Fick’s law for mass are very similar. One can convert from one transfer coefficient to another in order to compare all three different transport phenomena.

5. If the rain drop drags and enter into the atmosphere, which type of diffusion will it experience?
A. Energy
B. Osmosis
C. Momentum
D. Mass
Answer: C
Explanation: The drag experienced by a rain drop as it falls in the atmosphere is an example of momentum diffusion (the rain drop loses momentum to the surrounding air through viscous stresses and decelerates).

6. The S.I. unit of thermal diffusivity is ___________
A. m/s
B. m²/s
C. m/s²
D. m²/s²
Answer: B
Explanation: The units of thermal diffusivity are length²/time and a common set of SI units is m²/sec (the use of cm or mm as the length scale is frequent as it allows reporting of values closer to the value one).

7. In the below equation, what does “D” represents?

A. Length of the membrane
B. Distance
C. Diffusion
D. Thickness of the membrane
Answer: D
Explanation: It states that the rate of diffusion of a gas across a membrane is:
▪ Constant for a given gas at a given temperature by an experimentally determined factor, K.
▪ Proportional to the surface area over which diffusion is taking place, A.
▪ Proportional to the difference in partial pressures of the gas across the membrane, P₂ – P₁.
▪ Inversely proportional to the distance over which diffusion must take place, or in other words the thickness of the membrane, D.

8. A bioreactor of working volume 50 m³ produces a metabolite (X) in batch culture under given operation conditions form a substrate (S). The final concentration of metabolite at the end of each run was 1.1kg m^-3. The bioreactor was operated to complete 60 runs in each year. What will be the annual output of the system (production of metabolite (X)) in Kg per year?
A. 70
B. 66
C. 77
D. 60
Answer: B
Explanation: Volume = 50 m³
Total output = no of runs * product = 60 * 1.1 = 66.

9. Example of steady-state diffusion is _______________
A. Hydrogen purification by palladium sheets
B. Doping semi-conductors
C. Corrosion resistance of aluminium
D. Decarburization
Answer: A
Explanation: A practical example of steady-state diffusion – the purification of hydrogen gas. One side of a thin sheet of palladium metal is exposed to the impure gas composed of hydrogen and other gaseous species such as nitrogen, oxygen, and water vapor. The hydrogen selectively diffuses through the sheet to the opposite side, which is maintained at a constant and lower hydrogen pressure.

10. Fick’s second law is applicable to steady –state diffusion?
A. True
B. False
Answer: B
Explanation: Non- steady state diffusion – Concentration of solute atoms at any point in metal changes with time in this case. And the Fick’s second law states that rate of compositional change is equal to diffusivity times the rate of change of concentration gradient.

11. The most influencing factor of diffusivity of molecules is _______________
A. Lattice structure
B. Temperature
C. Presence of defects
D. Diffusing species
Answer: B
Explanation: Temperature. As temperature increases the average kinetic energy of particles increases. The diffusion coefficient is a physical constant dependent on molecule size and other properties of the diffusing substance as well as on temperature and pressure.

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Bioprocess Engineering Multiple Choice Questions on “Medium Optimization”.

1. What does X in “Xⁿ” represents in the large number of experiments?
A. Number of variables
B. Number of levels
C. Representation of any element
D. Number of elements
Answer: B
Explanation: To make a full factorial search which would examine each possible combination of independent variable at appropriate levels could require a large number of experiments, xⁿ, where x is the number of levels and n is the number of variables. This may be quite appropriate for three nutrients at two concentrations but not for six nutrients at three concentrations.

2. In the Plackett-Burman method, the evaluation of x-1 variables by x experiments, where x must be the multiple of?
A. 2
B. 4
C. 6
D. 8
Answer: B
Explanation: The Plackett-Burman method allows for the evaluation of x-1 variables by x experiments, x must be a multiple of 4, e.g. 8, 12, 16, 20, 24, etc. Normally one determines how many experimental variables need to be included in an investigation and then selects the Plackett-Burman design which meets that requirement most closely in multiples of 4.

3. Experimental error and dummy variables in Placket-Burman method are linked.
A. True
B. False
Answer: A
Explanation: Any factors not assigned to a variable can be designated as dummy variables. Alternatively, factors known to not have any effect may be included and designated as dummy variables. The incorporation of dummy variables into an experiment makes it possible to estimate the variance of an effect (experimental error).

4. The response surface optimization technique is also given by Plackett- Burman, which is another stage in medium optimization.
A. True
B. False
Answer: B
Explanation: The response surface optimization techniques were introduced by Box and Wilson in 1951.

5. The contour plot is __________
A. 1-D
B. 2-D
C. 3-D
D. Any dimension
Answer: B
Explanation: The axes of the contour plot are the experimental variables and the area within the axes is termed the response surface. To construct a contour plot, the results of a series of experiments employing different combinations of variables are inserted on the surface of the plot at the points delineated by the experimental conditions. Points giving the same results are then joined together to make a contour line. In its simplest form two variables are examined and the plot is two dimensional.

6. Is there any serum named as “Chicken serum”?
A. True
B. False
Answer: A
Explanation: Chicken serum is collected from healthy birds slaughtered for human consumption. Chicken serum is tested specifically for cytotoxicity. Test samples are examined for the ability to support the attachment and proliferation of three adherent cell lines. The test and reference cultures are monitored for evidence of nutritional deficiency, abnormal morphology, or cytotoxicity.

7. Is serum-free media beneficial?
A. True
B. False
Answer: A
Explanation: The advantages of removing serum from media include:
i) More consistent and definable medium composition to reduce batch variation.
ii) Reduction in potential contamination to make sterility easier to achieve.
iii) Potential cost savings because of cheaper replacement components.
iv) Simplifying downstream processing because the total protein content of the medium has been reduced.

8. What do you mean by the term “Trace elements”?
A. Needed in small amount
B. Needed at medium amount
C. Needed at very high amount
D. The elements which are discovered
Answer: A
Explanation: A chemical element required only in minute amounts by living organisms for normal growth.

9. Hybridoma technique is not required for antibody production.
A. True
B. False
Answer: B
Explanation: Hybridoma technology is a method for producing large numbers of identical antibodies (also called monoclonal antibodies).The myeloma cell line that is used in this process is selected for its ability to grow in tissue culture and for an absence of antibody synthesis.

10. What is Hepes?
A. An animal culture
B. A buffer
C. A type of non-ionic element
D. A horse serum
Answer: B
Explanation: HEPES (4-(2-hydroxyethyl)-1-piperazineethanesulfonic aciD. is a zwitterionic organic chemical buffering agent; one of the twenty Good’s buffers. HEPES is widely used in cell culture, largely because it is better at maintaining physiological pH despite changes in carbon dioxide concentration (produced by cellular respiration) when compared to bicarbonate buffers, which are also commonly used in cell culture.

11. Which of the following is not a foaming agent?
A. Sodium lauryl sulfate
B. Ammonium lauryl sulfate
C. Titanium hydride
D. Pluronic f-68
Answer: D
Explanation: Pluronic F68 is used in cell culture as a stabilizer of cell membranes protecting from membrane shearing and additionally acts as an anti-foaming agent.

12. Casein is converted to yoghurt because of _____________
A. Lactic acid
B. Salicylic acid
C. Benzoic acid
D. Picric acid
Answer: A
Explanation: Compared to other milk products such as cheese, ice cream, or butter, yogurt contains all milk proteins and salts whereas the milk sugar (lactose) is mostly converted into lactic acid which gives yogurt a pleasant acidic flavor.

13. A trickling filter is used for –
A. Antibiotic production
B. Beer production
C. Waste water treatment
D. Citric acid manufacturing
Answer: C
Explanation: A trickling filter, also called trickling biofilter, biofilter, biological filter and biological trickling filter, is a fixed-bed, biological reactor that operates under (mostly) aerobic conditions. Pre-settled wastewater is continuously ‘trickled’ or sprayed over the filter.

14. Blood agar is an example of which type of media?
A. Selective
B. Differential
C. Enriched
D. Enrichment
Answer: B
Explanation: Blood agar is a differential medium that distinguishes bacterial species by their ability to break down the red blood cells included in the media. Blood agar is often used to distinguish between the different species of pathogenic Streptococcus bacteria.

15. Sodium carboxy methyl cellulose is not a type of non-nutritional media supplements.
A. True
B. False
Answer: B
Explanation: Sodium carboxy methyl cellulose may be added to media at 0.1% to help to minimize mechanical damage caused by the shear force generated by the stirrer impeller.

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Chemical Reaction Engineering Multiple Choice Questions & Answers on “Reaction Rates – 1″.

1. The factors affecting the rate of homogeneous reaction are ____
A. Temperature only
B. Pressure only
C. Reactant Concentration only
D. Temperature, pressure and reactant concentration
Answer: D
Explanation: The rate constant in the rate expression is a function of temperature. Increasing pressure decreases the collisions between reactant molecules. This decreases the rate of reaction. Increasing the initial concentration of reactant increases the reaction rate. Hence, reaction rate is controlled by temperature and pressure conditions and initial concentration of reactant.

2. Which of the following is the correct expression for the rate of a reaction?
A. (frac{Moles , of , product , formed}{Volume , of , fluid×Time} )
B. (frac{Moles , of , reactant , initially , taken}{Volume , of , fluid×Time} )
C. (frac{Moles , unreacted}{Volume , of , fluid×Time} )
D. (frac{Moles , of , product , formed}{Volume , of , fluid} )
Answer: A
Explanation: Rate of the reaction is the number of moles of the reactant component disappearing per unit volume per unit time. The moles of the product formed are the number of moles of the reactant species disappearing during the course of reaction.

3. The rate of cellular reactions expressed as moles A disappearing/(m³.s) is in the range of ____
A. 10^-3-10^-4
B. 10²
C. 0.1
D. 10⁹
Answer: A
Explanation: The cellular reactions in living organisms occur very slowly. Hence, the rate is of the order 10^-3-10^-4 moles disappearing/(m³.s).

4. For the reaction aA+ bB → rR, which of the following is true?
A. (frac{-r_A}{a})=(frac{-r_B}{b}) ≤ (frac{r_R}{r} )
B. (frac{-r_A}{a}) ≥(frac{-r_B}{b}) ≤ (frac{r_R}{r} )
C. (frac{-r_A}{a})=(frac{-r_B}{b}) ≤ (frac{r_R}{r} )
D. (frac{-r_A}{a})≤(frac{-r_B}{b}) ≤ (frac{r_R}{r} )
Answer: C
Explanation: The rates of degradation of reactants and formation of product are related to each other as (frac{-r_A}{a} = frac{-r_B}{b} = frac{r_R}{r} ), where a, b and c denote the stoichiometry. The rate of disappearance of any reactant in turn is the rate of formation of products.

5. The rate of a reaction cannot be expressed in terms of ____
A. Volume of reacting fluid
B. Volume of solid
C. Amount of product
D. Interfacial surface
Answer: C
Explanation: The rate of the reaction can be expressed in terms of unit volume of reacting fluid, based on unit interfacial area and unit volume of solid. The amount of product formed has no influence on the reaction rate.

6. Order of a reaction is ____
A. Number of molecules of reactants taking part in the reaction
B. Power of any one of the reactant concentrations
C. Concentration of intermediate species formed
D. Sum of the powers of the concentrations of all the reactants
Answer: D
Explanation: The order of a reaction with respect to a given substance is the power to which its concentration term is raised in the rate equation. If there is more than one reactant molecules involved in the reaction, then the order of the reaction is the sum of the powers of concentrations of all reacting species in the rate expression.

7. The rate expression for a homogeneous reaction comprises of ____
A. A concentration dependent term only
B. A temperature dependent term only
C. A concentration dependent term and a temperature dependent term
D. A catalyst weight dependent term
Answer: C
Explanation: (-r_A) = kCⁿ,
Where,
k: Rate constant
C: Concentration
Rate constant, k is a function of temperature.

8. The number of molecules involved in an elementary reaction is termed as ____
A. Molecularity
B. Order of reaction
C. Unimolecular reaction
D. Rate of reaction
Answer: A
Explanation: Molecularity of an elementary reaction is the number of molecules of the reactant taking part in the reaction. Order of a reaction is the sum of the powers of the concentrations of all the reactants. Unimolecular reactions involve only one reactant. Rate of a reaction is the number of moles of the reactant component disappearing per unit volume per unit time.

9. Which of the following is true about elementary reactions?
A. They occur in multiple steps
B. They are complex in nature
C. Order of elementary reaction is an integer
D. All first order reactions are elementary
Answer: C
Explanation: The order of an elementary reaction can never take fractional values. Elementary reactions occur in a single step. First order reactions can be elementary or non- elementary.

10. The unit of frequency factor in Arrhenius equation is ____
A. (frac{mol}{m^3} )
B. Same as that of rate constant
C. (frac{mol}{m^3×s} )
D. mol
Answer: B
Explanation: The unit of frequency factor in Arrhenius equation is same as that of rate constant.
Arrhenius equation is, k = A e^-Ea/RT,
k: Rate constant
A: Frequency factor
The exponent term in Arrhenius equation gives an integer. Hence, unit of A depends on that of k.

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