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 “Large – Scale Production of Enzymes”.

1. The inactive cells are advantageous for enzyme activity.
A. True
B. False
Answer: A
Explanation: In some cases, it may be more advantageous to use inactive (dead or resting) cells with the desired enzyme activity in immobilized form. This approach eliminates costly enzyme separation and purification steps and is therefore economically more feasible.

2. Which of the following does not produces “Proteases”?
A. Bacillus
B. Rhizopus
C. Mucor
D. Bacillus coagulans
Answer: D
Explanation: A process in which a mutant atypical Bacillus coagulans strain is cultivated in a growth medium free of xylose. The invention relates to glucose isomerase, to methods for the production of this enzyme and to enzymatic isomerization of glucose to fructose with glucose isomerase.

3. Cellulase is used in which type of industry?
A. Food industry
B. Paper industry
C. Biofuel industry
D. Chemical industry
Answer: C
Explanation: Cellulase is used in biofuel industry and its application is class of enzymes that degrade cellulose to glucose monomers.

4. Which of the following is not included in immobilization process?
A. Absorption
B. Adsorption
C. Entrapment
D. Affinity
Answer: A
Explanation: Despite their excellent catalytic capabilities, enzymes and their properties must be improved prior to industrial implementation in many cases. Some aspects of enzymes that must be improved prior to implementation are stability, activity, inhibition by reaction products, and selectivity towards non-natural substrates. This may be accomplished through immobilization of enzymes on a solid material, such as a porous support. Immobilization of enzymes greatly simplifies the recovery process, enhances process control, and reduces operational costs. Many immobilization techniques exist, such as adsorption, covalent binding, affinity, and entrapment.

5. In Upstream processes, process development increases the mRNA hydrolysis and proteolysis?
A. True
B. False
Answer: B
Explanation: Process development is typically performed after genetic modification of the source organism, and involves the modification of the culture medium and growth conditions. In many cases, process development aims to reduce mRNA hydrolysis and proteolysis.

6. Which of the following is not an upstream process?
A. Selection of a suitable enzyme
B. Process development
C. Concentration and primary purification of enzymes
D. Large scale production
Answer: C
Explanation: Downstream processes are those that contribute to separation or purification of enzymes. Depending on the intended use of the enzyme, different levels purity is required. For example, enzymes used for diagnostic purposes must be separated to a higher purity than bulk industrial enzymes to prevent catalytic activity that provides erroneous results.

7. Which of the following purified enzyme is used in pharmaceutical industry?
A. Subtilisin
B. Novozym-435
C. Bromelain
D. Asparaginase
Answer: D
Explanation: Asparaginase enzyme as a desired product is used in pharmaceutical industry as an application for lymphatic cancer therapeutic.

8. Which type of fermentation is used for large scale manufacturing of enzymes?
A. Solid-state fermentation
B. Submerged fermentation
C. Solid-Gas state fermentation
D. Gas-state fermentation
Answer: B
Explanation: Submerged fermentation is a method of manufacturing biomolecules in which enzymes and other reactive compounds are submerged in a liquid such as alcohol, oil or a nutrient broth. The process is used for a variety of purposes, mostly in industrial manufacturing.

9. Which enzyme was first produced industrially?
A. Bacteria enzyme
B. Yeast enzyme
C. Fungal enzyme
D. Streptomyces
Answer: C
Explanation: Microbial enzymes have been utilized for many centuries without knowing them fully. The first enzyme produced industrially was taka-diastase (a fungal amylase) in 1896, in United States. It was used as a pharmaceutical agent to cure digestive disorders.

10. The production of enzyme is mostly carried out by?
A. Batch fermentation
B. Continuous fermentation
C. Fed-batch fermentation
D. Semi-batch fermentation
Answer: A
Explanation: The medium can be sterilized by employing batch or continuous sterilization techniques. The fermentation is started by inoculating the medium. The growth conditions (pH, temperature, O2 supply, nutrient addition) are maintained at optimal levels. The froth formation can be minimised by adding antifoam agents. The production of enzymes is mostly carried out by batch fermentation and to a lesser extent by continuous process.

11. Which is the inducer of enzyme invertase?
A. Starch
B. Sucrose
C. Galactosidases
D. Fatty acids
Answer: B
Explanation: Invertase is an enzyme that catalyzes the hydrolysis (breakdown) of sucrose. The resulting mixture of fructose and glucose is called inverted sugar syrup. For industrial use, invertase is usually derived from yeast. The inducer compounds are expensive and their handling (sterilization, addition at specific time) also is quite difficult.

12. What do you mean by “Nutrient repression”?
A. Inhibition of unwanted enzyme production
B. Production of unwanted enzymes
C. Inhibition of cell nutrients
D. Production of waste
Answer: A
Explanation: The native metabolism of microorganism is so devised that there occurs no production of unnecessary enzymes. In other words, the microorganisms do not synthesize enzymes that are not required by them, since this is a wasteful exercise. The inhibition of unwanted enzyme production is done by nutrient repression. The nutrients may be carbon, nitrogen, phosphate or sulfate suppliers in the growth medium. For large scale production of enzymes, nutrient repression must be overcome.

13. What is the method of screening?
A. To improve the microbial strain
B. To improve the growth of an enzyme
C. To choose appropriate microorganisms for the desired enzyme
D. To determine the optimum conditions for growth of microbes
Answer: C
Explanation: Screening is one of the key optimization parameters to understand the dynamics of the process, allowing for rapid understanding and enhancement of process conditions by analyzing culture metabolic rates and metabolites.

14. System of reaction in which no reactant leaves reaction mixture is termed as ___________
A. Open system
B. Closed system
C. Semi-open system
D. Partially closed system
Answer: B
Explanation: One of the fundamental foundations of bioprocess system design is the use of “closed” systems for production. As a key element of Good Manufacturing Practice (GMP) compliance, closed systems and equipment are utilized to prevent contamination of the product.

15. Which of the following is true for single cell protein?
A. Algae cannot be used in single cell protein
B. It is produced through fermentation
C. It does not contain carbohydrates and vitamins
D. Its utilization increases environmental pollution
Answer: B
Explanation: Single-cell proteins develop when microbes ferment waste materials (including wood, straw, cannery, and food-processing wastes, residues from alcohol production, hydrocarbons, or human and animal excreta). The problem with extracting single-cell proteins from the wastes is the dilution and cost. They are found in very low concentrations, usually less than 5%. Engineers have developed ways to increase the concentrations including centrifugation, flotation, precipitation, coagulation, and filtration, or the use of semi-permeable membranes.

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Bioprocess Engineering online test focuses on “Guidelines for Choosing Host-Vector Systems”.

1. Post-translational modification includes which type of protein modification?
A. Ionic
B. Non-covalent
C. Covalent
D. Metallic
Answer: C
Explanation: Post-translational modification (PTM) refers to the covalent and generally enzymatic modification of proteins following protein biosynthesis. Proteins are synthesized by ribosomes translating mRNA into polypeptide chains, which may then undergo PTM to form the mature protein product. PTMs are important components in cell signaling.

2. What is the full form of GRAS in the regulatory approval of food products?
A. Generally regarded as sacred
B. Generally recognized as safe
C. Generally recommended as standard
D. Generally recognized standard
Answer: B
Explanation: GRAS stands for in the regulatory approval of food products as “Generally recognized as safe”.

3. E.coli is not a perfect host due to __________
A. Non-proteolytic degradation
B. Proteolytic degradation
C. Retained intercellularly
D. Production at medium levels
Answer: B
Explanation: E. coli is not a perfect host. The major problems result from the fact E. coli does not normally secrete proteins. When proteins are retained intracellularly and produced at high levels, the amount of soluble active protein present is usually limited due to either proteolytic degradation or insolubilization into inclusion bodies.

4. Heat shock method uses ___________
A. Calcium rich environment
B. Magnesium rich environment
C. Potassium rich environment
D. Sodium rich environment
Answer: A
Explanation: In the laboratory, bacterial cells can be made competent and DNA subsequently introduced by a procedure called the heat shock method. Heat shock transformation uses a calcium rich environment provided by calcium chloride to counteract the electrostatic repulsion between the plasmid DNA and bacterial cellular membrane.

5. Inclusion bodies are devoid of proteins.
A. True
B. False
Answer: B
Explanation: Inclusion bodies, sometimes called elementary bodies, are nuclear or cytoplasmic aggregates of stable substances, usually proteins. They typically represent sites of viral multiplication in a bacterium or a eukaryotic cell and usually consist of viral capsid proteins.

6. Resolubilization is generally for the chemical alternations.
A. True
B. False
Answer: B
Explanation: The protein in the inclusion body is misfolded. The misfolded protein has no biological activity and is worthless. If the inclusion bodies are recovered from the culture, the inclusion bodies can be resolubilized and activity restored. When resolubilization is straightforward and recoveries are high, the formation of inclusion bodies can be advantageous, as it simplifies the initial steps of recovery and purification. It is important that during resolubilization the protein be checked by several analytical methods to ensure that no chemical modifications have occurred. Even slight changes in a side group can alter the effectiveness of the product.

7. Endotoxins are intracellular not harmful.
A. True
B. False
Answer: B
Explanation: If the product is retained intracellularly, then the cell must be lysed (broken) during recovery. Lysis usually results in the release of endotoxins (or pyrogens) from E. coli. Endotoxins are lipopolysaccharides (found in the outer membrane) and can result in undesirable side effects (e.g., high fevers) and death. Thus, purification is an important consideration.

8. Pyrogen is __________
A. Antibiotic
B. Non-toxic
C. Drug
D. Fever inducer
Answer: D
Explanation: Pyrogen (fever) is a fever inducing substance.

9. Secretion and excretion are two different terms.
A. True
B. False
Answer: A
Explanation: Secretion is defined here as the translocation of a protein across the inner membrane of E. coli. Excretion is defined as release of the protein into the extracellular compartment.

10. B. subtilis has a number of problems that have hindered its commercial adoption mainly due to:
A. Increased levels of proteins
B. Decreased levels of proteins
C. Increased levels of proteases
D. Decreased levels of proteases
Answer: C
Explanation: A primary concern has been that B. subtilis produces a large amount and variety of proteases. These proteases can degrade the product very rapidly. Mutants with greatly reduced protease activity have become available, but even these mutants may have sufficient amounts of minor proteases to be troublesome. B. subtilis is also much more difficult to manipulate genetically than E. coli because of a limited range of vectors and promoters.

11. What do you mean by glycosylation?
A. Addition of sugar
B. Non-addition of sugar
C. Lysis of sugar moieties
D. Blockage of sugar molecules
Answer: A
Explanation: Glycosylation is a critical function of the biosynthetic-secretory pathway in the endoplasmic reticulum (ER) and Golgi apparatus. Approximately half of all proteins typically expressed in a cell undergo this modification, which entails the covalent addition of sugar moieties to specific amino acids.

12. What is the full form of AOX in Pichia pastoris expression system?
A. Artificial oxidase
B. Acetone oxidase
C. Alcohol oxidase
D. Acetyl oxidase
Answer: C
Explanation: Pichia pastoris has two alcohol oxidase genes, Aox1 and Aox2, which have a strongly inducible promoter. These genes allow Pichia to use methanol as a carbon and energy source. The AOX promoters are induced by methanol and are repressed by e.g. glucose. Usually the gene for the desired protein is introduced under the control of the AOX1 promoter, which means that protein production can be induced by the addition of methanol.

13. Transformed cell lines are immortal.
A. True
B. False
Answer: A
Explanation: Cells that can be propagated indefinitely are called continuous, immortal, or transformed cell lines. Cancer cells are naturally immortal. All cancerous cell lines are transformed, although it is not clear whether all transformed cell lines are cancerous.

14. Baculovirus infects insect cell lines and are also pathogenic to humans.
A. True
B. False
Answer: B
Explanation: The baculovirus that infects insect cells is an ideal vector for genetic engineering, because it is nonpathogenic to humans and has a very strong promoter that encodes for a protein that is not essential for virus production in cell culture. The insertion of a gene under the control of this promoter can lead to high expression levels (40% of the total protein as the target protein).

15. Plant cell cultures are better than animal cultures.
A. True
B. False
Answer: A
Explanation: Plant cell cultures, compared to animal cell cultures, grow to very high cell density, use defined media, and are intrinsically safer.

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