AYYA NADAR JANAKI AMMAL COLLEGE (Autonomous), SIVAKASI M.Sc.

BIOINFORMATICS DEGREE COURSE THIRD SEMESTER CORE PAPER HF312 GENOMICS AND PROTEOMICS (For those admitted in June 2008 and later) MULTIPLE CHOICE QUESTIONS 1. What is a genome? a) An organism's complete genetic material b) The gene sequence involved in genetic recombination c) genetic fission d) allelo typing [ a ] 2. Shotgun cloning differs from the clone-by-clone method in which of the following ways? a. Genetic markers are used to identify clones in shotgun cloning. b. Computer software assembles the clones in the clone-by-clone method. c.The entire genome is sequenced in the clone-by-clone method, but not in shotgun sequencing d. No genetic or physical maps of the genome are needed [ d ] 3. Which bacterial genome was the first to be completely sequenced? a. E. coli b. Streptococcus pneumoniae c. Haemophilus influenzae d. Mycobacterium tuberculosis [ c ] 4. The study of the molecular organization of genomes, their information content and the gene products they encode a. Genetics b. Genomics c. Ergonomics d. Proteomics [ b ] 5. Celera is: a) An Italian government funded project to isolate the genes b) A genetically modified celery seed c) The company founded by Craig Venter d) DNA sequencing method [ c ] 6. Who is most likely to win a Nobel Prize for sequencing the human genome? a. Frances Collins b. Tony Blair c. No one d. Bill Clinton [ b ] 7. The finished human genome sequence will be a. Available for a fee on the internet as an insomnia treatment b. Available free of charge on the internet c. Serialized in the Daily Telegraph d. Read out by the BBC on Saturday afternoons in place of Grandstand [ b ] 8. What is C. elegans? a. A part of the male reproductive system b. Iceland's top boy band c. A species of worm d. A new leisurewear range from Calvin Klein [ c ] 9. What causes many diseases? a. SNP b.Stress c. Tiny mutations in our genes d. Supermodels [ c ] 10. Who are Crick and Watson?

a. The British family firm which invented the first gene sequencing machine b. A firm of lawyers specialising in gene patenting c. The Anglo-American scientific team who discovered the structure of DNA d. A popular singing pair from the 90s [ c ] 11. Which type of genomics studies the physical nature of genomes? a. Comparative genomics b. Structural genomics c. Functional genomics d. Pharmacogenomics [ b ] 12. The whole-genome shotgun sequencing approach depends primarily on a. rapidly sequencing thousands of small randomly cloned fragments b. methodical sequencing a few large cloned fragments of DNA c. sequencing the bacterial chromosome while it is still intact d. sequencing a small clone fragments [ b ] 13. Which of the following is sequence assembler? a. ARACHINE b. PHPRED c. JPRED d. BIND [ a ] 14. What outcome of genetics research is likely to have the biggest impact on society in the near future? a. Gene therapy b. Personalised medicine c. Most diseases will be curable d. Cloning [ a ] 15. Which type of genomics studies the transcripts and proteins expressed by a genome? a. Comparative genomics b. Structural genomics c. Functional genomics d. Pharmacogenomics [ c ] 16. Which type of genomics studies the similarities and differences among the genomes of multiple organisms? a. Comparative genomics b. Structural genomics c. Functional genomics d. Pharmacogenomics [ a ] 17. Who developed the DNA sequencing approach first using dideoxynucleoside triphosphates in DNA synthesis? a. Pauling b. Watson c. Sanger d.Craig Ventor [ c ] 18. How are the four different bases distinguished in automated sequencing systems? a. different radioactive tag b. distinctive fluorescent tag c. different colors d. unique antibody bound to it [ b ] 19. Contigs are a. overlapping genes b. sequence gaps c. physical gaps d. mapped segments [ a ] 20. Scaffolds are a. physical gaps b. sequence gaps c. set of contigs d. set of cloned segments [ a ] 21. Dideoxy nucleoside triphosphate a. will terminate DNA synthesis when incorporated into a growing DNA strand b. has an oxygen at the 3' carbon c. cannot bind to a growing DNA chain d. can form a sugar phosphate bond with a new nucleoside triphosphate [ a ]
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22. In manual Sanger sequencing, _____ sequencing reactions are performed. a. Four c. Two b. One d. Five [ a ] 23. Manual DNA sequencing gels are read from _____. a. the top down b. the bottom up c. from the right side d. from backside using infrared light [ b ] 24. The DNA sequence obtained by both the manual and automatic sequencing corresponds to: a. the complementary DNA strand b. the tRNA c. the template DNA strand d. the messenger RNA [ a ] 25. How many nucleotides are needed to code for a protein with 450 amino acids a. at least 450 b. at least 150 c. at least 900 d. at least 1,350 [ d ] 26. Active genes are associated with the loosely packed chromatin called __________. a. leucine zippers b. heterochromatin c. euchromatin d. heterodimers [ c ] 27. Bacteria use restriction enzymes to _____. a. synthesize RNA b. destroy foreign protein c. synthesize proteins d. destroy foreign DNA [ d ] 28. What is the approximate percentage of repetitive DNA sequences in human DNA? a. 20 to 30% b. 30 to 40% c. 40 to 50% b. 10 to 20% [ a ] 29. How many bases can be sequenced by Manual DNA sequencing? a. 70 b. 700 c. 5000 d. 7000 [ b ] 30. If we want to use DNA chip technology to determine which protein coding genes are expressed in heart vs lung tissue, what do we need to extract from these tissue? a. cDNA b. rRNA c. mRNA d.dsDNA [ c ] 31. As the complexity of an organism increases, all of the following characteristics emerge except __________. a. the gene density decreases b. the number of introns increases c. the gene size increases d. an increase in the number of chromosomes [ d ] 32. Why didn't Mendel find linkage? a. Some genes were linked, but they were too close together to cross over. b. All seven genes were on separate chromosomes. c. Mendel did detect linkage. He discovered this genetic phenomenon. d. Some genes were linked, but they were too far apart for crossing over to be distinguished from independent assortment [ d ] 33. Techniques used to identify the location of genes on a chromosome include __________. a.FISH b. repetitive DNA studies c. electrophoresis d.X-ray diffraction analysis [ a ]
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34. The human genome project was started in the Year a) 1980 b) 1990 c) 2000 d) 1985 [ b ] 35. If you unraveled the DNA in a single human cell, how long would it be? a. Long enough to reach the moon and back b. Exactly one furlong c. 500 miles d. Roughly the height of WTC [ a ] 36. If you have three genes (A, B, and C) linked on the same chromosome, how can you determine the gene order? a. Look for double crossover phenotypes involving the wild type and mutant alleles of genes A, B, and C. b. Look for single crossover phenotypes involving the wild type and mutant alleles of genes A, B, and C. c. Look for parental phenotypes. d. You cannot determine gene order by looking at the results of a cross. [ a ] 37. Genes A and B are farther apart than are genes A and C, and all three are linked. What cannot be concluded? a. B might be between A and C. b. C might be between A and B. c. A might be between B and C. d. More crossovers will occur between A and B than between A and C. [ a ] 38. Written out in its entirety, the deciphered genome would fill a. 200 telephone directories b. Enough telephone directories to fill the British Library c. A telephone directory d. 2000 telephone directories [ a ] 39. The field that is concerned with the management and analysis of biological data using computers a. Statistics b. Proteomics c. Genomics d. Bioinformatics [ d ] 40. Which of these organisms has the smallest genome? a. Haemophilus influenzae b. Mycoplasma genitalium c. Mycobacterium tuberculosis d. E. coli [ b ] 41. The minimum set of genes required for life is approximately: a. 50-100 genes b. 250-350 genes c. 1000-1500 genes d. 2000-2500 genes [ b ] 42. Deinococcus radiodurans is able to survive massive exposure to radiation because a. it produces a thick shell which acts as a shield from the radiation b. it has unique DNA repair mechanisms c. it has many copies of genes encoding DNA repair d. it produces thick cell wall [ a ] 43. Small solid supports onto which are spotted hundreds of thousands of tiny drops of DNA that can be used to screen gene expression.
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a. DNA microarrays b. cloning library c. Southern blot d. Western blot [ a ] 44. Bacteria use restriction enzymes to _____. a. synthesize RNA b. destroy foreign protein c. synthesize proteins d. destroy foreign DNA [ d ] 45. All of the following may play a role in determining whether or not a gene is transcribed except: a. the TATA box b.promoter regions in the DNA c. DNA methylation d.microtubules [ d ] 46. Y2H method is used to study------a. protein-protein interaction b. DNA-protein interaction c. DNA DNA interaction d. both a and b [ d ] 47. Yeast two-hybrid method is based on --------------------,the eukaryotic activator a. GAL4 b.TATA Box c. SW15 d.SBF [ a ] 48. What is the size of Mouse genome? a. 4.6 Mb b. 3200Mb c. 121Mb d. 3300Mb [ d ] 49. The size of D.melanogaster genome is a. 4.6 Mb b. 320Mb c. 121Mb d. 180Mb [ d ] 50. A.thaliana is -------------------a. ornamental plant b. non-flowering plant c. flowering plant d. shrubs [ c ] 51. Related genes that have diverged to provide separate functions in the same species are refered as -------------a. orthologs b. paralogs c. homologs d. xenologs [ b ] 52. Name the proteins involved in Y2H a.actin & myosin b.Bait & Prey c. activator & repressor d.binding and activating domain [ b ] 53. SAGE is used to study the Yeast -------------a. Sporulation b.Proteins c. genes d. RNA [ a ] 54. The number of mRNA genes present in S.cereviciae is ---------a. 600 b. 6000 c. 60 d. 60,000 [ b ] 55. The size of E.coli genome is a. 4.6 Mb b. 46Mb c. 64 Mb d. 4639bp [ a ] 56. The protein coding regions of bacterial genomes donot contain a. introns b. exons c. inteins d. repeats [ a ] 57. The workhorse of molecular biology genome is
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a. Haemophilus influenzae b. Mycoplasma genitalium c. Mycobacterium tuberculosis d. E. coli [ d ] 58. VNTRs are otherwise refered as a. Minisatelite b. Microsatellite c. Satelite DNA d. repeats [ a ] 59. STRs are otherwise refered as a. Minisatelite b. Microsatellite c. Satelite DNA d. repeats [ b ] 60. The number of chromosomes in yeast genome is a. 5 b. 10 c. 16 d. 20 [ b ] 61. SnRNAs are referd as a. Single stranded RNA b. Single nuclear RNA c. Small nuclear RNA d. Short segment of RNA [ b ] 62. Drugs and drug combinations are optimized for each individual's unique genetic makeup is termed as -----------------------. a. gene therapy b. personalized medicine c. gene testing d. Drug design [ b ] 63. What would be a likely explanation for the existence of pseudogenes? a. gene duplication b. gene duplication and mutation events c. mutation events d. unequal crossing over [ a ] 64. CpG islands and codon bias are tools used in eukaryotic genomics to __________. a. identify open reading frames b. find regulatory sequences c. look for DNA-binding domains d. identify a genes function [ a ] 65. An open reading frame (ORF) is a. the sequence of a complete genome b. a plasmid vector used in genome sequencing c. a possible gene predicted by DNA sequencing d. non-coding gene [ c ] 66. The goal of ________________ is to determine the location of specific genes within the genome. a. cloning b. annotation c. proteomics d. assembly [ b ] 67. Related genes that have same functions in different species are refered as -------------a. orthologs b. xenologs c. homologs d. paralogs [ a ] 68. Human and globin genes are a. homologs b. paralogs c. orthologs d. xenologs [ b ] 69. Human and Horse myoglobin genes are
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a. orthologs b. paralogs c. xenologs d. homologs [ a ] 70. Human transcriptome study helps to diagnose ---------------- disease a. Brain b. Diabetes c. cancer d. Heart [ c ] 71. Transcriptome analysis is caried out easily by-----------------a. ESI b.PAGE c. Microarray d.2DGE [ c ] 72. When a typical restriction enzyme cuts a DNA molecule, the cuts are staggered so that the DNA fragments have single-stranded ends. This is important in recombinant DNA work because _____. a. only single-stranded DNA segments can code for proteins b. the fragments will bond to other fragments with complementary single-stranded ends c. the single-stranded ends serve as starting points for DNA replication d. it allows a cell to recognize fragments produced by the enzyme [ b ] 73. How the eukaryotic transcription activators regulate transcription initiation? a. binding to activation domain b. binding to the promotor c. inhibit the binding domain d. inhibit binding &activating domain [ b ] 74. How the eukaryotic transcription repressors regulate transcription initiation? a. binding to activator b. binding to the promotor c. Inhibit the activator d. help RNA polymerase binding [ c ] 75. Which of the following is true of gene regulation in both eukaryotes and prokaryotes? a. lac and trp operons b. elaborate packing of DNA in chromosomes c. transcription is the usual point at which gene expression is regulated d. the removal of noncoding portions of RNA in the making of mRNA [ c ] 76. What does a microarray do? a. "one gene in one experiment" b. Monitor the whole genome on one chip c. Interactions among thousands of genes simultaneously d. Determination of expression level (abundance) of genes [ b ] 77. How many microarray spots do you think you would need to look at in a bacterial genome? a. hundreds b. a few c. a thousand d. thousands to millions [ d ] 78. Why is it going to take a long time to do the human genome? a.It's huge b.It's expensive c.It's complicated d. Its dense [ c ] 79. Why would you spot your two samples that you are comparing on one slide instead of separate ones? a. It's cheaper b. It's easier c. for less differences d. for decreased probability of changes [ a ] 80. KEGG is --------------------------------------- database a. metabolic b. chemical c. nucleic acid d. protein [ a ]
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81. Deposition of cDNA into inert structure is a. DNA finingerprinting b. DNA polymerase c. DNA probes d. DNA microarrays [ d ] 82. Human genome contains about a. 2 billion base pairs b. 3 billion base pairs c. 4 billion base pairs d. 5 billion base pairs [ c ] 83. The identification of drugs through genomic study a. Genomics b. Cheminformatics c. Pharmagenomics d. Phrmacogenetics [ c ] 84. How many potential open reading frames are present in a DNA sequence? a. One. b. Three. c. Six. d. Two. [ c ] 85. Scientists have recently succeeded in transferring genes into to increase levels of Vitamin A, iron and other micronutrients. a. rice b. wheat c. maize d. tomato [ a ] 86. SCID is a. severe combined immune deficiency b. severe combined immune disorder c. severe cancer infant deficiency d. sexual combined immune deficiency [ a ] 87. The first successful gene therapy treatment carried out for a. cancer b. ADA deficiency c. Sickle cell anemia d. thallasaemia [ b ] 88. Ex vivo gene therapy is carried out in a. any tissue b. WBC c. RBC d. Bone marrow [ d ] 89. Cystic fibrosis is a -----------------disorder. a. single gene b. multi gene b. enzyme d. inherited [ a ] 90. Which of the following is efficient gene transfer method in gene therapy? a. retrovirus b. adenovirus c. herpessimplex d. transfection [ d ] 91. Proteomics is: a. a branch of genome study b. the study of mRNA genes c. the study of the entire collection of proteins expressed by an organism d. the study of metabolic pathway of proteins [ c ] 92. If you were using a proteomics approach to find the cause of a muscle disorder, which of the following techniques might you be using? a. creating a genomic library b. sequencing the gene responsible for the disorder c. developing physical maps from genomic clones d. determining which environmental factors influence the expression of your gene of interest [ d ] 93. Two-dimensional gels are used to __________.
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a. separate RNA fragments b. separate different proteins c. observe a protein in two dimensions d. separate DNA from RNA [ b ] 94. The second dimension of separation for 2DGE is based on ------------a. molecular mass b. isoelectric point c. folding d. charge [ a ] 95. The first dimension of separation for two-dimensional electrophoresis is based on -------a. molecular mass b. isoelectric point c. folding d. charge [ b ] 96. The matrix used in MALDI is a. 2,5-dihydroxybenzoic acid b. 2,5-dinitrobenzoic acid c. 2,5-dihydroxyacetic acid d. 2,4-dihydroxybenzoic acid [ a ] 97. The term MALDI refers to a. Matrix assisted long desorption Ion b. Matrix Assisted Laser desorption Ionization c. Microarray Laser desorption Ionization d. Micro Laser Ionization [ b ] 98. The large scale identification and characterization of proteins in a cell, tissue, or organism is a. Genomics b. Cheminformatics c. Proteomics d. Bioinformatics [ c ] 99. In MALDI-TOF instruments deflecting ions with an electric field is done by a. TOF b. Detector c. Reflectron d. Laser [ c ] 100. In MALDI-TOF doubling the ion flight path and increasing the resolution is done by a. TOF b. Detector c. Reflectron d. Laser [ c ] 101. In Two-dimensional gels, the first dimension is by a. pH b.pKa c. IEF d.MW [ c ] 102. In Two-dimensional gels, the second dimension is by a. pH b.pKa c. IEF d.MW [ d ] 103. The Mass spectrometer spectrum is drawn based on the a. pH b.pKa c. Mass charge ratio d.MW [ d ] 104. Trypsin cleaves protein at a. K b. C c. D d.E [ a ] 105. The enzyme which cleave protein at R/K is a. protease b. trypsin c. CNBR d. pectin [ b ] 106. The analytical technique that measures the mass-to-charge ratio of charged particles is a. MS b. MALDI c.SELDI d. ESI [ a ] 107. In MS, the ion signal is processed into mass spectra. The X and Y axis comprises of
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a. Intensity Vs M/Z b. M/Z Vs Intensity c. Mass Vs charge ratio d. Mass Vs Intesity [ a ] 108. Which of the following method is used to study protein protein interaction? a. Microarray b.Y2H c. Blotting d. both a & b [ d ] 109. An analytical technique for protein identification is a. protein-protein interaction b. protein NA interaction c. Peptide mass fingerprinting d. proteome chip [ c ] 110. Peptide mass fingerprinting uses -----------------------to measure the masses of peptides. a. chromatography b. SELDI-TOF c. Mass spectrometer d. UV Spectrometer [ c ] 111. PMF samples are isolated proteins from --------------------a. chromatography b. 2D gels c. SDS-PAGE d. both b & c [ c ] 112. In PMF the ratio for sample: protease is ------------a. 50:1 b. 15:1 c. 1: 50 d. 1: 15 [ a ] 113. Which of the following is protein-protein interaction database? a. BIND b. PIP c. MDB d. PDB [ a ] 114. Ion-exchange chromatography is a process that allows the separation of ions and polar molecules based on their. a. mass b. charge c. pH d. pI [ b ] 115. Ion-exchange chromatography can be used for the purification of --------a. large proteins b. small nucleotides c. amino acids d. all the above [ d ] 116. The method of separating biochemical mixtures based on a highly specific biological interaction is .. a. Paper chromatography b. Column chromatography c. Affinity chromatography d. Ion-exchange chromatography [ c ] 117. The immobile phase of Affinity chromatography uses ----------a. agarose b. Polymer c. resin d. cellulose [ a ] 118. In MALDI, the ionization is triggered by a -------------laser beam. a. Hydrogen b. Neon b. Nitrogen d. None of the above [ b ] 119. In MALDI, Which protect the biomolecule from being destroyed by direct laser beam? a. reflectron b. TOF c. Mass analyser d. matrix 120. The matrix in MALDI is to facilitate a. vaporization b. ionization c. purification d. both a & b [ d ] 121. The first sequenced protein is
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a. bovine insulin b. porin c. calf insulin d. trypsin [ a ] 122. The sequencing of protein was first done by a. Craig Vendor b. Frederic Sanger c. Maxum Gilbert d. Wilkins [ b ] 123. Who got the Nobel prize for protein sequencing? a. Craig Vendor b. Frederic Sanger c. Maxum Gilbert d. Wilkins [ b ] 124. The reagent used for N-terminal analysis is named as a. Phenylisothiocynate b. carboxypeptidase c. Phenylthiocynate d. Phenylchloride [ a ] 125. The name of the Edman reagent is a. Phenylisothiocynate b. carboxypeptidase c. Phenylthiocynate d. Dansylchloride [ a ] 126. The used for N-terminal analysis is a. Aminopeptidase b. carboxypeptidase c. trypsin d. CNBR [ a ] 127. 1-dimethyl aminophthalene-5-sulfonyl chloride refers to a. PTIC b. dansylchloride c. DNFB d. DNBF [ b ] 128. N-terminal sequencing is otherwise termed as a. Edman degradation b. peptide sequencing c. PMF d. Sanger method [ a ] 129. PTH is detected from UV absorption at a.256nm b. 296 nm c.290nm d. 280nm [ b ] 130. Which of the following is protein sequencing method? a. mass spectrometry b. chromatography b. Microarray d. blotting [ a ] 131. Hydrolysis in N-terminal sequencing uses a. HNO3 b. H2 SO4 c. HCl d. KBr [ c ] 132. In the N-terminal sequencing, heating a sample of the protein is at a. 100 degrees Celsius b. 60 degrees Celsius c. 50 degrees Celsius d. 150 degrees Celsius [ a ] 133. Which of following amino acids may be degraded at higher temperature in N-terminal sequencing? a. S, Y, T b. L,K,M c. A.G, L d. D, L, M [ a ] 134. The Disulfides in protein molecules are reduced with the help of a. TEMED b. 2-mercaptoethanol c. HCl d. APS [ b ] 135. The experimental way to determine protein structure is a. X-ray b. NMR
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c. FT-IR d. both a & b [ d ] 136. The probes used in protein array are a. lipids b. DNA c. peptides d. All the above [ d ] 137. In protein array, the proteins are on glass chip. a. hybridized b. adsorbed c. immobilized c. complementary binding [ c ] 138. Drug is a -------a. Macro molecule b. Chemical compound c. Inhibitor d. target [ b ] 139. The naturally existing cellular or molecular structure involved in the pathology of interest that the drug-in-development is meant to act on is refers to ---------------. a. Target b. Receptor c. Messenger d. Template [ a ] 140. The majority of targets currently selected for drug discovery efforts are --------------a. Proteases b. Receptors c. Secondary Messenger d. GPCRs [ d ] 141. Protein kinases are used in drug discovery as ----------------a. Target b. Receptor c. Inhibitors d. Template [ a ] 142. The biological activity of drug molecule is studied by a. SAR b. QSAR c. ADME d. clinical trail [ b ] 143. The specific arrangement of functional groups is refered as a. Pharmacopore b. Receptor c. Ligand d. Lead [ a ] 144. The compound which has a desired biological activity on molecular target is a. Pharmacopore b. Receptor c. Ligand d. Lead [ d ] 145. CADD refers to a. Computer assited drug design b. Computer aided drug design c. Computer assited drug discovery d. Computational aided drug [ b ] 146. SBDD refers to a. Structure assited drug design b. Sequence based drug design c. Sequence assited drug discovery d. Structure based drug design [ d ] 147. The position of ligand in the active site of protein isand calculate binding affinity is a. QSAR b. Docking c. Modelling d. protein protein interaction [ b ] 148. Combinatorial chmistry and HTS depend on a. Genomics b. Cheminformatics c. Proteomics d. Pharmacogenomics [ b ] 149. The identification of drugs through genomic study a. Genomics b. Cheminformatics c. Pharmagenomics d. Phrmacogenetics [ c ] 150. The study of the hereditary basis for differences in a population is

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a. Orthology c. Pharmagenomics

b. Cheminformatics d. Phrmacogenetics

[ d ]

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