AYYA NADAR JANAKI AMMAL COLLEGE (Autonomous), SIVAKASIM.Sc. BIOINFORMATICS DEGREE COURSE – THIRD SEMESTER

CORE PAPER HF312 – GENOMICS AND PROTEOMICS(For those admitted in June 2008 and later)

MULTIPLE CHOICE QUESTIONS1. What is a genome?

a) An organism's complete genetic material b) The gene sequence involved in genetic recombination c) genetic fissiond) 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 sequencingd. 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. Genomicsc. 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 Venterd) DNA sequencing method [ c ]

6. Who is most likely to win a Nobel Prize for sequencing the human genome?a. Frances Collins b. Tony Blairc. 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 treatmentb. Available free of charge on the internetc. Serialized in the Daily Telegraphd. 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 systemb. Iceland's top boy bandc. A species of worm d. A new leisurewear range from Calvin Klein [ c ]

9. What causes many diseases?a. SNP b.Stressc. Tiny mutations in our genes d. Supermodels [ c ]

10. Who are Crick and Watson?

1

a. The British family firm which invented the first gene sequencing machineb. A firm of lawyers specialising in gene patentingc. The Anglo-American scientific team who discovered the structure of DNAd. A popular singing pair from the 90s [ c ]

11. Which type of genomics studies the physical nature of genomes?a. Comparative genomics b. Structural genomicsc. Functional genomics d. Pharmacogenomics [ b ]

12. The whole-genome shotgun sequencing approach depends primarily ona. rapidly sequencing thousands of small randomly cloned fragmentsb. methodical sequencing a few large cloned fragments of DNAc. sequencing the bacterial chromosome while it is still intactd. sequencing a small clone fragments [ b ]

13. Which of the following is sequence assembler?a. ARACHINE b. PHPREDc. 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 medicinec. 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 genomicsc. 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 genomicsc. 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 tagc. different colors d. unique antibody bound to it [ b ]

19. Contigs are a. overlapping genes b. sequence gapsc. physical gaps d. mapped segments [ a ]

20. Scaffolds are a. physical gaps b. sequence gapsc. set of contigs d. set of cloned segments [ a ]

21. Dideoxy nucleoside triphosphatea. will terminate DNA synthesis when incorporated into a growing DNA strandb. has an oxygen at the 3' carbonc. cannot bind to a growing DNA chaind. can form a sugar phosphate bond with a new nucleoside triphosphate [ a ]

2

22. In manual Sanger sequencing, _____ sequencing reactions are performed.a. Four c. Twob. 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. 700c. 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. rRNAc. mRNA d.dsDNA [ c ]

31. As the complexity of an organism increases, all of the following characteristics emerge except __________.

a. the gene density decreasesb. the number of introns increasesc. the gene size increasesd. 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 studiesc. electrophoresis d.X-ray diffraction analysis [ a ]

3

34. The human genome project was started in the Yeara) 1980 b) 1990c) 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 backb. Exactly one furlongc. 500 milesd. 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 filla. 200 telephone directoriesb. Enough telephone directories to fill the British Libraryc. A telephone directoryd. 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 genitaliumc. Mycobacterium tuberculosis d. E. coli [ b ]

41. The minimum set of genes required for life is approximately:a. 50-100 genes b. 250-350 genesc. 1000-1500 genes d. 2000-2500 genes [ b ]

42. Deinococcus radiodurans is able to survive massive exposure to radiation becausea. it produces a thick shell which acts as a shield from the radiationb. it has unique DNA repair mechanismsc. it has many copies of genes encoding DNA repaird. 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.

4

a. DNA microarrays b. cloning libraryc. 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 interactionc. DNA –DNA interaction d. both a and b [ d ]

47. Yeast two-hybrid method is based on --------------------,the eukaryotic activator a. GAL4 b.TATA Boxc. SW15 d.SBF [ a ]

48. What is the size of Mouse genome?a. 4.6 Mb b. 3200Mbc. 121Mb d. 3300Mb [ d ]

49. The size of D.melanogaster genome isa. 4.6 Mb b. 320Mbc. 121Mb d. 180Mb [ d ]

50. A.thaliana is --------------------a. ornamental plant b. non-flowering plantc. 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. paralogsc. homologs d. xenologs [ b ]

52. Name the proteins involved in Y2H a.actin & myosin b.Bait & Preyc. activator & repressor d.binding and activating domain [ b ]

53. SAGE is used to study the Yeast --------------a. Sporulation b.Proteinsc. genes d. RNA [ a ]

54. The number of mRNA genes present in S.cereviciae is ----------a. 600 b. 6000c. 60 d. 60,000 [ b ]

55. The size of E.coli genome is a. 4.6 Mb b. 46Mbc. 64 Mb d. 4639bp [ a ]

56. The protein coding regions of bacterial genomes donot contain a. introns b. exonsc. inteins d. repeats [ a ]

57. The workhorse of molecular biology genome is

5

a. Haemophilus influenzae b. Mycoplasma genitaliumc. Mycobacterium tuberculosis d. E. coli [ d ]

58. VNTR’s are otherwise refered as a. Minisatelite b. Microsatellitec. Satelite DNA d. repeats [ a ]

59. STR’s are otherwise refered as a. Minisatelite b. Microsatellitec. Satelite DNA d. repeats [ b ]

60. The number of chromosomes in yeast genome is a. 5 b. 10c. 16 d. 20 [ b ]

61. SnRNA’s are referd as a. Single stranded RNA b. Single nuclear RNAc. 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 medicinec. gene testing d. Drug design [ b ]

63. What would be a likely explanation for the existence of pseudogenes?a. gene duplicationb. gene duplication and mutation eventsc. mutation eventsd. unequal crossing over [ a ]

64. CpG islands and codon bias are tools used in eukaryotic genomics to __________.a. identify open reading framesb. find regulatory sequencesc. look for DNA-binding domains d. identify a gene’s function [ a ]

65. An open reading frame (ORF) isa. the sequence of a complete genomeb. a plasmid vector used in genome sequencingc. a possible gene predicted by DNA sequencingd. 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. xenologsc. homologs d. paralogs [ a ]

68. Human α and β globin genes are a. homologs b. paralogsc. orthologs d. xenologs [ b ]

69. Human and Horse myoglobin genes are

6

a. orthologs b. paralogsc. xenologs d. homologs [ a ]

70. Human transcriptome study helps to diagnose ---------------- diseasea. Brain b. Diabetesc. cancer d. Heart [ c ]

71. Transcriptome analysis is caried out easily by------------------a. ESI b.PAGEc. 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 endsc. 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 promotorc. 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 operonsb. elaborate packing of DNA in chromosomesc. transcription is the usual point at which gene expression is regulatedd. 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. It’s 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 --------------------------------------- databasea. metabolic b. chemical c. nucleic acid d. protein [ a ]

7

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. wheatc. 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 deficiencyc. Sickle cell anemia d. thallasaemia [ b ]

88. Ex vivo gene therapy is carried out in a. any tissue b. WBCc. RBC d. Bone marrow [ d ]

89. Cystic fibrosis is a -----------------disorder.a. single gene b. multi geneb. enzyme d. inherited [ a ]

90. Which of the following is efficient gene transfer method in gene therapy?a. retrovirus b. adenovirusc. herpessimplex d. transfection [ d ]

91. Proteomics is:a. a branch of genome studyb. the study of mRNA genesc. the study of the entire collection of proteins expressed by an organismd. 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 libraryb. sequencing the gene responsible for the disorderc. developing physical maps from genomic clonesd. determining which environmental factors influence the expression of your gene of

interest [ d ]93. Two-dimensional gels are used to __________.

8

a. separate RNA fragmentsb. separate different proteinsc. observe a protein in two dimensionsd. 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 pointc. folding d. charge [ b ]

96. The matrix used in MALDI is a. 2,5-dihydroxybenzoic acid b. 2,5-dinitrobenzoic acidc. 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. Detectorc. Reflectron d. Laser [ c ]

100. In MALDI-TOF doubling the ion flight path and increasing the resolution is done by a. TOF b. Detectorc. Reflectron d. Laser [ c ]

101. In Two-dimensional gels, the first dimension is by a. pH b.pKac. IEF d.MW [ c ]

102. In Two-dimensional gels, the second dimension is by a. pH b.pKac. IEF d.MW [ d ]

103. The Mass spectrometer spectrum is drawn based on the a. pH b.pKac. Mass charge ratio d.MW [ d ]

104. Trypsin cleaves protein at a. K b. Cc. D d.E [ a ]

105. The enzyme which cleave protein at R/K isa. protease b. trypsinc. CNBR d. pectin [ b ]

106. The analytical technique that measures the mass-to-charge ratio of charged particles isa. MS b. MALDIc.SELDI d. ESI [ a ]

107. In MS, the ion signal is processed into mass spectra. The X and Y axis comprises of

9

a. Intensity Vs M/Z b. M/Z Vs Intensityc. 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.Y2Hc. Blotting d. both a & b [ d ]

109. An analytical technique for protein identification isa. protein-protein interaction b. protein – NA interactionc. Peptide mass fingerprinting d. proteome chip [ c ]

110. Peptide mass fingerprinting uses -----------------------to measure the masses of peptides.a. chromatography b. SELDI-TOFc. Mass spectrometer d. UV Spectrometer [ c ]

111. PMF samples are isolated proteins from ---------------------a. chromatography b. 2D gelsc. SDS-PAGE d. both b & c [ c ]

112. In PMF the ratio for sample: protease is -------------a. 50:1 b. 15:1c. 1: 50 d. 1: 15 [ a ]

113. Which of the following is protein-protein interaction database?a. BIND b. PIPc. 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. chargec. 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 chromatographyc. Affinity chromatography d. Ion-exchange chromatography [ c ]

117. The immobile phase of Affinity chromatography uses -----------a. agarose b. Polymerc. resin d. cellulose [ a ]

118. In MALDI, the ionization is triggered by a -------------laser beam. a. Hydrogen b. Neonb. Nitrogen d. None of the above [ b ]

119. In MALDI, Which protect the biomolecule from being destroyed by direct laser beam? a. reflectron b. TOFc. Mass analyser d. matrix

120. The matrix in MALDI is to facilitatea. vaporization b. ionizationc. purification d. both a & b [ d ]

121. The first sequenced protein is

10

a. bovine insulin b. porinc. calf insulin d. trypsin [ a ]

122. The sequencing of protein was first done by a. Craig Vendor b. Frederic Sangerc. Maxum Gilbert d. Wilkins [ b ]

123. Who got the Nobel prize for protein sequencing? a. Craig Vendor b. Frederic Sangerc. Maxum Gilbert d. Wilkins [ b ]

124. The reagent used for N-terminal analysis is named as a. Phenylisothiocynate b. carboxypeptidasec. Phenylthiocynate d. Phenylchloride [ a ]

125. The name of the Edman reagent is a. Phenylisothiocynate b. carboxypeptidasec. Phenylthiocynate d. Dansylchloride [ a ]

126. The used for N-terminal analysis is a. Aminopeptidase b. carboxypeptidasec. trypsin d. CNBR [ a ]

127. 1-dimethyl aminophthalene-5-sulfonyl chloride refers to a. PTIC b. dansylchloridec. DNFB d. DNBF [ b ]

128. N-terminal sequencing is otherwise termed as a. Edman degradation b. peptide sequencingc. PMF d. Sanger method [ a ]

129. PTH is detected from UV absorption at a.256nm b. 296 nmc.290nm d. 280nm [ b ]

130. Which of the following is protein sequencing method? a. mass spectrometry b. chromatographyb. 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 Celsiusc. 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,Mc. A.G, L d. D, L, M [ a ]

134. The Disulfides in protein molecules are reduced with the help of a. TEMED b. 2-mercaptoethanolc. HCl d. APS [ b ]

135. The experimental way to determine protein structure is a. X-ray b. NMR

11

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 compoundc. 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. Receptorc. Messenger d. Template [ a ]

140. The majority of targets currently selected for drug discovery efforts are ---------------a. Proteases b. Receptorsc. Secondary Messenger d. GPCRs [ d ]

141. Protein kinases are used in drug discovery as -----------------a. Target b. Receptorc. Inhibitors d. Template [ a ]

142. The biological activity of drug molecule is studied by a. SAR b. QSARc. ADME d. clinical trail [ b ]

143. The specific arrangement of functional groups is refered as a. Pharmacopore b. Receptorc. Ligand d. Lead [ a ]

144. The compound which has a desired biological activity on molecular target is a. Pharmacopore b. Receptorc. Ligand d. Lead[ d ]

145. CADD refers toa. Computer assited drug design b. Computer aided drug designc. Computer assited drug discovery d. Computational aided drug [ b ]

146. SBDD refers to a. Structure assited drug design b. Sequence based drug designc. 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. Dockingc. 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

12

a. Orthology b. Cheminformatics c. Pharmagenomics d. Phrmacogenetics [ d ]

13