Bioinformatics I (BIF401)

1. In multiple sequence alignment (MSA), we have ________ .

   1. Local alignment
   2. Global alignment
   3. Both
   4. None of the given

2. The scoring of gaps in a MSA (Multiple Sequence Alignment) has to be performed in a different manner from scoring gaps in a pair-wise alignment?

   1. True
   2. False

3. Which of the following is untrue anout the modification of PAM matrices?

   1. At one time, the RAM250 scoring matrix was modified in an attempt to improve the aligment obtained
   2. All scores for matching a particular amino acid were normaliszed to the same mean and standarf deviation, and all amino acid identities were given the same score to provvide an equal contribution for each amino acid in sequence alignment
   3. This took palace in 1976
   4. These modifications were included as the default matrices for the GCG sequence alignment programs in in versions 8 and earlier and are optional in later versions

4. The major element of secondary structure in myoglobin and hemoglobin is:

   1. The P-strand
   2. The a-helix
   3. The reverse turn
   4. All of the given

5. All are nucleotide sequence database, except

   1. SwissProt
   2. EMBL
   3. DDBJ
   4. GenBank

6. Choose the incorrect statement out of the following?

   1. Only L-amino acids are found in the biological system
   2. Glycine is optical inactive
   3. Tyrosine is a modified amino acid
   4. Sereno cysteine is 21st proteinogenic amino acid

7. Which one of the following are Archaea?

   1. Firmicutes
   2. Chlamydiae
   3. Thermococci
   4. Chlorobi

8. Alpha Helices are formed by hydrogen bonding between ________ and ________ atoms in the protein backbone?

   1. Ci and Ni+4
   2. C and N
   3. O and H
   4. Oi and Hi+4

9. Which is the default scoring matrix used in BLAST?

   1. PAM62
   2. BLOSUM 62
   3. BLOSUM 60
   4. BLOSUM 80

10. To determine the number of each type of interaction within a protein, we need to find its inter atomic distances.

    1. True
    2. False

11. In GenBank, specific gene can be searched by using?

    1. Sequence ID
    2. Name
    3. Species
    4. All of the given

12. In dynamic programming we can do multiple sequence alignment upto ________

    1. 20 sequences
    2. 9 sequences
    3. 21 sequences
    4. 50 sequences

13. mRNA directs the building of proteins through a sequence of

    1. Introns
    2. Codons
    3. Exons
    4. Anticodons

14. A Protein Data Bank (PDB) data file for a protein structure contains only x and y coordinates of atoms.

    1. True
    2. False

15. Which of the following is not a benefit of BLAST?

    1. Handling of gaps
    2. Speed
    3. More sensitive
    4. Statistical rigor

16. All of the following are protein sequence databases except ________.

    1. PIR
    2. PSD
    3. Swiss Prot
    4. EMBL

17. X-Ray Crystallography data shows that hydrogen atoms of N-Term may come together with Oxygen atoms of C-term amino acid at ________ position.

    1. 2nd neighboring
    2. 3rd neighboring
    3. 4th neighboring
    4. None of the given

18. Which of the following is the smallest of the RNAs?

    1. Messenger RNA
    2. Transfer RNAs
    3. Ribosomal RNAs
    4. All of the given

19. Balls and sticks are solid spheres and rods, representing atoms and bond, respectively.

    1. True
    2. False

20. The study of full complement of proteins expressed by a genome is called

    1. Proteome
    2. Proteomics
    3. Genomics
    4. Protein formation

21. Which one of the following issues are addressed by using computational methods, data processing techniques and algorithms?

    1. Storage and Organization of data
    2. Analysis of many experiments
    3. For representation of biological information
    4. All of the given

22. Dynamic Programming uses a "________" to deal with matches, mismatches and gaps.

    1. Dynamic Algorithms
    2. Order of Algorithms
    3. Scoring Function
    4. Sequence Identification

23. Progressive alignment methods use the dynamic programming method to build a MSA starting with the most related sequences and then progressively adding less related sequences or groups of sequences to the initial alignment?

    1. True
    2. False

24. What are 2 things required in order to successfully use the dynamic programming technique?

    1. Optimal structure and overlapping subproblems
    2. A problem that can't be subdivided and is complex
    3. Non-overlapping subproblems and intervals
    4. Recursion and a problem that is complex

25. If two atoms are participating in a covalent bond, their distance will be equal to?

    1. 1 A
    2. ~0.96 A
    3. 0.096
    4. 0.0096

26. Which of these bonds is not involved in forming the secondary structure of a protein?

    1. Peptide
    2. Covalent
    3. Hydrogen
    4. Disulphide

27. The peptide bond in protein is:

    1. Planar, but rotates to three preferred dihedral angles
    2. Nonpolar, but rotates to three preferred dihedral angles
    3. Nonpolar, and fixed in a trans conformation
    4. Planar, and usually found in a trans conformation

28. How many proteins does the human body produce?

    1. As per hypothesis of "One gene = one protein" So, there should at least ~20,000
    2. Hypothesis of "One gene = two protein" So, there should at least ~40,000
    3. Hypothesis of "two gene = one protein" So, there should at least 10,000
    4. No relation of gene and protein

29. RNA is found in the nucleolus of the cell and DNA is found in

    1. Chromosomes
    2. Cytosol
    3. Cell Wall
    4. Vacuole

30. The BLAST program was developed in ________ .

    1. 1992
    2. 1995
    3. 1990
    4. 1991

31. The first RNA processing event is

    1. Capping
    2. Tailing
    3. Splicing
    4. Editing

32. The procedure of aligning two sequences by searching of patterns that is in the same order in the sequences?

    1. Sequence Alignment
    2. Pairwise Alignment
    3. Multiple Sequence Alignment
    4. All of the given

33. Name any two frequently used scoring matrices

    1. BLAST & FASTA
    2. Protparam & Protscale
    3. PSIPRED & FASTA
    4. BLOSUM & PAM

34. Which of the following methods are broad class of computational algorithms that rely on repeated random sampling to obtain numerical results.

    1. Martinez Algorithm
    2. N-J Algorithm
    3. Dynamic Programming
    4. Monte Carlo methods

35. The putative ORF can be translated into a protein sequence, which is then used to search against a protein database.

    1. True
    2. False

36. Which algorithm is used by global alignment?

    1. Needleman-Wunsch
    2. Smith-Waterman
    3. BLAST
    4. PAM

37. The ________ E-Value, the more significant the hit.

    1. Lower
    2. Higher
    3. Average
    4. Superior

38. Which of the following is the character based phylogenetic tree construction methods?

    1. N-J
    2. UPGMA
    3. Maximum Parsimony
    4. All of the given

39. C-Alpha atoms are traced to recreate the ________ protein structure.

    1. 2D
    2. 3D
    3. Can be used for both 2D and 3D
    4. None of the given

40. ________ are the units of proteins.

    1. Glucose
    2. Amino acids
    3. Nucleotides
    4. Nucleosides

41. Which of the following is the correct order of organization of genetic material from largest to smallest?

    1. Genome, Chromosome, Gene, Nucleotide
    2. Genome, Gene, Chromosome, Nucleotide
    3. Gene, Nucleotide, Chromosome, Genome
    4. Chromosome, Genome, Gene, Nucleotide

42. Bioinformatics can deliver:

    1. Provide us better understanding of life
    2. Provide us better understanding of evolutions and molecular mechanisms
    3. can help to store and process experimental Data
    4. All of the given

43. Ribbon diagram use cylinders or spiral ribbons to represent alpha-helices and broad, flat arrows to represent beeta-strands.

    1. True
    2. False

44. Who discovered diffraction pattern for DNA?

    1. Watson and Creeks
    2. Rosalyn Franklin
    3. Newton
    4. None of the given

45. Sum of stabilizing and destabilizing energies can help determine the ________.

    1. Quantity of 3' RNA structure
    2. Quantity of 2' RNA structure
    3. Quality of 3' RNA structure
    4. Quality of 2' RNA structure

46. Amino acids are joined together to form polypeptides. Each amino acid is attached to another by a peptide bond. What functional group is created when amino acids are joined together?

    1. Ester
    2. Amide
    3. Ketone
    4. No new functional groups are created

47. In multiple sequence alignment ________ .

    1. doing so many progressive alignments can be slow
    2. doing so many progressive alignments is easy
    3. doing so many progressive alignments is not possible
    4. None of the given

48. BLASTX uses protein sequences as queries to search against a protein sequence database.

    1. True
    2. False

49. GenBank database is maintained by ________.

    1. Brookhaven Laboratory
    2. DNA Database of Japan (DDBJ)
    3. European Molecular Biology Laboratory (EMBL)
    4. National Centre of Biotechnology Information (NCBI)

50. For which one of the following activities, bioinformatics is used in modern biological sciences?

    1. Developing algorithms for organizing data collected from experiments
    2. Data processing to determine the role of underlying biomolecule
    3. To perform wet lab experiments
    4. Both 1 & 2

51. X-ray diffraction data helps measure ________.

    1. Phi and angles
    2. C-Alpha atoms
    3. Protein structure
    4. Atomic positions

52. Which of the following is not protein fragmentation technique.

    1. Microarray
    2. CID
    3. ECD
    4. None of the given

53. Translation is the process in which

    1. DNA is formed on DNA template
    2. DNA is formed on RNA template
    3. RNA is formed on DNA template
    4. Protein is formed on RNA template

54. The secondary structure of a protein consists of all but one of the following, which is odd one out?

    1. Turns
    2. Alpha helices
    3. Beta Sheets
    4. Disulfide bridges

55. Mfold gives out (output) several structures along with their ________.

    1. Atomic positions
    2. Sequences
    3. Energetic stability
    4. All of the given

56. RNA is the genetic material in

    1. Viruses only
    2. In some viruses and some prokaryotes
    3. In some viruses and some prokaryotes and rarely in eukaryotes
    4. Only in some viruses

57. The greater the number of bonds between the amino acids, the ________ stable a protein becomes.

    1. More
    2. Less
    3. No relation of bonds with stability of protein -> Incorrect Statement
    4. Number of bonds direct proportional to stability of protein

58. All of the following are protein sequence database, except ________.

    1. Swiss Prot
    2. PIR
    3. TREMBL
    4. DDBJ

59. X-Ray data need a minimum of ________ resolution.

    1. 1
    2. 1.97
    3. 2
    4. 2.97

60. Dot plot of repeating elements would be small crosses on plot.

    1. TRUE
    2. FALSE

61. In the alpha helix the hydrogen bond:

    1. are roughly parallel to the axis of the helix.
    2. are roughly perpendicular to the axis of the helix
    3. occur mainly between electronegative atoms of the R groups.
    4. occur only between some of the amino acids of the helix.

62. In Bottom up proteomics, Enzyme ________ is used to cleave the proteins.

    1. Trypsin
    2. Lipases
    3. Amylase
    4. None of the given

63. The Alignment method suitable for finding out conserved patterns in DNA or Protein sequences is

    1. Multiple sequence alignment
    2. Pair wise alignment
    3. Global Alignment
    4. Local Alignment

64. Which of the following is not a variant of BLAST?

    1. BLASTN
    2. BLASTP
    3. BLASTX
    4. TBLASTNX

65. Addition or removal of amino acids from protein sequences or nucleotides from DNA or RNA sequences is known as?

    1. Insertion
    2. Deletion
    3. Indels
    4. None of the given

66. Single letter code of Tyrosine is ________.

    1. B
    2. J
    3. O
    4. Y

67. Alpha helices and beta sheets are formed because of ________.

    1. Hydrophobic interactions
    2. Hydrogen bonds
    3. Salt bridges
    4. All of the given

68. Black analysis methods use substitution matrices such as the PAM and BLOSUM matrices to score matches.

    1. TRUE
    2. FALSE

69. What is the source of protein structures in SCOP and CATH?

    1. UniPort
    2. Protein Databank
    3. Ensemble
    4. InterPro

70. Messenger RNA is only ________ of RNA content in the cell.

    1. 1-5%
    2. 5-10%
    3. 10-15%
    4. 15-20%

71. In Corey-Paulin-Koltun Diagram, each atom is represented by ________.

    1. Solid Sphere
    2. Balls and sticks
    3. Ribbons
    4. Folds

72. Bioinformatics is the interdisciplinary relative new development of ________.

    1. mathematics and biology
    2. physics and biology
    3. physics, chemistry, mathematics, computer science and biology
    4. maths, physics and biology

73. DNA makes RNA and RNA makes protein, this process is termed as

    1. Central Dogma
    2. Replication
    3. Translation
    4. Transcription

74. rRNA is synthesized by:

    1. Nucleus
    2. Cytoplasm
    3. RER
    4. Nucleolus

75. Which of the following is not a benefit or a factual of FASTA over BLAST?

    1. FASTA scans smaller window sizes
    2. It gives more sensitive results
    3. It gives less sensitive results
    4. It gives results with a better coverage rate for homologs

76. The correct order of progressive alignment steps for multiple sequence alignment is ________ .

    1. Guide tree, Pairwise alignment, Branching order in tree
    2. Pairwise alignment, Guide tree, Branching order in tree
    3. Guide tree, branching order in tree, Pairwise alignment
    4. Branching order in tree, Guide tree, Pairwise alignment

77. Which of the following is untrue about the Unweighted Pair Group Method Using Arithmetic Average?

    1. The simplest clustering method is UPGMA, which builds a tree by a sequential clustering method
    2. Given a distance matrix, it starts by grouping two taxa with the largest pairwise distance in the distance matrix
    3. The distances between this new composite taxon and all remaining taxa are calculated to create a reduced matrix
    4. The grouping process is repeated and another newly reduced matrix is created

78. Which of the following is not an ionization techniques in proteins?

    1. Matrix assisted laser desorption ionization
    2. MALDI
    3. Electro spray ionization
    4. X-ray crystallography

79. Your lab partner is using BLAST, and his best E-value is 3. This means that

    1. He's found 3 protein in the database that have the same sequence as his protein
    2. The chance that these similarities arose due to chance is one in 10^3
    3. There would be 3 matches that good in a database of this size by chance alone
    4. The match in amino acid sequence is perfect, except for the amino acids at 3 positions.

80. Block analysis methods use substitution matrices such as the PAM and BLOSUM matrices to score matches.

    1. True
    2. False

81. The Phi and Psi values of a Beta-strand composed of all D-amino acids will mainly occupy which quadrant in the Ramachandran plot?

    1. Upper Left
    2. Upper Right
    3. Lower Left
    4. Lower Right

82. 74- Scoring Matrices contains,

    1. Positive values
    2. Negative values
    3. Alphabets and characters
    4. Both +VE and -VE values

83. Which one of the following types of bond is principally responsible for holding the α-helix shape of a protein secondary structure?

    1. Disulphide
    2. Peptide
    3. Ionic
    4. Hydrogen

84. Beeta-pleated sheets are the examples of ________.

    1. Primary structure
    2. Secondary structure
    3. Tertiary structure
    4. Quaternary structure

85. An alpha helix is formed by hydrogen bonding between the hydrogen of an amine group and the backbone carbonyl group how many amino acids upstream of it?

    1. Two
    2. Three
    3. Four
    4. Five

86. Laboratory work using computers and computer-generated models generally offline is referred as:

    1. Dry-Lab
    2. In-vitro
    3. Web-Lab
    4. Dry-Lab and In-vitro

87. The interactions which holds and stabilizes the sub-units in 4' structure of proteins are:

    1. Hydrophilic interactions
    2. Hydrogen bonding
    3. Hydrophobic interactions
    4. Ionic bonding

88. Nussinov-Jacobson (NJ) Algorithm is a dynamic Programming (DP) strategy to predict ________.

    1. Stabilizing energies
    2. Destabilizing energies
    3. Optimal RNA 2' structures
    4. Optimal RNA 3' structures

89. Which of the following statements about amino acids is correct?

    1. Amino acids are uncharged at neutral pH
    2. Amino acids are classified according to the structures and properties of their side chains
    3. Amino acids in proteins are mainly in the D-configuration
    4. Twenty-four amino acids are commonly used in protein synthesis

90. The basic idea of thermodynamic stability is to maximize bonding in order to minimize the free energy.

    1. True
    2. False

91. In a similar way to structure prediction methods can be evaluated using RMSD to measure the similarity between two molecular complexes.

    1. True
    2. False

92. Beta Sheets are secondary structure that can be formed as a result of ________.

    1. Hydrophobic Bond
    2. Hydrogen Bond
    3. Ionic Bond
    4. All of the given

93. Amino acids are mostly synthesized from

    1. Fatty acids
    2. Mineral salts
    3. Alpha-ketoglutaric acid
    4. Volatile acids

94. Which of the following doesn't describe PAM matrices?

    1. This familt of matrics list the likelihood of change from one amino acid to another in homologous protein sequences during evolution
    2. There is presently no pther type of scoring matrix that is based on such sound evolutionary principles as are these matrices
    3. Even though they were originally based on a relatively small data set, the PAM matrices remain a useful tool for sequence alignment
    4. It stands for Percent Altered Mutation

95. GenBank and SWISSPORT are example of

    1. Primary Database
    2. Secondary Database
    3. Composite Database
    4. None of the given

96. ________ compares protein sequence against protein databases.

    1. blastp
    2. blastn
    3. blastx
    4. tblastx

97. CLUSTALW is a more recent version of CLUSTAL with the W standing for ________.

    1. Weakening
    2. Winding
    3. Weighting
    4. Wiping

98. Which of the following doesn't describe local alignment?

    1. A local alignment aligns a substring of the query sequence to a substring of the target sequence
    2. A local alignment is defined by maximizing the alignment score, so that deleting a column from either end would reduce the score, and adding further columns at either end would also reduce the score
    3. Local alignments have terminal gaps
    4. The substrings to be examined may be all of one or both sequences; if all of both are included then the local alignment is also global

99. GeneBank and UniPort have

    1. large number of sequences publically
    2. speciec name only
    3. RNA extraction techniques
    4. None of the given

100. Unfolding of a protein can be termed as ________.

     1. Renaturation
     2. Denaturation
     3. Oxidation
     4. Reduction

101. The identification of drugs through genomic study is known as

     1. Genomics
     2. Cheminformatics
     3. Pharma genomics
     4. Pharmacogenetics

102. How many types of secondary structures can be formed possibly by folding of RNA?

     1. 3
     2. 4
     3. 5
     4. 6

103. Which one of the following is not a tool for protein visualization?

     1. Rasmol
     2. CHIME
     3. Paymol
     4. None of the given

104. The ________ tool compares nucleotide sequence against DNA database.

     1. blastn
     2. blastp
     3. blastx
     4. tblastn

105. FASTA format start with ________ symbol.

     1. /
     2. *
     3. @
     4. >

106. Which one of the following methods can be used for statistical evaluation of data?

     1. T-test
     2. ANOVA
     3. Both 1 & 2
     4. None of the given

107. Zuker's Algorithm involves energy ________.

     1. Maximization
     2. Minimization
     3. Stabilizing
     4. Destabilizing

108. Analyzing or comparing entire genome of species known as,

     1. Bioinformatics
     2. Genomics
     3. Proteomics
     4. Pharmacogenomics

109. Elongation of transcription and RNA processing are all interconnected?

     1. TRUE
     2. FALSE

110. There are 64 codons in the genetic dictionary as:

     1. There are 64 amino acids to be coded
     2. Genetic code has a triplet nature
     3. There are 3 nonsense codons and 61 sense codons
     4. There are 64 different types of t-RNA

111. Amino acids are chained together by ________.

     1. hydrogen bond
     2. peptide bond
     3. covalent bond
     4. van der walls forces

112. Which one of the following is not a "Sequence Alignment Tool"?

     1. FASTA
     2. BLAST
     3. Rasmol
     4. ClustalW

113. Messenger RNA is

     1. Single stranded
     2. Double stranded
     3. Forms a sheet
     4. ?- Sheet

114. Visualization methods are very important in viewing molecular properties on molecules. Of particular note is the rendering of molecular surfaces according to their various properties (that can be expressed numerically).

     1. True
     2. False

Select a course code for Objective Questions:

ACC311 ACC501 BIF101 BIF401 BIF501 BIO101 BIO201 BIO202 BIO203 BIO204 BIO301 BIO302 BIO303 BIO401 BIO503 BNK603 BT101 BT201 BT301 BT302 BT401 BT402 BT403 BT404 BT405 BT406 BT501 BT504 BT505 BT604 CHE201 CHE301 CS001 CS101 CS201 CS202 CS204 CS301 CS302 CS304 CS311 CS401 CS402 CS403 CS408 CS501 CS502 CS504 CS506 CS508 CS601 CS602 CS604 CS605 CS607 CS609 CS610 CS614 CS707 CS710 ECO401 ECO402 ECO403 ECO404 EDU302 EDU401 EDU402 EDU501 EDU601 ENG101 ENG201 ENG301 ENG501 FIN611 FIN624 FIN625 ISL201 IT430 MCM101 MCM301 MGMT623 MGT101 MGT211 MGT301 MGT401 MGT402 MGT501 MGT502 MGT503 MGT510 MGT601 MGT603 MKT501 MKT610 MKT630 MTH101 MTH202 MTH302 MTH501 MTH601 MTH634 PAK301 PHY101 PHY301 PSY101 PSY403 PSY502 PSY512 SOC101 SOC301 SOC401 STA301 STA630 STA641 ZOO102 ZOO401 ZOO501 ZOO502 ZOO503 ZOO504 ZOO505 ZOO506 ZOO510 ZOO630

Select a course code for Subjective Questions:

ACC311 CS001 CS101 CS201 CS301 CS607 CS701 CS702 CS703 CS704 CS707 CS708 CS710 CS711 CS718 CS721 CS724 ECO401 ECO403 ENG101 ENG301 MGT703 MTH501 STA301