Part B

Ph.D Question paper

Course Title: Bioinformatics
Course Code: A

QUESTION 1 Even though a particular gene may be _____ ortholog of a gene of known
function in another organism, that gene may be acquired by a _____ function.
Option A a highly predicted, similar
Option B a highly predicted, same
Option C a highly predicted, novel
Option D less predicted, novel

QUESTION 2 The combined mixture of all labeled DNA fragments is electrophoresed to _____
the fragments by______ and the ladder of fragments is scanned for the presence
of each of the four labels.
Option A separate, size
Option B separate, pH
Option C assimilate, pH
Option D assimilate, size

QUESTION 3 To sequence larger molecules, individual chromosomes are purified and broken
into _____ or larger random fragments, which are cloned into vectors designed
for large molecules.
Option A 100 Mb
Option B 100 kb
Option C 500 Mb
Option D 500 kb

QUESTION 4 Many levels of clone redundancy may be required to build a consensus map
because individual clones can have _______
Option A Rearrangements
Option B Deletions
Option C two separate fragments
Option D Vectors

QUESTION 5 The retroposons include short _________ interspersed nuclear elements

(SINES).
Option A 90–4000 bp long
Option B 80–500 Mbp long
Option C 80–300 bp long
Option D 100–3000 bp long

QUESTION 6 More than _____ of the human genome consists of interspersed repetitive
sequences derived from TEs (transposable elements).
Option A one-third
Option B one-eighth
Option C one-fifth
Option D Half

QUESTION 7 _____ of the human genome comprises one particular family of the SINE
Element, designated Alu (1.2 million copies).
Option A 50%
Option B 40%
Option C 30%
Option D 10%

QUESTION 8 The human genome contains about _________ of class II of elements that
probably predate human evolution (Smit 1996).
Option A 2,000 copies
Option B 200,000 copies
Option C 2,00,00,000 copies
Option D 20,00,000 copies

QUESTION 9 A third category of TEs has features of both class I and class II TEs. These
miniature, inverted repeat TEs (MITES) are ________ in length.
Option A 500bp
Option B 300 bp
Option C 400 bp
Option D 100bp

QUESTION 10 Eukaryotic genes that encode proteins are interrupted by ________

Option A exons of varying length and number
Option B exons of varying length and but same number
Option C introns of varying number but same length
Option D introns of varying length and number

QUESTION 11 Using cDNA sequence with the __________ it is much simpler to locate
protein-encoding sequences in these molecules.
Option A exons taken out
Option B exons removed
Option C introns added
Option D introns removed

QUESTION 12 According to standard amino acid code letters which of the given pair is not
right?
Option A K- lysine
Option B Y- tyrosine
Option C R- serine
Option D Q- glutamine

QUESTION 13 Evolutionary modeling can include various types of analyses. Which is mostly
not one of them?
Option A The prediction of chromosomal rearrangements
Option B Eu/Hetero-chromatin structures
Option C Duplications at gene, chromosomal and full genome level
Option D Duplications at the protein domain level

QUESTION 14 In protein/domain analysis, each protein in the predicted proteome is again used
as a query of a curated protein sequence database such as ____ in order to locate
similar domains and sequences.
Option A PubChem
Option B Genbank
Option C MeSH
Option D SwissProt

QUESTION 15 Each DNA or protein sequence database entry has much information, including
______
Option A reference number type(s)
Option B source organism
Option C name of locus
Option D an assigned accession number(s)

QUESTION 16 Which of the given statements is incorrect about READSEQ?

Option A It is an extremely useful sequence formatting program developed by D. G.

Gilbert at Indiana University, Bloomington
Option B It was developed at Indiana University, Bloomington
Option C It can recognize a DNA or protein sequence file in any of the formats
Option D It can recognize a DNA or protein sequence file in some particular formats

QUESTION 17 Which of the following information Sequence comparisons do not provide?

Option A Gene relationships
Option B Gene locations
Option C Evolutionary history
Option D Function history

QUESTION 18 Which of the given statements is incorrect?

Option A Proteins may be clustered into families on the basis of either sequence or
structural similarity
Option B Proteins often comprise separate domains
Option C The number of protein sequences that are available is insufficient to determine
that domain shuffling occurs in evolution
Option D Proteins are modular

QUESTION 19 Which of the given statements is incorrect about Cluster analysis?

Option A Clustering organizes the proteins into groups by some objective criterion
Option B The P or E value from BLAST searches cannot be the criterion for a matching
protein pair
Option C One criterion for a matching protein pair is the statistical significance of their
alignment score
Option D A criterion for clustering proteins is the distance between each pair of sequences
in a multiple sequence alignment

QUESTION 20 Using boolean logic, the search looks for database entries that include the first
 term __________ the second, and subsequent terms repeated until the last term.
Option A AND
Option B OR
Option C NOT
Option D NAND

QUESTION 21 For a protein search, which of the following is the wrong choice for fields?
Option A Accession (number)
Option B E. C. number
Option C Issue
Option D Journal number

QUESTION 22 Knowing ________ should be enough to find the required entry quickly.
Option A publication date, protein name, journal name
Option B accession number, protein name, or name of gene
Option C publication date, protein name, or volume
Option D properties, protein name, or title word

QUESTION 23 The first bacterial genome to be sequenced was that of ________ a mild human
pathogen.
Option A Hemophilus influenza
Option B Lactobacillus
Option C Vibrio cholarae
Option D Clostridium botulinum

QUESTION 24 While sequencing of the first bacterial genome–A large number of random
overlapping fragments were sequenced and then a consensus sequence of the
entire ______ chromosome of Hemophilus was assembled by computer.
Option A 8.6 x 109 bp
Option B 1.8 x 106 bp
Option C 6.9 x 105 bp
Option D 1.8 x 104 bp

QUESTION 25 While sequencing of The first bacterial genome—Approximately ____ of the

____ predicted genes matched genes of another species, the bacterial species E.
coli K-12 that had been the subject of many years of genetic and biochemical
research.
Option A 46%, 1500
Option B 58%, 1496
Option C 58%, 1743
Option D 72%, 1743

QUESTION 26 After sequencing the Hemophilus genome and Organisms were selected for
sequencing based on minimum criteria. Which of the following is not one of
them?
Option A They had been subjected to a good deal of biological analysis
Option B They were model eukaryotic organisms
Option C They were an important human pathogen, e.g., Mycobacterium tuberculosis
(tuberculosis)
Option D They were of phylogenetic interest

QUESTION 27 The sequences of satellite DNA fall into different types, each with a different
repeat unit of length _____
Option A 5–400 Mbp
Option B 3–300 kbp
Option C 6–900 Mbp
Option D 5–200 bp

QUESTION 28 Minisatellites are made up of repeat units of up to ____ and microsatellites

compose of repeat units of ____ or less.
Option A 25 bp, 10 bp
Option B 70 bp, 6 bp
Option C 80 bp, 9 bp
Option D  25 bp, 4 bp

QUESTION 29 Genes that are transcribed are located in the ______

Option A Euchromatin
Option B Heterochromatin
Option C heterochromatin and euchromatin
Option D tightly bound DNA

QUESTION 30 ______ can comprise a large proportion of the eukaryotic genome as ______
Option A transposable elements, single copy sequences
Option B transposable elements, repetitive sequences
Option C macrosatellite DNA elements, single copy sequences
Option D satellite DNA elements, single copy sequences

QUESTION 31 (Transposable Elements) TEs have the potential to _____ in number until they
comprise a ____ proportion of the genome sequence.
Option A decrease, large
Option B decrease, micro
Option C increase, micro
Option D increase, large

QUESTION 32 There exist three types of interactions between domains. Which of the following
is not one of them?
Option A Stable complex
Option B Transient interaction
Option C Multi-domain protein
Option D Unstable interaction

QUESTION 33 Stable complexes consist of proteins that are _____ associated with each other,
like many ____ proteins for instance.
Option A temporarily, oligomeric
Option B temporarily, monomeric
Option C permanently, oligomeric
Option D permanently, monomeric

QUESTION 34 Sets of proteins that are part of stable complexes and sets of proteins involved in
transient interactions ____ in terms of the similarity in gene expression among
the set of proteins.
Option A are similar
Option B Differ
Option C are same
Option D show similar function

QUESTION 35 Correlation of gene expression for pairs of transiently interacting proteins is

______ compared to randomly chosen pairs of proteins.
Option A not significant
Option B only marginally significant
Option C totally significant
Option D significant to much extent

QUESTION 36 Which of the following is incorrect about Yeast-two-hybrid screens?

Option A The yeast-two-hybrid system uses the transcription of a reporter gene driven by
the Gal4 transcription factor to monitor whether or not two proteins are
interacting
Option B The DNA-binding domain chimeric protein will not bind upstream of the
reporter gene
Option C If the activation domain chimeric protein interacts with the DNA-binding
domain chimeric protein, the reporter gene will be transcribed
Option D Disadvantages of the method are that only pairwise interactions are tested, and
not interactions that can only take place when multiple proteins come together,
as well as a high false positive rate

QUESTION 37 Which of the following is incorrect about Purification of protein complexes

followed by mass spectrometry?
Option A Isolating protein complexes from cells allows identification of interactions
between ensembles of proteins instead of just pairs
Option B Systematic purification of complexes on a large scale is done by tagging
hundreds of genes with an epitope
Option C UnLike in the yeast-two-hybrid assay, this does not involve chimeric genes
Option D Affinity purification based on the epitope will then extract all the proteins
attached to the bait protein from cell lysates

QUESTION 38 Interactions between proteins can be predicted computationally by looking for

sets of genes that occur as a _______
Option A single gene in at least one genome
Option B multiple genes in at least one genome
Option C multiple genes in various genomes
Option D single gene in various genomes

QUESTION 39 Conservation of gene order due to operon structure is _______ so interactions of

 proteins specific to eukaryotes cannot be detected by method of Conservation of
gene order.
Option A not applicable to archea genomes
Option B not applicable to prokaryote genomes
Option C applicable to eukaryote genomes
Option D not applicable to eukaryote genomes

QUESTION 40 An approach for predicting ______ to look for cases across a set of genomes
where _____ are part of the same gene in one genome resulted in gene fusion
method.
Option A gene interactions, only three to four orthologs
Option B gene interactions, two orthologs
Option C protein interactions, two or more orthologs
Option D protein interactions, two orthologs