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WorksheetsBioinformatics 2
Total questions: 142
Worksheet time: 5hrs 44mins
Because there is no indication of which node represents an ancestor, there is no direction of an evolutionary path in an unrooted tree.
True
False
Molecular clock is an assumption by which molecular sequences evolve at varying rates.
True
False
A gene phylogeny only describes the evolution of a particular gene or encoded protein.
True
False
Evolution of a particular sequence _______ correlate with the evolutionary path of the species.
does not
always
does not necessarily
invariably
The species evolution is the ______ of evolution by _____ in a genome.
combined result, multiple genes
result, single genes
result, sole genes
distinct results, single gene
To obtain a species phylogeny, phylogenetic trees from a variety of gene families need to be constructed.
True
False
It is often desirable to define the root of a tree. There are two ways to define the root of a tree. One is to use an outgroup, which ______
is generally determined from similar or related sources of information
is generally determined from independent sources of information
is separated from those sequences at an early evolutionary time
is a sequence that is homologous to the sequences under consideration
Which of the following is incorrect statement about the Kimura model?
In this, the mutation rates for transitions and transversion are assumed to be different
According to this model, occur more frequently than transversions
According to this model, transversions occur more frequently than transitions
It is a model to correct evolutionary distances and is a more sophisticated model
Which of the following is incorrect statement about Choosing Substitution Models?
The evolutionary divergence is beyond the ability of the statistical models to correct
The statistical models used to correct homoplasy are called substitution models or evolutionary models
For constructing DNA phylogenies, there are nucleotide substitution models available
There is one substitution at a particular position, in divergent sequences
The second step in phylogenetic analysis is to construct sequence alignment. This is probably the most critical step in the procedure because it establishes positional correspondence in evolution.
True
False
What is the length of a motif, in terms of amino acids residue?
30- 60
10- 20
70- 90
1- 10
On average, what is the length of a typical domain?
About 300 residues
About 500 residues
About 900 residues
About 100 residues
Which of the following is false about the ‘loop’ structure in proteins?
They are more flexible and can adopt multiple conformations
They connect helices and sheets
They are never the components of active sites
They are more tolerant of mutations
Which of the common structural motifs are described wrongly?
β-hairpin – adjacent antiparallel strands
Greek key – 4 adjacent antiparallel strand
β-α-β – 2 parallel strands connected by helix
β-α-β – 2 antiparallel strands connected by helix
Which of the following least describes Long Loop β-hairpins?
Loop looks similar to the Greek Letter Ω
Wide-range of conformations with very specific sequence preferences
Generally they are referred to as the β-meander supersecondary structure
They are Often referred to as a ‘random coil’ conformation
Motifs that can form α/β horseshoes conformation are rich with which protein residue?
Proline
Arginine
Valine
Leucine
Which of the following wrongly describes protein domains?
They are made up of one secondary structure
Defined as independently foldable units
They are stable structures as compared to motifs
They are separated by linker regions
The protein structural motif domain- helix loop helix are contained by all of the following except ________
Scleraxis
Neurogenins
Leucine zipper
Transcription Factor 4
Which of the following is not the function of Short Linear Motifs?
Irreversible cleavage of the peptide at the SLiM
Reversible cleavage of the peptide at the SLiM
Moiety addition at targeted sites on SLiM
Structural modifications of the peptide backbone
In the zinc finger, which residues in this sequence motif form ligands to a zinc ion?
Cysteine and arginine
Cysteine and histidine
Histidine and proline
Histidine and arginine
Who coined the term Bioinformatics and when?
Robert Ledley, 1978
David W Mount, 1977
Paulien Hogeweg, 1979
Dr Margaret Oakley Dayhoff, 1976
GenBank, the Nucleic acid sequence database is maintained by
DNA database of Japan
European Molecular Biology Laboratory
National Centre for Biotechnology Information
Brookhaven laboratory
Each record in a database is called
Query
Entry
File
Record
All of the following are protein sequence databases except
SWISSPROT
EMBL
PIR
PDB
Which of the following is not a primary nucleic acid database?
GenBank
DDBJ
EMBL
TrEMBL
Margaret Dayhoff developed the first protein sequence database called
UniPROT
Atlas of sequence and structure protein
SWISS PROT
Protein sequence databank
The structural classification of proteins is based primarily on their
Amino acid sequence
Evolutionary relationships
function
Secondary structure content and arrangement
In the α helix the hydrogen bonds
occur only near the amino and carboxyl termini of the helix
are roughly parallel to the axis of the helix
are roughly perpendicular to the axis of the helix
occur only between some of the amino acids of the helix
Which of the following is a RefSeq accession number corresponding to an mRNA?
NP_52280
AAB134506
NM_15392
J01536
You have a favorite gene, and you want to determine in what tissues it is expressed. Which one of the following resources is likely the most direct route to this information?
Entrez
Pubmed
PCR
UniGene
Which of the following databases is derived from mRNA information?
HTGS
PBD
dbEST
OMIM
Which of the following databases can be used to access text information about human diseases?
PBD
OMIM
EST
What is the difference between RefSeq and GenBank?
RefSeq includes publicly available DNA sequences submitted from individual laboratories and sequencing projects
GenBank provides nonredundant curated data
GenBank sequences are derived from RefSeq.
RefSeq sequences are derived from GenBank and provide nonredundant curated data.
.Orthologs are defined as
Homologous sequences in the same species that arose through gene duplication
Homologous sequences in the same species which have similar and often redundant functions
Homologous sequences in different species that share an ancestral gene
Homologous sequences that share little amino acid identity but share great structural similarity
A single piece of information in a database is called
Dataset
Field
File
Record
Literature databases include
Pubmed and PDB
MEDLINE and PDS
MEDLINE and PUBMED
MEDLINE and PDB
Which of the following is false about the ‘loop’ structure in proteins?
They connect helices and sheets
They are more flexible and can adopt multiple conformations
They are more tolerant of mutations
They are never the components of active sites
Approximately how large is the human genome?
3000Mb
3Mb
300Mb
30,000Mb
You have a reasonably short, typical, double-stranded DNA sequence.Basically, how many proteins can it potentially encode?
6
1
2
3
Approximately what percentage of the human genome consists of repetitive elements of various kinds?
0.5
0.05
0.85
0.25
What percentage of the human genome is devoted to the protein-coding regions?
1-5%
5-10%
10-20%
20-30%
Bioinformatics is also being regarded as part of the
Molecular biology
Computational biology
Computational biotechnology
Computer Knowledge
The best estimate for the number of human genes is
100000
1000000
50000
30000
The Protein Data Bank (PDB)
Contains approximately as many structures as there are protein sequences in SwissProt/TrEMBL
Is operated jointly by the NCBI and EBI
Includes data on proteins, DNA–protein complexes as well as carbohydrates
Functions primarily as the major worldwide repository of macromolecular secondary structures
20 micron = ..........nm
20 x 10-9
20 x 109
2000
20000
A bucky ball is a molecule consisting of ..........carbon atoms
50
60
75
100
A compound that has desirable properties to become a drug is called
lead
find
fit drug
fit compound
An example of Homology & similarity tool?
PROSPECT
EMBOSS
RASMOL
BLAST
Analysing or comparing entire genome of species
Bioinformatics
Genomics
Proteomics
Pharmacogenomics
Application of bioinformatics include
data storage and management
drug designing
understand relationships between
all of the above
Analyzing or comparing entire genome of species is called
Pharmacogenomics
Genomics
Bioinformatics
Proteomics
Which of the following is untrue about SCOP?
It is a database for comparing and classifying protein structures
It is constructed almost entirely based on manual examination of protein structures
The proteins are grouped into hierarchies of classes, folds, superfamilies, and families
The SCOP families consist of proteins having low sequence identity
SCOP is _______ based on manual comparison of structures by human experts with no quantitative criteria to group proteins
Almost entirely
Not
Partially
never
In CATH, Structural domain separation is carried by
a combined effort of a human expert and compute r programs
Manual comparison only
computer programs only
human expertise only
The term “whole-genome shotgun sequencing” refers to
A strategy to sequence an entire genome by breaking up DNA, cloning it into libraries, sequencing small fragments, then reassembling the fragments into a complete map
A strategy to sequence an entire genome by breaking up DNA, cloning it into libraries, hybridizing
small fragments, then reassembling the fragments into a complete map
A strategy to sequence an entire genome by breaking up DNA and sequencing using oligonucleotide primers that span the genomic DNA
ktups, substitution matrix
The initiation of FASTA format has ____ symbol
<
>
/
*
______ the smallest amino acid, has a hydrogen atom as the R group
Threonine
Glycine
Valine
Proline
Step wise method for solving problems in computer science is called
Algorithm
Flowchart
Sequential design
Procedure
PRINTS are software used for
Detection of gene from genome sequence
dentification of functional domain/motifs of protein
Prediction of function of a new gene
Detecton of tRNAs gene
Human genome contains about
3 billion base pairs
2 billion base pairs
5 billion base pairs
4 billion base pairs
Which of the following is a protein structure database
SwissProt
Genbank
PDB
DDBJ
The identification of drugs through genomic study is called
Genomics
Biochemistry
Pharmacogenomics
Bioinformatics
SWISS PROT is related to
Sequence data
portable data
swiss bank
Sequence data bank
One centiMorgan is defined as ____ percentage of the total recombination events
0.01
0.1
One
Ten
In general, if you compare the size of a pattern (also called a motif or fingerprint) and a domain
They are about the same size
The pattern is larger
The comparison always depends on the particular proteins in question
The pattern is smaller
In comparing two homologous but distantly related proteins
They tend to share more percent amino acid identity in common than three-dimensional structure features
They tend to share three-dimensional structure features and percent amino acid identity to a comparable extent
It is not reasonable to generalize about the extent to which they share three-dimensional structure features and percent amino acid identity
They tend to share more three-dimensional structure features in common than percent amino acid identity
The CATH database offers a hierarchical classification of protein structures. The first three levels, class (C), architecture (A), and topology (T), all describe
Protein secondary structure (e.g., secondary structure composition, packing, shape, orientation, and connectivity)
Protein domain structure
Protein superfamilies grouped according to homologous Domains
Protein tertiary structure (e.g., tertiary structure composition, packing, shape, orientation, and connectivity)
What is the source of protein structures in SCOP and CATH?
UniPROT
Ensembl
InterPro
Protein Data Bank
In an α helix, the R groups on the amino acid residues
stack within the interior of the helix
are found on the outside of the helix spiral
alternate between the outside and the inside of the helix
cause only right-handed helices to form
In an α helix, the R groups on the amino acid residues
stack within the interior of the helix
are found on the outside of the helix spiral
alternate between the outside and the inside of the helix
cause only right-handed helices to form
The process of introduction of foreign DNA into an animal cell is called
Transversion
Conversion
Inversion
Transfection
A _______ is defined in SCOP as a collection of superfamilies
Primary structure
Secondary structure
mutated protein
Protein Fold
Which of the following is a sequence alignment tool?
PIR
BLAST
PRINTS
PROSITE
The stages of mRNA processing include all of the following except
Splicing
Export
Methylation
Polyadenylation
Genbank is maintained by
SIB
NIG
NCBI
EBI
which alignment is useful to detect for highly conserved regions?
Multiple
Pairwise
Local
Global
when you are comparing two or more than two sequences of same or different organisms, What is the type of alignment?
Global
Pairwise
Multiple
Local
Your lab partner is using BLAST, and his best E value is 3. This means that
he’s found 3 proteins in the database that have the same sequence as his protein.
the chance that these similarities arose due to chance is one in 10^3.
there would be 3 matches that good in a database of this size by chance alone.
the match in amino acid sequences is perfect, except for the amino acids at 3 positions.
If you enter a set of IUPAC codes into BLAST, you are probably trying to
find out whether a certain protein has any role in human disease.
search for the genes that are located on the same chromosome as a gene whose sequence you have.
find which section of a piece of DNA is transcribed into mRNA.
determine the identity of a protein.
What would be a likely explanation for the existence of pseudogenes?
gene duplication
gene duplication and mutation events
mutation events
unequal crossing over
Two-dimensional gels are used to __________.
separate DNA fragments
separate RNA fragments
separate different proteins
observe a protein in two dimensions
How are so many different antibodies produced from fewer than 300 major genes?
gene duplication
alternative splicing mechanisms
the formation of polyproteins
recombination, deletions, and random assortment of DNA segments
Gene duplication has been found to be one of the major reasons for genome expansion in eukaryotes. In general, what would be the selective advantage of gene duplication?
If one gene copy is nonfunctional, a backup is available.
Larger genomes are more resistant to spontaneous mutations
Duplicated genes will make more of the protein product.
Gene duplication will lead to new species evolution.
As the complexity of an organism increases, all of the following characteristics emerge except.__________
the gene density decreases
the number of introns increases
the gene size increases
an increase in the number of chromosomes
CpG islands and codon bias are tools used in eukaryotic genomics to.__________
identify open reading frames
differentiate between eukaryotic and prokaryotic DNA sequences
find regulatory sequences
look for DNA-binding domains
Shotgun cloning differs from the clone-by-clone method in which of the following ways?
The location of the clone being sequenced is known relative to other clones within the genomic library in shotgun cloning.
Genetic markers are used to identify clones in shotgun cloning.
Computer software assembles the clones in the clone-by-clone method.
No genetic or physical maps of the genome are needed to begin shotgun cloning.
.If you were using a proteomics approach to find the cause of a muscle disorder, which of the following techniques might you be using?
creating a genomic library
sequencing the gene responsible for the disorder
developing physical maps from genomic clones
determining which environmental factors influence the expression of your gene of interest annotating the gene sequence.
Characterizing molecular component is
Genomics
Cheminformatics
Proteomics
Bioinformatics
Analyzing or comparing entire genome of species
Bioinformatics
Genomics
Proteomics
Pharmacogenomics
The identification of drugs through genomic study
Genomics
Cheminformatics
Pharmagenomics
Phrmacogenetics
Human genome contains about
2 billion base pairs
3 billion base pairs
4 billion base pairs
5 billion base pairs
Deposition of cDNA into inert structure is
DNA fingerprinting
DNA polymerase
DNA probes
DNA microarrays
First molecular biology server Expasy in the year?
1991
1992
1993
1994
.An example of Homology & similarity tool?
PROSPECT
EMBOSS
RASMOL
BLAST
SWISSPROT protein sequence database began in
1985
1986
1987
1988
The first bioinformatics database was created by
Richard Durbin
Dayhoff
Michael j.Dunn
Pearson
Laboratory work using computers and associated web-based analysis generally online’ is referred as
dry lab
web lab
wet lab
insilico
Laboratory work using computers and computer-generated models generally offline’ is referred as
dry lab
web lab
wet lab
insilico
Laboratory work using chemicals, drugs etc using water’ is referred as
dry lab
web lab
wet lab
in silico
The term used to refer something ‘performed on computer or computer simulation”
dry lab
web lab
invitro
in silico
The first published completed gene sequence was of
M 13 phage
T 4 phage
phi X174
lambda phage
.............are the extensions of bucky balls.
Geodesic domes
Hexagons
Carbon nanotubes
AFM and STM
1 meter = ..................nm.
109
10-9
1010
10-10
1 mm = ............nm
106
10-6
107
10-7
1 nanometre = ...........cm.
10-9
10-8
10-7
10-6
20 micron = ..........nm
20 x 10-9
20 x 109
2000
20000
A bucky ball is a molecule consisting of ..........carbon atoms
50
60
75
100
A compound that has desirable properties to become a drug is called
lead
find
fit drug
fit compound
An example of Homology & similarity tool?
PROSPECT
EMBOSS
RASMOL
BLAST
Analysing or comparing entire genome of species
Bioinformatics
Genomics
Proteomics
Pharmacogenomics
Application of bioinformatics include
data storage and management
drug designing
understand relationships between
all of the above
BLAST programme is used in
DNA sequencing
Amino acid sequencing
DNA bar coding
Bioinformatics
BLOSUM matrices are used for
Multiple sequence alignment
Pair wise sequence alignment
Phylogenetic analysis
All of the above
Characterizing molecular component is
Genomics
Cheminformatics
Proteomics
Bioinformatics
Deposition of cDNA into inert structure is
DNA fingerprinting
DNA polymerase
DNA probes
DNA microarrays
First molecular biology server Expasy in the year?
1991
1992
1993
1994
In a bucky ball, each carbon atom is bound to ...........adjacent carbon atoms.
1
2
3
4
invitro in latin means
within the
within the lab
outside the lab
outside the glass
Margaret Dayhoff developed the first protein sequence database called
SWISS PROT
PDB
Atlas of protein sequence and structure
Protein sequence databank
Nanotechnology, in other words, is
Carbon engineering
Atomic engineering
Small technology
Microphysics
Phylogenetic relationship can be shown by
Dendrogram
Gene Bank
Data retrieving tool
Data search tool
PRINTS are software used for
detection of genes from genome sequence
detection of tRNA genes
prediction of function of a new gene
Identification of functional domains/motifs of proteins
Proteomics is the study of
set of proteins
set of proteins in a specific region of the cell
entire set of expressed proteins in a cell
none of these
Step wise method for solving problems in computer science is called
flowchart
sequential design
procedure
algorithm
SWISS PORT is related to
Portable data
Swiss Bank data
Sequence data bank
Sequence data
SWISSPROT protein sequence database began in
1985
1986
1987
1988
The computational methodology that tries to find the best matching between two molecules, a receptor and ligand is called
molecular matching
molecular docking
molecular fitting
molecule affinity checking
The cut-off limit of human eye to see is ..................nm
10
100
1000
10000
The diameter of a bucky ball is about
1 Armstrong
100 Armstrong
1 nm
10 nm
The diameter of a bucky ball is about
1 Armstrong
10 Armstrong
100 Armstrong
1000 Armstrong
The diameter of fly ash particles is .............Âμm
10-May
20-Oct
20-30
100
The diameter of human hair is ....................m
75000
75
7.5 x 10-5
7.5 x 10-9
The diameter of hydrogen atom is ..............nm.
10
1
0.1
0.01
The hardest material found in nature is
steel
topaz
diamond
quartz
The most important property of nanomaterials is
force
friction
pressure
temperature
The size of a quantum dot is .............m.
5
5 x 10-9
5 x 10-10
5 x 10-11
The size of E. coli bacteria is .................nm.
75000
2000
200
5
The tensile strength of a carbon nanotube is ...........times that of steel.
10
25
100
1000
The term used to refer something performed on computer or computer simulation
dry lab
web lab
invitro
in silico
The tool for identification of motifs?
COPIA
Pattern hunter
PROSPECT
BLAST
The width of carbon nanotube is ............nm.
1
1.3
1.55
10
There is a plenty of room at the bottom. This was stated by
Issac Newton
Albert Einstein
Richard Feynman
Eric Drexler
