Chapter-Genomics and Bioinformatics

(a)

Exp: Human genome project was officially started on October 1,1990.

(c)

Exp: The first set of whole genome sequences of the smallest genome Mycoplasma genitalium and Haemophilus influenzae.

(a)

Exp: Celera genomics is dedicated to sequencing of human and mouse genomes. Celera focuses on genetic sequencing and related technologies.

(b)

Exp: BAC vectors are used in making a genomic library in which insert size is 80-100 kb.

(b)

Exp: A single base difference in the ApoE gene is associated with Alzheimer’s disease.

(a)

Exp: Huntington is an autosomal dominant disease located on 4^th chromosome.

(c)

Exp: Nick translation was developed by Rigby and Paul Berg in 1977.

(d)

Exp: In comparative hybridization experiments, comparisons between the amounts of mRNA are done in two cell populations.

(c)

Exp: The reporters that are used in comparative cDNA hybridization microarray are fluorescent dyes (fluors).

(b)

Exp: Microarrays are made from a collection of purified DNA molecules using an arraying machine.

(a)

Exp: The number of chromosome in E.coliis 1, genome size in bp is 500,000 and the number of predicted gene is 5,000.

(d)

Exp: Gene prediction is done by using programs like GeneMark (bacterial genome) and GENSCAN (eukaryotes). GENSCAN can identify introns, exons, promotor sites and poly A signals and other gene identification algorithms.

(c)

Exp: Gene prediction is done by using programs like GeneMark (bacterial genome) and GENSCAN (eukaryotes).

(b)

Exp: In eukaryotes the gene prediction is quite complex as the genome is the combination of exons and introns. Prokaryotes do not have introns and the gene is continuous.

(d)

Exp: EST data is used to infer expression patterns by counting the number of ESTs corresponding to each gene divided by the total number of ESTs. Millions of ESTs are deposited in a special database called dbESTs.

(c)

Exp: The genomic DNA refers to the nuclear DNA. The GST approach is similar to EST. One read of sequence was obtained from either end. This data is referred to as genomic sequence tags.

(a)

Exp: All Web based tools are available free e.g. BLAST, Gene level sequence etc.

(c)

Exp: The taxonomic browser provides information on taxonomic classification of various species. This database has information on over 79,000 organisms.

(d)

Exp: Locus link carries information on the official gene names and other descriptive information about genes. By this one can access information on homologous genes.

(a)

Exp: The sequences being similar does not mean that they are homologous. Homology is defined as similarity due to common ancestry. BLAST is used for analyzing sequence information

(b)

Exp: Duplicated genes within a genome have similarities and these are referred as paralogs. Homologues will have the same function whereas paralogs may differ in functions.

(c)

Exp: Homologene is a database of orthologs and homologs for human, mouse, rat, zebrafish and cow genes represented in UniGene and Locus Link. It is very easy to find homologous relations using this database.

(a)

Exp: RefSeq is a well-verified database of mRNAs and proteins of human, mouse and rat. This data is used in many cases e.g. DNA chips and describing the sequence features of human genome.

(c)

Exp: The history of bioinformatics began when Ingram demonstrated that there is homology between sickle cell haemoglobin and normal haemoglobin.

(c)

Exp: Genome annotation is the attachment of biological information to the provided sequences.

(a)

Exp: The two sequences are different from each by one base i.e. T in place of C. Hence it is a SNP.

(c)

Exp: Unigene database is created to manage the redundancy in EST data. The objective is to group ESTs into sets called clusters that belongs to ‘one’ gene; here Uni means one.

(c)

Exp: The genomic library of Plasmodium falciparum can be easily generated by digestion with Mnase. This library is used for gene identification in P. falciparum.

(a)

Exp: DNA is present in nucleus as well as in mitochondria and chloroplast.

(d)

Exp: The real significance of genomics began with the introduction of Human Genome Project (HGP) in the mid-1980s.

(c)

Exp: Structural genomic involves high-throughput DNA sequencing followed by assembly, organization and management of DNA sequences. It also includes determination of three-dimensional structure of all the proteins.

(a)

Exp: This technology is DNA Microarray that promises to monitor the whole genome on a single microchip.

The principal behind DNA Microarray Technology is base pairing or hybridization between the nucleotides. Base pairing allows probes to hybridize to targets on the Microarray.

(d)

Exp: There are several names to DNA microarray technology such as DNA arrays, gene chips, biochips, DNA chips and gene arrays.

(c)

Exp: DNA microarrays work on the principle of base pairing. Base pairing allows probes to hybridize to targets on the Microarray.

(b)

Exp: FISH (Fluorescent in situ hybridization) is a cytogenetic technique that can be used to detect and localize the presence or absence of specific DNA sequences on chromosomes.

(d)

Exp: FISH technology is useful in detecting the status of disease during interphase of cell division.

(a)

Exp: Comparative Genomic Hybridization (CGH) is a molecular- cytogenetic method for the analysis of copy number changes (gains or losses) in DNA. Comparative cDNA hybridization microarray compares the amounts of different mRNA in two cell populations.

(c)

Exp: Expressed Sequence Tag is a unique stretch of DNA within a coding region of a gene. Craig Venter and co-workers isolated mRNA molecules and constructed cDNA molecules to create expressed sequence tags or ESTs.

(a)

Exp: Expressed Sequence Tag is a unique stretch of DNA within a coding region of a gene. It is useful for identifying full-length genes and serves as a landmark for mapping.

(b)

Exp: Gene prediction is an important problem for computational biology.Homology based Gene prediction is the first and most commonly used tool to discover new genes.

(c)

Exp: Annotation is a process that identifies genes, their regulatory sequences, and their function. After a genome sequence has been obtained and checked for accuracy, the next task is to find all the genes that encode proteins.

(b)

Exp: The data library was established to collect, Organize and distribute nucleotide sequence data and related information at the European Molecular Biology Laboratory (EMBL) in 1980.

(a)

Exp: The National Biomedical Research Foundation (NBRF) as a resource to assist researchers in the identification and interpretation of protein sequence information established the Protein Information Resources (PIR) in 1984.

(c)

Exp: The nomenclature system in bioinformatics is based on the recommendations of International Union of Pure and Applied Chemistry (IUPAC). Different Laboratories of the world follow nomenclature system of IUPAC so that the data set can be uniformed and easy to compare.

(b)

Exp: Nucleotides are the building blocks of DNA and each nucleotide consists of three components -

I. a nitrogenous base (purine or pyrimidine)

II. a pentose sugar and

III. a phosphate residue

(a)

Exp: The purines (adenine and guanine) are present in both deoxyribonucleotides and ribonucleotides

c) Each nucleotide consists of three components-

A nitrogenous base (purine or pyrimidine)

A pentose sugar and

A phosphate residue

(b)

Exp: A nucleic acid is a macromolecule composed of chains of monomeric nucleotides.

(b)

Exp:The DNA molecule is constituted by nucleotides consisting of adenine, guanine, thymine and cytosine. Uracil is found only in RNA while thymine is found only in DNA.

(c)

Exp:The constituents of nucleotides are nucleoside and phosphate. Nucleotides are molecules, which comprise the structural units of RNA and DNA.

(a)

Exp: Humans can produce 10 of the 20 amino acids. The others must be supplied in the food.

d)

Exp: The Mouse genome database (MGD) is the primary public catalogue for mouse genome. It includes information on mouse genetic markers, nomenclature, molecular segments, physical maps and many other aspects of mouse genome.

b)

Exp:The genome database (GDB) maintains data created for genome mapping of Human genome project. The GDB stores a vast data submitted by hundreds of investigators.

(a)

Exp: To develop information systems in molecular biology the NCBI was established at the National institute of health (USA). The NCBI is the first and foremost store of publicly available genomic and proteomics data.

(b)

Exp: Locuslink provides a single query interface to organize sequence and descriptive information about genetic loci. It presents information on official nomenclature, sequence accessions, phenotypes, EC numbers, MIM numbers, UniGene clusters, homology, map locations.

(a)

Exp: The taxonomy browser is an original data analysis tool for visualizing the taxonomic relationships among the prokaryotes. It provides information on taxonomic classification of various species; it has information on over 79,000 organisms.

(d)

Exp: Duplicated genes within a genome may have similarities but these are referred as paralogs. Homologues will have the same function whereas paralogs may differ in functions.

(c)

Exp: FASTA stands for FAST ALL. It can be used for fast protein comparison or fast nucleotide comparison. This program achieves high level of sensitivity for similarity searching at high speed.

(d)

Exp: A curator is one who reviews and checks newly submitted data. This process is called curation. He ensures that all necessary information is given for e.g.

1. Biological features are adequately described.

2. Translation of any coding regions obeys universal translation rules.

(b) This term was coined by H.Winkler in 1920 for the full set of chromosomes. He was Professor of Botany at the University of Hamburg, Germany.

(b) According to IUPAC nomenclature S codes for G or C.

(b) ENTREZ is a database through which all of its component databases can be accessed and retrieved.

(b) Reverse transcriptase is used in making cDNA to mRNA. DNase produces single stranded nicks and these nicks are sealed by DNA ligase.

(c) According to IUPAC nomenclature sometime the complement symbol is same.

(d) SWISS- PROT is a database resource provided by NCBI for annotated protein sequence.

(d) According to IUPAC nomenclature Ile is the code for Isoleucine.

(a) According to IUPAC nomenclature R codes for G or C.

(d) Many redundant in ESTs are generated during the course of its production. Because several cDNA clones represent the same gene, to manage the redundancy in EST data UniGene database was created. The objective is to group ESTs into sets called clusters that belong to one gene.

(a) According to IUPAC nomenclature for G or T is K.

(b) According to the concept of directionality proteins are synthesized in N’ to C’ direction.

(a)

(b) According to IUPAC nomenclature T is the complementary nucleotide for A

(a) According to IUPAC nomenclature Glu is the three-letter code for Glutamine.

(a) According to the concept of directionality nucleotides are synthesized in 5’ to 3’ direction.

(a) According to IUPAC nomenclature M codes for A or C.

(c) The locus link presents information about official nomenclature, sequence accessions, phenotypes, EC numbers, MIM numbers, UniGene clusters, and homology, map locations.

(d) According to IUPAC nomenclature complement of H is D.

(b) Stands for FAST ALL. It can be used for fast protein comparison or fast nucleotide comparison. This program achieves high level of sensitivity for similarity searching at high speed.

(a) According to IUPAC nomenclature G or A or T is coded by D.

(c) As Random sequencing does not require any pexisting information about the sequence hence it is also known as de nova sequencing.

(c) Fluorescent in situ hybridization.

(d) According to IUPAC nomenclature Y codes for T or C.

(c) This term was coined first time in 1986 by Thomas Roderick. He described scientific discipline of mapping, sequencing and analyzing genomes under genomics.

(c) By gene prediction and gene counting it is known that out of 25,500 genes only 20% are encodes for protein.

(d) According to IUPAC nomenclature W codes for tryptophan.

(c) Reverse transcriptase is used in making cDNA to mRNA. DNase produces single stranded nicks and these nicks are sealed by DNA ligase.

(a) FISH (Fluorescent in situ hybridization) is a cytogenetic technique that can be used to detect and localize the presence or absence of specific DNA sequences on chromosomes.

(a) According to IUPAC nomenclature N codes for G or A or T or C.

(c) A probe can be a sequence of either RNA or DNA but in microarray technology DNA is used as a probe.

(c) Gene prediction is done by using programs like GeneMark (bacterial genome) and GENSCAN (eukaryotes). GENSCAN can identify introns, exons, promotor sites and poly A signals and other gene identification algorithms.

(c) According to IUPAC nomenclature the complement for R is Y.

(b) This technology is DNA Microarray that promises to monitor the whole genome on a single microchip.

The principal behind DNA Microarray Technology is base pairing or hybridization between the nucleotides. Base pairing allows probes to hybridize to targets on the Microarray.

(b) Variation in cell cycle can be studied by DNA microarray technology.

(c) Messenger RNA is transcribed from DNA and carries message for protein synthesis.

(d) Caenorhabditis elegans is one of the organism whose genome has been sequenced.

(b) Defects in regulatory genes can be identified by DNA microarray technology.

(c) According to IUPAC nomenclature the one letter code for amino acid lysine is K.

(b) Complementary DNA or cDNA is synthesized from mature RNA catalyzed by reverse transcriptase.