Biotechnology Question Bank, Functional and Structural Genomics, Genetic Variations

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7. Differentiate between functional and structural genomics?

  • Functional genomics- this is a field of study which co-relates the structure and sequence of the genome to its function. In this field the information provided by structure genomics is used to study the function of genes or protein in a systematic manner.

  • Structural Genomics- In structural genomics, one studies the sequence-structure relationship of a genome. It represents an initial phase of genome analysis which involves creating high resolution genetic physical and transcript maps and ultimately sequencing the genome. Because of rapid advances in the field of proteomics the study of three dimension structure of all proteins has also become easier because of structural genomics.

8. What causes genetic variations in individuals?

  • The genetic variations are caused due to single nucleotide polymorphisms or SNPs which can occur both in the coding and non-coding regions of the genome. It is believed that SNPs occur at 1.6 million to 3.2 million sites in the human genome and may affect gene function, depending upon exact base change and where it occurs.

  • 9. If you are given a sequence without any label, how will you find out whether it is a DNA sequence or RNA sequence or a protein sequence?The usual approach taken by standard computer programs like sequence search programs scan the first 20 symbols. If the symbols encountered switch between any of the 4 bases only, then the sequence at hand is taken as a DNA sequence. Instead of T if U is encountered, then it is an RNA sequence. But if the symbols switch between any of the 20 (other than 4), then it is taken as protein sequence.

  • The usual approach taken by standard computer programs like sequence search programs scan the first 20 symbols. If the symbols encountered switch between any of the 4 bases only, then the sequence at hand is taken as a DNA sequence. Instead of T if U is encountered, then it is an RNA sequence. But if the symbols switch between any of the 20 (other than 4),

10. What is Human Genome Project?

  • The Human Genome project officially started on 1 Oct, 1990 in the United States, as a 15 year programme to map and sequence the complete set of human chromosomes, as well as those of general model organisms. The strategy of this international project was to make a series of maps of each human chromosome at increasingly finer resolution.

  • In this approach chromosomes were divided into smaller fragments that could be cloned and fragments were arranged to correspond to their locations on a chromosome. After mapping, each of these ordered fragments would be sequenced.

11. How can FISH technique help in the detection of chromosomal abnormalities?

  • The application of FISH can be illustrated by taking an example of chronic mylogenous leukaemia (CML). It was observed from the karyotype analysis of the lymphocyte preparation made from blood samples of CML patients that there was a 9-22 translocation in the chromosome (Philadelphia chromosome). Although by counting the number of such cells it was possible to find out the severity of the disease, it was not an easy procedure.

  • The regions on the chromosomes involved in translocation were identified on chromosomes 9 and 22 from the DNA library it was possible to pick up clones carrying the particular genes involved in CML. Using nick translation, it was possible to fluorescently label chromosome 9 region with red colour and chromosome 22 region with green colour and prepare the probe. It was observed that when CML lymphocytes smeared cells were hybridized with the two probes in situ and when observed under fluorescent microscope, the cells, which were affected, appeared as red and green.

12. What are the reasons for completely sequencing a genome?

The reasons for completely sequencing a genome are:

  • It provides a base for the discovery of all inventories of genes.

  • The sequence shows the relationship between genes.

  • It provides a set of tools for future experimentation.

  • The sequencing provides an index to draw and organize all genetic information about the organism.

  • Ultimately the whole genome sequence becomes an archive for further containing all the genetic information required to make the organism.

13. How can microarray be used for comparative studies?

  • If one were to study the effect of certain drugs or say a cancerous cell so as to see which genes are activated or switched off vis-à-vis a normal cell one can use the Microarray technology as a comparative tool. Now in order to study the expression of different genes under different conditions one needs to look into the different mRNA population in the cell since it is the mRNA which gets converted into proteins. mRNA accounts for only 3% of the total RNA of a cell. The m-RNA is first converted into its cDNA by RT PCR since the mRNA is very unstable and prone to attack by RNase in vitro conditions.

  • The cDNA is more stable. Reporter fluorescent molecules are tagged on to the cDNA. Two samples are taken one of a normal people and another of the cancerous person which is to be compared. The normal persons and the cancerous person’s cDNAs are labeled with different (for example Red and Green) fluorescent dyes.

  • The samples are then spotted on to the various DNA spots on the microarray. If there is a match i.e. the sample DNA hybridize with the DNA on the microarray then the spots whose mRNA is present at a higher level in one or the other cell population shows up as predominantly red or green. Yellow spots have roughly equal amounts of bound cDNA from each cell population. This way the whole genome can be monitored for expression studies on a single glass slide.

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