Bioinformatics Exercises
  A.Biology. Basic Knowledge in Biology
  Writer : Seyeon Weon   Updated : 10-13   Hit : 2236   Updates 
The questions below are to check some basic knowledge in biology. You don't need to write long answers at all. Just write down very brief answers for each. This assignment is not to give you a heavy load of work, but to give you a chance to review and refresh your knowledge in biology.
Briefly answer the following questions:
  1. Why is DNA more stable than RNA?
  2. What will happen if we put DNA duplex into pure distilled water?
  3. Why is thymine used in DNA instead of uracil?
  4. The whole E. coli genome is about 4.6 Mbp. How many copies of E. coli genome can be present in 1 micro gram of DNA sample?
  5. Promoters are the region located at the 5' end of genes. They are recognized by RNA polymerases and the recognition is the most important step for the initiation of gene expression. If we assume that there are 1000 promoters in E. coli genome and all of them have the same sequence, what would be the minimum length of this promoter sequence, assuming that RNA polymerases recognize bases as we read alphabets?
  6. What is the average size of the DNA fragments that are obtained from the full digestion by 2 different restriction enzymes in a single reaction mixture, in which one is 6 base and the other one is 4 base recognition?
  7. The communication of information in life is done by the complementarity of molecules. Protein sequence is determined by mRNA sequence, which is in turn copied from DNA sequence. We call this flow of information from DNA to RNA to protein as the central dogma of life. RNA can easily be copied from DNA by the molecular complementarity since they use the same complementary pairs of bases. (The difference between uracil and thymine does not hinder the complementarity.) In contrast, protein has no such obvious complementarity with RNA. Then, how can the information in protein sequence be copied from mRNA? What is the key step in this inter-lingual communication?
  8. Transcription is the process of making RNA from DNA. (Translation is making protein from mRNA.) Chromosomes are either closed circles (for eubacteria and archaebacteria) or very long linear strings (for eukaryotes). What could happen physically on these chromosomes while a region within them is being transcribed?
  9. What is the fundamental reason that we can only separate DNA fragments of about one thousand bases or so at the very best using the current sequencing machines?
  10. What is the most important discovery done by James D. Watson for the elucidation of DNA structure?
  11. There was a great fuss about being human genome sequencing done in the first half of this year. But, in reality only 20 some percent (as of this writing) of the human genome is in finished stage, which is still not the one we would expect when we say "the exact sequence of the human species". Write your opinion about why this discrepancy could happen. (No 7 line limitation)
  12. DNA microarrays could be described as "high density dot blot" or "reverse Southern blot in a high-throughput style". If the changes in the DNA microarrays comparing to the conventional molecular biology methods were only being "high density" or "high-throughput, what you need to learn to become the competent biologist of the 21st century would not be this much. What are the things that give us this pain? Focus your discussion on DNA microarrays. (No 7 line limitation)
  13. Numerous reports have been seen for the discoveries of the genes that are responsible for cancers, schizophrenia, cardiovascular diseases, etc. It seems that we have been stuck on this stage for years. Just keep on reporting new genes. Of course, these complex diseases should be caused by several genes. Except being caused by many genes, what could be the main reason beneath this slow progress? The question is not about "gene therapy", which is the subject of next question.
  14. Gene therapy has been around us (i.e., molecular biologists) for many years. But, we all know that it is still far way from being practical. There are many problems to overcome, such as delivery problem, targeting problem, and so on. Suppose that you somehow discovered a perfect method that could deliver a reagent only to target cells without degradation and the reagent could perfectly and only block the expression of the target gene. With this absolutely precise weapon, would you think that we could finally conquer the diseases in question 13?
  15. Recently the result of an extensive study about Y chromosomal Adam was reported. This result does not match well with the previous result from mitochondrial Eve. What could be the cause of this discrepancy? (Actually, no need to consult the original research paper. Just use your basic knowledge in biology for your discussion.)