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Exam in Gene Technology & Molecular Biology (BB1110), Saturday 28/1-2012, 9:00-13:00h. The answers should be brief!!

Max: 82p; pass: 41p. Write your name on all papers! Dont forget to write your email address on the cover, as this is the means by which you will receive your result!
1. The gene concept has changed somewhat over time. Why is that so and explain, in your own words, how a gene is defined today (post ENCODE project). (4p) 2. Transcription factors are important in transcription regulation, but their specificity and activity differ a lot. Explain how this works, and how it is possible that certain regulatory gene elements function well despite being located far away, either upor downstream, from the actual transcription start site. (4p) 3. What are the different sources of dsRNA and antisense RNA molecules that affect gene expression, and how do they operate? (5p) 4. Mention three common vectors used in recombinant DNA technology, and some of their important, common as well as specific, properties/features. (5p) 5. PCR reactions should be specific, but will sometimes also result in the amplification of unintended products. Explain why that is, and how the PCR procedure can be modified for greater specificity. (3p) 6. Pyrosequencing is central to the relatively new high-throughput 454-sequencing platform by Roche, which can be used for whole genome sequencing and transcriptome analysis. Briefly, describe how pyrosequencing works, and how it is applied in the 454 platform. (5p) 7. You have got an assignment to express a eukaryotic protein. Unfortunately, it seems that the protein cannot be successfully/functionally expressed in your prokaryotic host. What might be the reasons for this, and how can it be addressed? (4p) 8. Many different cell types can be used as hosts for recombinant protein production. Compare the utility of E. coli, yeast and mammalian expression systems with respect to parameters relevant for protein production (e.g., cost efficiency, PTMs, productivity, ease of use etc.). (6p) 9. Explain how baculovirus insect cell expression systems can be used in heterologous protein production. (3p) 10. Metabolic load is an issue associated with recombinant protein expression. Explain what metabolic load is, and give examples of measures (at least three) that can be undertaken to overcome high metabolic load. (4p) 11. There exist several types of genetic markers that can be used for genotyping. Explain the difference behind three such markers, and how they can be used/analyzed in this context. (5p) 12. In the field of protein engineering, it is common to work with protein libraries instead of specific protein mutants when one wants to identify/obtain novel variants with desired properties. Why is that the case, and explain/mention some important considerations when creating and working with such libraries. (5p)

13. A researcher is planning a project where she needs to create a peptide library, each peptide consisting of five amino acid residues. She would like to display the peptides on phage and then through bio-panning identify peptide variants that bind a certain target protein. Help her design a so-called degenerate codon (for the coding strand) that may encode isoleucine, asparagine, threonine or lysine in each of the five amino acid positions. Theoretically, how many peptide variants and nucleotide variants would such a library contain? (4p) 14. Describe the difference between traditional and subunit vaccines? What are the potential advantages and disadvantages with the two vaccine types? (4p) 15. Explain (a) what gene therapy is, and (b) what vector type used for gene delivery that is the most common one, and why this is the case. Briefly, also discuss/mention some issues (at least three) that have to be considered to get an efficient gene therapy system. (5p) 16. What is the difference between a transgenic plant and one that allows transient expression of the transgene? (2p) Agrobacterium carrying a Ti plasmid can be used to introduce transgenes in plants. Another useful method is gene-gun/micro particle bombardment. State some advantages and disadvantages of the gene-gun approach in comparison to that of using Agrobacterium? (2p) 17. Knockout mice are a valuable tool for investigation of the gene function behind embryonic development or certain diseases. How can you create a knockout mouse, and how would you deal with genes that are important during embryonic development? (5p) 18. Explain the concept of proteome and proteomics, and why this research field is an important complement to that of genomics and transcriptomics. (5p) 19. What is the difference between genomics and metagenomics? (2p)

Single letter code: B= C or G or T D= A or G or T H= A or C or T K= G or T M= A or C N= A or C or G or T R= A or G S= C or G V= A or C or G W= A or T Y= C or T