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Assignment sample solution:
Lecture 5
overview
• Generic types of regulation control
• Regulation of the “sugar” lactose gene(s) for the bactria e. coli [ referred to as the lac operon]
• Regulation of the expression of the “amino acid” gene tryptophan in E. Coli. [try operon]
Part 1
• Two/three elements– What is its overall function defence (…– How the enzyme works (cleaves peptide bonds…)– Abnormal activity: break down connectivity tissue
(support structure) in lung…
Part 2: Regulation of Elastase• Brief overview of regulation at transcription
level (promoter enhancer/silencer); can also refer to other levels of regulation
• The specific regulation of elastase: where/when its transcription occur.
• Some elements involved it the expression of the gene. Some reference used by previous , unnamed, students include [1, 2,3,]
Part 3
• Show prokaryotic gene: transcription/transcription example (DNA -> mRNA ->AA) and explain the a contiguous DNA sequence is translated to give, via codons, to give an amino acid strand.
• Eukaryotic CDS structure: introns/exons (could also refer to A.S.)
• Explain, illustrate, that DNA is first converted into a pre-mRNA and then removal of introns gives an mRNA which is not identical to the DNA and so its translation will not be the same as in prokaryotic regulation
Part 4
• Describe how to find ORF: – Translated DNA sequence over all 6 reading frames (use a diagram
or otherwise to illustrate this) – Determine all possible start stop regions.– Look for regions that have a start /stop sequences
• Ways to eliminate false positives [4]:– Size of ORF– Proximity of promoter– Bases sequences (specific bp ratios and other sequence structures) – Determine similarity to existing “known” coding sequences
Part 5a code• A script that retrieves a DNA sequence (only)• Translates the sequence into amino acids (single letters and not
abbreviations (M not Met)• Repeat the above overall 6 reading frames:• Frames 1 to 3 :
– shifting the sequences 1 character and repeating the translation process
• Frames 4-6 – get the compliment of the primary stand and revers it;– Repeat the translation process
• Search each seq for starts and stops•
Part 5b code• Determine the position of the start and stop• Determine the length of sequences where you
have a start followed by a stop • Eliminate those whose length is less than 20• Display the results for all 6 reading frames in a
user friendly format.
Reference • [1] Nuchprayoon, I., Simkevich, C. P., Luo, Friedman, A. D. , and M.,
Rosmarin, A. G., (2012). “GABP Cooperates With c-Myb and C/EBP to Activate the Neutrophil Elastase Promoter”. Blood June 15, 1997 vol. 89 no. 12 4546-4554.
• [2] Oelgeschläger, M., Nuchprayoon, I., Lüscher, B., and Friedman, A.D. (1996). “C/EBP, c-Myb, and PU.1 cooperate to regulate the neutrophil elastase promoter”. Mol Cell Biol. 1996 September; 16(9): 4717–4725.
• [3] Zimmer, M., Medcalf, R. L, Fink, 1. M., Mattmann, C., Lichter, P., Jenne, D. E. (1992). “Three human elastase-like genes coordinately expressed in the myelomonocytic lineage are organized as a single genetic locus on l9pter”. Proc. No4. Acad. Sci. USA 89, 8215-8219.
• Zhang, M.Q. 2002 Computational prediction of eukaryotic coding genes. Nat Rev. Genet. 3 698-709 .