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 [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 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, Zhang, M.Q Computational prediction of eukaryotic coding genes. Nat Rev. Genet Zhang, M.Q Computational prediction of eukaryotic coding genes. Nat Rev. Genet