BIOINFORMATIK I UEBUNGEN

Regulation of transcription

TF classification by DNA-binding A. Zinc fingersB. Helix-turn-helix C. Leucine zipperD. Helix-loop-helix

hetero dimerization homo dimerization Transcription factor dimerization Leucine zippers

Protein 3D-structure Example: PPARg::RXRa+Rosi, 9-cis RA, NCOA2 (3dzy) PDB JMol Cn3D POLYVIEW-3D Proteopedia PDB identification code

Recombinant DNA technology Protein synthesis In vitro expression Libraries Gene transfer in animals and plants

Recombinant DNA technology Polymerases Nucleases

restriction enzymes Recombinant DNA technology

Ligases

Cloning

Cloning vector (pBR322) Plasmid Ampicillin resistance Tetracycline resistance Polylinker Origin of replication (ori)

Selection by antibiotics

Selection by X-gal

Exercise 3 1. CLONING EXPERIMENT Starting from a cloning sequence and find out which cloning vector (name, accnr, length) was used (e.g. using the tool VecScreen) Where is the insert in the given sequence located (position from-to, length) Identify the insert (name, accnr, organism, length, amino acid sequence, function) Determine the restriction enzyme (6bp cutter) used for incorporating the insert (name, sequence) Are there homolog proteins in humans (name, accnr, description, conserved domains) 2. PROTEIN 3D-STRUCTURE Show 3D protein structure of a homolog human protein (including DNA binding) (from 1) and give PDB identification code for this structure