Using Python to Analyze a Protein By Aaron

Using Python to Analyze a Protein By Aaron Mathieu for AP Biology (grades 11 & 12)

Start By Picking Protein and Finding Amino Acid Sequence MALWMRLLPLLALLALWGPDPAAAF VNQHLCGSHLVEALYLVCGERGFFY TPKTRREAEDLQVGQVELGGGPGA GSLQPLALEGSLQKRGIVEQCCTSIC SLYQLENYCN

Use the Model to Analyze the Protein Amino Acid Sequence Human Hemoglobin subunit alpha MVLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVADA LTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVS TVLTSKYR Human Alpha-amylase 1 MKLFWLLFTIGFCWAQYSSNTQQGRTSIVHLFEWRWVDIALECERYLAPKGFGGVQVSPPNENVAIH NPFRPWWERYQPVSYKLCTRSGNEDEFRNMVTRCNNVGVRIYVDAVINHMCGNAVSAGTSSTCGS YFNPGSRDFPAVPYSGWDFNDGKCKTGSGDIENYNDATQVRDCRLSGLLDLALGKDYVRSKIAEYM NHLIDIGVAGFRIDASKHMWPGDIKAILDKLHNLNSNWFPEGSKPFIYQEVIDLGGEPIKSSDYFGNG RVTEFKYGAKLGTVIRKWNGEKMSYLKNWGEGWGFMPSDRALVFVDNHDNQRGHGAGGASILTF WDARLYKMAVGFMLAHPYGFTRVMSSYRWPRYFENGKDVNDWVGPPNDNGVTKEVTINPDTTCGN DWVCEHRWRQIRNMVNFRNVVDGQPFTNWYDNGSNQVAFGRGNRGFIVFNNDDWTFSLTLQTGL PAGTYCDVISGDKINGNCTGIKIYVSDDGKAHFSISNSAEDPFIAIHAESKL Human Catalase MADSRDPASDQMQHWKEQRAAQKADVLTTGAGNPVGDKLNVITVGPRGPLLVQDVVFTDEMAHFD RERIPERVVHAKGAGAFGYFEVTHDITKYSKAKVFEHIGKKTPIAVRFSTVAGESGSADTVRDPRGFAV KFYTEDGNWDLVGNNTPIFFIRDPILFPSFIHSQKRNPQTHLKDPDMVWDFWSLRPESLHQVSFLFSD RGIPDGHRHMNGYGSHTFKLVNANGEAVYCKFHYKTDQGIKNLSVEDAARLSQEDPDYGIRDLFNAIA TGKYPSWTFYIQVMTFNQAETFPFNPFDLTKVWPHKDYPLIPVGKLVLNRNPVNYFAEVEQIAFDPSN MPPGIEASPDKMLQGRLFAYPDTHRHRLGPNYLHIPVNCPYRARVANYQRDGPMCMQDNQGGAPN YYPNSFGAPEQQPSALEHSIQYSGEVRRFNTANDDNVTQVRAFYVNVLNEEQRKRLCENIAGHLKDA QIFIQKKAVKNFTEVHPDYGSHIQALLDKYNAEKPKNAIHTFVQSGSHLAAREKANL

Observing Python to Analyze a Protein

For your protein answer the following questions: 1. How many positive amino acids are in your chosen protein? 2. How many negative amino acids are in your chosen protein? 3. How many non-polar, hydrophobic amino acids are in your chosen protein? 4. How many polar, hydrophilic amino acids are in your chosen protein? 5. How many “special” amino acids are in your chosen protein?

Coding Challenge Determine the number of each amino acid in protein Figure out how many regions of the sequence are likely to form alpha helixes (alpha-helix tend to be rich in Glu, Ala, Leu, Met, Lys, Arg, Gln, His) Figure out how many regions of the sequence are likely to form beta pleated helixes (beta-sheets are rich in Val, Ile, Tyr, Cys, Trp, Phe, Thr) Find how many regions of the sequence are likely to form turns and loops (turns and loops are rich in Gly, Asn, Asp, Pro, Ser) Identify if there any large regions that are hydrophobic Predict how many disulfide bonds might form in a protein’s tertiary structure (these form in Cystine)