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Using Python to Analyze a Protein

Learn how to analyze a protein using Python. Find amino acid sequences, identify types of amino acids, predict secondary structures, and determine the presence of disulfide bonds.

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Using Python to Analyze a Protein

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

  2. Start By Picking Protein and Finding Amino Acid Sequence MALWMRLLPLLALLALWGPDPAAAFVNQHLCGSHLVEALYLVCGERGFFYTPKTRREAEDLQVGQVELGGGPGAGSLQPLALEGSLQKRGIVEQCCTSICSLYQLENYCN

  3. Use the Model to Analyze the Protein

  4. Observing Python to Analyze a Protein

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

  6. 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 are any large regions that are hydrophobic • Predict how many disulfide bonds might form in a protein’s tertiary structure (these form in Cystine)

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