KP Ramirez Week 2

Notes

four plants from the wild: two green, one red, and one white.

Your customers would really like to have purple flowers from this plant. You set out to create a true-breeding purple flower.

Hypothesis Testing In the three Aipotu labs, you will use a process much like that used by practicing scientists as they conduct research. Although this process almost never follows a formula, it often proceeds as follows: 1. Observe Patterns. Observe the natural world and look for patterns, exceptional events, etc. For example, you might observe that red proteins tend to have long thin shapes. 2. Develop hypotheses. From the observations, you define testable hypotheses – statements or questions that can be addressed experimentally. Continuing the example, you might reasonably hypothesize that long thin proteins will be red. 3. Test hypotheses. You then set up experiments or observations that will collect data that bear on your hypothesis. In the example, you might type in a sequence of amino acids that would be expected to fold into a long thin shape, fold the protein, and observe its color. If your hypothesis is correct, it will be red. If you get another result, your hypothesis is incorrect. 4. Revise hypotheses as necessary. If your results do not match your prediction, you need to revise your hypothesis and go to Step (3) again until they do match.

Tasks: Work together as a class to: • Determine the differences in amino acid sequence between the proteins produced by the alleles you found in Part I. • Determine how the amino acid sequence of a pigment protein determines its color. • Explain, in terms of the proteins present, the interactions between the alleles you found in part I. o Why is the color phenotype of some pigment proteins dominant while others are recessive? o How do the pigment proteins combine to produce the overall color of the plant? • Construct a purple protein to demonstrate your understanding of this process.

Assignment

Specific Tasks for this section Work as a class, using the data blog to:

• What are the differences in the amino acid sequences of the proteins produced by the

alleles you define in Part I? Hint: use the Compare menu to find the difference(s) between the amino acid sequences.

• What features of the amino acid sequence make a protein pigmented?
• What features of the amino acid sequence make a protein a particular color?
• How do the colors combine to produce an overall color? How does this explain the

genotype-phenotype rules you found in part (I)?

• Which proteins are found in each of the four starting organisms?
• Using this knowledge, construct a purple protein.

Notes

Allele Protein Structures

• Green:Met-Ser-Asn-Arg-His-Ile-Leu-Leu-Val-Tyr-Trp-Arg-Gln
• Blue:Met-Ser-Asn-Arg-His-Ile-Leu-Leu-Val-Tyr-Cys-Arg-Gln
• Yellow:Met-Ser-Asn-Arg-His-Ile-Leu-Leu-Val-Trp-Cys-Arg-Gln
• Red:Met-Ser-Asn-Arg-His-Ile-Leu-Leu-Val-Phe-Cys-Arg-Gln
• White:Met-Ser-Asn-Arg-His-Ile-Leu-Leu-Val-Val-Cys-Arg-Gln

Flowers

• Green green/green
• Green2 Blue/Yellow
• Red: Red/nothing
• White: White/White