KP Ramirez Week 2

Notes

four plants from the wild: two green, one red, and one white. Create a True Breeding Purple Allele

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

1. Met non polar, hydrophobic. Ser polar uncharged. Asn polar uncharged. Arg polar uncharged. His Polar uncharged. Ile Nonpolar hydrophobic. Leu Nonpolar hydrophobic. Val Nonpolar hydrophobic. TYR polar uncharged. TRP nonpolar hydrophobic. Arg polar uncharged. Gln polar uncharged.

• Blue:

Met-Ser-Asn-Arg-His-Ile-Leu-Leu-Val-Tyr-Cys-Arg-Gln

TYR-polar uncharged, CYS-polar uncharged

• Yellow:

Met-Ser-Asn-Arg-His-Ile-Leu-Leu-Val-Trp-Cys-Arg-Gln

TRP-Nonpolar hydrophobic, CYS-polar uncharged

• Red:

Met-Ser-Asn-Arg-His-Ile-Leu-Leu-Val-Phe-Cys-Arg-Gln

PHE-nonpolar hydrophobic CYS-Polar uncharged

• White:

Met-Ser-Asn-Arg-His-Ile-Leu-Leu-Val-Val-Cys-Arg-Gln

Val-Nonpolar hydrophobic, CYS polar uncharged.

Flowers

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

Phenotypes & Genotypes

• Green-CgCg
• White-CwCw
• Red -CrCr
• Blue -CbCb
• Orange-Needs yellow and red CrCy
• Yellow-CyCy
• Purple -Needs Red and blue CrCb
• Black -Needs red and green CrCg

Charged, acidic (-) basic (+) form ionic bonds Uncharged polar form H-bonds Hydrophobic(nonpolar) hydrophobic interaction, van der waals

There are positions that are important, look at the characteristics of amino acid side chains. Figure out how to make the purple flowers, look at the properties and make an educated guess

Assignment

Put your data in the tables below:

1. allele color amino acid sequence (highlight differences)

1. What features of a protein make it colored?
2. What features of the amino acid sequence make a protein a particular color?
3. How do the colors combine to produce an overall color? How does this explain the genotype-phenotype rules you found in part (I)?
4. Which proteins are found in each of the four starting organisms?

• Green-1
• Green-2
• Red
• White