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Alex George

Apoitu II: Biochemistry

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

1. Tyr- Polar, uncharged; Trp- Nonpolar, hydrophobic; Cys- Polar, uncharged; Phe- Nonpolar, hydrophobic; Val- Nonpolar, hydrophobic

• The aromatic side chains of Tyr and Phe are aromatic, which contribute to the color of the flower. The presence of both in the protein structure produce a purple color.

Flowers

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

Allele Combination-->Color

• Blue/Red--> Purple

Phenotype ---> Genotype

• Green ---> cg/cg
• Blue ---> cb/cb
• White ---> cw/cw
• Red ---> cr/cr
• Orange ---> cr/cy
• Yellow ---> cy/cy
• Purple ---> cr/cb
• Black ---> cr/cg
• Definite Alleles: cg, cb,cw,cr,cy

Assignment: Part II: Biochemistry

Specific Tasks

1. What are the differences in the amino acid sequences of the proteins produced by the alleles you define in Part I?
   • The differences are present in the 10th and 1lth positions of the 13 amino acid sequence of the protein.
2. What features of the amino acid sequence make a protein pigmented?
   • It appears if there is an aromatic amino acid in either of these positions, then the flower will be pigmented.
3. What features of the amino acid sequence make a protein a particular color?
   • Aromaticity also explains the reason for a particular pigment of color. It appears that the level or the number of aromatic side chains in the 10th and 11th positions produces different colors. For example, Tyr-Cys in the 10th and 11th positions produces a blue pigment, whereas Val-Cys has no pigment, otherwise white.
4. How do the colors combine to produce an overall color? How does this explain the genotype-phenotype rules you found in part (I)?
   • The different colors represented by the protein reflect a particular pigment, therefore if you combine two proteins that reflect red and blue, the apparent color will be purple. This explains the "Green 2" flower that was resulted from the "Blue" and "Yellow" proteins.
5. Which proteins are found in each of the four starting organisms?
   • Green-1: Green x Green
   • Green-2: Yellow x Blue
   • Red: Red x ----
   • White: White x White
6. Using this knowledge, construct a purple protein.
   • 1 Possible Purple Protein:Met-Ser-Asn-Arg-His-Ile-Leu-Leu-Val-Tyr-Phe-Arg-Gln

Table of Color/Amino Acid Sequence