Janelle N. Ruiz Assignment 2
Assignment II
Part II: Biochemistry
- Question 1: 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.
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
The differences in the amino acid sequences are found at position 10 and 11.
- Question 2: What features of the amino acid sequence make a protein pigmented?
The properties of amino acid side chains make a protein pigmented as well as the sequence of the amino acids which make up the protein. How a protein is structured (i.e. its amino acid sequence) will ultimately determine how and to what degree it is able to reflect and absorb specific wavelengths of light and therefore its percieved pigment.
- Question 3: What features of the amino acid sequence make a protein a particular color?
The differences in color between different proteins depends upon a protein's amino acid sequences as explained above. The particular pigment which is reflected by a given protein will likely be determined by the amount of and interaction between aromatic amino acid side chains. Aromatic compounds, because of the alternating double- and single-bond ring system, absorb light and are colored because of this. The size of the molecule (i.e. the amount of aromatic amino acid side chains) and the structure of the aromatic side chain (i.e. the amount and order of the double and single bond ring system) will determine the color of the protein.
- Question 4:How do the colors combine to produce an overall color? How does this explain the genotype-phenotype rules you found in part (I)?
Because we are working under the assumption that the two proteins (allele colors) found in a diploid organism work alone as monomers rather than dimers, each protein will be reflecting and absorbing its own specific wavelength of light. When two proteins of different colors are found in a diploid organism, either one color allele will be observed in the organism or a different, new color allele will be observed. The following genotype/phenotypes were observed:
- Green 1: green/green
- Green 2: blue/yellow
- Green 3: green/yellow
- Green 4: green/blue
- Green 5: green/white
- Red: red
- Red 1: white/red
- White: white/white
- Black: green/red
- Purple: blue/red
- Orange: yellow/red
- Blue: blue/white
- Yellow: yellow/white
Because an observed color of white indicates that all color is absorbed and non is reflected, it makes sense that a white allele would become "hidden" and therefore not observed when combined with an allele of another color. In situations where two color alleles are combined, such as with blue/red, yellow/red, and blue/yellow, genetic co-dominance is observed in which the combination of two proteins which reflect and absorb different wavelengths of light cause a new color appearing as a "blend" of the two alleles to be observed. The green allele, when combined with all other color alleles except red, exhibits a genetic dominance. ASK
- Question 5: Which proteins are found in each of the four starting organisms?
- 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
- Question 6: Using this knowledge, construct a purple protein.
- Purple:
Met Ser Asn Arg His Ile Leu Leu Val Tyr Phe Cys Arg Gln
Met Ser Asn Arg His Ile Leu Leu Val Tyr Phe Arg Gln
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Links
Notes
Format
- allele
- color
- amino acid sequence (highlight differences)
