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 

TABLE

White:

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

Met Ser Asn Arg His Ile Leu Leu Val Phe Tyr Arg Gln

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

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

Met Ser Asn Arg His Ile Leu Leu Val Trp Tyr Arg Gln

When you add amino acids with non-aromatic side chains to these positions (10 and 11), you get a white protein. Also, though Phe and Tyr, which are amino acids with aromatic side chains, at postion 10 and 11, respectively, will give a purple protein, when you SWITCH Phe and Tyr, you get white… It looks like any combination fo an aromatic proteisn gives a color but the combo of TWO aromatic proteins gives purple… no also others – depends on the aromatic ring. Just TYR (aromatic) and you get WHITE

Orange:

Met Ser Asn Arg His Ile Leu Leu Val Phe Trp Arg Gln

Met Ser Asn Arg His Ile Leu Leu Val Trp Phe Arg Gln

Met Ser Asn Arg His Ile Leu Leu Val Trp Phe Phe Arg Gln

Red:

Met Ser Asn Arg His Ile Leu Leu Val Phe Phe Arg Gln Lots of Phe = red

Black:

Met Ser Asn Arg His Ile Leu Leu Val Tyr Phe Trp Arg Gln

Met Ser Asn Arg His Ile Leu Leu Val Trp Tyr Phe Arg Gln

Met Ser Asn Arg His Ile Leu Leu Val Phe Tyr Trp Arg Gln

All three aromatic, get black

Yellow:

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

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

ADD lots of TRPs, get yellow

JUST TYR AND YUOU GET WHITE!!!

Blue: Lots of TYR (aromatic) and you get blue

It doesn’t seem to matter when you add non-aroamtic to the mix…. Stays the same color

Green:

Met Ser Asn Arg His Ile Leu Leu Val Tyr Trp Arg Gln A few more tyr – green Lots of tyr – blue Add a fe/lot of trp – green SWITCH -- white  add a few more trp to this switch – yellow  Add a few more try -- green

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Links

BIOL398-01/S10:Week 2

Format

• allele
• color
• amino acid sequence (highlight differences)