Electronic Lab Notebook

Week 2: Aipotu Biochemistry Lab

Specific Tasks:

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.

Methods

In this lab, I used Aipotu Biochemistry software to analyze the effects of amino acid sequence on flower phenotype. First, I decided to look for patterns and correlations between amino acid sequences and phenotype (that is, protein color). Using the list of 'interesting' amino acid sequences provided (see page 12), I made my initial observations. Inputting the sequences in the folding window, I took note of various features of the 2D structures formed including hydrophobic interactions (indicated by patterns of clustering of like-colored amino acid residues; the darker the amino acid, the more hydrophobic), ionic interactions, and behavior of hydrogen bond forming amino acids. To add to my initial observation set, I looked at the alleles for the proteins of the four organisms in the Greenhouse. To help aid in my observations, I used the 'Compare'>'Upper vs. Lower' function on Aipotu. This allowed me to locate changes between similar amino acid sequences. Based off these observations, I came up with my initial hypotheses for this investigation:

Proteins will be colored depending on the presence of absence of specific amino acid residues
1. Proteins with amino acid Phe will be red
2. Proteins with amino acid Trp will be yellow
3. Proteins with amino acid Tyr will be blue
Secondary colors (i.e. orange and green) are formed due to the combination of color-determining amino acids
Thus, combining two alleles that code for protein pigments Red and Blue will create a flower of Purple color.

Using this, I constructed a number of proteins consisting of the various amino acids. By constructing a colorless protein using Phe, Trp or Tyr, my hypothesis would be deemed inadequate.

Results

Starting Organism	Allele	Color	Amino Acid Sequence
Green-1	C^G	Green	Met Ser Asn Arg His Ile Leu Leu Val Tyr Trp Arg Gln Met Ser Asn Arg His Ile Leu Leu Val Tyr Trp Arg Gln
Green-2	C^BC^Y	Green	Met Ser Asn Arg His Ile Leu Leu Val Tyr Cys Arg Gln Met Ser Asn Arg His Ile Leu Leu Val Trp Cys Arg Gln
Red	C^R -	Red	Met Ser Asn Arg His Ile Leu Leu Val Phe Cys Arg Gln
White	C^WC^W	white	Met Ser Asn Arg His Ile Leu Leu Val Val Cys Arg Gln Met Ser Asn Arg His Ile Leu Leu Val Val Cys Arg Gln

What features of a protein make it colored?
1. Colored proteins must have at least 6 hydrophilic molecules, 7 hydrophobic molecules, and at least 1 of: Phe, Trp or Tyr
What features of the amino acid sequence make a protein a particular color?
1. Presence of specific amino acids determine color. Phe is red, Trp is yellow and Tyr is blue.
How do the colors combine to produce an overall color? How does this explain the genotype-phenotype rules you found it Part (I)?
Show your TA that you have made a purple protein. For full credit, you need to explain to your TA why it is purple

Discussion

Weekly Assignments

Class Journals