Dramir36 Week 2

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Purpose

To understand how changing an amino acid sequence of a plant can cause a change in expression of a hypothetical flower color.

Methods

a) 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.

Method: All 4 of the given Greenhouse flower colors were compared among each other and identified the difference of the amino acid sequences by using the Compare option in the Aipotu program to dispay the differences between the Upper and Lower Folding Window.

Answer: Green-1 contains both amino acid sequences that code for a green colored flower, whereas Green-2 is a mixture between Blue and Yellow amino acid sequences. The difference between the Blue and Yellow sequences is that the Blue amino acid sequence contains a "Tyr" whereas a Yellow amino acid sequence contains a "Trp" instead. The Red flower only contains a single Red amino acid sequence. Lastly, the White flower contains two identical White amino acid sequences.

b) What features of the amino acid sequence make a protein pigmented?

Method: The White flower amino acid sequence was compared to the other colored flowers, then found relations between the colored flowers and finding the common amino acid sequence to make a protein pigmented.

Answer: In the white flower, there is a "Val" in the 10th position, whereas the other pigmented flowers do not contain a "Val" in the 10th position, but a different amino acid is in its place to make the protein pigmented. Although, the 11th position is switched from "Cys" to "Trp" in order to make an amino acid sequence for green plants.

c) What features of the amino acid sequence make a protein a particular color?

Method: In order to identify which amino acid makes a protein a particular color, the sequences of each color flower were compared.

Answer: In order to get Green-1, the 11th position has to be "Trp" and the 10th position is "Tyr". To get Green-2, which is the mixture between Blue and Yellow flowers, is that the Blue sequence need a "Cys" in the 11th position and a "Tyr" in the 10th position. The Yellow sequence is the same as the Blue sequence, except that "Trp" is in the 10th position. To get a Red protein, the sequence is similar to the Blue sequence but "Phe" is placed in the 10th position instead. Lastly, to get a White protein, which also has a similar sequence to the Blue protein but "Val" is in the 10th position.

d) How do the colors combine to produce an overall color? How does this explain the genotype-phenotype rules you found in part (I)?

Method: The amino acid sequence of Green-1 was compared to the Green-2, which is a heterozygote of Blue and Yellow proteins.

Answer: The amino acid that is different between both sequence proteins that are combined, will be inserted near the 10th position. As to say that the new overall color with have both amino acids in its sequence. For example, the "Tyr" from the Blue and the "Trp" of the Yellow are placed in the same sequence at the 10th position to combine into a Pure Green protein.

e) Which proteins are found in each of the four starting organisms?

Method: The Amino acid sequence of each of the four organisms were recorded.

Answer:

Protein of Each Starting Organism

Color	Amino Acid Sequence
Green-1	MSNRHILLVYWRQ
Green-2
Red
White

f) Using this knowledge, construct a purple protein.

Method:

Answer:

Screenshot of Purple flower using Aipotu program

Hints:

A) It may be useful, before formulating any hypotheses, to look for patterns in the data. Which features do colored proteins have in common that uncolored proteins lack?

• Try comparing the amino acid sequences of proteins with different colors.

• Here are some additional interesting sequences to try:

• FFFFFFFRRRRRR

• RRRFFFFFFFRRR

• KKKKKKLLLLLLF

• KKKKKKLLLLLLL

• SLQLNITMEVDFW

• EEEWWWWWWWEEE

B) Scientists, including yourselves, often find it useful to use mutation to study phenomena like this. Go to Genetics and make some mutants. Save any ones with interesting colors to the Greenhouse. Switch back to Biochemistry and look at the proteins they have.

Procedure:

1. Compare the proteins found in the starting strains to answer questions (a) and (b) on the following pages.

2. Your TA will assign your group one particular colored protein to study. Compare its sequence and shape to the “sample protein” that you get by clicking the Load Sample Protein button on one of the Folding Windows and then choosing from the Compare menu.

3. A representative from each group will come to the board to describe the sequence and shape difference(s) between their protein and the sample. Note that each subsequent group should relate their findings to the previously-presented data.

4. Based on these data, as a class, make several specific hypotheses that can be tested.

5. Each group should work on one or more of their hypotheses and post them to the blog.

6. Your TA may stop for a mini-symposium to share data and design new hypotheses.

7. You will then be able to complete parts (d) through (f).

Put your data in the tables below:

(a) Which proteins are found in each of the four starting organisms?

Green-1

Green-2

Red

White

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

(c) What features of a protein make it colored?

(d) What features of the amino acid sequence make a protein a particular color?

(e) How do the colors combine to produce an overall color? How does this explain the genotype-phenotype rules you found in part (I)?

(f) Show your TA that you have made a purple protein. For full credit, you need to explain to your TA why it is purple.