Dramir36 Week 2
User:Dramir36 template:Dramir36 Skinny Genes
- Week 1
- Week 2
- Week 3
- Week 4
- Week 5
- Week 6
- Week 7
- Week 8
- Week 9
- Week 10
- Week 11
- Week 12/13
- Week 14
- Week 15
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.
- b) What features of the amino acid sequence make a protein pigmented?
- c) What features of the amino acid sequence make a protein a particular color?
- d) How do the colors combine to produce an overall color? How does this explain the genotype-phenotype rules you found in part (I)?
- e) Which proteins are found in each of the four starting organisms?
- f) Using this knowledge, construct a purple protein.
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.
