KP Ramirez Week 2: Difference between revisions

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Notes
==='''Notes'''===
This was a collaboration between [[User:Kevin A Paiz-Ramirez|KP Ramirez]], [[User: Janelle N. Ruiz|Janelle Ruiz]], and [[User:Alex J. George|Alex George]]


four plants
from the wild: two green, one red, and one white.
Create a True Breeding Purple Allele


Your customers would really like to have
purple flowers from this plant. You set out to create a true-breeding purple flower.
Hypothesis Testing
In the three Aipotu labs, you will use a process much like that used by practicing scientists as
they conduct research. Although this process almost never follows a formula, it often proceeds
as follows:
1. Observe Patterns. Observe the natural world and look for patterns, exceptional events,
etc. For example, you might observe that red proteins tend to have long thin shapes.
2. Develop hypotheses. From the observations, you define testable hypotheses –
statements or questions that can be addressed experimentally. Continuing the example,
you might reasonably hypothesize that long thin proteins will be red.
3. Test hypotheses. You then set up experiments or observations that will collect data
that bear on your hypothesis. In the example, you might type in a sequence of amino
acids that would be expected to fold into a long thin shape, fold the protein, and
observe its color. If your hypothesis is correct, it will be red. If you get another result,
your hypothesis is incorrect.
4. Revise hypotheses as necessary. If your results do not match your prediction, you
need to revise your hypothesis and go to Step (3) again until they do match.
Tasks:
Work together as a class to:
• Determine the differences in amino acid sequence between the proteins produced by
the alleles you found in Part I.
• Determine how the amino acid sequence of a pigment protein determines its color.
• Explain, in terms of the proteins present, the interactions between the alleles you found
in part I.
o Why is the color phenotype of some pigment proteins dominant while others are
recessive?
o How do the pigment proteins combine to produce the overall color of the plant?
• Construct a purple protein to demonstrate your understanding of this process.
===Assignment===
Specific Tasks for this section
Work as a class, using the data blog to:
*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.
==='''Notes'''===
'''Allele Protein Structures'''
'''Allele Protein Structures'''
* '''Green:'''
* '''Green:'''
Line 92: Line 43:
There are positions that are important, look at the characteristics of amino acid side chains. Figure out how to make the purple flowers, look at the properties and make an educated guess
There are positions that are important, look at the characteristics of amino acid side chains. Figure out how to make the purple flowers, look at the properties and make an educated guess


==Assignment==
=='''Assignment'''==
Put your data in the tables below:
*'''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 color amino acid sequence (highlight differences)
*This occurs for the amino acid sequence found at position 10 and 11
'''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 2''': What features of the amino acid sequence make a protein pigmented?
*The amino acid side chains cause protein pigmentation as well as the structure. This in turn presents how light is reflected and perceived. 
 
 
*'''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 interaction between the aromaticity in the amino acid side chains.
 
*'''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
 
Our group worked together to determine what would be the best way to go about finding a purple flower. The protein is purple because of the way in which '''Tyr''' and '''Phe''' this order was imperative.  reflect and absorb light. Because both amino acids have aromatic side chains with alternating double and single bond ring structures, they reflect and absorb different wavelengths of light. Because the presence of '''Tyr''' tends to reflect blue light, as seen in the table below with the blue protein allele, and the presence of '''Phe''' tends to reflect red light, as seen in the table below with the red protein allele. Combined these two produced the purple pigment.
 
==='''TABLE'''===
*Note: the following was the initial table completed in the computer lab, however, Janelle was able to provide a more detailed one seen below. [[Media:Untitled-1.jpg‎| Table of Color/Amino Acid Sequence]]
 
*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, will yeild a purple protein when at postions 10 and 11, respectively, when you SWITCH '''Phe''' and '''Tyr''',  you get a white protein. Just '''Tyr''' (aromatic) and you get a white protein.
 
*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''' at those positions gives a red protein.
 
*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
 
Having all three amino acids in any combination at between positions 9 and 12 yeilds a black protein.
 
*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
 
If many '''Trp'''s are added to these positions, get a yellow protein.
 
*Blue:
Lots of '''Tyr''' (aromatic) at these positions, and you get a blue protein.
 
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
 
If you add a few more '''Tyr''' or '''Trp''' to these positions, get a green protein. If you switch '''Trp''' and '''Tyr''', you get a white protein.
 
{{Kevin A Paiz-Ramirez}}
 
 
back to [[User:Kevin A Paiz-Ramirez|KP Ramirez]]
 
==Links==
[[BIOL398-01/S10:Week 2]]


#What features of a protein make it colored?
[[Category:BIOL398-01/S10]]
#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?
*Green-1
*Green-2
*Red
*White

Latest revision as of 21:26, 7 February 2010

Notes

This was a collaboration between KP Ramirez, Janelle Ruiz, and Alex George


Allele Protein Structures

  • Green:
Met-Ser-Asn-Arg-His-Ile-Leu-Leu-Val-Tyr-Trp-Arg-Gln
  1. Met non polar, hydrophobic. Ser polar uncharged. Asn polar uncharged. Arg polar uncharged. His Polar uncharged. Ile Nonpolar hydrophobic. Leu Nonpolar hydrophobic. Val Nonpolar hydrophobic. TYR polar uncharged. TRP nonpolar hydrophobic. Arg polar uncharged. Gln polar uncharged.
  • Blue:
Met-Ser-Asn-Arg-His-Ile-Leu-Leu-Val-Tyr-Cys-Arg-Gln

TYR-polar uncharged, CYS-polar uncharged

  • Yellow:
Met-Ser-Asn-Arg-His-Ile-Leu-Leu-Val-Trp-Cys-Arg-Gln

TRP-Nonpolar hydrophobic, CYS-polar uncharged

  • Red:
Met-Ser-Asn-Arg-His-Ile-Leu-Leu-Val-Phe-Cys-Arg-Gln

PHE-nonpolar hydrophobic CYS-Polar uncharged

  • White:
Met-Ser-Asn-Arg-His-Ile-Leu-Leu-Val-Val-Cys-Arg-Gln

Val-Nonpolar hydrophobic, CYS polar uncharged.

Flowers

  • Green green/green
  • Green2 Blue/Yellow
  • Red: Red/nothing
  • White: White/White

Phenotypes & Genotypes

  • Green-CgCg
  • White-CwCw
  • Red -CrCr
  • Blue -CbCb
  • Orange-Needs yellow and red CrCy
  • Yellow-CyCy
  • Purple -Needs Red and blue CrCb
  • Black -Needs red and green CrCg

Charged, acidic (-) basic (+) form ionic bonds Uncharged polar form H-bonds Hydrophobic(nonpolar) hydrophobic interaction, van der waals

There are positions that are important, look at the characteristics of amino acid side chains. Figure out how to make the purple flowers, look at the properties and make an educated guess

Assignment

  • 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.
  • This occurs for the amino acid sequence found at position 10 and 11
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 2: What features of the amino acid sequence make a protein pigmented?
  • The amino acid side chains cause protein pigmentation as well as the structure. This in turn presents how light is reflected and perceived.


  • 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 interaction between the aromaticity in the amino acid side chains.
  • 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

Our group worked together to determine what would be the best way to go about finding a purple flower. The protein is purple because of the way in which Tyr and Phe this order was imperative. reflect and absorb light. Because both amino acids have aromatic side chains with alternating double and single bond ring structures, they reflect and absorb different wavelengths of light. Because the presence of Tyr tends to reflect blue light, as seen in the table below with the blue protein allele, and the presence of Phe tends to reflect red light, as seen in the table below with the red protein allele. Combined these two produced the purple pigment.

TABLE

  • Note: the following was the initial table completed in the computer lab, however, Janelle was able to provide a more detailed one seen below. Table of Color/Amino Acid Sequence
  • 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, will yeild a purple protein when at postions 10 and 11, respectively, when you SWITCH Phe and Tyr, you get a white protein. Just Tyr (aromatic) and you get a white protein.

  • 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 at those positions gives a red protein.

  • 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

Having all three amino acids in any combination at between positions 9 and 12 yeilds a black protein.

  • 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

If many Trps are added to these positions, get a yellow protein.

  • Blue:

Lots of Tyr (aromatic) at these positions, and you get a blue protein.

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

If you add a few more Tyr or Trp to these positions, get a green protein. If you switch Trp and Tyr, you get a white protein.

Journal Assignments

KP Ramirez Week 2 KP Ramirez Week 6 KP Ramirez Week OFF
KP Ramirez Week 3 KP Ramirez Week 7 KP Ramirez Week 11
KP Ramirez Week 4 KP Ramirez Week 8 KP Ramirez Week 12
KP Ramirez Week 5 KP Ramirez Week 9 KP Ramirez Week 13

Shared Journals

  1. Week 2
  2. Week 3
  3. Week 4
  4. Week 5
  5. Week 6
  6. Week 7
  7. Week 8
  8. Week 9
  9. Week 10
  10. Week 11
  11. Week 12
  12. Week 13


Useful Links


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Links

BIOL398-01/S10:Week 2

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