1. Ap Biology Discussion Notes
Monday 5/2

2. Goals for the Day
Be able to tie together multiple disciplines in biology
Be prepared for the AP test

3. Question of the Day 5/2
Is it possible that things that are advantageous in one environment are “maladaptive” or disadvantageous in others? Give an example to explain your answer.
Emphasize not just structure but FUNCTION that is tied to what is going on in our cells! All cells have same DNA, but do different things based on gene expression.

5. Dichromatic Vision

6. Trichromatic Vision

7. Day 3

8. The Cell Biology of Color Vision in Monkeys
** Notes for this section:
The following slides are included as an overview of the cell biology of the Monkey Opsins case.
For more information visit:
A retinal chromophore opsin molecule is activated by a photon of light. This in turn stimulates the opsin protein that tells the cone cell to send a signal to the brain.

9. How Does Color Vision Work? Cell Biology
The retina has two types of cells: rod cells and cone cells. There are more rod cells than cone cells. Cone cells are responsible for color vision.

10. How Does Color Vision Work? Cell Biology
The retina has two types of cells: rod cells and cone cells. There are more rod cells than cone cells. Cone cells are responsible for color vision.

11. How Does Color Vision Work?
There are three types of cone cells. More accurately, any given cone cell may be using only one of three types of transmembrane opsin proteins.
On the left – photo of cone and rod cells.
On the right – cartoon representation.

12. How Does Color Vision Work?
There are three types of cone cells. More accurately, any given cone cell may be using only one of three types of transmembrane opsin proteins.
There are three types of cone cells. More accurately, any given cone cell may be using only one of three types of transmembrane opsin proteins.
On the left – photo of cone and rod cells.
On the right – cartoon representation.

13. Three types of Cone Cell
Different kinds of opsin proteins embedded in the membrane of cone cells make each kind able to receive different information from the others.
Central Dogma of Molecular Biology:
DNA  RNA  Protein
Genes code for…. Proteins which lead to function!.

14. Chromatic Vision: Cone Cells
Cone cells in the retina of the eye allow light of different wavelengths to be interpreted as color in the brain. The following slides describe how this pathway works.
The Brain
Light Waves
Color
The Cone cell

15. (i) Non-animated version of slide opsin-chromophore-brain slide
To produce the signal for color vision, retinal must stimulate the opsin protein but this cannot occur while the retinal molecule is in its cis- conformation.

16. (ii) Non-animated version of slide opsin-chromophore-brain slide
When 11-cis-retinal absorbs a photon (a basic unit of light), it changes from 11-cis-retinal to All-trans-retinal.

17. (iii) Non-animated version of slide opsin-chromophore-brain slide
All-trans-retinal stimulates the opsin in the membrane of the cone cell.

18. The cone cell sends a signal to the brain, resulting in vision.
(iv) Non-animated version of slide opsin-chromophore-brain slide
The cone cell sends a signal to the brain, resulting in vision.

19. The cone cell sends a signal to the brain, resulting in vision.
Opsin Image modified from Scientific American, April 09
All-trans-retinal
ATTENTION! ANIMATION SLIDE!
This slide contains an animation and is meant to be played in slide show format.
The following four slides contain a non-animated version of this slide.
If you do not wish to show this slide, right click it in the slide layout (to the left) and select “Hide” in this slide and in the ones that follow would be specific to only ONE type of opsin molecule.
11-cis-retinal
Opsin
To produce the signal for color vision, retinal must stimulate the opsin protein but this cannot occur while the retinal molecule is in its cis- conformation.
The cone cell sends a signal to the brain, resulting in vision.
All-trans-retinal stimulates the opsin in the membrane of the cone cell.
When 11-cis-retinal absorbs a photon (a basic unit of light), it changes from 11-cis-retinal to All-trans-retinal.

20. The Cell Biology of Color Vision in Monkeys
A retinal chromophore opsin molecule is activated by a photon of light. This in turn stimulates the opsin protein that tells the cone cell to send a signal to the brain.
** Notes for this section:
The following slides are included as an overview of the cell biology of the Monkey Opsins case.
For more information visit:
A retinal chromophore opsin molecule is activated by a photon of light. This in turn stimulates the opsin protein that tells the cone cell to send a signal to the brain.

21. The Role of Opsins
There are three types of opsins: Short Wave Sensitive (SWS) Medium Wave Sensitive (MWS) Long Wave Sensitive (LWS) An individual possessing only SWS and MWS opsins will have dichromatic vision. An individual possessing SWS, MWS and LWS opsins will have trichromatic vision.

22. How Does Color Vision Work?
When cone cells with the MWS opsin protein are stimulated, green color is perceived by the brain.
When cone cells with the LWS opsin protein are stimulated, red color is perceived by the brain.
When cone cells with the SWS opsin protein are stimulated, blue color is perceived by the brain.
When cone cells with the MWS opsin protein are stimulated AND cone cells with the LWS opsin are stimulated, yellow color is perceived by the brain.
When cone cells with the MWS opsin protein are stimulated AND cone cells with the SWS opsin are stimulated, violet color is perceived by the brain.
When cone cells with the SWS opsin protein are stimulated AND cone cells with the LWS opsin are stimulated, cyan color is perceived by the brain.
When all cone cells are stimulated in equal proportions, white light is perceived by the brain.
We perceive different shades of light when our different types of cone cells are stimulated in different proportions.

23. How Does Color Vision Work?
When cone cells with the MWS opsin protein are stimulated, green color is perceived by the brain.
When cone cells with the LWS opsin protein are stimulated, red color is perceived by the brain.
When cone cells with the SWS opsin protein are stimulated, blue color is perceived by the brain.
When cone cells with the MWS opsin protein are stimulated AND cone cells with the LWS opsin are stimulated, yellow color is perceived by the brain.
When cone cells with the MWS opsin protein are stimulated, green color is perceived by the brain.
When cone cells with the LWS opsin protein are stimulated, red color is perceived by the brain.
When cone cells with the SWS opsin protein are stimulated, blue color is perceived by the brain.
When cone cells with the MWS opsin protein are stimulated AND cone cells with the LWS opsin are stimulated, yellow color is perceived by the brain.
When cone cells with the MWS opsin protein are stimulated AND cone cells with the SWS opsin are stimulated, violet color is perceived by the brain.
When cone cells with the SWS opsin protein are stimulated AND cone cells with the LWS opsin are stimulated, cyan color is perceived by the brain.
When all cone cells are stimulated in equal proportions, white light is perceived by the brain.
We perceive different shades of light when our different types of cone cells are stimulated in different proportions.

24. How Does Color Vision Work?
When cone cells with the MWS opsin protein are stimulated AND cone cells with the SWS opsin are stimulated, violet color is perceived by the brain.
When cone cells with the SWS opsin protein are stimulated AND cone cells with the LWS opsin are stimulated, cyan color is perceived by the brain.
When all cone cells are stimulated in equal proportions, white light is perceived by the brain.
We perceive different shades of light when our different types of cone cells are stimulated in different proportions.
When cone cells with the MWS opsin protein are stimulated, green color is perceived by the brain.
When cone cells with the LWS opsin protein are stimulated, red color is perceived by the brain.
When cone cells with the SWS opsin protein are stimulated, blue color is perceived by the brain.
When cone cells with the MWS opsin protein are stimulated AND cone cells with the LWS opsin are stimulated, yellow color is perceived by the brain.
When cone cells with the MWS opsin protein are stimulated AND cone cells with the SWS opsin are stimulated, violet color is perceived by the brain.
When cone cells with the SWS opsin protein are stimulated AND cone cells with the LWS opsin are stimulated, cyan color is perceived by the brain.
When all cone cells are stimulated in equal proportions, white light is perceived by the brain.
We perceive different shades of light when our different types of cone cells are stimulated in different proportions.

25. Chromatic Vision: Opsins
What is the building block ( ________mer) of an opsin protein?
3D Visualization

26. Chromatic Vision: Opsins
3D Visualization
2D Visualization
The opsin protein is composed of a string of amino acids.
Each green dot in the 2D visualization represents one amino acid.

27. Opsin Structure
MWS
opsin
LWS
opsin
The LWS opsin differs from the MWS opsin in three significant places in the amino acid sequence:
Position 180: alanine to serine
Position 277: phenylalanine to tyrosine
Position 285: alanine to threonine

28. Opsin Structure
The LWS opsin differs from the MWS opsin in three significant places in the amino acid sequence:
Position 180: alanine to serine
Position 277: phenylalanine to tyrosine
Position 285: alanine to threonine
MWS
opsin
LWS

29. Opsin Response to Light
The responses to light of each opsin protein (S, M and L) in trichromats are shown to the right. Note how similar the curves look for M and L. The L curve is shifted by about 30 nm response maximum to the right (longer wavelength).

30. Opsin Response to Light
A third opsin provides another channel for sending color signals to the brain. Three opsin proteins allow the eye to detect a richer variety of light wavelengths resulting in the ability to distinguish more colors.

31. The Genetics of Color Vision in Monkeys
** Notes for this section:
The following slides are included as an overview of the genetics of the Monkey Opsins case.
Trichromatic vision arises from gene duplication and gene mutation of the MWS opsin protein, resulting in the creation of the LWS opsin protein.
For more information visit:

32. The Genetics of Color Vision
The section of DNA on a chromosome that codes for an opsin protein is called an opsin gene.

33. Location of Opsin Genes
The gene coding for the SWS opsin protein is located on chromosome #7. The gene coding for the MWS and LWS opsins are located on the X-chromosome.
OPTIONAL ACTIVITY! See activity notes.

34. Evolution of LWS Opsin Gene
The LWS gene arose through gene duplication and gene mutation of the MWS gene on the X-chromosome.

35. Origin of the LWS Opsin Gene
The LWS gene arose through gene duplication and gene mutation of the MWS gene on the X-chromosome.

36. Gene Duplication
Gene duplication happens during meiosis in prophase I where unequal crossing over can occur.

37. Unequal Crossing Over (Meiosis, Prophase 1)
For more information see:

38. Origin of the LWS Opsin Gene
The LWS gene arose through gene duplication and gene mutation of the MWS gene on the X-chromosome.

39. Origin of the LWS Opsin Gene
The LWS gene arose through gene duplication and gene mutation of the MWS gene on the X-chromosome.

40. This slide may be useful in an ecology/organismal course where a brief refresher of DNA and nucleotides may be helpful.

41. The MWS Opsin Gene
This slide may be useful in an ecology/organismal course where a brief refresher of DNA and nucleotides may be helpful.

42. The MWS Opsin Gene 1092 Nucleotides
This slide may be useful in an ecology/organismal course where a brief refresher of DNA and nucleotides may be helpful.
When we write out the DNA sequence of a gene, we just write out the sequence of the coding strand since nucleotides are complimentary.
1092 Nucleotides

43. The MWS Opsin Gene  GTCGTTAGATAG  1092 Nucleotides
This stretch of the DNA strand would be written out as a series of letters, as shown.
1092 Nucleotides

44. MWS Opsin Gene vs. LWS Opsin Gene
Each opsin gene is exactly the same length (1092 nucleotides)
MWS Opsin Protein vs. LWS Opsin Protein
These 1092 nucleotides undergo transcription and translation and result in a protein that is 364 amino acids in length.

45. MWS Opsin Gene vs. LWS Opsin Gene (mutations at the nucleotide level that result in protein functional changes)
G  T T  A G  A
Three simple substitution mutations change the properties of the opsin protein.
Now, rather than being maximally stimulated at ~534nm, the resulting opsin protein is maximally stimulated at ~564nm.

46. What difference does this make at the protein level?

47. Evolution of LWS Opsin Gene
The LWS gene arose through gene duplication and gene mutation of the MWS gene on the X-chromosome.
Summary/recap slide.

48. Fact or Fiction? A monkey researcher in South America discovered that some monkey females are trichromatic.
Definitely Fact
Possibly Fact
Possibly Fiction
Definitely Fiction

49. The Case of Trichromatic Females

50. Genes code for opsin proteins; the opsin proteins facilitate color vision.
Some new world monkey species have two different MWS alleles. If a female is heterozygous for these alleles she can produce three different types of opsin protein. This means that SOME females in SOME new world species are trichromatic. Females that are homozygous for the MWS gene on the x-chromosome are dichromatic.

51. Genes code for opsin proteins; the opsin proteins facilitate color vision.
Some new world monkey species have two different MWS alleles. If a female is heterozygous for these alleles she can produce three different types of opsin protein. This means that SOME females in SOME new world species are trichromatic. Females that are homozygous for the MWS gene on the x-chromosome are dichromatic.
Some new world monkey species have two different MWS alleles. If a female is heterozygous for these alleles she can produce three different types of opsin protein. This means that SOME females in SOME new world species are trichromatic. Females that are homozygous for the MWS gene on the x-chromosome are dichromatic.

52. The Phylogenetics of Color Vision in Monkeys
** Notes for this section:
The following slides are included as an overview of the phylogenetics and biogeography of the Monkey Opsins case.
For more information visit:

53. Biogeography of Global Monkeys
Photo: Frans de Waal, M Arunprasaad, D Wright, P Gonnet, L DeVoldor, W Endo

54. Monkeys of the World
Old world monkeys have two different opsin genes on their X chromosomes whereas new world monkeys only have one.

55. Phylogenetics – Exploring Relationships Among Species
This tree is a representative sample of new world and old world monkeys. It is not meant to encapsulate all species.
From a genetic perspective, Old World Primates are more closely related to one another than they are to New World Primates (and vice versa). Evidence suggests that they share a common ancestor in whom the gene duplication and mutation events occurred.

56. Geology: Plate Tectonics and Drift
When did color vision evolve? The next few slides bring in aspects of geology and paleontology to help answer this question.

57. Primates In New/Old World
Squirrel Monkey
Owl Monkey
Spider Monkey
Wooly Monkey
Chimpanzee
Human
Gorilla
Orangutan
Gibbon
Rhesus
Baboon
Mangabey
Mona
Langur
Colobus
Capuchin
Marmoset
Sakis
Continents Split
50 Million Years Ago
ATTENTION!!! ANIMATED SLIDE!
A non-animated version of this slide follows.
These events can now be mapped onto the phylogenetic tree to give a fuller picture.
Research suggests that color vision evolved around 40 million years ago:
Old World
New World
Color Vision Evolves!
Gene Duplication and Mutation
Primates In New/Old World
55 Million Years Ago
Rise of Primates
75 Million Years Ago

58. Ancestral Characteristic
An Ancestral Characteristic is a characteristic shared through common ancestry. A characteristic that is thought to have also been present in the common ancestor.
In primates for example DICHROMATIC vision would be considered an “ancestral characteristic” while trichromatic vision would be considered a derived characteristic (one not present in the common ancestor of 2 groups)

59. Primates In New/Old World
Squirrel Monkey
Owl Monkey
Spider Monkey
Wooly Monkey
Chimpanzee
Human
Gorilla
Orangutan
Gibbon
Rhesus
Baboon
Mangabey
Mona
Langur
Colobus
Capuchin
Marmoset
Sakis
Continents Split
50 Million Years Ago
ATTENTION!!! ANIMATED SLIDE!
A non-animated version of this slide follows.
These events can now be mapped onto the phylogenetic tree to give a fuller picture.
Research suggests that color vision evolved around 40 million years ago:
Old World
New World
Color Vision Evolves!
Gene Duplication and Mutation
Primates In New/Old World
55 Million Years Ago
Rise of Primates
75 Million Years Ago

60. Day 3 Questions