Biology 1002B Notes
Cycle 1: Trapping Light for Energy and Information
Characteristics of Chlamydomonas that make it a
Useful Model System
Unicellular, soil-dwelling green alga with
multiple mitochondria, two anterior flagella for
motility and mating, an eyespot, and a
chloroplast that houses the photosynthetic
apparatus and critical metabolic pathways
Reflects basic eukaryotic structure
Reproduces and grows rapidly, so lots of them
can be grown quickly
Normally haploid, so mutations are obvious
There is DNA in its nucleus and chloroplast
Contains both plant (chloroplasts) and animal
(flagella) traits
Ability to manipulate its genetics
Grows in the dark on an organic carbon source while maintaining a functional photosynthetic
apparatus
Relatedness of Chlamydomonas to Plants and Animals
Classified as a plant
Lineage diverged from land plants over 1 billion years ago
Genes can be traced to the green plant or plant-animal common ancestor by comparative
genomic analyses
Related to plants by having chlorophyll and being photosynthetic, related to animals by having
motility due to flagella and having an eyespot that can sense the environment which is similar to
animals
More closely related to plants due to their position on the phylogenetic tree, however they have
traits similar to animals, which is why they are a good model organism to test things on
Relationship Between Genome Size and Protein Coding Genes
No relationship because some genomes contain more junk DNA than others, meaning less
protein coding gene areas
Chlamydomonas has a small genome size but because it has less junk DNA it has a high number
of protein coding gene regions
Humans have a large genome but a lot of junk DNA and therefore less protein coding gene areas,
therefore showing no relation between the genome size and PCG #
Phototransduction from Eyespot to Flagella
, Each cell contains a light sensor called an eyespot
allowing it to gather info about the location and
intensity of a light source
Cells can move toward or away from the light source,
for efficient photosynthesis
All cells are polarized (inside is -, outside is +)
Channelrhodopsin
o Photoreceptor molecule of the eyespot
o Has a channel through which ions can move
o Opens up when light is absorbed and ions can move across the membrane
o Depolarization causes an action potential which causes the flagella to move
o Process is called phototaxis – movement of an organism in response to light, either
towards or away from the source of the light
Advantages to Chlamydomonas in Being Phototactic
Light harvesting for photosynthesis
Can reduce damage from light if source is too strong, or move closer if more light is needed
Distinctions Between Primitive, Complex, Simple
Just because an organism is simple, does not mean it is primitive
Primitive organisms are earlier on in evolution
Complex organisms have specialized tissues (i.e. nerves, organs, or flowers)
Reasons why Chlamydomonas Might Move Towards a Light Source
It needs energy (which is produced from photosynthesis, therefore it needs light)
Reasons why Chlamydomonas Might Move Away From a Light Source
The light intensity is too much for the cell, so it moves away to create as minimal damage as
possible
Possible mutations that could cause a Chlamydomonas cell not to be Phototactic
Mutation which affects the section of the DNA which codes for the channelrhodopsin protein
(does not absorb light)
Mutation which causes a great depletion in the amount of channelrhodopsin receptors,
eventually ceasing the cells ability to be phototactic
Mutations in the ability for the Channelrhodopsin/plasma membrane to conduct a proper action
potential, therefore not enabling the flagella to receive the action potential, and stripping the
flagella of its ability to move
The Electromagnetic Spectrum
Defined as the range of wavelengths or frequencies of electromagnetic radiation extending from
gamma rays to the longest radio waves and including visible light
Light
Defined as the portion of the electromagnetic spectrum that humans can detect with their eyes
It is a stream of photons (photons – discrete particles or packets of energy)
Has no mass
, Behaves as a wave as it travels through space
Particle-Wave duality – behaves as a particle (photon) and a wave
The longer the wavelength, the lower the energy of the photons it contains
Functions:
o Source of energy that sustains all organisms
o Provides organisms with info about the physical world that surrounds them
Light Interaction with Matter
When a photon of light hits an object, it can be reflected, transmitted or absorbed
Absorption must take place for it to be used as a source of energy or for information
o Occurs when the energy of the photon is transferred to an electron in the molecule
o Promotes electron from its ground state to a higher energy level (excited state)
o Photon can only be absorbed if the energy of the photon matches the amount of energy
needed to move electron to a specific excited state
If energies don’t match, photon is transmitted or reflected
Pigments
Efficient at absorbing photons
o All pigments have a region where carbon atoms are covalently bonded to each other with
alternating single and double bonds
o Called a conjugated system
o Allows electrons to be delocalized and can therefore freely interact with photons of light
The colour of a pigment corresponds to the photons of light that are not absorbed (reflected or
transmitted)
Why Biological Systems Only Absorb Visible Wavelengths of the Electromagnetic Spectrum
Visible light is used by organisms because it is the most dominant form of electromagnetic
radiation reaching Earth’s surface
Shorter wavelengths than those in the visible spectrum:
o Absorbed by ozone layer
o Contain higher amounts of energy that can break the bonds in a molecule (harmful to
living organisms)
Longer wavelengths than those in the visible spectrum:
o Absorbed by water vapour and CO2 in the atmosphere
o Don’t contain enough energy to move an electron from a ground state to excited state
Relationship Between Pigments and Associated Proteins
Pigments are always bound to proteins, creating pigment-protein complexes
Most proteins (cytosolic proteins) don’t have pigments associated with them
Proteins do not absorb light, pigments do
Pigments take energy of photons and trap them in a molecule
If you isolate the proteins carefully, you can keep pigments attached
Can see pigments in pigment-protein complexes with protein gel electrophoresis
Four Fates of the Excited State of Chlorophyll Resulting from Absorption of Photons
1. Heat – lose the energy as heat get to ground state
, 2. Fluorescence – lose a little energy as heat get
to a sub-excited state, then spit photon back
out, and lose the rest as fluorescence (photon
released has lower energy/longer wavelength)
3. Photochemistry – uses energy to break/make
bonds
4. Energy transfer – if two pigments are close
enough together, then excited state migrates to
next pigment (only energy is transferred, not
electrons)
Relationship Between Energy of Photon and Electron Excited States to Explain Pigment Colour
and Absorption Spectrum
All of the photon’s energy must be absorbed – the electron’s excited state energy must match the
photon’s energy
The absorption spectrum shows which wavelengths match up to a pigment’s excited state (which
means they can be absorbed)
The wavelengths that are not absorbed are the colour of the pigment
Distinctions of Photochemistry Between Phototransduction (vision, eyespot) & Photosynthesis
Phototransduction (Eyespot)
o Photon of light absorbed by channelrhodopsin changes the stereochemistry of retinal
o When retinal absorbs light it undergoes photoisomerization, and it will change from trans
to cis
o The conformational change of retinal causes change in the shape of opsin, causing
channelrhodopsin channel to open up
Phototransduction (Human eye)
o 1000s of rhodopsins in rods and cones
o When retinal absorbs light it undergoes photoisomerization, and it will change from cis to
trans
o The conformational change of retinal causes change in the shape of opsin
o G-protein can now bind, ions can flow, which causes electrical impulses that go to the
visual centers of the brain
Photosynthesis (chlorophyll)
o Light energy is converted into chemical energy
o Due to energy transfer and oxidation of the chlorophyll
o Leftover electron is used to make energy/sugar
Major Similarities and Differences Between Eyespot and Eye
Eyespot Eye
Channelrhodopsin: trans to cis Rhodopsin: cis to trans
Channelrhodopsin absorbs light and Light activates a pathway that eventually changes ion
directly alters ion flow: channel goes movement into and out of the cell: doesn’t DIRECTLY
from closed to open and allows ions to change the flow, but it activates a single signalling
flow pathway that eventually does
Cycle 1: Trapping Light for Energy and Information
Characteristics of Chlamydomonas that make it a
Useful Model System
Unicellular, soil-dwelling green alga with
multiple mitochondria, two anterior flagella for
motility and mating, an eyespot, and a
chloroplast that houses the photosynthetic
apparatus and critical metabolic pathways
Reflects basic eukaryotic structure
Reproduces and grows rapidly, so lots of them
can be grown quickly
Normally haploid, so mutations are obvious
There is DNA in its nucleus and chloroplast
Contains both plant (chloroplasts) and animal
(flagella) traits
Ability to manipulate its genetics
Grows in the dark on an organic carbon source while maintaining a functional photosynthetic
apparatus
Relatedness of Chlamydomonas to Plants and Animals
Classified as a plant
Lineage diverged from land plants over 1 billion years ago
Genes can be traced to the green plant or plant-animal common ancestor by comparative
genomic analyses
Related to plants by having chlorophyll and being photosynthetic, related to animals by having
motility due to flagella and having an eyespot that can sense the environment which is similar to
animals
More closely related to plants due to their position on the phylogenetic tree, however they have
traits similar to animals, which is why they are a good model organism to test things on
Relationship Between Genome Size and Protein Coding Genes
No relationship because some genomes contain more junk DNA than others, meaning less
protein coding gene areas
Chlamydomonas has a small genome size but because it has less junk DNA it has a high number
of protein coding gene regions
Humans have a large genome but a lot of junk DNA and therefore less protein coding gene areas,
therefore showing no relation between the genome size and PCG #
Phototransduction from Eyespot to Flagella
, Each cell contains a light sensor called an eyespot
allowing it to gather info about the location and
intensity of a light source
Cells can move toward or away from the light source,
for efficient photosynthesis
All cells are polarized (inside is -, outside is +)
Channelrhodopsin
o Photoreceptor molecule of the eyespot
o Has a channel through which ions can move
o Opens up when light is absorbed and ions can move across the membrane
o Depolarization causes an action potential which causes the flagella to move
o Process is called phototaxis – movement of an organism in response to light, either
towards or away from the source of the light
Advantages to Chlamydomonas in Being Phototactic
Light harvesting for photosynthesis
Can reduce damage from light if source is too strong, or move closer if more light is needed
Distinctions Between Primitive, Complex, Simple
Just because an organism is simple, does not mean it is primitive
Primitive organisms are earlier on in evolution
Complex organisms have specialized tissues (i.e. nerves, organs, or flowers)
Reasons why Chlamydomonas Might Move Towards a Light Source
It needs energy (which is produced from photosynthesis, therefore it needs light)
Reasons why Chlamydomonas Might Move Away From a Light Source
The light intensity is too much for the cell, so it moves away to create as minimal damage as
possible
Possible mutations that could cause a Chlamydomonas cell not to be Phototactic
Mutation which affects the section of the DNA which codes for the channelrhodopsin protein
(does not absorb light)
Mutation which causes a great depletion in the amount of channelrhodopsin receptors,
eventually ceasing the cells ability to be phototactic
Mutations in the ability for the Channelrhodopsin/plasma membrane to conduct a proper action
potential, therefore not enabling the flagella to receive the action potential, and stripping the
flagella of its ability to move
The Electromagnetic Spectrum
Defined as the range of wavelengths or frequencies of electromagnetic radiation extending from
gamma rays to the longest radio waves and including visible light
Light
Defined as the portion of the electromagnetic spectrum that humans can detect with their eyes
It is a stream of photons (photons – discrete particles or packets of energy)
Has no mass
, Behaves as a wave as it travels through space
Particle-Wave duality – behaves as a particle (photon) and a wave
The longer the wavelength, the lower the energy of the photons it contains
Functions:
o Source of energy that sustains all organisms
o Provides organisms with info about the physical world that surrounds them
Light Interaction with Matter
When a photon of light hits an object, it can be reflected, transmitted or absorbed
Absorption must take place for it to be used as a source of energy or for information
o Occurs when the energy of the photon is transferred to an electron in the molecule
o Promotes electron from its ground state to a higher energy level (excited state)
o Photon can only be absorbed if the energy of the photon matches the amount of energy
needed to move electron to a specific excited state
If energies don’t match, photon is transmitted or reflected
Pigments
Efficient at absorbing photons
o All pigments have a region where carbon atoms are covalently bonded to each other with
alternating single and double bonds
o Called a conjugated system
o Allows electrons to be delocalized and can therefore freely interact with photons of light
The colour of a pigment corresponds to the photons of light that are not absorbed (reflected or
transmitted)
Why Biological Systems Only Absorb Visible Wavelengths of the Electromagnetic Spectrum
Visible light is used by organisms because it is the most dominant form of electromagnetic
radiation reaching Earth’s surface
Shorter wavelengths than those in the visible spectrum:
o Absorbed by ozone layer
o Contain higher amounts of energy that can break the bonds in a molecule (harmful to
living organisms)
Longer wavelengths than those in the visible spectrum:
o Absorbed by water vapour and CO2 in the atmosphere
o Don’t contain enough energy to move an electron from a ground state to excited state
Relationship Between Pigments and Associated Proteins
Pigments are always bound to proteins, creating pigment-protein complexes
Most proteins (cytosolic proteins) don’t have pigments associated with them
Proteins do not absorb light, pigments do
Pigments take energy of photons and trap them in a molecule
If you isolate the proteins carefully, you can keep pigments attached
Can see pigments in pigment-protein complexes with protein gel electrophoresis
Four Fates of the Excited State of Chlorophyll Resulting from Absorption of Photons
1. Heat – lose the energy as heat get to ground state
, 2. Fluorescence – lose a little energy as heat get
to a sub-excited state, then spit photon back
out, and lose the rest as fluorescence (photon
released has lower energy/longer wavelength)
3. Photochemistry – uses energy to break/make
bonds
4. Energy transfer – if two pigments are close
enough together, then excited state migrates to
next pigment (only energy is transferred, not
electrons)
Relationship Between Energy of Photon and Electron Excited States to Explain Pigment Colour
and Absorption Spectrum
All of the photon’s energy must be absorbed – the electron’s excited state energy must match the
photon’s energy
The absorption spectrum shows which wavelengths match up to a pigment’s excited state (which
means they can be absorbed)
The wavelengths that are not absorbed are the colour of the pigment
Distinctions of Photochemistry Between Phototransduction (vision, eyespot) & Photosynthesis
Phototransduction (Eyespot)
o Photon of light absorbed by channelrhodopsin changes the stereochemistry of retinal
o When retinal absorbs light it undergoes photoisomerization, and it will change from trans
to cis
o The conformational change of retinal causes change in the shape of opsin, causing
channelrhodopsin channel to open up
Phototransduction (Human eye)
o 1000s of rhodopsins in rods and cones
o When retinal absorbs light it undergoes photoisomerization, and it will change from cis to
trans
o The conformational change of retinal causes change in the shape of opsin
o G-protein can now bind, ions can flow, which causes electrical impulses that go to the
visual centers of the brain
Photosynthesis (chlorophyll)
o Light energy is converted into chemical energy
o Due to energy transfer and oxidation of the chlorophyll
o Leftover electron is used to make energy/sugar
Major Similarities and Differences Between Eyespot and Eye
Eyespot Eye
Channelrhodopsin: trans to cis Rhodopsin: cis to trans
Channelrhodopsin absorbs light and Light activates a pathway that eventually changes ion
directly alters ion flow: channel goes movement into and out of the cell: doesn’t DIRECTLY
from closed to open and allows ions to change the flow, but it activates a single signalling
flow pathway that eventually does
