Lecture 1 – Introduction to Chlamydomonas
Independent Outcomes:
1. Locate the eyespot on an image of Chlamydomonas.
Lecture Outcomes:
1. Characteristics of Chlamydomonas that make it a useful model system
A single cell system that has attributes of both plants and animals
Has a simple life cycle in addition to a relatively simple genome
Compact DNA and the less junk DNA compared to humans; easier to sequence
Since chlamy are normally haploid, the effects of mutations are seen immediately
without further crosses
2. Relatedness of Chlamydomonas to plants and animals
Has a flagella (eukaryotic trait) and chloroplasts (plant trait)
More related to plants than to animals
3. Relationship between genome size and protein coding genes (PCGs)
No relation, since some genomes contain more junk DNA than others
Humans have a large genome, lot of junk DNA and less PCG regions
Chlamy have a small genome, but the same # of PCG regions and less junk DNA
4. Phototransduction from eyespot to flagella
Part of the eyespot is in the chloroplast and part of it is in the plasma membrane
Phototransduction is the ability of converting light energy to an electrical signal
o Occurs with the help of aid proteins called channelrhodopsin, which spans the
plasma membrane at the eyespot
o Outside the membrane, there is a positive (+) charge and inside is negative (-)
o When the eyespot absorbs a photon of light, it changes the conformation of the
protein, and the channel opens, allowing charged calcium and hydrogen ions to
diffuse across the membrane
o This diffusion causes a voltage difference and results in depolarization
o If the voltage passes the threshold, action potential is created and travels to the
base of the flagella, which causes it to swim in a certain direction
5. Advantages to Chlamydomonas in being phototactic.
Phototactic is the bodily movement of a motile organism in response to light
, This is an advantage for chlamy because it allows it to move in the direction where it will
maximize how much light it is receiving in order to harness energy of photons in
photosynthesis
6. Distinctions between primitive, complex, simple.
Primitive Genetically old or earliest of the kind in its existence
Simple Basic or uncomplicated in form, nature or design
Complex Consists of many different and connected parts
Eyespot is not more primitive than the eye because both of them have been around for
the same amount of time
o BUT, the eyespot is more simple than the eye
7. Reasons why Chlamydomonas might move towards a light source.
To gather information about their surroundings
To increase its rate of photosynthesis, thus providing itself with the energy it needs
To get the “right” amount of light it needs for survival
8. Reasons why Chlamydomonas might move away from a light source.
Once it has received the correct amount of light, it will move away to avoid
overconsumption
Too much light absorbed can increase the rate at which ROS (reactive oxygen species) are
formed, which can result in harmful mutations and/or kill cell
May already have sufficient energy, thus it moves away from light, allowing itself to
allocate energy to other tasks (e.g. reproduction) instead of photosynthesis
Will move towards dim light, but away from very intense or potentially mutagenic light as
it can be damaging
9. Possible mutations that could cause a Chlamydomonas cell not to be phototactic.
Mutation in channelrhodopsin – may cause defectiveness (no conformational change),
which could destroy its depolarization mechanism, so as a result, the eyespot would lose
its ability to discern between light intensities and direct the movement of flagella
Mutation in the length or function of flagella – results in the lack of locomotion
Lecture 2 – Energy and Information
Lecture Outcomes:
1. Relationship between wavelength and energy content of a photon.
Inversely proportional (high energy = short wavelength and low energy = long
wavelength)
Blue light has more energy than red light
2. Molecular characteristic of pigments that make them able to absorb light.
Proteins don’t absorb light, pigments do
Pigments are planar and have a conjugated ring system, where carbon atoms are
covalently bonded to each other with alternating single and double bonds
o Results in an abundance of non-bonding pi orbital electrons available to trap light
3. Relationship between pigments and associated protein.
Pigments are not free in the cell; they are bound to proteins very specifically (protein-
pigment complex)
When pigments absorb a photon of light, they can change shape and thereby trigger
change to the protein molecule they are bound to
,4. Four “fates” of the excited state of chlorophyll resulting from absorption of photons.
Heat – for most compounds that absorb light, the electron simply returns to the ground
state and all the absorbed energy is released as heat
Fluorescence – it can release some of the absorbed energy as heat and then release a
photon of light (fluorescent photon has less energy and longer wavelength than original)
Photochemistry – energy is used to do work (breaking/making bonds) which changes the
structure of a molecule
Energy transfer – energy is used to excite a neighbouring pigment (no electrons
transferred, only energy transferred)
5. Relationship between energy of photon and electron excited states to explain pigment colour and
absorption spectrum.
One photon can excite only one electron
All of the photon’s energy must be absorbed; therefore, the pigment’s excited state
energy must match the photon’s energy
Absorption spectrum shows which wavelengths match up to a pigment’s excited state
High excited state Blue photons of light absorbed (high absorption peak)
Low excited state red photons of light absorbed (low absorption peak)
The wavelengths that are not absorbed are the colour we see of the pigment
Chlorophyll is green because there is no green excited state; no state that can absorb a
green photon
6. Distinctions of photochemistry between phototransduction (vision, eyespot...) & photosynthesis
Phototransduction process of converting light energy into electrochemical signals
o Absorption of light by photoreceptors triggers rapid changes in the
concentrations of ions which generates an action potential
o When retinal absorbs light, it undergoes photoisomerization, where the double
bond changes to a single bond for a split second, allowing it to rotate freely and
becomes either cis or trans depending on the original conformation
Photosynthesis process of converting light energy into chemical energy
o Instead of causing a change in conformation, it excites electrons through
oxidation-reduction reactions
o Uses photosystems to oxidize chlorophyll
7. Major similarities and differences between phototransduction in eyespot vs eye.
SIMILARTIES:
o Both, at their most basic level use photoreceptors to absorb light
o Eye has a protein called rhodopsin, while eyespot has channelrhodopsin, but
both are types of pigment-protein complexes with 7 membrane spanning
domains
Channelrhodopsin = retinal (pigment) + opsin (protein)
Rhodopsin = retinal + opsin too, but not the same opsin
When they absorb light, they change conformation
Light causes channelrhodopsin to undergo photoisomerization (switch
from cis to trans) and alter its conformation
o Light triggers the proteins to change ion concentration within their respective
cells (changes in ions occurs at plasma membrane)
DIFFERENCES:
o Rhodopsin in eye converts from cis to trans during photoisomerization
o Channelrhodopsin in eyespot goes from trans to cis
, 8. Reasons why life has evolved to detect the narrow band of energy represented by “visible light”.
Visible light is the most dominant form of EM radiation reaching earth’s surface
Shorter wavelengths of ER contain too much energy to destroy the chemical bonds of
molecules (x-rays and gamma rays)
Longer wavelengths of ER are energetically weak and wouldn’t supply enough energy to
move an electron from a ground to a higher state (microwaves and radiowaves)
9. Basics of bioluminescence.
Chemical energy in the form of ATP is used to excite an electron in a substrate molecule
from the ground state to a higher excited state
When the electron returns to the ground state, the energy is released as a photon of light
(therefore light is produced)
This process is expensive for organisms (because they need to invest energy to excite
electrons), but may increase overall fitness of organism
Lecture 3 – Protein Structure and Function
Independent Outcomes:
1. Basic structure of an amino acid and what are the different classes of amino acids.
A central atom attached to an amino group, a carboxyl group and a hydrogen atom
i. Remaining R group is 1 of 20 side chains
4 different classes of amino acids, grouped according to properties of side chains:
i. Non-polar
ii. Uncharged polar
iii. Negatively charged (acidic) polar
iv. Positively charged (basic) polar
2. Chemistry of the peptide bond and how it is formed.
Covalent bonds link amino acids into chains called polypeptides
A peptide bond is the link between each pair of amino acids
It is formed by a dehydration synthesis reaction between the –NH2 group of one amino
acid and the –COOH group of a second
3. The four levels of protein structure.
Primary, secondary, tertiary, and quaternary structures
4. What bonding arrangements give rise to primary, secondary and tertiary structure.
Primary structure – particular & unique sequence of amino acids forming a polypeptide
Secondary structure – twists and turns of the amino acid chain (alpha helix and beta
sheets) based on hydrogen bonds between atoms of the backbone
Tertiary structure – folding of the amino acid chain, with its secondary structures, into the
overall 3-D shape of a protein
i. Includes bonds, hydrogen bonds, hydrophobic interactions and disulfide bridges
Quaternary structure – optional structure that refers to the arrangement of polypeptide
chains in a protein that is formed from more than one chain
5. How are alpha helices and beta sheets formed.
Alpha helix coil shape formed when hydrogen bonds form between every N-H group
of the backbone and the C=O group of the amino acid
Beta sheet side-by-side alignment of beta strands, formed by hydrogen bonds
between atoms of each strand
Independent Outcomes:
1. Locate the eyespot on an image of Chlamydomonas.
Lecture Outcomes:
1. Characteristics of Chlamydomonas that make it a useful model system
A single cell system that has attributes of both plants and animals
Has a simple life cycle in addition to a relatively simple genome
Compact DNA and the less junk DNA compared to humans; easier to sequence
Since chlamy are normally haploid, the effects of mutations are seen immediately
without further crosses
2. Relatedness of Chlamydomonas to plants and animals
Has a flagella (eukaryotic trait) and chloroplasts (plant trait)
More related to plants than to animals
3. Relationship between genome size and protein coding genes (PCGs)
No relation, since some genomes contain more junk DNA than others
Humans have a large genome, lot of junk DNA and less PCG regions
Chlamy have a small genome, but the same # of PCG regions and less junk DNA
4. Phototransduction from eyespot to flagella
Part of the eyespot is in the chloroplast and part of it is in the plasma membrane
Phototransduction is the ability of converting light energy to an electrical signal
o Occurs with the help of aid proteins called channelrhodopsin, which spans the
plasma membrane at the eyespot
o Outside the membrane, there is a positive (+) charge and inside is negative (-)
o When the eyespot absorbs a photon of light, it changes the conformation of the
protein, and the channel opens, allowing charged calcium and hydrogen ions to
diffuse across the membrane
o This diffusion causes a voltage difference and results in depolarization
o If the voltage passes the threshold, action potential is created and travels to the
base of the flagella, which causes it to swim in a certain direction
5. Advantages to Chlamydomonas in being phototactic.
Phototactic is the bodily movement of a motile organism in response to light
, This is an advantage for chlamy because it allows it to move in the direction where it will
maximize how much light it is receiving in order to harness energy of photons in
photosynthesis
6. Distinctions between primitive, complex, simple.
Primitive Genetically old or earliest of the kind in its existence
Simple Basic or uncomplicated in form, nature or design
Complex Consists of many different and connected parts
Eyespot is not more primitive than the eye because both of them have been around for
the same amount of time
o BUT, the eyespot is more simple than the eye
7. Reasons why Chlamydomonas might move towards a light source.
To gather information about their surroundings
To increase its rate of photosynthesis, thus providing itself with the energy it needs
To get the “right” amount of light it needs for survival
8. Reasons why Chlamydomonas might move away from a light source.
Once it has received the correct amount of light, it will move away to avoid
overconsumption
Too much light absorbed can increase the rate at which ROS (reactive oxygen species) are
formed, which can result in harmful mutations and/or kill cell
May already have sufficient energy, thus it moves away from light, allowing itself to
allocate energy to other tasks (e.g. reproduction) instead of photosynthesis
Will move towards dim light, but away from very intense or potentially mutagenic light as
it can be damaging
9. Possible mutations that could cause a Chlamydomonas cell not to be phototactic.
Mutation in channelrhodopsin – may cause defectiveness (no conformational change),
which could destroy its depolarization mechanism, so as a result, the eyespot would lose
its ability to discern between light intensities and direct the movement of flagella
Mutation in the length or function of flagella – results in the lack of locomotion
Lecture 2 – Energy and Information
Lecture Outcomes:
1. Relationship between wavelength and energy content of a photon.
Inversely proportional (high energy = short wavelength and low energy = long
wavelength)
Blue light has more energy than red light
2. Molecular characteristic of pigments that make them able to absorb light.
Proteins don’t absorb light, pigments do
Pigments are planar and have a conjugated ring system, where carbon atoms are
covalently bonded to each other with alternating single and double bonds
o Results in an abundance of non-bonding pi orbital electrons available to trap light
3. Relationship between pigments and associated protein.
Pigments are not free in the cell; they are bound to proteins very specifically (protein-
pigment complex)
When pigments absorb a photon of light, they can change shape and thereby trigger
change to the protein molecule they are bound to
,4. Four “fates” of the excited state of chlorophyll resulting from absorption of photons.
Heat – for most compounds that absorb light, the electron simply returns to the ground
state and all the absorbed energy is released as heat
Fluorescence – it can release some of the absorbed energy as heat and then release a
photon of light (fluorescent photon has less energy and longer wavelength than original)
Photochemistry – energy is used to do work (breaking/making bonds) which changes the
structure of a molecule
Energy transfer – energy is used to excite a neighbouring pigment (no electrons
transferred, only energy transferred)
5. Relationship between energy of photon and electron excited states to explain pigment colour and
absorption spectrum.
One photon can excite only one electron
All of the photon’s energy must be absorbed; therefore, the pigment’s excited state
energy must match the photon’s energy
Absorption spectrum shows which wavelengths match up to a pigment’s excited state
High excited state Blue photons of light absorbed (high absorption peak)
Low excited state red photons of light absorbed (low absorption peak)
The wavelengths that are not absorbed are the colour we see of the pigment
Chlorophyll is green because there is no green excited state; no state that can absorb a
green photon
6. Distinctions of photochemistry between phototransduction (vision, eyespot...) & photosynthesis
Phototransduction process of converting light energy into electrochemical signals
o Absorption of light by photoreceptors triggers rapid changes in the
concentrations of ions which generates an action potential
o When retinal absorbs light, it undergoes photoisomerization, where the double
bond changes to a single bond for a split second, allowing it to rotate freely and
becomes either cis or trans depending on the original conformation
Photosynthesis process of converting light energy into chemical energy
o Instead of causing a change in conformation, it excites electrons through
oxidation-reduction reactions
o Uses photosystems to oxidize chlorophyll
7. Major similarities and differences between phototransduction in eyespot vs eye.
SIMILARTIES:
o Both, at their most basic level use photoreceptors to absorb light
o Eye has a protein called rhodopsin, while eyespot has channelrhodopsin, but
both are types of pigment-protein complexes with 7 membrane spanning
domains
Channelrhodopsin = retinal (pigment) + opsin (protein)
Rhodopsin = retinal + opsin too, but not the same opsin
When they absorb light, they change conformation
Light causes channelrhodopsin to undergo photoisomerization (switch
from cis to trans) and alter its conformation
o Light triggers the proteins to change ion concentration within their respective
cells (changes in ions occurs at plasma membrane)
DIFFERENCES:
o Rhodopsin in eye converts from cis to trans during photoisomerization
o Channelrhodopsin in eyespot goes from trans to cis
, 8. Reasons why life has evolved to detect the narrow band of energy represented by “visible light”.
Visible light is the most dominant form of EM radiation reaching earth’s surface
Shorter wavelengths of ER contain too much energy to destroy the chemical bonds of
molecules (x-rays and gamma rays)
Longer wavelengths of ER are energetically weak and wouldn’t supply enough energy to
move an electron from a ground to a higher state (microwaves and radiowaves)
9. Basics of bioluminescence.
Chemical energy in the form of ATP is used to excite an electron in a substrate molecule
from the ground state to a higher excited state
When the electron returns to the ground state, the energy is released as a photon of light
(therefore light is produced)
This process is expensive for organisms (because they need to invest energy to excite
electrons), but may increase overall fitness of organism
Lecture 3 – Protein Structure and Function
Independent Outcomes:
1. Basic structure of an amino acid and what are the different classes of amino acids.
A central atom attached to an amino group, a carboxyl group and a hydrogen atom
i. Remaining R group is 1 of 20 side chains
4 different classes of amino acids, grouped according to properties of side chains:
i. Non-polar
ii. Uncharged polar
iii. Negatively charged (acidic) polar
iv. Positively charged (basic) polar
2. Chemistry of the peptide bond and how it is formed.
Covalent bonds link amino acids into chains called polypeptides
A peptide bond is the link between each pair of amino acids
It is formed by a dehydration synthesis reaction between the –NH2 group of one amino
acid and the –COOH group of a second
3. The four levels of protein structure.
Primary, secondary, tertiary, and quaternary structures
4. What bonding arrangements give rise to primary, secondary and tertiary structure.
Primary structure – particular & unique sequence of amino acids forming a polypeptide
Secondary structure – twists and turns of the amino acid chain (alpha helix and beta
sheets) based on hydrogen bonds between atoms of the backbone
Tertiary structure – folding of the amino acid chain, with its secondary structures, into the
overall 3-D shape of a protein
i. Includes bonds, hydrogen bonds, hydrophobic interactions and disulfide bridges
Quaternary structure – optional structure that refers to the arrangement of polypeptide
chains in a protein that is formed from more than one chain
5. How are alpha helices and beta sheets formed.
Alpha helix coil shape formed when hydrogen bonds form between every N-H group
of the backbone and the C=O group of the amino acid
Beta sheet side-by-side alignment of beta strands, formed by hydrogen bonds
between atoms of each strand
