January 17, 2013
• Light interacting with biology
○ Energy point of view and information point of view
• Similarities and differences of the light capturing and photochemistryof phototransduction
(retinal) vs. photosynthesis(chlorophyll).
• Where in the cell does the following occur? What does it do? Free energy? Requires O2? Where
is the carbon?
○ Citric Acid Cycle
○ Electron transfer
Energy fixation - occurs in the thylakoid membranes
Electron transport system
○ Carbon fixation ( Calvin Cycle) - occurs in the stroma
• Compare photosynthesiswith cellular respiration General Good Questions
January 15, 2013
Why is fluorescence higher with isolated chlorophyll?
There is less fluorescence in the cell sample because the cell requires a lot of energy for it to run the cell processes it needs to function
properly. Therefore, the energy produced by the excitation could be used by essential molecules and cell organelles to perform these
processes. The energy can also be transferred to the reaction center to drive photochemistry as part of photosynthesis. It is possible that the
cell has developed an evolutionary mechanism(s) which help utilize light energy by minimizing energy loss and the amount of fluorescence
In the isolated chlorophyll, there is no pathway for the energy produced to be utilized so it is released via fluorescence. Since none of the
energy is being utilized by other processes like in the cell, most of the energy is released as fluorescence, producing a higher amount of
fluorescence than in the cell.
How are the excited states of pigments A through D organized to allow for tranfer from A to B to C to D?
Yes there is bound to be some heat loss so the pigments further away (A) need to have the highest excited state and the one in the reaction
centre the lowest.
Why is a bacterium smaller than a eykaryotic cell?
How is the tertiary bonding arrangements different among the four groups of organisms, and why?
Tertiary bonds are responsible for the correct structure of enzymes. Varying temperatures result in the denaturation of these enzymes
because these enzymes tert bonds are not suitable to the change in environment. The presence of more tertiary bonds should increase the
strength of tertiary structure (more R group interactions/polypeptide sequence) and therefore make enzymes more resistant to higher
temperatures. If a hyperthermophile that requires regularly higher temperatures get placed in a colder environment its structure takes more
energy to bend (stronger R group bonding) and therefore can't flex to meet the shape of the incoming substrate (equally detrimental to
growth rate and survival).
Outcomes Page 2 Lecture 1 - Light: Energy & Information Homework:
i) Pages 370 - 372 in Evolution: principles and processes.
January 7, 2013 ii) Section 1.1 in Biology: Exploring the Diversity of Life, 2nd Ed. Check out Fig. 1.1.
12:45 PM iii) the scientific article posted below. It is a complicated paper so jLec 1-ad the
Introduction and Conclusions. Skim over whatever else is interesting to you.
Independent Study Outcomes
1. Identify criteria used to measure complexity.
○ Genomesize - total # of genes in an organism
○ Gene (copy) number - the number of copies of a gene in a given gene family resulting from a
○ Increase in size of organismsover the course of evolution
○ The number of genes that encode proteins
○ The number of parts or units in an organism(where parts = segments, organs, tissues etc)
○ The number of cell types possesed by an organism
○ Increased compartmentalization, specialization or subdivision of function over the course of
○ The number of gene, gene networks or cell-to-cell interactions required to form the parts of
○ The number of interactionsbetween the parts of an organism, reflecting the increasing
functional complexity and/orintegration over the course of evolution
2. Identify the main structural components of Chlamydomonas cells.
soil-dwelling green alga
two anterior flagella for motility and mating,
& a chloroplast that houses the photosynthetic apparatusand critical
3. Identify the relationship between Chlamydomonas and the evolutionary common ancestor of
animals and plants.
○ Many Chlamydomonas and angiosperm genes are derived from ancestral green plant genes,
including those associated with photosynthesis and plastidfunction.
• roles of light as used by life
○ A source of energy
○ A source of information about the environment
• characteristics of Chlamydomonas that make it a useful model system
○ Attributes of both animal and plant
○ Easy to mass produce
○ Model system for looking at flagella and comparing to humans/other organims
○ Have both chloroplasts and mitocohondria
• function of basic components of Chlamydomonas cells
○ Basal body: is an organelle formed from a centriole,and a short cylindrical array of
microtubules. It is found at the base of a cilium or flagellum and serves as a nucleation site
for the growth of the axonememicrotubules.
○ Nucleus: a membrane-enclosedorganelle; contains most of the cell's geneticmaterial
○ Mitochondrion: a membrane-enclosed organelle; they generatemost of the cell's supply of
adenosine triphosphate(ATP), are also involved in other tasks such as signaling, cellular
differentiation, cell death, as well as the control of the cell cycle and cell growth.
○ Chloroplast: Photosynthesis is their main function, where chloroplastscapture the sun's
light energy,and store it in the energy storage moleculesATP and NADPH while breaking
down water molecules.Pyrenoid: within chloroplast - where carbon fixation takes place.
○ Eyespot: allows the cells to sense light direction and intensity and respond to it by
swimming either towards the light
• relative usefulness of various biological characteristics as measures of complexity
○ Cell size
○ Genomesize - however because of the cvalue enigma, isn’t always correct
○ PCG - Protein coding genes - may mislead you too?
○ Single cell organismsvs multicellular organisms
• advantages to Chlamydomonas in beingphototactic.
○ Moveaway from the light when there's too much that might harm the cell
○ Movetowards the light when needed
• reasons why Chlamydomonas might move AWAY from a light source.
○ It's harmful or damaging to the cells if the cells harvest too much of it
○ Produces reactive oxygen species that hurts the cell if there's too much.
• basic structure of rods and cones as photoreceptor cells.
○ Rods - visual receptors that function underlow light and do not give rise to colour
○ Cones - photoreceptors that function best in bright light and are differentially sensitiveto
red, green, or blue wavelengths (the retina'scolour receptors)
Outcomes Page 3 red, green, or blue wavelengths (the retina'scolour receptors)
• major components involved in phototransduction and their role.
1. A light photon interacts with the retinal in a photoreceptor cell. The retinal undergoes
isomerisation, changing from the 11-cis to all-trans configuration.
2. Retinal no longer fits into the opsin binding site.
3. Opsin thereforeundergoes a conformational change which activates phosphodiesterase.
4. Phosphodiesterase (an enzyme) breaks down cGMP to 5'-GMP. This lowers the
concentration of cGMP and therefore the sodium channels close.
5. Closure of the sodium channels causes hyperpolarizationof the cell due to the ongoing
6. Hyperpolarization of the cell causes voltage-gated calcium channels to close.
7. As the calcium level in the photoreceptorcell drops, the amount of the neurotransmitter
glutamatethat is released by the cell also drops. This is because calcium is required for the
glutamate-containing vesiclesto fuse with cell membraneand release their contents.
8. A decrease in the amount of glutamate released by the photoreceptors causes
depolarization of On center bipolar cells (rod and cone On bipolarcells) and
hyperpolarization of cone off-center bipolar cells.
Outcomes Page 4 Lecture 2 - Light
January 9, 2013
• Relationship between excited states of a pigment and its absorption,fluorescence emission spectra.
○ Absorption bands will be the peaks in the flouresenceemission spectra
○ The higher the absorption,the taller the peaks
○ Peaks with mini peaks attached show the energy leaving as heatloss, then as fluoresence. (i.e. two minor excited states)
• Region of the electromagnetic spectrum known as “visible light”.
○ longer wavelengths than UV light, but shorter wavelengths of infared radiation
○ The energy of the light is inverselyrelated to its wavelength
• Relationship between wavelength and energycontent of a photon.
○ The shorter the wavelength, the higher the amountof energy in the photon
e.g The amountof energy in a blue photon of light is higher than the amount of energy in a red photon
• Molecular characteristic of visible pigments that make them able to absorb light.
○ Conjugted system - alternation between double bond and single bond
Results in many non-bonding electronsthereforeavailabe interact with light and are
• Relationship between pigments and associated protein.
○ Pigments are bound specificly to proteins
○ Non-covalentbonds btween the two
• Four “fates” of the excited state of chlorophyll resulting from absorption of photons.
○ Lose all energyas heat
○ Lose a little as heat, and the rest as floresence.
○ Energy transfer
• Reason(s) why relative fluorescenceis different in isolated chlorophyll vs. intact cells when exposed to light.
• What accounts for the fact that chlorophyll is green in colour
○ There is no green excited state, green light is not absorbed and therefore the photon is reflected back
• Quantitative relationship between photons and excited electrons.
• Relationship between energyof photon and energy required to excite electrons in orderfor photons to be absorbed.
• General structureof photosystem.
○ In photosynthesis:
Antenna - protein with individuallybound chloryphil. Antenna surrounds the reaction centre.
□ No photochemisty - only energy transfer
□ Chloryphil absorbs photon of light and electron gets excited to higher energy state.
□ Excited state can transfer to neighbouring chloryphyl.
Reaction centre - when energy from the antenna reachesthe reaction centre
□ Oxidization of chlorophyl occurs.
□ Electron released from reaction centre drives electron transport.
• Similarities and differences of the light capturingand photochemistry of phototransduction (retinal) vs. photosynthesis (chlorophyll).
Photo Receptor Photosystem
• How are excited states of antennae pigments organized to provide for energytransfer to reaction center.
Outcomes Page 5 • How are excited states of antennae pigments organized to provide for energytransfer to reaction center.
• Structure of rhodopsin.
○ Protein opsin + cofactor retinal.
• Effect of photon absorption by 11-cis retinal on retinal structurefollowed by association with opsin protein followed by interaction of
transducin with opsin.
○ 11-cis absorbsphoton --> breaks doublebond --> reformsinto trans position } (photoisomerization)
○ Retinal no longer fits into opsin bonding site
○ Opsin undergoesa formation change; there is a 'cleft' for transducin to bind;
○ Activates phosphodiesteraise
• Reasons why life has evolved to detect the narrow band of energy represented by “visible light”.
○ Most dominantform of electromagnetic radiation
UV absorbedby ozone
Infared absorbedby other molecules like O2, H2O
○ Energy in visible light is just perfect to do photochemistry
To excite a pigment
Or change a conformation of a molecule
Too much energy from Gama Rays - bons break etc.
Not enough energy from microwaves,radio waves; can't excite an electron.
Outcomes Page 6 Understanding the PROTEIN section of the Purple Pages of the textbook - specifically from page F29 -
Lecture 3 - Protein Structure and Fuction F35. Focus on the outcomes.
January 13, 2013
Independent Study Outcomes
1. Basic structure of an amino acid and what are the different classes of amino acids.
○ Classes of amino acids:
Non-polar amino acids
□ e.g Alanine, Valine, Leucine…
Uncharged polar amino acids
□ e.g. serine, threonine, tyrosine…
Positively charged (BASIC) polar amino acids
□ e.g. asparic acid, glutamic acid
Negatively charged (ACIDIC) polar amino acids
□ e.g. Lysine, Arginine,
2. Chemistry of the peptide bond and how it is formed.
○ Formed through a dehydration synthesis reaction.
3. The four levels of protein structure.
○ Primary structure: the sequence of amino acids in a protein
○ Secondary structure: regions of alpha helic, beta strand or random coil in a polypeptide chain
○ Tertiary structure: overall three dimensional folding of a poly peptide chain
○ Quaternary structure (ONLY SOMETIMES): the arrangement of polypeptide chains in a protein that contains
more than one chain
4. What bonding arrangements give rise to primary, secondary and tertiary structure.
○ Primary Structure: Covalent bonds linking residues together
○ Secondary structure: Hydrogen bonds between N-H and C=O groups
○ Tertiary structure: 4 weak forces: ionic bonds, hydrogen bonds, hydrophobic interactions, disulfide bridges
5. How are alpha helices and beta sheets formed.
○ Alpha helices: coil shape formed when hydrogen bonds form between every N-H group of the backbone and
the c=O group of the amino acid four residues earlier
○ Beta sheets: formed by hydrogen bonds between backbone atoms on adjacent regions of the peptide
1. reasons why photosystems have antenna proteins while the eye doesn’t.
○ because in the eye you don’t want to use the energy - you want to reflect the image instead of just
harvesting the energy (like you would want to do in photosystems).
2. points of control for regulation of protein abundance.
○ mRNA decay
3. factors affecting mRNA transcript abundance.
○ Balance between the rate of transcription and mRNA decay.
4. steps in making a Northern Blot for measuring mRNA transcript abundance.
○ Isolate RNA from cell or tissue samples
○ Gell electrophoresis
○ Lab created single stranded radioactive DNA will bind to complementary mRNA that we're looking at
○ Measure radioactive markers & voila! Northern Blot
5. relative abundance of various types of RNA in typical cells.
○ Ribosomal RNA is the most abundant (~90%)
6. steps in making a Western Blot for measuring protein abundance.
○ uses gel electrophoresis to separate native proteins by 3-D structure or denatured proteins by the length of
○ The proteins are then transferred to a membrane (typically nitrocellulose or PVDF),
○ where they are stained with antibodies specific to the target protein.
7. characteristics of constitutive vs. induced vs. repressed gene expression kinetics.
Constitutive expression if the gene doesn’t change
Outcomes Page 7 ○ Constitutive expression if the gene doesn’t change
○ Induced - it goes up; transcript abundance or protein accumulation goes up
○ Repressed - it goes down; transcript abundance goes down or protein accumulation goes down
8. varieties of defects that might account for lower levels of functional photoreceptors.
○ Could be a simple muatation in the opposite gene, so that the wrong protein is made
○ Problem with translation
○ mRNA decay of the opsin
○ Protein abundance has been repressed
Or anything that lowers the amount of opsin
○ Protein decay - breaks down much faster than a normal one would
9. relationship among polypeptide, apoprotein, cofactor and functional protein.
○ Sometimes a polypeptide needs to interact with a non-protein after translation
○ Cofactor is a non-protein chemical compound that is bound to a protein and is required for the protein's
○ Apoprotein is the polypeptide chain that isn't functional without the cofactor.
10. relationship between protein folding and function.
○ Protein has to fold ( which occurs after translation) to be functional
○ Spontaneous, in miliseconds
11. factors affecting proper protein folding (Anfensen's dogma)
○ Dependent dolely on primary sequence
○ Urea - disrups tertiary bonding, causes it to unfold
Outcomes Page 8 Lecture 4 - Energy & Enzymes Section4.1 (Energy and the laws ofthermodynamics)from the textbook. Focus on reallyunderstanding
sections 4.1d and 4.1e. A must.
January 16, 2013
Independent Study Outcomes
1. Isolated,closed and open systems.
2. Firstlaw of thermodynamics
a. Energy can be transformedfrom one form into anotheror transferred fromone pace to
another,but it cannotbe createdor destroyed
3. Second law of thermodynamics
a. The total disorderof a systemandits surroundsingsalways increases
4. What is meant bythe phrase "it takes energyto maintain low entropy" (section 4.1e)
a. Livingthings bringin energy and matterand use them to generateorder out ofdisorder
○ potential,kinetic, chemical energy,
○ Entropy:Lack of order or predictability;gradualdeclineinto disorder
○ spontaneous reaction ∆G
○ enthalpy (H),
○ exothermic, endothermic,
○ Gibbs Free Energy,
○ exergonic, endergonic,
○ rate of reaction