Biology 1002B Outcomes
Lecture 1: Chlamydomonas and Intro
Characteristics of Chlamydomonas that make it a useful model system. It is a useful model system for
flagella because their flagella are the same as the ones found in humans. It also shares many common
traits with animals which make it a useful model system. It is a model system for photosynthesis, cell
structure. It is also very easy to induce mutations in chlamydomonas so it is useful as a model.
Relatedness of Chlamydomonas to plants and animals large level of similarity between chanelrodopsin
Relationship between genome size and protein coding genes there is really no relationship, genome sizes
can range largely without much change in protein coding genes. It all depends so no relationship can be
Phototransduction from eyespot to flagella. This is the ability to convert light into an electrical signal. The
signal is then used to initiate various functions in the body and or reactions.
Advantages to Chlamydomonas in being phototactic. Phototaxis is the ability to move towards or away
from light. The advantage
Distinctions between primitive, complex, simple. Primitive is an old thing that is not to be confused with
simple. Complex is complex. i.e. eyespots are not primitive they are just simple.
Reasons why Chlamydomonas might move towards a light source. In order to use it as an energy source.
Reasons why Chlamydomonas might move away from a light source. Perhaps it is a recognized
wavelength that they cannot use for energy or it is suspected to be a predator.
Possible mutations that could cause a Chlamydomonas cell not to be phototactic. Perhaps a mutations
that does not allow chanelrodhopsin to function irregularly.
Lecture 2: Light Energy and Information
Relationship between wavelength and energy content of a photon. The shorter the wavelength the higher
Molecular characteristic of pigments that make them able to absorb light. Delocalized electrons in a
conjugated ring system are the electrons that interact with the photons of light. These pigments tend to be
Relationship between pigments and associated protein.
Four “fates” of the excited state of chlorophyll resulting from absorption of photons. 1. When an electron is
excited it can eventually decay and drop back to its ground state. 2. You can also use the excited electron
to cause photochemistry and use the extra energy to break bonds and create new bonds.3. There can
also be an energy transfer if there are two pigments close together. 4. It can also lose a small amount of
energy and then produce a photon (with a longer wavelength than it initially had because of the small loss
Relationship between energy of photon and electron excited states to explain pigment colour and
absorption spectrum. Pigments can only absorb specific wavelengths of light and thus they are the color
of whatever wavelength they reflect. The absorption spectrum is what wavelengths a particular electron
Key features of eyespot that allow for directionality and amplification of light signal This is the globules
behind which act as a reflecting barrier so that only light coming in from the top 180 degrees can triggerthe channelrhodopsin. Light from behind gets bounced back and does not trigger the rhodopsin. This
allows for a direction of the light source to be established.
Distinctions between photochemistry & photoisomerization photoisomerization is when a photon causes
one isomer to change to another, photochemistry is when a photon causes a breaking or forming of
Major similarities and differences between phototransduction in eyespot vs eye. They both use very
similar rhodopsin molecules and they both use depolarization to send the signal that light has been
Reasons why life has evolved to detect the narrow band of energy represented by “visible light”. This is
because ti is the most abundant on earth. And because it has the perfect amount of energy to excite
electrons whereas light outside this will either not excite the electron or will destroy the molecule.
Basics of bioluminescence. An electron is excited in a chemical reaction and then as the electron falls
back to its ground state a photon is emitted and it produces light.
Lecture 3: Protein Structure and Regulation
1. role of ER bound ribosomes and free ribosomes ribosomes on the ER make the proteins that are
going to be secreted or that are found in the plasma membrane. The free ribosomes make everything
2. points of control for regulation of protein abundance. A point of control for abundance of proteins is
transcription. i.e. the abundance of proteins can be controlled by controlling transcription. The same
holds true for translation, transcript abundance and the rate of mRNA decay.
3. factors affecting mRNA transcript abundance. Environment such as temperature and what the cells
needs a proteins in the particular situation.
4. steps in making a Northern Blot for measuring mRNA transcript abundance. Isolate RNA from cells or
tissue samples. Use the electrophoresis to align all of the RNA on the gel. Then transfer the RNA from
the gel to the plastic sheet and take a “probe” that is single stranded (like all the stuff on the sheet)
which is a compliment to the strand you are isolating. Then use some sort of technique to make the
tags on the probe to glow or become apparent and then measure the levels In each test.
5. relative abundance of various types of RNA in typical cells.Ribosomal RNA bands represents 97%
of total RNA. All of the mRNA accounts for 3%.
6. steps in making a Western Blot for measuring protein abundance.Protein abundance is similar to
the northern blot except for the proteins there has to be a specific antibody made to attach to
it so that you can see the specific protein.
7. characteristics of constitutive vs. induced vs. repressed gene expression kinetics. Constitutive
expression: when the abundance does not change Induced: when expression goes up i.e.
you have induced an expression of the protein Repressed: when the expression goes down
8. varieties of defects that might account for lower levels of functional photoreceptors.There could be a
genetic mutation in the opsin. Or tere could be a mutation in the enzymes that produce the
retinal and cause a decrease in the numbers of functional retinal.
9. relationship among polypeptide, apoprotein, cofactor and functional protein.apoprotein is a protein
without its cofactor, which it needs to become a functional protein. A cofactor is a non-protein
attachment to an apoprotein. A polypeptide is essentially the unfolded protein in a chain of
10. relationship between protein folding and function. The protein folding determines the function
because of the complex 3D shape.
11. factors affecting proper protein folding (Anfinsen's dogma) If a protein is folded and is then unfolded
by something that denatures it, it will fold itself back up again because of the charges of its parts.
12. Role of energy in protein native confirmation the native protein conformation is the one with the
lowest associated energy level.Lecture 4: Energy and Enzymes
1. Isolated (no matter or energy transfer), closed (no matter trnaser but energy transfer) and open (both
energy and matter transfer) systems.
2. First law of thermodynamics Energy cannot be created or destroyed, only changed from one form or
moved from one place to another.
3. Second law of thermodynamics the total disorder of a system and its surroundings always increases
4. What is meant by the phrase "it takes energy to maintain low entropy" (section 4.1e) We eat food to
maintain a low entropy so that out cells stay ordered and in order to do this we need to pump energy into
them, and then increase the disorder of our surroundings. Living organisms can be thought of as islands
of low entropy in a sea of disorder.
meaning of potential (energy that is not kinetic but that is “stored” as situational energy
of the chemical or object”, kinetic (energy of movement”, chemical energy (energy used
and created by breaking and making chemical bonds), entropy a thermodynamic quantity
representing the unavailability of a system's thermal energy for conversion into mechanical
work, often interpreted as the degree of disorder or randomness in the system , spontaneous
reaction (a reaction that occurs without the input of energy), enthalpy (H)
(thermodynamic quantity equivalent to the total heat content of a system. It is equal to the
internal energy of the system plus the product of pressure and volume). , exothermic when
energy is released into the environment, endothermic whne energy is absorbed into the
product, Gibbs Free Energy energy that is freed from a reaction, exergonic where there
is a positive free energy ie there is energy leaving the system, endergonic where energy
is being brought into a reaction, catalyst a substance that increases the rate of a chemical
reaction without itself undergoing any permanent chemical change. , rate of reaction How
quickly a reaction tales place, energy of activation (E )(thA input of energy required to
begin the reaction), transition state The state of a molecule when it is ready to undergo
a reaction and it has already absorbed its activation energy, kinetic stability how stable
a molecule is and resistant to spikes in kinetic energy, active site a region on an enzyme
that binds to a protein or other substance during a reaction. , catalytic cycle A catalytic cycle in
chemistry is a term for a multistep reaction mechanism that involves a catalyst. The catalytic
cycle is the main method for describing the role of catalysts in biochemistry
Why life needs to consume energy Life needs to consume energy to offset the effect of the second law of
thermodynamics. And we need that low enthalpy energy to continue to function.
Components of Gibbs Free Energy equation and how they affect whether or not a reaction will be spontaneous
∆G =∆H - T∆S
∆G (free energy) =∆H (enthalpy) - T∆S (entropy)…. if the free energy is greater on the left side of the equation this
endergonic, if the free energy goes down it is exergonic. If it is an exergonic reaction it is a spontaneous reaction.
It will likely be exothermic. (This means that the lowest energy state has been reached, or it would not have been
Role of enzymes in endergonic vs. exergonic reactions enzymes cannot supply energy to the reaction, and thus
they cannot create an endergonic reaction. However, they do make exergonic reactions go very quickly, where
they may take a very long time to occur.
Relationship between activation energy and rate of reaction. The lower the activation energy the quicker the rate
How enzymes increase rate of chemical reactions. Enzymes lower the activation energy for the reaction.
Why biological systems need enzymes. Reactions would take way too long to happen and biological systems
would be left without the necessary building blocks for life.Importance of tertiary structure to enzyme function this is because the tertiary structure holds the enzyme in
shape. And it would not work without its shape.
Link between enzyme function and growth rate if the enzymes are functioning well then there will be a faster
How tertiary structure bonding arrangements are different depending upon the temperature habitat of the
organism. (homework question) the arrangements differ to counteract the effects of the hear so that when the
heat morphs their shape they still work? No clue.
Lecture 5: Membrane Structure and Function
What are the fundamental aspects of the Fluid Mosaic Model This model shows that membranes are a
fluid and that they approximately have the viscosity of olive oil. It also says that the lipid cells move
around in the membrane by switching places with other lipid cells (hence being a liquid). It is rare for a
lipid to switch from one side of the membrane to the other. It also states that there are proteins in the lipid
bilayer and that they move around as well, albeit more slowly because of their size. There are a wide
assortment of proteins with types including transport, attachment, signal, transduction and processes
such as the electron transport chain.
Basic structure of a lipid, a fatty acid. From the bottom up; there are the non-polar carbon chain lipids at
the bottom which are like tails to the molecule. They can be straight and saturated or kinked and
unsaturated. Above that there is glycerol, which is then attached to a phosphate group. The phosphate
group is then attached to a polar unit.
Role of hydrophobic effect in membrane formation The structure of a phospholipid being one part
hydrophobic and another part hydrophilic means that in a aqueous solution such as the environment
inside the body that they will arrange with the hydrophobic section all facing in and the hydrophilic section
facing out. This makes the formation of a lipid bilayer very probable and energetically favorable.
What is meant by the terms saturated and unsaturated. Saturated is when the lipid carbon chain is fully
saturated with hydrogen atoms meaning the carbon chain is straight and has no double bonds. An
unsaturated molecule is one where it is not fully saturated with hydrogen and thus must have one of more
double bonds to compensate. These lipids are “kinked” where there is a double bond.
meaning of hydrophilic Water loving, hydrophobic Water fearing, fatty acid A fatty acid is a
single carbon chain with a carboxyl group on the end (COOH)., saturated All bonds ar filled
with hydrogen, membrane fluidity the viscosity of the membrane whether it exhibits more fluid
or more solid characteristics, desaturase a class of enzymes that introduce a double bond into
fatty acids to control the membrane fluidity. (more saturated=more fluid-like), membrane
permeability the permeability of a membrane and what can travel through it and what cant,
transmembrane protein a protein that spans the lipid bilayer in a membrane, simple diffusion a
diffusion that will occur naturally because the gradients are in favor of it. , facilitated diffusion
when a protein is the source of the diffusion where otherwise there could be no diffusion. All
proteins on membranes, whether passive or active are examples of facilitated diffusion , active
transport this is the opposite of simple diffusion. It is when you move ions where the gradient is
not energetically favorable. To do this you need energy and it requires a transporter protein
(and energy) to move ions from a low concentration to a high concentration., “ATP-Binding
Cassette” (ABC) transporter Moves ions into high gradient areas and requires energy to do
so., cystic fibrosis A genetic disease where the CTFR protein has a mutation which causes it to
function improperly, Cystic Fibrosis Transconductance Regulator (CFTR) This is a protein that
pumps cl- ions out of the cell to form a pressure gradient and eventually keeps the lining of the
lungs and intestines moist., ∆F508 describes a space in the CFTR gene where there is a
deletion on one of the bases, chaperone protein Essentially the quality control they bind to the
folding proteins in the ER and if they are folded properly they let them go, however if they areimproperly folded they will tag them and the protein will be degraded, “ER quality control”
essentially the chaperone proteins, proteosomes, proteases
role of fatty acids in membrane structure. They form the lipid bilayer. The hydrophilic heads
point out and the hydrophobic lipids pint inwards. There are two layers of this and hence a
bilayer. (back to back lipids)
relationship of fatty acid saturation levels on membrane fluidity. The more saturation the less
fluid. Or, the more double bonds (unsaturation) the more fluid.
relationship of temperature on membrane fluidity. Higher temperature means higher fluidity.
relationship of fluidity to membrane functions such as transport. The more fluid the easier it is
to move around and to have proteins move and function.
properties of saturated vs. unsaturated fats. Saturated is straight and unsaturated has a kink.
Unsaturated means that the cell will be more fluid.
role of desaturases in fatty acid biosynthesis. They are used to put double bonds on carbon
chains of the fatty acids, effectively controlling the fluidity of the membrane.
relationship of bacterial desaturase expression vs. temperature. As the temperature decreases
so does the expression of the desaturase. (this is to make the lipid bilayer more fluid in colder
conditions, which would normally make it much more solid)
Structure of desaturase there is a channel in the desaturase and the fatty acid goes all the way
to the bottom of the channel into the desaturase. Once the string can go no farther the active
site puts the double bond in the fatty acid effectively making it unsaturated.
role of size and charge in movement of molecules across biological membranes. If the
molecule is large or if it is charged it will not be able to pass through the lipid bilayer. If it is
small and non-polar it will be able to pass through unaffected. Ex. O2
characteristics of transmembrane proteins that enable them to interact with hydrophobic core
of membrane. They must have a hydrophobic stretch of amino acids that will let them
transverse the lipid bilayer and the other sections that do not traverse but are on one side or
the other will be hydrophilic. It takes around 20 amino acids to traverse the lipid bilayer. This is
also made possible by the alpha helix structure which makes the structure of the amino acids
inside the membrane essentially non-polar making it easier for them to interact.
factors influencing simple & facilitated diffusion. Whether or not there is a membrane. If it is
facilitated there must be some kind of barrier and if there is diffusion happening on its own then
it must be simple diffusion.
transport against a concentration gradient (active transport) This is achieved by proteins in the
membrane and requires energy in order to go against the pressure gradient and get the ion
into the high concentration area.
basic structure of ABC transporter. There are clamps for the ATP and it moves the ion through
the channel similar to opsin. It uses the ATP as energy to do this.
genetics underlying cystic fibrosis. There is a genetic mutation to the gene that build the CFTR
transporter protein in the membrane. This means that people with CF have trouble in moving
cl- ions across a membrane.
cystic fibrosis phenotype. Carriers have no symptoms or noticeable effects. However, if you
are homozygous then you have full blown CF. 1 in 22 Canadians are carriers of the CFTR
mutation.possible link between CF an Cholera (heterozygote advantage) There is a heterozygote
advantage because you are slightly less able to move water out of the cells and into the lungs
etc… this means that when you get cholera you will not lose as much water and have a higher
chance of surviving. Thus, the CF allele has continued to persist because it confers an
advantage to heterozygotes.
physiological function of CFTR. Moves Chlorine ions out of the cell to keep a strong gradient
Because of this the water will then diffuse out and follow the cl- and overall it keeps the lining
of the lungs wet (same idea with intestines).
relationship of CFTR synthesis and folding in the intra-cellular secretory system. The mutation
causes it to fold improperly.
what happens to the deltaF508 form of CFTR it gets caught in the ER and will not be allowed
role of chaperone proteins They bind to the proteins and “sense” whether or not they are
folded or not. If they are not folded correctly they are tagged and then degraded.
role of proteasomes
Lecture 6: Photosynthesis
1. How is the structure of ATP linked to the fact that its hydrolysis is strongly exergonic. There are three
reasons. 1. Both the products of the reaction are negatively charged. 2. The release of the terminal
phosphate allows for a greater opportunity for hydration (which is favorable). 3. The third phosphate group
can exist in a large number of resonance forms, not all of which are available when bonded. Thus release
of the phosphate increases the overall disorder of the system.
2. What is the biochemical "goal" of the Calvin Cycle. The goal of the Calvin cycle is to synthesize simple
sugars from an input of carbon dioxide.
3. What is the relationship between G3P and glucose. G3P is the starting point from which the body
makes glucose and other more complex sugars and carbohydrates.
4. What is the importance of ribulose 1,5-bisphosphate (RuBP) in the cycle...what's a cycle anyway?
They are important in the cycle because they are needed to “kickstart” the next round. The reason it is a
cycle is because it needs the products (ribulose) at the end of the cycle to start the new round.
5. The three stages of the Calvin Cycle are Fixation, Reduction and Regeneration...what do these
terms mean, biochemically? The fixation step takes the incoming CO2 and the leftover ribulose form the
previous cycle and creates the bisphosphoglycerate with them. Reduction uses up 6 ATP and results in
one molecule of G3P. the regeneration step produces two more G3P molecules. It also produces the next
round of materials to be used to start off the cycle again.
6. If I take a culture of Chlamydomonas cells and isolate all the chlorophyll, the isolated chlorophyll will
produce much more fluorescence than an intact culture of Chlamydomonas containing the same amount
of chlorophyll. Why? Watch the video below. Florescence: Giving off light as a result of incident
radiation with a shorter wavelength. (ie starts with short wavelength, loses some energy, comes back as
Red light causes chlorophyll's electron to jump one "energy level." Since blue light has more energy, it
excites the chlorophyll's electrons even more: They jump two levels. However, it's very difficult for the
electron to stay at such high energy in a chlorophyll molecule, so the electron falls very quickly from the
blue energy level to the red energy level. (The extra energy is lost as heat.)
OK: now all of the energy associated with the chlorophyll is "red" energy. When the chlorophyll is properly
arranged in the chloroplast, that red energy is used to do the work of photosynthesis. However, if you take
the chlorophyll out of the chloroplasts, there's no place for the energy to go, except heat or light! Much of
the energy is released in the form of red fluorescence, so the chlorophyll looks red.Absorption of light energy by photosystem II results in the
primary acceptor. P680
is rapidly reduced back to P68O by an
electron from H2O transferred from the oxygen evolving complex.
2 From the primary acceptor the electron is passed to the mobile
carrier molecule plastoquinone (PQ). As it accepts an electron from
through the membrane before binding to the cytochrome complex,
thylakoid lumen. From the cytochrome Complex the electron is
donated to plastocyanin
Absorption of light energy by photosystem Iresults in the
oxidation of P7Oo. The liber
d by th
tase complex. P7OO is
reductase Cormplex, NADP is reduced to NAD
Proton pumping by plastoquinone (red arrows) creates a
into the stroma throue h the ATPase corr mplex, which drivees the
synthesis of ATP from ADP and Pi
Absorption of light energy by photosystem II results in the primary acceptor. P680 is rapidly reduced back to P68O by an electron from H2O transferred from the oxygen evolving complex. 2 From the primary acceptor the electron is passed to the mobile carrier molecule plastoquinone (PQ). As it accepts an electron from PC2 diff through the membrane before binding to the cytochrome complex, thylakoid lumen. From the cytochrome Complex the electron is donated to plastocyanin Electron transport cytochrome Ph of light of light Oxygen evolving Plastocyanin Thylakoid Lumen Calvin Cycle ADP P Absorption of light energy by photosystem Iresults in the oxidation of P7Oo. The liber d by th tase complex. P7OO is OO b reaches NAD reductase Cormplex, NADP is reduced to NAD Proton pumping by plastoquinone (red arrows) creates a hy Th into the stroma throue h the ATPase corr mplex, which drivees the synthesis of ATP from ADP and Pi Calvin cycle CHT NADP ATP synthasedefinition of photosynthesis the process by which green plants and some other organisms
use sunlight to synthesize foods from carbon dioxide and water. Photosynthesis in plants
generally involves the green pigment chlorophyll and generates oxygen as a byproduct. ,
oxidation combine or become combined chemically with oxygen. , reduction Reduction
reactions is when an oxidation reaction is reversed and a chemical loses its oxygen, oxidation-
reduction reaction Redox (reduction-oxidation) reactions include all chemical reactions in which
atoms have their oxidation state changed; in general, redox reactions involve the transfer
of electrons between species, light reactions The reactiosn that take place when a photon
of light interacts with a pigment, Calvin cycle The other half of the photosynthetic cycle
which is in the chloroplast, redox potential The ability of a molecule to undergo a
reduction or oxidation reaction, chloroplast In plant cells which contain photosynthesis
reaction with photons and the ETC, thylakoid membrane The membrane in the thylakoid
which holds the ETC, lumen Inside of the thylakoid and holds the positive proton
gradient., P680 chlorophyll in PSII and P680* is the excited state P680+ is the
chlorophyll is when it loses its electron so it takes an electron back from water and
starts the cycle again, P700 Chlorophyll in the PSI and P700* is the excited state.
P700+ is when it loses its electron and starts the cycle over again by getting another
electron. ( and * for each), chemiosmosis Is when you are using a proton gradient to
do work. (in the case of the ETC it uses the proton gradient to create ATP),
Structure of chloroplast (use your model of Chlamydomonas and link that to structures
and compartments seen in Figure 7.3) see pictures The chloroplast has the light reactions
that occur in the chloroplast and the result is atp, this then powers the calvin cycle to produce
adp (which is turned back into ATP in the chloroplast) and simple sigars for the plant to use as
Source of electrons and products of electron transport The source of electrons is the
water that goes into the electron transport chain. Also, the products are ATP and
Structure of photosynthetic electron transport The electron transport chain is present in
the thylakoid membrane (which is in the chloroplast). The chlorophyll is located in the
photosystem 2 and photosystem 1. This is the only point where chlorophyll can be
found. Inside the “reaction center” in photosystem 2 is special chlorophyll “p680”. InLight
Glucose and other
Electrons carried by
NADH and FADH
system and oxidative
components of the thylakoid membrane
nized according to their energy level.
is also referred to as the Z scheme.
Isorbing a photon of light, an electron
n the reaction centre chlorophyll of
ll P680) gets excited to a higher
level (P680 which enables electron
port to be spontaneous (downhill) to
osystem I. However, the energy level
ADP is greater than that of P700.
difference is overcome by photosystem I
rbing a photon of light, producing P700
two photons of light, one absorbed by
osystem II and another absorbed by
osystem I, are required to overcome the
difference between HTO and NADP
Light energy Photosystem II Primary acceptor P68 Pla poo P68 phnt I Glycolysis Glucose and other fuel molecules Pyruvate Pyruvate oxidation Acetyl-CoA Citric acid cycle Electrons carried by NADH and FADH Electron transfer system and oxidative phosphorylation ptor edoxin NADP reductase NADPH NADP re 7.12 components of the thylakoid membrane nized according to their energy level. is also referred to as the Z scheme. Isorbing a photon of light, an electron n the reaction centre chlorophyll of system ll P680) gets excited to a higher level (P680 which enables electron port to be spontaneous (downhill) to osystem I. However, the energy level ADP is greater than that of P700. difference is overcome by photosystem I rbing a photon of light, producing P700 two photons of light, one absorbed by osystem II and another absorbed by osystem I, are required to overcome the difference between HTO and NADPphotosystem 1 there is another special chlorophyll “p700”. The protons (because they
have built up a strong gradient) flow through the ATP synthase multi-protein and you
cause photophosphorylation to construct ATP. Water is extremely difficult to oxidize and
how P680+ can take an electron from water is remarkable. This is only because it is the
strongest biological known oxidant.
Mechanism of electron flow The mechanism is the redox potential of the molecules so
that the electron will flow to the molecule with the higher redox potential (or the hardest
to oxidize) and is more electronegative meaning that the molecule will hold the electrons
more strongly (and so attract the electrons) than the preceding molecules of a lower
redox potential. This is because the lower the redox potential the lower the electron
Anoxygenic photosynthesis This only takes one photosystem. So it is much more
efficient. However, instead of water it uses hydrogen sulfide. The problem is that this is
not abundant and water is, so that nearly all systems use the water version. Both
systems produce the same amount of ATP and NAHPH. However, just based off of not
having any hydrogen sulfide means this system will not work in nature even though it is
Reaction catalyzed by rubisco This reaction takes the 5 carbon sugar at the end of the
Calvin cycle (the product) and adds the incoming CO2 that enters the cycle to make two
3 carbon molecules called PGA. Rubisco is an ancient enzyme.
Difference between carboxylation reaction and oxygenation (photorespiratory) reaction.
Carboxylation is when the Calvin cycle goes as planned which creates the 2PGA
molecules to go onto the second step. (5+1=6 then divide by two products = 3).
However, Oxygen can take the place of the CO2 you then have a reaction called
oxygenation this then gives you one molecule of PGA and another molecule called
phosphoglycolate which you lose during respiration. So, carboxylation = good and
oxylation = bad because it is less efficient.
Implication of photorespiration (oxygenation) on growth This decreases the growth
because there is a overall net loss of carbon.
Mechanism by which Chlamydomonas concentrates carbon dioxide There is a pump on
the membrane of the cell that pumps in bicarbonate. This gets broken down into CO2
and so there is a high concentration of CO2 in the cell and this allows it to keep the
carboxylation reaction high and low on the Oxygenation reaction just based on
concentrations.Lecture 7: Cellular Respiration
What are the major molecules that control the rate of cellular respiration? Phosphofructokinase allows the
cellular respiration to continue and the ATP and Citrate inhibit it to stop the cycle if there is too much ATP.
location, products, distribution in nature and purpose of pathways such as glycolysis, CA cycle,
respiratory electron transport etc. Anaerobic bacteria only have glycolysis. Everything else has the full
role of energy coupling in early steps of glycolysis It allows the first reaction of glycolysis to occur by
spending 2 ATP molecules (and thus having the hybrid reaction that can occur spontaneously) to get the
end product of pyruvate.
relative potential energy of various intermediate compounds (eg. glucose vs. pyruvate vs. CO2) Glucose
has the most potential energy then pyruvate has a bit less and is in the middle, then CO2 has the least
link between glycolysis and Citric Acid Cycle Pyruvate is used to start the CA cycle so it is transported into
the mitochondria where the rest of respiration takes place. Then pyruvate loses its carboxyl group
(because there is no free energy left in it). There is then a dehydrogenase that comes into pyruvate and
makes the NADH. Then the Coenzyme A binds to what is left of the pyruvate and it makes it much more
reactive. Then it’s off to the CA cycle. The CA cycle oxidizes the acetyl CoA. Then the carbon is lost, and
the citrate holds the energy with the 6 carbons. It then goes through the CA cycle to make NADH and
role of pyruvate dehydrogenase complex It creates an NADH from the broken down pruvate.
diagnostic value of relative ratios of bioenergetic intermediates (eg. ATP, pyruvate, NAD etc.) ATP is the
most useful, then Pyruvate is less useful, and NAD is the least useful? The most ATP is made in the ETC.
relative location of electron transport chain components relative to mitochondrial membrane, matrix,
intermembrane space It is in the membrane that goes between the matrix and the inter membrane space.
role of oxygen in electron transport The oxygen allows to remove the excess product of H2O by
absorbing the electron at the end of the chain.
role of NADH in electron transport It gets oxidized and donates the initial electron for the chain to start the
role of cofactors in ETC They allow the electrons to flow down the ETC and pump protons into the inter-
membrane space (complexes).relationship between redox potential of ETC intermediates and “flow” of electrons The components will
allow electrons to flow down the chain because each molecule has a higher electron affinity than the
previous one. This means the electrons get pulled down the chain.
link between ETC and synthesis of ATP The ETC creates the proton gradient which is used by ATP
synthase which makes the ATP.
effect of uncoupling agents on ATP synthesis The uncoupling has no effect on ETC but it means that the
ATP synthase will no longer work.
goal of making lactate under conditions of hypoxia (low oxygen) IF there is not enough NAD+ then there
is no glycolysis. Ie, Glycolysis stops. So taking pyruvate and turning it into lactate makes some NAD+ so
that glycolysis can continue.
role of NAD+/NADH in sensing hypoxia It senses it because if it is a very high ratio it means that the cell
is able to oxidize. And the ETC is working fine. However, if it is low then it meas the ETC may have a
role of HIF1 regulation in sensing hypoxia This is a transcription factor which will activate transcription
when it senses the hypoxia.
effects of HIFI activity on pyruvate metabolism It prevents the pyruvate dehydrogenase and so effectively
stops the pyruvate from continuing the respiration. This will shut down the rest of the CA cycle other than
glycolysis so that it can use up all of the NADH and will get some ATP as opposed to getting none. So this
is an emergency measure in the presence of a lack of oxygen.
feedback regulation of glycolysis, CA cycle and ETS (not covered in class) ok….
various characteristics that compare/contrast with those of photosynthesis The pumps on respiration
pump out H+. ‘
Lecture 8: Integrated Metabolism
What prevents Chlamydomonas from being a heterotroph that grows on glucose? Even if you put it in an
environment with glucose there is no glucose transporter and so it cannot acquire glucose from the
environment. It could use the glucose if it acquired it however, it cannot get the glucose in the first place.
change in respiration rate (oxygen consumption) in isolated mitochondria by addition of NADH, ADP,
uncoupler etc. The consumption increases when you add NADH. The consumption will Increase
when you add ADP and Pi. The oxygen consumption will greatly increase the rate of electron
definition of respiratory control and how it is accomplished (proton gradient). The influence that the
presence that ADP and Pi have on the rate of electron transport. It is accomplished by creating a
large gradient in protons if there is low ADP (because ATP synthase stops working). So the electron
change slows down because it is too hard to pump protons in when the gradient is already so high. If
there is lots of ADP then there is an increase in electron flow because ATP synthase is working. If
there is an uncoupling (like poking holes in the membrane) then the ETC is unhindered and will
operate at a maximal speed.
metabolic link(s) between chloroplast and mitochondria. ATP made in the chloroplast stays in the
chloroplast and is used by the Calvin cycle. There is a transporter on the chloroplast membrane that
can transport the G3P outside of the chloroplast. G3P is not only a product of the Calvin cycle; it is
also an intermediate of glycolysis. G3P and Glucose represent the carbon backbone to build a huge
array of other useful molecules such as fatty acids etc… The energy form that is exported is the
carbon in the form of sugars not the ATP from the chloroplast.
Just to be clear: All/most plants have mitochondria, no matter whether they photosynthesize or not.
Chloroplasts (for photosynthesis) are required to product glucose, food for the plant. Mitochondria, on theNADP
the CO2 acceptor
Co. at a time
Phase 1: Carbon fixation
NADP Ribulose bisphosphate (RuBP) 3 ADP ATP ase 3 Regeneration of the CO2 acceptor RUB G3P Input 30 Entering one Co. at a time Phase 1: Carbon fixation Short-lived intermediate 3-phosphoglycerate ATP 6 ADP CALVIN CYCLE 1.3 Bisphosphoglycerate 6 NAD 6 NADP Glyceraldehyde-3-phosphate Phase 2 (G3P) Reduction G3P Glucose and a su other organic Output compoundsother hand, are sites of respiration, where this glucose is broken down and ATP is produced.
They have completely different roles, and thus mitochondria are still required in photosynthesizing plants.
Without mitochondria, plants would not be able to break down whatever they photosynthesize.
reasons why Chlamydomonas can grow as a heterotroph on certain reduced carbon compounds -
but not others. It can grow on acetate. It does have transporters on its membrane that can transport
acetate. Whereas with glucose it has no transporter. So, Chlamy can use acetate but not glucose.
Lecture 9: Integrated Metabolism II
how to measure carbon fixation in Chlamydomonas Place chlamy in a flask and add light from an external
source and have a co2 analyzer on the top of the flask. (this is a closed system). The units are
micromole/cell/min or something like that
how one can distinguish between gas exchange in mitochondria from that taking place in the chloroplast
of a Chlamydomonas cell. The gas exchange in the mitochondria will cause the carbon fixation rate to
decrease as it is spewing out lots of CO2. If the chloroplast is working then the carbon fixation rate will be
positive because it is taking CO2 in and using it to make sugars.
Identify major parts of a light response curve for carbon fixation Carbon fixation means how much CO2 is
being turned into organic carbon. So, if carbon gas is being spewed out then there is a negative carbon
fixation. If CO2 is being brought into the cells then there is a positive carbon fixation.
What metabolic processes and external factors may influence the change in rate as a function of light. If
the intensity of the light changes the rate will change as well. More light means more chloroplast function
which means higher fixation rate. The opposite it true for no or low levels of light.
Light compensation point The point where the chloroplast is bringing CO2 in at the same rate as the
mitochondria is spitting it out. The light saturation point is the point where everything is working as fast as
possible and cannot work any faster. This can be damaging to plants if there is too much light because it
will keep absorbing it even though it can’t be used.
Principal of measuring enzyme kinetics as a function of substrate concentration. Easiest way is to
measure the rate of product formation. If this can be related somehow to a color change then it can be
seen. We can then see how the substrate concentration affects the rate of product formation for an
km, Vmax Vmax is the maximum velocity for an enzyme. This is how fast an enzyme can process
substrate at its peak operating potential. Enzymes will differ by a lot in their Vmax. Km is ½ of Vmax. This
is the substrate concentration that gets you ½ Vmax. This is a measure of affinity.
Effect of a competitive inhibitor on enzyme kinetics (Vmax, Km) V max remains unchanged but the km
changes and it makes it much larger because the slope has been decreased. Ie. The value for ½ Vmax is
larger meaning we need more substrate to make it to Vmax.Non-competitive inhibition will lover both Vmax and km values. This is because it binds to a site that is not
the active site so it can bind without competing for the spot. It can then warp the enzyme ad make it un-
Role of allosteric activation and inhibition in the regulation of metabolism It can control the enzymes. For
example, if the atp levels are low in the cell that means there is high ADP maybe ADP activates an
enzymes that influences the rate of ATP production. Likewise if these is a lot of ATP then you don’t want
to make more so an allosteric activation or inhibition could change that so that there is a reasonable level
of concentrations in the cell at all times.
Lecture 10: The Origin of Eukaryotes
meaning of endosymbiosis When one cell absorbs another free living cell, cyanobacteria Bacteria that were the
first to undergo oxidative photosynthesis, lateral gene transfer Gene transfer from the mitochondria to the nucleus.
origin of endomembrane system, nuclear membrane, ER etc. These all come from the in-folding of the lipid
membrane folding into the center of the cell. This eventually segregated into an organelle in the center of the cell
and not attached to the original membrane whatsoever.
origin of mitochondria and chloroplasts Through endosymbiosis. That is, a cell essentially engulfed a mitochondria
and a chloroplast.
evidence supporting theory of endosymbiosis Morphology is the same. The formation and division; I.e. you don’t
make a chloroplast or mitochondria you can only get them when one divides into two. Electron transport chains
are present in their membranes. This supports that they were free living. They have their own genomes. They
have translational and transcriptional machinery.
factors driving development of early eukaryotic cells The oxygen in the atmosphere, the membrane infolding to
form the organelles and the absorbtion of the mitochondria and the chloroplast.
why eukaryotic cells can be larger and more complex than prokaryotic cells They can be larger and more