Bio 201 lecture 1

The cell is the basic unit of life

- Yeast, plant cell, human cell

The cell is the basic unit of medicine

- Wallerian degeneration
o In diseased tissue what’s going on is break down in cellular function and cellular
organization that leads to tissue function
- Double-cortex syndrome
o Outer surface of brain is smooth, brain doesn’t have the curves that normally see in
human brain. This disease is caused by a single amino acid substitution in one protein.
An arginine becoming serine in a protein called double cortin
o Now brain won’t form curves
- African ox-eye daisy
o Targets of these molecules are individual proteins that drug has to bind to some protein
and protein has some function and leads to
o Why would changing function of single protein in our cells be important?
The cell is the basic unit of evolution

- Antibiotic resistance. These organisms could evolve in such a way they escape the antibody. A
clear example of that cells are involving and evolution has negative consequences for treating
diseases.
- Uni cellular organisms are capable of more than we think. Scientists must see how bags of
enzymes have sophisticated behaviors, memory formation at the level of individual cells.

How many proteins are there in a human cell?

- Around 20,000 protein coding genes in the protein genome. So the upper number is around
25,000 types of proteins
- Understand the basic cell biology of neurons that help you understand what comes next.

Part1: biological energetics

- Where do cells get their energy from? How do they convert it one way to another are they
energy efficient? The mitochondria and sometime biochemical reaction that’s happening in the
mitochondria

Part2: building a cell

- How cells create organization and structure. How they put components into one place and
another. how cells build complex structures and polarize themselves.

Part3: cell physiology

 - Complex cellular behaviors. How cells take these basic organizational building blocks and how
do they then use them to accomplish physiological behaviors

Do animals consume energy? no

- It seems like we consume energy, but we actually don’t by James Prescott joules. The first law of
thermodynamics
- The total amount of energy remains constant over time. Isolated systems we have heat coming
into body, heat exiting, we’re consuming food and etc.
o Basic idea is that basic is never created or destroyed, it’s transferred from one form to
another

Living organism convert energy from one form to another

- Sun light photons go into plant and turn into chemical bonds and then animals eat the plant
matter and take the chemical bonds and convert the energy stored into them into energy and
heat.
- In general, in metabolism, metabolism is the science of energy conversion.
- How do organisms accomplish these conversions?

Caveat 1: organism store energy during growth

- Plants produce cellulose fibers, animals produce muscle fibers as your body expands in size,
that’s energy being captured and permanently stored in your body

Caveat 2: organisms store energy temporarily during activity

- Consuming energy in the form of glucose and convert it into ATP and then will get consumed
- There will be a period of time when it’s stored. Eventually, it’s converted to heat and work and
it’ll be no longer be a part of our bodies and be released

Organisms devote 20% of their genomes to metabolismmp0 -

- Converting one energy to another E.coli 1/3 genes in E.coli is associated with metabolic function

We’re taking glucose, and converting it into brain, it doesn’t seem to make sense. Making complex
activity from simple building blocks but not consuming anything in the process

- There is something else that’s going on and that is the second law of thermodynamics
o An isolated system also tends towards disorder
- But order seems to be increasing as simple structures build complex structures

Not all energy is equal

- Did joule’s experiment. A weight is attached to a pully that you can spin with a handle
- If you spin the handle, you’d lift the weight. As you lift the weight, you’d give it potential energy.
If you release it weight will fall and release the potential energy
 - He attached the pully to a paddles that are in a tank of water and there’s also a thermometer in
the water
o He wound up the mass and let it fall and the kinetic energy of the motion of the mass
downwards could cause the paddles to spin. One type of kinetic energy is turning into
another. and that would heat up the water and cause the temp of water to increase
- “high quality energy” potential energy of mass on a pully
- ‘low quality’ energy HEAT. Heat is just a form of kinetic energy.
o Heat is the random movement of molecules
- Once the energy be turned into random kinetic motion it cannot be organized into a
coordinated kinetic motion.

What are animals consuming?

- Quality energy and we convert it into low quality energy.

- Complex chemical bonds linking together molecules in the food, but we consume that and the
amount of energy in the bar will be equal to the amount to leaves our body in terms of heat and
work
- Increased entropy while keeping total amount of energy equal
o Order of the energy is what determines the quality of energy.
Living organisms convert high quality energy into low quality energy

- Photons in sun, high quality, chemical bonds, also high quality of energy but also some
dissipation of low quality energy (entropy) and then we use that and produce low quality energy

the quality of energy depends on how much is ‘free’

- Gibbs free energy. H = enthalpy = total energy

- G = free energy’ or available energy
- G = H – “unavailable energy”
- G = H – TS
- S is disorder

Lecture #2 energy in cells

- Not all energy is equal
o Mass on pulley and paddles. Potential energy is high quality energy and spinning the
paddle and increasing temperature of water (heat) due to random kinetic energy of
water molecules in the tank is lower quality than initial quality of energy

Living organisms convert high-quality energy into low-quality energy

- High quality photons to high quality chemical bonds and energy (entropy) with lwo quality

The change in free energy determines whether a process occurs spontaneous

 - Delta G = Gfinal – Ginitial
- Delta G = deltaH – TdeltaS
- If system is isolated delta H is 0
- Entropy has to be increasing as delta S > 0
- If delta G < 0 for a spontaneous process

Free energy values are “standardized”

- Standard free energy can be additive during standard STP (298K, 1atm, 7.0 pH, and
concentrations being 1M)

Cells capture the free energy released by ATP hydrolysis to create order

- Delta G for a to b positive, but delta G for c to d negative

o Positive delta G to create ordered structures.
- A negative delta G coupled with a positive delta G
- Coupling reactions: the trick living reactions do. Capture energy from environment and take
negative delta G and use it to do positive delta G
- What do we mean by coupling? How do we take 2 reactions that are happening in different
phases and put them together.
o Take negative delta G reaction and use it to drive positive delta G reactions
ATP binding/hydrolysis can distort the 3D structure of proteins

- Enzymes + ATP that sticks to it and the binding is going to distort physical process and reacts to
the binding of the ATP and energy will cause protein to distort.
- ATP can induce strain in protein structure.
- All the amino acids in the globular form move out where they want to be based on protein
folding
- Distortion allows them to create a chemical reaction. ATP binds, protein breaks and energy is
used to break apart the molecule
o Glycogen phosphorylate, has a couple ATP binding sites. Binding of ATP will change the
shape of protein
- Cells spend energy by changing protein structure by ATP and causing distortion of the protein

Redox reactions provide a basis for energy transduction

- Reduction: gaining an electron

- Oxidation: losing an electron
- Taking glucose to turn it into Co2 and H2O. harvesting out the electrons oxidizing the glucose.
- Fuels are oxidized by metabolic enzymes.
o Goal of metabolic enzymes is to taking electrons out of the structure they started with
- Electrons carry a lot of energy with it
- Goal of metabolic enzyme is to capture energy by capturing that electron
NAD+ is the principal electron acceptor in metabolic redox reactions

- It will gain electron and become reduced and it’s the reduction of NAD + to NADH that is core
energy harvesting reaction that’s inside our bodies when we’re oxidizing glucose to make fuel

GAPDH brings NAD+ into position to be reduced.

- There’s tiny NAD+ and that’s where the NAD sits in the GAPDH. So the
glyceraldehyde 3-phosphate (substrate) will bind to GAPDH which stands
for glyceraldehyde 3-phosphate dehydrogenase
- Electrons will pop out of the glyceraldehyde 3-phosphate and form 1,3-
bisphosphoglycerate
- That’s where the NAD sites, they go around the phosphate and bind to GAPDH+ and the
electrons will come out of glycerol that reaction is that electrons are liberated and captured
- That’s a tall order, how do you catch electrons they’re tiny and they will react with the first thing
they hit and reduce whatever they smack first
- So you have a protein that has evolved over time to hold and get substrate directly adjacent to
the NAD+ so when the glyceraldehyde 3-phosphate breaks and its electron comes out of it, the
NAD+ is right there and captures it to make NADH. Electron can then be released from NADH to
make NAD+

NAD+ may be useful in a wide range of therapies

- Tuberculosis Drug Isoniazid active and form binds to NADH and because it has those electrons in
them, the release of electrons can be used to drive processes and NADH is energy source for cell
wall synthesis enzyme
- By binding on the NADH, you inhibit cell wall synthesis enzyme and shut down tuberculosis drug
- Wallerian degermation happens happen injury
- Wlds mice have delayed neurodegeneration
o The neural degeneration is caused by overproduction of NAD+ neurodegeneration is
fundamentally a metabolic effect due to injury, neuron is degenerating quickly due to
metabolic break down
o If more electron acceptor better job at harvesting electrons maybe less susceptible to
this type of degeneration.

FAD is used when available free energy could not reduce NAD+

- Oxidized FAD, reduced is FADH2+

- There are other electron acceptors and FAD is used when NAD
cannot be used

How much energy does a cell harvest from a reduction reaction?

- How much energy do you get from capturing the electron? How much energy is there in ATP
hydrolysis? How much in an electron?
- Standard energy of NAD+ reduction to NADH -> Delta G is 52.6kcal/mol
 - FAD reduction delta G is 43.4kcal/mol
o If the electron coming out doesn’t have enough energy in it to reduce NAD+ cells will
then use FAD instead

How much energy is available when ATP is hydrolyzed?

- Energy currency of the cell.

- Delta G = -7.3kcal/mol
- ATP is energy currency? How much is it worth?
- When you hydrolyze ATP, you get whatever you want done. You cannot make change. In order
to answer that question, we establish scale.
- If inefficient, the extra energy is just dissipated into heat. ATP wants to be a perfect amount, so
we don’t waste or need too many.

Thermal energy can serve as a baseline for cellular energy scales

- Based line is thermal energy which is random kinetic energy of molecules bouncing around in
solutions. They’re under constant motion. The hotter the water, the faster they move. We can
use that amount of random kinetic energy as a baseline
o How does everything compare to random Collison of water molecules at room
temperature?
- Ludwig Boltzmann E = 3/2KbT
- Average amount of energy that a molecule moving in a solution will have is that
equation (Kb is the Boltzmann’s constant)
o This energy is average, there will be time when it’ll be a lot and more, so the angle
brackets mean the average.
- KbT = 0.6 kcal/mol (37 degrees)
- We think about energy in units of KbT, kcal/mol is for people dealing with large volumes of
buffers and chemical reactions. With individual molecules and how they’re behaving, think
about energy regarding units of KbT.
- Translate all the energies into these units of KbT.
o Consider the physiological concentrations of ATP but ATP doesn’t exist in 1 molar.
Reaction is ATP goes to ADP + Pi and delta G is only if all the reagents are at one mole
o ATP hydrolysis is equal to 20 KbT
- Turns out the thermal motion of molecules is one of the most significant is cells and proteins

Molecules move continuously due to Brownian motion

- Constantly jiggling around called Brownian motion. Robert Brown.

- “These motions were such as to satisfy me, after frequently repeated observation that they
arose neither from currents in the fluid, not from its gradual evaporation, but belonged to the
particle itself.”

Molecules diffuse with a characteristic diffusion coefficient (D)

 - Every protein in the cell that’s not anchored is moving in random way inside cells.
- Small molecules have a “faster” diffusion and a larger diffusion coefficient and don’t get dragged
down and will move around and they’ll move around
- Large molecules move slower.
- Moves anywhere in a random way and anything not anchored to something is doing this right
now.
o All the ATP, molecules are moving random in the cell.
Brownian motion is a “random walk”

- Starting at one point (0) and a 50% chance step right or left and random steps. Wiggle back and
forth in this random walk in this 1-Dimension random walk. 50% right and 50% left.
- All the molecules start at position 0 at the origin and spread outward and spread crosses.
- Drives dispersion of proteins out throughout the cytoplasm.

Brownian motion explores a lot of space, but you get nowhere (on average)

- random walk 100 walkers take 120 steps and at the end you plot the histogram and looks like
gaussian distribution. The peak is at position 0 because if you flip heads or tails
120 times, most probably outcome is the same number of times, so you go
nowhere.
- Based on probability that is correct most molecules go nowhere but some
proteins that make it out in the distribution.
- Describe distribution that the mean value of the squared displacement is 2Dt (2
times diffusion coefficient times time)
- Thermal energy is dominant inside cells and nothing is ever stationary.
o Protein will start moving around in 3D.
- The distribution so at 2Dt, 63% if them will still be in the first distribution

How do other energies compare to thermal energy?

- Chemical energy: chemical bonds we can ask how strong a hydrogen bond or noncovalent bond
is compared to thermal energy
- Mechanical energy: like work, our muscles produce force and how does this compare to thermal
energy
- Electromagnetic energy: attraction and repulsion of charges, photons and how do these
energies compare

Cells and subcellular structures both feel and produce mechanical forces

- White threads are microtubules, and the arrows look like they’re
buckling in response to force.
- Cell has hit wall and in response it’s buckling
 - Microtubules and the arrows feel like they’re buckling
- Tissue culture cell in a dish and its complicated but grid little dots. Embedded substrate plastic
beads and substrate itself is stretchy
- The first thing cells do is they start pulling on their environment.
o Creates movement of fluorescent beads in the substrate and can measure magnitude of
displacement and see how much force the cells are producing
- Heat map showing hotspots where cells have landed and pulled on its environment

Magnitude of cellular forces

- Most measured in newtons. 1N = 1kg x m/s 2

- Cellular forces are measured at pN to nN (10^ -12 to 10^-9)
o The same force as laser force to your hand and the photons as they hit your hand
- A force is not an energy. If comparing 1 KbT to one force, we use work terms
- 1 KbT = 4.1 pN nm (4 pN of work over 1 nm)
- Cellular forces very low and ATP = 80pN nm of work
- Muscle contraction. Most relevant way is when we contract muscles that’s when we do the
most work. How is it we can lift that much mass?

Electromagnetic energies

- Can come from photons absorbed or emitted

- Or electrostatic potentials
o Attraction of opposite charges and repelling of same charges
Cells absorb and sometimes produce photons

- Chloroplasts absorb photos during photosynthesis. Cells produce photons with

bioluminescence.
o Fireflies chemical reaction that produces photons
- E = hv (Planck’s constant times frequency in hz)
- Visible photon = 2 eV (electron volts)
- 1 KbT = 25meV
- Visible photon = 80KbT 4 times the energy of ATP hydrolysis comes from visible photon

The surface of protein contains many charged residues.

- Surfaces of proteins contain many charged residues.

- Proteins bind to each other due to the positive regions interacting with the
negative regions of the protein surfaces they’re binding to
- From coulomb’s law, moving 2 opposite charges from 0.3nm to 0.15nm apart,
- E = 2.3KbT
How strong is a non covalent bond like a hydrogen bond

- Strength of these are hard to calculate but the range is from E = 2-12KbT
- When things are stuck together, they bind with strength around that much KbT

So how are non-covalent bonds and electrostatic bonds energy broken?

- Comes back to Boltzmann and the energy of the proteins are constantly fluctuating
- P = e– E/(KbT) : the probability that the molecule has a particular energy at a given time
- Ex: if strength of non covalent bond is 3KbT, p = e -3 = 0.05. collisions coming from thermal
energy 1/20 be sufficient to pop the two proteins back apart.
- 1/20 break a hydrogen bond and 10 11 collisions per second.
o Very weak bonds based on only a few hydrogen bonds will be quickly broken
- Energy of a molecule fluctuates

How do you ever make it over a transition state

- Probability of breaking a bond can be explained of how chemical reactions

ever make it over their transition state
- The free energy of reactants is higher than product. In order to make It over, a
positive delta G is needed.
- If only negative delta G is spontaneous, why? This works because energy of
molecules is constantly fluctuating a probability thermal energy alone is
enough for the molecule to pop up and gain free energy and then undergo transition and come
back down

What about covalent bonds?

- Very strong. E = 100KbT

- Probability of breaking a covalent bond is E -100
- A collision breaks a
covalent bond every
1024 years
- Thermal energy is way
down at 100
- And all relatively close

Cells must balance chemical mechanical thermal and electromagnetic

energies
 - The plot of amount of energy (Y) and length of energy (X). as you get to longer and longer things,
some energy goes way up and some go way down.
o A point where they all overlap at the length scale of 1nm
o Very relevant scale for cells and proteins
- Thinking about cell functions, must think about heat, mechanics, non-covalent bonds, covalent
bonds, electrostatic potentials
 There’s no other area where you have to worry about so many types of
energetic type

ATP hydrolysis is a 20-dollar bank note. Its relatively equal to 20KbT

- It’s big enough to do something with but it is small enough to avoid too much waste.

Lecture 3
Life for a protein inside of cells. Cytoplasm is more rich, complex and unknown than expected.

- More energy to bend a longer and longer rod and the electron binding energy of a box is the
amount of energy involved in electrostatic potentials. As charges get further and further away.
Energy decreasing because those charges don’t feel each other anymore
- Red line in the middle is thermal energy. At 10 -9 the thermal, mechanical energies are all
converging.
o Plot showing you all these energy scales are converging
Cytoplasm: the material in which organelles are imbedded.

What is cytoplasm like: if you can stick your finger in it what would it feel like?

- Depending on who you ask. Protein complex or ion and its different based on the size of the
structure you want to talk about.
1.) Cytoplasm is crowded
o Consists of: Ions Measured in -0.1nm, there’s sugars, amino acids, small molecules,
proteins, DNA RNA, large protein assemblies with 10-100nm, organelles sizes of 1
micron meter.
o A huge range of size
o Surrounded by tiny sugars/ions etc
- How crowded?
o Compare it to somebody that we know. Talking about a protein crystal
o When trying to solve structure of protein, purify it and make it crystalize.
o Put in x-ray beam and from scatter determine structure of the structure.
 Protein structure is 20-60% protein by weight
o Red blood cells are 35% protein by weight. Can just look at protein density.
 Compare to dilute solution
o It is about as crowded as a protein crystal
 2.) Cytoplasm is a rough and tumble place
o Constantly hit by neighbours because they’re all moving by energy. Proteins all shaking
and colliding with one another. from perspective of single proteins like being in a mosh
pit
o Constantly being smacked around by everything else causing you to move this way.
o They diffuse by characteristic diffusion coefficient. Smaller, larger D. the movement is
characterized by the Brownian random walk. Gets you nowhere by average.

The structure of individual proteins is distorted by collisions

- Molecular dynamics simulation take the 3D structure of protein and put in computer and said
what would happen to this structure? It’s constantly being distorted
- Why isn’t it always in one stable food? Because thermal energy distorting it and causes large
arrangements

Bacterial cytoplasm can be simulated in a computer

- The 3D structure of proteins is constantly being distorted and small molecules are able to make
descent progress but large protein assembles are effectively trapped
- Collisions physically distortion and trapping protein

3.) Cytoplasm is viscous

o Inertia: resistance of an object to any change in its state of motion
o Viscosity: a measure of a fluid’s resistance to flow.
o The Reynold’s number = inertial forces/viscous forces
- Cells, organelles, and proteins are in a low Reynold’s number environment.
- for human, Re = 10^4, for bacteria 10^-4
o what this means is that when a bacteria is swimming, viscous forces are 10^4 larger
than inertial forces, Viscosity dominates
o when bacteria stops swimming, it comes to an immediate stop. If not actively
swimming, no inertia
4.) cytoplasm is elastic
o tendency for an object to return to original shape after deformation
o if you poke a cell with a needle without puncturing and just denting the membrane, cell
will return to original shape
5.) cytoplasm is a meshwork
o cytoskeleton will create a mesh like environment inside of cells.
o Organelles, polymers, and other structures define the ‘pore size’
o Smaller the pore size, able to get out throughout the holes in the chain link fence
What is the cytoplasm like: depends on who you are.

- It’s like salty water if you’re an ion.

 - Starts to become like jelly or petroleum jelly you would get high viscous forces and you struggle
to diffuse.
- Becomes like glass (still a liquid) when you become very large. The nucleus is effectively trapped

6.) Cytoplasm is an active material

o Living systems, cytoplasm is far from equilibrium. Lots of energy consumptions
happening with ATP hydrolysis and metabolism and electrons coming out of glucose
o Very far from equilibrium system. What does this mean? What is this consequence of
this enzymatic activity on those types of things? Brownian motion, viscosity, elasticity
etc.

Carbon starvation of bacteria turn their cytoplasm into glass

- Bacteria, time passing and pictures of bacteria. M2G is the name of type of food bacteria is
getting.
- There’s a fluorescent labelled protein (white dot) you can see the protein starts at the top and
then moves up and down appears to be diffusing in something like a random walk.
- If you starve the bacteria and did carbon starvation and removed food, now the protein goes
nowhere and becomes stuck.
o Diffusion that was previously observed has been significantly reduced.
- When metabolism goes down, the entire cytoplasm just freezes, and bacteria becomes like a
glass pill in response to that.

Rapid ATP depletion also freezes the cytoplasm of E.coli

- 3 untreated cells, colored things are trajectories. Tracing out wherever the marker proteins
were. 4 trajectories shown and the tracer molecules is going around quite fine
- Add DNP (causes rapid ATP depletion) and now the trajectory is frozen. Protein molecules are
effectively frozen.
o They are still moving but the diffusion coefficient has gone way down.
- What that means, the diffusion we see inside the cells is active diffusion and not purely thermal
- When Brown was looking at fat globular, it was coming from purely thermal energy. Diffusion in
cells not purely thermal energy. Energy source from metabolism itself.
- All the enzymatic activity is shaking everything up, and then metabolic process is mixing things
inside the cytoplasm
- Take the active process away, you only get thermal diffusion
- Diffusive is ACTIVE not thermal
- Even in our cells, density of cytoplasm is regulated and related to cell development,
differentiation, disease and disease states can be associated with cytoplasm density
o Change in active and vigorous shaking of cytoplasm
It’s unknown what the cytoplasm is like.

- Some refer as weak elastic solid

 - Other say soft glassy material
- Poroelastic material
- Viscoelastic gel.

At the end of the day, we don’t know there’s no single way to describe the cytoplasm.

Lecture 4 Glycolysis
Focus on phosphorfructokinase1. Enzymatic regulation that is a case study how cells can control the flux
through a metabolic process.

Redox reaction provide a basis for energy transduction

- Electrons jumping out has a lot of free energy. What we want to do is to capture that free
energy and use it

Metabolism happens in 4 stages

- The first step is glycolysis happens outside the mitochondria,

take a single glucose and break into 2 pyruvates
- Pyruvate goes into inner matrix mitochondria past outer and
inner mitochondrion membrane to do the citric acid cycle or
CREB cycle
o Citric acid cycle is where most of electrons come out
and turn into NADH
- Stage 3 turn electron into proton gradient in the inner mitochondrion membrane through
electron transport chain.
- Proton gradient generated is converted to ATP by ATP synthase.

Glycolysis means “sugar breaking”

- Start with glucose, break it in half and turn it into 2 pyruvates

- Allows cells to get access to electrons that are in glucose because they can pull them out of the
pyruvate through citric acid cycle
- Glycolysis is preparing glucose to get its electrons harvested

Glycolysis is a multi-step process

1.) phosphorylate glycose

o attach phosphate group. This reaction catalysed
by hexokinase
o glucose to glucose6-phosphate.
o Glucose 6-phosphate fed into lots of
downstream reactions for example, glycogen if
we want to store for future use. Can go in many
different directions besides glycolysis
2.) Change the ring structure
 o From a glucose ring into a fructose ring
o From glucose 6 phosphate into fructose 6-phosphate
 Phosphoglucose isomerase enzyme
o This is also a precursor for downstream metabolic processes like glycolipids
3.) Phosphorylate again
o This is performed by phosphofructosekinase1 or PFK.
o Reaction happens by ATP input
 Now there is a charged up double phosphorylated molecule and now we can
smash it
4.) Smash it and turn into 2 glyceraldehyde 3-phosphate by aldolase
o We cracked open the ring structure that’s not as stable.
o One of the two has to get isomerized into
glyceraldehyde 3 phosphate before it can
move on
5.) Oxidize it and make NADH catalyzed by
glyceraldehyde 3-phosphate dehydrogenase. To
give 1-3 bisphosphoglycerate
6.) Now dephosphorylate and make 3
phosphoglycerate by phosphoglycerate kinase.
 Enzyme is named after reverse
reaction
7.) Mutate it and move the phosphate. From 3
phosphoglycerate to 2-phosphoglycerate through
phosphoglycerate mutase
8.) Condense It and remove a water molecule with Enolase. Makes it Phosphoenolpyruvate
9.) Dephosphorylate one more time get a pyruvate by pyruvate kinase.

The first step is referred to pump-priming reaction

- Primes the pump of glycolysis. It generates a

useful metabolite.
- If well hadn’t be used, refill the pipes with water
in order to get the pumping mechanism to work.
- Through catalysis and energy would lower the
transition state.
- The other way to easily get over is to raise the
free energy of the reactants.
o If we can take the line where reactants
are shown and move it up
- The amount of free energy you need to gain also
decreases not because you lowered it through
catalysis but because free energy of reactants are
going up.
 - This molecule has larger amount and that further transition states get down.
o Put some energy in as a way to facilitate the enzymology.
The glucose “disassembly line” is performed by large machines

- Break into 2 pieces and then disassembly is performed by large machines like the enzymes. They
are huge.
o The size difference between the substrate and enzyme is even more than you think
- Think of control of glycoses as an effort to control these large machines
- How do they control?

Modern assembly lines are continuously monitored

- Engineers can change the flux through an assembly line by monitoring the flux.
o Speed of assembly line can speed up or slow down
How do cells monitor their disassembly machines?

- Cancer cells show increased glycolytic flux.

- Once the cell has become malignant, glycolysis has happening too fast. Huge flux through
glycolytic process
- Mutations in glycolytic enzymes are frequently found in patient tumours
o How cells control in this rate of flow due to critical link to disease
Cancer was once thought to be caused by misregulation of glycolysis

- Cancer cells stop doing oxidative respiration and stop using it and start getting all ATP through
glycolysis alone.
- Drink radioactive glucose and then you see increase in absorption of radioactive glucose by
tumors.
- Cancer is caused by transformation of DNA. Glycolysis result is caused by the transformation.

Where does a cell want to control glycolysis

- Where should the interruption be?

- Find which steps in the process have large delta Gs.
o Reactions with those are effectively irreversible
o A small -delta G there will be movement back and forth between products and
reactants.
o And delta G depends on concentration. If low negative delta, it will be proceeded
forward with abundance of product. And then if product piles up, reverse flow.
- A few steps with large delta Gs and such reactions are in principle irreversable,

PFK1 is the ‘gatekeeper’ of glycolysis

 - the enzyme that gates the very large negative delta G. fructo 6 phosphate into fructose 1-6
bisphosphate.
- Controlling whether this enzyme is active or not by regulating glycolysis

PFK switches between active and inactive states

- A conformational change that causes the molecule to switch between the two states
- It’s an example of an allosteric enzyme. This happens through an allosteric molecule.
- Sticking this molecule at one place will change the state
- Inactive state (tense state), then active state (relaxed state)
o In the relaxed state, substrate able to bind into substrate pocket
o In tense state, substrate binding site is not accessible.
- Only interaction in relaxed state.
- The A is the activator, and the I is the inactivator.
o In relaxed state, activators are bound to the activator binding sites and stabilized
o In inactive state, inactivators bind to inactivator site and keep in tense state
- Binding elsewhere not the substrate binding site.
- Substrate is F6P. this enzyme is a dimer of a dimer so a tetramer
- The switching of the 4 subunits switches at once. Tetramer. Best understanding: hemoglobin

The MWC model for allostery successfully explained hemoglobin

- Need an enzyme that needs something to suck oxygen up and release it

- the occupancy of hemoglobin compared to oxygen partial pressure (mmHg) concentration of
oxygen basically
- in blue, curve that would describe hemoglobin that was not an allosteric enzyme and all
behaved independently
o at low, binding is low, at high, binding is high.
- But the way hemoglobin works is by having each individual subunit communicate with
each other about whether there’s oxygen in binding pocket or not
o Circle, inactive state, square, active state
- As the circle binds to oxygen, it can cause hemoglobin to switch from inactive to
active where it has a higher affinity for oxygen
o Binding of one oxygen will trigger conformation of hemoglobin that makes
the other 3 empty sites to have higher affinity.
o Consequence: as you look at occupancy
o At high oxygen, you occupy the hemoglobin. But fully occupied state actually
goes to a lower concentration not just the lungs
o Hit threshold of oxygen concentration where hemoglobin spits out all its
oxygen and drop down to occupancy of 0.
  If no coordinated switching of hemoglobin between active and inactive states,
there would be regions where blue line is below red line
 You would’ve given up oxygen before u want to
 Coordinated switching allows hemoglobin on or off.
 Maybe individual subunits can switch between active or inactive but this is
essentially what’s happening with phosphate fructose kinase.
 If one subunit gets switched, coordinate the switch of the other 3 subunits of
the tetramer at the same time

PFK is inhibited by its product, ATP and citrate

- Want to turn off glycolysis if no need for energy. (citrate first thing pyruvate turns into)
- This suggests, downstream, the disassembly line is
packed.
- As concentration increases, rate decreases
o Can identify residue on the molecules when
mutated in cancer cause citrate inhibition to go
away.
- Cancer mutations block product inhibition
o Even when citrate is piled up, the glycolysis
continues. It can’t turn off PFK tetramer.

AMP is both a substrate and an inhibition

- Initial spike as ATP binds but as ATP increases, decrease in rate except for
blue curve N46S. another mutation that blocks inhibition of PFK.
- PFK has 2 binding sites for ATP, one for substrate and one for kinase
reaction for inhibitory site to switch to inactive site.

PFK is active directly by AMP and indirectly by excess fructose 6- phosphate

- Increase concentration of F6P, relative velocity of rate increases

- Active binding site is by those

Phosphofructokinase (PFK1) determines the rate of glycolytic flux

- High citrate and high ATP acting as inhibitors.

They all control concerted switch between
active and inactive conformation
 - Fructose 6 phosphate into fructose 2 bis phosphate then acts as activator

Cells monitor their disassembly lines by sticking things to them

Lecture 5 Mitochondria
Electron tomogram: images taken from electron microscope. Load sample into electron microscope and
take it from tilt angles and take pictures and each picture is only 2D but by rotating it, you can
reconstruct a 3D structure.

- The mitochondria is not like rugby balls, but most don’t. instead, they look like long slender
tubes that branch, overlap, connect etc
- Mitochondria form a complex and interconnected network

Mitochondria were bacterial once

- Endosymbiotic hypothesis: we had ancestral proto eukaryote. The idea is that this early proto
eukaryote engulfed a bacterium that was capable of oxidative phosphorylation. In the absence
of oxygen, cells are much less efficient because we stop at glycolysis and just go to lactic acid.
- It engulfed and has its own mitochondrial genome and persist inside the cell as a symbiont.
- Aerobic respiration as the putative drive for endosymbiosis.
o That’s why the ancestral cell ingulfed the mitochondria.
Mitochondria make their own ribosomes, segregate their own DNA

- Mitochondria are maintaining their own genome and duplicating it. Maybe they were at one
point free living organisms
- The idea of endosymbiosis was controversial

Lynn Margulis: proposed the origin of Mitosing cells. This paper proposed not only mitosis is
endosymbionts, also other structures. Rejected by 15 journals before it was accepted. Not everybody
agreed and making counter arguments against her.

What was the alternative hypothesis to endosymbiosis?

- Aerobic proto-eukaryotic that enlarged and engulfed its respiratory surfaces.

Sequence analysis carried the day for endosymbiosis

- Sequenced the genome of bacteria and mitochondria and complex eukaryotes.

- Discovered that mitochondrial proteins and genes are significantly more closely related to
prokaryotic genes than to other eukaryotic genes.
- 1981 completed sequence of human mitochondrial genome. With the full sequence of
mitochondrial genome, it’s clear they have strong homology to prokaryotic genes and not other
nuclear genes

Why did endosymbiosis occur?

 - If it wasn’t because they need aerobic respiration, what’s the driving force
- The amount of power cells can produce (power/gene)
o Eukaryote with mitochondria on the bottom
o Shows that they can produce a lot stronger power/gene
o Idea is that it wasn’t mitochondria brought a new magic trick to the ancestral proto
eukaryote. Rather they allowed it to become more efficient and much better
o The genome of that proto eukaryote free to expand and become more complex and
become eukaryotic genome
- Hypothesis: mitochondria increased power/gene
- Unclear at the moment why endosymbiosis occurs

Mitochondria have their own genetic code

- Protein products of different lengths (predictable) based on where the new stop codons showed
up

Mitochondrial proteins are built from a combination of nuclear and mtDNA

- Very small compared to the nuclear genome. Most proteins are built from a combination of
nuclear DNA and mitochondria DNA.
- Each protein and each complex of the electron transport chain that are made of components of
nuclear DNA and some come from mitochondrial DNA
- Own unique genetic code meaning mitochondrial DNA is not segregated by strict rule of mitosis
but segregated randomly depending on which copy ends up in which daughter cell
- Can give rise to interesting genetic phenotypes

The petit mutation in yeast is a model for mtDNA inheritance

- They make tiny colonies. Instead of normal colonies. The rate of colony growth is lower meaning
the colonies are small
o If you mate petit yeast with normal healthy yeast, you end up most case in normal yeast
o Occasionally, these petit colonies will raise again
Mutations in mtDNA segregates differently

- the yeast fuses, and now the diploid zygote have both petit and normal mitochondrial. No
forced segregation when it divides
- it can be the case you get mixing and each of these cells have some normal and some petit
mitochondria
- occasionally, segregation events where the first segregation everybody is fine but after the
second one, you end up with one daughter cell that happens to inherent only mitochondria with
the petit mutation
o these cells will form petit colonies and all their off springs will form petit colony.
Mitochondrial function influences your lifespan
 - some mice start to die and right around 400 days, mice with mitochondrial mutation start to die
whereas their heterozygous and wild type continue to live
- deleterious mutations in mitochondria genes can limit our life span
o if the cells are less good at generating ATP and metabolism defective, it makes sense
that life will grind you down a bit faster
- the opposite can also occur

mutations in the electron transport chain can extend lifespan in C.elegans

- some mutation made the C.elengans life longer.

- The electron transport chain can be improved and C.elegans can live twice as long but this
mutation hasn’t occurred yet etc
o This observation is profound because it suggests that life span is genetically determined.
- Organisms could (if wanted and evolutionary advantageous) could live twice as long.
o If we put this mutation into human baby, there would be a baby that could live twice as
long
o Why haven’t C.elegans discovered this mutation? It must not be evolutionary
advantageous to live twice as long
o Our life span is genetically determined. Not just life grinds us down but we are
programmed to die
 Reasons: many organisms, our total life span is longer than our fertile life span.
After off springs, all you’re doing is competing for resources with off spring and
the competition is disadvantageous to the off spring kids. Get out of the way to
let off spring thrive.

Lecture 6
Mitochondria part 2!

Mutations in mitochondria affects 1 in 5000 live births

- Lots of diseases associated with breakdown of mitochondria functions.

- A break down of mitochondria functions should mess up everything,
but in many cases, these diseases are focused on organ systems

Mitochondria morphology varies in different tissues

- Tissue specific genes expressed that impact mitochondria morphology

and function. Start to understand why there’s specific breakdown of
mitochondria function in different organs
o Associated with tissue specific function
o That universally expressed protein is modulated and regulated by a variety of other
genes that are tissue specific. So then you’d get tissue specific disease phenotype.

Mitochondrial form an interconnected tubular network

 - They are not the little beans shaped
- What are the genes and proteins for establishing this network? Why are mitochondria shaped
that way?
- How these mitochondria are able to fuse and split

Mitochondria undergo fusion and fission

- They undergo both.

o Fusion: come together
o Fission: split
- This process is continuous and going on in all of the cells and the network is continuously
rebuilding itself, fusing, breaking apart to achieve a steady state size to have a distribution of
mitochondrial sizes
o Due to thickness of tube is constant, there’s a distribution of mitochondrial lengths that
will tell you state of mitochondrial network
o If everything is fused together, a few very long mitochondria, if everything breaks apart,
a lot but very short mitochondria

Fusion is a 2 step process

- Because mitochondria have 2members, outer and inner. To get true

fusion so the mitochondrial matrix will be shared, both the membranes
must fuse.
o The outer membrane (OMM)
o Outer membrane (IMM)
o Inner space (IMS)
o Matrix
- There are proteins linking the outer mitochondrial membrane called mitofusin (MFN)
o The MFN form dimers and through a conformational change, they smash the
membranes together and make the fuse happen
- Now proteins on the inside called OPA1. The two will come in and dimerize and under go change
and the inner mitochondrial membranes will be fused
o It’s a 2-step process. Fusion of outer membrane and then followed by fusion of inner
membrane.

Fission uses a GTPase to squeeze the mitochondria apart

- Just break apart and assume the inner and outer membranes will close itself.
- Protein called DRP1 (dynamin related protein 1) the DRP1 form an oligomeric structure around
the mitochondria. By polymerizing the protein, it becomes a collar with increasing polymer size.

Fusion uses a GTPase to squeeze mitochondria apart

 - The balance is created by a balance of all the proteins as there’s fission and fusion events
happening at all times.

Fission and fusion mutants have opposite phenotypes

- In wild type, there’s no mutations so everything is normal

- Now if there’s no fusion caused by Mfn-null mutation, then the mitochondrial network becomes
fragmented because the DRP is still active but it’s not being counterbalanced by the fusion effect
- If no fission, there’s a point mutation in DRP1 in K38A the GTP binding pocket that inhibits the
GTP activity of the protein without source of energy coming from GTP, there fission cannot
happen
o Then inactive form of DRP1 and get instead a mitochondrial network fully fused
together.
- If they need to shift mitochondrial network to slightly more fragmented or more fused state, can
do that by upregulating and down regulating the two classes of proteins. (OPA and mitofusin
and the DRP1)

Mitochondrial accumulate damage to their DNA and protein contents

- Mitochondria is main source of reduced oxygen species (reactive oxygen species)

o Because glucose is being smashed and some electrons don’t get caught by the electron
carrier and hit an oxygen and get a reactive oxygen species.
o Those species are a biproduct of metabolism and occur inside mitochondrial themselves
and although they will spread and damage cellular components more widely

Fission and fusion promote the mixing of mitochondrial contents

- if fuse two cells together, the red contents would mix with the green contents and
mitochondrial would appear yellow. There’s exchange of components between mitochondrial
through this process of fission and fusion
o if there’s a fusion mutant, then the two mitochondrial won’t mix together and will
persist red and green.
o One of the things happening in fission and fusion is the exchange of internal
components

Fission and fusion enable mitochondrial rescue

- 3 mitochondrial, 2 healthy and 1 that is defective.

- Normally, expect mitochondria can replace the damaged protein
by synthesizing more.
o Mitochondrial genome (green dots)
o If you have a copy of mitochondria genome, you can fix
the protein but if you don’t have one, you can’t fix
yourself.
 - The defect mitochondria fuse with a healthy one. Give defect mitochondria mtDNA and then it
can synthesize the protein again.
o Then if they fission and split and the original damaged part happens to get a copy of the
mitochondrial DNA, then it’ll be fixed.
- Promotes exchange, cycling of mitochondria DNA to enable rescue,

Fission promotes the equal segregation of mitochondria into daughter cells

- Petit mutation in yeast is inherited by yeast.

- Right before M phase, the mitochondria get fragmented to create as many tiny mitochondria as
possible such that each copy of the mitochondria genome is enclosed in one tiny mitochondrion
compact, then when the cleavage plane happens, you get daughter cells that get approx. equal
number of mitochondria they inherit.

DRP1 mutant cells segregate their mitochondria asymmetrically (knockout for DRP)

- This is because the network does not fragment. So each daughter cell will get different amounts
of mitochondria.

Mitochondria make close contact with the endoplasmic reticulum

- Mitochondria associated membrane (MAM) where the ER and the

mitochondria touches. they are the location of most fusion effects.
o Fission often occurs at the point of ER-mitochondrial contact.
o Over time, that is the location the mitochondria fission occurs
 A lot of the organelles are all in contact with one another and
rates of contact are regulated and biochemistry are happening
where organelles touch each other.
o Something about contact of ER membrane and mitochondria
membrane is responsible for the recruit of DRP1.
 There’s where DRP1 polygamized and constricts
- How do we get rid of mitochondria that has just died?

Cells degrade their mitochondria in a process called mitophagy

- Eating of mitochondria. The digestive membrane compartment envelopes mitochondria by an

organelle that’s targeted for degradation
- Mitophagy clears out dysfunctional mitochondria and controls mitochondria number.
- Mitophagy is very tightly linked to disease

A form of Parkinson’s disease is linked to mis regulated mitophagy.

- Autosomal recessive early-onset Parkinson’s disease

o PINk1 mutations, Parkin mutations. Those are critical for mitophagy.
o If cells can’t properly dispose bad mitochondria, you’ll develop Parkinson’s.
Parkin tags mitochondria for degradation and is targeted by PINK1

- Parkin says this mitochondria needs to go and the targeting

happens with the PINK1 kinase.
o Parkin interacting kinase (pink1)
- PINK1 comes in and sticks to the outside of damaged
mitochondria
o If bad import and export components
- Starts phosphorylating everything around the outer surface of the mitochondria and get a lot of
phosphate groups
- Leads to the protein parkin which is a ubiquitin ligase.
o Attachment of ubiquitin group is signal to degrade the substrate.
- Parkin ubiquinates and then it becomes a target to mitophagy. Enveloped, degraded and broken
down.
o Now it cannot continue to mess up
- Inability to recruit parkin, won’t degrade bad mitochondria, breakdown of cellular function due
to inability to recycle bad mitochondria will cause Parkinson’s.

Lecture 7: citric acid cycle

- Pyruvate enters the mitochondria.

Glycolysis means “sugar breaking”

- At the end of it, it turns into 2 pyruvates and they enter the citric acid cycle

Pyruvate the cycle as c2 acetyl group on acetyl-CoA

- Pyruvate starts off with 3 carbons and one of them leaves

- Pyruvate becomes a part of acetyl-CoA (co-enzyme A)
o The acetyl group is just the little bit.
- 3 step reaction
o Decarboxylation
 Loss of a carbon dioxide
o Oxidation
 Harvest an electron using NAD+
to NADH
o Transfer of the acetyl group
 Transfer it onto the big co-
enzyme A structure.

Pyruvate dehydrogenase is an enormous complex

- It’s a number of enzymes not just one enzyme that completes these 3 steps
 - The images correspond to various views/perspective on that complex. Take a bunch of pictures
from different perspectives.
o Take the images and use them to reconstruct what the complex should look like
o Crystallographers solved crystal structure of different components of
the pyruvate dehydrogenase complex
o Can dock into 3D structure these crystal structures, then can come up
with models of what it looks like
- Made up of several different enzyme groups.
o Pink spot is the substrate
- This movie is somewhat accurate with Brownian motion but the swaying back
and forth of the arms is unrealistic.
o Those arms would undergo thermal motion and fluctuate back and
forth
o The proteins moving in straight lines. Corresponds to physical understanding of what
things look like in our world but not inside cells

Citric acid, tricarboxylic acid, Krebs

- Acetyl-coA will then enter the cycle. Citric acid going in at the first step of the cycle called the
tricarboxylic acid cycle because there’s 3 in the citric acid, or Kreb cycle after the
person who discovered it (Hans Krebs)
o Individual steps of this process have been worked out but Kreb saw that it was in a cycle
and put together all the individual steps into a cyclical nature.

Krebs measured O2
consumption of Pigeon
muscle using manometer

- U shaped glass tube

that is opened on
the top and the
bottom
- If just take and fill it
with some dense
liquid, then the
pressure of
atmosphere will
push down on both
sides, liquid will rise
on equal height
because pressure is
equal
- Attach one side of tube a small reaction vessel, he would put a gram of Pigeon muscle.
o Used it as a source of all the components of the citric acid cycle
 o He used that and measured how much oxygen does this pigeon muscle produce.
o Put alkaline substance that would absorb any carbon dioxide produced by tissue.
 As CO2 released, it’s disappearing
o The stopper is so they can close the reaction side of the vessel.
- As oxygen being consumed, it’s taking molecule from the gas and its decreasing
- Oxygen coming out of gas phase in the reaction side so number of moles of gas on the other
side is dropping so less pressure of the gas on the reaction side
o More pressure from atmosphere.
- What Kreb was measuring is the height changes in the manometer as oxygen is consumed.
o Has equations based on ideal gas law that allowed him to convert the height difference
into # of mols of oxygen consumed
- He’s adding things in there and seeing how it changes mole of oxygen consumed
- Addition of citrate increased the rate of oxygen consumption

Warburg manometers were a stable of biochemistry

- It was good until micro electrode responsible to electrodes was invented

o Closed circuit.
o Direct reading. Gas binds to microelectrode changing resistance
The C2 acetyl group is added to oxaloacetate, a C4 “carrier”

- Can go through a closed transition. What you’re meant to see

is that the first thing that happens is that oxaloacetate binds
and the binding is what causes the conformational changes.
And the binding that creates the acetyl coA site.
o It needs to bind to oxaloacetate first because every
enzyme, will always have some forward rate constant
o If the acetyl coA were to bind into the site where a cleavage reaction will happen,
(separate into acetyl and coA) want to confirm the oxaloacetate is there so then the
acetyl group can stick on the enzyme binding site.
o If reaction site wasn’t there, then you’d cleave and have no
receiver group there for the acetyl. So this is induced fit
protein biochemistry

Citrate is converted into a less stable form

- remove water and then add water, into aconitase and then turn into
isocitrate
- same except the location of OH groups vs CH2 groups are switched.

C6 isocitrate is broken down in 2 steps to form C4 succinyl coA

- take isocitrate and harvest an electron, break it, to get alpha

ketoglutarate by isocitrate dehydrogenase.
 - There’s a decarboxylation (loss of CO2), an oxidation reaction (creation of new NADH) and the
coA will come in as a carrier for the remaining carbons and we get Succinyl coA by alpha
ketoglutarate dehydrogenase
- cells want to keep everything together, so they make a mega complex and then channel
substrate between each enzyme

large metabolic complexes enable “substrate channeling”

- channel the substrate from point A, B to C.

- at the level of protein structure, you can see there are 3 enzymes that are ether
separate or in a complex
- the color is meant to indicate the charge residues on that protein
- then there’s channel of positive charge residue created on the surface of the
complex so there’s electrostatic steering of the substrate from active site 1,2, to
3
o CS, MDH, ACCN an idea that these 3 enzymes would form large
metabolic complexes (citric synthase, malate dehydrogenase, and
aconitase)
o The large negatively charged substrate would hop between active sites
passing through the channel.
- Channels increase reaction rates and preserve orientations
- Applying chemical cross-linking agent to trap any enzymes together
o If we cross link we can identify large complexes and we can see those are faster at doing
their job.
 But if you add glue, of course things will be glued together. If you tried to purify
ACCN by itself and pull it down, you wouldn’t get citric synthase coming with it
unless there’s glue added.
o Arguments: whether large metabolic complexes were legit occurring inside cells or
artifact caused by cross linking agent
o Not uncommon for complexes inside cells to fall apart when you lyse the cells.
o People cross linking said, we’re not just gluing, we’re preserving native complexes.
- The bioID method: take the gene for ACCN and attach to it a ligase and attaches a molecule
called Biotin. Then biotin tags protein that comes in close proximity to ACCN
o By varying length of linker that connects biotin ligase, you can expand the range of the
biotin ligase and get spatial resolution.
o When attached really close, it’ll only attach to a few things, but if a chain, can go out
further
 - The enzymes in the disassembly line are connected and substrate rolls
down

C4 succinyl coA is converted back to oxaloacetate in 4 steps

- Go from Succinyl coA to succinate and get a GTP

- Then use the succinate dehydrogenase complex to turn into fumarate
o Here, The free energy in the electron coming out of succinate is
not enough to reduce NADH so make FAD and FADH2 so that’s
the succinate dehydrogenase complex
- Add water with fumarase to get to malate
- Then use malate dehydrogenase to harvest the last electron out using
malate dehydrogenase to get oxaloacetate.

Radioactive carbons allowed scientists to track the fates of metabolites

- Can add radioactive pyruvate and inhibit process in any step, and see in the carbon dioxide
released, do I detect radioactivity.
- By adding radioactive carbons at various states (radioactive citrate etc) and looking when in the
cycle the radioactive carbons are released, are able to see the 2 carbons that enter the cycle
didn’t leave on their first go around.
- The carbon comes off the bottom not the top. So the carbons enter at the top and continue all
the way around
o When you get to succinate, succinate is symmetric molecule, so you don’t know which
orientation went into the next step of the process. Can reorient themselves.
- In the next round, the two carbons become the bottom carbons and they leave.
- Because succinate is symmetric, you can assume 50% go in one orientation so track progressive
release of carbon to the turn around.

TCA enzymes are major oncogenes

- IDH mutations: > 85% of low-grade gliomas (isocitrate dehydrogenase)

- Significant driver of particular type of cancer
o Why would that mutation be an oncogenic mutation? What does it have to do with
cancer?
o Especially, because cancer was thought to be caused by mis regulation of glycolysis.
- Cancer cell isn’t even using TCA cycle, but…

TCA metabolites are a source of biosynthetic precursors and cofactors

- The red arrows leaving it are places that intermediates is

shuttled off to use in another process beyond the process
of creating ATP.
 - The reason why cancer cells rely on glycolysis because they’re using the TCA cycle to produce
biosynthetic precursors to drive proliferation and growth
- The pyruvate is being used to starting use for biosynthetic precursor
o The production of the precursors is the step that goes wrong
Mutation in isocitrate dehydrogenase produce an oncogenic metabolite

- Normally, producing alpha keta glutarate, if you have mutation, you produce 2-
hydroxy glutarate.
- And this is an oncogenic metabolite. It then goes and drives cancer progression
- It inhibits of histone demethylation.
o Histone tails are major determines of gene expression. Then this changes the pattern of
gene expression

Glucose has been fully converted into Co2, NADH, and a few ATP

- Produce carbon dioxide, NADH, a few ATP, GTP, and a FADH2

- Harvested all the energy out of the glucose and captured into reduced carriers.
- Now we go to the electron transport change which then gets converted into protein gradient.
And then that will be converted into ATP synthesis.

Lecture 8: electron transport chain

- Looking at how the electrons we harvested out of glucose put into NAD and FAD and how the
energy is converted into a proton gradient across inner mitochondrial membrane.

Glucose has been fully converted into Co2, NADH, and a few ATP

- We had gone through glycolysis. The pyruvate went into mitochondria through transporter and
went through citric cycle. A number of NAD+ converted to NADH, one FADH2 come out as well.
- Now, must get the energy contained in the electrons carried by NADH and get it all the way to
ATP.
o 2 steps, the conversion of the electrons in NADH into a proton gradient across the inner
mitochondrial membrane.

The electron transport chain converts NADH reduction into a proton gradient

- How does it convert NADH reduction into proton gradient?

- Complexes of the electron transport chain (complex1, complex 3 and complex 4)
o Complex 2 appears briefly
- Multistep process.
o NADH enters at the base of complex 1, and gives 2 electrons to complex 1. Those
electrons take a long path and travel through complex 1.
o Complex 1 is somehow going to put 4 protons across the inner mitochondria membrane
as those electrons pass through
 o Carried through carrier where it goes
through to complex 3 and complex 3 will
also take a couple protons across and
electrons go to Cytochrome C
o Cytochrome C diffuse around the space
until it lands on complex 4
o Electrons leave cytochrome C and go to
complex 4 and then they hit oxygen and
make water.
 Ultimately, oxygen is the last
electron acceptor.
- Convert movement of electrons to pumping of proton across membrane

Iron clusters and other “prosthetic groups” pass the electrons downhill

- Large aromatic organic complex (hemes) with an iron in the middle. A structure like this is a
decentralized electron cloud
o Large number of atoms that are sharing electron in this cloud
o The electrons passing through these electron transport chain moves from cloud to cloud
 Not the same electron that makes their way through the same process
o The one NADH releases is not the one that makes it all the way to oxygen.
- Electron that enters, enters the decentralized electron cloud and then one of the other
electrons leave.
- Iron sulfur cluster. There’s a distributed cloud of
electrons that is releasing electrons as new electrons
come in and passing it from one to the other
- In complex 1, a series of iron sulfur cluster. Electrons
move between these clusters as it makes its way
through the protein

The ‘reduction potential’ of each electron carrier increases

down the chain

 Must have free

energy released so it would happen spontaneously
 The reduction potential must increase as you move down
the chain
 Reduction potential: readiness to gain an electron
(Arbitrary zero point)
 As reduction potential increases, free energy decreases. A
negative delta G associated with each step o the process
 Like passing a bucket chain downhill.
 Moving bucket of water downhill, releasing free energy (potential
energy gradient) in the cells, it’s a free energy reduction potential in
heme groups
  Electron reaches in and until it exits and reaches
ubiquinone

Electrons are first passed to ubiquinone (CoQ), a lipid like carrier

- Can be reduced to CoQH2,

- CoQ is a vitamin supplement
o Provide cells with additional amounts with the idea that it helps
you have better energy metabolism.
- It might not be possible for healthy individual to supplement CoQH2

Ubiquinone deficiencies cause disease

- Phenotypes of ubiquinone deficiency

o Encenphalomyopathy
o Severe infantile multisystemic disease
o Cerebellar ataxia
o Isolated myopathy
o Nephrotic syndrome
- If ubiquinone is an important electron shuttle from compelx 1 to 3 to 4, it’ll cause disease if
deficient

CoQH2 transfers the electrons to Complex 3

- CoQH2 takes the electron and makes its way to

complex 3.
- The electrons are going through and liberating free
energy moving through deliberated electron clouds but
how does the 4 protons move through the membrane?
o How do we couple the movement of electron in
the cloud to the pumping of protons?

In Complex 1, electron transfer and proton translocation are

separated

- They’re physically separated in space.

- The proton crossing is far away from where the
electrons move.
 - The path of the electron and the 4 protons are moving across membrane far away
- There are free energy liberated as these electrons move, somehow, that free energy has to be
harnessed to pump protons.
o The protons are going from the matrix into the intermembrane space and in the space,
the concentration of proton is higher.
o Costs energy. Where is this energy hidden in electrons come from?
- How in CoQ reduction coupled to H+ movement?

How to construct a gated proton channel

- It has to be able to open and close in ways you can control

o A little hole in the membrane like a ungated channel, the proton will flow down
concentration gradient
o Have to allow channel open so proton only move in one direction.
o Horse track gates! What is the signal that carries up length of complex 1 and how is the
gate controlled

Proton translocation channels have residues with a regulated pKa

- Ka = acid dissociation constant “Affinity for protons”

o Measuring eq for protonated state and deprotonated state of any structure
- pKa = -log10Ka
- the lysine can take on or release individual protons.
- Need lysine residues in Complex 1 that can bind and release protons in response to CoQ
reduction
o The CoQ to CoQH2 will need to cause Lysine to change their Ka.

The gate is two such residues connected to half channels in the membrane

- Need proton to go through one half channel to bind to lysine

- And then lysine 2 will hold onto it and drop it
- How does complex 1 construct this kind of gate? How does it open and
close gate in a coordinated way with CoQH2 reduction
- How to keep protons happy in tiny disks of plasma membrane such that
he can crystalize the entire structure and solve it.
o Leonid Sazanov was able to identify residues that have regulatable pKa and the protons
will bind initially to one side chain and then when that residue changes conformation
the proton will move to the next adjacent side chain that has a pKa such that the
sidechain wants the protein
o Proton will then go there and fall through. He was able to chart the path through the
proton structure.
o He noticed the alpha helix running parallel to the membrane
  Very unusually to see alpha helix parallel to plasma membrane. All the rest are
perpendicular to membrane. Almost always the case
 Maybe that is a part of the mechanism of pumping of protons

Transverse helix couples changes at the CoQ site to changes in the pKa of Lysines

- Each of the thing, there’s little dots these are residues with regulatable pKa. Can see that the
protons are shown bound when in blue state
- The electrons come down and hit the CoQ, and
that causes large conformational change in the
proton structure at the CoQ site.
- Causes a sliding of the transverse helix that
reconfigures all the proteins structures along
complex 1
- All the local regions around are changed.
o That change causes proton to hop down
and out the bottom channel
- Lysine catches proton, tosses it and drops it.
- 4 subunits that are doing this of catching proton, throwing it catching it, and dropping it.
- Which residue holding on the proton will depend on the state of the transverse helix.
- Lysine surrounded by other amino acids with are influencing how the lysine side group takes on
and releases protons
o The binding proton state and giving away proton state, the pumping changes the lysine
wants to bind or give it away.
 The two lysines are in opposite states and switch back and forth and transverse
helix cause the lysine to pop between the two states.
 Lysine its self changes its physical chemical properties by changing the amino
acids which interact with the side groups.
- 4 times for 4 protons for pumping of transverse helix
o Complex 1 of ET is a pump
- Transverse helix pumping back and forth happens 200 times a second.
- The pumping of the protons are coupled with the movement of the electrons along the iron
sulfide groups and eventually to the reduction of CoQ, so the electron trigger the movement of
transverse helix

Complex II transfers electron to CoQ from succinate

- Succinate CoQ reductase has electron passing through and reducing CoQ to CoQH2.
- The succinate turns into Fumarate + 2H+

Complex 3 transfers electrons from CoH2 to cytochrome C

- THE Q CYCLE
 - Complex 3 with CoQH2 and to the known as Q0 site. Two electrons coming in with CoQH2
- The 2 electrons coming in don’t both go in the same direction
- One of them go up through a series of iron sulfur cluster and reach cytochrome C
o Sequential: first electron goes up and second electron goes down related to reduction
potential. The most probably movement is up
o The CoQH2 arrives the Q0 site, it’s a probability answer. Even if one direction has a
larger delta G the other direction will also have a negative delta G.
- Triggers cytochrome C to dissociate and go to complex 4 in the form of
reduced cytochrome C
o There’s a new Cytochrome C that comes in after the reduced one
leaves. It’ll wait until the next electron comes
- The other goes down through a different series of delocalized electron
cloud
- The electron going down hits the Qi site and that site has the ability to
bind to oxidized CoQ.
o CoQ with no electrons attached to it yet
- It will sit there as partially reduced CoQ plus that electron
o Then turns into fully reduced CoQH2 and then leaves Qi site
o This CoQH2 can leave and enter another complex 3 and those
electrons will ultimately get harvested.
o Complex process so electron can get spit out one at a time to the cytochrome C
- CoQ from top Q0 leaves and new CoQH2 comes in

In: 2CoQH2, 1 CoQ, 2H+

Out: 1CoQH2, CoQ, 4H+, 2e-

Complex 4 passes the electrons from cytochrome C to O2

- Electrons come in from cytochrome C and passing through copper based decentralized
electron clouds and ultimately back down where the electrons hit oxygen and get
converted into water
o The ultimate destination of the oxygen we inhale.
o Probably through regulated pKa of lysine
The electron transport chain

- NADH going to NAD+ electron coming out of

complex 1. Pumps out 4 protons with transverse
helix going back and forth.
- The Coq gets reduced to CoQH2 with the Q cycle
on complex 3 that causes cytochrome C to pop off
in the reduced state
 - Cytochrome C flows to complex 4 and hits oxygen and gets a couple more protons across the
membrane
- If the protons working in coordinated matter, why have diffusible signals? Why can’t we stick
them together?

ETC complexes form supramolecular assembles

- Can be observed directly in membranes and get structures of how it works

- Remember electrons are continuously moving from higher free energy to lower free energies.

Electrons moved to higher reduction potential groups all the way to O2

- Every step, a negative delta G that drives the process

- Free energy liberated all the way down and converted to pumping
of protons

The activity of electron transport chain by measuring the pH changes

- Put pH electrode in solution that contains mitochondria, and it

starts pumping protons across the intramitochondrial membrane
will cause detectable changes in the solution
- Changing in H+ concentration. Once oxygen is added, now the
electrons start to flow and protons start to pump, a spike in H+
concentration as the mitochondria works.

Without O2, the TCA cycle and ETC stop because NAD+ is depleted.

- If we can no longer take the electrons out of the process by

converting O2 to water, the entire process backs up
o If cannot pass electrons from the very bottom of complex 4 to oxygen, all the heme
groups become backed up with electrons
o Complex 4 becomes full of electrons and then complex 3 becomes fully reduced and go
back
o Now the NADH has nowhere to go. All the NAD+ gets converted to NADH and now
inside mitochondria no more NAD+ and cannot do citric acid cycle
o Citric acid cycle components are full. It’s a pile up.
o Can’t even do glycolysis the citric concentration so high the PFK is shut off.
Now we make the proton gradient into ATP! ATP synthase.

Lecture 9 ATP Synthesis

- ATP synthesis and transport. The ATP synthase is the large complex that produces ATP for cell
and very important complex
- Electrons flow into electron transport chain at the base of complex I and the electron gets
passed to coQ to make CoQH2, then to Complex III and then complex 4 is where electron
reaches oxygen the final electron acceptor
 o During this process, protons are getting pumped and setting up a gradient and the
protons want to flow back across the concentration gradient
- The transverse helix pumping of protons in complex one
- Without oxygen, the TCA cycle and ETC stop because NAD+ is depleted.
- You need a electron shuttle and that’s how the electrons are brought from cytoplasm into the
matrix of the mitochondria. At the same time converting cytoplasmic NADH into NAD+

Cells regenerator their cytoplasmic NAD+ pools by the malate aspartate shuttle

- By using intermediates in the TCA cycle, they can carry electron through the cycle.
- Malate comes in becomes oxaloacetate and the NAD+ matrix turns into NADH and then there’s
a. whole conversion which converts back and forth.
- That’s how you bring in electrons from cytosol into mitochondrial matrix

ATP Synthase harness the proton-motive force to make ATP

- The ATP synthase. The C ring brings in the proton and gets them flowing back
across the membrane
- There’s 2 proton half channels and work similarly in protons that work in
complex I. same basic idea that have residues that have regulatable pKa
- Protons will travel through half channels to get back across membrane
- At the top, there are head domains made up of alpha and beta subunits.
o 3 alpha 3 beta
- That’s where the ATP synthesis reaction occurs.
- Connecting the C ring to the alpha beta subunits there’s the gamma subunit (the
stick)
- Then there’s a subunit, b subunit and delta subunit that provides structural integrity to keep the
structure together.
- Can be shown as 2 fragments. F0 and F1
o That comes from the original purification of this complex sometimes large protein
complexes come in 2 pieces during purification (F1 large fragment F0 separate large
fragment) and those pieces came off when first purified.
- A green portion and orange portion, the green parts are rotating and the orange parts are
stationary in space.
- Similar to complex 1 of electron transport chain. The location of energy liberation is separate
from location of reaction.
- Protons flowing through green subunit (C ring) and proton comes up from half channel, goes
around C ring and exists through other half channel to the other half channel.
- Energy being liberated in the C ring but the ATP synthesis happens in the head domain.
- How does this turn into chemical activity that is physically distant from
where free energy is being liberated
- How does the thing spin and how does the spin couple with ATP reaction
The F0 subunit c ring rotates as protons pass through it.

- Most of them have a proton in it and its happy there because there’s an adjacent negative
charge
- But below the charge in the half tube, there’s no H+, but there’s a positively charged arginine-
210 residue and interacts with negative charge.
- High concentration of protons down there, so protons will start coming up through bottom half
channel and compete with the arginine for the negatively charged residue.
o Since concentration of proton is high, it will win. It kicks the arginine-210 to the side and
causes it to click from its position so the arginine clicks over and now there’s both
arginine and proton competing to the charge (above)
o Arginine-210 will win and that proton leaves because low concentration of proton on
that side
o The C ring will be rotated over the bottom channel and then flick back into original
position and back but we’ve rotated the entire C ring by one subunit and had a proton
that entered from the bottom and left from the top.
- Throughout this entire time, it clicks in and out of the position. It’s in the arginine-210 is in the a
subunit it doesn’t actually rotate and nota. Not a part of the c-ring
- In general 10-14 C subunits.
o A continuous rotation of C ring and during that protons are entering, and exiting
through the top
- Brownian motion is driving this
- The C ring is wiggling back and forth and every time it wiggles enough, it clicks into position and
then the proton leaves.
- Brownian Rachet

Brownian rachets must be ’rectified’ to avoid breaking the 2nd law

- Rotate rachet up the slope and then it clicks and snaps back so then it can’t go back.
- If you can build microscopic rachet driven by thermal energy, it would just rotate? Evetime
rotate far enough it would snap. If attach to pully, you can lift weight
- But that’s not possible (Richard P.Feyman)
- A Brownian rachet will rotate equally in both directions because of the vibration in order to get
it to work, must put some source of energy into it so it rectifies that motion such that it does not
snap back and must push down on the pull from preventing it from popping back up.

Recent cryo-EM has determined the structure of the C ring

- When proton leaves, go to low concentration space, when proton

comes in, comes in from high concentration space
 - That free energy is enough to buy energy from the two-half channel and clicks and rotates in
only one direction
- Arginine -210 interacts with asparte 61 and that’s the negative residue
that interacts with the proton.
- How is that process (liberating free energy) coupled to the synthesis of
ATP all the way up there?

F1 subunit exists in 3 discrete conformations

- alpha is there for structural

support. 3 conformations
- O position means open
 Nucleotides can pop in
and out
 L is loose
 ADP and Pi trapped but
non-reactive. Loosely
held
 T is tight
 ADP and Pi converted
(reversibly) to ATP
- These beta subunits must cycle through these different steps to accomplish ATP synthesis.
- What’s driving this in these beta subunits is the rotation of the gamma subunit embedded
within them

Rotation of the F0 gamma subunit pushes the F1 beta subunit through their 3-state cycle

- When the gamma subunit rotates, then beta 2 in opens releases the ATP and beta 1 is loose. The
dark green = loose.
- The rotation of the C ring causes rotation of the gamma subunit and as it rotates, it pushes the
betta subunits through this conformational cycle causing them to grab ADP and Pi and smash
together to make ATP and let them go.
- 12 H+ is equal to 3ATP
o 1 full rotation because 12 c subunits and one full rotation we’d get 3ATP molecules out.
- The gamma subunit is a nanoscopic version that mechanical engineers build known as a cam.

ATP synthases is the world’s smallest turbine generator

- ATP synthase smallest turbine and generates electricity. Generating electricity through a
turbine. The rotating shaft has a large ring of magnet so the rotation of motor relative to the
stator generates current flow in the stator and that is effectively the source of electricity.
 o Here taking potential energy (of water as it flows downhill) and that potential energy is
being converted into a rotation of turbine shaft and that rotation is converted into
electricity.
o Turbines are huge
- In ATP synthase, it’s a lipid bilayer and it’s a flow of protons across a membrane and that is the
source of potential energy but downhill flow of the proton being converted to rotation and
turned into chemical energy.

The movement of ATP synthase has been directly visualized

- The max speed is 130 rev/second

- They purified the F1 fragment (has gamma, alpha beta subunits) missing the C ring
- Attach through chemical cross linking and actin filament it’s a fluorescent labeled stick.
- Running backwards but hydrolysis of ATP is pushing the gamma subunit through rotation so it’s
the opposite effect
- Major break through: Japanese hot spring and thought oh we can’t purify good F1 fragment how
can we find a better source of F1 fragments.
- Get ATP synthase F1 filaments from thermophilic bacterial from hot springs. So even at elevated
temperatures, they won’t denature. Protein more stable.

Rotary ATpases: ancient innovation

- Found in a lot of type of organism bacteria (bacillus) in 2019, Yeast (Cerevisiae) in 2018,
Coloplast (spinach) 2018.
- Used throughout all the domains of life.

ATP escapes the mitochondrial matrix via an ATP/ADP antiporter

- Takes ATP out of the mitochondria matrix and brings ADP in

- Have to take phosphate in so a phosphate transporter is also necessary
- The phosphate transporter works as an antiporter and uses the flow of
OH- in the opposite direction as the source of free energy to drive
phosphate in
- That OH that goes out sticks to one of protons generated by electron
transport chain.
o Meaning one of proton pumped by complex I gets consumed by
binding to OH- group. It’s free energy used to get phosphate in
- Each ATP needs 1H+ for transport purposes!

African herbal remedy is an inhibitor of ATP/ADP antiporter

- So you hope it kills the antiporter of the virus before it kills you

Funky tempeh!

- Tempeh Bongkrek (fermented soybeans and coconut)

 - Can become contaminated by G.gladioli and bacteria produces Bonkrek acid which is an
ATP/ADP antiporter inhibitor. If you eat too much your mitochondria can’t get ADP Pi back into
matrix

How efficient is the entire system?

- The reduction of one NADH into NAD+ is delta G of 52.6kcal/mol

o Energy put into electron transport chain
o Got protons across membrane in result
- Need 3 protons to make 1 ATP through C ring and in general approx. 3ATP per NAD+ reduction
- 3 ATP molecule is 22kcal/mol in terms of final energy
o The overall system is 50% efficient in terms of how much energy you get out vs how
much you put in.

A pump and a turbine are the nano scale machines that drive all life on earth

- Complex 1 pump to push protons across the membrane and the ATP synthase 1 with ratcheting
mechanism that converts proton motor force back into ATP
- Tons of mitochondria inside cell

Lecture 10: photosynthesis

Looking at chloroplast and how they harvest energy from photons for electron flow

ATP synthase harness the proton-motive force to make ATP

- Harness energy source to make ATP. Rotation of c ring subunit by the flow of protons cause a
number of conformational changes that occur in the alpha and beta subunits that drive through
chemical cycle that drives through synthesis of ATP

Accounting:

- 1NADH reduced = 12 H+ transferred

- 4H+ = 1ATP (assuming there’s a certain number of C ring subunits which can vary)
- 1 proton at the start
- 1NADH reduced = 3ATP
- Efficiency = 50% efficient

The proton-motive force is conserved in bacterial,

mitochondria, and chloroplast

- Invention life made is how to create

concentration differences across a membrane
- Early on, cells acquired the ability to make
concentration gradients in proton across
gradients essentially making batteries they
charge up which can produce ATP.
 - Flow back up thylakoid in chloroplasma and the green is thylakoid

Photosynthesis takes place on the thylakoid membrane of chloroplasts

- Stacks of thylakoid membrane and that’s the granum. Where the

light of the sun is being harvested
- Pancake stack acting like location where light is harvested
- If we look closely in thylakoid membrane and looking at protein
complexes found there, we find that the architecture is quite
similar to mitochondrial and electron transport chain

The architecture is reminiscent of

mitochondria and the ETC

- Stage one, where light is

coming in
- as light hits, it liberates
electrons, and it moves
through PSII
- the Q/QH2 takes the
electron through called
plastocyanin and carries it
further until it takes it
out.
- 2 diffusible electron carriers and flow of electron through system is used to pump protons
against membrane
- In ATP synthesis proton flow back and coupled to ATP hydrolysis.
- The reaction which light liberates electrons.
- How is photon from sun are able to cause proton to flow through the thylakoid membrane

Photosynthesis takes advantage of the photoelectric effect

- Metal surface and shine a powerful light the impinging light will cause
electrons in the metal to leave their orbitals and flow through the metal
- Now, photon energy into movement of electron.
- Photon has the hit the electron in an orbital and liberate it.
- Essential for breaking down of classical understanding of light (light is wave)
and the quantum understanding (photons)
- Measurement of photoelectric effect is what gave proof for quantum nature of light.
- Einstein said light e = hv, and that disagreed with classical view of light as a wave
o Then amount of energy comes from amplitude not from frequency of the wave.
- Millikan said no! amount of energy is not a function of frequency and color it’s a function of
amplitude
 - Developed apparatus for shining light on metal and current coming off and voltage for light
coming out
- Predicted amount of electron liberate will increase with intensity of light. Saying each electron
will absorb more energy and by increasing brightness should get increase energy per electron
o If frequency shouldn’t matter, should be able to change color of light and as long as
amplitude is same, amount of energy coming off per electron should stay the same
- Millikan thought energy per electron and intensity but no relationship between energy per
electron and color.
- Did not vary with light intensity but varied with frequency.
- Millikan actually measured of Planck’s constant and proved Einstein right.
o Some scientists really want to make correct measurements. Like Millikan
Absorption of a photon can push an electron into an excited state

- In order to understand how the photo electric effect works, we

have to use Jablonski Diagrams
- Horizontal lines are different energy states for particular
electron
- Bottom: ground state, the electron in its standard orbital
- Excited states: where electron can jump to if require more
energy
- Several lines above excited states are vibrational states that are
surround that excited state. Still in the same energetic band but the electron is able to reach
slightly above the base line excited state.
- The incoming light hits the electron in the ground state and as energy from photon is absorbed,
it will knock the electron up into excited state and giving its energy to the electron and pushing
it onto the vibrational modes.
- That excited state is very short lived, during the time its short lived, the electron might vibrate
its way down to the bottom-line excited state.
o Then the electron will land at the base of excited state and decay out of excited position
back to its ground state
o When that happens, a large amount of energy released as photon (emitted light) that
comes out
o That emitted light is another photon that we can’t observe
- This is the basis of types of fluorescents. Like GFP.
- Absorb photon, get pushed up, go down to base excited state, then electron drops to ground
state and emits a green photon so GFP.
o Light is caused by decay of electron from excited state to ground state.
- The amount of energy in the absorption reaction is greater than the emission, if energy of a
photon is equal to hv, if energy goes down, meaning frequency of light has gone down. So
absorbs blue but emit green.
- Color of light that excites is higher frequency than the light emitted.
 - Always a shift towards red, so a shift towards lower frequency of emitted photons due to the
loss of energy in the vibrational states of excited states.
- In photosynthesis, not remitting colored light, we’re transferring it to an electron acceptor. So
we can capture energy and turn into proton flow.
- Energy from photons can destroy covalent bonds of fluorophore, can use fluorescence over
time.

Chlorophyll molecules have delocalized electrons that easily

jump and transfer

- Large decentralized electron and when light knocks it out

it can go through another cluster.
- Light comes in and electron liberated and bounces
around in delocalized electron cloud until goes to
primary acceptor

Photosystem II transfers the excited electrons to a

quinone

- Two photons pop the electrons out and then

go through the QB molecule and take a
couple H+ from stroma to make QH2 and
then push proton across thylakoid
membrane and the electron will make its
way to plastocyanin.
- There’re similarities between chloroplasts
and electron transport chain.
- The electrons are leaving the PSII and they
do have to be replaced by the electron from
water.
- From the oxygen evolving complex, the water molecules make 2H+ and one of the electron from
water molecule will go into replacing electron liberated from light reaction and that is the
source of oxygen we breathe.
- When we eventually inhale the oxygen, it’ll get converted back into water.
- The two cycles are counter to each other and that’s the path it takes.