"mindmap"

Here is a link to the mind map I did for photosynthesis and respiration. Read More…

Photosynthesis

Photosynthesis:


Plants are examples of “Autotrophs,” or, organisms that can support themselves and don’t need to eat other things (we are “heterotrophs;” we do eat other things). In particular, plants are “photoautotrophs,” supporting themselves with light.
484px-Simple_photosynthesis_overview
This is the basic scheme we have been following. Photosynthesis can be broken into two parts, the “photo” part (light reactions” and the “Synthesis part” (Calvin Cycle). The light reactions produce two main things: ATP and NADPH (It’s just like NADH, except it has an extra phosphate). The processes that result in look like the ones we learned about in respiration (except, backward). The ATP synthase works the same way as it does in respiration.
The ATP and reduced nucleotide cofactor (NADPH) are used in the synthesis part (Calvin Cycle) to pull CO2 out of the air and synthesize carbohydrates. In the process, the oxidized NADP+ and ADP are produced…and fed back into the light reactions.

Light Reactions


The general idea is that photons of light hit electrons, exciting them to a higher energy level. Instead of “falling” back down and emitting light, the high energy electrons are passed to other molecules, reducing them, and the electrons are passed down an electron transport chain of proteins or smaller molecules that are reduced, then oxidized by the next player in the chain. In this way, just like in respiration, protons are pumped across the membrane and those drive the ATP synthase. The first recipient in the chain is called “Plastoquinone” and it looks like this:
Plastoquinone
(That structure in the brackets is repeated 9 times). (The protein complex that gets the electrons next is called “cytochrome b6f”). There are two different photosystems (called PSI and PSII) that can work together. Photosystem I can also work on its own. Each has their own chlorophyl and accessory pigments in the “antenna complex.” In a pattern known as the “Z scheme,” electrons starting in PSII get passed though electron transport to PSI, where light excites it. Another electron RedOx reaction can pass two electrons onto NADP+, generating NADPH, the reduced form. This will be passed to the “synthesis” part, or Calvin Cycle. The Z scheme looks like this:Thylakoid_membrane

Some key points:
  1. In the Z scheme, PSII is excited “first,” (there are many reaction centers all being hit more or less simultaneously. It’s just that to see the “scheme,” we have to imagine things happening in sequence).
  2. Electrons leave PSII. They are replaced by electrons taken from oxygen in water (a rare case of oxygen being oxidized). This generates O2, which is good for us.
  3. At some point PSI also gets hit by a photon of the right energy. That electron is can be passed directly to an iron-containing protein called “Ferrodoxin” and eventually used to reduce NADP. The electrons are replaced by electrons coming down the from the PSII system.
  4. The Z scheme is also called “linear flow” of electrons because they appear to start at one place (PSII) and pass down the chain, eventually leaving the system. You could call it an “open” pathway, since electrons will leave the system at the end, transferred to NADP+ to make the reduced NADPH, and therefore need to be replaced by electrons from oxygen, obtained in PSII.
  5. Photosystem 1 (PSI) can work on its own without PSII. In that case the electrons excited from PSI get passed down the chain to Cytochrome b6f and passed back into a PSII reaction center. When this happens: Oxygen is NOT released and NADPH is not made. In some organisms, the electrons can be taken from some other source and NADPH can be made, but, oxygen is not produced.
  6. From an evolutionary point of view, PSI appears to be older. If that’s the case, photosynthesis was going on for a long time without oxygen being produced. This is still somewhat debated.

The "Synthesis" Part



Basic. There are three phases.


Calvin-cycle4
  1. Carbon Fixation: The starting molecule is Ribulose 1-5 bisphosphate, a 5-carbon sugar derivative with a phosphate on each end. CO2 is pulled from the air and attached to one end, creating a very unstable 6-carbon molecule that breaks almost immediately in to two 3-carbon molecules called 3 phosphogycerate. If you’re counting Carbons (and you should be), you started with 5, added 1 CO2 to get 6, then broke that into two 3-carbon molecules.
  2. Reduction: This molecule may be used for some biosynthetic pathways. However, to be really useful, it needs to be reduced from the carboxyl (COO-) form to the aldehyde form (C=O). This goes in two steps involving first ATP, then reduction with NADPH. This yields the very useful glyceraldehyde 3-phosphate (G3P). I’m sure you remember that one from glycolysis.
  3. Regeneration: For it to be a “cycle,” the starting material Ribulose, 1-5 bisphosphate has to be regenerated. This actually has several steps and if you don’t look a little at the details, the math doesn’t seem to work. For that reason, I’ll do a little detail here. What happens is the first two steps are run 3 times, (requiring 3 Ribulose 1-5 bisphosphate molecules), which gets you 6 G3P. One of those can be syphoned off to use for other things such as glucose synthesis. The remaining 5 G3P are rearranged through several enzymatic steps to get you back your 3 Ribulose 1-5 bisphosphate. (Five 3-carbon molecules get you three 5-carbon molecules…15 carbons in each case)
So, running the Calvin cycle 3 times gets you a net gain of one G3P. Run it 3 more times and you can use two of those to make a glucose. That takes more ATP and is essentially the reverse of the first few steps of glycolysis. It takes a total of 6 times round the cycle to make a single glucose.



Detail


You don't need to memorize this. It's here for context. Please keep reading. There is more after this.
  1. We start with Ribulose 1-5 bisphosphate (that means 2 phosphates, one on each end of the molecule at positions 1 and 5). Note that ribulose is a ketose, with a carbonyl at position 2. The attack of the CO2 is at position 4, one from the right end.
  2. RuBP-2D-skeletal
  3. The intermediate, 3-keto-2-carboxyarabinitol-1,5-bisphosphate (hope you appreciate that I wrote out the name of the “β-keto intermediate”, Brian), is immediately broken into two 3-phosphoglycerates. These have a phosphate on position 3, a carboxyl group (acid) at position 1. Note that here they are assumed to be deprotonated, as they would be at normal pH.rubismech
  4. Phosphoglycerate can itself be used as starting material for many biosynthetic pathways. Some molecules may get syphoned off for other uses.
  5. ATP is used to add a phosphate to the other end (carbon 1) of 3-phosphoglycerate (3-PG), yielding 1,3 bisphosphoglycerate (you need two ATP because you have two 3-PG). Note that the carboxyl end (left side) now goes COOPO3-. In ATP hydrolysis, ADP would be left with the extra oxygen and the Pi picks up its fourth O from water. Here, the transferred Phosphate gains its fourth Oxygen from the carboxyl.
    BIPGLYC
  6. NADPH is the reducing agent for the next step, which removes the phosphate. Note that if you now remove the Pi, the oxygen that was the end of the carboxyl is removed, leaving just the carbonyl. So, it’s now an aldehyde (terminal carbonyl) and is Glyceraldehyde 3-phosphate. It can be used in biosynthetic pathways too. The H from NADPH is now at the end of the molecule, where the O used to be.
  7. Once you build up enough G3P, you can syphon one off for Glucose synthesis (note that this particular version of the cycle implies that it’s the 3 phosphoglycerate that is syphoned off. This is a bit of a controversy...and may just be a point of view. Let’s stick with the G3P as being the main intermediate used to build glucose.
  8. I’m not going to go into any more detail on the regeneration process than I did above in phase 3.


CAM and C4 Plants


The problem of Oxygen


We discovered that Photosystem II has such an extremely high RedOx potential that it can oxidize Oxygen, removing it from water and releasing it as molecular O
2. That’s good for us, but creates quite a few problems. The main problem as far as we are concerned here is that RuBisCO has a very odd property: it can carry out a very unproductive reaction called “photorespiration.” In this reaction, instead of binding CO2 and adding that to ribulose-bisphosphate (RuBP), it binds O2 and adds that to RuBP.
RuBisCO binds CO
2 preferentially. But, if there is a lot of O2 around photorespiration happens.
The exact biochemistry is not that important here. There are a whole series of reactions that take place and the net result is that CO2 is released (that’s why it’s called “respiration;” oxygen is consumed and CO
2 is released). But, unlike cellular respiration, ATP is consumed in the process. Thus, it is considered a wasteful process.
There is some debate how much of a problem this is for plants. Photorespiration may be helpful to some plants under some circumstances. However, it
is clear that other plants have evolved specific strategies to minimize it.
Plants that have no strategy to prevent photorespiration are called C3 plants (because the product of carbon fixation are two, 3-carbon molecules…3 phosphoglycerate). They do photosynthesis the way I have taught it so far. They include most of our agriculturally important plants, such as wheat, rice, soybean, potato, fruit trees and nut trees and others. They tend to do well in cool, moist climates, but not at all well in hot, dry climates. In such climates, the plants will keep their stoma closed to conserve water. Gradually, this will deplete the CO
2 and build up O2,) leading to photorespiration).

The Biochemistry


Plants that live in hot, dry climates have evolved mechanisms to prevent photorespiration. One such type of plants is called C4 plants and the other CAM plants. Both these strategies involve keeping the concentration of CO
2 relatively high when the Calvin Cycle is running. While there is some variation on these themes, the biochemistry is similar in both cases. I will present the simplest variant:
Both fix CO2 onto phosphoenolpyruvate (PEP) forming the 4-carbon molecule Oxaloacetate. That is converted to Malate by the enzymes indicated.
C4Path

CO2 can be released from Malate, generating pyruvate. Remember “Pyruvate Kinase” from glycolysis? It will take pyruvate and add phosphate from ATP to regenerate PEP so the plant can do this again.

C4 Plants: Spatial separation.


These include a few important agricultural plants, such as corn and sugar cane as well as some grasses. “Crabgrass” is a C4 plant, which is why it takes over your lawn, especially in dry weather.
When grown in the same environment, at 30°C, C3 grasses lose approximately 833 molecules of water per CO
2 molecule that is fixed, whereas C4 grasses lose only 277 water molecules per CO2 molecule fixed. This increased water use efficiency of C4 grasses means that soil moisture is conserved, allowing them to grow for longer in arid environments.
Thus, the grass we like requires roughly
THREE TIMES the water as crabgrass. I still hate crabgrass.

C4 plants separate oxygen production from the Calvin cycle in two different sets of cells, known as the “mesophyll” and “bundle-sheath” cells, respectively. The set up looks like this:
Pasted Graphic 6
This image is used without permission from this website: http://www.bio.umass.edu/biology/conn.river/photosyn.html

They transport the malate made above into the bundle-sheath cells and released the CO
2 in the chloroplast of those cells. This keeps the concentration of CO2 high in those cells and minimizes photorespiration. Another depiction of the overall scheme is below:
C4scheme

CAM Plants: Temporal separation


CAM stands for Crassulacean acid metabolism. There is no chemical named “Crassulacean acid.” The name comes from the family of plants that use this approach,
Crassulaceae, and the fact that the chemicals oxaloacetate and malate are organic acids.
CAM plants include succulents. The only agriculturally important plants in this category are pineapple and agave.
They keep their stomata closed during the day, minimizing water loss. Then, at night, when temperatures are generally cooler, they open stomata and allow gas exchange. They save the Malate generated in the pathway above in the vacuole, then use it during the day to keep CO
2 concentrations high. This image is from wikipedia and yes, the labels are in German.
CAMPicture


Side point:


PBS ran a documentary by Ken Burns not long ago on the “Dust Bowl,” in case any of you have trouble falling asleep, you can look it up. However, there is a good point to be made connecting this element of history to biology. The native grasses on the great southern plains, such as buffalo grass, Are C4 plants. These have typically deep roots and use less than ⅓ the water for each glucose generated than the shallow-rooted C3 plants, such as wheat, that we planted there in their place.

Respiration Continued

Some details on where the high-energy electrons come from.
Read More…

Intro Respiration

Big Picture:
You should review this figure on mitochondria:
https://upload.wikimedia.org/wikipedia/commons/b/b5/Mitochondrion_mini.svg
Remember that oxidation/reduction (RedOx) reactions involve electrons being traded from positions of high potential energy to ones of lower potential energy, with the resulting release of some free energy (the difference, or delta) between the start and final state.
The overall reaction in respiration combines carbon and hydrogen gotten from carbohydrates and other carbon-containing molecules with oxygen to make CO
2 and water. But, instead of doing that all at once, there is a long series of reactions releasing smaller amounts of free energy, some of which is captured in nice, “bite-sized,” chunks of energy we can use. What “bite-sized” chunk really means is electrons in compounds easily oxidized. The two main bites of energy for the cell are ATP and NADH.
We will produce ATP through simple reactions called “substrate level phosphorylation” and through oxidative phosphorylation. In this second process, NADH is the source of electrons for the electron transport system, which uses RedOx reactions to pump protons to the inter-membrane space. Finally, the ATP synthase uses that proton gradient to synthesize ATP.
We will start at the end, because it makes more sense this way.

ATP Synthase


  1. Enter the ATP synthase:
  2. Atp_synthase
    This machine is almost too good to be true. It’s in the mitochondrial inner membrane, the chloroplast inner membrane and the plasma membrane or inner membrane of bacteria. The protons flow down gradient through a channel, which leads to mechanical changes that spin the rotor (more like a ratchet). This mechanical energy is then used to drive ATP synthesis. Thus, we convert mechanical energy to chemical potential energy. The process is also called “chemiosmosis.”
  3. Too cool. Here is a video. It’s not the one from the creationist site.

All this needs to run is a proton gradient. How do you get that? Well, that depends. In the mitochondria and chloroplast, the proton gradient comes from a system called “Electron Transport,” also taking place in the inner membrane of the mitochondria (or chloroplast).
Electron Transport is a series of RedOx reactions taking place in or near the membrane that result in protons being removed from various chemicals and released into a confined space between two membranes (such as between the inner and outer membrane of the mitochondria).

Reducing equivalents or “Reduced Cofactors”


To run electron transport, you need electrons in a high energy state. That is, you need something that has electrons that are relatively easy to remove to a lower state. The thing donating the electrons is the “reducing agent” (it gets oxidized) and therefore we call it a “reducing equivalent” or “reduced cofactor.” It will be one or more “B” vitamin derivatives in its reduced form.

  1. A word about “cofactors.” I hope all of you were starting to see the patterns in the nucleotide cofactors. Take a look at the separate entry on cofactors if you like.
  2. NAD clearly has a lot in common with ADP. NADH has particularly high RedOx potential and is sometimes used directly in enzymatic reactions requiring free energy. These really are variations on a theme. The cofactors in electron transport are variations on another theme, or, pardon the pun, variations on a Heme. These are the iron-containing rings that you are familiar with from Hemoglobin, which can carry oxygen in your blood. But, similar cofactors will be used in electron transport.
  3. If you want to carry electrons in a membrane, you need something that is hydrophobic to do it. The go-to cofactor there is “Coenzyme Q.” It is not based ADP. The “MeO” in the structure stands for a Methyl-Oxygen or “methyl ether.”
CoQ
  1. You will see these structures over and over. They will always be doing similar tasks.

Oxidative phosphorylation.

  1. Technically, this includes two stages: the phosphorylation by the ATP synthase we’ve already discussed, and the Electron Transport System which uses oxidation/reduction reactions to move protons to the inter-membrane space to drive the ATP synthase.
  2. I stole the figure below from a great text book called “Molecular Cell Biology.”

ETS2
The key players here are called either electron carriers such as Cytochromes and cofactors such as coenzyme Q, or oxido/reductases, enzymes that catalyze the transfer of electrons, frequently while pumping protons across the membrane. You don’t need to know the names of them, though I might use them. The complexes are just labeled with Roman Numerals.
The cytochromes are small-ish proteins that contain bound within them, usually, an Iron atom/ion. This is cytochrome c, one of the
  1. Most well characterized cytochromes.Cytochrome_C The multi-ring structure in the middle is not part of the protein per se. It is called a “heme,’ as in “hemoglobin,” and is held in place by the protein. The red dot is an iron.
  2. Technically, the heme is not a cofactor, but a “prosthetic group.” That is fairly subtle distinction. A cofactor generally enters the active site of a protein when it is needed, is altered, then has to be replaced. A prosthetic group stays in the protein continuously. Below are two images of a heme chelating an iron.
HemeHemeSpacefill
  1. Look at the general scheme on page 171, figure 9.13. Electrons are passed from NADH or FADH2. These enter the “electron transport system” which is the string of cytochromes and other acceptor/donor molecules in the inner membrane. The electrons pass down through a series of RedOx reactions, the acceptor for one step being the donor for the next. Finally, the electrons are passed to Oxygen, which pairs with protons to make water.
  2. At three steps along the way, just due to the orientation in the membrane, the H+ product of the dehydrongenation (oxidation) is spit into the intermembrane space (between the two membranes—we’re so clever with names). This leads to an electrochemical gradient.
  3. Key Points:

  1. The donor of electrons are cofactors NADH and FADH2 .
  2. The oxidation/reduction reactions pass electrons from one carrier to another in or near the inner membrane.
  3. The reactions result in protons being pumped to the inter-membrane space, establishing the electrochemical gradient that runs the ATP Synthase.
  4. The final recipient of the electrons is oxygen, which combines with H+ to make water. That’s why you breath out water.
The remaining question is: Where did the reduced cofactors NADH and FADH2 come from? We’ll get to that next.

Cofactors

Small-ish molecules that are bound to a protein and required for it to complete it's function. Read More…