Intro Respiration

Cellular Respiration.

Here is a link to a screencast from last year. It actually covers much more than we did today. If you want to watch the first 15 minutes of it, you might find it good review. If you want to watch all 40 minutes of it, it will take you through pretty much the whole chapter 9.

We break down glucose (and lots of other things) to make CO
2 and H2O. Both are much lower in chemical potential energy than the starting food item, so free energy is released. But, the convoluted steps we use to do this allow us to harvest little bits of energy to make molecules with a convenient amount of chemical potential energy (such as ATP and NADH+H+).
Big Picture:
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 a more efficient process called "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).

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 is 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.
  2. NAD clearly has a lot in common with ADP. NADH is sometimes used directly in enzymatic reactions requiring 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 pump 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. 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 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.