October 29, 2007

Mad Scientist: Update on Chloroplasts

Posted in Mad Scientist at 10:54 pm by D. Borst

So it turns out that a natural experiment has developed that tests exactly what I questioned in my last mad scientist post– Sea Slugs ingest algae and are able to extract the chloroplasts from these cells and use them to fix their own carbon.  These sea slugs only extract the chloroplasts though, and they are able to use the products of the fixation reaction in their own bodies.  Cool!  Read about it in this article here. Free article from NCBI.

Electron Carrier Molecules

Posted in Cell Biology tagged , , , , , , at 4:15 am by D. Borst

So, in Mitochondria Pt. 2 I threw a whole lot of information at you, some of it without much context. In this post, I will hopefully provide some of that context. Specifically, we will explore the the different types of electron carrier molecules that are present in the electron transport chain.

Heme Group from Cytochrome CMost electron carrier molecules are proteins that have had electron accepting functional groups added to them. The cytochrome series of molecules are a good example of this. Cytochrome electron carriers all have a heme functional group added to them. The heme group from cytochrome c is imaged with pymol to the left. It is this heme group that allows the cytochrome carriers to accept the electrons that they carry–without such functional groups, the electron transport chain couldn’t work. If you are wondering where you might have heard of a heme group before, they are also present in molecules of hemoglobin, the protein that carries oxygen in the bloodstream.
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October 24, 2007

Fatty Acid Oxidation, Krebs Cycle and Glycolysis

Posted in Cell Biology at 2:51 am by D. Borst

So my cell biology class is taking a very modular approach to Fatty Acid Oxidation, the Krebs Cycle and Glycolysis. Im sure that my biochemistry class will not be nearly so informal, however, for completeness in my discussion of the mitochondria and because I said I would, here is a quick overview of these three important cycles that lead to the cell getting energy from food.

There are two standard food inputs that the cell uses to make ATP–Fatty Acids and Glucose. Ultimately, Glucose is reduced to two molecules of pyruvate in the cytosol, which are then further reduced to two molecules of Acetyl-CoA in the matrix space. In the fatty acid cycle, fatty acids are reduced in length to make units of Acetyl-CoA. This supply of Acetyl-CoA is what drives the Citric acid cycle in the cell.

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October 23, 2007

Ramachandran Plots and the Alpha Helix

Posted in Biochemistry tagged , , , , at 7:28 am by D. Borst

Structure = Function. This is the creed of the biochemist. However, there are many levels of structure for the biochemist–four is the classical number. We will start in this posted review of my biochemistry class at PSU with discussing how primary structure (the sequence of amino acids in a protein) gives rise to secondary structure (local conformation of the Carbon-nitrogen backbone.)

Amino acids are generally thought of as starting with a amino group (the N terminus) and ending with a carboxilic acid (the C terminus). However, for purposes of thinking about secondary structure, it is more conveinent to think of the peptide backbone as jumping from α-carbon to α-carbon. This is because the conformation of the peptide bond is very rigid, due to it having partial double bond character. The double bonded oxygen shares some of its electrons with the nitrogen, making the Cα to Cα stretch unusually rigid. This makes it possible to think of the peptide as a series of planes that meet at the alpha carbons. In each plane are the atoms between each α-carbon. The planes meet corner to corner at the alpha carbons, not including the R groups.

There are other generalizations that we can make about local structure: Generally the peptide bond assumes a trans-conformation relative to the placement of the R-groups on the α-carbons. This leads to the one-up, one down general representation of the peptide backbone.

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Electron Transport Shuttles in the Mitochondria

Posted in Cell Biology tagged , , , , at 5:06 am by D. Borst

So in Mitochondria Pt. 2 I mention that thare are a few ways for NADH produced in the cytosol to enter the mitochondria to take part in ATP synthesis. I mentioned one of these ways: the Glycerol Phosphate Shuttle. Electrons from cytosolic NADH imported by the glycerol phosphate shuttle end up reducing FAD. However, the way in which they do this is of interest.

NADH from the cytosol gives up its two electrons and Hydrogen (becoming NAD+), to Dihydroxyacetone phosphate (DHAP). The keytone on DHAP is totally reduced, transforming DHAP into Glycerol 3-phosphate. Glycerol 3-phosphate will then float untill it encounters inner membrane bound Glycerol 3-phopshate dehydrogenase. G3PDH has a FAD prosthetic group attached to it, as shown in the figure to the left (the FAD group is the orange organic molecule inside the protein). When Glycerol 3-phosphate encounters G3PDH, it transfers its electrons to the FAD prosthetic group. This is now This has the effect of making FAD prosthetic group in a membrane bound protein oxidized. Ubiquinone can come along and encounter the FAD group, and take the electrons away, shuttling the electrons into the electron transport chain at the same point that electrons coming through Succinate dehydrogenase enter the chain. Thus cytosolic NADH electrons is equivalent to a mitochondria generated FAD electrons. In the process of giving up its electrons to G3PDH, Glycerol 3-phosphate re-oxidizes to form DHAP once more, and the cycle can begin again. This whole process is very nicely summed up in this schematic from Stryer’s Biochemistry Fifth Edition, which is available for free on the NCBI bookshelf.
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October 22, 2007

Happy 50th to Bone Marrow Transplantation

Posted in Articles of Interest tagged , at 11:25 pm by D. Borst

There was an interesting historical article in the New England Journal of Medicine one and a half weeks ago (ok, Im a little behind, but it comes every week!) about the history of Hematopoietic-Cell Transplantation. It is a story of courage and perseverance of a physician-scientist in the face of confusing data and poor understanding of the biology behind how the body recognizes self from not-self. If you have some time, and you are interested in how things all began, give it a read. Its work that yielded a Nobel Prize. The article is freely available via the NEJM website.

October 21, 2007

My First PyMol Image

Posted in Biochemistry, Software tagged , , , at 8:08 am by D. Borst


So eventually, if you want to do work with proteins, you have to actually look at some. I suppose it is inevitable. You will want to know the locations of alpha helices and beta sheets, you will want a sense of the way the thing all hangs together. These days, we don’t have to search through card catalogs of images of different proteins, painstakingly hand drawn by some poor soul to show the view that he thinks is most informative (but for your purposes blows goat chunks). Instead we can get files that detail the locations of each atom in the protein, and then generate the image automatically on our computer. Time to get a Molecular Visualizer.

I was faced with this task this weekend, as my Cell Biology and Biochemistry classes are quickly moving into the territory where I will be regularly required to look at the structures of proteins of interest. I came across 3 programs in my search (out of about 20 that I know of), all free. I’ll dally a bit with you here to discuss them.

Chimera was the first program that I downloaded. It appears to run fine on Mac OSX systems, though it is a X11 program, so devotees of the “Mac Look” may be disappointed when their cursor turns around and they are forced to interact with non-aqua rendering of windows. If this means nothing to you the take home message is: Its ugly.

Chimera probably works fine. I found it somewhat difficult to figure out immediately, as in, I did not look at any manuals, did not look up anything online, and frankly did not spend too much time on it. It appears to import pdb files from the Protein Database just fine, and may work better in this respect to the program I will discuss later, PyMol. I’m kinda a techy-linuxey kinda guy, so any high end program that doesn’t involve a text interface kind of frightens me. The though of spending arduous hours searching scroll down menu’s makes me shiver in my britches (to mix a metaphor). So Chimera now sits alone and abandoned in my applications folder, waiting for me to be neurotic enough to delete a 10 mb program in the search for extra space on my hard drive.

I also did some work with the KiNG viewer, a program made by the good people at Duke. KiNG obviously supports the “cartoon” view of proteins, but in the five minutes that I spent playing with it, I couldn’t get that feature to work. Furthermore, KiNG translates a pdb file into a so called kinemage (kinetic image), presumably to let you do cool and sophisticated things with it. But it also lacks a text interface and frankly, I didn’t like the feel of it too much. It is very likely that I would have gotten over this if I had honestly taken the time to learn to use it, which I may in the future. But I was already pretty taken with PyMol by this point.

On the upside, KiNG is a java application, which means that it is kind of half in and half out of the aqua interface. It is undoubtedly prettier than Chimera, so I guess if that is important to you, go for it.

As I have mentioned, the application that has won me over for the moment is PyMol. PyMol is made by Delano Scientific and it is the weird bastard son of people who put their faith early in open source but have become disenchanted.

According to their website, a high proportion of the images of proteins in journals like Nature and Science are made with PyMol. They pride themselves on the ability of their program to quickly make publication quality images.

Pymol comes in several flavors: Old, Expensive and Do-it-yourself. Pymol started as an open source project, but the developers have since begun charging for pre-compiled binaries the program for specific operating systems. You can get non-current versions of the software (0.99 is the latest freely available as of this writing) online for free, though you sacrifice in what ever new and improved features that they have added in the latest version, or whatever corrections to the drawing algorithms they may have made. If you want to pay money, you can become a subscriber, get the latest program, and support. If your school or institution is site licensed, you may be able to freely download it anyway. Will update this blog if PSU is so licensed. The do it yourself option is for those people who are willing to get their hands a little sweaty from some command line fu and linux trickery (not that sweaty).

Delano Scientific offers the source code for the latest versions of pymol for free. This means that you can download the source code, compile it on your own machine, and have a version of pymol specifically made for your own machine. (In the linux environment this individualization is preferred, but for the rest of us, it means that you cant just drag and drop the program onto your friend’s computer. ) If you want to do this, the easiest way is to install fink, a package manager program that will install linux apps onto your computer in a fairly automated way. If you install fink, simply enter:

fink install pymol-py25

on the command line, and presto! Your computer will make a lot of buzzing noises, the fan will spin, text will flash across your terminal interface and in about an hour, PyMol will be hidden away in the linux side of your shiny Macbox. If you want to do this, you need Xcode and X11, but those are free too.

You could simply go for PyMol 0.99, which runs in aqua and still has the text interface, but compared with the beauty of automatically compiling binaries on your own machine.

Anyway, I found pymol to be very straightforward. It has a somewhat non-intuitive UI, but once you get it (about 5 minutes for me) it became straightforward. It has a command line interface that I find very useful. I can enter:

load 2gmh.pdb
hide sticks
hide nonbonded
color yellow, ss h
color green, ss ""
color red, ss s
show cartoon
png foo.png

and get the image at the start of this overly long entry. Furthermore, I was easily able to find good documentation for the program online, in the form of outdated user manuals for versions 0.99 and a community wiki. I have not been able to load the form of ATP synthase yet–there is some problem that I don’t understand. But other than that, I have been very pleased with the program. Four out of five stars.

UPDATED: I was using pdb file 1qo1 to try and play around with ATP synthase. This appears to simply be a file of atom locations, and not actually a file that will give you secondary structure. Thus when I loaded 1c17 and 1e79 (two other pdb files with full secondary structure data, I was able to move them both onto the 1oq1 file with the “align” command, and I was aces. PyMol all the way.

Updated 2:  I have received information that PSU does not have a site license to  pymol.  Well shucks, guess you will have to stick with v 0.99 if you cant use Fink.  If you can use fink, just type ‘fink install pymol-py25’ and you are golden.  In the half hour that it takes to download and compile.  So go get coffee.

Mad Scientist Dreams: Chloroplasts in Animal Cells

Posted in Cell Biology, Mad Scientist at 8:07 am by D. Borst

So animals cells need the universal energy currency ATP just like plant cells. We animals get our ATP from the catabolic processing of carbohydrates and fats. Which is really, really cool, as I will go over in another post. Plants, as every 3rd grader learns, use chloroplasts to generate high energy electrons (in the form of NADPH) which are then used to make ATP through oxidative phosphorlation. But for the first episode of Mad Scientist’s Question Period, what would happen if you were to insert chloroplasts into an animal cell, or even just a eucaryote that normally doesn’t contain them? Would the cell be able to attain the ATP generated by the chloroplasts? Chloroplasts, like mitochondria have transferred many of the genes for their machinery to the host genome, but even in the absence of this information the chloroplast should be able to last for a while. Does this sort of transgenic cell work? Furthermore, would it be possible to insert the genes for chloroplasts into the genome of a mouse or a nematode and get a photosynthetic animal?

I am trying to approach the issue of modularity in genetics and cell biology. Some aspects of cellular life appear to be fairly modular–they can be mixed and matched between organisms with relative ease, adding features without disrupting the symmetry of the pattern. In my mind, lateral gene transfer in prokaryotes is a prime example of this.

For example, the genes of an ABC transporter that confers drug resistance can be transferred from one prokaryote to the next, making the spread of drug resistance much faster than it would be if microbes followed a strictly hereditary system of evolution. But the point is, the gene for the transporter protein can be transferred to a new type of bacteria through lateral transfer, and the protein can be expressed and implanted in the membrane, where it will serve its function without necessarily gumming up the rest of the organisms works.

Now the chloroplast is a much larger and more complex possible “module” than a single Transporter Protein, and multicellular eucaryotic cells are much more complex than prokaryotic cells. It is very likely that this wouldn’t work at all. But it sounds to me like a question for science.

Any papers describing an attempt at such a crazy task would be greatly appreciated.


The Mitochondrion Pt. 2 — The Electron Transport Chain

Posted in Cell Biology at 8:03 am by D. Borst

We will be skipping over a detailed description of the Krebs (or TCA) cycle temporarily to talk about ATP production on the inner mitochondrial membrane. This is perhaps the most important function of the mitochondria–each molecule of ATP/ADP travels between the mitochondria and the cytosol approximately once a minute. Each day, 2 x 1016 molecules of ADP are phosphorylated in our bodies: 160kg/day. Each ATP Synthase complex can phosphorylate up to 100 molecules of ADP per second. This phosphorylation is a chemiosmotic process, or driven the flow of ions across a selectively permeable membrane. In this case, the ions flowing are protons. A concentration, charge and pH gradient is set up across the inner membrane, and the osmotic pressure to return to equilibrium is used to synthesize ATP from ADP.

However, in order for a gradient to be taken advantage of, it must first be established. The way the mitochondria sets this up is through the electron transport chain. The big picture here is that high energy electrons created by the TCA cycle are used to reduce molecules of O2 into water, and the energy given off is used to drive a series of proton pumps pumping protons out of the matrix space and into the intermembrane space of the mitochondria. These protons are then let back in by ATP synthase, driving the phosphorylation of ADP into ATP. It is important to note that the electron transport chain consists of the transfer of the high energy electrons through more than 60 different electron carriers. The change in energy from the point at which they are produced to the point where they reduce molecular oxygen is so great that the energy must be carefully lowered by successive transfers in order to keep the release of energy from being too explosive. The directionality of the chain is produced by each successive transporter molecule having a higher affinity for the electrons than its predecessor. Thus the chain allows 50% of the energy in the electrons to be captured in productive work, the other half being released as heat energy.

Why is oxygen the end for the electron transport chain? Well, molecular oxygen is very electronegative, and thus a lot of energy can be take from the electron before it is handed over to oxygen. However, the end point in the electron transport chain does not have to be Oxygen. Anerobic bacteria use almost the same process to catalyze production of ATP as eukaryotes, but end up depositing the electrons on other electronegative species such as as Sulfur and Nitrogen. It was only the rapid accumulation of atmospheric oxygen 1.6 billion years ago that made it possible for this process to end in the reduction of molecular oxygen.

Let us first focus on the electron transport chain. For each molecule of Acetyl-CoA the Krebs cycle produces 5 molecules of NADH, one molecule of FADH2 and one molecule of GTP. NADH and FADH2 are both electron carriers that are used as inputs to the electron transport chain and NADH is probably the most important. NADH is the reduce form of NAD+, which is free floating in the matrix space. NADH will diffuse to the edge of the membrane, where it will eventually associate with the first proton pump, NADH Dehydrogenase (also called Complex 1). NADH Dehydrogenase is a complex of more than 40 different polypeptides. Most of these polypeptides are themselves electron carriers, mostly of the iron-sulfur center variety.

Each NADH carries two electrons. These electrons are released one at a time to Complex 1, and each pulls two H+ ions through the complex to the other side of the membrane before it is passed off, for a total of 4 H+ from each NADH that is dehydrogenated by Complex 1. The electrons are then passed off to the second free electron carrier in the electron transport chain, Ubiquinone.

Of the 60+ electron carriers in the electron transport chain, only NADH, Ubiquinone and Cytochrome C are not part of one of the four large electron transport complexes. While Ubiquinone (also known as coenzyme Q) is not a part of one of the major complexes, it is implanted in the membrane. Ubiquinone is a freely diffusing molecule within the membrane, acting as a transporter. Part of the beauty of this system is that while each electron travels along a specific path from type of complex to next type of complex, if one complex becomes damaged, the electrons being ejected from a previous complex are not stalled–they simply are carried by Ubiquinone to another instance of the same complex.

Ubiquinone picks up the two electrons originally from NADH and transfers them to complex 3 (there is a complex two, but it is not part of the NADH electron transport chain), also referred to as the cytochrome b-c1 complex. Complex three is smaller than complex one, containing only 11 polypeptide chains, and has carriers predominantly of the cytochrome variety. On their way through complex 3, each electron pulls two H+ across the membrane, for a total of 8 protons thus far per molecule of NADH.

Cytochrome C is the next free floating electron transporter. Cytochrome C binds the electrons it carries via a heme group, and travels on the outside of the inner membrane to complex 4, the cytochrome oxidase complex. The cytochrome oxidase complex is slightly larger than complex 3, as it is a dimer containing 13 polypeptides. The transfer of each electron through this complex pulls 1 proton through the complex to the intermembrane space, for a total of 10 protons per original molecule of NADH from the Krebs cycle. This is the last stop on the electron transport chain. At this point, the electrons are transferred four at a time to molecular oxygen, to make two molecules of water.

However, NADH is only one of the three sources of high energy electrons to the electron transport chain. As mentioned previously, the Krebs cycle also produces reduced FAD, another electron carrier. At one step in the Krebs cycle, succinate is transformed into fumarate by Succinate Dehydrogenase. Succinate Dehydrogenase is bound up on the inner membrane, the only enzyme in the Krebs cycle that isn’t free floating in the matrix space. FAD (and when reduced FADH2) is complexed with Succinate Dehydrogenase, and together, they form the aforementioned Complex 2. Electrons entering the transport chain through complex 2 are of lower energy than electrons entering the cycle through NADH. Thus electrons from FADH2 are transferred directly to Ubiquinone, and do not pass through complex 1. From then on the cycle is the same as for electrons from NADH. Thus for each molecule of FAD reduced, six protons are pumped across the inner membrane (four from complex 3, and two from complex 4).

The third source of high energy electrons is from cytosolic NADH. For each molecule of glucose that is processed by glycolysis there are two molecules of NADH that are produced. Most of this cytosolic NADH gets used up in cytosolic processes, however some of it is transported into the mitochondria for use in the electron transport chain. However, since it has to be transported across the inner membrane (it can simply float through the porins in the outer membrane), its electrons loose some of their energy. Specifically, electrons from cytosolic NADH are transported into the electron transport chain via the glycerol phosphate shuttle. This process uses the electrons on the cytosolic NADH to reduce FAD, producing FADH2. These electrons then enter the transport chain via ubiquinone, and have the same contribution per cytosolic NADH as per mitochondrial FADH2.

The net effect of this electron transport chain is to create a gradient in charge, pH and concentration of hydrogen ions. There is a tenfold concentration of protons on the outside of the matrix space, leading to the matrix space having a pH of approximately 8 (the intermembrane space is for all intents and purposes continuous with the cytosol, so its pH does not drop). Furthermore, from the concentration of hydroxide on the inside and the resulting high concentration of ATP, there is charge gradient across the inner membrane of 200 mV. These three gradients together form the proton motive force, which is then used to drive ADP phosphorylation.

The proton motive force is also used to generate heat. In brown fat, (a high density fat possessed by infants and animals living in very cold environments. Also referred to as baby fat.) the proton gradient is expended by special hydrogen ion channels that let the protons back in. This releases energy, creating heat. This heat is used to protect organisms particularly sensitive to heat changes.

Protons are guided back into the matrix space primarily via ATP Synthase (also called ATPase). ATPase has two major subunits, F0 which is lodged in the inner mitochondrial membrane, and F1 which protrudes into the matrix space. F0 unit grabs onto a proton and ligates it to one of the 10-14 identical proteins that make up a rotor. This then causes the rotor to spin. A proton is carried around for one full spin, after which it is deposited upon the inside of the membrane. The spinning rotor turns inside the F1 subunit, which does not spin. Thus ATPase changes the chemical energy of the the proton motive force into the mechanical energy of the spinning rotor. It is this mechanical energy that brings ADP and inorganic phosphate into correct alignment to produce ATP. It requires between 2 and 3 Hydrogen ions to catalyze the production of 1 molecule of ATP. This means that each NADH has enough energy to make about 2.5 molecules of ATP from ADP through oxidative phosphorylation. All told, this yields around 30 molecules of ATP from 1 molecule of glucose, when the 2 ATP’s from Glycolysis are added in.

If you found this description confusing, check out this movie in which an actin fiber has been connected to the spinning rotor. You can also check out this movie or this one:

So, to sum it all up:

  • The proton motive force is generated by the process of pumping hydrogen ions from the matrix space into the intermembrane space.
  • The major source of high energy electrons for the electron transport chain is NADH from the Krebs Cycle.
  • The electron transport chain is responsible for pumping protons, and contains three major proton pumps, complex 1: NADH Dehydrogenase, Complex 3: Cytochrome bc1, and Complex 4: Cytochrome Oxidase.
  • The electron transport chain is made up of 60+ electron carriers, each which has a higher affinity for electrons than the last.
  • The de-energized electrons are deposited in the reduction of molecular oxygen to water. This accounts for 90% of the cells need for oxygen.
  • The proton motive force is used by ATP Synthase to spin its F0 subunit, generating mechanical force to catalyze the phosphorylation of ADP to ATP.
  • Each NADH provides enough energy to catalyze the phosphorylation of about 2.5 molecules of ADP.
  • Well that is all for this post. Thanks for stopping by. The information for this post was attained from Alberts’ Molecular Biology of the Cell, and the Friday, October 19th lecture by Dr. Todd Rosentiel.

    Previous Relevant Posts: Mitochondria Pt. 1 — Structure

    The Mitochondrion Pt. 1 — Structure and Layout

    Posted in Cell Biology at 3:59 am by D. Borst

    So we learned in grade school that the mitochondria is the cell’s energy powerhouse. Lets expand upon that a little bit.

    Mitochondria (along with chloroplasts and other plastids) are thought to have originally been independent entities. As such, they had their own DNA, the remains of which can be found in the mitochondria in our cells. It is thought that originally a mitochondria was endocytosed but never fully digested by a early pre-eucaryote. Over time, mitochondria have come to develop a symbiotic relationship with eucaryotic cells, to the point where all but a handful of the mitochondiral genome is now present in the host genome. The mitochondria in turn provides its host cell with incredibly large ammounts of ATP by processing Acetyl-CoA in the Krebs Cycle.

    There are two views of the noble mitochondria, one in which it is a small, rigid little bean shaped organelle that is somewhat static in its shape and size, and the other, more recently supported view that the mitochondria is a dynamic and quickly changing organelle. Mitochondria are now thought to quickly change conformation, bind and split with other mitochondria, and in some case form one huge reticulated super entity. Two theories attempt to explain our earlier oversight:

  • One is that when isolating the parts of the cell, the contents were disrupted in order to get them out of the plasma membrane. However, this disruption also caused the mitochondrial membrane to be split in many places leading to smaller mitochondria to be characterized by explorers.
  • The other theory has to do with or techniques for looking at the cell, and how they are based upon actual or optical sectioning of the cell (i.e. physically sectioning or by using a particular focusing plane, which led to the observation of individual small mitochondria that were connected out of the section.
  • In any case, the new model suggests that mitochondria are much more fluid and less bean shaped than what you may see in your textbook, so remember that.

    Structure of Mitochondria

    The structure of the mitochondria is one of the important epigenetic features of the cell. Cells in which mitochondria or chloroplasts have been ”zapped” are not able to reconstruct the mitochondria. Rather the information to construct mitochondria seems to be contained within the structure of the mitochondria themselves. The mitochondria somehow, and Im not clear on the details, replicate themselves without being directly reliant upon cell machinery. Similarly, mitochondria are not regulated during the cell cycle, but it is just a matter of brownian motion that all cells splitting off get some mitochondria. The mitochondria then regulate their own replication (or expansion in the case of the reticulated mitochondrial super entity.

    Mitochondria have two membranes, an outer and an inner. The outer membrane has a whole bunch of porin transporter molecules that allow molecules of 5 kd or less to easily diffuse across the membrane. It, along with the inner membrane, forms a intermembrane space that is semicontinuous with the cytosol. This semi-continuity is important for the proton gradient that is generated across the inner membrane. The outer membrane of the mitochondria has proteins responsible for fatty acid elongation.

    The inner membrane is solid, and jam packed full of proteins. It is estimated that there is one protein for every 3 lipid molecules in the inner membrane. The inner membrane contains special lipid molecules termed ‘cardiolipids.’ These lipids have four fatty acid tails rather than the two that most membrand lipids have. It is continuous with itself, and forms an inner “matrix space” where the more important processes to energy production occur. This matrix space also contains the remains of the mitochondria’s own DNA, which because the mitochondria is highly conserved, has been useful for relatedness studies, i.e. mitochondrial eve. The inner membrane is also much longer than the outer membrane, making it fold back in upon itself to form long christae that protrude into the matrix space. This structure increases the surface area of the membrane, allowing a greater number of worker proteins to exist. ATP production is located on this inner membrane, so a greater surface area yields more possibilities for production. As will be discussed later, ATP production is driven by a proton gradient that is established across this membrane the electron transport process. Cardiolipids are thought to make this membrane more impermeable to protons because of their four tails.

    So to remember:

  • Mitochondria may have originally been free organisms that have been engulfed by proto-eucaryotes.
  • Mitochondra form dynamic entities within animal cells, quickly combining with other mitochondria to form large and irregular reticulated organelles.
  • Cells cannot make mitochondria de novo, they must inherit them from their progenitors and allow them to reproduce.
  • Mitochondria have two membranes, an outer membrane that has many porin channels within it, and a inner membrane that has special cardiolipids that make it a good barrier to protons.
  • The inner membrane of the mitochondria is the site of much of the cells ATP production.
  • That is all for this segment. The information for this post came from two sources–either Alberts’ Molecular Biology of the Cell, or the October 17 Cell Biology lecture by Dr. Todd Rosentiel at PSU.

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