The Mitochondria: BioVisions Video/Explanations

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The Mitochondria: BioVisions Video/Explanations

Postby BioWizard on March 29th, 2014, 12:24 pm 

Here is the second BioVisions video depicting a mitochondrion inside the cell carrying out the process of oxidative phosphorylation, leading to the production of ATP - the cell's energy currency. And below are captions of every scene along with a brief synopsis (better late than never). If you have any comments, questions, corrections, etc, please feel free to post them here.




Scene by scene explanation:

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The video opens with a mitochondrion gliding along an organized network of of microtubules. The microtubles appear to be directionally arranged, with the mitochondrion being transported unidirectionally. In the distance, you see a two more mitochondria being transported in the same direction. This indicates active transport of mitochondria towards a location in the cell where there are high energy demands. This transport occurs when mitochondria associate with motor proteins that undergo anterograde or retrograde movement along the microtubule highways. You also see some Glogi stacks (right), and what I suspect is the nucleus and some ER folds above it (left).


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here you see a protein destined for mitochondrial delivery gliding along the outer mitochondrial membrane (OMM). The protein is bound to three chaperon proteins which stabilize it meanwhile its being delivered and possibly target it for the correct transport channel.


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Once the protein arrives at the membrane channel that will transport it into the mitochondrion, a signal peptide on the protein is recognized and threaded into the channel. The rest of the protein follows, and the chaperon molecules fall off as the entire polypeptide chain snakes through the opening. Such transport channels in the outer membrane are called TOMs, and those in the inner membrane are called TIMs.


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Here you see the protein being transported across the OMM, and then further through the inner mitochondrial membrane (IMM).


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After taking a little stroll in the inter membrane region (remember mitochondria has two membranes, OMM and IMM), we arrive at yet another protein being snaked across the outer and inner membranes. This time, the camera follows the protein through the channel in the inner membrane, and allows us to finally enter the lumen of the mitochondrion.


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Once inside the matrix, we see a large variety of proteins floating around. A lot of these proteins are presumably enzymes of the Tricarboxylic Acid (TCA) cycle (Also known as Kreb's cycle). This is the pathways that takes glucose metabolites produced from glycolysis, and then uses them to produce reduced NADH and FADH2. These nucleotides pick up electrons and protons stripped off in the TCA cycle and carry them over to the Electron Transport Chain (ETC) proteins, where the oxidative phosphorylation process if continued. You also notice a strand of DNA double helix. This is part of the mitochondrion's chromosome, with like it's bacterial ancestors, is circular. You see another part of this circle back in the "distance".


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We encounter this structure and we go through it. I'm not 100% sure what it is, though to me is looks like a HSP complex, which is a complex of proteins that help other proteins to fold. Perhaps this is here to remind us that mitochondria still carry out some protein synthesis of their own genes inside them, the way their ancestral cells (possibly alpha proteobacteria) used to do independent of the eukaryotic cell that currently host them.


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As we venture around, we encounter the ETC proteins lining the inside of the IMM.


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This is either Complex I or Complex II, the first entry points for electrons into the ETC. Complex one will extract electrons from NADH, while Complex II will extract them from FADH2. The electrons are passed on through the membrane (via CoQ) to a neighboring complex III.

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Complex III picks up the electrons and reduces a molecule of Cytochrome C floating on the opposite side of the inner membrane (so in the intermembrane region). Reduced Cytochrome C glides over to a neighboring Complex IV. There it passes the electrons on the to Complex, which uses them to reduce Oxygen to H2O (and this is why we breathe O2 - it acts as an electron sink, which in effect drives this entire process and is therefor called oxidative phosphorylation).


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And now we get to the beast that is Complex V. Complex V is where the magic happens. Complex V has two main parts, one that runs across the inner membrane (this is the one that you see rotating), and one that hangs out on the inside of the mitochondrion. As Complexes I, II, and IV pass electrons through them, they also pump out protons (H+) from inside the mitochondrion, to the opposite side of the inner membrane (so the protons linger in the intermembrane space and create a gradient: the extra concentration of protons on the outer side of the inner membrane vs the lower concentration of protons on the inner side of the inner membrane - so the mitochondria's gut, or matrix). This gradient makes the protons "want" to run down the gradient back towards the inside (where it is slightly negatively charged now), and one place they are able to do so is through Complex V. As they rush through the membrane part of Complex V, they cause it to turn.


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As the "rotor" of complex V turns, it causes structural changes in the part that hangs out inside the mitochondrion. This transfer of energy is what allows the inner part of the Complex to combine one ADP and one Phosphate ion to make ATP. So you see the ADP coming in (drab greenish orange), get converted to ATP (bright orange), then leaves the complex.


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Nearby, an ADP/ATP exchange channel spits out one ATP molecule for each ADP molecule that goes into the mitochondrion. The ATP is now outside the inner membrane, and can leak out through the outer membrane into the cell to serve as energy currency for most cellular processes.


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Finally, you see the destination where all these mitochondria are headed. It seems to be a location with much activity going on, with some filaments forming, and lots of endo or exo cytosis happening in distance. My guess here is that these mitochondria are being transported along a cellular processes (such as a neurite), where they are provide necessary energy required for further growth, or performing some energy demanding function.


And finally, here's a summary of the ETC chain for reference:
phosphoralytion_.jpg
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Re: The Mitochondria: BioVisions Video/Explanations

Postby SciameriKen on March 29th, 2014, 2:50 pm 

Fantastic write up Bio -- as I look at this I notice the creators are portraying the environment of ultra-slowed down molecular interactions behaving as if they were sea creatures in an aquarium. Do you think this is a correct dipiction?
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Re: The Mitochondria: BioVisions Video/Explanations

Postby Paralith on March 29th, 2014, 2:55 pm 

Great write up Bio! Thanks so much for taking the time to do this.
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Re: The Mitochondria: BioVisions Video/Explanations

Postby BioWizard on March 29th, 2014, 4:49 pm 

SciameriKen » 29 Mar 2014 02:50 pm wrote:the creators are portraying the environment of ultra-slowed down molecular interactions behaving as if they were sea creatures in an aquarium. Do you think this is a correct dipiction?


Excellent point SciKen. We covered this in the thread discussing the previous video, but it's important enough to mention it here as well. The truth is that some things were slowed down while other things were sped up (relatively speaking) for cinematographic purposes. Also, there are a lot of things that are depicted to translocate directly between points A and B, but in reality the trajectories are rather stochastic (Brownian motion and all). They also removed all the water molecules, since these wouldn't be entirely transparent at that scale and you wouldn't be able to see well through them.
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Re: The Mitochondria: BioVisions Video/Explanations

Postby Page370 on August 12th, 2014, 6:33 am 

Thank You!
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Re: The Mitochondria: BioVisions Video/Explanations

Postby Atique on February 28th, 2015, 2:21 pm 

can you share the video of above mentioned topic. thanks
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Re: The Mitochondria: BioVisions Video/Explanations

Postby BioWizard on February 28th, 2015, 6:09 pm 

Atique » 28 Feb 2015 01:21 pm wrote:can you share the video of above mentioned topic. thanks


It's included in the first post. Click on the video insert and it should start playing. I just tested it on my phone - it still works.
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Re: The Mitochondria: BioVisions Video/Explanations

Postby neuro on March 2nd, 2015, 6:07 am 

Great job, Bio.
I'd just add that though mitochondria do travel as isolated entities, as shown here, to other locations in the cell, our current view is that they generally are not peanut-shaped things, but most of the time they constitute a reticulum, which they may detach from or fuse back with, and this is an important aspect, so that worn out "pieces" of the network can detach as single mitochondria and be degraded, thereby permitting the mitochondrial network to turnover and get continuously renewed, as all other elements in the cell do...

Thanks.
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Re: The Mitochondria: BioVisions Video/Explanations

Postby BioWizard on March 2nd, 2015, 9:36 am 

neuro » 02 Mar 2015 05:07 am wrote:Great job, Bio.
I'd just add that though mitochondria do travel as isolated entities, as shown here, to other locations in the cell, our current view is that they generally are not peanut-shaped things, but most of the time they constitute a reticulum, which they may detach from or fuse back with, and this is an important aspect, so that worn out "pieces" of the network can detach as single mitochondria and be degraded, thereby permitting the mitochondrial network to turnover and get continuously renewed, as all other elements in the cell do...

Thanks.


Very true, neuro.
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