mitochondrial matrix

Citric Acid Cycle

The citric acid cycle (sometimes called the Krebs cycle) occurs in the mitochondrial matrix and is the third stage in the aerobic breakdown of glucose. The first, of course, is glycolysis, which creates pyruvate, NADH, and ATP. The second—which isn’t long enough to get its own post—is the linking reaction in which pyruvate is converted to Acetyl CoA. This is a coenzyme that the citric acid cycle breaks down to use later in energy production. Basically, the purpose of the linking reaction is to make pyruvate into something the cycle can use.

The main goal of the citric acid cycle is to convert bond energy (in the form of Acetyl CoA) into its reducing equivalents: i.e., to make some more NADH and FADH2, which are electron carriers. These then go through the electron transport chain and use their electron energy to create ATP. Remember, to reduce a compound is to add electrons to it—think of the mnemonic OILRIG.

So, how does the citric acid cycle do this?

Some diagrams get pretty complicated, especially when you include the enzymes responsible and the carbon compounds formed at every stage, but I’m going to break it into relatively simple steps.

  1. An enzyme joins acetyl-CoA to oxaloacetate in order to form citric acid, which is where the cycle gets its name. Then, a water molecule “attacks” the acetyl, and CoA is ejected from the cycle.
  2. Next, water is ejected and then put back in to help facilitate the reduction of NAD+ into NADH. For every turn of the cycle, 3 NADH molecules are created, and 2 molecules of CO2 are released.
  3. ADP plus a free phosphate group (denoted as “Pi”) is put into the cycle, and these are smushed together to form an ATP.
  4. Finally, FAD+ is reduced to FADH2. (FAD and NAD are both very similar coenzymes, performing the same oxidative and reductive roles in a reaction, but they’re different because they work on different classes of molecules: FAD oxidises carbon-carbon bonds, and NAD oxidises carbon-oxygen bonds)

A diagram might make it a little clearer:

So, let’s do a quick round-up of what’s happened:

  • Acetyl-CoA has been released as two CO2 molecules
  • 3 NAD+ were reduced to 3 NADH
  • 1 FAD+ was reduced to 1 FADH2
  • 1 ADP+Pi formed 1 ATP molecule

This isn’t the end—the main goal of citric acid cycle is to prepare the electron carriers NADH and FADH2 for the electron transport chain, where much more ATP will be made.

Onwards to the ETC!

Further resources: Khan Academy: Krebs Cycle

Scientists Keep a Molecule from Moving Inside Nerve Cells to Prevent Cell Death

Amyotrophic lateral sclerosis (ALS, or Lou Gehrig’s disease) is a progressive disorder that devastates motor nerve cells. People diagnosed with ALS slowly lose the ability to control muscle movement, and are ultimately unable to speak, eat, move, or breathe. The cellular mechanisms behind ALS are also found in certain types of dementia.

A groundbreaking scientific study published in Nature Medicine has found one way an RNA binding protein may contribute to ALS disease progression. Cells make RNA to carry instructions for making proteins from DNA to protein-constructing machinery.

The culprit protein, TDP-43, normally binds to small pieces of newly read RNA and helps shuttle the fragments around inside nerve cell nuclei. The study describes for the first time the molecular consequences of misplaced TDP-43 inside nerve cells, and demonstrates that correcting its location can restore nerve cell function. Misplacement of TDP-43 in nerve cells is a hallmark of ALS and other neurological disorders including frontotemporal dementia (FTD), Alzheimer’s, Parkinson’s, and Huntington’s diseases. Studies that characterize common mechanisms behind these diseases could have widespread implications and may also accelerate development of broad-based therapies.

To find the misplaced TDP-43, the researchers viewed nerve cells donated by people who died from ALS or FTD under high powered microscopes. They discovered TDP-43 accumulates in nerve cell mitochondria, critical structures responsible for generating the enormous amount of energy nerve cells require. By physically isolating the affected mitochondria the researchers were able to pinpoint TDP-43’s exact location inside the subcellular structures. They were also able to characterize variations of the protein most likely to get misplaced.

This important work was led by Xinglong Wang, PhD, from the department of pathology at Case Western Reserve University School of Medicine and a team of scientists from his laboratory.

“By multiple approaches, we have identified the mitochondrial inner membrane facing matrix as the major site for mitochondrial TDP-43,” explained Wang. “Mitochondria might be major accumulation sites of TDP-43 in dying neurons in various major neurodegenerative diseases.”

The researchers discovered that once inside the mitochondria, TDP-43 resumes its RNA binding role and attaches itself to mitochondrial genetic material. This disrupts the mitochondria’s ability to generate energy for the cell. Wang’s team was able to precisely identify the RNA in mitochondria that was bound by TDP-43 and observe the resultant disassembly of mitochondrial protein complexes. This finding provides much needed clarity on the consequences of TDP-43 misplacement inside nerve cells and opens the door for deeper studies involving a range of neurological disorders. Although the study focused on ALS and FTD, according to Wang “mislocalization of TDP-43 represents a key pathological feature correlating strongly with symptoms in more than half of Alzheimer’s disease patients.”

Mutations in the gene encoding TDP-43 have long been linked to neurodegenerative diseases like ALS and FTD. Wang’s team found that disease-associated mutations in TDP-43 enhance its misplacement inside nerve cells. The researchers also identified sections of TDP-43 that are recognized by mitochondria and serve as signals to let it inside. These sections could serve as therapeutic targets, as the study found blocking them prevents TDP-43 from localizing inside mitochondria. Importantly, Wang’s team was able to keep TDP-43 out of nerve cell mitochondria in mice using small proteins which “almost completely” prevented nerve cell toxicity and disease progression.

“We, for the first time, provide the novel concept that the inhibition of TDP-43 mitochondrial localization is sufficient to prevent TDP-43-linked neurodegeneration,” said Wang. “Targeting mitochondrial TDP-43 could be a novel therapeutic approach for ALS, FTD and other TDP-43-linked neurodegenerative diseases.”

Wang has begun to develop small proteins that prevent TDP-43 from reaching mitochondria in human nerve cells, and has a patent pending for the therapeutic molecule used in the study.

There is no treatment currently available for ALS or FTD. The average life expectancy for people newly diagnosed with ALS is just three years, according to The ALS Association.