Mitochondrial dysfunction 

Mitochondria are best known as the powerhouses of our cells since they produce the cell's energy. But they also lead the genetic orchestra which regulates how every cell ages, divides, and dies. They help dictate which genes are switched on or off in every single cell of our organism. They also provide the fuel needed to make new brain connections, repair and regenerate our bodies. 

Whether we are housewives, sportsmen or labor people, energy is a topic that concerns us all, every day and in every way. Our well being, behavior and ability to perform the tasks in front of us to do is our individual measure of energy. But how we derive energy from the foods that we eat? 

There are many man-made myths surrounding energy production in the body and which foods supply energy. Mainstream science says that carbohydrates are what mitochondria use as fuel for energy production. This process is called oxidative metabolism because oxygen is consumed in the process. The energy produced by mitochondria is stored in a chemical "battery", a unique molecule called adenosine triphosphate (ATP). Energy-packed ATP can then be transported throughout the cell, releasing energy on demand of specific enzymes. In addition to the fuel they produce, mitochondria also create a by-product related to oxygen called reactive oxygen species (ROS), commonly known as free radicals. But what we are not told is that mitochondria were specifically designed to use fat for energy, not carbohydrate.

Source: Christian B. Allan, PhD and Wolfgang Lutz, MD, Life Without Bread. 

There are several very complicated steps in making ATP within mitochondria, but a look at 5 major parts of ATP production will be all that you need to know in order to understand how energy is created within our mitochondria and why fats are the key to optimize their function. Don't get focused on specific names, just try to see the whole picture. 

Step 1 - Transportation of Food-Based Fuel Source into the Mitochondria 

Fuel must first get into the mitochondria where all the action happens. Fuel can come from carbs or it can come from fats. Fatty acids are the chemical name for fat, and medium and large sized fatty acids get into the mitochondria completely intact with the help of L-carnitine. Think of L-carnitine as a subway train that transports fatty acids into the mitochondria. L-carnitine (from the Greek word carnis means meat or flesh) is chiefly found in animal products. 

Fuel coming from carbs needs to get broken down first outside the mitochondria and the product of this breakdown (pyruvate) is the one who gets transported inside the mitochondria, or it can be used to produce energy in a very inefficient way outside the mitochondria through anaerobic metabolism which produces ATP when oxygen is not present. 

Step 2 - Fuel is Converted into Acetyl-CoA 

When pyruvate - the product of breaking down carbs - enters the mitochondria, it first must be converted into acetyl-CoA by an enzymatic reaction. 

Fatty acids that are already inside the mitochondria are broken down directly into acetyl-CoA in what is called beta-oxidation. 

Acetyl-CoA is the starting point of the next step in the production of ATP inside the mitochondria. 

Step 3 - Oxidation of Acetyl-CoA and the Krebs Cycle 

The Krebs cycle (AKA tricarboxylic acid cycle or citric acid cycle) is the one that oxidizes the acetyl-CoA, removing thus electrons from acetyl-CoA and producing carbon dioxide as a by-product in the presence of oxygen inside the mitochondria. 

Step 4 - Electrons Are Transported Through the Respiratory Chain 

The electrons obtained from acetyl-CoA - which ultimately came from carbs or fats - are shuttled through many molecules as part of the electron transport chain inside the mitochondria. Some molecules are proteins, others are cofactors molecules. One of these cofactors is an important substance found mainly in animal foods and it is called coenzyme Q-10. Without it, mitochondrial energy production would be minimal. This is the same coenzyme Q10 that statins drug block producing crippling effects on people's health. Step 4 is also where water is produced when oxygen accepts the electrons. 

Step 5 - Oxidative phosphorylation 

As electrons travel down the electron transport chain, they cause electrical fluctuations (or chemical gradients) between the inner and outer membrane in the mitochondria. These chemical gradients are the driving forces that produce ATP in what is called oxidative phosphorylation. Then the ATP is transported outside the mitochondria for the cell to use as energy for any of its thousands of biochemical reactions. 

But why is fat better than carbs? 

If there were no mitochondria, then fat metabolism for energy would be limited and not very efficient. But nature provided us during our evolution with mitochondria that specifically uses fat for energy. Fat is the fueled that animals use to travel great distances, hunt, work, and play since fat gives more packed-energy ATPs than carbs. Biochemically, it makes sense that if we are higher mammals who have mitochondria, then we need to eat fat. Whereas carb metabolism yields 36 ATP molecules from a glucose molecule, a fat metabolism yields 48 ATP molecules from a fatty acid molecule inside the mitochondria. Fat supplies more energy for the same amount of food compared to carbs. But not only that, the burning of fat by the mitochondria - beta oxidation - produces ketone bodies that stabilizes overexcitation and oxidative stress in the brain related to all its diseases, it also causes epigenetic changes that produce healthy and energetic mitochondria and decreasing the overproduction of damaging and inflammatory free radicals among many other things!

Mitochondria regulate cellular suicide, AKA apoptosis, so that old and dysfunctional cells which need to die will do so, leaving space for new ones to come into the scene. But when mitochondria function becomes impaired and send signals that tell normal cells to die, things go wrong. For instance, the destruction of brain cells leads to every single neurodegenerative condition known including Alzheimer's disease, Parkinson's disease and so forth. Mitochondrial dysfunction has wide-ranging implications, as the health of the mitochondria intimately affects every single cell, tissue and organ within your body.

The catalysts for this destruction is usually uncontrolled free radical production which cause oxidative damage to tissues, fat, proteins, DNA; causing them to rust. This damage, called oxidative stress, is at the basis of oxidized cholesterol, stiff arteries (rusty pipes) and brain damage. Oxidative stress is a key player in dementia as well as autism. 

We produce our own anti-oxidants to keep a check on free radical production, but these systems are easily overwhelmed by a toxic environment and a high carb diet, in other words, by today's lifestyle and diet. 

Mitochondria also have interesting characteristics which differentiate them from all other structural parts of our cells. For instance, they have their own DNA (referred as mtDNA) which is separate from the widely known DNA in the nucleus (referred as n-DNA),. Mitochondrial DNA comes for the most part from the mother line, which is why mitochondria is also considered as your feminine life force. This mtDNA is arranged in a ring configuration and it lacks a protective protein surrounding, leaving its genetic code vulnerable to free radical damage. If you don't eat enough animal fats, you can't build a functional mitochondrial membrane which will keep it healthy and prevent them from dying. 

If you have any kind of inflammation from anywhere in your body, you damage your mitochondria. The loss of function or death of mitochondria is present in pretty much every disease. Dietary and environmental factors lead to oxidative stress and thus to mitochondrial injury as the final common pathway of diseases or illnesses. 

Autism, ADHD, Parkinson's, depression, anxiety, bipolar disease, brain aging are all linked with mitochondrial dysfunction from oxidative stress. Mitochondrial dysfunction contributes to congestive heart failure, type 2 diabetes, autoimmune disorders, aging, cancer, and other diseases. 

Whereas the nDNA provides the information your cells need to code for proteins that control metabolism, repair, and structural integrity of your body, it is the mtDNA which directs the production and utilization of your life energy. A cell can still commit suicide (apoptosis) even when it has no nucleus nor nDNA. 

Because of their energetic role, the cells of tissues and organs which require more energy to function are richer in mitochondrial numbers. Cells in our brains, muscles, heart, kidney and liver contain thousands of mitochondria, comprising up to 40% of the cell's mass. According to Prof. Enzo Nisoli, a human adult possesses more than ten million billion mitochondria, making up a full 10% of the total body weight.[9] Each cell contains hundreds of mitochondria and thousands of mtDNA. 

Since mtDNA is less protected than nDNA because it has no "protein" coating (histones), it is exquisitely vulnerable to injury by destabilizing molecules such as neurotoxic pesticides, herbicides, excitotoxins, heavy metals and volatile chemicals among others. This tips off the balance of free radical production to the extreme which then leads to oxidative stress damaging our mitochondria and its DNA. As a result we get overexcitation of cells and inflammation which is at the root of Parkinson's disease and other diseases, but also mood problems and behavior problems. 

Enough energy means a happy and healthy life. It also reflects in our brains with focused and sharp thinking. Lack of energy means mood problems, dementia, and slowed mental function among others. Mitochondria are intricately linked to the ability of the prefrontal cortex - our brain's captain- to come fully online. Brain cells are loaded in mitochondria that produce the necessary energy to learn and memorize, and fire neurons harmoniously. 

The sirtuin family of genes works by protecting and improving the health and function of your mitochondria.[10] They are positively influenced by a diet that is non-glycating, i.e. a low carb diet as opposed to a high carb diet which induces mitochondrial dysfunction and formation of reactive oxygen species. 

Another thing that contributes to mitochondrial dysfunction is latent viral infection such as the ones of the herpes family. As I mentioned in On Viral "Junk" DNA, a DNA Enhancing Ketogenic Diet, and Cometary K..., most, if not all of your "junk" DNA has viral-like properties. If a pathogenic virus takes hold of our DNA or RNA, it could lead to disease or cancer. 

Herpes simplex virus is a widespread human pathogen and it goes right after our mitochondrial DNA. Herpes simplex virus establishes its latency in sensory neurons, a type of cell that is highly sensitive to the pathological effects of mt DNA damage. 
[11] A latent viral infection might be driving the brain cell loss in neurodegenerative diseases such as Alzheimer's disease.[12] As I speculated in Heart attacks, CFS, herpes virus infection and the vagus nerve , a latent herpes virus infection might drive more diseases than we would like to admit. 

Members of the herpes virus family (i.e. cytomegalovirus and Epstein-Barr virus which most people have as latent infections!), can go after our mitochondrial DNA, causing neurodegenerative diseases by mitochondrial dysfunction. But a ketogenic diet is the one thing that would help stabilize mtDNA since mitochondria runs the best on fat fuel. As it happens, Alzheimer's disease is the one condition where a ketogenic diet has its most potential healing effect.[4] 

The role of mitochondrial dysfunction in our "modern" age maladies is a staggering one. Optimal energetic sources are essential if we are to heal from chronic ailments. It is our mitochondria which lies at the interface between the fuel from foods that come from our environment and our bodies' energy demands. And it is a metabolism based on fat fuel, a ketone metabolism, the one which signals epigenetic changes that maximizes energetic output within our mitochondria and help us heal.

I am incredulous at how my body is responding. I think I am totally carb intolerant. I've struggled with extreme fatigue/exhaustion for so many years, even with improved sleep in a dark room that I can't tell you how wonderful it is to wake up in the morning, get out of bed and not long to crawl back in, going through the day by will mostly. Also chronic long-standing intestinal issues are finally resolving. A couple of people at work have made comments to the effect that I'm a "different woman", calmer, no more hyperness under pressure, stress seems to roll off of my back as well. I've lost a little weight and although I don't weigh myself, my clothes are definitely looser. I've had the round middle for so many years I was resigned to struggling to bend over to pull my shoes on! -Bluefyre, 56 years old, United States. Sott.net forum