Change Your Biochemistry to Change Your Health

Article at-a-glance:

  • Biochemistry is how the body uses nutrients.
  • Unlike genetics, diet, our environment and even what we think changes our biochemistry.
  • Symptoms that don’t always seem connected actually are when you evaluate them through the lens of the body’s biochemistry.
  • This article is an extract from Dr. Neustadt’s Amazon Top 100 book, A Revolution in Health Through Nutritional Biochemistry.

by Dr. John Neustadt

Unlike genetics, which we’re born with and can’t change, our environment, what we eat and even what we think alters our biochemistry. Biochemistry is the process by which your body uses. Nutrients turn on and off genes, are used to repair DNA and creates the chemical reactions that allow our bodies to thrive.

These nutrients include vitamins, minerals, amino acids, fats and non-vitamin phytonutrients. Our bodies exist in a web of interactions among biochemical pathways and body systems. Since biochemistry is a web of interactions and a single nutrient can be used for hundreds of different activities in the body, nutrient deficiencies can disrupt biochemical function and cause symptoms that don’t always seem connected.

This article introduces basic concepts in biochemistry and nutrition that will help you when discussing diseases, thinking about ways in which you can improve your diet, considering which dietary supplements to take and possible options with your healthcare provider.

Amino Acids

Amino acids are composed simply of carbon, oxygen, hydrogen, nitrogen, and sometimes sulfur. They are the building blocks of proteins. Proteins contain multiple amino acids strung together like letters of an alphabet. These letters (amino acids) can be combined in almost an infinite number of ways to produce the diversity of proteins seen in humans.

People produce about five hundred thousand different proteins, which act as hormones to control mood, energy, and appetite; connective tissue such as skin, hair, and nails; and muscles. For example, phenylalanine is an amino acid. Phenylalanine travels down its pathway to produce tyrosine, dopamine, and epinephrine. It also produces niacin (vitamin B3), thyroid hormones, and melanin, a skin pigment.

You may see phenylalanine sometimes on a food or dietary supplement label with the warning, “Phenylketonurics—contains phenylalanine.” Phenylketonuria (PKU) is a disorder is screened for at birth and has an incidence of 1 in 10,000. People with this condition have difficulty transforming phenylalanine to tyrosine. Phenylalanine, therefore, accumulates in the blood and causes mental and physical retardation.

Phenylalanine is found in all protein foods, and neonates diagnosed with this condition are placed on a phenylalanine-restricted diet and supplemented with tyrosine, vitamins, minerals, and other amino acids. While effective, maintaining this severely limited diet is quite difficult in school-age children, it leads to socially awkward situations for adults, and it is complicated in pregnant women. Fortunately, as you will discover reading this book, the problem in people with phenylketonuria is simply a problem with inefficient transformation of phenylalanine to tyrosine. The enzyme (protein that facilitates a biochemical reaction) that converts phenylalanine to tyrosine in many people with PKU still functions, although inefficiently.

Since 1999, several clinical trials have reported positive results in decreasing serum phenylalanine in people with this condition by administering pharmacological doses of tetrahydrobiopterin (BH4), a nutrient required for this enzyme to function. In one small study involving five children, serum phenylalanine concentrations declined in four of five of them with a loading dose of ten milligrams of BH4 per kilogram body weight. A larger study conducted in 2002 showed that BH4 significantly lowered phenylalanine in 87% of the children by as much as 92%. Infants and children with this disorder should now also be tested for their responsiveness to BH4 therapy, as it may allow many of them to consume a less restrictive diet and some to even cease the therapeutic diet altogether.

What this study showed is that even in seemingly severe genetic conditions, there may be some enzyme activity that can be stimulated with pharmacologic dosages of nutrients, and diseases once viewed as incurable may, in fact, be ameliorated with nutrients. This study also reminds the authors of an observation by Roger Williams, PhD, in 1956, when he wrote, “Whenever an extreme genetic character appears in an individual organism, it should be taken as an indication (unless there is proof to the contrary) that less extreme and graduated genetic characters of the same sort exist in other individual organisms.”


Vitamins are nutrients required for essential metabolic reactions in the body. Vitamins are divided into two general categories—fat-soluble and water-soluble. The fat-soluble group includes vitamin A, D, K, and E. Fat-soluble vitamins are better absorbed when ingested with some fat and can be stored in fat within the body. The reason why fat-soluble vitamins are absorbed more effectively when you consume them with additional fat, as with a meal, is because fat causes the excretion of bile into the small intestines from the gallbladder. The bile surrounds the fat and makes it more absorbable by the small intestines. Fat-soluble vitamins can be stored in tissues, meaning that there is a risk for toxicity. For example, high dosages of vitamin A can cause liver damage in children and adults, and in pregnant women it can cause damage to fetuses.

Water-soluble vitamins include the B-complex vitamins—B1 (thiamin), B2 (riboflavin), B3 (niacin), B5 (pantothenic acid), B6 (pyridoxine), B12 (cobalamin) folic acid, and biotin—as well as vitamin C (ascorbic acid). Water-soluble vitamins do not need fat for absorption, and they also carry a much lower risk for toxicity. Water-soluble vitamins are not stored in fat and are excreted in the urine. The only water-soluble vitamins that carry any appreciable risk for toxicity are vitamins B3 and B6. If you get too much of the other water-soluble vitamins, you simply urinate them out. Vitamin B2 may cause a harmless yellowish-green discoloration to the urine.

Patients frequently ask whether or not they are absorbing the vitamins since they see their urine change color. They believe and have heard, that people shouldn’t take high doses of the water-soluble vitamins because they don’t absorb them. The simple answer is yes; they are absorbing them. In order for vitamins to appear in urine, people must absorb them through the intestines, where they enter the bloodstream, circulate through the body, and bathe cells with their nutrients prior to appearing in the urine. The cells will extract from the blood the amounts they need, and the excess appears in the urine.

The amount of these vitamins the body needs depends on many factors, including diet, stress, and ongoing infections. For example, one of the places in the body where vitamin C is most concentrated is in white blood cells. These cells comprise our immune system that protects us from bacteria and viruses. When people get a cold or flu, their bodies’ ability to absorb vitamin C from the bowels increases. That is, they find that when they’re sick they absorb up to tens times more vitamin C than when they’re healthy. This reflects the body’s ability to adapt to different situations that require different amounts of nutrients. To test this, people can do what’s called the Bowel Tolerance Test.

“To bowel tolerance” means that they take ever-increasing amounts of vitamin C, such as one thousand milligrams every hour for one day, then two thousand milligrams every hour for the next day, and so on, until their intestines cannot absorb any more. When this happens, they may experience some burning, loose stools, or watery diarrhea when they have a bowel movement. This signals that they’ve reached bowel tolerance and need to decrease the amount taken to the dose at which these discomforts did not appear. Bowel tolerance can vary from person to person and can be as low as one thousand milligrams per day when healthy and greater than ten thousand milligrams per day when sick.


Examples of minerals include calcium, magnesium, manganese, copper, zinc, selenium, iron, and vanadium. Except for calcium, which concentrates outside of cells, all other minerals are pumped into cells where they concentrate and do their work. For example, magnesium, which is required for more than three hundred biochemical reactions in the body, concentrates in cells where it is required for the generation of cellular energy, called adenosine triphosphate (ATP). Muscles also use magnesium to allow them to relax after a contraction, thereby explaining why a low magnesium level sometimes manifests itself as muscle cramps. Unfortunately, conventional medical labs only measure magnesium in the serum (the liquid portion of blood) and not intracellular magnesium, which gives a false impression that someone has normal magnesium when, in fact, their intracellular magnesium may be low. Many people have a deficiency in intracellular magnesium since it’s been estimated that 56% of people do not eat the recommended daily value of magnesium. Additionally, magnesium deficiency can cause DNA damage and may contribute to the development of cancer.

Selenium is used in the body for many different functions. One of its functions is to produce active thyroid hormone, T3, from the conversion of the inactive thyroid hormone, T4, in different tissues in the body. This conversion also requires zinc. This is important because symptoms of low thyroid function include fatigue, depression, weight gain, and low body temperature. Low thyroid function can also cause increased cholesterol, a risk factor for heart disease and stroke. However, conventional screening tests for thyroid function do not test for the actual thyroid hormones themselves or for selenium and zinc. Instead, the standard screening test for low thyroid function, called hypothyroidism, is a measurement of thyroid-stimulating hormone (TSH). TSH is actually produced in a region of the brain called the anterior pituitary gland, and its role is to stimulate the production T4 and T3 by the thyroid gland, which is located in the lower end of a person’s neck. Doctors find that people can have “functional hypothyroidism,” which means that their TSH and T4 levels are normal, but their T3 is low. People who only receive the conventional medical workup can experience fatigue, difficulty losing weight, and frequent coldness when the underlying cause may be low thyroid function because of low selenium or zinc.

Non-Vitamin Nutrients

In addition to the vitamins listed above, there are nutrients derived from plants, called phytonutrients (phyto means plant in Greek), which have specific beneficial properties. One class of these compounds, called flavonoids, are powerful antioxidants. An antioxidant “quenches” free radicals, which are unstable molecules that damage proteins, DNA, and cell membranes. A urine test measures free-radical damage to DNA, which is a risk factor for cancer. Free-radical damage to lipids (fats)is a risk factor for heart disease, and a blood test measures this condition. Free radicals are produced naturally as the byproducts of cellular processes, such as the production of cellular energy. Additionally, free radicals make up a vital component of the immune system since they are produced by white blood cells to kill viruses and bacteria.

Like everything in life, balance is the key. The body needs a certain amount of free radicals to function properly, but excessive free radicals cause diseases. Antioxidants keep free radicals in balance. These antioxidant molecules include flavonoids, vitamins A, C, and E, glutathione, alpha lipoic acid, and many others. They can donate an electron that neutralizes the free radical. By quenching free radicals, antioxidants stop them from doing additional damage to other molecules.

Flavonoids are found in high amounts in darkly pigmented fruits such as blueberries, blackberries, plums, and cherries; and also in vegetables. Flavonoids are more powerful antioxidants than vitamin C, and they can help increase the strength of blood vessels, decrease inflammation, and lower the risks for cancer and cardiovascular diseases. Frequently, the advice given to patients is to “eat a rainbow a day” of fruits and vegetables, meaning that people should eat a variety of differently colored, fresh whole fruits and vegetables each day to ensure an ample supply of phytonutrients. Additionally, when fresh fruit is not available, it can be helpful to purchase frozen fruits, such as cherries or blueberries, and eat a cup a day of frozen fruit.


While many people believe low-fat diets are healthy, the fact is that our bodies require fats for proper function. Fats make up 60% of the brain and central nervous system. The membranes that surround every cell are comprised of two layers of fats, called the lipid bilayer. These fats are involved in communication between cells and the production of hormones and other vital chemicals.

There are different classes of fats, including saturated and unsaturated fatty acids. The unsaturated fatty acids are further defined as omega-6 and omega-3 fatty acids. Modern diets that are high in animal meats are high in omega-6 fats and low in omega-3 fats. Omega-6 fatty acids can contribute to chronic degenerative diseases and promote inflammation. High amounts of omega-3 fatty acids are found in fish and plants, and they are considered anti-inflammatory and protective against some chronic, degenerative diseases such as cardiovascular disease. Saturated fats, another class of fatty acids, are found in beef and other land animals and can contribute to heart disease. Unsaturated fatty acids are liquid at room temperature while saturated fatty acids are solid at room temperature.

Diet and Nutrients

A discussion of nutrients would be incomplete without mentioning the role proper nutrition plays in our health. Food contains the vital nutrients required for our bodies to function, but there are several reasons why most people become deficient in nutrients as they age. One simple reason is that people do not eat an optimal diet. The Mediterranean Dietary Pattern has been studied for more than thirty years and has been shown repeatedly to reduce the risk of cancer, diabetes, cardiovascular disease, obesity, and premature death. This diet is essentially the opposite of the Standard American Diet (SAD) that promotes cancer, diabetes, cardiovascular disease, obesity, and premature death. The SAD diet is propagated by multi-million dollar advertising campaigns that convince people that eating processed foods and high amounts of beef is necessary and beneficial. This, in fact, is completely false. The Mediterranean Diet is a whole-foods, plant-based diet that stresses consuming whole grains, whole fruits and vegetables, and fish. It is low in saturated fat and high in fiber from complex carbohydrates.

A word about eggs

Eggs are excellent sources of protein and biotin, a water-soluble vitamin, and lutein and zeaxanthin, two fat-soluble vitamins that can help preserve eyesight. One egg contains approximately five grams of protein.

There is a misconception that eggs increase cholesterol. The fact is that ingestion of moderate amounts of eggs does not adversely affect lipid levels in the majority of patients. Instead, it is when eggshells are cracked and the yolk is scrambled that free radicals create problems. When egg whites and yolks are exposed to air and heat, such as when you make an omelet, the fats in the egg become rancid, and it’s just like eating a wonderfully delicious meal of free radicals that enter your body and cause damage to your blood vessels and other cells. On the other hand, hard-boiled eggs are good for you and do not contain the free radicals found in scrambled or fried eggs because the shell in hard-boiled eggs is left intact; therefore the egg yolk and egg white are not exposed to oxygen.

Fatty acids surround every cell in our bodies and are crucial for proper cell functions. There are two major classes of fatty acids—omega-3 fatty acids and omega-6 fatty acids. Omega-3 fatty acids are anti-inflammatory, while omega-6 fatty acids promote inflammation and heart disease. Omega-3 fatty acids are found in high amounts in plant oils and cold-water fish, while meats (e.g., beef) contain higher amounts of omega-6 fatty acids.Meat consumption in the Mediterranean Diet is monthly, while people following a SAD pattern of eating consume red meat multiple times each week. In most parts of the United States, this means eating farm-raised beef that was finished on corn and treated throughout its life with hormones and antibiotics. In contrast, wild game and meat that is hormone free, antibiotic free, and grass fed and grass finished contains a healthier profile of fatty acids than conventional meats.

Different concentrations of fatty acids exist in foods, and both omega-3 and omega-6 fatty acids are required for proper health. However, the SAD contains too much omega-6 fatty acid and too little omega-3 fatty acid. This unfavorable ratio promotes inflammation and plays an important role in many diseases such as heart disease and dementia. In short, the SAD is comprised mostly of processed foods and red meat and is high in saturated fat, simple sugars, and trans fats, and it is low in fiber.

Many food products in the American diet are inherently low in vitamins and minerals. For example, the conventional agricultural system in the United States has depleted the soils of vitamins and minerals, which are then not available for the plants to take up from the soils. The result, which has been confirmed in multiple studies, is that conventionally grown foods are lower in vitamins and minerals compared to organically grown foods.

A word about frozen versus fresh foods

In some instances, frozen foods may actually be healthier than “fresh” fruits and vegetables. This has to do with one simple rule: the farther fruits and vegetables have to travel from the farm to your table, the longer they have to degrade and spoil. The moment a fruit or plant is detached from the soil, it stops taking up nutrients and begins the sometimes slow, sometimes rapid, process of decaying and dying. During this process, nutrients are depleted. Therefore, in instances where fresh fruits and vegetables from a nearby farm are not available, frozen fruits and vegetables may be more nutritious because the process of freezing locks in nutrients, as long as the food is not processed first (that is, heat is not applied).

These deficiencies set in motion dysfunctions in biochemical pathways that cause chronic, degenerative conditions such as cardiovascular disease, and they parallel the extremely common deficiencies detected by laboratory panels that test for vitamin and mineral deficiencies.Processed foods such as white rice, pasta, potato chips, and baked goods that use white flour are nearly devoid of vitamins and minerals. These foods are consumed in large quantities in the United States and are a cause of nutritional deficiencies. For example, about 85% of magnesium and 60% of calcium are lost during the process of refining wheat to make white flour for breads, muffins, cookies, and pizza dough. The naturally occurring nutrients are stripped out during the processing of these foods by removing the most nutrient-dense portion of the grain and applying heat during the manufacturing process that destroys vitamins.

Agte V, Tarwadi K, Mengale S, Hinge A, Chiplonkar S. Vitamin profile of cooked foods: how healthy is the practice of ready-to-eat foods? International journal of food sciences and nutrition. 2002;53(3):197-208. [Article]

Ames BN. Low micronutrient intake may accelerate the degenerative diseases of aging through allocation of scarce micronutrients by triage. PNAS. 2006;103(47):17589-17594. [Article]

Arts IC, Hollman PC. Polyphenols and disease risk in epidemiologic studies. Am J Clin Nutr. 2005;81(1):317S-325. [Article]

Aviram M, Dornfeld L, Kaplan M, et al. Pomegranate juice flavonoids inhibit low-density lipoprotein oxidation and cardiovascular diseases: studies in atherosclerotic mice and in humans. Drugs Exp Clin Res. 2002;28(2-3):49-62. [Article]

Aviram M, Fuhrman B. LDL oxidation by arterial wall macrophages depends on the oxidative status in the lipoprotein and in the cells: role of prooxidants vs. antioxidants. Mol Cell Biochem. 1998;188(1-2):149-159. [Article]

Banks RE, Dunn MJ, Hochstrasser DF, et al. Proteomics: new perspectives, new biomedical opportunities. Lancet. 2000;356(9243):1749-1756. [Article]

Berry MJ, Larsen PR. The role of selenium in thyroid hormone action. Endocr Rev. 1992;13(2):207-219. [Article]

Bralley J, Lord R. eds. Laboratory Evaluations for Integrative and Functional Medicine, 2d Edition. Duluth, GA: Metametrix Institute; 2008. [Book]

Bravo L. Polyphenols: chemistry, dietary sources, metabolism, and nutritional significance. Nutr Rev. 1998;56(11):317-333. [Article]

Bruckdorfer KR. Antioxidants, lipoprotein oxidation, and arterial function. Lipids. 1996;31 Suppl:S83-85. [Article]

Cathcart RF. The method of determining proper doses of vitamin C for the treatment of diseases by titrating to bowel intolerance. Australas Nurses J. 1980;9(4):9-13. [Article]

Cathcart RF. Vitamin C, titrating to bowel tolerance, anascorbemia, and acute induced scurvy. Med Hypotheses. 1981;7(11):1359-1376. [Article]

Cestaro B, Giuliani A, Fabris F, Scarafiotti C. Free radicals, atherosclerosis, ageing and related dysmetabolic pathologies: biochemical and molecular aspects. Eur J Cancer Prev. 1997;6 Suppl 1:S25-30. [Article]

Cordain L, Eaton SB, Sebastian A, et al. Origins and evolution of the Western diet: health implications for the 21st century. Am J Clin Nutr. 2005;81(2):341-354. [Article]

Donovan JL. Flavonoids and the risk of cardiovascular disease in women. Am J Clin Nutr. 2004;79(3):522-523. [Article]

Fernandez ML. Dietary cholesterol provided by eggs and plasma lipoproteins in healthy populations. Curr Opin Clin Nutr Metab Care. 2006;9(1):8-12. [Article]

Fung TT, Willett WC, Stampfer MJ, Manson JE, Hu FB. Dietary Patterns and the Risk of Coronary Heart Disease in Women. Arch Intern Med. 2001;161(15):1857-1862. [Article]

Gaby AR. Sub-laboratory hypothyroidism and the empirical use of Armour thyroid. Altern Med Rev. 2004;9(2):157-179. [Article]

Groff JL, Gropper SS. Advanced Nutrition and Human Metabolism. Third ed. Belmont: Wadsworth; 2000. [Book]

Harbige LS. Dietary n-6 and n-3 fatty acids in immunity and autoimmune disease. Proc Nutr Soc. 1998;57(4):555-562. [Article]

Hasler CM. The Changing Face of Functional Foods. J Am Coll Nutr. 2000;19(90005):499S-506. [Article]

Hickey S, Roberts H. Misleading information on the properties of vitamin C. PLoS Med. 2005;2(9):e307; author reply e309. [Article]

Hubbard RW, Ono Y, Sanchez A. Atherogenic effect of oxidized products of cholesterol. Prog Food Nutr Sci. 1989;13(1):17-44. [Article]

Jacob RA, Sotoudeh G. Vitamin C Function and Status in Chronic Disease. Nutrition in Clinical Care. 2002;5(2):66-74. [Article]

Jovanovic SV, Simic MG. Antioxidants in nutrition. Ann N Y Acad Sci. 2000;899:326-334. [Article]

Knekt P, Kumpulainen J, Jarvinen R, et al. Flavonoid intake and risk of chronic diseases. Am J Clin Nutr. 2002;76(3):560-568. [Article]

Kohrle J. The deiodinase family: selenoenzymes regulating thyroid hormone availability and action. Cell Mol Life Sci. 2000;57(13-14):1853-1863. [Article]

Kralik A, Eder K, Kirchgessner M. Influence of zinc and selenium deficiency on parameters relating to thyroid hormone metabolism. Horm Metab Res. 1996;28(5):223-226. [Article]

Kure S, Hou D-C, Ohura T, et al. Tetrahydrobiopterin-responsive phenylalanine hydroxylase deficiency. The Journal of Pediatrics. 1999;135(3):375-378. [Article]

Lichtenstein AH. Dietary fat and cardiovascular disease risk: quantity or quality? J Womens Health (Larchmt). 2003;12(2):109-114. [Article]

Mackness MI, Durrington PN, Mackness B. How high-density lipoprotein protects against the effects of lipid peroxidation. Curr Opin Lipidol. 2000;11(4):383-388. [Article]

Maron DJ. Flavonoids for reduction of atherosclerotic risk. Curr Atheroscler Rep. 2004;6(1):73-78. [Article]

Muntau AC, Roschinger W, Habich M, et al. Tetrahydrobiopterin as an Alternative Treatment for Mild Phenylketonuria. N Engl J Med. 2002;347(26):2122-2132. [Article]

Mutanen M, Freese R. Fats, lipids and blood coagulation. Curr Opin Lipidol. 2001;12(1):25-29. [Article]

Nesheim RO. Nutrient changes in food processing. A current review. Fed Proc. 1974;33(11):2267-2269. [Article]

Neustadt J. Mitochondrial dysfunction and disease. Integr Med. 2006;5(3):14-20. [Article]

Neustadt J. The food pyramid and disease prevention. Integr Med. 2005;4(6):14-19. [Article]

Neustadt J. Western Diet and Inflammation. Integr Med. 2006;5(4):14-18. [Article]

Reddy MB, Love M. The impact of food processing on the nutritional quality of vitamins and minerals. Adv Exp Med Biol. 1999;459:99-106. [Article]

Ross JA, Kasum CM. Dietary flavonoids: bioavailability, metabolic effects, and safety. Annu Rev Nutr. 2002;22:19-34. [Article]

Ross SA, McCaffery PJ, Drager UC, De Luca LM. Retinoids in Embryonal Development. Physiol Rev. 2000;80(3):1021-1054. [Article]

Schroeder HA. Losses of vitamins and trace minerals resulting from processing and preservation of foods. Am J Clin Nutr. 1971;24(5):562-573. [Article]

Segal AW. How Neutrophils Kill Microbes. Annual Review of Immunology. 2005;23(1):197-223. [Article]

Shils ME. Magnesium. In: Shils M, Olson J, A., Shike M, Ross AC, eds. Modern Nutrition in Health and Disease. 9th ed. Baltimore: Williams & Wilkins; 1999:169-192. [Book]

Simopoulos AP. The importance of the ratio of omega-6/omega-3 essential fatty acids. Biomed Pharmacother. 2002;56(8):365-379. [Article]

Simopoulos AP. The Mediterranean Diets: What Is So Special about the Diet of Greece? The Scientific Evidence. J Nutr. 2001;131(11):3065S-3073. [Article]

Steinberg D. Low density lipoprotein oxidation and its pathobiological significance. J Biol Chem. 1997;272(34):20963-20966. [Article]

Valenzuela A, Sanhueza J, Nieto S. Cholesterol oxidation: health hazard and the role of antioxidants in prevention. Biol Res. 2003;36(3-4):291-302. [Article]

Vita JA. Polyphenols and cardiovascular disease: effects on endothelial and platelet function. Am J Clin Nutr. 2005;81(1):292S-297. [Article]

Williams R. Biochemical Individuality: the basis for the genotrophic concept. New York: McGraw-Hill; 1998. [Book]

Worthington V. Nutritional quality of organic versus conventional fruits, vegetables and grains. Journal of alternative and complementary medicine. 2001;7(2):161-173. [Article]

Ashwagandha for Sleep, Health and Longevity

Ashwagandha (Withania somnifera) is an herb native to India, Pakistan and Sri Lanka. It is in the Solanaceae family, which also contains such plants as eggplant (Solanum melongena), belladonna (Atropa belladonna), cayenne pepper (Capsicum spp.), potato (Solanum tuberosum), tobacco (Nicotiana spp.) and tomato (Lycopersicon esculentum).



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