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We’re attempting to provide unpretentious, plain English descriptions of the most important concepts in medicine, aimed at students in their basic science years.

Division welcome (concepts!)
Division welcome (details!)
Summary of pathways
Disorders of fructose metabolism
Disorders of galactose metabolism
Lactase deficiency
Glycolysis / ATP production
Glycolysis regulation, key enzymes
Hexokinase vs. glucokinase
Regulation by F2,6BP
Gluconeogenesis, irreversible enzymes
Pyruvate metabolism
Pyruvate dehydrogenase complex
Pyruvate dehydrogenase deficiency
TCA cycle (Krebs cycle)
Electron transport chain and oxidative phosphorylation
Ethanol metabolism
Ethanol hypoglycemia
HMP shunt (pentose phosphate pathway)
Glycogenolysis / glycogen synthesis
Glycogen storage diseases
Amino acids intro
Amino acids
Amino acid derivatives
Catecholamine synthesis
Alkaptonuria (ochronosis)
Maple syrup urine disease
Hartnup disease
Transport of ammonium by alanine and glutamate
Urea cycle
Ornithine transcarbamoylase (OTC) deficiency
De novo pyrimidine and purine synthesis
Orotic aciduria
Purine Salvage Pathway
Purine salvage deficiencies
Cholesterol synthesis
Fatty acid metabolism
Lipoprotein functions
Major apolipoproteins
Lipid transport, key enzymes
Familial dyslipidemias
Metabolic fuel use
Glycogen regulation by insulin and glucagon/epinephrine
Metabolic fuel use (continued)
Ketone bodies
Vitamins: fat soluble
Vitamin A (retinol)
Vitamin D
Vitamin E
Vitamin K
Vitamins: water soluble
Vitamin B1 (thiamine)
Vitamin B2 (riboflavin)
Vitamin B3 (niacin)
Vitamin B5 (pantothenate)
Vitamin B6 (pyridoxine)
Folic acid
Vitamin B12 (cobalamin)
Vitamin C (ascorbic acid)
Enzyme terminology
Metabolism sites
Rate-determining enzymes of metabolic processes
Activated carriers
Universal electron acceptors

Division welcome (concepts!)

Rather than just start with “chromatin structure,” “heterochromatin,” “euchromatin,” and all the other “smallest parts” of biology, we think it’s best to begin Biochemistry with what is, conceptually, the most important idea: metabolism.

You are a human organism; so, let us understand what keeps this human body going: ATP. By ATP, we mean ATP and any other “chemical equivalent” – things that can push an energetically unfavorable reaction forward, usually through the dissociation of a high energy phosphate-phosphate bond. (That’s how ATP does it!)

Entropy makes elements of us all. Entropy gradually and inevitably decomposes us all. Entropy favors our literal coming apart. The body, miraculously, has evolved to slow this process long enough for us to divide, procreate and, thereby, pass on our precious genes! We do this, interestingly, by breaking down compounds (carbohydrates, fats, and, as a last resort, proteins) which themselves have quite a bit of chemical energy stored in the form of bonds.

However, we don’t break these bonds all willy-nilly, releasing that precious chemical energy as uncaptured heat! No, my friends, that energy is transferred. It is transferred to an extremely useful chemical equivalent known as ATP.

Our cells know how to handle, store, and use, on demand, ATP. Putting the energy that was once in our food into the small molecule known as ATP allows us to “ship” and use that energy in nearly any enzymatic reaction (which cannot be said for molecules like glucose, fatty acids, and peptides). So, our body converts chemical energy in food to ATP, the common currency which all cells and most all reactions accept! (Kinda like VISA! hehe.)

ATP, in turn, drives all sorts of reactions in the body that entropy disfavors. What we mean by that is, while entropy wants things to come apart (since coming apart is actually energetically favorable), our bodies use ATP to drive reactions that keep things together.

So, ATP facilitates certain reactions which favor the “together-ness” of our bodies. Without ATP, we quite literally fall apart, decompose as it were.

So, let’s begin Biochemistry by talking about how we generate ATP. We’ve evolved to do so using three major categories: carbohydrates, fats and amino acids. (We can also breakdown nucleotides to form ATP but this is almost negligible when it comes to the overall ATP production of the body.)

Division welcome (details!)

There are many things related to metabolism to learn about, but don’t get overwhlemed; just remember, the primary purpose of all metabolic systems is to produce ATP.

Every living organism has a set of enzymes that converts macromolecules from one form to another and, in the process, makes ATP. As odd as it may sound, “biological death” begins when an organism fails to make ATP at a rate required by the enzymes which make ATP! Without sufficient ATP, a cell cannot maintain, repair, or reproduce itself – and a cell that cannot respond to the dynamic world around it is as good as dead.

Fortunately, the human body can generate ATP from the three major macromolecule categories:

Not all macromolecules, however, are “created equal.” Each has a different “cost” to the body.

Carbohydrates are only made up of carbon, hydrogen, and oxygen, and the cost of carb metabolism is the lowest because the body can fully metabolize carbohydrates to H2O and CO2. Fatty acids, too, are only made up of carbon, hydrogen, and oxygen, but their metabolism results in the production of ketoacids. Unlike CO2, ketoacids cannot be eliminated via exhalation; their accumulation increases the acidity of the blood and can cause body-wide problems. Proteins are most costly because their degradation means a loss of structural integrity as well as the generation of ketoacids and ammonium ions.

Because of these associated costs, the body has evolved to greatly favor glucose for fuel. When glucose is low, it relies on fatty acids and then only shifts to proteins in dire conditions.

Amino acids intro

Amino acids are used for three main purposes. They can form structural and enzymatic proteins; they are precursors for a variety of signaling molecules (hormones and neurotransmitters); and they can be catabolized to generate ATP.

Unlike carbohydrates and fatty acids, amino acids are nitrogen-rich. Their catabolism occurs via the urea cycle, which transfers nitrogen from the amino acid to urea -- a small, non-polar molecule which can be excreted in urine. Without the urea cycle, nitrogens become ammonium ions (NH4+) and lower blood pH.

Disorders of amino acid metabolism typically cause clinical problems because of a build-up of toxic precursors along a degradation pathway or because of an inability to eliminate nitrogen in the form of urea. For this reason, treatment often includes avoidance of foods high in a particular amino acid.

Vitamins: fat soluble

Vitamins are tiny little molecules which we, as humans, cannot synthesize on our own. We need to acquire them by eating things around us. Pretty much every vitamin is a “cofactor” or a “coenzyme” (these terms mean the same thing). Scientists discovered that in the absence of certain tiny molecules, important enzymes would not work! Hence, they called these molecules “cofactors” or a “coenzymes”.

So, in the future, when you come across a vitamin, you can say to yourself, “Oh, right! Without this tiny little molecule, certain essential enzymes of the human cell don't work!”

National Library of Medicine
Vitamins = Organic substances that are required in small amounts for maintenance and growth, but which cannot be manufactured by the human body.

Note that vitamins are not defined “chemically”; vitamin is a functional definition; that is, we have said nothing about the organic structure or chemical composition required to be a vitamin; only that a vitamin is any small molecule which (1) cannot be synthesized by the human body but which (2) is required for normal processes and, thus, (3) must be obtained from the diet!

Vitamins: water soluble

See the entry for Vitamins: fat soluble.