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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!)

ATP is the evolved engine by which our body slows the spontaneous and inevitable death march of entropy. The universe doesn’t like being organized. The universe wants to maximize its free energy by getting all its constitutent parts in the most disordered jumble possible. The heat death of the universe is when every atom in the universe dances with the maximum degree of freedom. Every time a bond is formed between two atoms, well, their maximum degrees of freedom are reduced.Think about it, when you are by yourself, you can wiggle and dance with a maximum range of motion; but if you hold hands with someone, or if you’re daring enough, place your hands on your partner’s hips, well, you place constraints on your movement (since you’re trying to move in unison). This is what separates you and I as dancers from professional tango pairs who move with such synchrony it’s like they’re one, beautiful flowing unit.

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 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