Jamie Hale

Jamie Hale

Sunday, June 7, 2009

Biochemistry 101

The following is an excerpt from Knowledge and Nonsense: the science of nutrition and exercise

Appendix 1: Biochemistry and Genetics

I decided to include this section for all of the biochemistry fans. Many of the terms mentioned in this section are often discussed in scientific texts and research studies. If you read much research, you may occasionally stumble across a word or phrase that you might not understand. I put together this section to help you understand some of those words and phrases. The terms are not presented in any particular order.

These are the fundamental substances that make up the matter of the universe. An element is any substance that can’t be subdivided further by chemical means. Another way of saying this is that an element is composed of only one kind of atom. Examples of elements include oxygen, nitrogen, sulfur, carbon,and calcium.

This is the smallest part of an element that still retains the chemical and physical properties of that element. Atoms are composed of three types of subatomic particles.
1. Protons: These are positively charged particles found in the center or nucleus of the atom.
2. Neutrons: These are also found in the nucleus but bear no electrical charge (neutral).
3. Electrons: These particles move around the nucleus in orbits. They have a negative electrical charge. Electrons are arranged in shells around the nucleus. Each shell can contain only a finite number of electrons before a new shell must be formed. The first shell is filled when it has two electrons. The second and each
succeeding shell are filled with eight electrons.

A molecule is the chemical combination of two or more atoms. Atoms chemically combine by interactions with their respective electron shells. Such interactions are termed bonds, and these bonds are what hold the atoms together. One of the most
important chemical bonds is the covalent bond, which is where two or more atoms share their electrons with one another. This can effectively fill all of the outer shells of the participant atoms,thereby making them extremely stable. A good example is water.

Macromolecules are large molecules. Many organic molecules are characteristically large and are thus called macro. These macromolecules are usually formed from smaller repeating subunits. Macromolecules are often termed polymers, and the
subunits which compose them are termed monomers. Monomers are assembled into polymers by a special kind of covalent bond forming reaction termed dehydration synthesis or condensation. The name is due to the fact that water is always one of the products.

Hydrogen bonds
These are weak electrical attractions that occur between the hydrogen atoms in a molecule and the oxygen or nitrogen atoms in the same molecules or in separate molecules. Hydrogen bonds are important because they give macromolecules a threedimensional shape, which is critical to their proper functioning.

Basic organic compounds
Organic compounds are those which contain carbon. There are four major classes of organic compounds that are significant to organisms (carbohydrates, lipids, proteins, and nucleic acids).

Enzymes are protein bio-catalysts that speed up reactions but are
not altered by those reactions. Coenzymes are small organic molecules, frequently vitamins. The enormous diversity of proteins ensures that there will be adequate kinds of enzymes for each and every reaction. Each enzyme is specific for one
particular reaction. This means that each of the hundreds of reactions that occur within the cell must have its own enzyme. The types of reactions a cell can execute are dependent upon the kinds of enzymes present. There are six major classes of enzymes.
1. Oxireductases: Catalyze oxidation reduction reactions.
2. Transferases: Catalyze the movement of functional
groups between molecules.
3. Hydrolases: Catalyze the breakdown of polymers by the
addition of water.
4. Lyases: Catalyze the breakdown of molecules but not by
the addition of water.
5. Isomerases: Catalyze internal rearrangements of
6. Ligases and synthetases: Catalyze the linkage of
molecules together.

Biological oxidations
Oxidation is a type of chemical reaction in which electrons are removed from an atom or molecule. Reduction is a type of chemical reaction in which an atom or molecule gains electrons. Oxidation and reduction always go together. It is not possible to
have electrons floating freely about. Whenever one molecule is oxidized another must be simultaneously reduced. In other words, the electron removed from one molecule must be transferred to another molecule.

Metabolism by definition is the sum total of all chemical reactions that occur within the cell or organism. It can be generally categorized into two subsections—catabolism and anabolism. Catabolic reactions are breakdown reactions in which
large complex molecules are reduced to smaller fragments (macromolecules are turned into micromolecules). Anabolic reactions are synthesis reactions whereby smaller molecules are joined to form larger or more energetic ones. Catabolic reactions
are exergonic (energy yielding) while anabolic reactions are endergonic (energy consuming). In the cell, catabolic reactions provide the energy necessary to drive the anabolic reactions.

Kreb’s cycle (tricarboxylic acid cycle, citric acid cycle)
Krebs cycle is a series of catabolic reactions occurring in the mitochondrial matrix. The main purpose of these reactions is the transfer of energy carried in the bonds of acetyl-CoA to electron carrier molecules. The molecules receiving the hydrogens and electrons are the coenzymes NAD+ and FAD, which transfer the hydrogens and electrons to the respiratory chain for the phosphorylation of ADP to ATP. Refer to The Biochemistry of Human Nutrition by Sareen Gropper for a detailed description of what happens in the Krebs cycle.

Thermic effect of food
The thermic effect of food (diet-induced thermogenesis) is an increase in the metabolic rate that occurs following the ingestion of food. It is thought to account for an increase in the basal metabolic rate of between 5 percent and 15 percent. The increase in metabolism is a result of increased oxidation associated with the digestion of food, absorption, transport, metabolism, and storage of energy following eating. Protein has the highest thermic effect of the three macronutrients. Carbohydrates have the next highest and fats the least thermic effect.

Nucleic acids
There are two types of nucleic acid—DNA and RNA. DNA is the largest molecule and it has two essential functions. It is the hereditary molecule containing the genetic blueprint that it transmits from generation to generation, and it regulates the
activity of the cell by controlling protein synthesis. All RNA is synthesized off of the DNA molecule. Part of the DNA unwinds and ribose, containing nucleotides, are locked into position in place of the deoxyribose nucleotides. Therefore, all RNA
represents a copy of some of the information contained in the DNA molecule.

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