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Amino Acids

By Matthew Lewis

In this tutorial we will look at what amino acids are, how they are obtained, and the specific structure of cystine.

Table of Contents
Definition and General Structures
Functions and Origins
Cystine Structure

Definition and General Structures:

An amino acid is generally defined as an organic compound (meaning it contains carbon) containing at least one amino group and at least one carboxyl group. This can be easily explained by showing the general structure for an amino acid, where each letter stands for an elemental atom (N=nitrogen, H=hydrogen, C=carbon, and O=oxygen) and the lines drawn between them represent chemical bonds.

In the "general form" you can see the central carbon atom connected to 4 different "groups". Starting at the left, the H2N- group (shown in yellow) is called the "amino group". Moving across, the H is simply a hydrogen atom, and to the right, the -COOH (shown in green) is the "carboxyl group". All three of these groups are present in all amino acids. The 4th group is a variable, meaning that it is different in composition for each individual amino acid. This group is commonly denoted by an "R" (shown in blue). The letter R does not code for any specific elemental atom.

While the general form is a good representation of the basic amino acid structures, they usually exist in a slightly modified form within our bodies. Because of the effects of pH on the amino and carboxyl groups, amino acids can exist in "ionic" forms which are slightly modified (by the addition or removal of one hydrogen atom) and, as a result, charged like a magnet (denoted by + and - symbols). Similarly, charges can exist for any functional groups (amino, carboxyl, or otherwise) found within the "R" group.

Functions and Origins:

Amino acids function as the building blocks of proteins which in turn have a vast number of uses in the body, essentially making us who we are. A single protein is nothing more than a folded strand of amino acids held together by chemical links called "peptide bonds".

The length and amino acid sequence of these strands are unique to the specific protein they are being instructed to form. To look at this process of building a protein, we will start from the beginning with DNA .

The DNA within our cells (shown below) codes for the many proteins needed by our body. The two processes by which proteins are formed from a DNA template are called "transcription" and "translation". In transcription, the DNA molecule containing the gene of interest (coding for the protein of interest), is essentially copied, creating a mobile strand of RNA (called RNA instead of DNA because of a slight difference in the new molecule's building blocks). This RNA molecule is sent outside of the nucleus (the area of the cell where DNA is kept, shown below in purple) to a complex that "reads" the RNA like a set of instructions and makes the appropriate protein. Thus, the RNA is called a "messenger RNA" or mRNA for short, since it acts as a messenger by carrying the instructions for building a protein from the DNA gene out to the appropriate cellular machinery. The process of "reading" RNA messages and making the corresponding proteins by joining the appropriate amino acids together is translation. The amino acids are linked via the formation of peptide bonds, and the completed amino acid chain (called a polypeptide) folds to form a complete functional protein.

In short, DNA codes for a series of amino acids which become the building blocks of proteins. Those proteins then go off within the cell or out into the body to perform any number of functions, from making possible many of our bodies chemical reactions, to establishing our eye color, to forming and repairing our many muscles.

We obtain these building blocks in two ways. Non-essential amino acids can be synthesized within the body or supplemented by diet. The rest, the essential amino acids , must be obtained from our diet because they are either not synthesized by the body at all, or not in large enough amounts to fulfill our physiological requirements. Amino acids obtained through diet come from the protein we eat, found in such foods as soy and nuts as well as meat sources. These ingested proteins are initially broken down in the stomach. First, whole proteins are broken down into polypeptides and shorter peptide chains (di- and tripeptides, etc., meaning chains of two and three amino acids). A small amount of free amino acids are also produced by this digestion. These amino acids and amino acid chains then move into the small intestine, where the chains are further broken down bit by bit into more single amino acids, which are then absorbed through the cell membranes of the intestine wall by active transport. A small amount of di- and tripeptides are also actively absorbed, but are quickly broken down into individual amino acids within the cells just after getting through the cell membrane . From there, the amino acids exit the cell and enter the blood stream.

The Structure of Cystine:

The defective transport found in cystinuric patients prevents proper absorption of particular amino acids, including cystine, in the intestine and kidneys. Cystine is particularly insoluble, and thus precipitates from solution at high concentrations, forming aggregates we know of as stones. Cystine itself is actually a product of two cysteine amino acids (note the extra "e") that forms when they undergo oxidation and are joined their sulfur groups. The structures of cysteine and cystine are shown below.

The bond that occurs between the two sulfur atoms of the cysteine amino acids is called a disulfide bond. The bond is the result of the oxidation (a reversible chemical reaction) of their -SH groups. The -SH group at the end of cysteine's "R" group is commonly called a "thiol", "sulfhydryl", or "mercapto" group. All names are equally valid. In the urine, cysteine exists mostly in its disulfide form (cystine). Once transported into the kidney cells, the disulfide bond is reduced (the opposite of oxidation) and each molecule of cystine becomes two cysteine amino acids. Additionally, it is through the formation of these sulfur-to-sulfur disulfide bonds that thiol drugs (containing the -SH thiol group) are able to form complexes with cysteine.

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