Amino acids to Proteins

The amino acids are responsible for many functions in the human body. Without amino acids, we could not survive. I will provide a brief explanation of the general structure of the twenty amino acids, and show why they are so important for life.

As mentioned, there are twenty common amino acids which are used by the body. There are also a number of uncommon amino acids, however they are less frequently encountered and I will not deal with them in this post. The general structure of amino acids is to have a carbon atom (called the alpha carbon), bonded to a carboxyl and amine functional group and a hydrogen atom. The fourth space for bonding to the alpha carbon is used by a group (called the R-group) which differs for each amino acid. The R group gives the amino acid its characteristics, determines what it can do and what function it will have.

The amino acids join together by a peptide bond which is between the carbonyl group of one amino acid, and the peptide group of another. This results in the loss of a water molecule, and hence is classified as a condensation reaction. Amino acids can link together to form peptides (two, three or four amino acids), polypeptides (less than one hundred amino acids in the chain) or proteins (greater than 100 amino acids). It is when amino acids form proteins that they are used to perform specific functions in the human body.

The sequence that amino acids are in when they join together, is called their primary structure. The secondary structure is the spatial arrangement of the main chain atoms (this is not related to how the R-groups are arranged). The following types of secondary structures are quite common and called regular. They are the alpha-helix, beta-sheet and the beta-turns. If a regular pattern is not found, the structure can be described as random coil. The tertiary structure is the overall 3-D arrangement of all atoms in the protein. This is predominantly determined by Van der Waal forces, the presence (or absence) of hydrogen bonds, ionic interactions and the hydrophobic effect.

Myoglobin is a protein that is completely necessary for life. It is a relatively small protein that is found in muscle cells. It is able to bind to oxygen, and in this way, can supply muscles with oxygen. It contains 8 alpha-helices which vary in length. Most of the hydrophobic R-groups of the amino acids are inside these helices and so are internal to the protein. The protein is so closely packed that even the relatively weak Van der Waal interactions do a good job at stabilizing the protein. The heme group within myoglobin has two bonding positions – one of which is to the R group of histidine, the other allows an oxygen molecule to bind to it. This is where the oxygen is stored and from there, it can then be distributed throughout the muscle. It has been found that there is a higher abundance of myoglobin in diving animals such as whales and seals. This allows them to bind more oxygen, therefore have a greater supply of oxygen, which allows them to stay submerged for longer periods of time.

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