STRUCTURE OF PROTEINS

There are an estimated 100,000 different proteins in the human body alone, and each of these is a polymer with a combination of unique sequences derived from only 20 amino acids. Every protein has a different structure and performs a different function in the body.

1) Nonribosomal Peptides are synthesized using a modular enzyme complex (which functions much like a factory conveyor belt). Nonribosomal peptides are confined primarily to fungi, plants and unicellular organisms. In general, these peptides are cyclic, although linear nonribosomal peptides are common. Hybrid compounds are often found.

2) In the field of genetics it is well understood that Ribosomal Peptides are synthesized during the translation process by messenger RNA (preceded by transcription from the DNA template by transfer RNA). http://en.wikipedia.org/wiki/Translation_%28genetics%29

In higher organisms, these peptides may function as hormones. In some lower organisms peptides are produced as antibiotics. http://en.wikipedia.org/wiki/Peptide They are often subjected to proteolysis (page 9) to generate the mature form.

3) Digested peptides are the result of nonspecific proteolysis as part of the digestive cycle. It has also been documented that, when certain food proteins such as spinach protein, casein, egg protein, and gluten are broken down, opioid peptides are formed. These short polymers mimic the effects of morphine, and those individuals that are unable to break them down will experience mental illness. They have been given names such as casomorphine, dermorphine and gluten exorphine. Ultimately, digested peptides are ribosomal peptides; although they aren't made on the ribosome of the organism that contains them.

4) Peptide Fragments are sections of proteins that can used forensically to identify or quantify the source protein. Often these are the products of enzymatic degradation performed in the laboratory on a controlled sample, but they can also be paleontological samples, which have been degraded by natural effects.

Like that of nucleic acids, the molecular structure of proteins has several levels of organization. As with DNA or RNA, the primary structure of a protein is its sequence of amino acids. Through interaction between neighboring amino acids, a polypeptide chain twists and folds into a secondary structure. Secondary structures interact and further fold to form a tertiary structure. Finally, some proteins consist of multiple polypeptide chains in a particular association that produces a quarternary structure. Proteins obviously, are also therefore, polymers.

Since proteins may be either a “single polypeptide molecule”, or consist of multiple polypeptide subunits, a debate has raged for years over when a polypeptide becomes a

protein and vice-versa. There seems to be more agreement with the general distinction that peptides are short and proteins are long (at least 50 amino acids in length). It used to be accepted that certain polypeptide chains short enough to be made synthetically from their constituent amino acids could properly be called peptides. The past disagreement between what is a peptide and what is a polypeptide seems to have been resolved in favor of any sequence in excess of 10 amino acids now being classified as a polypeptide, but what of proteins?

With the advent of better synthetic techniques, polypeptides as long as hundreds of amino acids can be made, including full proteins like ubiquitin. There have been several different conventions proposed to sort out the peptides, polypeptides and proteins, once and for all, but reportedly, each of them seems to suffer from at least one flaw.

A fairly current idea, seeming to be gaining popularity, is that in order for a polypeptide to become a protein, it has to have some sort of biological function in the body. This definition contemplates a division of purpose as part of the equation. Further, there is the notion that "a peptide is an amino acid molecule without secondary structure (i.e., free-floating, random or without a recognizable systematic pattern of twists or folds) ; on gaining defined structure, it is a protein." This seemingly welcome compromise allows for the same molecule to be either a peptide or a protein depending upon its environment, for there a there are some peptides that cannot be proteins. http://en.wikipedia.org/wiki/Peptide

Thus, it would seem that there are regarded to be both structural proteins and functional proteins. Structural Proteins form most of the solid material in an organism. For example, the structural proteins collagen and keratin are the main component of skin, hair or fur, muscles, and tendons. On the other hand, Functional proteins help carry out activities and functions in the body. Hemoglobin is exemplified as a functional protein that occurs in the red blood corpuscles and helps to transport oxygen throughout the body, whereas, Myosin is also a protein, but its responsibility is afford muscle tissue the ability to contract. Insulin is yet another functional protein. It helps to regulate the storage of glucose for further metabolism.

When we humans eat protein-containing foods (such as beans, nuts, eggs, cheese, meat, fish, etc.) most polypeptide chains are broken down in the digestive tract and the individual amino acids generally are absorbed within our bodies. These absorbed amino acids may then become recombined into proteins specific to each individual in a process known as “protein synthesis”. In order to accommodate the different bodily functions each individual protein is directed to a specific task.

A subclass of the functional proteins is that group of “long” polypeptides referred to as Enzymes. Specific chemical reactions in the body are fostered by enzymes. An example is amylase. This enzyme occurs both in the intestines and in human saliva, and helps break apart the glucose-glucose bonds in carbohydrates. This enables the human body to absorb the glucose so that it may be used for energy.

Proteolysis is the directed degradation (digestion) of proteins by cellular enzymes called proteases or by intramolecular digestion. Curiously, certain venoms, such as those produced by poisonous snakes, can also cause proteolysis. These venoms are, in fact, highly evolved digestive fluids that begin their work outside of the body. Proteolytic venoms cause a wide range of toxic effects, including: cytoxis (cell-destroying), hemotoxic (blood-destroying), myotoxic (muscle-destroying), and hemorrhagic (bleeding). http://en.wikipedia.org/wiki/Proteolysis

Enzymes in fact may be divided into subunits referred to as “moieties” (halves) that must be united for there to be a viable enzyme, more technically known as a holoenzyme. The corresponding moieties are called apoenzymes and coenzymes. To appreciate the relationship of apoenzymes and coenzymes and their catalytic properties when properly constituted as a fully active holoenzyme first click on the coenzyme link (just two lines above).

The following two links will tie our discussion up till now to soil, its component parts, and a practical application of all the chemistry you’ve been reading about up till now in a straightforward, informative way. The third website link is an excellent source of an even more technical presentation if you really want to dig in after reading the next two links.

Humus, Humic Acid and Humates

http://www.up.wroc.pl/~weber/humic.htm#start

Finally, please log on to www.montmorillonite.org for additional information about the role of trace elements and minerals in soil science and nutrition.