This is the first of a series on the importance of amino acids in the diet. It attempts to lay to rest the problem of defining what is an amino acid, as much confusion exist when any organic molecule that has an acidic group as well as containing a nitrogen either as an amino group or otherwise contained within the structure is called an "amino acid". A simplified approach has been to only class as amino acids, those molecules that either are, in fact, amino acids or may be derived from them and that have not previously been classified as belonging to some other biochemical-metabolic grouping. Thus carnitine, a metabolic product of lysine, and taurine, a metabolic product of cysteine are called amino acids, while niacin a metabolic product of tryptophan is called a vitamin and gamma amino butyric acid, a metabolic product of glutamic acid is without a proper name.
A more reasoned approach is to classify only those carboxylic acids with an alpha amino group as an amino acid, when, and only when, there is a genetic codon for their inclusion into protein. The various transfer ribonucleic acids, tRNAs, have been well characterized and the three-letter genetic code for them is well established and widely published in textbooks. As example, in a basic course in general, organic and biochemistry it is taught that lysine has the "nature-assigned" codon of either AAA or AAG which represents the ribonucleotides adenine, adenine, adenine, or adenine, adenine, guanine. There is no codon for carnitine. Likewise, cysteine has the codon assigned as UGU or UGC where the ribonucleotides are uridine, guanine, uridine or uridine, guanine, cytosine. There is no codon for taurine. Further, tryptophan has the codon assigned as UGG where the ribonucleotides are uridine, guanine, guanine. There is no codon for niacin. And finally for this discussion, glutamic acid has the codon assigned as GAA or GAG where the ribonucleotides are guanine, adenine, adenine or guanine, adenine, guanine. There is no codon for gamma amino butyric acid.
The question arises; what do you call those biologically active products of
amino acid catabolism (broken down by enzymatic processes)? If no other
classification has been given it seems that the term, "pseudo-amino acid" is
appropriate. Here is what Abraham Cantarow and Bernard Schepartz, writing
about peptides, said in their classic textbook,
The other compounds, since they contain some residues which are definitely not amino acids, also belong to the category of pseudopeptides. They are more closely related to peptides than to amides, however, because in each case one constituent of the compound is either an amino acid or closely related to an amino acid. Pantothenic and "folic" acid belong to the group of B vitamins. Hippuric acid, phenylacetylglutamine, and dibenzoylornithine are substances which result from the coupling of a foreign substance for excretion from the organism (detoxication). .... Under proper conditions, carbon dioxide, which may be considered the anhydride of carbonic acid, combines with the amino groups of amino acids or proteins to form "carbamino" compounds. The resulting linkage bears some resemblance to an amide or peptide bond."
Thus we have a suggestion that "pseudo" be applied to those compounds that appear like a biologically similar one but are uniquely different.
This is an overworked term. If the diet is inadequate in protein for a prolonged time, all amino acids are essential. With intravenous therapy involving nitrogen metabolism, a goodly supply of amino acids is required with emphasis on what's essential being less important than getting the patient into a positive nitrogen balance. (That is having more nitrogen going into the system than coming out as excretory products.) And, stage of growth is important. Young animals have additional requirements for amino acids as they build body tissue whereas an adult can "get-by" as they have body reserves to draw upon. Nevertheless a group of amino acids that cannot be synthesized in the body are termed essential.
If you want to memorize the essential amino acids here's a handy tool: The executive's name was tt hallim vp (vice president, no less.) This stands for threonine, tryptophan, histidine, alanine, lysine, leucine, isoleucine, methionine, valine and phenylalanine. For chicks (chickens that is), you can add: gg which stands for great guy (or glutamic acid and glycine if you prefer.)
When a varied diet is consumed, a "typical" individual has a balance of the different nutrients which includes carbohydrates, fats, proteins, minerals and vitamins. And, when the diet becomes somewhat fixed in one class of constituents at the disadvantage of another, there is enough float in the system to permit normal processes to continue. In fact it takes quite an insult to the system to provoke a disaster in which cell or organ functions are disrupted. An example of this type of result can be demonstrated with rats (since the use of humans for such purpose, would to say the least, be unethical.)
Growing rats fed an adequate diet in proteins that contain an abundance of the essential amino acids rapidly reach mature size. Their hair coat glistens, they are alert and active, they are not aggressive nor or they either obese or overly muscled. The essential amino acids are so termed because they are building blocks for all the proteins of the cell and must be supplied in the diet. Other so called non-essential amino acids are synthesized by the cells typically as degradation products of the other amino acids or are formed by minor alterations in structure which does not require complex chemistry.
When protein in the diet supplies amino acids in quantities in excess of requirements of protein synthesis, the amino acids are metabolized by a process that removes the "amino" part of the molecule resulting in a residue of carbon, hydrogen, oxygen and sometimes nitrogen or sulfur depending upon the starting amino acid. The majority are simply burned (oxidized) in processes that nature has designed to scavenger energy. However, in a few instances, the skeletal remainder from the amino acid serves as a precursor for other useful substances. In the four cases presented here; taurine, gamma amino butyric acid, niacin and carnitine, are formed from the amino acids, cysteine, glutamic acid, lysine and tryptophan respectively.
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(Hopefully, to avoid confusion, I add the following: DNA contains the genetic code for the synthesis of all proteins. The code is a three letter shorthand made up of the same nucleotides as RNA with the exception that Uridine is present exclusively in RNA and its counterpart Thymine is present exclusively in DNA. Nucleotide are said to pair, thus adenine pairs with thymine (AT) and guanine pairs with cytosine (GC). When the process of transcription takes place, that is to say, DNA is read and a molecule of RNA is formed as its counterpart, these base pairings occur with the exception that uridine now takes the place of thymine in the evolving RNA polymer chain. The product just formed is called messenger RNA or mRNA and it leaves the nucleus of the cell where the DNA is stored and enters the soup of the cells chemical factory. Messenger RNA which now contains the "anti-codon" for the nucleotides of DNA is read in a organized structure called a ribosome. There each base is again paired with a nucleotide structure which is called "transfer RNA". These small (by comparison to DNA and RNA) molecules have at a hairpin turn in their structure, and three nucleotides in the hairpin pair with a three nucleotide sequence in the messenger RNA. The codon in the transfer RNA is the "anti-codon" for the messenger RNA. The result is that the information from DNA is flawlessly transferred to a sequence of amino acids that will be zippered into a protein. Formed proteins then go about the business of being the structure and enzyme factories of the cell. It would appear that two distinctly different messenger RNAs could be formed in the nucleus which would cause to appear two distinctly different protein polymers. This is not the case as in the reading of DNA, one strand is the so-called informational strand and the other the template strand. It is always the template strand that is transcribed yielding up the information for amino acid sequences in protein.)
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