Non-Standard Amino Acids

Dhristi JEE 2022-24

About Non-Standard Amino Acids

Non- amino acids are organic molecules that are not composed of amino acids. There are many different types of non-amino acids, and they can be found in both natural and synthetic forms. Some of the most common non-amino acids include sugars, lipids, and nucleic acids. Non-amino acids are used in various areas of the plant and even humans for different purposes. For example, when the non-amino acid ribonucleic acid (RNA) is combined with DNA, it becomes messenger RNA (mRNA), which serves as a transcriptional control protein that works in the nucleus of a cell. The cell can then use this messenger RNA to produce proteins and the cell is thus able to function. The same concept applies to amino acids in which some of the non-amino acids can be utilized as a building block and others will be degraded. The role of the non-amino acids can be diverse. Some of them will be used in metabolic processes. However, some of them may not be used for a long time and then will become no longer usable. In addition to the need for amino acids in biological processes, there are also non-amino acids that must be present in a certain amount. 


These non-amino acids are known as essential amino acids. The different types of non-amino acids are not the same, and they are not all manufactured the same way. For example, there are certain metabolic processes that do not require the presence of certain non-amino acids. Examples of non-essential amino acids include hydroxyproline, glycine, serine, threonine, lysine, arginine, and aspartic acid. In cases of long-term starvation, the body may use its protein stores and depleted non-essential amino acids will be used instead of the essential ones. To maintain a healthy body and to prevent many health problems, it is very important that we consume certain essential amino acids on a regular basis. Supplements With Essential Amino Acids for Health The body needs the essential amino acids in different quantities and it is not possible to provide them through supplements. When the body is not supplied with the required amount of essential amino acids, these amino acids will be converted into other compounds, which are called by-products. Some of these by-products are toxic. For example, the body makes some proteins that are harmful to the liver. The main amino acids that the body needs are listed below. We should remember, however, that the recommended daily amount of each of these amino acids depends on an individual's gender, age, and weight.


Non-Standard Amino Acids Definition

Non-standard amino acids are amino acids that are considered to be chemically modified after they are incorporated into a protein; this is known as post-translational modification. This type of amino acid is known to be found in various living organisms but does not occur in all proteins. They are not found in the genetic code of any organism. This type of amino acid can get created naturally as well as artificially in the laboratory. They are known to be present in meteorites and are capable of getting used in prebiotic experiments.


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Standard and Non-Standard Amino Acids

Amino acids are considered to be molecules that are characterized by the presence of an amino group and a carboxylic group in the molecular structure of the compounds. Hence, these molecules are termed amino acids. The main function of an amino acid is to act as a manometer for the purpose of the synthesis of proteins and peptides. From all the amino acids that exist naturally, there is a set of 20 amino acids which are termed standard amino acids. These standard amino acids serve as building blocks for the proteins that are produced in a living organism. These acids are studied widely all over the world. The standard amino acids are:

  • Glycine

  • Alanine

  • Proline

  • Valine

  • Leucine

  • Isoleucine

  • Methionine

  • Phenylalanine

  • Tyrosine

  • Tryptophan

  • Serine

  • Threonine

  • Cysteine

  • Asparagine

  • Glutamine

  • Lysine

  • Arginine

  • Histidine

  • Aspartate

  • Glutamate


Besides standard amino acids, there are some acids that are found in some proteins and are known as non-standard amino acids. The acids have a different composition that doesn't match the composition of standard amino acids. They are known for presenting different physicochemical properties. Therefore, when it becomes necessary to introduce a local in a particular protein with specific properties, and it can't get incorporated by the standard amino acids, then the non-standard amino acids come into the scene, and they are used for incorporation. So it is clear that the only difference between standard and non-standard amino acids is their composition.


Some examples of non-standard amino acids are:

  • Cystine, desmosine, and isodesmosine

  • Hydroxyproline and hydroxylysine

  • Gamma-carboxyglutamate

  • Phosphoserine, phosphothreonine, and phosphotyrosine

  • N-acetyl lysine

  • Methyllysine


Non-Standard Amino Acids and Their Functions

Non-standard amino acids being an essential molecule in biochemistry, have some key functions that help humans to produce different things which act as useful products in their daily lives.


Some of the important functions of non-standard amino acids are as follow:

  • The most important posttranslational modification of amino acids occurring in eukaryotic organisms is considered to be the reversible addition of a phosphate molecule to the hydroxyl portion of the R groups of serine, threonine, and tyrosine. The event is referred to as phosphorylation and gets used for regulating the activity of proteins that seem to be functioning in cells continuously. This is considered to be an important function of non-standard amino acids.

  • Non-standard amino acids that are produced in industries are considered to have some important functions that can be very useful. The first commercial production of amino acids was in the year 1908. At that time, a flavouring agent, monosodium glutamate, was prepared using a type of large seaweed. Glycine and cysteine can also do the work as food additives, and some mixtures of amino acids are also used as flavour enhancers in some food industries. This is considered to be another important function of amino acids that is useful to humans.


List of Non-Standard Amino Acids

Non-standard amino acids which one cannot find in proteins are lanthionine, 2-aminoisobutyric acid, dehydroalanine, and the neurotransmitter gamma-aminobutyric acid. Non-standard amino acids are considered to be intermediaries that are present in the metabolic pathway of standard amino acids. In order to have a clear understanding, let's discuss an example: ornithine and citrulline seem to occur in the urea cycle, which is considered to be a part of amino acid catabolism. Some other examples of non-standard amino acids are as follows:

  • Cystine, desmosine, and isodesmosine: This type of amino acid is known to be found in extracellular matrix proteins such as elastin.

  • Hydroxyproline and hydroxylysine: This type of amino acid is known to be found in one type of extracellular matrix, which is known as collagen.

  • Gamma-carboxyglutamate: These are found in osteocalcin, which is considered to be a type of extracellular matrix that is found in bones but also in the prothrombin. This is considered to be important for the coagulation cascade.

  • Phosphoserine, phosphothreonine, and phosphotyrosine: These are found in many different proteins. They're known to be phospholipids and also to be found in intracellular membranes.

  • Inositol: This type of amino acid is found in many kinds of viruses.

FAQs on Non-Standard Amino Acids

1. What is an amino acid?

The simplest substance of which proteins are composed is called an amino acid. An amino acid is an organic compound composed of carbon, hydrogen, oxygen and nitrogen. The carbon, hydrogen and oxygen atoms are bonded to each other in such a way that two carboxyl groups are covalently bonded to the nitrogen atom. The carbon atom attached to one of the carboxyl groups is bonded to the nitrogen atom through a single covalent bond. The hydrogen atom attached to the other carboxyl group is bonded to the carbon atom of the amino group through two covalent bonds. When the amino group is bonded to another molecule, the nitrogen atom is called the amine group. Amino acids are derived from the amino group in the molecule lysine and the two carbon atoms of each molecule. The simplest amino acid is called glycine. It has the formula HOCH(NH2)CH3. Glycine occurs in two forms. When one carbon atom of the molecule is substituted with another carbon atom, the molecule has the form (H3NCH2C6H4) HCH(NH2)CH3, where the carbon atom on which lysine is attached is called a carbon atom of the carboxyl group and the nitrogen atom attached to the other carboxyl group is called the amine group. When the carbon atom to which lysine is attached is substituted with two other carbon atoms, the molecule has the form (H3NCH2C6H4)2 HCH(NH2)CH3.

2. What is the use of non-standard amino acids?

As a handy way to highlight that these molecules have special physical and chemical properties, several aliphatic non-standard amino acids have been proposed in the scientific literature. In one paper they're even called "non-standard" but this term is rather misleading as they are only a bit different from standard amino acids in their chemical structure. Their name originates from their being non-standard in the way they are synthesized and expressed in cells. But as you'll see on a closer look, many of these molecules also exhibit properties that differ a lot from those of standard amino acids. Amino Acid Tautomeric Form Heterotrophic Metabolism Heterotrophic organisms get their carbon (and energy) from non-photosynthetic sources. They don't directly use light to make ATP through a process called photosynthesis, as plants do. The majority of organisms that live on land today and in the past, have converted carbon dioxide into organic compounds through a process called heterotrophic metabolism.

3. What are nonstandard amino acids?

Nonstandard amino acids (nsaa) refer to the 20 common amino acids that have not been designated as standard amino acids. The nsaas have been developed from naturally occurring amino acids. They are incorporated in certain proteins and functional fragments. Although all amino acids are built up from standard-designated residues and stop-transfer RNAs, the sequence of any given amino acid may consist of sequences that were produced by alternative pathways. In some cases, different reactions yield functionally distinct products. For example, in addition to valine and isoleucine, the biosynthesis of methionine may include a combination of dehydrogenation (conserving one hydrogen) and reductive amination (conserving two hydrogens).

4. What is the importance of non-standard amino acids?

The first thing to know is that some amino acids are of great biological importance and are produced by many organisms (and plants), but are not known in proteins of other organisms. These are called "non-standard amino acids". For example, the amino acid "isoleucine" (Ile) is found in chicken egg yolk and some plants, but it is not a standard amino acid. Such an amino acid is sometimes called a "non-standard amino acid". On this page, I will use the term "non-standard amino acid" to refer to any amino acid other than the 20 common standard amino acids. Second, there are two main ways that non-standard amino acids can be incorporated into proteins. The most important way is by covalent modification of standard amino acids during translation.

5. What is the difference between non-standard amino acids and standard amino acids?

There are about 20 amino acids that are considered standard in foods. That does not mean you can’t find them in other places, but it is a great place to start. Those 20 are: The next level of amino acids is known as non-standard amino acids. These are not standard amino acids that occur naturally. They are in foods and supplements. For example, there is a very popular essential amino acid called ornithine that is considered a non-standard amino acid.

6. State the classification of standard amino acids.

One of the best ways to classify standard amino acids is based on the polarity of the R group. Polarity is considered to be the distribution of electric charge. The two types based on polarity are as follows:

 

Non-Polar Amino Acids: Non-polar amino acids are glycine, alanine, valine, leucine, isoleucine, proline, phenylalanine, methionine, and tryptophan. The R groups of this type of amino acids are considered to have either aliphatic or aromatic groups.

 

Polar Amino Acids: Polar amino acids are serine, cysteine, threonine, tyrosine, asparagine, and glutamine. The side chains in these groups of amino acids possess a spectrum of functional groups.

7. What are the basic amino acids?

The three basic types of amino acids that are known to humans and are included in the biochemistry course are arginine, lysine, and histidine. These three amino acids have basic side chains at neutral pH. Their side chains are known to have side chains that contain nitrogen in them and are also capable of resembling ammonia which is considered to be a base. Their pKa's are considered to be high enough that they have the ability to bind protons; thus; as a result, they gain a positive charge during the process. This is what basic amino acids mean; in order to get more knowledge, one has to choose biochemistry as his/her career.

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