Amino acids – building blocks of Proteins

By | July 31, 2021
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Amino acids (aa) are the building blocks of proteins, which happens to be one of the 4 important biological macromolecules. Amino acids are organic compounds made up of nitrogen, carbon, hydrogen and oxygen, along with a variable side chain group. All amino acids share a similar fundamental structure. The central carbon atom, or also termed as a alpha (α) carbon, bound to an amino group (NH2), a carboxyl group (COOH), and to a hydrogen atom. Every amino acid also has a important atom or group of atoms bonded to the central atom known as the R group.

amino acid structure

In most of the living organisms, proteins are synthesized using 20 amino acids and all these 20aa’s differ in their R group and rest of the structure remains similar. proteins are formed by a process called as Translation ( mainly involves different types of RNAs). The primary sequence of a protein is formed by a process called as dehydration synthesis. Here, the carboxylic acid of the upstream amino acid is linked to the amine functional group of the downstream amino acid to form a peptide bond and release of water molecule. Subsequent amino acids will be added onto the carboxylic acid terminal of the growing protein. It is important point to remember that the new amino acids are always added onto the carboxylic acid tail, never onto the amine of the first or earlier amino acid in the chain and this linking of aa’s follow in a specific pattern, starting with the amine and ending with the carboxylic acid tail.

Linking of amino acids by peptide bonds

As mentioned earlier, in our body, a total of 20 alpha amino acids that are commonly incorporated into protein structures. They are

Non Polar or Hydrophobic amino acids : Glycine ( Gly – G), Alanine ( Ala- A), Valine ( VLA – V), Leucine ( Leu -L), Isoleucine (ile – I), Phenylalanine (Phe – F), Tyrosine (Tyr – T), Tryptophan (Trp – W), proline ( pro – P), Methionine ( Met – M)

Polar or Hydrophilic amino acids: Cysteine (Cys – C ), Serine (Ser – S), Threonine (Thr – T ), Asparagine (Asn -N), Glutamine (Gln – Q)

Acidic amino acids : Aspartic acid (Asp – D), and Glutamic acid ( Glu -E)

Basic amino acids: Lysine ( Lys-K), arginine (Arg – R), Histidine ( His – H)

All amino acids are represented as a single upper case letter or a three-letter abbreviation . For example, the letter H or the three-letter symbol His represent Histidine.

20 alpha amino acids used in synthesis of proteins

Essential amino acids:

Humans can synthesize 11 out of 20 aa required for normal function of the body. The remaining 9 are essential” to be supplemented through the diet, hence termed as essential aa. This doesn’t mean that the remaining 11 which our body has the capability to produce, are non essential aa in real sense. They non essential aa are also vital for our growth and survival but are termed non essential aa only because there is no need to supply them through the diet. Even absence of any one of these 9 essential aa in our diet leads to defects in proteins synthesis. Our body can store excess fat and starch for emergency use but similar mechanism is not observed when it comes to storing store excess amino acids for later use—Hence these aa must be supplemented through food every day.

The following are categorized as essential amino acids:

Histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan and valine.

There is another category of aa’s termed as conditional essential aa, which are required only during certain times such as illness or stress. eg; Arginine in cancer cells.

Synthesis of amino acids:

As we have seen in the blog post “4 major biological macromolecules” has made up of individual components termed as monomers. In case of protein macromolecule, they are polymers of amino acid monomers. But how does our body synthesize there monomers in the first place or what is the source for these monomers?

So far more than 500 amino acids ( Thanks to pioneering work of Gordon, Martin, & Synge 1943 using partition chromatography) are known to present in nature. However, only 20 amino acids are required for the protein synthesis. Out of these 20 amino acids, our body can synthesize only 11 of them.

Amino acid synthesis is a highly energy consuming process and also all the enzymes involved in various aa synthesis processes are regulated tightly at the level of transcription by regulators of gene expression within the cells. Our body has devised mechanisms to synthesize amino acids using required for different functions within the body.

The process by which our body synthesizes there amino acids involves set of biochemical reactions, where the substrate or starting material for synthesis is usually some compounds present in the food we eat or any intermediate compound formed during biochemical pathways ( Krebs cycle, Glycolysis etc.).

This allows us to understand that our cells doesn’t always start from scratch when it comes to synthesis of molecules required for any important function. In this case of aa synthesis, the cell doesn’t start accumulating nitrogen, carbon, sulfur, oxygen, hydrogen etc. and rather use best available intermediate compounds present in the cell, as the substrates to produce required amino acids. This way cells preserve lots of energy, which is required to start everything from start as it might have happened at origin (beginning) of life.

Energy is a prerequisite for forming chemical bonds between elements to form compounds. Sometimes, synthesis of a particular aa requires multiple steps and each catalyzed by different enzyme. Cells also need to spend lot of energy in transcription and translations of all involved enzymes in various aa synthesis steps. Significant amount of energy can be saved by using already available intermediate compounds, which can by pass some steps of the biosynthetic pathway to produce desired amino acid.

The citric acid cycle (also called as Krebs cycle or tricarboxylic acid cycle) which occurs in the mitochondria in which 36 mol of ATP are formed from a single glucose molecule. This cycle involves many organic compounds at different steps, which serve as intermediates for the biosynthesis of amino acids (e.g., glutamate is synthesized from α-ketoglutaric acid, an intermediate in the citric acid cycle).

The amino acids synthesis pathways can be grouped into several units. This grouping is based on similarities of mechanism employed to form amino acids eg: enzymes use for synthesis of more than one amino acid. These groups are: simple reactions, aromatic amino acids, threonine / lysine, serine/glycine, and branch chain amino acids. Synthesis of some aa involve unique pathways as evident in synthesis of cysteine, methionine, proline, histidine and arginine. The aromatic amino acids, threonine/lysine and serine/glycine pathways have a common beginning and then diverge to form the amino acid of interest.

For detailed synthesis reactions of all amino acids, Please refer

Functions of amino acids:

Apart from their role in composing proteins, amino acids have many other biologically important functions.

  • serves as energy metabolites
  • Nutrients
  • Function as as chemical messengers in communication between cells eg: 3-hydroxytyramine (dopamine) is also a key neurotransmitter.
  • Amino acids such as Glycine, cysteine, and alanine serve as food additives and mixture of these work as flavor enhancers in the food industry. 
  • Commercial production of amino acids is a huge industry. Monosodium glutamate (MSG) – sodium salt of glutamic acid, is used to intensify the natural flavor of certain foods especially in cuisines of China and Japan

Amino acids and early life on earth:

In a bid to understand how life might have formed on our planet Earth. Two scientists – Miller and Urey in the year 1953, recreated conditions of early life on earth in a pioneering experiment. They took ammonia, hydrogen, methane, and water vapor in a flask and to this they provided electrical sparks. Then they analyzed the contents in the flask.

They inferred that their experiment led to formation of new molecules and among these were eleven standard amino acids. This allowed them to propose that the simple (first) organisms or life might have arose millions of years ago, in an environment similar to the one they recreated in their flask and this what we know as primordial soup.

This hypothesis was further extended to explain the origin of slightly complex organisms, evolving from simple life forms. This constant competition between organism to make use of available organic supplements in the environment present during that time. This competition might had led to the evolution of organisms to biosynthesize their own nutrients / monomers required for synthesis of macromolecules for growth and proper functioning of the cell. Scientists are of the opinion that significant amounts of organic compounds on early Earth may have been derived from comet and meteorite impacts. These resultants organic compounds serves as precursors to amino acids and other molecules or compounds required for biosynthesis of major biological macromolecules of the cell.

Image credit :


amino acids synthesis overview – Wikipedia