Amino acids-building block of proteins

Amino acids are organic compounds that serve as the building blocks of proteins, which are essential components of living organisms. The basic structure of an amino acid consists of a central carbon atom, often referred to as the alpha carbon, attached to four different chemical groups: a hydrogen atom, an amino group (-NH2), a carboxyl group (-COOH), and a side chain, also known as the R-group. Amino acids are not only essential for protein synthesis but also contribute to the synthesis of other important molecules, such as neurotransmitters, hormones, and certain coenzymes.

general structure of amino acids

Amino acids are compounds containing carbon, hydrogen, oxygen and nitrogen and serves as monomers of proteins. These compounds contains both an amino group and carboxylic group. In an amino acids, the amino and carboxylic group are attached to the same carbon atom which is called an alpha carbon.

The various amino acids differ with respect to the side chain called the R- group. It is the unique side chain that differentiates one amino acid from another. 

Amino acids are often associated with chiral carbon atoms. A chiral carbon, or stereocenter, is a carbon atom that is bonded to four distinct groups, creating a non-superimposable mirror image known as a stereoisomer. In the case of amino acids, the alpha carbon (the central carbon atom) is the chiral carbon.

The simplest amino acid is the glycine which contains H as a R- group. Tryptophan is often considered one of the most complex amino acids due to its large and intricate side chain. It contains a two-ring structure, including an indole ring, making it relatively bulky compared to other amino acids.

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Amino acids as Zwitter ion:-

When an amino acid is dissolved in water, it exists in solution as the dipolar ion, or zwitterion. A zwitterion can act as either an acid (proton donor) or a base (proton acceptor).Substances having this dual nature are amphoteric and are often called ampholytes.

A Zwitter ion can acts as either an acid a proton donor o a base as a proton acceptor. At low pH, the positively charged species predominates and the pH increases the electrically neutral Zwitter ion becomes predominant and at higher pH, the negatively charged species predominates.

At physiological pH, the amino groups are protonated and the carboxylic groups are deprotonated.

standard and non-standard amino acids 

there are 22 different amino acids participates in protein synthesis which are incorporated by ribosomes into proteins. such amino acids are called standard amino acids or can be called as proteinogenic amino acids.

Amino acids that are occur naturally in cells but are not incorporated by ribosomes into proteins are called non-standard amino acids , these are synthesized proteins by ribosomes post translational modifications of standard amino acids.

Among these uncommon amino acids are 4-hydroxyproline, a derivative of proline, and
5-hydroxylysine, derived from lysine. Another important uncommon amino acid is -carboxyglutamate, found in the blood-clotting protein prothrombin and in certain other proteins that bind Ca2+ as part of their biological function. 

Selenocysteine is a special case, it is the 21st amino acid . This rare amino acid residue is introduced during protein synthesized rather than created through a post synthetic modification. It contains selenium rather than the sulfur of cysteine. Actually derived from serine, selenocysteine is a constituent of just a few known proteins. it is specified by the stop codon, (UGA).

classification of standard amino acids

Nonpolar, Aliphatic R Groups- The R groups in this class of amino acids are nonpolar and hydrophobic. The sidechains of alanine, valine, leucine, and isoleucine, Glycine has the simplest structure. Methionine, one of the two sulfur-containing amino acids, has a non-polar thioether group in its side chain. Proline has an aliphatic side chain with a distinctive cyclic structure. The secondary amino (imino) group of proline residues is held in a rigid conformation that reduces the structural flexibility of polypeptide regions containing proline.

Aromatic R Groups- Phenylalanine, tyrosine, and tryptophan, with their aromatic side chains, are relatively nonpolar (hydrophobic). Tyrosine and tryptophan are significantly more polar than phenylalanine, because of the tyrosine hydroxyl group and the nitrogen of the tryptophan indole ring. 

Polar, Uncharged R Groups- The R groups of these amino acids are more soluble in water, or more hydrophilic, than those of the nonpolar amino acids, because they contain functional groups that form hydrogen bonds with water. This class of amino acids includes serine, threonine, cysteine, asparagine, and glutamine. The polarity of serine and threonine is contributed by their hydroxyl groups; that of cysteine by its sulfhydryl group; and that of asparagine and glutamine by their amide groups.

Positively Charged (Basic) R Groups -The most hydrophilic R groups are those that are either positively or negatively charged. The amino acids in which the R groups have significant positive charge at pH 7.0 are lysine, which has a second primary amino group at the position on its aliphatic chain; arginine, which has a positively charged guanidine group; and histidine, which has an imidazole group.

Negatively Charged (Acidic) R Groups- The two amino acids having R groups with a net negative charge at pH 7.0 are aspartate and glutamate, each of which has a second carboxyl group.

configuration of amino acids:-

A chiral carbon amino acids can exist in 2 configuration and these two configurations are called enantiomers. 

Enantiomers are a type of stereoisomer, which means they are molecules with the same molecular formula and connectivity of atoms but differ in their three-dimensional spatial arrangement. Specifically, enantiomers are mirror-image isomers, much like left and right hands are mirror images of each other.

D and L system:-

Special nomenclature has been developed to specify the absolute configuration of the four substituents of asymmetric carbon atoms. The absolute configurations of simple sugars and amino acids are specified by the D, L system based on the absolute configuration of the three-carbon sugar glyceraldehyde, a convention proposed by Emil Fischer in 1891.

For all chiral compounds, stereoisomers having a configuration related to that of L-glyceraldehyde are designated L, and stereoisomers related to D-glyceraldehyde are designated D.

NOTE:- The D and L designations specify the configuration of a single reference carbon. all the amino acids which are ribosomically incorporated into proteins exhibit L configuration. therefore they are all L amino acids.

R and S system:-

The R and S system, also known as Cahn-Ingold-Prelog priority rules, is a method used in organic chemistry to assign a specific label (either R or S) to chiral centers in molecules.

The rules for determining whether a chiral center is labeled as R or S are as follows:

1. Assigning Priority:

   • Assign priority to each substituent attached to the chiral center based on the atomic number of the atoms directly bonded to the chiral carbon.
   • The higher the atomic number, the higher the priority.

2. Orienting the Molecule:

   • Arrange the molecule so that the lowest priority substituent (usually hydrogen) is pointing away from you in three-dimensional space.

3. Determining Rotation:

   • Observe the sequence of priorities (from highest to lowest) as you move in a clockwise or counterclockwise direction around the chiral center.

4. Assigning Configuration:

• If the sequence of priorities is clockwise, the configuration is labeled as "R" (from the Latin "rectus" meaning right).
• If the sequence of priorities is counterclockwise, the configuration is labeled as "S" (from the Latin "sinister" meaning left).
5. The R and S labels describe the absolute configuration of a chiral center and provide a standardized way of communicating the three-dimensional arrangement of substituents. Enantiomers will have opposite R/S configurations at chiral centers.

conclusion:-

1) Amino acids are the building blocks of proteins that composed of a hydrogen group, the amino group. the carboxylic group and the side chain which is different for different amino acids.

2) Amino acids are chiral carbons that are optically active carbons that are called enantiomers.

3) These enantiomers shows 2 types of configuration systems first is D and L system and the second is the R and S system.

4)Amino acids are classified into 4 types first Nonpolar, Aliphatic R Groups ,   Aromatic R Groups, Polar, Uncharged R Groups, Positively Charged (Basic) R Groups and Negatively Charged (Acidic) R Groups.

FAQs:-

Q1)  What amino acid means?

Ans:- Amino acids are organic compounds that serve as the building blocks of proteins. Proteins are essential macromolecules in living organisms, and they play crucial roles in various biological processes. Amino acids are characterized by having both amino (-NH2) and carboxyl (-COOH) functional groups. The structure of an amino acid consists of a central carbon atom (alpha carbon) bonded to a hydrogen atom, an amino group, a carboxyl group, and a side chain (often referred to as "R group").

Q2) What are the 4 types of amino acids?

Ans:- Amino acids are classified into 4 types first Nonpolar, Aliphatic R Groups ,   Aromatic R Groups, Polar, Uncharged R Groups, Positively Charged (Basic) R Groups and Negatively Charged (Acidic) R Groups.

Q3) What is 20 amino acids?

Ans:- Alanine (Ala, A), Arginine (Arg, R), Asparagine (Asn, N), Aspartic Acid (Asp, D), Cysteine (Cys, C), Glutamic Acid (Glu, E), Glutamine (Gln, Q), Glycine (Gly, G), Histidine (His, H), Isoleucine (Ile, I), Leucine (Leu, L), Lysine (Lys, K), Methionine (Met, M), Phenylalanine (Phe, F), Proline (Pro, P), Serine (Ser, S), Threonine (Thr, T), Tryptophan (Trp, W), Tyrosine (Tyr, Y), Valine (Val, V).

Q4) What is the R group?

Ans:- The "R group" (also known as the "side chain") is a term used to describe the variable part of an amino acid's structure. The R group is what distinguishes one amino acid from another. It can be as simple as a single hydrogen atom (in the case of glycine) or a complex structure in other amino acids.

Q5) what are the benefits of amino acids?

Ans:- Protein Synthesis: Amino acids are the building blocks of proteins. They are essential for the synthesis of structural and functional proteins in the body. Proteins are vital for the growth, repair, and maintenance of tissues, including muscles, skin, and organs.

1. Muscle Growth and Repair: Amino acids, particularly branched-chain amino acids (BCAAs) such as leucine, isoleucine, and valine, are essential for muscle protein synthesis. They contribute to muscle growth and repair, making them important for athletes, bodybuilders, and individuals engaged in physical activities.

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3. Energy Production: Certain amino acids can be converted into energy through processes like gluconeogenesis and the citric acid cycle. During periods of increased energy demand, amino acids can serve as an energy source.

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5. Immune Function: Amino acids are involved in the production of antibodies and immune system components. They play a role in supporting the body's defense mechanisms and help maintain a healthy immune system.