Amino Acid Structure and Classification

Amino Acid Structure and Classifications 🧮

Amino acids are the essential building blocks of proteins. Each protein's unique composition of amino acids determines its specific structure and function, much like how Lego pieces can be put together to create many different unique 3D models. Each amino acid contains an amino group (–NH2) and a carboxyl group (–COOH). The 20 proteinogenic alpha amino acids have both the amino and carboxyl groups attached to the alpha carbon, which is also attached to an R group specific to each amino acid. The alpha carbon is chiral (unless R = H, as with glycine).

The image above depicts the general structure of an amino acid. Note the central alpha carbon bonded to an amino group, a carboxyl group, a hydrogen atom, and the unique R group, which determines the amino acid's identity and properties.

Each of the 20 amino acids has a one-letter and a three-letter abbreviation. These abbreviations are like shorthand codes that make it easier to communicate complex biochemical information.

The image above shows a comprehensive table of amino acids, categorized into distinct groups based on their properties. The table is divided into four sections: nonpolar/hydrophobic amino acids, nonpolar/hydrophobic aromatic amino acids, polar/hydrophilic uncharged amino acids, and polar/hydrophilic charged amino acids. Each section provides detailed information about the amino acids, including their names, abbreviations, and symbols.

Each amino acid and its classification ➗

As shown in the table above, the 20 amino acids can be classified into various groups depending on their hydrophilicity, charge, and aromaticity. Because amino acids have unique side chains, they have unique chemical properties and roles in proteins.

1. Nonpolar, Nonaromatic Amino Acids 🧲

These amino acids have hydrophobic side chains that avoid water and stabilize protein structures by aligning towards the interior of the protein molecule. Examples include:

• Glycine (Gly, G):

  This is the simplest amino acid, with just a hydrogen atom as its side chain, providing flexibility to protein structures. It can be found on the inside or outside of proteins.

  The image above shows the chemical structure of glycine, highlighting its simple structure with a hydrogen atom as its side chain.

• Alanine (Ala, A), Valine (Val, V), Leucine (Leu, L), and Isoleucine (Ile, I):

  These amino acids have alkyl side chains of varying lengths, contributing to the hydrophobic core of proteins.

  The image above shows the structures of alanine, valine, leucine, and isoleucine. Notice the variations in their alkyl side chains, contributing to their hydrophobic properties.

• Methionine (Met, M):

  This amino acid contains a sulfur atom within a thioether group, and it's often involved in initiating protein synthesis.

  The image above illustrates the chemical structure of methionine, emphasizing the presence of a sulfur atom in its side chain.

• Proline (Pro, P):

  This amino acid is unique due to its cyclic structure that incorporates the amino nitrogen, restricting flexibility; it's often found in turns and loops of proteins.

  The image above shows the structure of proline. Notice the cyclic structure incorporating the amino nitrogen.

2. Aromatic Amino Acids 🧲

These amino acids have aromatic rings in their side chains, which can absorb UV light, making them useful in determining protein concentration via spectroscopy. Examples include:

• Phenylalanine (Phe, F):

  This amino acid is nonpolar, with a benzyl side chain, contributing to the hydrophobic core.

  The image above depicts the structure of phenylalanine, highlighting its benzyl side chain.

• Tyrosine (Tyr, Y):

  This amino acid is polar due to a hydroxyl group attached to the benzyl ring. Its structure is vital to signaling pathways using tyrosine kinase receptors.

  The image above illustrates the chemical structure of tyrosine, emphasizing the hydroxyl group attached to its benzyl ring.

• Tryptophan (Trp, W):

  This is the largest amino acid, with a complex double ring that includes a nitrogen atom, and plays an important role in protein-protein interactions.

  The image above shows the structure of tryptophan, highlighting its large, complex double ring structure.

3. Polar, Uncharged Amino Acids 🧲

These amino acids have side chains that can form hydrogen bonds with water, making them hydrophilic. Examples include:

• Serine (Ser, S) and Threonine (Thr, T):

  These both contain hydroxyl groups, which are often involved in phosphorylation.

  The image above depicts the structures of serine and threonine. Take note of the hydroxyl groups in both.

• Cysteine (Cys, C):

  This amino acid has a thiol group, making it reactive and prone to forming disulfide bonds, which are crucial for protein stability.

  The image above shows the chemical structure of cysteine. Note the thiol group (SH) in its side chain.

• Asparagine (Asn, N) and Glutamine (Gln, Q):

  These contain amide groups that do not gain or lose protons, remaining neutral in charge and often involved in hydrogen bonding.

  The image above shows the structures of asparagine and glutamine. Notice the presence of amide groups in their side chains.

4. Charged Amino Acids 🧲

These amino acids can be further divided into acidic and basic amino acids based on their side chain charges. They are often important for enzymatic activity and for creating electrostatic interactions that help to stabilize protein structure.

Acidic (Negatively Charged):

• Aspartic Acid (Asp, D) and Glutamic Acid (Glu, E):

  These amino acids have carboxyl groups in their side chains, which lose protons and become negatively charged. They are often involved in active sites of enzymes.

  The image above shows the structures of aspartic acid and glutamic acid. Note the carboxyl groups in their side chains.

Basic (Positively Charged):

• Lysine (Lys, K):

  This amino acid has a terminal primary amino group, often involved in binding to negatively charged molecules.

  The image above depicts the chemical structure of Lysine, showcasing its functional groups and side chain.

• Arginine (Arg, R):

  This amino acid contains a guanidinium group, making it highly basic and often involved in protein binding.

  The image above depicts the chemical structure of Arginine. The molecule consists of a central carbon chain with an amino group (NH2) and a carboxyl group (COOH) attached, as well as a guanidinium group, which is a positively charged functional group.

• Histidine (His, H):

  This amino acid contains an imidazole ring, which can shuttle protons, playing a crucial role in enzyme active sites and buffering.

  The image above depicts the chemical structure of Histidine, showcasing its functional groups and side chain.

Amino Acid Metabolism and Synthesis 🧪

• Essential Amino Acids: Cannot be synthesized by the human body and must be obtained from the diet. These include histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, and valine.

• Non-Essential Amino Acids: Can be synthesized by the body. These include alanine, asparagine, aspartic acid, glutamic acid, serine, arginine, cysteine, glutamine, glycine, proline, and tyrosine.

Post-Translational Modifications 🧬

Amino acids in proteins can undergo various post-translational modifications that affect protein function, localization, and interactions:

• Phosphorylation:

  Addition of phosphate groups (usually to serine, threonine, or tyrosine), playing a critical role in signaling pathways.

• Glycosylation:

  Attachment of carbohydrate groups, affecting protein folding, stability, and cell recognition.

• Acetylation and Methylation:

  Modifications that typically occur on lysine residues, influencing gene expression and protein function.

• Ubiquitination:

  Attachment of ubiquitin to lysine residues, tagging proteins for degradation.