Amino Acids

Amino Acid alpha Helix

Core Concepts-Amino Acids

In this tutorial you will learn about the building blocks of an amino acids, as well as what they are used for and how the contribute to the formation of proteins.

Topics Covered in Other Articles

Key Terms

  • Peptide Bond – A peptide bond is the result of a condensation reaction between two amino acids: the carboxyl group of one amino acid reacts with the amino group of an adjacent amino acid, releasing a molecule of water. Short chains of amino acids linked by peptide bonds are referred to as peptides.
  • Polypeptide – A polypeptide is a polymer with a defined sequence of amino acids linked together through covalent peptide bonds.
  • Amino Acid – molecules that combine to form proteins.
  • Monomer – small subunit of a chain
  • Polymer – many subunits linked together.
  • Confirmation – three dimensional shape of a molecule

Building Blocks of Amino Acids

Amino acids are the building blocks of a larger (well known) macromolecule, proteins. They consist of a carbon bonded to a hydrogen atom, carboxyl group, amino group, and a variable group.

Amino Acid Structure

The COOH on the right hand side of the photo above is the carboxyl group. The carboxyl group is usually very important in enzymatic protein transport. On the left hand side of the photo above, the H2N, is what is known as the amino group. The large letter R in the center of the model above signifies the variable group in an amino acid. This group is what makes each amino acid different from one another, it also determines its properties. There are only 20 different R variations, meaning there are only 20 amino acids.

Twenty Standard Amino Acids

Here are the 20 different amino acid strands. The variable groups are at the bottom of each amino acid.

Polymers and Monomers

In chemistry and biology a broad term for a single subunit in a chain is a monomer. Monomer’s are the smallest building blocks. Two monomers put together create a dimer. Dimers are also just two subunits of a chain. Trimer’s link three subunits (monomers) together. Finally, the polymer is many of those subunits linked together. Each time two monomers link together to form a dimer, they go through a process known as dehydration synthesis. Similarly, two dimers (or larger chains) linking together go through the same process.

Dehydration synthesis

Therefore, dehydration synthesis links two monomers together to form one water molecule.

Amino acids are the monomers of proteins. By removing water, they form long chains of amide bonds through dehydration synthesis reactions. Peptide bonding is when amino acids link together. When just two amino acids bond this is a peptide bond, but when multiple amino acids bond together they from a polypeptide.

Amino Acids to Protein

When amino acids form polypeptides they are on the path to becoming a protein, but are not a protein yet. A polypeptide is a protein when it is in a 3D shape. There are four levels of protein structure.

Primary Structure

The primary structure is the order of amino acids in the chain, acquired by the DNA. A slight change in the primary structure can change the function of the protein.

Protein primary structure

Secondary Structure

The secondary structure is coiling and folding of a chain of amino acids. There are multiple possible secondary structures.

A common secondary structure is the alpha helix. The alpha helix is stabilized by a hydrogen bond between every fourth peptide bond. Below is the characteristic shape of an alpha helix.

Secondary Structure of Amino Acids - Alpha Helix
Alpha Helix

The beta pleated sheet is another type of secondary structure. The beta pleated sheet: non parallel polypeptide chains folded in an accordion style.

Beta Pleated Sheet of Amino Acids
Beta Pleated Sheet

Tertiary Structure

The next level of structure is the tertiary structure. The tertiary structure of a protein is the proteins three dimensional shape. This shape occurs due to the bonding of side chains, hydrophobic interactions, and Van der Wall interactions.

202101 Protein tertiary structure.png

Quaternary Structure

The quaternary structure is due to the interactions between several polypeptide chains. Usually this is a protein with one or more amino acid chains. Below the quaternary strucuture occurs because of the different color polypeptide chains interacting.

202101 Protein quaternary structure containing amino acid chains
In this diagram the blue and the pink represent different amino acid chains

Functions of Amino Acids and the Proteins they Form

The shape of a protein will determine how and if this protein is going to work. A protein can only work properly if the shape is correct for its function.

The process of denaturation alters the native confirmation of a protein. As a result, function can be dramatically altered. There are some things that denature proteins. Adding a chemical agent that disrupts hydrogen bonding, getting too hot, or changing pH can all denature proteins.