Amino Acids and Proteins (Biology Link)

Amino Acids Structure

Amino acids are the building blocks of proteins. Each amino acid has three main parts:

• Amino group (-NH₂): a basic group containing nitrogen.
• Carboxyl group (-COOH): an acidic group.
• Variable R group: this is different for each amino acid and determines its properties.

In solution, amino acids exist as zwitterions. This means the amino group gains a hydrogen ion (H⁺) becoming -NH₃⁺, and the carboxyl group loses a hydrogen ion becoming -COO⁻. The molecule has both positive and negative charges but is overall neutral.

For example, glycine, the simplest amino acid, has an R group of just a hydrogen atom (H). Its structure is:

NH₂–CH₂–COOH

The zwitterion form of glycine in water is:

NH₃⁺–CH₂–COO⁻

Peptide Bond Formation

Amino acids join together to form proteins through peptide bonds. This happens in a condensation reaction, where a molecule of water is removed.

The peptide bond forms between the carboxyl group (-COOH) of one amino acid and the amino group (-NH₂) of another.

When two amino acids join, they form a dipeptide. Many amino acids joined together form a polypeptide, which folds to become a protein.

The general reaction is:

Amino acid 1 + Amino acid 2 12 Dipeptide + Water

The water molecule comes from the -OH of the carboxyl group and an -H from the amino group.

For instance, if glycine and alanine join, the peptide bond forms between glycine's carboxyl group and alanine's amino group, releasing water.

Example: When two amino acids join, the peptide bond forms and one water molecule is released. This is why proteins are called natural polymers made from amino acid monomers.

Protein Structure Levels

Proteins have complex structures organised into four levels:

Primary Structure

This is the sequence of amino acids in the polypeptide chain. The order is determined by genetic information and affects the protein's final shape and function.

Secondary Structure

This is the local folding of the polypeptide chain into shapes like:

• Alpha helix: a spiral shape held by hydrogen bonds.
• Beta pleated sheet: folded, sheet-like structures also stabilised by hydrogen bonds.

Tertiary Structure

This is the overall 3D folding of the polypeptide chain. It is held together by various interactions:

• Hydrogen bonds
• Disulfide bridges (strong covalent bonds between sulfur atoms in cysteine amino acids)
• Ionic bonds between charged R groups
• Hydrophobic interactions where non-polar R groups cluster inside

The tertiary structure determines the protein's specific shape and function.

Quaternary Structure

Some proteins consist of more than one polypeptide chain. The quaternary structure is the arrangement of these multiple chains into a functional protein.

For example, haemoglobin has four polypeptide chains working together to carry oxygen in blood.

Example: The primary structure is like a string of beads (amino acids). The secondary structure is how the string coils or folds locally. The tertiary structure is how the whole string folds into a specific 3D shape. The quaternary structure is when several folded strings join to form a larger protein.

Functions of Proteins

Proteins have many vital roles in living organisms:

• Enzymes: Proteins that act as biological catalysts, speeding up chemical reactions without being used up. Each enzyme has a specific shape that fits its substrate.
• Structural proteins: Provide support and strength. For example, collagen in skin and keratin in hair and nails.
• Transport proteins: Carry substances around the body. Haemoglobin transports oxygen in the blood.
• Signalling proteins: Hormones like insulin regulate body processes.
• Antibodies: Proteins that help the immune system recognise and fight pathogens.

The shape of a protein is crucial to its function. If the shape changes (denaturation), the protein may no longer work properly.

Example: Enzymes have an active site that fits a specific substrate. If the enzyme's tertiary structure changes due to heat or pH, the active site changes shape and the enzyme stops working.