Organic Chemistry - Polymers

Proteins: Structure and Description

Proteins are large biomolecules made up of amino acids. They play crucial roles in biological systems, acting as enzymes, structural components, and more. The structure of a protein is hierarchical, meaning it exists in distinct levels of organization.

Levels of Protein Structure

Proteins are typically described at four levels of structural complexity:

• Primary Structure: The linear sequence of amino acids in the polypeptide chain. This sequence is determined by the genetic code.
• Secondary Structure: Local folding patterns within the polypeptide chain, stabilized by hydrogen bonds between atoms in the peptide backbone. Common secondary structures include alpha-helices and beta-sheets.
• Tertiary Structure: The overall three-dimensional shape of a single polypeptide chain. This is determined by various interactions between the side chains (R-groups) of the amino acids, including hydrogen bonds, ionic bonds, disulfide bridges, and hydrophobic interactions.
• Quaternary Structure: The arrangement of multiple polypeptide chains (subunits) to form a functional protein complex. Not all proteins have quaternary structure.

Amino Acid Structure

Amino acids are the building blocks of proteins. Each amino acid has a central carbon atom (alpha-carbon) bonded to four different groups: an amino group (-NH₂), a carboxyl group (-COOH), a hydrogen atom (-H), and a side chain (R-group). The R-group is unique to each amino acid and determines its chemical properties.

Amino Acid	R-Group	Properties
Glycine	-H	Smallest amino acid, allows for flexibility in protein structure.
Alanine	-CH3	Non-polar, hydrophobic.
Valine	-CH(CH3)2	Non-polar, hydrophobic, branched chain.
Leucine	-CH2CH(CH3)2	Non-polar, hydrophobic, branched chain.
Proline	-CH2CH2-	Cyclic structure, often disrupts alpha-helices.
Serine	-CH2OH	Polar, hydrophilic.
Threonine	-CH(OH)CH3	Polar, hydrophilic, branched chain.
Lysine	-CH2CH2CH2NH3+	Basic, positively charged at physiological pH.
Arginine	-CH2CH2CH2NH2+	Basic, positively charged at physiological pH.
Aspartic Acid	-CH2COOH	Acidic, negatively charged at physiological pH.
Glutamic Acid	-CH2CH2COOH	Acidic, negatively charged at physiological pH.

Protein Function and Importance

The specific three-dimensional structure of a protein is essential for its function. Different types of proteins perform a wide variety of tasks:

• Enzymes: Proteins that catalyze biochemical reactions. Their active site has a specific shape that binds to the substrate.
• Structural Proteins: Provide support and shape to cells and tissues (e.g., collagen, keratin).
• Transport Proteins: Carry molecules across membranes or throughout the body (e.g., hemoglobin).
• Hormones: Chemical messengers that regulate bodily functions (e.g., insulin).
• Antibodies: Proteins produced by the immune system to fight off foreign invaders.

Denaturation of Proteins

Proteins can lose their native three-dimensional structure through a process called denaturation. This can be caused by factors such as heat, changes in pH, or exposure to certain chemicals. Denaturation disrupts the weak bonds (hydrogen bonds, ionic bonds, hydrophobic interactions) that maintain the protein's shape, leading to a loss of function.