Proteins and Amino Acids: Biochemistry Lecture

Proteins

• Proteins are macromolecules formed from amino acids united by peptide bonds, accounting for over 50% of the dry mass of most cells.
• There are 20 amino acids that all protein molecules are made of, and some proteins contain just a few amino acids in a chain, while others are chains of thousands of amino acids.
• Polymers of proteins are called polypeptides, and a protein consists of one or more polypeptide chain.

Structure of Amino Acids

• Amino acids are organic molecules with an asymmetric carbon atom called the alpha (α) carbon at their center.
• An amino acid has four main groups: 1) Amino group (NH2), 2) Carboxyl group (COOH), 3) Hydrogen atom (H), and 4) Side chain or radical group (R).
• The 20 amino acids are distinguished by their R-group.

Amino Acid Polymers

• Amino acids are joined together through a dehydration reaction, removing a hydroxyl group from the carboxyl end of one amino acid and a hydrogen atom from the amino group of another.
• The resulting covalent bond is called a peptide bond, and repeating this process creates a polypeptide chain.
• A polypeptide chain has an amino acid with a free amino group (N-terminus) at one end and an amino acid with a free carboxyl group (C-terminus) at the other end.

Classification of Amino Acids

• Amino acids are classified into two main groups: essential and non-essential amino acids.
• Essential amino acids are not synthesized by the body and must be obtained through diet; there are 9 essential amino acids.
• Non-essential amino acids can be synthesized by the body using essential amino acids; there are 11 non-essential amino acids.

Classification of Proteins

• Proteins are classified based on their function:
  • Catalytic proteins (enzymes)
  • Structural proteins (collagen, elastin, keratin)
  • Contractile proteins (myosin, actin)
  • Transport proteins (hemoglobin, myoglobin, albumin, transferrin)
  • Regulatory proteins or hormones (ACTH, insulin, growth hormone)
  • Genetic proteins (histones)
  • Protective proteins (immunoglobulins, clotting factors)
• Proteins are also classified based on their composition:
  • Simple proteins (albumin, globulins, histones)
  • Conjugated proteins (lipoprotein, glycoprotein)
  • Derived proteins (peptones, peptides, denatured proteins)

Protein Structure

• There are four orders of protein structure: primary, secondary, tertiary, and quaternary.
• Primary structure refers to the sequence of amino acids in a polypeptide chain.
• Secondary structure is the folding or coiling of the polypeptide into a repeating configuration, resulting from hydrogen bonds between the polypeptide backbone.
• Tertiary structure is the overall three-dimensional shape of a polypeptide, resulting from interactions between amino acids and R groups.
• Quaternary structure is the overall protein structure that results from the aggregation of two or more polypeptide subunits.

Forces Controlling Tertiary Protein Structure

• Hydrogen bonds between polar side chains of amino acids
• Hydrophobic forces between non-polar (R) groups of amino acids
• Electrostatic forces (ionic bonds, salt bridges) between oppositely charged (R) groups of amino acids
• Disulfide bonds between sulfur amino acids (cysteine)

Protein Denaturation

• Protein denaturation results in the unfolding and disorganization of the protein's secondary and tertiary structures, without hydrolysis of peptide bonds.
• Denaturing agents include heat, organic solvents, high pressure, mechanical mixing, strong acids or bases, detergents, and ions of heavy metals.
• Denaturation may be reversible or, more commonly, irreversible, and denatured proteins are often insoluble and precipitate from solution.