In-Depth Notes on Amino Acids and Proteins

Functions of Proteins

• Proteins are polymers made from 20 different amino acids.

• Their characteristics and functions depend on the sequence of amino acids.

• Functions include:

  • Forming structural components (cartilage, muscles, hair, nails).

  • Acting as enzymes to regulate biological reactions (digestion, metabolism).

  • Transporting oxygen in the blood (e.g., hemoglobin, myoglobin).

Amino Acids

• Amino acids are the building blocks of proteins.

• Each amino acid has:

  • A central carbon atom (α-carbon).

  • An ammonium group (—NH₃⁺).

  • A carboxylate group (—COO⁻).

  • A hydrogen atom.

  • An R group (side chain) that varies among amino acids.

Classification of Amino Acids

• Amino acids are classified as:

  • Nonpolar (hydrophobic): Have hydrocarbon side chains (e.g., Valine).

  • Polar (hydrophilic): Have polar or ionic side chains (e.g., Asparagine).

Nonpolar Amino Acids

• Nonpolar when the R group is:

  • H, alkyl, or aromatic structure.

Polar Amino Acids

• Polar when the R group is:

  • An alcohol, thiol, or amide.

Structural Formulas of Amino Acids

• General structural features:

  • α-carbon attached to:

  • —NH₃⁺ group.

  • —COO⁻ group.

  • A hydrogen atom and an R group.

  • Each amino acid has a unique three-letter or one-letter abbreviation.

Acidic and Basic Amino Acids

• Acidic Amino Acids: R group contains a carboxylic acid.

• Basic Amino Acids: R group contains an amine.

Amino Acid Stereoisomers

• All α-amino acids (except glycine) are chiral due to:

  • α-carbon connected to four different groups.

  • Configurations lead to D or L enantiomers based on the position of —NH₃⁺.

Essential Amino Acids

• Of the 20 amino acids, 11 can be synthesized by the body.

• 9 essential amino acids must be obtained from diet.

Isoelectric Point (pI)

• The pH at which the amino acid has balanced charged groups (neutral).

• Exists as:

  • Positive ion in acidic solution (pH < pI).

  • Negative ion in basic solution (pH > pI).

Ionized Forms of Amino Acids

• pI values for nonpolar and polar neutral amino acids range from pH 5.1 to 6.3.

• Example: Alanine at pI 6.0 has zero charge, being a zwitterion with:

  • Carboxylate anion (—COO⁻).

  • Ammonium cation (—NH₃⁺).

• Acidic solutions add H⁺ to the carboxyl group, while basic solutions remove H⁺ from the ammonium group.

Formation of Peptides

• Peptide bond formation occurs through:

  • Linkage of two or more amino acids.

• Types of peptides:

  • Dipeptides (2 amino acids).

  • Tripeptides (3 amino acids).

  • Tetrapeptides (4 amino acids).

• Peptide bond: Amide bond between the —COO⁻ of one amino acid and the —NH₃⁺ of another.

Structural Levels of Proteins

• The primary structure: Sequence of amino acids linked by peptide bonds (e.g., Ala–Leu–Cys–Met).

• Secondary Structure:

  • Alpha Helix: Hydrogen bonds between amide groups create a spiral shape.

  • Beta-Pleated Sheet: Hydrogen bonds between carbonyl oxygen atoms and amide hydrogen create a sheet structure.

  • Triple Helix: Three polypeptide chains woven together, typical in collagen.

Tertiary Structure

• Overall 3D shape caused by interactions of different parts of the peptide chain.

• Interactions include:

  • Hydrophobic interactions (nonpolar amino acids).

  • Salt bridges (ionic bonds between charged R groups).

  • Hydrogen bonds (between R groups).

  • Disulfide bonds (between cysteine R groups).

Quaternary Structure

• Combination of two or more protein units.

• Consists of subunits (e.g., hemoglobin has four polypeptide chains).

• Stabilized by similar interactions as tertiary structure.

Denaturation of Proteins

• Disruption of bonds in secondary, tertiary, and quaternary structures by:

  • Heat or organic compounds breaking H bonds.

  • Acids/base disrupting ionic bonds.

  • Heavy metal ions reacting with S–S bonds.

  • Agitation that stretches peptide chains.

• Example: Cooking an egg denatures its proteins by disrupting tertiary structure.