Overview
This lecture introduces the basics of amino acids: their structures, classification, properties, and how they form proteins via peptide bonds. The focus is on understanding amino acid side chains and their influence on protein characteristics.
Course Introduction & Structure
- The course covers structures/functions of biomolecules, bioenergetics, and metabolism.
- Topics include amino acids, proteins, enzymes, vitamins, co-enzymes, carbohydrates, lipids, and nucleic acids.
- Recommended textbooks: Stryer, Lehninger, Voet & Voet.
Central Dogma & Biological Alphabets
- Central dogma: DNA → RNA → Protein.
- DNA alphabet: A, G, T, C (nitrogenous bases).
- RNA alphabet: A, G, C, U (U replaces T).
- Protein alphabet: 20 amino acids, each with unique side chains.
Amino Acid Structure
- Amino acids have a central (alpha) carbon bonded to an amino group, carboxyl group, hydrogen, and variable R group (side chain).
- Most amino acids are chiral (asymmetric); glycine is the exception (not chiral).
Classification of Amino Acids
- Unique Amino Acids: Glycine (simple, achiral), Proline (imino acid; side chain forms a ring).
- Hydrophobic Amino Acids: Side chains contain only carbon/hydrogen; avoid water (e.g., alanine, valine, leucine, isoleucine, methionine).
- Polar Amino Acids: Side chains contain O or N; can form hydrogen bonds (e.g., serine, threonine, cysteine, asparagine, glutamine, histidine).
- Acidic Amino Acids: Side chains have additional carboxyl groups; negatively charged at physiological pH (aspartic acid, glutamic acid).
- Basic Amino Acids: Side chains have additional amino groups; positively charged at physiological pH (lysine, arginine).
- Aromatic Amino Acids: Contain aromatic rings (phenylalanine, tyrosine, tryptophan); absorb UV light at 280 nm.
Properties of Amino Acids
- Side chain properties (size, shape, charge, polarity, hydrophobicity, aromaticity) determine protein folding and function.
- Hydrophobic residues tend to be buried inside proteins; polar/charged residues often on the surface.
Peptide Bonds & Protein Representation
- Amino acids link via peptide bonds (dehydration reaction) forming proteins.
- Peptide chains have an N-terminus (NH3⁺) and C-terminus (COO⁻).
- Protein sequences are represented by three-letter or one-letter amino acid codes.
Key Terms & Definitions
- Amino acid — building block of proteins, contains central carbon, amino, carboxyl, hydrogen, and R group.
- Peptide bond — covalent bond linking amino acids in proteins, formed by condensation.
- Zwitterion — molecule with both positive and negative charges but overall neutral (common amino acid form at physiological pH).
- Chirality — property of a molecule having a non-superimposable mirror image; most amino acids are chiral.
- Aromaticity — presence of stable ring structures; in amino acids, this allows UV absorption.
- Hydrophobicity — tendency to repel water; applies to amino acids with nonpolar side chains.
- Polarity — presence of uneven charge distribution; enables hydrogen bonding.
Action Items / Next Steps
- Memorize the 20 amino acids, their structures, three-letter, and one-letter codes.
- Review side chain properties (size, charge, polarity, hydrophobicity, aromaticity).
- Read assigned textbook chapters on amino acids and peptide bond formation.