Overview
This lecture covers the elemental composition of living organisms, the structure and classification of amino acids, peptide and protein structure, properties of amino acid ionization, and the hierarchical organization of protein structures.
Elements in Living Organisms
- Only a small subset of elements from the periodic table are abundant in living organisms.
- The major elements in biomolecules are carbon, hydrogen, nitrogen, oxygen, phosphorus, and sulfur.
- Minor and trace elements comprise about 3% of body weight and include essential and non-essential elements.
Biomolecules and Monomers
- Four major biomolecule types: amino acids, carbohydrates, nucleotides, and lipids.
- Amino acids form proteins, simple sugars form polysaccharides, and nucleotides form nucleic acids.
- Lipids do not form true polymers and are structurally diverse and water-insoluble.
- Monomers are simple forms; once linked in polymers, they are called residues.
Amino Acids: Structure and Classification
- Amino acids have an amino group, carboxyl group, hydrogen,and variable R group bonded to the alpha carbon.
- Most amino acids are chiral (L and D isomers), but only L-amino acids are found in proteins.
- Glycine is achiral; proline has a secondary amino group and a ring structure.
- Amino acids are grouped by side chain properties: non-polar, polar uncharged, aromatic, positively charged, and negatively charged.
- Branched-chain amino acids (valine, leucine, isoleucine) are energy sources for muscles.
Essential and Non-Essential Amino Acids
- Essential amino acids cannot be synthesized by the body and must be obtained from the diet.
- Non-essential amino acids are synthesized within the body.
Ionization of Amino Acids
- Each amino acid has at least two ionizable groups: the alpha-carboxyl and alpha-amino groups.
- Amino acids may have a third ionizable group in the side chain.
- The pKa value indicates the pH at which half of a group is ionized.
- The isoelectric point (pI) is the pH where the net charge is zero.
Peptides and Protein Structure
- Peptide bonds join amino acids via a condensation reaction between the carboxyl and amino groups.
- Peptides have direction: N-terminus (free amino) to C-terminus (free carboxyl).
- Peptides: oligopeptides (few residues), polypeptides (more than 40), proteins (large polypeptides, may have multiple subunits).
Levels of Protein Structure
- Primary: linear amino acid sequence.
- Secondary: regular local structures (alpha helix, beta sheet) stabilized by hydrogen bonds.
- Tertiary: overall 3D folding of a polypeptide, stabilized by side chain interactions and disulfide bonds (between cysteine residues).
- Quaternary: arrangement of multiple polypeptide subunits.
Folding and Function
- Correct folding is essential for protein function; misfolded proteins may aggregate or degrade.
- Hydrophobic residues cluster inside proteins, hydrophilic residues are surface-exposed.
- Disulfide bridges stabilize extracellular proteins.
Key Terms & Definitions
- Amino Acid — Organic molecule with an amino group, carboxyl group, hydrogen, and R group attached to alpha carbon.
- Chirality — Property where molecules exist in non-superimposable mirror images (L- and D- forms).
- Peptide Bond — Covalent bond joining the carboxyl group of one amino acid to the amino group of another.
- Primary Structure — Linear sequence of amino acids in a protein.
- Alpha Helix/Beta Sheet — Regular secondary structures in proteins stabilized by hydrogen bonds.
- Tertiary Structure — Full 3D shape of a single polypeptide chain.
- Quaternary Structure — Assembly of multiple polypeptide chains into a functional protein.
- pKa — pH at which an ionizable group is half protonated.
- Isoelectric Point (pI) — pH at which a molecule has no net electric charge.
- Disulfide Bridge — Covalent bond formed between sulfur atoms of two cysteine residues.
Action Items / Next Steps
- Practice determining net charge of amino acids at various pH values.
- Review amino acid side chain classifications.
- Look for warning labels about phenylalanine in food products (aspartame-containing).
- Read assigned textbook chapters on amino acids and protein structure.