General Biochemistry Lecture - Chapter 3: Amino Acids, Peptides, and Proteins

Key Principles

• Understand and expand upon 4 key principles from the chapter.

Amino Acids

Review of Isomers

• Isomers: Same chemical formula, different properties.
  • Structural Isomers: Different bonds.
  • Stereoisomers: Same bonds, different spatial arrangements.
    • Diastereomers: e.g., cis vs. trans arrangements.
    • Enantiomers: Mirror images (focus of this lecture).

Generic Structure

• All amino acids (except glycine) have a chiral center (α-carbon).
• Common components: amino group, carboxyl group, hydrogen, R group (side chain).
• Enantiomers: L and D configurations; L-forms are primary in proteins.

Classes of Amino Acids

• Nonpolar, Aliphatic: Stabilize protein structure via hydrophobic effect.
• Aromatic: Absorb light (270-280 nm), contribute to hydrophobic effect.
• Polar, Uncharged: Form hydrogen bonds, cysteine forms disulfide bonds/bridges.
• Positively Charged (pH 7): e.g., lysine, arginine, histidine.
• Negatively Charged (pH 7): e.g., aspartate, glutamate.

Uncommon Amino Acids

• Examples: 4-Hydroxyproline in collagen, pyrolysine, phosphorylation, metabolites like ornithine.

Acid-Base Properties

• Amino acids can act as acids or bases.
• Non-ionic form: No charge.
• Zwitterion form: Net zero charge (neutral pH).
• Zwitterions act as buffers by donating/accepting protons.
• Titration Curves: Identify species at different pH levels, important for understanding amino acid behavior.

Isoelectric Point (pI)

• Calculate pI: (pK₁ + pK₂) / 2 for amino acids without ionizable side chains.
• pH < pI: Net positive charge.
• pH > pI: Net negative charge.
• pI corresponds to zwitterion form.

Peptides and Proteins

• Peptides: Chains of amino acids, formed by condensation reactions (peptide bond).
  • Types: dipeptides, tripeptides, oligopeptides, polypeptides, proteins.
• Naming: Start with N-terminal end (amino end) to C-terminal end (carboxyl end).
  • Know 3-letter and 1-letter codes for amino acids.

Protein Purification

Methods and Properties

• Separate proteins based on size, charge, binding properties, and solubility.
• Column Chromatography: Ion-exchange, size exclusion (gel filtration), affinity chromatography.
• Electrophoresis: SDS-PAGE to estimate molecular weight and check for purity.
• Specific Activity: Total enzyme units/weight of protein. Increases as purification progresses.

Protein Structure Levels

• Primary: Amino acid sequence.
• Secondary: Alpha helices, beta sheets.
• Tertiary: 3D shape of a single polypeptide.
• Quaternary: Complexes of multiple subunits.

Protein Sequencing

• Edman Degradation: Classic method.
• Proteases: Enzymes that hydrolyze peptide bonds at specific sites.
• Mass Spectrometry: Identify protein masses and sequences; used in combination with liquid chromatography.

Chemical Synthesis of Proteins

• Method: Use protecting groups (e.g., Fmoc) to sequentially add amino acids on a resin.

Using Amino Acid Sequences

Biochemical Information

• Structure and Function: Sequence informs 3D structure and likely function.
• Cellular Location: Specific sequences may indicate cellular compartments.
• Evolution: Conserved sequences across species can indicate important functions.
  • Consensus Sequences: Highlight highly conserved residues.
• Protein Families: Homologs (family members), paralogs (within species), orthologs (across species).

Practical Considerations

• Tune into live lectures for hands-on practice and review of complex topics in preparation for exams and assignments.