Chapter 5: Amino Acids

Overview

• Amino acids are monomer units forming peptides and then proteins.
• Properties include polymerization, acid-base properties, and chiral nature.

Structure of Amino Acids

• Basic Structure: Central Alpha carbon (not the first carbon; carboxyl group carbon is carbon 1).
  • Alpha carbon bonded to an amino group, hydrogen, side chain (R-group), and carboxyl group.
  • Chiral molecule due to four distinct groups around alpha carbon.
  • Zwitterion forms by losing an H from carboxylic group, keeping H on the amine group.

Chirality and Stereoisomerism

• Enantiomers: Non-superimposable mirror images (L and D forms).
• Example: Alanine with structures showing L-Alanine (Levorotary) and D-Alanine (Dextrorotary).

Categories of Amino Acids

• Aliphatic (hydrophobic): Glycine, Alanine, Valine, Leucine, Isoleucine, Methionine.
• Aromatic (hydrophobic): Phenylalanine, Tyrosine, Tryptophan.
• Polar Uncharged (hydrophilic): Serine, Threonine, Asparagine, Glutamine, Cysteine.
• Polar Basic (positive charge): Histidine, Lysine, Arginine.
• Polar Acidic (negative charge): Aspartic Acid, Glutamic Acid.

Detailed Amino Acid Structures

• Aliphatic Amino Acids: Proline, Glycine, Alanine, Valine, Leucine, Isoleucine, Methionine.
  • Proline: Cyclic structure, helps with protein turns.
  • Glycine: Only non-chiral amino acid.
  • Alanine: Simple methyl side chain.
  • Valine: Iso-propyl group (looks like an inverted V).
  • Leucine: Iso-butyl group.
  • Isoleucine: Sec-butyl group, additional chiral center.
  • Methionine: Contains sulfur, start codon amino acid.
• Aromatic Amino Acids: Phenylalanine, Tyrosine, Tryptophan.
  • Absorb UV light at 280 nm.
  • Tyrosine: Alcohol group with a pKa of 10.5.
• Polar Uncharged Amino Acids:
  • Serine (alcohol group), Threonine (two-carbon chain with alcohol), Asparagine (amide form of aspartic acid), Glutamine (amide form of glutamic acid), Cysteine (contains SH group).
• Polar Basic Amino Acids:
  • Histidine (buffer at physiological pH, imidazole side chain), Lysine (diamino group), Arginine (guanidinium group, most basic).
• Polar Acidic Amino Acids:
  • Aspartic Acid, Glutamic Acid.

Titration Curves

• Neutral Side Chain Example (Alanine):
  • Protonated form (low pH), zwitterion form (pI = 6.15), fully deprotonated form (high pH).
• Acidic Side Chain Example (Glutamic Acid):
  • Three ionizable groups, pKa’s: 2.2 (carboxyl), 4.1 (side chain carboxyl), 9.7 (amine).
  • Zwitterion at pI = 3.3.
• Basic Side Chain Example (Lysine):
  • Three ionizable groups, pKa’s: 2.2 (carboxyl), ~9 (amine), 10.5 (side chain amine).
  • Zwitterion at pI = 9.8.

pKa Values for Various Side Chains

• Aspartate/Glutamate: 4
• Histidine: 6 (buffer in biological systems)
• Cysteine: 8.4 (SH group)
• Tyrosine: 10.5 (OH group)
• Lysine: 10.5 (amine side chain)
• Arginine: 12 (guanidinium group)