MCAT Biochemistry Series: Amino Acids, Peptides, and Proteins

Introduction

• Presenter: Iman
• Objective: Start a new series on biochemistry focusing on amino acids, peptides, and proteins for the MCAT.
• Format: Review chapter content and solve practice problems.

Proteins: Functions and Importance

• Proteins account for more than 50% of dry mass in cells.
• Functions:
  • Speed up chemical reactions (enzymes)
  • Defense against invaders (immune function)
  • Storage
  • Transport
  • Cellular communication
  • Structural support
• Enzymes: Proteins that act as catalysts, lowering activation energy and speeding up reactions.
• Structural complexity: Proteins have unique 3D shapes.

Amino Acids: Building Blocks of Proteins

• 20 amino acids form proteins.
• Amino acids are linked by peptide bonds to form polypeptides.
• Amino acid structure:
  • Central carbon
  • Amino group (NH2)
  • Carboxyl group (COOH)
  • Hydrogen
  • Variable side chain (R group)
• Side chains (R groups) determine properties and functions.
• Categories:
  • Electrically charged side chains
  • Polar vs nonpolar
  • Hydrophobic vs hydrophilic

Memorization Tips

• Know the structure, three-letter code, and one-letter code for each amino acid.
• Use flashcards and frequent drawing for memorization.

Special Cases

• Glycine: Not chiral (two hydrogens attached to central carbon).
• Cysteine: R configuration, unlike others which are S.
• Proline: Causes kinks in polypeptide chains.

Acid-Base Chemistry of Amino Acids

• Amino acids can accept or donate protons.
• Ionizable groups:
  • Gain protons under acidic conditions, lose them under basic conditions.
  • Low pH: Protonated; High pH: Deprotonated
• PKA value: pH at which half of the molecules are deprotonated.
• All amino acids have at least two PKA values for the amino and carboxyl groups.
• Third PKA for some amino acids with ionizable side chains.

Titration Curves and Isoelectric Point

• Titration curves demonstrate dissociation constants.
• Isoelectric point (pI) is the pH where net charge is zero.
• Formula: pI = (pka1 + pka2) / 2
• Henderson-Hasselbalch equation relates pH, pKa, and concentration ratios.

Peptide Bond Formation

• Formed by dehydration reaction.
• Polypeptides have N-terminus (free amino group) and C-terminus (free carboxyl group).
• Peptide bonds are stable due to resonance.

Protein Structures

• Primary Structure: Linear sequence of amino acids.
• Secondary Structure: 3D structures like alpha helices and beta sheets due to interactions in the chain.
• Tertiary Structure: Overall 3D conformation due to side chain interactions.
• Quaternary Structure: Arrangement of multiple polypeptides or subunits.

Conclusion

• In the next session, practice problems related to this chapter will be tackled.
• Encouragement for further study and memorization.