Recording-2025-03-07T14:41:19.246Z

Protonation States of Amino Acids

• Different forms of amino acids can exist based on protonation:

  • Amine groups gain a plus charge when protonated.

  • Carboxylic acids typically remain neutral.

• The concept of alpha carbon:

  • The alpha carbon is the central carbon to which the R group is attached.

  • Indicates the proximity of other functional groups in the structure.

pKa Values and Ionization

• pKa values vary across amino acid side chains; exact numbers are not to be memorized but understood in context.

• Important points regarding histidine:

  • Has a pKa close to physiological pH (around 6 to 7).

  • Allows for easy protonation and deprotonation in biological systems, making histidine common in enzyme active sites.

  • At pH below its pKa, histidine predominantly exists in a protonated state.

• General rule for determining predominant charge forms:

  • If pH < pKa, protonated form predominates.

  • The closer the pH is to the pKa, a 50/50 mix of charge forms may occur.

Classifying Amino Acids

• Four major classes of amino acids:

  1. Basic

  2. Acidic

  3. Neutral Polar

  4. Hydrophobic

• Key examples:

  • Basic: Arginine (負 charge above pH 7)

  • Acidic: Aspartate, Glutamate

  • Neutral Polar: Asparagine, Glutamine

  • Hydrophobic: Glycine, Alanine, Proline, Methionine

• Understanding these classifications is crucial for analyzing protein function and interactions.

Structure and Side Chains

• Different amino acid properties affect their behavior in proteins:

  • Neutral polar amino acids (e.g., Asparagine) do not typically become protonated due to resonance effects with carbonyl groups.

• Phylogenetic similarity in amino acids based on side chains can impact protein structure.

• Examples:

  • Aspartate and Glutamate differ from Asparagine and Glutamine primarily by one CH2 group.

Peptide Bond Formation and Structure

• Peptide bonds link amino acids through an amide linkage (N-C bond):

  • Formed in ribosome during protein synthesis (translation).

  • Amino group (NH2) attacks carboxyl group (COOH) of another amino acid.

• Characteristics of peptide linkage:

  • Exhibits partial double bond character due to resonance, preventing free rotation.

  • Enforces a cis or trans configuration, impacting protein folding and flexibility.

Limitation of Flexibility in Protein Structure

• Peptide backbones show limited flexibility due to resonance of the peptide bond,

  • The nitrogen and carbon atoms have restricted movement, creating rigid structural features.

  • Important angles between various bonds are theta and phi angles, affecting the overall structure.

• Ramachandran plots specify preferred angles for phi (N-C) and psi (C-C):

  • Visualization of allowed angles in peptide chains indicates steric hindrance.

• Glycine and proline show unique flexibility as compared to other amino acids:

  • Glycine provides flexibility without large side chains.

  • Proline has a distinct structure that causes unique rigidity and influences turning and folding of peptide chains.