Lecture 12: Secondary Structures (copy)

Exam Preparation

• Emphasis on providing students with a clear answer by Thursday.

• Open questions can be challenging and may frustrate students.

• When difficulty arises, focus on breaking complex material into smaller sections.

Sequence Alignment

• Importance of understanding sequence alignments in protein studies.

• Key observations from alignment:

  • Certain amino acid positions are invariant, indicating essential functions for the protein.

  • Some residues show high variability, suggesting functional flexibility or redundancy in the protein structure.

• Importance of the three-dimensional structure in protein functionality.

Protein Structure Fundamentals

Polypeptide Backbone

• Polypeptide consists of a repeating backbone of nitrogen, alpha carbon, and carbonyl carbon.

• Each amino acid contributes the following:

  • Nitrogen atom

  • Alpha carbon (Cα)

  • Carbonyl carbon (C=O)

• Understanding the directionality:

  • Amino terminus (N-terminus) starts the chain.

  • Carboxyl terminus (C-terminus) ends the chain.

Amide Linkage

• Amide linkages create flat, planar structures with no rotation due to partial double bond character.

• The amide plane connects alpha carbons.

  • Provides structural stability in the polypeptide chain.

  • Rotation occurs around the bonds that connect the alpha carbon to nitrogen and carbonyl carbon.

Folding of Polypeptides

• Folding is influenced by bond rotations which dictate protein conformation.

Phi (φ) and Psi (ψ) Angles

• Phi (φ) and Psi (ψ) angles define the conformation of the polypeptide:

  • Measured in degrees from 0 to 360 degrees.

  • Many configurations are energetically unfavorable due to steric hindrance.

• Flesh out acceptable combinations of phi and psi angles across amino acids.

Secondary Structures

Alpha Helices

• Definition: A helical structure that rotates around a central axis.

• Properties:

  • Helix type can be left-handed or right-handed.

  • Pitch of the helix = 5.4 Å.

  • Each turn contains approximately 3.6 residues.

Beta Sheets

• Structure description: Arranged in pleated formations, stabilized by hydrogen bonds.

• Types: Parallel and anti-parallel configurations.

• Loops connect the ends of beta strands; may contain helices.

• Noted as regular elements of secondary structure with a tendency to twist.

Visual Representations in Proteins

• Realistic depictions help understand structural dynamics:

  • Protein structures often exhibit loops and pleated sheets.

  • Hydrophobic residues predominate in the surface structure of proteins, influencing interaction with the environment.