Ramachandran Plots and Amino Acids Quiz

Amino Acid Structure and Properties

• The chemical and structural properties of amino acids are defined by their unique side chains and central α-carbon atom.
• Most naturally occurring L amino acids are found in the S-stereochemistry configuration.

Polypeptide Composition and Bonds

• Typically, 20 different amino acids are found in polypeptides.
• A peptide bond connects the α-carboxylate of one amino acid to the α-amino group of another amino acid.
• The formation of a peptide bond results in the loss of NH3+ and COO- groups.

Polypeptide Structure and Ends

• The free positively charged amino terminus is located at the N-terminus of a polypeptide.
• The repeating part of a polypeptide is called the backbone.
• The central α-carbon atom of an amino acid has attached amino, carboxyl, and hydrogen groups.

Unique Amino Acid Properties

• Glycine and proline have unique Ramachandran plots.
• In a pentapeptide, the motion of all residues is frozen except for the central residue, except for glycine.

α-Helix Structure

• The linear distance per residue in an α helix is approximately 0.15 nm.
• Hydrogen bonds between CO and NH groups stabilize local structural elements in secondary structures of proteins.
• In an α helix, the CO and NH groups form hydrogen bonds in a clockwise pattern.
• All backbone CO and NH groups of alanine, leucine, and arginine residues are involved in hydrogen bonding in an α helix.
• Essentially all α helices found in proteins have a right-handed structure.
• The φ value in a Ramachandran plot can change due to the peptide bond.
• Backbone amide to carbonyl oxygen hydrogen bonds are stabilized by the planarity of the peptide bond in proteins.

Other Secondary Structures

• Glycine is rarely found in α helices due to its small size and lack of steric hindrance.
• The β-pleated sheet structure can accommodate bulkier amino acid side chains.
• Proline is not suitable for α helices due to its rigid, non-planar structure.
• Antiparallel β-sheets are stabilized by hydrogen bonds between CO and NH groups of amino acids on adjacent strands.
• An abrupt (tight) reverse turn in the polypeptide chain direction characterizes a β-turn.

Polypeptide Chain Properties

• The charge and hydrophobicity of a peptide structure are contributed by the amino acid side chains.
• i to i+3 hydrogen bonds are commonly found in β-hairpin loops.
• There is no free rotation about the peptide bond due to its planarity.
• The distance between adjacent residues in a fully extended β-strand is approximately 0.35 nm.
• In a β-strand, the side chains of adjacent amino acids point in opposite directions.
• The peptide bond is planar, with the atoms lying in a plane.
• Parallel β-sheet structures are stabilized by hydrogen bonds between CO and NH groups of amino acids on adjacent strands.

Ramachandran Plot and Higher-Order Structure

• The Ramachandran plot illustrates the possible conformations of a polypeptide chain.
• The critical property for consideration of higher-order protein structure is the path of a polypeptide chain.
• Proline is distinguished from other amino acids by its ability to have two different configurations for its peptide bond.
• The attribute that distinguishes proline from other amino acids regarding its peptide bond is the lack of a hydrogen atom on its α-carbon atom.
• The path of a polypeptide chain is determined by the amino acid sequence and the interactions between amino acid side chains.