Lecture 12: Secondary Structures (copy)

Sequence Alignment

A method to arrange sequences of DNA, RNA, or proteins to identify regions of similarity.

Invariant Amino Acid Positions

Positions in a protein sequence that are unchanged, indicating essential functions.

Variable Residues

Amino acid positions that show high variability, suggesting flexibility or redundancy.

Polypeptide Backbone

The repeating structure in a polypeptide consisting of nitrogen, alpha carbon, and carbonyl carbon.

Amino Terminus (N-terminus)

The start of a polypeptide chain, where the first amino acid is located.

Carboxyl Terminus (C-terminus)

The end of a polypeptide chain, where the last amino acid is located.

Amide Linkage

A bond that links amino acids; creates flat, planar structures with no rotation.

Phi (φ) Angle

An angle that defines the conformation of a polypeptide, measured from 0 to 360 degrees.

Psi (ψ) Angle

An angle that describes the rotation around the alpha carbon in a polypeptide.

Alpha Helix

A helical structure in proteins that rotates around a central axis, with specific pitch and residue count.

Beta Sheets

A secondary structure in proteins characterized by pleated formations stabilized by hydrogen bonds.

Hydrophobic Residues

Amino acids that repel water, often found on the surface of proteins, affecting environmental interactions.