Physical Biochemistry Basics

Study Notes

Physical biochemistry focuses on the physical properties of biological molecules, including proteins, RNA, and DNA (biopolymers).
These properties describe their structure from the atomic level to the multi-subunit level.
Properties are studied through interactions with different kinds of radiation, their behavior in electromagnetic and centrifugal fields, and quantitative aspects.
Symmetry, mathematical analysis, and diffraction methods contribute to understanding these properties.

Configuration refers to the arrangement of atoms or groups of atoms in a molecule, specifically their position around one or more nonrotating bonds or chiral centers.
A chiral center is an atom with no plane or center of symmetry, such as carbon with four different groups attached.
Conformation refers to different spatial arrangements of a molecule generated by rotation about single bonds.
- Gauche/anti, eclipsed/staggered conformations are examples, which can influence strain on a molecule.
- Torsion angle (θ) describes the angle between two groups on either side of a freely rotating chemical bond.
Key point: The terms anti and gauche apply only to bonds (or groups) on adjacent carbons, and only to staggered conformations.
Conformation change does not create a new molecule, but can alter its properties.
Native confirmation of a protein is its properly folded form, which is functional.
The unfolded or denatured conformation is nonfunctional, leading to proteolysis of the cell.
Both configuration and conformation are crucial for protein shape and function, but they represent distinct characteristics.