General Overview of Basic Concepts in Molecular Biophysics

Abstract

This chapter provides a brief overview of the basic concepts and current questions facing biophysicists in terms of the structural characterization of proteins, protein folding, and protein-ligand interactions. Although this chapter is not meant to provide an exhaustive coverage of the entire field of molecular biophysics, the fundamental concepts are explained in some detail to enable anyone not directly involved with the field to understand the important aspects and terminology. COVALENT STRUCTURE OF BIOPOLYMERSBiopolymers are a class of polymeric materials that are manufactured in nature. Depending on the building blocks (or repeat units using polymer terminology), biopolymers are usually divided into three large classes. These are polynucleotides (built of nucleotides), peptides and proteins (built of amino acids), and polysaccharides (built of various saccharide units). In this chapter we only consider the general properties of biopolymers using peptides and proteins as examples; questions related to polynucleotides and polysaccharides will be discussed in some detail in Chapter 9.All polypeptides are linear chains built of small organic molecules called amino acids. There are 20 amino acids that are commonly considered canonical or natural. This assignment is based on the fact that these 20 amino acids correspond to 61 (out of a total 64) codons within the triplet code with three remaining codons functioning as terminators of protein synthesis (Table 1.1) (1, 2), although there