Stryer's Biochemistry, 4th Edition
Chapter 2. "Protein Structure and Function" and 3. "Exploring Proteins"

Today's task-A step back and a step forward.
Review key concepts presented in Chapter 1.
Complete presentation of the Chapter 2 material.
Launch into Chapter 3, "Exploring Proteins".

Key concepts

Reversible Interactions of Biomolecules are mediated by three kinds of noncovalent bonds:

1. Electrostatic bonds. In chemistry you learned that opposite charges attract while like charges repel. The case is the same in biochemistry. A charged group on a substrate may be attracted by an oppositely charged group on an enzyme. The Force of such an interaction is highly dependent on the distance between the charges and the dielectric constant of the medium (i.e., F = q₁q₂/r²D); "q" denotes the charge on each atom. In water, the dielectric constant (D) is high and therefore the charges need to be within ~2.8 Angstroms to effect a strong electrostatic interaction. Also referred to as ionic bond, salt linkage, salt bridge, or ion pair. (1 Angstrom = 10¹⁰m)

2. Hydrogen bonds. H-bonds can be formed between uncharged molecules as well as charged ones. In hydrogen bonding, a hydrogen atom is shared by two other atoms. The atom to which it is most tightly associated is called the hydrogen donor, whereas the other atom is the hydrogen acceptor. The acceptor has a partial negative charge which attracts the hydrogen. In biological systems, the donor is typically an oxygen or a nitrogen with hydrogen covalently attached. Hydrogen bonds are generally stronger than van der Walls bonds but far weaker than covalent bonds. Typical bond length = 2.6 to 3.1 Angstroms.

3. Van der Waals bonds. These are non-specific and attractive in the range of 3 to 4 Angstroms distance between any two atoms. At a shorter distance, very strong repulsive forces result. For two atoms separated by their respective van der Waals contact radii, the bond energy is generally about 1 kcal/mol or roughly 1/3rd to 1/7th that of a Hydrogen bond and an Electrostatic bond.

4. Hydrophobic/hydrophilic interactions. As you are well aware dispersed oil droplets come together to form a single large oil drop. At the atomic level and in the biologic system the same phenomenon occurs: nonpolar molecules or residues group together in the aqueous environment. Water is very polar and forms hydrogen bonds with neighboring water molecules. When nonpolar compounds are placed in water, the nonpolar molecules are squeezed together by water but held together by hydrophobic interactions.

2 transparencies.