Introduction to
Chemical Bonds and
Interactions in Biology
Chemistry and Chemical Biology
Rutgers University

Overview
•   Atoms and Bonds
•   Properties of single bonds (covalent)
–   Chirality
–   Configuration
–   Conformation
•   Interactions in Biology
–   Non-covalent
•   Hydrogen bonding
•   Hydrophobic interactions
•   Electrostatic interactions
–   Covalent
•   Disulfide bridges
•   Coordinate bonds

Atoms

Bonds
•   The atoms of the elements form characteristic number of bonds.
•   The grey atoms represent atoms of elements that can form one, two or three bonds.

More on Bonds

Even more on Bonds

Representing Bonds

Properties of Single Bonds
(Covalent)
•   Chirality
•   Configuration
•   Conformation

Chirality

Molecular Chirality

Configuration
•   To go from α -D-glucose to β -D-glucose a bond has to be broken

L- and D- configurations of amino acids

Conformation
•   Described in terms of torsion angles
•   Rotation around bond
•   No bonds broken
•   Minimize non bonded interactions

Nomenclature
Saenger, Wolfram. Principles of Nucleic Acid Structure . Springer-Verlag New York Inc., 1984, p. 16.

Conformation Examples
Cyclohexanes
Pyranose sugars
Voet, Donald and Judith G. Biochemistry . John Wiley & Sons, 1990, pp. 249-250.

Non-covalent Interactions in Biology
•   Non-covalent:
–   Hydrogen bonds
–   Hydrophobic interactions
–   Electrostatic interactions
•   Covalent:
–   Disulfide bonds
–   Coordinate bonds

Hydrogen bonding

Examples of Hydrogen Bonding
Water Hydrogen Bonding Ice structure
Voet, Donald and Judith G. Biochemistry . John Wiley & Sons, 1990, p. 30.

Hydrophobic interactions
Clathrate hydrates
Voet, Donald and Judith G. Biochemistry. John Wiley & Sons, 1990, p. 179.

Electrostatic interactions
Example of electrostatic interaction in PDB entry 1HSA (MHC complex)

Disulfide Bridges
Example of a disulfide bond in
PDB entry 1HSA (MHC complex)

Coordinate Bonding
N-ter
Example of a
Zinc Finger domain
From PDB entry 1ZAA
(ZIF268 protein)
C-ter

References
Creighton, Thomas. Proteins: Structures and Molecular Principles.
W. H. Freeman and Company, 1984, p. 160.
Saenger, Wolfram. Principles of Nucleic Acid Structure .
Springer-Verlag New York Inc., 1984, pp. 15-16.
Voet, Donald and Judith G. Biochemistry .
John Wiley & Sons, 1990, pp. 30-33, 68-69, 179, 248-250.