NJMS Department of Biochemistry and Molecular Biology

Covalent Bonds: These are the type of bonds formed by two atoms sharing a pair of electrons. Covalent bonds are what lead to a primary structure of a molecule. These are high energy bonds with single bond energies of 50-100 Kcal/mole. See more at Birkbeck College (University of London). The following table summarizes covalent bond information of common elements of Biochemistry.
For a description of all types of bonding see MIT's Chemistry Review.

ELEMENT	CHARGE	# COVALENT BONDS	EXAMPLE	STRUCTURE
Nitrogen (N)	positive charge on nitrogen	4	Ammonia	H \|+ H--N--H \| H
Oxygen (O)	negative charge on oxygen	1	ionized ethanol	H H \| \| _ H--C--C--O \| \| H H
Sulfur (S)	negative charge on the sulfur	1	ionized mercaptoethanol	H H \| \| - H--C--C--S \| \| H H

Hydrogen Bonds: In the case of "hydrogen bonds", the terms bonds and interactions are used interchangeably.

diagram of water molecule with hydrogen bonding

This is a water dimer with H bond between oxygen of one water and H atom of another molecule.

   Here, first the H is covalently bonded to an elecronegative atom (such as an O).
   Secondly, the shared electron cloud is shifted somewhat toward the electronegative element (the O), so leaving a partial positive charge on H.
   Third, the partially positively charged H is able to interact (form a hydrogen bond) with the partially negatively charged electronegative atom ( O) of another molecule.

Hydrogen bonds (interactions) are weaker than covalent bonds. They have a bond energy of ~5 Kcal/mole. The bonds are useful iin proteins, enzymes and DNA because they provide structural stability.

The partially positively charged H of alcohol and the H bond to the N of primary amine. Note: that R stands for any side group.	H \| R--O--H ...... N--R \| H
The partially positively charged H of an amine and the H bond to the carbonyl oxygen of a ketone.	R₂--N--H ...... O=CR₂

Ionic Bonds
Note: Ionic Bonds or Electrostatic Interactions are terms that are used interchangeably.

The interaction is between a negatively charged oxygen atom of a group like a carboxylate of glutamate or aspartate and a positively charged side chain of of lysine, arginine or histidine.
This kind of interaction occurs in proteins at physiological pH because the carboxylate groups are negatively charged at pH 7.4 (pKa is ~4.0), and the Arg, Lys, and His side chains are positively charged.
For additional information, see a review by MIT-Birkbeck.

Hydrophobic Interactions or Bonds: These interactions occur between hydrophobic chains present in organic compounds or side chains of hydrophobic amino acids.
    A simple example of hydrophobia is a drop of oil in water. Oil is not miscible with water because hydrophobic chains of fatty acids hate water and prefer each other. A vigorous shaking (providing energy) breaks up the oil droplet into micelles but if you let them sit for a while, strong hydrophobic interactions will force the micelles into the original drop.
    The hydrophobic bonds are stronger than H bonds but weaker than covalent bonds.
    In a globular protein (which is soluble in water), hydrophobic side chains tend to point to the interior of the protein structure and away from bulk water.
   On the other hand, hydrophobic side chains of membrane proteins interact with the membrane's phospholipid membrane bilayers, and so do not tend to aggregate to the interior.