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Biology LibreTexts

1:IV: Biochemical bonds/weak interactions

A. Hydrogen bonds (H-bonds)

The "H-bond donor" - a hydrogen bound to an electronegative atom (usually "O" or "N") in an organic compound forms this bond with an "H-bond acceptor" - an electronegative atom in the same or another compound (also usually and "O" or an "N").
H-bond donors: the "H" in -OH, -NH3+
H-bond acceptors: an "O" in -OH, -C=O, -CO2- or the "N" in -NH2 or the equivalent.

B. Salt bridges

The weak interaction between fully charged ions (e. g. Na+, K+, Cl-, -CO2-, -NH3+) when they are dissolved in an aqueous solution. The water shields the ions making their normally strong interactions much weaker.

C. Van der Waals interactions


(D. Hydrophobic interactions)


Some take home information


Bond/interaction energy length
Van der Waals 0.08 kJ/mole for single atoms (~7 kJ for benzene rings) 0.1 - 0.17 nm
H-bond 12 - 30 kJ/mol 0.2 - 0.27 nm
Ionic Bond ~500 kJ/mol  
Salt Bridge ~30 kJ/mol  
Covalent Bond 350 - 450 kJ/mol 0.1 - 0.15 nm
Hydrophobic interaction 0.01 kJ/mol per square angstrom (13 kJ/mol for benzene rings)  

Two quarters of organic chemistry are one of the prerequisites for BIS102. What organic chemistry should I remember? Largely the properties of a few kinds of molecules that are important in biochemistry. At a minimum, you should recall the structure and properties of the following compounds/functional groups:

  1. Carboxylic acids
  2. Alcohols
  3. Amines
  4. Aromatic rings
  5. Alkanes
  6. C-C single and double bonds (e. g. geometry - tetrahedral, free rotation vs. planar, restricted rotation)
  7. Aldehyde/ketone (i. e. carbonyl oxygen)

Also, you should be familiar with the basics of the processes of nucleophilic attack, acid catalysis and base catalysis.