1:IV: Biochemical bonds/weak interactions

Last updated
Save as PDF

Page ID: 7275

\( \newcommand{\vecs}[1]{\overset { \scriptstyle \rightharpoonup} {\mathbf{#1}} } \) \( \newcommand{\vecd}[1]{\overset{-\!-\!\rightharpoonup}{\vphantom{a}\smash {#1}}} \)\(\newcommand{\id}{\mathrm{id}}\) \( \newcommand{\Span}{\mathrm{span}}\) \( \newcommand{\kernel}{\mathrm{null}\,}\) \( \newcommand{\range}{\mathrm{range}\,}\) \( \newcommand{\RealPart}{\mathrm{Re}}\) \( \newcommand{\ImaginaryPart}{\mathrm{Im}}\) \( \newcommand{\Argument}{\mathrm{Arg}}\) \( \newcommand{\norm}[1]{\| #1 \|}\) \( \newcommand{\inner}[2]{\langle #1, #2 \rangle}\) \( \newcommand{\Span}{\mathrm{span}}\) \(\newcommand{\id}{\mathrm{id}}\) \( \newcommand{\Span}{\mathrm{span}}\) \( \newcommand{\kernel}{\mathrm{null}\,}\) \( \newcommand{\range}{\mathrm{range}\,}\) \( \newcommand{\RealPart}{\mathrm{Re}}\) \( \newcommand{\ImaginaryPart}{\mathrm{Im}}\) \( \newcommand{\Argument}{\mathrm{Arg}}\) \( \newcommand{\norm}[1]{\| #1 \|}\) \( \newcommand{\inner}[2]{\langle #1, #2 \rangle}\) \( \newcommand{\Span}{\mathrm{span}}\)\(\newcommand{\AA}{\unicode[.8,0]{x212B}}\)

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:

Carboxylic acids
Alcohols
Amines
Aromatic rings
Alkanes
C-C single and double bonds (e. g. geometry - tetrahedral, free rotation vs. planar, restricted rotation)
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.