1:IV: Biochemical bonds/weak interactions
- Page ID
- 7275
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\(\newcommand{\avec}{\mathbf a}\) \(\newcommand{\bvec}{\mathbf b}\) \(\newcommand{\cvec}{\mathbf c}\) \(\newcommand{\dvec}{\mathbf d}\) \(\newcommand{\dtil}{\widetilde{\mathbf d}}\) \(\newcommand{\evec}{\mathbf e}\) \(\newcommand{\fvec}{\mathbf f}\) \(\newcommand{\nvec}{\mathbf n}\) \(\newcommand{\pvec}{\mathbf p}\) \(\newcommand{\qvec}{\mathbf q}\) \(\newcommand{\svec}{\mathbf s}\) \(\newcommand{\tvec}{\mathbf t}\) \(\newcommand{\uvec}{\mathbf u}\) \(\newcommand{\vvec}{\mathbf v}\) \(\newcommand{\wvec}{\mathbf w}\) \(\newcommand{\xvec}{\mathbf x}\) \(\newcommand{\yvec}{\mathbf y}\) \(\newcommand{\zvec}{\mathbf z}\) \(\newcommand{\rvec}{\mathbf r}\) \(\newcommand{\mvec}{\mathbf m}\) \(\newcommand{\zerovec}{\mathbf 0}\) \(\newcommand{\onevec}{\mathbf 1}\) \(\newcommand{\real}{\mathbb R}\) \(\newcommand{\twovec}[2]{\left[\begin{array}{r}#1 \\ #2 \end{array}\right]}\) \(\newcommand{\ctwovec}[2]{\left[\begin{array}{c}#1 \\ #2 \end{array}\right]}\) \(\newcommand{\threevec}[3]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \end{array}\right]}\) \(\newcommand{\cthreevec}[3]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \end{array}\right]}\) \(\newcommand{\fourvec}[4]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \\ #4 \end{array}\right]}\) \(\newcommand{\cfourvec}[4]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \\ #4 \end{array}\right]}\) \(\newcommand{\fivevec}[5]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \\ #4 \\ #5 \\ \end{array}\right]}\) \(\newcommand{\cfivevec}[5]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \\ #4 \\ #5 \\ \end{array}\right]}\) \(\newcommand{\mattwo}[4]{\left[\begin{array}{rr}#1 \amp #2 \\ #3 \amp #4 \\ \end{array}\right]}\) \(\newcommand{\laspan}[1]{\text{Span}\{#1\}}\) \(\newcommand{\bcal}{\cal B}\) \(\newcommand{\ccal}{\cal C}\) \(\newcommand{\scal}{\cal S}\) \(\newcommand{\wcal}{\cal W}\) \(\newcommand{\ecal}{\cal E}\) \(\newcommand{\coords}[2]{\left\{#1\right\}_{#2}}\) \(\newcommand{\gray}[1]{\color{gray}{#1}}\) \(\newcommand{\lgray}[1]{\color{lightgray}{#1}}\) \(\newcommand{\rank}{\operatorname{rank}}\) \(\newcommand{\row}{\text{Row}}\) \(\newcommand{\col}{\text{Col}}\) \(\renewcommand{\row}{\text{Row}}\) \(\newcommand{\nul}{\text{Nul}}\) \(\newcommand{\var}{\text{Var}}\) \(\newcommand{\corr}{\text{corr}}\) \(\newcommand{\len}[1]{\left|#1\right|}\) \(\newcommand{\bbar}{\overline{\bvec}}\) \(\newcommand{\bhat}{\widehat{\bvec}}\) \(\newcommand{\bperp}{\bvec^\perp}\) \(\newcommand{\xhat}{\widehat{\xvec}}\) \(\newcommand{\vhat}{\widehat{\vvec}}\) \(\newcommand{\uhat}{\widehat{\uvec}}\) \(\newcommand{\what}{\widehat{\wvec}}\) \(\newcommand{\Sighat}{\widehat{\Sigma}}\) \(\newcommand{\lt}{<}\) \(\newcommand{\gt}{>}\) \(\newcommand{\amp}{&}\) \(\definecolor{fillinmathshade}{gray}{0.9}\)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
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.