Humboldt State University ® Department of Chemistry

Richard A. Paselk

Chem 438 - Introductory Biochemistry - Spring 2013

Lecture Notes:


Cells and Organelles, cont.

Compartmentation in Eukaryotes, cont.

Let's look at where different major metabolic pathways occur in a "typical" liver cell. [overhead-Animal cell]

eukaryote cell image

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Not shown - Glycogen Granules: enzymes of glycogen synthesis and breakdown. including branching and debranching.

Let's look at a "typical" plant cell for a moment. All of the organelles (except for centrosomes) we saw in animals are here as well, but with a few additions:

plant cell structure diagram

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Chapter 2: Water

Water is a very unusual, even incredible substance whose amazing properties are often unappreciated because of its ubiquitousness.[Slide] Water's special properties include extremely high mp and bp (0 °C & 100 °C K, compare to methane, -183 °C & -161 °C, with a MW of 16 vs. water's 18); a high heat capacity (18 cal/°C mol vs. 8 cal/°C mol for methane); it has a high viscosity; its solid form is less dense than the liquid form at the same temperature (ice floats on water - very rare), it has a large surface tension, and it has a high dielectric constant (78.5 vs. 1.9 for hexane).The high mp, bp, and heat capacity of water all predict relatively strong bonding between water molecules, so let's first review the types of bonding which occur between atoms and molecules. The most stable bonds are of course covalent bonds (with bond energies of 50 [S-S] to 80 [C-C] to 110 [O-H] kcal/mol), occurring when we have significant overlap of atomic orbitals.

Water of course is a covalent structure: H-O-H. But what gives it its special properties is the polarity of its O-H bonds and the resultant dipole moments of the bonds and the molecule itself.

The water molecule itself is bent, with an angle of 104.5° between the hydrogens (compare to 109.5° for sp3 tetrahedron) as seen in Figure 2.1, p 27of your text. [slide]

Structural diagram of water molecule showing bond angles and lengthsSpace-filling image of water molecule

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Because of the very strong dipole moments of these bonds and the very small size of the hydrogen substituents on water, a slight degree of orbital overlap occurs between adjacent water oxygens and hydrogens to give partial covalent bonds known as H-bonds (effectively, can only form with O, N, & F).

#-D image of H-bonding between space-filling images of water molecules

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Within solid bulk water (ice):

image of ice crystal structure

In addition to covalent bonds and H-bonds there are a variety of non-covalent bonds/interactions as seen in the table below:


 Interaction Type
Example Average Strength, kcal/mol (kJ/mol) Range**
Charge-charge (ionic) -NH3+ Cl-   1/r
Charge-dipole -NH3+ClCH3   1/r2
Dipole-dipole ClCH3 ClCH3    1/r3
Dipole-induced dipole* CH4 ClCH3 0.1-0.2 (0.4-4)  1/r6
(induced dipole-induced dipole)

0.1-0.2 (0.4-4)
Hydrogen bond  two H-bonded water molecules 3-8 (12-30)  

 van der Waals repulsion

*van der Waals interactions, **from Zubay Biochemistry 3rd. (1993) Table 4.3, pg. 89.

Water is an excellent solvent for polar substances since its dipolar structure enables it to insulate them from each other and it can make good dipole-dipole and dipole-charge bonds. Figure 2.6 on p 30and the figure below (Slide) shows the hexavalent liganding (note that the image should be seen in 3D so that two of the waters are actually out of the plane of the image, one in front and one behind) of water to sodium and chloride ions to form hydration shells (For sodium ions, the waters in the inner hydration-shell exchange every 2-4 nsec.). Anything which can H-bond will also of course be quite soluble.

Flattened image of the hydration of sodium ion

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© R. A. Paselk 2010;

Last modified 1 February 2013