Humboldt State University ® Department of Chemistry

Richard A. Paselk

Chem 438 - Introductory Biochemistry - Spring 2013

Lecture Notes:

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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]

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1. Nucleolus: localized region of the nucleus in which ribosomal RNA's are synthesized and processed.
2. Nucleus: DNA replication, synthesis and processing of messenger RNA's.
3. Ribosome: Ribonucleoprotein machines for translating RNA information into proteins.
4. Vesicle:small membrane enclosed vessels used in transporting proteins between different organelles (e.g. sER and Golgi etc.)
5. Rough Endoplasmic Reticulum: Biosynthesis and modification of membrane and export proteins.
6. Golgi Complex: Further modification of membrane and export proteins.
7. Cytoskeleton: multi-subunit fibrous proteins such as actin and microtubulin providing support for cell shape
8. Smooth Endoplasmic Reticulum: Lipid Synthesis; Steroid synthesis; Phase one detoxification reactions.
9. Mitochondria: Kreb's Citric Acid Cycle; Electron transport system and Oxidative Phosphorylation; Fatty acid oxidation; Amino acid catabolism; Interconversion of carbon skeletons.
10. Lysosomes: Hydrolytic (digestive) enzyme localization.
11. Cytosol: Glycolysis and most of gluconeogenesis; Pentose Phosphate shunt; Fatty acid biosynthesis.
12. Peroxisomes: Amino acid oxidases, catalase-oxidative degradation reactions.
13. Centrioles within Centrosome: Centrioles are barrel-shaped structures composed of nine microtular triplet-strands. A pair of associated centrioles in amorphous stuff makes up the centrosome which is involved in organizing the mitotic spindle in cell division in animal and most fungal cells (they are not present in plants). It is also essential for flagella and celia formation.
14. Plasma Membrane: Active and passive transport systems; receptors and signal processing systems (synthesis of various second messengers etc.).

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:

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• Chloroplasts: Light capturing processes and electron transport & oxidative phosphorylation for photosynthesis; Calvin cycle (dark reactions of photosynthesis).
• Glyoxisomes: location of glyoxalate cycle.
• Cell wall: made up of cellulose glued together with lignin (a plastic-like polymer) - maintains cell integrity against high osmotic pressure, gives cell rigidity.
• Vacuole: storage of dilute aqueous solutions, provides fluid for osmotic pressure.  

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]

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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).

• Note that the partial covalent character means that they are directional! Figures 2.3 & 2.4 (p 28-9) show representations of H-bonds in water.
• Compare the bond length of water H bonds (0.18 nm) to the covalent bond-length between O and H of 0.096 nm - notice that the bond distance is nearly twice the true covalent bond distance, but significantly less than the van der Waals radius of 0.26 nm.

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Within solid bulk water (ice):

• every water molecule is bonded to 4 others, as in the ice structure seen in Figure 2.5 on pg. 29 [Slide]
  

• In liquid water the molecules are still bonded to a large degree (the heat of fusion for ice is only 13% of the heat of vaporization for ice, thus most of the H-bonds must survive melting).
• Of course in liquid water the bonds are very unstable (average lifetime about 10 psec = 10^-11 sec), exchanging constantly to give a "flickering cluster" structure.
• The various properties of water arise from this structure. (Note hi bp & mp, heat cap., viscosity, and, less obviously, that ice floats.
• Ice floats because the molecules are in an open lattice rather than close-packed. Garrett & Grisham (in their text, Biochemistry, 2nd ed) note that close-packed water molecules would only occupy about 57% of the volume of ice. This would lead one to expect that ice would float "high." It doesn't because most of the structure remains in the liquid phase at 0° C.)

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 Dispersion* (induced dipole-induced dipole) CH4 CH4 0.1-0.2 (0.4-4) 1/r6 Hydrogen bond   3-8 (12-30)    van der Waals repulsion     1/r12 *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.

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© R. A. Paselk 2010;

Last modified 1 February 2013