Humboldt State University ® Department of Chemistry

Richard A. Paselk

Chem 431	Biochemistry	Fall 2008
Lecture Notes: 27 August	© R. Paselk 2008
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The Characteristics of Life

• Chemical complexity and extraordinary organization on the microscopic level.
• Systematic extraction, transformation and utilization of environmental energy.
• Mechanisms for precise self-replication and self-assembly.
• Sensory-response systems.
• Defined component functions and regulatory interactions.
• Redundancy.
• A history of and capacity for evolutionary change.
• A history of and capacity for evolutionary change.

All of these characteristics come together in the fundamental unit of life, the cell. All cells share a few features (text Figure 1-3):

• The plasma membrane defines the cell, separating the interior from the exterior. Composed of lipids and proteins it is hydrophobic and an effective barrier to the passage of ions and polar molecules.
  • The topolgical integrity of the plasma membrane is maintained during cell division.
• The cytoplasm encompasses the entire content of the cell exclusive of the nucleus.
  • The cytosol is the aqueous solution portion of the cytoplasm, including,
    • enzymes, RNA molecules and their component molecules (amino acids and nucleotides),
    • metabolytes (small molecular intermediates in metaboolism),
    • coenzymes (organic catalytic enzyme ligands) and
    • ribosomes.
• A nucleus or nucleiod where DNA is localized.

There are three domains of life recognized today (text Figure 1-4, figure below), with two fundamental types of cell organization: prokaryote (no nuclear envelope or membrane bound organelles) and eukaryote (membrane bound organelles and a nuclear envelope).

Cells and Organelles

A typical idealized prokaryote cell is shown in text Figure 1-6. [overhead- E. coli cell]

A prokaryote cell: size and composition

Let's look at E. coli for a moment just to get an idea of its size, and also to get an idea of the sizes of various molecules. The image in your text and as shown above gives the major components.

E. coli cell x 100,000 [overhead] is an artists rendition of a typical E. coli cell, with the various components drawn to scale. E. coli cytosol [overhead] magnifies a square section of that cell to 1,000,000 times so that particles such as ribosomes, proteins and DNA are readily visible. This view leaves out all of the small molecules though, to simplify the visualization. Finally a corner of the square is magnified a further ten times and water and small metabolites are shown in a very thin slice of our bacterial cell.

To give some additional perspective, lets look at the relative sizes of these objects. [overhead-sizes of molecules, one million times magnification]

Cool facts about E. coli :70% water, 15% protein, 7% nucleic acids, 3% polysaccharides, 3%, lipids, 1% inorganic ions, & 0.2% metabolites.

Complex, generalized organisms such as E. coli exhibit an amazing level of redundancy in enzymes etc. For example, of the approximately 4,000 genes in E. Coli less than 300 have been found to be "essential," where essential means the organism cannot grow on rich medium if the gene is deleted. Many genes also appear to be "silent" under more restrictive conditions as well - that is the organism often has more than one pathway to accomplish a given metabolic activity. (Cornish-Bowden & Cárdenas, Nature 14 Nov 2002, p 129)

Eukaryotic Cells, Compartmentation and Organelles

As mentioned earlier we will be focusing on eukaryotes in the rest of this course. Eukaryotes differ from prokaryotes in having a nucleus and cell organelles (their cells are physically compartmentalized). As a point of reference, an E. coli cell is about the size of a typical mammalian mitochondria.

Let's look at where different major metabolic pathways occur in a "typical" liver cell. (text Figure 1-7a) An image of a more generalized cell is shown below.

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: Complex RNA-protein machine for code-directed protein biosynthesis.
4. Vesicle: small membrane enclosed transport sack.
5. rough Endoplasmic Reticulum: Biosynthesis and modification of membrane and export proteins.
6. Golgi Complex: Further modification of membrane and export proteins.
7. Cytoskeleton: Protein fibers such as actin and microtubules used to maintain cell shape, transport tracks, and mechanical scafolding.
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. Vacuole: storage of dilute aqueous solutions, provides fluid for osmotic pressure.  
11. Cytosol: Glycolysis and most of gluconeogenesis; Pentose Phosphate shunt; Fatty acid biosynthesis.
12. Lysosomes: Hydrolytic (digestive) enzyme localization/Peroxisomes: Amino acid oxidases, catalase-oxidative degradation reactions.
13. Centriole:

Not identified in the image above are:

• Glycogen Granules: enzymes of glycogen synthesis and breakdown. including branching and debranching.
• Plasma Membrane: Active and passive transport systems; receptors and signal processing systems (synthesis of various second messengers etc.).

Pathway Diagrams

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Last modified 24 August 2008