Kinematic Self-Replicating Machines
© 2004 Robert A. Freitas Jr. and Ralph C. Merkle. All Rights Reserved.
Robert A. Freitas Jr., Ralph C. Merkle, Kinematic Self-Replicating Machines, Landes Bioscience, Georgetown, TX, 2004.
4.3.4 Prokaryotic Cells
Bacteria are unicellular microorganisms capable of independent metabolism, growth, and replication , but lacking a distinct nucleus (prokaryotes). Their shapes are generally spherical or ovoid (cocci), cylindrical or rodlike (bacilli), and curved-rod, spiral or comma-like (spirilla). Bacilli may remain associated after cell division and form colonies configured like strings of sausages. Bacteria range in size from 0.2-2 microns in width or diameter, and up to 1-10 microns in length for the nonspherical species. The largest known bacterium is Thiomargarita namibiensis, with spheroidal diameters from 100-750 microns . Spherical bacteria as small as 50-500 nm in diameter have been reported . It has been theorized that the smallest possible cell size into which the minimum essential molecular machinery can be contained within a membrane is a diameter on the order of ~40-50 nm , though the current consensus among biologists is that a somewhat larger minimum size may be required (Section 5.3). Many spherical bacteria are ~1 micron in diameter; an average rod or short spiral cell is ~1 micron wide and 3-5 microns long. Each bacterial cell consists of a mass of protoplasm enclosed within the usual thin lipid bilayer plasma membrane. Most Gram-positive bacteria are surrounded by a thick, mechanically strong but porous peptidoglycan cell wall. Gram-negative bacteria like E. coli surround themselves with an additional two-layer coat atop the peptidoglycan layer.
Bacterial cells possess small internal vacuoles, ribosomes, granules of stored food, and usually one or more externally-attached flagella, but have no internal membranous surfaces, no internal organelles (although some functional compartmentalization does exist ), and no distinct nucleus. A single circular chromosome is organized into one or more compact aggregates, called nucleoids, that may occupy about one-third of cell volume . E. coli, a well-studied cylindrical bacterium typically measuring 0.65 microns wide and 1.7 microns long (cell volume ~ 0.6 micron3), has one double-stranded DNA chromosome that measures ~1.3 mm (~4.2 megabases or ~109 daltons) in length (strand volume ~ 0.002 micron3), organized in ~40 kilobase loops , during resting phase.
During binary fission (Figure 4.18), the normal method of bacterial self-replication, the bacterium starts with its genetic material, a circular chromosome of DNA, attached at one spot on the inner cell membrane, but otherwise fairly loose inside the cell. Chromosomal replication  begins at a specific sequence of nucleotides called the origin. Enzymes called helicases recognize this specific sequence, bind to this site, and begin unwinding the DNA by breaking the hydrogen bonds that hold the double strand together, creating a “replication fork.” Single-stranded binding proteins attach in chains along the separated strands for stabilization and to prevent rewinding. After the enzyme primase creates a short priming sequence, highly reactive free nucleoside triphosphates in the cytoplasm begin pairing up with their complementary bases on the exposed parental strand. Once properly aligned, the triphosphates are joined to the growing strand by an enzyme called DNA polymerase which catalyzes the hydrolysis of the phosphates as the nucleotide is added to the strand, forming a phosphodiester bond.
The polymerase continues around an entire strand until the duplicate copy is complete. The two duplicate chromosomes are attached at different ends of the cell membrane, called “pole preference” . The cell continues to take in food, metabolizing nutrients, building proteins via ribosomal translation of mRNA transcripts, increasing its mass and elongating, causing the two points of chromosome attachment on the cell membrane to grow apart. Once the bacterium has reached twice its initial size, its plasma membrane thickens and forms a division septum , pinching inward at the center of the cell, the full invagination finally causing the cell to divide, with a new cell wall separating two now-independent “daughter cells” having duplicate chromosomes. When each daughter again reaches a threshold “parental” size, the replication cycle can begin anew. Under optimal growth conditions the cycle may take only 15-20 minutes in E. coli . Note that the logic of replication in bacteria is, first, to duplicate the information tape, and then, second, to manufacture the construction engine, the same as the classical von Neumann kinematic replication scheme (Section 2.1.1).
In modern biotechnology, bacteria are often employed as “self-replicating factories” [1779-1781] for various useful products.
Last updated on 1 August 2005