All cells, both eukaryotic and prokaryotic, are bounded by a plasma membrne. Prokaryotic cells' membranes can differ greatly
depending on the organism's metabolic functions: "various prokaryotes do have a number of specialized membranes that perform many of their
metabolic functions." (Campbell et all, 2002, p. 530).

Eukaryotes, more complex than prokaryotes, have internal membranes which compartmentalize the cell, increasing efficiency of metabolism.
Furthermore, each internal membrane is specialized according to the
compartment's function - for example, the enzyme embedded specifically in the smooth endoplasmic reticulum of a liver cell removes the
phosphate from glucose phosphate, the first product of glycogen hydrolysis. This removal of a phosphate enables the liver cell to release
glucose into the blood. Releasing glucose into the blood is crucial to the liver's job: regulating blood sugar levels. The liver cannot
release glucose phospate into the blood, as it is an ionic compound. This specialized membrane with the enzymes embedded in it is found
in the smooth endoplasmic reticulum of the liver; thus, specialization does exist at the cellular level as each cell has a particular
function to carry out.

A major difference in prokaryotes and eukaryotic cells is the prescence of a nucleus: eukaryotes have a nucleus, but
prokaryotes do not. Prokaryotic cells do have a nucleoid in which their DNA is mainly "concentrated" (Campbell et al, 2002, p. 112), but
unlike a eukaryotic cell, this structure is not enclosed and not separated from the rest of the cell by any kind of internal membrane.
In a eukaryotic cell, between the nucleus and the plasma membrane are many organelles which aid the cell in metabolic processes. These
many organelles include mitochondria, peroxisomes, lysosomes, golgi bodies, vacuoles, cytoskeletons, flagella, and plastids.
A prokaryotic cell lacks all of these membrane-enclosed organelles. It does contain flagella for locomotion, but the flagella of
prokaryotes and eukaryotes differ greatly.

Because of the lack of complexity of a prokaryotic cell, prokaryotic cells' size typically range from 1.0 and 10.0 picometers, SMALLER than
the 10 to 100 picometers from which eukaryotic cells range. Not only do prokaryotes not have any membrane-enclosed organelles, but they
also only have one double-stranded DNA molecule with few proteins associated with it. All major functions are powered by this one
molecule, but there are also plasmids inside a prokaryotic cell. Plasmids are small rings of DNA that consist of a small number of genes.
They aid in the metabolism of unusually-found-in-the-environment nutrients.

Regarding metabolism, "every type of nutrition observed in eukaryotes is represented among prokaryotes" (Campbell et al, 2002, p. 532)
There are also two types of nutrition that are nonexistant in any cell other than prokaryotic cells. For instance, photoautotrophic cells
need light energy for the synthesis of organic compounds from carbon dioxide, their carbon source. Chemoheterotrophic cells cannot
synthesize organic molecules; they must consume organic food molecules for their energy and carbon. Both photoautotrophic and
chemoheterotrophic prokaryotic cells exist, but prokaryotes can obtain energy and a carbon source to build organic molecules in two other
ways: chemoautotrophic cells and photoheterotrophic cells. The former needs carbon dioxide as their source of carbon but does not need
light or organic food molecules for energy; they can extact energy from inorganic substances via oxidation. The latter
uses light as an energy source but cannot synthesize organic molecules from carbon dioxide; it needs to consume carbon that is already in its
organic form.

As aforementioned, prokaryotes and eukaryotes use flagella as a method for locomotion. The flagella are arranged from
microtubules which protrude from the cell: in eukaryotes, the flagella are extensions of the plasma membrane; in prokaryotes, the flagella
are attached to the cell surface (Campbell et al, 2002, p. 54. The structure of the flagella fits its function: chains of flagellin are
wound up and spiraled into a helical filament; this makes up the filament. The filament is connected to the basal protein that motors it
through a curved hook. The basal apparatus, composed of 35 different proteins, acts a motor for the flagella. H+ ions power the basal
apparatus. Proton pumps in the plasma membrane diffuse the H+ ions into the cell; these ions power the basal apparatus. In eukaryotes, the
flagella undulate while the cilia (another organelle for locomotion) move back and forth. The flagella force movement and always move toward
the axis of flagellum, while the cilia move in the direction perpendicular to its axis. The flagella are arranged in a pattern in which
nine doublets of microtubules enclose two doublets. Then, cross-linking proteins connect the two center doublets together
and then to the outer nine doublets of microtubules. The motor of eukaryotic flagella and archaea are the dynein proteins that connect all
the nine doublets together, that is to say they connect each doublet with its neighboring doublet. These dynein arms cause the bending
movement of cilia and flagella through "a complex cycle of movements caused by changes in the conformation of the protein, with ATP providing
energy for these changes." (Campbell et al, 2002, p. 130).

Reproduction of prokaryotes is unlike eukaryotes because prokaryotes reproduce only through binary fission. In other words, prokaryotes
reproduce only asexually. There is no mitosis nor meiosis in prokaryotes. The prokaryote population is, essentially, a constantly mutating
clonal cell line. Mutation is very abundant in the prokaryote population. Prokaryotes can accumulate large numbers of mutations.
There does exist some transfer of genes: Transduction, in which viruses transfer genes across cell lines, conjugation, in which a gene
is unilaterally transfered from one prokaryote to another, and transformation, in which genes from the surrounding environment enter a
prokaryotic cell. "Unlike most eukaryotic populations, every prokaryotic population represents a mixture of genetically diverging clonal cell
lines on which natural selection acts". (Torsvik et al, 2002.) Eukaryotes commonly reproduce through sexual reproduction, but not all.
SOme protists, for example, reproduce asexually but perform the sexual processes of meiosis and syngamy so that genes are shuffled and then
recombined. Specifically, in paramecium caudatum, two genetically diverging cells can partially fuse. The 2 partially fused paramecia,
through meiosis, produces four haploid micronuclei - four
indentical micronuclei that each carry the exact same genetic code. Through mitosis, one of the four haploid micronuclei divides into two
daughter micronuclei. Now, within each paramecium, there are 2 genetically identical micronuclei. The protists each swap one micronuclei.
Now there are 2 genetically diverging micronuclei within each parmecium. Through syngamy, the 2 micronuclei fuse together. This new
diploid nucleus now has a mixture of chromosomes. After syngamy, the new parcemium reproduces itself asexually: through mitosis, it
divides into 8 indentical micronuclei. 4 of the micronuclei replicate their DNA to form a new macronuclei. The other four remained as
micronuclei in the cell. This cell divided once and then divided again to create 4 new individuals. Not all eukaryotes' reproduction
is exactly like this, but most, unlike prokaryotes, involve some kind of fusion of two organisms and recombination of genes for the new
organism. Pollen germinates the egg in a plant. Sperm germinates the egg in an animal. In fungi, "germinating aerospores give rise
to new haploid mycelia." (Campbell et al, 2002, p. 623).

Cell walls of prokaryotes differ. Bacteria have cell walls made of peptidoglycan. Gram-positive bacteria's cell walls consist only
of peptidoglycan and a few protiens. Gram-negative bacteria have a thin layer of peptidoglycan surrounde in a periplasmic gel betwixt
the plasma membrane and the outer membrane, proteins among rows of lipids and some carbohydrates bound to the lipids. See Figure 27.5.
Archaea's cell walls do not contian peptidoglycan altogether. Not all eukaryotes have cell walls; animals, for instance, do not.
Plant cell walls help to maintian the cell's shape and prevent excessive uptake of water. The cell walls, however, do not isolate
one cell from the next: plasmodesmata are openings within the cell wall that allow for continuation of cytoplasm and endoplasmic
reticulum via desmotubules.

Prokaryotes are classified under 2 domains: bacteria and archaea. The cells of archaea have completely different membranes that
are made of isoprenes - lipids with hydocarbons branched on, as opposed to the fatty acids that make up bacterial cells.
(University of Albany School of Public Health, 2004.) Eukaryotes are all in the same domain, grouped under four kindgdoms.
Fungi are heterotrophs that obtain nutrition by absorption. Animals are sexually-reproducing heterotrophs without cell walls.
Plants have cell walls and are autotrophic. Protists are any eukaryotes that aren't already animals, plants, or fungi.

The theory of endosymbiosis offers an explanation as to the origin of eukaryotes. According to the theory, eukaryotes' mitochondria
and plastids evolved from prokaryotes living symbiotically inside a larger cell. The relationship between the prokayote,
which is called an endosymbiont, and the larger cell which engulfed the prokaryote, which is called the host cell, was likely a symbiotic
relationship as a heterotrophic host would have needed the nutrients from a plastid, and an anerobic cell would have benefitted from an
aerobic host to synthesize oxygen into something else that the anerobic host cell could use (Campbell et al, 2002, p. 550). The evidence of
this theory is highly dependent upon the fact that the modern prokaryotic cells bear a striking relationship with the organelles in modern
eukaryotic cells into which the prokaryotes theoretically evolved. For example, the plasma membrane of a modern aerobic prokayote is highly
reminiscient of christae in a modern eukaryotic cell. Christae are infoldings in the inner membrane of the mitochondrion. These folds
increase the surface area of the inner membrane, into which ATP synthases are bulit, establishing efficiency within cell respriration. ATP
synthase is the enzyme that makes ATP. The respiratory membranes of prokaryotic cells "do indeed have several enzymes and transport systems"
(Campbell et al, 2002, p. 550) on them for making ATP also. Choloroplasts and mitochondria replicate themselves by similar processes of
binary fission prokaryotes use to reproduce. The ribosomes found in chloroplasts are similar to the ribosomes of the cyanobacteria; in terms
of "size, biochemical characteristics, and sensitivity to certain antibiotics" (Campbell et all, 2002, p. 500) the similarity between
chloroplast ribosomes and bacterial ribosomes is GREATER than the similarity between chloroplast ribosomes and other ribosomes within the
same plant cell. Organelles and their respective prokaryotes are also similar in size. However, the notion that mitochondria and plastids*
evolved from prokaryotic endosymbionts is just one part of the whole theory of endosymbiosis; specifically, it's the theory of serial
endosymbiosis. The theory of secondary endosymbiosis which explains the diversity of plastids among organisms. The two membranes in a
chloroplast contrast with the three or four membranes found in some algae groups. The algae groups with three or four membranes evolved
from a host cell engulfing an endosymbiont, like in serial endosymbiosis. But this time, the host cell was a heterotrophic protist and
the endosymbiont was not a prokaryote but another eukaryote - an algae that already hosted a prokaryote, or more specifically, a
cynobacteria. The plasid having acted as an endosymbiont twice, the second engulfment added a membrane from the vacuole of the former
host cell. Sometimes the new plastid loses the midochondria and nucleus of its original host cell; for example, the plastid in a
cryptomonad algae protist contains a nucleomorph, derived from the nucleus of the host cell that engulfed a cyanobacteria. Needless to say,
the theory of endosymbiosis convolutes traditional evolutionary theory that all organisms are derived from a common ancestor and that the
relatedness of two organisms is proportional to how recently the organisms shared a common ancestor. Now, considering that an aerobic
prokaryote and a mitochondrion are structurally very similar, yet the mitochondrion is an organelle from a eukaryote, and the aerobic
prokaryote is not even in the same domain as a eukaryote, the traditional evolutionary theory does not explain the similarity. Not even
convergent evolution does; the organelle and the organism have not acquired similar adaptive values from living in similar environments
despite not being genetically related. The fact that a eukaryote engulfed a bacteria early in its evolutionary history now creates a branch
in the cladogram that goes across the branch of archaea, as shown in Figure 28.7.


















Torsvik, Vigdis, Ovreas, Lise, and Thingstad, Tron Frede. (2002, May). Prokaryotic Diversity - Magnitude, Dynamics, and Controlling
Factors. Science, 296 1064-1065.

www.sci.sdsu.edu/plants/bio201/4-Prokaryotes-red.pdf


Campbell, NA and JB Reece. (2002) Biology, Sixth Edition. Pearson Prentic Hall: new Jersey.