Prepared July, 2010


       

In Celebration of Psalm Nineteen:
God's handiwork in Creation

Chapter 7
The Third Genesis:
Creation of the Proper Cell
(Eukaryotic Life)
ca. 1.8 Ba

UNDER CONSTRUCTION

"An organic being is a microcosm, a little universe  formed of a host of self propagating organisms inconceivably minute, and as numerous as the stars in heaven."
 - Charles Darwin
Animals and Plants ii, p483 (1868)




NOTE: Ba (Ma) = Billions (Millions) of years before the present time.

NOTE: see the lecture A Fit Place to Live for a synopsis of Chapters 5-??.


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Introduction. The first living matter was bacterial life, created nearly four billion years ago. Bacteria flourished for the next two billion years, slowly preparing the earth to support a much more complex life based on the eukaryotic cell, or the "proper cell". To say the proper cell is "much more complex" is not to imply that the bacterial cell is simple. In fact, as we saw in earlier chapters, even the simplest of bacterial cells is vastly complex.

But if the bacterial cell is complex, the eukaryotic cell is much, much more complex. Because of this added complexity, the
eukaryotic cell can only survive and propagate in an environment that has readily available supplies of food and other products of bacterial life: the tasks that the eukaryotic cell must carry out take so much effort that it requires these prepared supplies in order to keep up its pace of living. Even plants and other so-called autotrophs need organic food.

For example, no
eukaryotic cell is able to fix nitrogen, a laborious and energy-intensive task that was carried out by specialized bacteria over the two billion years since the first life appeared (and that continues today). The product of that effort is an abundant supply of organic matter distributed throughout the earth -- almost all organic matter of whatever kind includes a supply of fixed nitrogen.

In addition, most advanced species of life, including all animals and many eukaryotes, are based on oxygen metabolism, and this required that the earth had to be changed from a strongly reducing environment to an oxidizing environment (the atmosphere, the  oceans and the earth's crust). That process occurred over the same two billion years, and ended up with a stable 20% oxygen atmosphere, and most reduced ocean salts oxidized and precipitated to form the major ore deposits.


Bacteria, the only life forms present to this point, do not have the basic design that is needed for complex life. A new cell type is needed, so radically different that it amounts to a new creation of life. The new creation is called the eukaryote cell, and occurred around 1.8 billion years ago. All plants and animals are made from eukaryotic cells.

The most visible distinction between bacteria and eukaryotes is the presence of a nucleus - think of the yolk of an egg (Figure 1). All eukaryotes have the genetic material - the DNA - in long strands called chromosomes, enclosed in a nucleus that is separated from the rest of the cell by a protective membrane. In contrast, prokaryotes - the bacteria - have looped DNA that is not separated from the rest of the cell. The nucleus protects the DNA from damage by contact with food or cell invaders. Passage of material across the nuclear membrane is controlled by ports formed of complex molecules that are designed to allow only certain kinds of material to pass.

DNA in proper cell
Figure 1
DNA in Prokaryotes and Eukaryotes
dcb


Many single-celled species are eukaryotes (such as the familiar paramecium -- Figure 2) and all visible plants and animals are eukaryotes.

paramecium-diag
Figure 2
Paramecium

There is such a large difference between prokaryotes and eukaryotes that the creation of eukaryotes is virtually a total re-design, a second creation on a par with with the original creation of prokaryote life. For one thing, the simplest eukaryotes have over 10 times the DNA found in the most complex prokaryote[FOOTNOTE: Scott F. Gilbert, Developmental Biology, 5th Ed. p.5] and are much larger. Figure 3 illustrates one prominent feature of eukaryotes: the extensive use of membranes to form controlled micro-environents where various specialized activities occur.

Eukaryote Membrane Structure
Figure 3
Eukaryote Membrane Structures


The nucleus which encloses the genetic material is the most characteristic feature of a proper cell. The nuclear membrane surrounds the genetic material and serves as a gate-keeper to control access. A proper cell also has other membrane-enclosed structures called organelles which perform specialized tasks.

Another characteristic feature is the fact that it has structure. Bacteria come in a few typical shapes that can be characterized as "balloon shapes" (Figure 4) -- what occurs when the shape is determined primarily by internal pressure acting on a closed surface membrane. There is little or no internal structural support. In contrast a proper cell has a cytoskeleton for internal structural support. The cytoskeleton
allows the proper cell to assume a fantastic range of shapes and sizes (Figure 5).

Bacterialshapes-Merc
Figure 4
Bacterial Shapes
From the Merck Manual


Ciliates
Figure 5
Ciliate Shapes (Eukaryotes)
Bar at right is 1 mm.
Source: P. Eigner
used by permission

The cytoskeleton also allows a proper cell to be much larger than a bacterial cell because the cytoskeleton itself supports an internal transport system to convey food and wastes within the cell. In contrast, bacteria rely on diffusion for internal transport (See Note). This limits the practical bacterial cell size to something on the order of ten microns (about the size of a period in Figure 5). Eukaryotes can reach sizes that are easily visible to the naked eye -- the extreme is nerve cells in animal bodies that can reach lengths of several meters.

The first eukaryotic cells were single-celled, as bacteria are. Multicellular structures formed by bacteria are actually individual single-celled microbes that live together and may have some cell specialization such as the nitrogen-fixing heterocysts, and akinetes. But the structural and transport features of the proper cell have the potential for far more, and thus led in time to multi-celled species, and eventually to the visible, multi-cellular plants and animals.

This anticipation of future biological innovation is a characteristic of the creation of living species. In later chapters we will also discuss the formation of homeobox and development gene packages during the Cambrian explosion (about 550 Ma), which anticipated many innovations in animal life that would occur hundreds of millions of years later.


MAJOR INNOVATIONS IN THE EUKARYOTIC CELL
Internal Membranes
 -- nuclear
Membranes enclose a number of specialized parts of the cell -- the nucleus and the various organelles of a typical cell. The nuclear envelope controls the passage of molecules between the nucleus and the rest of the cell using access ports that recognize particular molecules.

Error Correction
Error-detecting and correcting schemes ensure the accuracy of the dna and rna copies. In bacteria, insertions and changes to the dna code occur frequently, because the dna is located in the cell cytoplasm and can come in contact with portions of dna derived from food and viruses. In addition the transcription of the bacterial dna is more prone to errors. Overall for a bacterial dna, transcription accuracy is on the order of one transcription error per ??? codons.  In contrast, overall transcription accuracy for a eukariotic cell is on the order of one error per billion codons. [CHECK]. This still results in about ??? errors per cell per second. [CHECK]

Cytoskeleton
• Provides structure to the cell
• Provides an internal transport network
       Uses the Kinesin linear motor molecule to transport large molecules between the cell wall and organelles.
       Allows task specialization in the organelles.


organelles


cellular  comms








sex - mitosis/meiosis


chromosomes



Protection of the genetic code. 
All eukaryotes have the genetic material - the DNA - in long strands called chromosomes, enclosed in a nucleus that is separated from the rest of the cell by a protective membrane. In contrast, prokaryotes - the bacteria - have looped DNA that is not separated from the rest of the cell.

The nucleus protects the DNA from damage by contact with food or cell invaders. When the DNAs genes are copied prior to building the various proteins and other complex molecules of life, the genes are processed within the nucleus to remove un-needed information, and to correct copying errors.

It is hard to overemphasize how this contrasts with bacteria. The DNA of bacteria comes in constant contact with the cell contents, and as a result is subject to both random and deliberate changes in the DNA code itself. That is how viral infection works: a virus injects its genetic material into a bacterial cell, and the material then inserts itself into the cell's own DNA. From this point the cell begins to reproduce the virus, using the cell's own genetic machinery.

Bacteria are designed in this loose genetic way because one of the strong points about bacteria is the ability to respond to environmental changes by changing its genetic make-up. Bacteria can even share segments of DNA from other bacterial species, perhaps through snips of DNA that enter the cell as food. This is why bacterial species, such as the common E. Coli have so many different subspecies, both harmful and beneficial. One biologist, Lynn Margulis, argued that the concept of species is not really appropriate for bacteria because there is so much genetic variation. She notes: "Because bacteria that differ in nearly every measurable trait can receive and permanently incorporate any number of genes from each other or from the environment, the concept of "species," applicable to named eukaryotes, seems inappropriate for the Prokarya. For higher species, that advantage is overshadowed by the need to guard the genetic code's accuracy. The code is much more complex, and changes are very likely to be unwelcome. So for eukaryotes, the emphasis is on limiting changes in the code and controlling the accuracy when the code is copied. This work takes place within the nucleus.

More remarks along these lines will be made in the next chapter.


<INSERT SHARP POINT -- ANTICIPATION IN BIOLOGY?? -- here or in evolution chapter??>


Structure of a Eukaryotic Cell. Hints of many features that are characteristic of a eukaryotic cell can be found in isolated instances in certain bacteria.

A typical eukaryotic cell has a number of specialized organelles in addition to the charcteristic nucleus (Figure 6).  These organelles provide a suitable micro-environment to conduct specialized tasks. Bacteria have a few such organelles, such as the thylakoid in photosynthetic bacteria
. Eukaryotes are a major advance over bacteria in the number of these specialized organelles and in the way that the organelles are physically linked by a cytoskeleton that is used to exchange food and waste between the organelles and the exterior of the cell.

Examples of these organelles and their primary function include:
• Nucleolus -- controls cell division
• Mitochondria -- produce the ATP energy "batteries"
• Rough Endoplastic Reticulum --
• Golgi Apparatus --

organelles
Figure 6
Typical Eukaryotic Cell
dcb


The cytoskeleton (Figure 7) provides internal structure to the cell, which is how a eukaryotic cell can take on the broad variety of body plans of Figure 5. All of the organelles are interconnected by the cytoskeleton. The Kinesin motor molecule follows the cytoskeleton microtubules to carry food and waste throughout the cell. This use of motorized transport is the reason why a eukaryotic cell can be much larger than a bacterial cell which relies on diffusion to move food and waste internally.

Microtubule Cytoskeleton
Figure 7
Microtubule Cytoskeleton
Source: Harvard


The Kinesin Transport molecules.
The kinesin transport molecules are  designed to use electrostatic  attraction to move two "legs" of the molecule along tubulin.

Sharp Point: Kinesin transport.


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NOTES

Dr. Ronald E. Hurlbert, Washington State University Microbiology 101/102 Internet text.   Chapter IX Microbial Exchange of Genetic Material. [MAYBE APPROPRIATE FOR EVOLUTION CHAPTER]



Sharp Point          Eigen's Paradox -- Error Correction Coding

Error correction mechanisms in prokaryotes and eukaryotes. Eigen's paradox.






The Cytoskeleton
Structure in the "amorphous protoplasm"
   
When mid-19th Century biologists looked at cells through a microscope, they saw the cell protoplasm as an amorphous jelly. The prominent evolutionary proponent Ernst Haeckel viewed the protoplasm as the "life force" of living cells, and assumed that it, and therefore the essence of life, to be essentially simple[FOOTNOTE:
Ernst Haeckel, The History of Creation (1876): Vol. I, On the Protoplasm Theory, p.99ff. [100] "protoplasm (the original slime) is the most essential (and sometimes the only) constituent part of the genuine cell." [p406] "the general explanation of life is now no more difficult to us than the explanation of the physical properties of inorganic bodies."John Theodore Merz, A History of European Thought in the Ninetenth Century (1907-1914):  Vol. II. Chapter 10 "On the Vitalistic View of Nature" pp 444ff. The term "protoplasm" was coined by Hugo von Mohl in 1846 for the "visible but apparently structureless forms of cells and protoplasm".]. However, by the end of the 19th century it was generally understood through numerous scientific investigations that there is much more structure and content to the protoplasm[FOOTNOTE: George L. Goodale, Protoplasm and its History (Botanical Gazette Vol. XIV No. 335, Oct. 1889) Pdf (2.8 Megs) "Protoplasm is no longer regarded by any one in any sense as a comparatively simple substance. ... By better methods of staining, and by the use of homogeneous immersion [compound microscope] objectives, the apparently structureless mass is seen to be made up of parts which are easily distinguishable. There has been, and in fact is now, a suspicion that some of these appearances, under the influence of staining agents, are post-mortem changes, and do not belong to protoplasm in a living state. But it seems to be beyond reasonable doubt that protoplasm is marvellously complex in its morphological and physical as well as its chemical constitution.].

The basic problem is the resolution of light microscopes which can only see things down to a dimension of a few microns -- the size of small bacteria. Therefore the elaborate structure within a bacterial cell was almost completely invisible.

The structural content of the "protoplasm" is built up of cytoskeleton threads that are only a few nanometers in diameter (a few molecules across), and can be viewed only with electron microscopes, first built in the 1940s. Even then, the essentially colorless threads can only be viewed if they were tagged with dyes or doped with heavy atoms such as gold.

The cytoskeleton performs a number of functions in the cell (see Figure 8): it provides:
• Structure, support and spatial organization;
• Food and waste transport between cell organelles and the cell wall;
• Contraction, dilation and movement;

Cytoskeleton Diagram
Figure 8
Functions of the cytoskeleton

The food and waste transport involves the Kinesin transport molecule which is a linear motor that carrys waste and food along the microtubules which connect the cell wall and all internal organelles.




The Kinesin Transport Molecule
A molecular motor.
   

The Kinesin molecule transports food and wastes between the organelles of a eukaryotic cell, moving along microtubules of the cell's cytoskeleton (Figure 9).
 
031b-kinesin
Figure 9
Kinesin motor molecule
See the YouTube animation "Fantastic Vesicle Traffic"

 
Kinesin motors were first discovered by accident in 1981
[FOOTNOTE: The description by Pamela Clapp neglects to note that Dr. Allen's wife Nina worked closely with him and participated in the discovery] by a Dartmouth professor, Robert D. Allen, when he used a television camera to view squid nerve fiber under a light microscope. By adjusting the image brightness it was discovered that details could be seen that are a tenth of the size that is normally visible in a light microscope, and for the first time, it was actually possible to see little round objects moving along the nerve fiber. These turned out to be kinesin.




Modes of Internal Cell Transport
Diffusion vs. Kinesin Transport
   
Bacteria rely on ordinary diffusion to move food and waste within a cell. Diffusion depends on random movement due to molecular collisions, and is typified by the dispersion of a dye in a beaker of water (Figure 10):

031c-diffusion
Figure 10
Diffusion




golgi apparatus -- and animation

cytoskeleton microtubules
centrosome (near nucleus) organizes microtubules. "All eukaryotic cells have a microtubular organizing center"
http://www.youtube.com/watch?v=5rqbmLiSkpk&feature=related

endoplasttic reticulum Protein Translocation


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REFERENCES

Bruce Alberts, et al. Essential Cell Biology: An Introduction to the Molecular Biology of the Cell (1998),
David C. Bossard, A Fit Place to Live. (2003)
Wallace S. Broecker, How to Build a Habitable Planet (1985)
Guillermo Gonzalez & Jay W. Richards, The Privileged Planet (2004)
George L. Goodale, Protoplasm and its History (Botanical Gazette Vol. XIV No. 335, Oct. 1889) Pdf (2.8 Megs)
Ernst Haeckel, The History of Creation (1876): Vol. I On the Protoplasmic Theory, p.99ff.
Robert Hasselkorn, The Cyanobacterial genome core and the origin of photosynthesis (Proceedings of the National Academy of Sciences, 2006)
Dr. Ronald E. Hurlbert, Washington State University Microbiology 101/102 Internet text.
D. T. Johnston et al, Anoxygenic photosynthesis modulated Proterozoic oxygen and sustained Earth's middle age (Proceedings of the National Academy of Sciences, 2006)
Lynn Margulis and Kathlene V. Schwartz, Five Kingdoms: An Illustrated Guide to the Phyla of Earth,Third Edition, W.H. Freeman, 1999, p79. The most recent edition of this work has been renamed Kingdoms and Domains (2009) by Lynn Margulis and Michael J. Chapman.
John Theodore Merz, A History of European Thought in the Ninetenth Century (1907-1914)
Harold J. Morowitz, Beginnings of cellular Life, Yale University Press, (1992).
J. Willliam Schopf, Cradle of Life: The Discovery of Earth's Earliest Fossils (1999).
Peter D. Ward &  Donald Brownlee, Rare Earth: Why Complex Life is Uncommon in the Universe. (2000)


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Prepared July, 2010