Friday, April 10, 2009

Making of Eukaryotic cells

On page 88 Carroll discusses the creation of eukaryotic cells. Explain how eukaryotic cells are a fussion of archaen bacteria and other prokaryotic bacteria. What are some of the traits that eukaryotes share with the ancestoral bacteria.
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  1. Mark LeeApril 10, 2009 at 3:53 PM

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  2. Mark LeeApril 10, 2009 at 3:56 PM

    Eukaryotic cells are a fusion of archaen and other prokaryotic bacteria because of endosymbiosis. The endosymbiont states that a long time ago one cell (the early eukaryote) may have ingested another prokaryote through phagocytosis. If the lysosomes of the eukaryotic cell did not break down the prokaryotic cell, the prokaryotic cell could divide within the eukaryotic cell. Therefore when the eukaryotic cell divided, both new cells would have the same prokaryotic cells inside of them. Over time the two cells (now referred to as the cell and organelle) would form a mutually beneficial relationship. It is entirely likely that over the course of evolutionary history, eukaryotes took on both bacteria and archaea as endosymbionts. An example of endosymbiosis in modern eukaryotic cells would be the mitochondria and the chloroplast. Both were formerly bacteria, and at some point in evolutionary history were consumed by eukaryotes. They now work in conjunction with eukaryotic cells to produce sugars from light (chloroplasts) and to break down sugars into ATP (mitochondria). It is entirely likely that over the course of evolutionary history, eukaryotes took on both bacteria and archaea as endosymbionts. Furthermore, over time it is very likely, as stated by Carroll, that the genes of the endosymbiont and the host fused, resulting in eukaryotic cells having elements of both archaen and other bacterial DNA.

    Both prokaryotes and eukaryotes have similar, though not identical, features, which show the similarities of their genetic makeup. The fact that there are few identical features between prokaryotes and eukaryotes is to be expected due to the fact that the two types of cells differentiated long ago in evolutionary history, meaning that there was plenty of time for the two types of cells to evolve independently. The similarities are as follows. Both prokaryotes and eukaryotes have a lipid bi-layer plasma membrane, both have flagella and cilia, both have ribosomes that are similar in structure, and both have cytoskeletons arranged in similar manners.

    http://74.125.95.132/search?q=cache:eU9PSbM0p6sJ:biology.suite101.com/article.cfm/similarities_of_prokaryotic_and_eukaryotic_cells+shared+eukaryotic+and+prokaryotic+traits&cd=5&hl=en&ct=clnk&gl=us

    Campbell

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  3. Kimberly KenyonApril 10, 2009 at 3:57 PM

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  4. Jennifer JooApril 10, 2009 at 4:29 PM

    Carroll explains that bacteria were the “product of a mixed marriage – a genetic fusion of archaean and bacterial parents” (88). This is because when sequencing of archaen and bacterial genomes were compared, many archaean genes showed a large similarity to their bacterial counterparts. Eukaryotic genes were then suggested to be more related to genes of bacteria than of archaea. Many of the similarities between arachaea and eukaryotes were in “informational genes whose products dealt with copying and decoding DNA” (87). Eukaryotes and bacteria also had similarities in operational genes involved in metabolism of nutrients and cellular materials. Carroll notes that eukaryotes seem to have inherited informational genes from one ‘parent’ and operational genes from the other.
    Fusion between two different organisms has been suggested before. Margulis “proposed that mitochondria and chloroplasts . . . arose from bacteria livening within eukaryotes” (88) in a process called serial endosymbiosis. Both mitochondria and chloroplasts used to be small prokaryotes living within larger cells, the host cell. Aerobic heterotrophic prokaryotes that eventually became endosymbionts, a cell that lives within another cell, are the proposed ancestors of mitochondria while photosynthetic prokaryotes that became endosymbionts are the proposed ancestors of chloroplasts (textbook). As said above, eukaryotes took on both bacteria and archaea as endosymbionts as a result of a mutually beneficial relationship.
    The idea of fusion between archaen bacteria and prokaryotic bacteria exemplifies science as a process as the “conventional” tree of life (figure 3.4) is now replaced by the new tree of the tree of eukaryotes (figure 3.5), also called the “ring of life” by others. The accepted ‘diagram of life’ has always been changing, from plant/animal kingdoms in1735 to the addition of protists in 1866. Norman Pace, a microbiologist and RNA scientist from the University of Colorado at Boulder, has even suggested the abolishment of the word ‘prokaryote’ (source: Source: http://www.sciencenews.org/view/generic/id/42241/title/Dissing_a_loaded_label_for_some_unicellular_life) Woese of the University of Illinois at Urbana-Champaign in 1977 described the three domains of life as eukaryotes, bacteria, and archaea and used differences in the rRNA to determine relationships between the organisms. This suggests that bacteria and archaea are distinct groups and that eukaryotes and archaea are more closely related than bacteria and archaea. According to this, the LUCA (last universal common ancestor) split into two domains, bacteria and archaea, and then eukaryotes formed from a branch of the archaea.
    The eukaryotes’ dual heritage was further examined for shared genes; by analyzing the shared gene patterns, the eukaryotic genome was said to be a “product of a fusion between a relative type of archaean and a type of bacterium” (88). Symbiosis, “the term used to describe ecological relationships between organisms of different species that are in direct contact” (text), is common among organisms that live together such as Thermus aquaticus, of Yellowstone National Park.

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  5. Sofia HossainApril 10, 2009 at 4:47 PM

    In Carroll’s specific discussion of natural selection in terms of immortal genes he briefly highlights the role of endosymbiosis in developing the compartmentalization of eukaryotes in comparison to prokaryotes. According the figure 3.5 in the book, the root of the complexity of eukaryotes is the fusion of the characteristics of Bacilli, Cyanobacteria, Proteobacteria, Eocyta, and Euryarchaea. However, in this process, though, these species were not lost in the mix of eukaryotes. Because the structure of the tree of eukaryotic evolution is a ring, it is continual: these organisms formed the eukaryote while continuing on a divergent path of evolution.
    Before we delve into the specifics of eukaryotic evolution from some primordial organism, we should first briefly examine what characteristics are shared by the present-day eukaryote from the present-day prokaryote and what characteristics separate the two. From a first glance, there are obvious physical characteristic the separate the two, namely size. A eukaryotic cell is significantly larger than a prokaryotic cell. In terms of natural selection an obvious reason for this increased size is that with time the eukaryote acquired more “things” than the prokaryote and thus had to increase its size to accommodate these structures. In addition, because of the acquired endomembrane system, the eukaryotic cell is able to efficiently transport particles from one side of the cell to the other through the use of vesicles formed off the ER which travel through the cytoplasm to the golgi apparatus, are packaged to be digested/morped by lysosomes, or presented/pass through the membrane of the cell. The eukaryotic cell can compensate for diffusion through this vesicle system, thus enabling it to have a larger size than that of the prokaryote because the prokaryote lacks such intricate endomembrane systems and has to chiefly rely on the slow process of diffusion.
    Despite the apparent difference in size, these cells do share rudimentary structures and carry out the same basic processes. They perform most of the same kinds of functions, and in the same ways. Both are enclosed by plasma membranes, filled with cytoplasm, and loaded with ribosomes. Both have DNA which carries the archived instructions for operating the cell. The DNA in the two cell types is precisely the same kind of DNA, and the genetic code for a prokaryotic cell is exactly the same genetic code used in eukaryotic cells. Carroll explains the prevalence of shared structures such as ribosomes in his discussion of immortal genes. The code for ribosomes is essential to all organisms in order to translate the genetic code and carry out the metabolic purposes of life. Although throughout evolutionary time the code for ribosomes may have been independently by tampered with, natural selection irons out any harmful injuries to the code through different processes (e.g. redundancy in the genetic code) as to maintain the same basic function of these immortal genes.
    Scientists of the Nara Institute of Science and Technology and Japan used power spectrum analysis techniques to prove the universal genetic code (immortal genes) shared by both eukaryotes and prokaryotes in terms of periodicity in the genetic code. They used a power spectrum method to identify periodic patterns in nucleotide sequence, and characterized nucleotide sequences that confer periodicities to prokaryotic and eukaryotic genomes. A 10-bp periodicity was prevalent in hyperthermophilic bacteria and archaebacteria, and an 11-bp periodicity was prevalent in eubacteria. Thus, the initial results of their experiments validate the basis of the ring like structure to explain evolution by showing the similarities between bacteria and archae. The 10-bp periodicity was also prevalent in the eukaryotes such as the worm Caenorhabditis elegans. Additionally, in the worm genome, a 68-bp periodicity in chromosome I, a 59-bp periodicity in chromosome II, and a 94-bp periodicity in chromosome III were found. In human chromosomes 21 and 22, approximately 167- or 84-bp periodicity was detected along the entire length of these chromosomes. Because the 167-bp is identical to the length of DNA that forms two complete helical turns in nucleosome organization, the respective sequences may correspond to arrays of a special compact form of nucleosomes clustered in specific regions of the human chromosomes. This periodic element contained a high frequency of the triplet TGG. TGG-rich sequences are known to form a specific subset of folded DNA structures, and therefore, the sequences might have potential to form specific higher order structures related to the clustered occurrence of a specific form of the speculated nucleosomes. The specific similarities detected in the experiment reveal that there is a profound relation, shaped by natural selection among these organisms.

    The most widely-accepted theory for the evolution of prokaryotes is the theory of endosymbiosis. Endosymbiosis is the process by which one cell is taken up by another and retained internally, such that the two cells live together and integrate at some level, sometimes permanently. In two cases, endosymbiotic events had far-reaching effects on the evolution of life: these are the origins of mitochondria and plastids.
    Mitochondria are generally known as the energy-generating powerhouses of eukaryotic cells, where oxidative phosphorylation and electron transport metabolism takes place. They are also involved in oxidation of fatty acids, amino acid metabolism, and assembly of iron-sulfur clusters. They are bounded by two membranes, the innermost of which is generally highly infolded to form ‘cristae.’ The presence of mitochondria is an ancestral trait in eukaryotes. Mitochondria can be traced back to a single endosymbiosis of an alpha-proteobacterium
    Plastids are the photosynthetic organelles of plants and algae. As in the case of mitochondria, plastids in many lineages have been radically reduced or transformed, primarily through the loss of photosynthesis. Plastids can also be traced back to a single endosymbiosis event involving a cyanobacterium and the ancestor of the Archaeplastida. However, unlike mitochondria, plastids then spread to other eukaryotic lineages by secondary and tertiary endosymbiotic events. In these events, one eukaryotic cell took up another eukaryote that already contained a plastid (an alga), and this second, endosymbiotic eukaryote was then reduced and integrated. In most cases all that remains of this alga is the plastid surrounded by the remains of the endosymbiont’s plasma membrane. However, in cryptomonads and chlorarachniophytes a tiny relict of the algal nucleus called a “nucleomorph” is also retained, the study of which helped elucidate the complex evolutionary history of plastids.
    To go back to our discussion of the divergent features of prokaryotes and eukaryotes, we see that some eukaryotes lack a cell wall while all prokaryotes have a cell wall. This seems like is would be a disadvantage in terms of fitness because now the cell is more vulnerable to being infected by foreign matter and also it loses the rigidity provided by the cell wall. Again, natural selection has overcome such faults by introducing a complex cytoskeleton structure consisting of two structures: actin filaments and microtubules. The actin filaments resist pulling forces and convert chemical activity into mechanical motion. Microtubules resist compression and shearing forces and can be used as rails to slide components through the cytoplasm. In addition, microtubules contribute to another divergent feature of prokaryotes and eukaryotes: reproduction. Bacteria reproduce through the process of binary fission which takes advantage of the fact that the DNA is circular, not linear, in order to clone the cells. Animal and plant cells, undergo the process of mitosis, which is facilitated by the microtubules which attach onto the kinetochores of centromeres and stretch the cell in order to clone it.
    An alternative hypothesis has developed to the theory of endosymbiosis because of certain fallacies in the evidence for theory. For example, it is possible to find some chloroplasts the same size and shape as some bacteria, but the range in size and shape is so great we cannot rule out that they are similar just by chance. The theory to compensate for such fallacies is autogenous model. According to the autogenous model, the eukaryotes arose directly from a single prokaryote ancestor by compartmentalization of functions brought about by infoldings of the prokaryote plasma membrane. This model is usually accepted for the endoplasmic reticulum, golgi, and the nuclear membrane, and of organelles enclosed by a single membrane (such as lysosomes). According to the autogenous hypothesis, mitochondria and chloroplasts have evolved within the protoeukaryote cell by compartmentalizing plasmids (vesicles of DNA) within a pinched off invagination of the cell membrane. Similarities between mitochondria or chloroplasts and eubacteria can be accounted for by mosaic evolution in which the components in the compartment evolve more slowly than other parts of the cell, and thus retain many eubacterial features. Mitochondria or chloroplasts may have acquired their double-membrane status by secondary invagination or more elaborate folding of membranes. Thus, we see that there is still much to explore regarding the evolution of a basic cell.

    Sources:
    http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T39-478RSC2-5&_user=10&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=6c7a70a7552ff068ee0d53012ccedb58

    http://tolweb.org/Eukaryotes/3
    http://www.gwu.edu/~darwin/BiSc151/Eukaryotes/Eukar
    yotes.html

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  6. Kimberly KenyonApril 16, 2009 at 8:46 PM

    In the book, Carroll talks about the studies Maria Rivera and James Lake conducted. Their studies helped prove that eukaryotic cells are a fusion of archean bacteria and prokaryotic bacteria by analysis and understanding that eukaryotes had to have come from two different origins. This is also known as the endosymbiotic theory. This would have occurred through phagocytosis of a prokaryote. During the digestion of this cell the lysosome could not break down the cell, therefore the prokaryotic cell could continue to live and divide and grow in the eukaryotic cell. Symbiotic relationships are believed to have allowed this to happen. A relationship between two different organisms can eventually lead to endosymbiosis and eventually over time, the fusion would occur and they would become one organism instead of two. Bacteria is very similar to the functions and structures of the mitochondria which further provides evidence of endosymbiosis.

    There are many similarities and differences in eukaryotic and prokaryotic cells. Eukaryotic cells have a nucleus and prokaryotic cells lack a nuclear envelope. Eukaryotic cells are more complex and larger then prokaryotes cells. However, eukaryotes do have similarities with ancestral bacteria. They both accomplish tasks with the same functions. Both are enclosed in plasma membranes. Each of these cells has DNA. The DNA is the same type. Eukaryotes have the same basic molecular mechanisms that govern their lives. Also, the mitochondria in eukaryotic cells and prokaryotic cells are very similar suggesting that they might be connected. It has also been said that prokaryotes and eukaryotes evolved independently then they fused together, both cells contain ribosomes with similar structures and a plasma membrane. This helps prove that eukaryotes have evolved from a fusion of bacteria.

    http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=cooper.section.90
    http://www.cod.edu/PEOPLE/FACULTY/FANCHER/ProkEuk.htm
    http://www.gwu.edu/~darwin/BiSc151/Eukaryotes/Eukaryotes.html

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