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1.3Phylogeny of Organisms

1.3.1

Classification by the Phylogenetic Tree

Figure 1-1 shows the phylogenetic tree of all organisms currently known. The classification is primarily based on differences in DNA sequence. Here, organisms are divided into three main categories (i.e., domains) - bacteria, archaea and eukarya (or eukaryotes). The former two do not have a clearly defined nucleus, and are also known as prokaryotes. Bacteria and archaea not only have different lipid compositions in the cell membrane, but also have clearly different gene compositions. As for eukaryotes, which include humans and plants, there is mounting evidence suggesting their evolution from the branch of archaea rather than that of bacteria.

Fig. 1-1. Phylogenetic tree of all organisms

The phylogenetic tree of all organisms on earth estimated based on genome sequence. Eukaryotes are closer to archaea than to bacteria.

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Viruses and Prions

Viruses generally have a simple structure; their nucleic acids (gene segments), DNA and RNA are surrounded by proteins, and they do not have a cell shape. Although viruses self-replicate, they cannot do so using only their intrinsic components, and must rely on the materials of the host organism. In addition, viruses themselves do not respond to external stimuli and do not have the ability to synthesize ATP.
Viruses do not satisfy the definition of organisms outlined in II. Column Figure. 1-1 shows the gene structure of the Rous sarcoma virus. In 1911, Peyton Rous demonstrated that sarcomas are caused by elements on a sub-cell scale. To do this, he mashed and filtered sarcoma tissue and injected the extract into healthy chickens, which subsequently developed sarcomas. The relevant element was later found to be an RNA-genome-based virus with a typical retrovirus structure. It has only four genes coded into its genome, of which v-src - an oncogene - causes sarcomas in chickens.

Column Fig. 1-1. Gene structure of the Rous sarcoma virus


Another molecule with odd properties is the prion. Prions were isolated as elements that cause transmissible spongiform encephalopathy in cattle and humans, and are made of one type of protein. It has also been shown that infectious prions are not derived from other organisms and that the gene coding them exists in the human genome, and that normal prion proteins are expressed in our brains. Since both normal and infectious prions have identical primary protein structures, it has been suggested that the infection mechanism follows the path shown in Column Figure. 1-2 (Prion hypothesis). Although prions multiply, they are a single protein type and do not satisfy the definition of organisms shown in II.

Column Fig. 1-2. Prion hypothesis

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1.3.2

Classification Based on Organelles

Turning our attention to organelles, not all eukaryotes have mitochondria, and some protista also lack them. Since mitochondria are surrounded by double membranes and have circular DNA, it is believed that aerobically respiring bacteria began to live symbiotically with primitive eukaryotes and subsequently adapted to an intracellular environment by discarding unnecessary genes, thus becoming organelles (Endosymbiotic hypothesis: see Column in Chapter 5). Similarly, chloroplasts found in plant cells are believed to have originated as cyanobacteria that were able to photosynthesize while living symbiotically with plants (Table 1-1).
The earliest stage of eukaryotes is protista, which include mastigotes, plasmodia and red-tide-causing dinoflagellates. Protista also include euglena, which perform photosynthesis, and slime molds, which differentiate and change shape despite being unicellular organisms.
From this stage, the group of organisms known as plants was diverged. Plants are multicellular organisms that have cells surrounded by cell walls and perform photosynthesis. Plants are autotraphs, meaning that they can synthesize organic matter from carbon dioxide and water. As producers, plants provide nutrients to all other organisms on earth.
Then, fungi (such as molds and mushrooms, nutritionally classified as decomposers) with cell walls but no photosynthesis (i.e., heterotrophs) were diverged, followed finally by animals. Animals neither have cell walls nor perform photosynthesis, making them heterotrophs, and are nutritionally classified as consumers.

Table 1-1. Similarities between organelles and prokaryotes

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1.3.3

Sizes of Biological Materials

Figure 1-2 shows the sizes of cells and the organelles they contain.
The naked eye enables observation of specimens as small as 0.1 mm (100 μm) in size, which includes the diameter of a human egg (ovum), a human hair and a paramecium (200 μm). The resolution of light microscopes allows the subjects of just a few micrometers to be viewed. The average size of bacteria is 0.5-5μm, and the size of mitochondria in higher animals is slightly larger than that. Generally, eukaryotic cells are larger - up to 40 μm in diameter - and their volume is 1,000 to 10,000 times that of prokaryotic cells. Some cells are very long; sciatic nerve cells in humans, for example, are nearly 1 m in length. Cells smaller than 1 μm can be observed only by electron microscopes. The diameter of DNA molecules in a cell is 2 nm, the thickness of the cell membrane is 10 nm, and the diameter of ribosomes is 20 nm.

Fig. 1-2. Sizes of biological materials

This figure shows the general scheme of the size order for biological components, organelles, cells and individuals. The resolutions of the naked eye and light microscopes are 100 μm and a few micrometers, respectively, whereas that of electron microscopes is a few nanometers.

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